Clostridial Toxin Activatable Clostridial Toxins

[01] This patent application claims priority pursuant to 35 U.S. C. §119(e) to United States provisional patent application Serial No. 60/718,616 filed on September 19, 2005, the contents of which is hereby incorporated by reference in its entirety.

[02] The ability of Clostridial toxins, such as, e.g., Botulinum neurotoxins (BoNTs), BoNT/A, BoNT/B, BoNT/CI , BoNT/D, BoNT/E, BoNT/F and BoNT/G, Tetanus neurotoxin (TeNT), Baratium neurotoxin (BaNT) and Butyricum neurotoxin (BuNT) to inhibit neuronal transmission are being exploited in a wide variety of therapeutic and cosmetic applications, see e.g., William J. Lipham, COSMETIC AND CLINICAL APPLICATIONS OF BOTULINUM TOXIN (Slack, Inc., 2004). Clostridial toxins commercially available as pharmaceutical compositions include, BoNT/A preparations, such as, e.g., BOTOX ^® (Allergan, Inc., Irvine, CA), Dysport ^® /Reloxin ^® , (Beaufour Ipsen, Porton Down, England), Linurase ^® (Prollenium, Inc., Ontario, Canada), Neuronox ^® (Medy-Tox, Inc., Ochang-myeon, South Korea) BTX-A (Lanzhou Institute Biological Products, China) and Xeomin ^® (Merz Pharmaceuticals, GmbH., Frankfurt, Germany); and BoNT/B preparations, such as, e.g., MyoBloc™/NeuroBloc™ (Elan Pharmaceuticals, San Francisco, CA). As an example, BOTOX ^® is currently approved in one or more countries for the following indications: achalasia, adult spasticity, anal fissure, back pain, blepharospasm, bruxism, cervical dystonia, essential tremor, glabellar lines or hyperkinetic facial lines, headache, hemifacial spasm, hyperactivity of bladder, hyperhidrosis, juvenile cerebral palsy, multiple sclerosis, myoclonic disorders, nasal labial lines, spasmodic dysphonia, strabismus and VII nerve disorder.

[03] The increasing use of Clostridial toxin therapies in treating a wider range of human afflictions necessitates increasing the efficiency with which these toxins are produced. However, meeting the needs for the ever increasing demand for such toxin treatments may become difficult. One outstanding problem is that all Clostridial toxins need to be converted into the di-chain form of the molecule in order to achieve optimal activity. Historically, this conversion has been done in one of two ways. The first method simply purifies a Clostridial toxin from the bacterial strain itself, thereby relying on the naturally-occurring endogenous protease used to convert the single-chain form of the toxin into the di-chain form. The second method utilizes an exogenous protease that converts the single-chain form into the di-chain by either taking advantage of a fortuitous cleavage site found in the appropriate location or by genetically engineering a protease cleavage site of commonly used, commercially available exogenous proteases. However, there are several drawbacks to both of these methods. For example, methods employing an endogenous protease produce low toxin yields because native Clostridial strains usually produce little toxin. In addition these strains are poorly suited for research, thus hindering the efforts to genetic manipulation Clostridial toxins to improve their therapeutic and cosmetic attributes. Lastly, several Clostridial strains do not produce the endogenous protease necessary to convert the single-chain form of the toxin to the di-chain form. A drawback to the use of exogenous proteases is a lack of protease specificity that results in inactive toxin because of proteolytic cleavage in inappropriate locations. In

addition, many of the currently available proteases are from animal sources that lack Good Manufacture Standard (GMS) approval, requiring additional purification steps during the manufacturing process. Thus, methods currently used to convert the single-chain form of the toxin into the di-chain form are inefficient, cumbersome and lead to higher overall production costs. These drawbacks represent a significant obstacle to the overall commercial production of Clostridial toxins and are thus a major problem since di- chain forms of these toxins are needed for scientific, therapeutic and cosmetic applications. In addition, both the amount of Clostridial toxins anticipated for future therapies and the demand for toxins with enhanced therapeutic properties are increasing. Therefore, there is a need to develop better methods for producing Clostridial toxin di-chain molecules in order to meet this need.

[04] The present invention provides modified Clostridial toxins that rely on a novel method of converting the single-chain form of the toxin into the di-chain form. These and related advantages are useful for various clinical, therapeutic and cosmetic applications, such as, e.g., the treatment of neuromuscular disorders, neuropathic disorders, eye disorders, pain, muscle injuries, headache, cardiovascular diseases, neuropsychiatric disorders, endocrine disorders, cancers, otic disorders and hyperkinetic facial lines, as well as, other disorders where a Clostridial toxin administration to a mammal can produce a beneficial effect.

BRIEF DESCRIPTION OF THE DRAWINGS

[05] FIG. 1 shows a schematic of the current paradigm of Clostridial toxin posttranslational processing. Clostridial toxins are translated as a single-chain polypeptide of approximately 150 kDa comprising an enzymatic domain, a translocation domain and a binding domain. A disulfide bridge formed from a cysteine residue in the enzymatic domain and a cysteine residue from the translocation domain form a di- chain loop. Within this di-chain loop is a protease cleavage site for a naturally-occurring protease that can be produced endogenously from the Clostridial strain synthesizing the toxin, or exogenously from a source found in the environment. Cleavage of the protease cleavage site by the naturally-occurring protease converts the single-chain form of the toxin into the di-chain form. The di-chain form of the toxin is held together by the disulfide bond and non-covalent interactions between the two chains.

[06] FIG. 2 shows a schematic of the current paradigm of neurotransmitter release and Clostridial toxin intoxication in a central and peripheral neuron. FIG. 2a shows a schematic for the neurotransmitter release mechanism of a central and peripheral neuron. The release process can be described as comprising two steps: 1) vesicle docking, where the vesicle-bound SNARE protein of a vesicle containing neurotransmitter molecules associates with the membrane-bound SNARE proteins located at the plasma membrane; and 2) neurotransmitter release, where the vesicle fuses with the plasma membrane and the neurotransmitter molecules are exocytosed. FIG. 2b shows a schematic of the intoxication mechanism for tetanus and botulinum toxin activity in a central and peripheral neuron. This intoxication process can be described as comprising four steps: 1) receptor binding, where a Clostridial toxin binds to a Clostridial

receptor system and initiates the intoxication process; 2) complex internalization, where after toxin binding, a vesicle containing the toxin/receptor system complex is endocytosed into the cell; 3) light chain translocation, where multiple events result in the release of the active light chain into the cytoplasm; and 4) enzymatic target modification, where the active light chain of Clostridial toxin proteolytically cleaves its target SNARE substrate, such as, e.g., SNAP-25, VAMP or Syntaxin, thereby preventing vesicle docking and neurotransmitter release.

[07] FIG. 3 shows a schematic of the subcellular localization and cleavage sites of SNAP-25, VAMP and Syntaxin. VAMP is localized to synaptic vesicle membrane, whereas SNAP-25 and Syntaxin are localized to the plasma membrane. BoNT/A and BoNT/E cleave SNAP-25 close to the carboxyl-terminus, releasing nine or 26 residues, respectively. BoNT/B, BoNT /D, BoNT /F, BoNT /G and TeNT act on the conserved central portion of VAMP (white box) and release the amino-terminal cytosolic half of VAMP into the cytosol. BoNT/Ci cleaves SNAP-25 close to the carboxyl-terminus as well as cleaving Syntaxin at a single site near the cytosolic membrane surface. The action of BoNT/ C1 results in release of a large portion of the cytosolic domain of Syntaxin, while only a small portion of SNAP-25 is released by selective proteolysis of BoNT/C1.

[08] FIG. 4 shows a schematic of modified Clostridial toxins. FIG. 4a shows a modified Clostridial toxin comprising an enzymatic domain, a translocation domain and a binding domain and a di-chain loop including a Clostridial toxin substrate cleavage site comprising a BoNT/A cleavage site, derived, e.g., from a member of the SNAP-25 family susceptible to BoNT/A cleavage. Cleavage of the BoNT/A cleavage site by BoNT/A converts the single-chain form of the modified toxin into the di-chain form. FIG. 4b shows a modified Clostridial toxin comprising an enzymatic domain, a translocation domain and a binding domain and a di-chain loop including a Clostridial toxin substrate cleavage site comprising a BoNT/E cleavage site, derived, e.g., from a member of the SNAP-25 family susceptible to BoNT/E cleavage. Cleavage of the BoNT/E cleavage site by BoNT/E converts the single-chain form of the modified toxin into the di-chain form.

[09] FIG. 5 shows a schematic of modified Clostridial toxins. FIG. 5a shows a modified Clostridial toxin comprising an enzymatic domain, a translocation domain and a binding domain and a di-chain loop including a Clostridial toxin substrate cleavage site comprising a BoNT/B cleavage site, derived, e.g., from a member of the VAMP family susceptible to BoNT/B cleavage. Cleavage of the BoNT/B cleavage site by BoNT/B converts the single-chain form of the modified toxin into the di-chain form. FIG. 5b shows a modified Clostridial toxin comprising an enzymatic domain, a translocation domain and a binding domain and a di-chain loop including a Clostridial toxin substrate cleavage site comprising a BoNT/D cleavage site, derived, e.g., from a member of the VAMP family susceptible to BoNT/D cleavage. Cleavage of the BoNT/D cleavage site by BoNT/D converts the single-chain form of the modified toxin into the di-chain form. FIG. 5c shows a modified Clostridial toxin comprising an enzymatic domain, a translocation domain and a binding domain and a di-chain loop including a Clostridial toxin substrate

cleavage site comprising a BoNT/F cleavage site, derived, e.g., from a member of the VAMP family susceptible to BoNT/F cleavage. Cleavage of the BoNT/F cleavage site by BoNT/F converts the single- chain form of the modified toxin into the di-chain form. FIG. 5d shows a modified Clostridial toxin comprising an enzymatic domain, a translocation domain and a binding domain and a di-chain loop including a Clostridial toxin substrate cleavage site comprising a BoNT/G cleavage site, derived, e.g., from a member of the VAMP family susceptible to BoNT/G cleavage. Cleavage of the BoNT/G cleavage site by BoNT/G converts the single-chain form of the modified toxin into the di-chain form. FIG. 5e shows a modified Clostridial toxin comprising an enzymatic domain, a translocation domain and a binding domain and a di-chain loop including a Clostridial toxin substrate cleavage site comprising a TeNT cleavage site, derived, e.g., from a member of the VAMP family susceptible to TeNT cleavage. Cleavage of the TeNT cleavage site by TeNT converts the single-chain form of the modified toxin into the di-chain form.

[010] FIG. 6 shows a schematic of modified Clostridial toxins. FIG. 6a shows a modified Clostridial toxin comprising an enzymatic domain, a translocation domain and a binding domain and a di-chain loop including a Clostridial toxin substrate cleavage site comprising a BoNT/C1 cleavage site, derived, e.g., from a member of the Syntaxin family susceptible to BoNT/C1 cleavage. Cleavage of the BoNT/C1 cleavage site by B0NT/CI converts the single-chain form of the modified toxin into the di-chain form. FIG. 6b shows a modified Clostridial toxin comprising an enzymatic domain, a translocation domain and a binding domain and a di-chain loop including a Clostridial toxin substrate cleavage site comprising a BoNT/C1 cleavage site, derived, e.g., from a member of the SNAP-25 family susceptible to BoNT/C1 cleavage. Cleavage of the BoNT/C1 cleavage site by BoNT/C1 converts the single-chain form of the modified toxin into the di-chain form.

[011] FIG. 7 shows a plasmid map of prokaryotic expression construct pET29b/BoNT/A-A17 comprising a polynucleotide molecule of SEQ ID NO: 225 encoding a modified BoNT/A of SEQ ID NO: 203, operably- linked to a carboxyl-terminal polyhistidine binding polypeptide. A Trypsin protease cleavage site is operably-linked between the polyhistidine binding polypeptide and the modified BoNT/A. Abbreviations are as follows: P ₇₇ , a bacteriophage T7 promoter region; ED, a polynucleotide molecule encoding a BoNT/A enzymatic domain; A17, a polynucleotide molecule encoding a BoNT/A substrate cleavage site; TD, a polynucleotide molecule encoding a BoNT/A translocation domain; BD, a polynucleotide molecule encoding a BoNT/A binding domain; Trypsin, a polynucleotide molecule encoding Trypsin cleavage site; 6xHis, a polynucleotide molecule encoding a polyhistidine binding polypeptide; T7 TT, a bacteriophage T7 transcription termination region; f1 origin, a bacteriophage f1 origin of replication; Kanamycin, a polynucleotide molecule encoding an am inophosphotransf erase that confers Kanamycin resistance; pBR322 ori, a pBR322 origin of plasmid replication region; lacl, a polynucleotide molecule encoding a lactose I.

[012] FIG. 8 shows a plasmid map of prokaryotic expression construct pET29b/BoNT/λ-BT35 comprising a polynucleotide molecule of SEQ ID NO: 227 encoding a modified BoNT/A of SEQ ID NO: 205, operably-linked to a carboxyl-terminal polyhistidine binding polypeptide. A Trypsin protease cleavage site is operably-linked between the polyhistidine binding polypeptide and the modified BoNT/A. Abbreviations are as follows: Pi ₇ , a bacteriophage T7 promoter region; ED, a polynucleotide molecule encoding a BoNT/A enzymatic domain; BT35, a polynucleotide molecule encoding a BoNT/B substrate cleavage site and a TeNT substrate cleavage site; TD, a polynucleotide molecule encoding a BoNT/A translocation domain; BD, a polynucleotide molecule encoding a BoNT/A binding domain; Trypsin, a polynucleotide molecule encoding Trypsin cleavage site; 6xHis, a polynucleotide molecule encoding a polyhistidine binding polypeptide; T7 TT, a bacteriophage T7 transcription termination region; f1 origin, a bacteriophage f1 origin of replication; Kanamycin, a polynucleotide molecule encoding an am inophosphotransf erase that confers Kanamycin resistance; pBR322 ori, a pBR322 origin of plasmid replication region; lacl, a polynucleotide molecule encoding a lactose I.

[013] FIG. 9 shows a plasmid map of prokaryotic expression construct pET29b/BoNT/A-Csyn8 comprising a polynucleotide molecule of SEQ ID NO: 229 encoding a modified BoNT/A of SEQ ID NO: 207, operably-linked to a carboxyl-terminal polyhistidine binding polypeptide. A Trypsin protease cleavage site is operably-linked between the polyhistidine binding polypeptide and the modified BoNT/A. Abbreviations are as follows: P ₁₇ , a bacteriophage T7 promoter region; ED, a polynucleotide molecule encoding a BoNT/A enzymatic domain; Csynδ, a polynucleotide molecule encoding a BoNT/01 substrate cleavage site; TD, a polynucleotide molecule encoding a BoNT/A translocation domain; BD, a polynucleotide molecule encoding a BoNT/A binding domain; Trypsin, a polynucleotide molecule encoding Trypsin cleavage site; 6xHis, a polynucleotide molecule encoding a polyhistidine binding polypeptide; T7 TT, a bacteriophage T7 transcription termination region; f1 origin, a bacteriophage f1 origin of replication; Kanamycin, a polynucleotide molecule encoding an aminophosphotransferase that confers Kanamycin resistance; pBR322 ori, a pBR322 origin of plasmid replication region; lacl, a polynucleotide molecule encoding a lactose I.

[014] FIG. 10 shows a plasmid map of prokaryotic expression construct pET29b/BoNT/A-DF39 comprising a polynucleotide molecule of SEQ ID NO: 231 encoding a modified BoNT/A of SEQ ID NO: 209, operably-linked to a carboxyl-terminal polyhistidine binding polypeptide. A Trypsin protease cleavage site is operably-linked between the polyhistidine binding polypeptide and the modified BoNT/A. Abbreviations are as follows: P ₇₇ , a bacteriophage T7 promoter region; ED, a polynucleotide molecule encoding a BoNT/A enzymatic domain; DF39, a polynucleotide molecule encoding a BoNT/D substrate cleavage site and a BoNT/F substrate cleavage site; TD, a polynucleotide molecule encoding a BoNT/A translocation domain; BD, a polynucleotide molecule encoding a BoNT/A binding domain; Trypsin, a polynucleotide molecule encoding Trypsin cleavage site; 6xHis, a polynucleotide molecule encoding a polyhistidine binding polypeptide; T7 TT, a bacteriophage T7 transcription termination region; f1 origin, a bacteriophage f1 origin of replication; Kanamycin, a polynucleotide molecule encoding an

am inophosphotransf erase that confers Kanamycin resistance; pBR322 ori, a pBR322 origin of plasmid replication region; iacl, a polynucleotide molecule encoding a lactose I.

[015] FIG. 11 shows a plasmid map of prokaryotic expression construct pET29b/BoNT/A-E8 comprising a polynucleotide molecule of SEQ ID NO: 233 encoding a modified BoNT/A of SEQ ID NO: 211 , operably-linked to a carboxyl-terminal polyhistidine binding polypeptide. A Trypsin protease cleavage site is operably-linked between the polyhistidine binding polypeptide and the modified BoNT/A. Abbreviations are as follows: P-rr, a bacteriophage T7 promoter region; ED, a polynucleotide molecule encoding a BoNT/A enzymatic domain; E8, a polynucleotide molecule encoding a BoNT/E substrate cleavage site; TD, a polynucleotide molecule encoding a BoNT/A translocation domain; BD, a polynucleotide molecule encoding a BoNT/A binding domain; Trypsin, a polynucleotide molecule encoding Trypsin cleavage site; 6xHis, a polynucleotide molecule encoding a polyhistidine binding polypeptide; T7 TT, a bacteriophage T7 transcription termination region; f1 origin, a bacteriophage f1 origin of replication; Kanamycin, a polynucleotide molecule encoding an am inophosphotransf erase that confers Kanamycin resistance; pBR322 ori, a pBR322 origin of plasmid replication region; Iacl, a polynucleotide molecule encoding a lactose I.

[016] FIG. 12 shows a plasmid map of prokaryotic expression construct pET29b/BoNT/A-G8 comprising a polynucleotide molecule of SEQ ID NO: 235 encoding a modified BoNT/A of SEQ ID NO: 213, operably-linked to a carboxyl-terminal polyhistidine binding polypeptide. A Trypsin protease cleavage site is operably-linked between the polyhistidine binding polypeptide and the modified BoNT/A. Abbreviations are as follows: Pi ₇ , a bacteriophage T7 promoter region; ED, a polynucleotide molecule encoding a BoNT/A enzymatic domain; G8, a polynucleotide molecule encoding a BoNT/G substrate cleavage site; TD, a polynucleotide molecule encoding a BoNT/A translocation domain; BD, a polynucleotide molecule encoding a BoNT/A binding domain; Trypsin, a polynucleotide molecule encoding Trypsin cleavage site; 6xHis, a polynucleotide molecule encoding a polyhistidine binding polypeptide; T7 TT, a bacteriophage T7 transcription termination region; f1 origin, a bacteriophage f1 origin of replication; Kanamycin, a polynucleotide molecule encoding an am inophosphotransf erase that confers Kanamycin resistance; pBR322 ori, a pBR322 origin of plasmid replication region; Iacl, a polynucleotide molecule encoding a lactose I.

[017] FIG. 13 shows a plasmid map of yeast expression construct pPICZ A/BoNT/A-A17 comprising a polynucleotide molecule of SEQ ID NO: 236 encoding a modified BoNT/A of SEQ ID NO: 203, operably- linked to carboxyl-terminal c-myc and polyhistidine binding polypeptides. Abbreviations are as follows: P _A OXL an aldehyde oxidase 1 promoter region; ED, a polynucleotide molecule encoding a BoNT/A enzymatic domain; A17, a polynucleotide molecule encoding a BoNT/A substrate cleavage site; TD, a polynucleotide molecule encoding a BoNT/A translocation domain; BD, a polynucleotide molecule encoding a BoNT/A binding domain; c-myc, a polynucleotide molecule encoding a c-myc binding polypeptide; 6xHis, a polynucleotide molecule encoding a polyhistidine binding polypeptide; AOX1 TT, an

aldehyde oxidase 1 transcription termination region; Zeocin™, a polynucleotide molecule encoding a Zeocin™ resistance polypeptide; pUC ori, a pUC origin of plasmid replication region.

[018] FIG. 14 shows a plasmid map of baculovirus transfer construct pBACgus3/BoNT/A-A17 comprising a polynucleotide molecule of SEQ ID NO: 237 encoding a modified BoNT/A of SEQ ID NO: 203, operably-linked to carboxyl-terminal polyhistidine binding polypeptide. A Thrombin protease cleavage site is operably-linked between the modified BoNT/A and the polyhistidine binding polypeptide. Abbreviations are as follows: P _PH , an polyhedrin promoter region; gp64, a polynucleotide molecule encoding a gp64 signal polypeptide; ED, a polynucleotide molecule encoding a BoNT/A enzymatic domain; A17, a polynucleotide molecule encoding a BoNT/A substrate cleavage site; TD, a polynucleotide molecule encoding a BoNT/A translocation domain; BD, a polynucleotide molecule encoding a BoNT/A binding domain; Thrombin, a polynucleotide molecule encoding a Thrombin protease cleavage site; 6xHis, a polynucleotide molecule encoding a polyhistidine binding polypeptide; pUC ori, a pUC origin of plasmid replication region; Ampicillin, a polynucleotide molecule encoding a β-lactamase that confers Ampicillin resistance; f1 ori, a bacteriophage f1 origin of replication; gus, a polynucleotide molecule encoding a β-glucuronidase.

[019] FIG. 15 shows a plasmid map of mammalian expression construct pSecTag2/BoNT/A-A17 comprising a polynucleotide molecule of SEQ ID NO: 238 encoding a modified BoNT/A of SEQ ID NO: 203, operably-linked to carboxyl-terminal c-myc and polyhistidine binding polypeptides. Abbreviations are as follows: P _C M _V . an cytomegalovirus promoter region; IgK, a polynucleotide molecule encoding an immunoglobulin K polypeptide; ED, a polynucleotide molecule encoding a BoNT/A enzymatic domain; A17, a polynucleotide molecule encoding a BoNT/A substrate cleavage site; TD, a polynucleotide molecule encoding a BoNT/A translocation domain; BD, a polynucleotide molecule encoding a BoNT/A binding domain; c-myc, a polynucleotide molecule encoding a c-myc binding polypeptide; 6xHis, a polynucleotide molecule encoding a polyhistidine binding polypeptide; BGH pA, a bovine growth hormone polyadenylation site; f1 ori, a bacteriophage f1 origin of replication; Psv ₄ o. a simian virus 40 promoter region; Zeocin™, a region encoding an Zeocin™ resistance polypeptide; pUC ori, a pUC origin of plasmid replication region; Ampicillin, a polynucleotide molecule encoding a β-lactamase that confers Ampicillin resistance.

DETAILED DESCRIPTION

[020] Clostridia toxins produced by Clostridium botulinum, Clostridium tetani, Clostridium baratii and Clostridium butyricum are the most widely used in therapeutic and cosmetic treatments of humans and other mammals. Strains of C. botulinum produce seven antigenically-distinct types of Botulinum toxins (BoNTs), which have been identified by investigating botulism outbreaks in man (BoNT/A, /B, /E and /F), animals (BoNT/C1 and /D), or isolated from soil (BoNT/G). BoNTs possess approximately 35% amino acid identity with each other and share the same functional domain organization and overall structural

architecture. It is recognized by those of skill in the art that within each type of Clostridial toxin there can be subtypes that differ somewhat in their amino acid sequence, and also in the nucleic acids encoding these proteins. For example, there are presently four BoNT/A subtypes, BoNT/A1 , BoNT/A2, BoNT/A3 and BoNT/A4, with specific subtypes showing approximately 89% amino acid identity when compared to another BoNT/A subtype. While all seven BoNT serotypes have similar structure and pharmacological properties, each also displays heterogeneous bacteriological characteristics. In contrast, tetanus toxin (TeNT) is produced by a uniform group of C. tetani. Two other species of Clostridia, C. baratii and C. butyricum, also produce toxins, BaNT and BuNT respectively, which are similar to BoNT/F and BoNT/E, respectively.

[021] Clostridial toxins are each translated as a single chain polypeptide of approximately 150 kDa that is subsequently cleaved by proteolytic scission within a disulfide loop by a naturally-occurring protease (FIG. 1). This cleavage occurs within the discrete di-chain loop region created between two cysteine residues that form a disulfide bridge. This posttranslational processing yields a di-chain molecule comprising an approximately 50 kDa light chain (LC) and an approximately 100 kDa heavy chain (HC) held together by the single disulfide bond and non-covalent interactions between the two chains. The naturally-occurring protease used to convert the single chain molecule into the di-chain is currently not known. In some serotypes, such as, e.g., BoNT/A, the naturally-occurring protease is produced endogenously by the bacteria serotype and cleavage occurs within the cell before the toxin is release into the environment. However, in other serotypes, such as, e.g., BoNT/E, the bacterial strain appears not to produce an endogenous protease capable of converting the single chain form of the toxin into the di-chain form. In these situations, the toxin is released from the cell as a single-chain toxin which is subsequently converted into the di-chain form by a naturally-occurring protease found in the environment.

[022] Each mature di-chain molecule comprises three functionally distinct domains: 1) an enzymatic domain located in the LC that includes a metalloprotease region containing a zinc-dependent endopeptidase activity which specifically targets core components of the neurotransmitter release

apparatus (Table 1); 2) a translocation domain contained within the amino-terminal half of the HC (H _N ) that facilitates release of the LC from intracellular vesicles into the cytoplasm of the target cell (Table 1); and 3) a binding domain found within the carboxyl-terminal half of the HC (H _c ) that determines the binding activity and binding specificity of the toxin to the receptor complex located at the surface of the target cell (Table 1).

[023] The binding, translocation and enzymatic activity of these three functional domains are all necessary for toxicity. While all details of this process are not yet precisely known, the overall cellular intoxication mechanism whereby Clostridial toxins enter a neuron and inhibit neurotransmitter release is similar, regardless of type. Although the applicants have no wish to be limited by the following description, the intoxication mechanism can be described as comprising at least four steps: 1) receptor binding, 2) complex internalization, 3) light chain translocation, and 4) enzymatic target modification (see FIG. 2). The process is initiated when the H _c domain of a Clostridial toxin binds to a toxin-specific receptor complex located on the plasma membrane surface of a target cell. The binding specificity of a receptor complex is thought to be achieved, in part, by specific combinations of gangliosides and protein receptors that appear to distinctly comprise each Clostridial toxin receptor complex. Once bound, the toxin/receptor complexes are internalized by endocytosis and the internalized vesicles are sorted to specific intracellular routes. The translocation step appears to be triggered by the acidification of the vesicle compartment. This process seems to initiate two important pH-dependent structural rearrangements that increase hydrophobicity and promote formation di-chain form of the toxin. Once activated, light chain endopeptidase of the toxin is released from the intracellular vesicle into the cytosol where it specifically targets one of three known core components of the neurotransmitter release apparatus. These core proteins, vesicle-associated membrane protein (VAMP)/synaptobrevin, synaptosomal-associated protein of 25 kDa (SNAP-25) and Syntaxin, are necessary for synaptic vesicle docking and fusion at the nerve terminal and constitute members of the soluble N-ethylmaleimide- sensitive factor-attachment protein-receptor (SNARE) family. BoNT/A and BoNT/E cleave SNAP-25 in the carboxyl-terminal region, releasing a nine or twenty-six amino acid segment, respectively, and BoNT/C1 also cleaves SNAP-25 near the carboxyl-terminus. The botulinum serotypes BoNT/B, BoNT/D, BoNT/F and BoNT/G, and tetanus toxin, act on the conserved central portion of VAMP, and release the amino-terminal portion of VAMP into the cytosol. BoNT/C1 cleaves syntaxin at a single site near the cytosolic membrane surface. The selective proteolysis of synaptic SNAREs accounts for the block of neurotransmitter release caused by Clostridial toxins in vivo. The SNARE protein targets of Clostridial toxins are common to exocytosis in a variety of non-neuronal types; in these cells, as in neurons, light chain peptidase activity inhibits exocytosis, see, e.g., Yann Humeau et al., How Botulinum and Tetanus Neurotoxins Block Neurotransmitter Release, 82(5) Biochimie. 427-446 (2000); Kathryn Turton et al., Botulinum and Tetanus Neurotoxins: Structure, Function and Therapeutic Utility, 27(11) Trends Biochem. Sci. 552-558. (2002); Giovanna LaIIi et al., The Journey of Tetanus and Botulinum Neurotoxins in Neurons, 11 (9) Trends Microbiol. 431-437, (2003).

[024] The present invention discloses modified Clostridial toxins that can be converted from the single- chain polypeptide form into the di-chain form using the enzymatic activity of a Clostridial toxin. This is accomplished by replacing the naturally-occurring protease cleavage site found within the di-chain loop region with a Clostridial toxin substrate cleavage site. In a modification where the Clostridial toxin substrate cleavage site replacement is the substrate for the Clostridial toxin, activation is accomplished using a Clostridial toxin having BoNT/A enzymatic activity. This cleavage site replacement will enable these modified toxins to activate one another, eliminating the reliance of a different protease. For example, a modified BoNT/A comprising a BoNT/A substrate cleavage site will enable a Clostridial toxin having BoNT/A enzymatic activity to cleave the BoNT/A substrate cleavage site of the modified BoNT/A, thereby producing the di-chain form of the toxin. In a modification where the Clostridial toxin substrate cleavage site replacement is the substrate for a different Clostridial toxin, activation is accomplished using a Clostridial toxin having BoNT/C1 enzymatic activity. For example, a modified BoNT/A comprising a BoNT/C1 substrate cleavage site will enable a Clostridial toxin having BoNT/C1 enzymatic activity to cleave the BoNT/C1 substrate cleavage site of the modified BoNT/A, thereby producing the di-chain form of the toxin.

[025] Aspects of the present invention provide modified Clostridial toxins comprising a Clostridial toxin substrate cleavage site, wherein the Clostridial toxin substrate cleavage site is located within a di-chain loop region of the modified Clostridial toxin. It is envisioned that any Clostridial toxin substrate cleavage site can be used, including, without limitation, a BoNT/A substrate cleavage site, a BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site, a BoNT/G substrate cleavage site, a TeNT substrate cleavage site, a BaNT substrate cleavage site and a BuNT substrate cleavage site.

[026] Other aspects of the present invention provide polynucleotide molecules encoding modified Clostridial toxins comprising Clostridial toxin substrate cleavage site, wherein the Clostridial toxin substrate cleavage site is located within the di-chain loop region.

[027] Other aspects of the present invention provide methods of producing a modified Clostridial toxin comprising Clostridial toxin substrate cleavage site, wherein the Clostridial toxin substrate cleavage site is located within the di-chain loop region. Other aspects of the present invention provide methods of producing in a cell a modified Clostridial toxin comprising Clostridial toxin substrate cleavage site, wherein the Clostridial toxin substrate cleavage site is located within the di-chain loop region and expressing the expression construct in the cell.

[028] Aspects of the present invention provide, in part, a Clostridial toxin. As used herein, the term "Clostridial toxin" means any polypeptide that can execute the overall cellular mechanism whereby a Clostridial toxin enters a neuron and inhibits neurotransmitter release and encompasses the binding of a Clostridial toxin to a low or high affinity receptor complex, the internalization of the toxin/receptor complex,

the translocation of the Clostridial toxin light chain into the cytoplasm and the enzymatic modification of a Clostridial toxin substrate.

[029] A Clostridial toxin includes, without limitation, naturally occurring Clostridial toxin variants, such as, e.g., Clostridial toxin isoforms and Clostridial toxin subtypes; non-naturally occurring Clostridial toxin variants, such as, e.g., conservative Clostridial toxin variants, non-conservative Clostridial toxin variants, Clostridial toxin chimeric variants and active Clostridial toxin fragments thereof, or any combination thereof. As used herein, the term "Clostridial toxin variant," whether naturally-occurring or non-naturally- occurring, means a Clostridial toxin that has at least one amino acid change from the corresponding region of the disclosed reference sequences (see Table 1) and can be described in percent identity to the corresponding region of that reference sequence. As non-limiting examples, a BoNT/A variant comprising amino acids 1-1296 of SEQ ID NO: 1 will have at least one amino acid difference, such as, e.g., an amino acid substitution, deletion or addition, as compared to the amino acid region 1-1296 of SEQ ID NO: 1 ; a BoNT/B variant comprising amino acids 1-1291 of SEQ ID NO: 2 will have at least one amino acid difference, such as, e.g., an amino acid substitution, deletion or addition, as compared to the amino acid region 1-1291 of SEQ ID NO: 2; a BoNT/C1 variant comprising amino acids 1-1291 of SEQ ID NO: 3 will have at least one amino acid difference, such as, e.g., an amino acid substitution, deletion or addition, as compared to the amino acid region 1-1291 of SEQ ID NO: 3; a BoNT/D variant comprising amino acids 1 -1276 of SEQ ID NO: 4 will have at least one amino acid difference, such as, e.g., an amino acid substitution, deletion or addition, as compared to the amino acid region 1-1276 of SEQ ID NO: 4; a BoNT/E variant comprising amino acids 1-1252 of SEQ ID NO: 5 will have at least one amino acid difference, such as, e.g., an amino acid substitution, deletion or addition, as compared to the amino acid region 1-1252 of SEQ ID NO: 5; a BoNT/F variant comprising amino acids 1-1274 of SEQ ID NO: 6 will have at least one amino acid difference, such as, e.g., an amino acid substitution, deletion or addition, as compared to the amino acid region 1-1274 of SEQ ID NO: 6; a BoNT/G variant comprising amino acids 1- 1297 of SEQ ID NO: 7 will have at least one amino acid difference, such as, e.g., an amino acid substitution, deletion or addition, as compared to the amino acid region 1 -1297 of SEQ ID NO: 7; and a TeNT variant comprising amino acids 1-1315 of SEQ ID NO: 8 will have at least one amino acid difference, such as, e.g., an amino acid substitution, deletion or addition, as compared to the amino acid region 1-1315 of SEQ ID NO: 8.

[030] Any of a variety of sequence alignment methods can be used to determine percent identity, including, without limitation, global methods, local methods and hybrid methods, such as, e.g., segment approach methods. Protocols to determine percent identity are routine procedures within the scope of one skilled in the art and from the teaching herein.

[031] Global methods align sequences from the beginning to the end of the molecule and determine the best alignment by adding up scores of individual residue pairs and by imposing gap penalties. Non- limiting methods include, e.g., CLUSTAL W, see, e.g., Julie D. Thompson et al., CLUSTAL W: Improving

the Sensitivity of Progressive Multiple Sequence Alignment Through Sequence Weighting, Position- Specific Gap Penalties and Weight Matrix Choice, 22(22) Nucleic Acids Research 4673-4680 (1994); and iterative refinement, see, e.g., Osamu Gotoh, Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinement as Assessed by Reference to Structural Alignments, 264(4) J. MoI. Biol. 823-838 (1996).

[032] Local methods align sequences by identifying one or more conserved motifs shared by all of the input sequences. Non-limiting methods include, e.g., Match-box, see, e.g., Eric Depiereux and Ernest Feytmans, Match-Box: A Fundamentally New Algorithm for the Simultaneous Alignment of Several Protein Sequences, 8(5) CABIOS 501-509 (1992); Gibbs sampling, see, e.g., C. E. Lawrence et al., Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment, 262(5131) Science 208-214 (1993); Align-M, see, e.g., Ivo Van WaIIe et al., Align-M - A New Algorithm for Multiple Alignment of Highly Divergent Sequences, 20(9) Bioinformatics,:1428-1435 (2004).

[033] Hybrid methods combine functional aspects of both global and local alignment methods. Non- limiting methods include, e.g., segment-to-segment comparison, see, e.g., Burkhard Morgenstern et al., Multiple DNA and Protein Sequence Alignment Based On Segment-To-Segment Comparison, 93(22) Proc. Natl. Acad. Sci. U.S.A. 12098-12103 (1996); T-Coffee, see, e.g., Cedric Notredame et al., T-Coffee: A Novel Algorithm for Multiple Sequence Alignment, 302(1) J. MoI. Biol. 205-217 (2000); MUSCLE, see, e.g., Robert C. Edgar, MUSCLE: Multiple Sequence Alignment With High Score Accuracy and High Throughput, 32(5) Nucleic Acids Res. 1792-1797 (2004); and DIALIGN-T, see, e.g., Amarendran R Subramanian et al., DIALIGN-T: An Improved Algorithm for Segment-Based Multiple Sequence Alignment, 6(1) BMC Bioinformatics 66 (2005).

[034] As used herein, the term "naturally occurring Clostridial toxin variant" means any Clostridial toxin produced without the aid of any human manipulation, including, without limitation, Clostridial toxin isoforms produced from alternatively-spliced transcripts, Clostridial toxin isoforms produced by spontaneous mutation and Clostridial toxin subtypes. Non-limiting examples of a Clostridial toxin isoform include, e.g., BoNT/A isoforms, BoNT/B isoforms, BoNT/C1 isoforms, BoNT/D isoforms, BoNT/E isoforms, BoNT/F isoforms, BoNT/G isoforms, and TeNT isoforms. Non-limiting examples of a Clostridial toxin subtype include, e.g., BoNT/A subtypes BoNT/A1 , BoNT/A2, BoNT/A3 and BoNT/A4; BoNT/B subtypes BoNT/B1 , BoNT/B2, BoNT/B bivalent and BoNT/B nonproteolytic; B0NT/CI subtypes B0NT/CI- 1 and BoNT/Ci-2; BoNT/E subtypes BoNT/E1 , BoNT/E2 and BoNT/E3; and BoNT/F subtypes BoNT/F1 , BONT/F2, BONT/F3 and BoNT/F4.

[035] As used herein, the term "non-naturally occurring Clostridial toxin variant" means any Clostridial toxin produced with the aid of human manipulation, including, without limitation, Clostridial toxins produced by genetic engineering using random mutagenesis or rational design and Clostridial toxins produced by chemical synthesis. Non-limiting examples of non-naturally occurring Clostridial toxin

variants include, e.g., conservative Clostridial toxin variants, non-conservative Clostridial toxin variants, Clostridial toxin chimeric variants and active Clostridial toxin fragments.

[036] As used herein, the term "conservative Clostridial toxin variant" means a Clostridial toxin that has at least one amino acid substituted by another amino acid or an amino acid analog that has at least one property similar to that of the original amino acid from the reference Clostridial toxin sequence (Table 1). Examples of properties include, without limitation, similar size, topography, charge, hydrophobicity, hydrophilicity, lipophilicity, covalent-bonding capacity, hydrogen-bonding capacity, a physicochemical property, of the like, or any combination thereof. A conservative Clostridial toxin variant can function in substantially the same manner as the reference Clostridial toxin on which the conservative Clostridial toxin variant is based, and can be substituted for the reference Clostridial toxin in any aspect of the present invention. A conservative Clostridial toxin variant may substitute one or more amino acids, two or more amino acids, three or more amino acids, four or more amino acids, five or more amino acids, ten or more amino acids, 20 or more amino acids, 30 or more amino acids, 40 or more amino acids, 50 or more amino acids, 100 or more amino acids, 200 or more amino acids, 300 or more amino acids, 400 or more amino acids, or 500 or more amino acids from the reference Clostridial toxin on which the conservative Clostridial toxin variant is based. A conservative Clostridial toxin variant can also substitute at least 10 contiguous amino acids, at least 15 contiguous amino acids, at least 20 contiguous amino acids, or at least 25 contiguous amino acids from the reference Clostridial toxin on which the conservative Clostridial toxin variant is based, that possess at least 50% amino acid identity, 65% amino acid identity, 75% amino acid identity, 85% amino acid identity or 95% amino acid identity to the reference Clostridial toxin on which the conservative Clostridial toxin variant is based. Non-limiting examples of a conservative Clostridial toxin variant include, e.g., conservative BoNT/A variants, conservative BoNT/B variants, conservative BoNT/C1 variants, conservative BoNT/D variants, conservative BoNT/E variants, conservative BoNT/F variants, conservative BoNT/G variants, and conservative TeNT variants.

[037] As used herein, the term "non-conservative Clostridial toxin variant" means a Clostridial toxin in which 1) at least one amino acid is deleted from the reference Clostridial toxin on which the non- conservative Clostridial toxin variant is based; 2) at least one amino acid added to the reference Clostridial toxin on which the non-conservative Clostridial toxin is based; or 3) at least one amino acid is substituted by another amino acid or an amino acid analog that does not share any property similar to that of the original amino acid from the reference Clostridial toxin sequence (Table 1). A non- conservative Clostridial toxin variant can function in substantially the same manner as the reference Clostridial toxin on which the non-conservative Clostridial toxin variant is based, and can be substituted for the reference Clostridial toxin in any aspect of the present invention. A non-conservative Clostridial toxin variant can delete one or more amino acids, two or more amino acids, three or more amino acids, four or more amino acids, five or more amino acids, and ten or more amino acids from the reference Clostridial toxin on which the non-conservative Clostridial toxin variant is based. A non-conservative Clostridial toxin variant can add one or more amino acids, two or more amino acids, three or more amino

acids, four or more amino acids, five or more amino acids, and ten or more amino acids to the reference Clostridial toxin on which the non-conservative Clostridial toxin variant is based. A non-conservative Clostridial toxin variant may substitute one or more amino acids, two or more amino acids, three or more amino acids, four or more amino acids, five or more amino acids, ten or more amino acids, 20 or more amino acids, 30 or more amino acids, 40 or more amino acids, 50 or more amino acids, 100 or more amino acids, 200 or more amino acids, 300 or more amino acids, 400 or more amino acids, or 500 or more amino acids from the reference Clostridial toxin on which the non-conservative Clostridial toxin variant is based. A non-conservative Clostridial toxin variant can also substitute at least 10 contiguous amino acids, at least 15 contiguous amino acids, at least 20 contiguous amino acids, or at least 25 contiguous amino acids from the reference Clostridial toxin on which the non-conservative Clostridial toxin variant is based, that possess at least 50% amino acid identity, 65% amino acid identity, 75% amino acid identity, 85% amino acid identity or 95% amino acid identity to the reference Clostridial toxin on which the non-conservative Clostridial toxin variant is based. Non-limiting examples of a non- conservative Clostridial toxin variant include, e.g., non-conservative BoNT/A variants, non-conservative BoNT/B variants, non-conservative BoNT/C1 variants, non-conservative BoNT/D variants, non- conservative BoNT/E variants, non-conservative BoNT/F variants, non-conservative BoNT/G variants, and non-conservative TeNT variants.

[038] As used herein, the term "Clostridial toxin chimeric variant" means a molecule comprising at least a portion of a Clostridial toxin and at least a portion of at least one other protein to form a toxin with at least one property different from the reference Clostridial toxins of Table 1. One class of Clostridial toxin chimeric variant comprises a modified Clostridial toxin were the endogenous cell binding domain of a naturally-occurring Clostridial toxin is either modified or replaced with a cell binding domain of another molecule. Such modified Clostridial toxin possesses an altered cell binding activity because the modified toxin can, e.g., use the same receptor present on the surface of a naturally occurring Clostridial toxin target cell, referred to as an enhanced cell binding activity for a naturally-occurring Clostridial toxin target cell; use a different receptor present on the surface of a naturally occurring Clostridial toxin target cell, referred to as an altered cell binding activity for a naturally-occurring Clostridial toxin target cell, or use a different receptor present on the surface of the non-Clostridial toxin target cell, referred to as an altered cell binding activity for a non-naturally-occurring Clostridial toxin target cell.

[039] A Clostridial toxin chimeric variant can be a modified Clostridial toxin with an enhanced cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell, e.g., a motor neuron. One way this enhanced binding activity is achieved by modifying the endogenous targeting domain of a naturally-occurring Clostridial toxin in order to enhance a cell binding activity of the toxin for its naturally- occurring receptor. Such modifications to a targeting domain result in, e.g., a enhanced cell binding activity that increases binding affinity for an endogenous Clostridial toxin receptor present on a naturally- occurring Clostridial toxin target cell; an enhanced cell binding activity that increases binding specificity for a subgroup of endogenous Clostridial toxin receptors present on a naturally-occurring Clostridial toxin

target cell; or an enhanced cell binding activity that increases both binding affinity and binding specificity. Non-limiting examples of modified Clostridial toxins an enhanced cell binding activity for a naturally- occurring Clostridial toxin receptor are described in, e.g., Lance E. Steward, et al., Modified Clostridial Toxins with Enhanced Targeting Capabilities For Endogenous Clostridial Toxin Receptors, International Patent Publication No. 2006/008956 (Mar. 14, 2006), Lance E. Steward, Modified Clostridial Toxins with Enhanced Translocation Capability, and Enhanced Targeting Activity, U.S. Provisional Patent Application No. 60/807,063 (JuI. 11 , 2006); the content of which are all hereby incorporated by reference in their entirety.

[040] A Clostridial toxin chimeric variant can be a modified Clostridial toxin with an altered cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell, e.g., a motor neuron. One way this altered capability is achieved by replacing the endogenous targeting domain of a naturally- occurring Clostridial toxin with a targeting domain of another molecule that selectively binds to a different receptor present on the surface of a naturally occurring Clostridial toxin target cell. Such a modification to a targeting domain results in a modified toxin that is able to selectively bind to a non-Clostridial toxin receptor (target receptor) present on a Clostridial toxin target cell. This enhanced binding activity for a naturally occurring Clostridial toxin target cell allows for lower effective doses of a modified Clostridial toxin to be administered to an individual because more toxin will be delivered to the target cell. Thus, modified Clostridial toxins with an enhanced binding activity will reduce the undesirable dispersal of the toxin to areas not targeted for treatment, thereby reducing or preventing the undesirable side-effects associated with diffusion of a Clostridial toxin to an unwanted location. Non-limiting examples of modified Clostridial toxins with an altered cell binding capability for a Clostridial toxin target cell are described in, e.g., Lance E. Steward et al., Modified Clostridial Toxins with Altered Targeting Capabilities For Clostridial Toxin Target Cells, International Patent Publication No. 2006/009831 (Mar. 14, 2005); Lance E. Steward et al., Multivalent Clostridial Toxin Derivatives and Methods of Their Use, U.S. Patent Application No. 11/376,696 (Mar. 15, 2006); and Lance E. Steward, Modified Clostridial Toxins with Enhanced Translocation Capabilities and Altered Targeting Activity for Clostridial Toxin Target Cells, U.S. Provisional Patent Application No. 60/807,062, (JuI. 11 , 2006); the contents of all of which are hereby incorporated by reference in their entirety.

[041] A Clostridial toxin chimeric variant can be a modified Clostridial toxin with an altered cell binding activity capable of intoxicating a cell other than a naturally occurring Clostridial toxin target cell, e.g., a cell other than a motor neuron. These modified toxins achieve this intoxication by using a target receptor present on non-Clostridial toxin target cell. This re-targeted capability is achieved by replacing a naturally-occurring targeting domain of a Clostridial toxin with a targeting domain showing a selective binding activity for a non-Clostridial toxin receptor present in a non-Clostridial toxin target cell. Such modifications to a targeting domain result in a modified toxin that is able to selectively bind to a non- Clostridial toxin receptor (target receptor) present on a non-Clostridial toxin target cell (re-targeted). A modified Clostridial toxin with an altered targeting activity for a non-Clostridial toxin target cell can bind to

a target receptor, translocate into the cytoplasm, and exert its proteolytic effect on the SNARE complex of the non-Clostridial toxin target cell. Non-limiting examples of modified Clostridial toxins with an altered targeting activity for a non-Clostridial toxin target cell are described in, e.g., Keith A. Foster et al., Clostridial Toxin Derivatives Able To Modify Peripheral Sensory Afferent Functions, U.S. Patent 5,989,545 (Nov. 23, 1999); Clifford C. Shone et al., Recombinant Toxin Fragments, U.S. Patent 6,461 ,617 (Oct. 8, 2002); Conrad P. Quinn et al., Methods and Compounds for the Treatment of Mucus Hypersecretion, U.S. Patent 6,632,440 (Oct. 14, 2003); Lance E. Steward et al., Methods And Compositions For The Treatment Of Pancreatitis, U.S. Patent 6,843,998 (Jan. 18, 2005); Stephan Donovan, Clostridial Toxin Derivatives and Methods For Treating Pain, U.S. Patent Publication 2002/0037833 (Mar. 28, 2002); Keith A. Foster et al., Inhibition of Secretion from Non-neural Cells, U.S. Patent Publication 2003/0180289 (Sep. 25, 2003); J. Oliver Dolly et al., Activatable Recombinant Neurotoxins, WO 2001/014570 (Mar. 1 , 2001); Keith A. Foster et al., Re-targeted Toxin Conjugates, International Patent Publication WO 2005/023309 (Mar. 17, 2005); Lance E. Steward et al., Multivalent Clostridial Toxin Derivatives and Methods of Their Use, U.S. Patent Application No. 11/376,696 (Mar. 15, 2006); and Lance E. Steward, Modified Clostridial Toxins with Enhanced Translocation Capabilities and Altered Targeting Capabilities for Non-Clostridial Toxin Target Cells, U.S. Provisional Patent Application No. 60/807,059, (JuI. 11 , 2006); the contents of all of which are hereby incorporated by reference in their entirety. The ability to re-target the therapeutic effects associated with Clostridial toxins has greatly extended the number of medicinal applications able to use a Clostridial toxin therapy. As a non-limiting example, modified Clostridial toxins retargeted to sensory neurons are useful in treating various kinds of chronic pain, such as, e.g., hyperalgesia and allodynia, neuropathic pain and inflammatory pain, see, e.g., Foster, supra, (1999); and Donovan, supra, (2002); and Stephan Donovan, Method For Treating Neurogenic Inflammation Pain with Botulinum Toxin and Substance P Components, U.S. Patent 7,022,329 (Apr. 4, 2006). As another non-limiting example, modified Clostridial toxins retargeted to pancreatic cells are useful in treating pancreatitis, see, e.g., Steward, supra, (2005).

[042] Thus, in an embodiment, a Clostridial toxin chimeric variant can comprise a modified Clostridial toxin disclosed in the present specification where the binding domain comprises an enhanced cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell. In another embodiment, a Clostridial toxin chimeric variant can comprise a modified Clostridial toxin disclosed in the present specification where the binding domain comprises an altered cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell. In still another embodiment, a Clostridial toxin chimeric variant can comprise a modified Clostridial toxin disclosed in the present specification where the binding domain comprises an altered cell binding activity capable of intoxicating a non-naturally occurring Clostridial toxin target cell.

[043] It is also envisioned that any of a variety of Clostridial toxin fragments can be useful in aspects of the present invention with the proviso that these active fragments can execute the overall cellular mechanism whereby a Clostridial toxin proteolytically cleaves a substrate. Thus, aspects of this

embodiment can include Clostridial toxin fragments having a length of, e.g., at least 300 amino acids, at least 400 amino acids, at least 500 amino acids, at least 600 amino acids, at least 700 amino acids, at least 800 amino acids, at least 900 amino acids, at least 1000 amino acids, at least 1100 amino acids and at least 1200 amino acids. Other aspects of this embodiment, can include Clostridial toxin fragments having a length of, e.g., at most 300 amino acids, at most 400 amino acids, at most 500 amino acids, at most 600 amino acids, at most 700 amino acids, at most 800 amino acids, at most 900 amino acids, at most 1000 amino acids, at most 1100 amino acids and at most 1200 amino acids.

[044] It is also envisioned that any of a variety of Clostridial toxin fragments comprising the light chain can be useful in aspects of the present invention with the proviso that these light chain fragments can specifically target the core components of the neurotransmitter release apparatus and thus participate in executing the overall cellular mechanism whereby a Clostridial toxin proteolytically cleaves a substrate. The light chains of Clostridial toxins are approximately 420-460 amino acids in length and comprise an enzymatic domain (Table 1). Research has shown that the entire length of a Clostridial toxin light chain is not necessary for the enzymatic activity of the enzymatic domain. As a non-limiting example, the first eight amino acids of the BoNT/A light chain (residues 1-8 of SEQ ID NO: 1) are not required for enzymatic activity. As another non-limiting example, the first eight amino acids of the TeNT light chain (residues 1-8 of SEQ ID NO: 8) are not required for enzymatic activity. Likewise, the carboxyl-terminus of the light chain is not necessary for activity. As a non-limiting example, the last 32 amino acids of the BoNT/A light chain (residues 417-448 of SEQ ID NO: 1) are not required for enzymatic activity. As another non-limiting example, the last 31 amino acids of the TeNT light chain (residues 427-457 of SEQ ID NO: 8) are not required for enzymatic activity. Thus, aspects of this embodiment can include Clostridial toxin light chains comprising an enzymatic domain having a length of, e.g., at least 350 amino acids, at least 375 amino acids, at least 400 amino acids, at least 425 amino acids and at least 450 amino acids. Other aspects of this embodiment can include Clostridial toxin light chains comprising an enzymatic domain having a length of, e.g., at most 350 amino acids, at most 375 amino acids, at most 400 amino acids, at most 425 amino acids and at most 450 amino acids.

[045] It is also envisioned that any of a variety of Clostridial toxin H _N regions comprising a translocation domain can be useful in aspects of the present invention with the proviso that these active fragments can facilitate the release of the LC from intracellular vesicles into the cytoplasm of the target cell and thus participate in executing the overall cellular mechanism whereby a Clostridial toxin proteolytically cleaves a substrate. The H _N regions from the heavy chains of Clostridial toxins are approximately 410-430 amino acids in length and comprise a translocation domain (Table 1). Research has shown that the entire length of a H _N region from a Clostridial toxin heavy chain is not necessary for the translocating activity of the translocation domain. Thus, aspects of this embodiment can include Clostridial toxin H _N regions comprising a translocation domain having a length of, e.g., at least 350 amino acids, at least 375 amino acids, at least 400 amino acids and at least 425 amino acids. Other aspects of this embodiment can

include Clostridial toxin H _N regions comprising translocation domain having a length of, e.g., at most 350 amino acids, at most 375 amino acids, at most 400 amino acids and at most 425 amino acids.

[046] It is also envisioned that any of a variety of Clostridial toxin H _c regions comprising a binding domain can be useful in aspects of the present invention with the proviso that these active fragments can determine the binding activity and binding specificity of the toxin to the receptor complex located at the surface of the target cell execute the overall cellular mechanism whereby a Clostridial toxin proteolytically cleaves a substrate. The H _c regions from the heavy chains of Clostridial toxins are approximately 400- 440 amino acids in length and comprise a binding domain (Table 1). Research has shown that the entire length of a H _c region from a Clostridial toxin heavy chain is not necessary for the binding activity of the binding domain. Thus, aspects of this embodiment can include Clostridial toxin H ₀ regions comprising a binding domain having a length of, e.g., at least 350 amino acids, at least 375 amino acids, at least 400 amino acids and at least 425 amino acids. Other aspects of this embodiment can include Clostridial toxin Hc regions comprising a binding domain having a length of, e.g., at most 350 amino acids, at most 375 amino acids, at most 400 amino acids and at most 425 amino acids.

[047] Thus, in an embodiment, a Clostridial toxin comprises a Clostridial toxin enzymatic domain, a Clostridial toxin translocation domain and a Clostridial toxin binding domain. In an aspect of this embodiment, a Clostridial toxin comprises a naturally occurring Clostridial toxin variant, such as, e.g., a Clostridial toxin isoform or a Clostridial toxin subtype. In another aspect of this embodiment, a Clostridial toxin comprises a non-naturally occurring Clostridial toxin variant, such as, e.g., a conservative Clostridial toxin variant, a non-conservative Clostridial toxin variant or an active Clostridial toxin fragment, or any combination thereof. In another aspect of this embodiment, a Clostridial toxin comprises a Clostridial toxin enzymatic domain or an active fragment thereof, a Clostridial toxin translocation domain or an active fragment thereof, a Clostridial toxin binding domain or an active fragment thereof, or any combination thereof. In other aspects of this embodiment, a Clostridial toxin can comprise a BoNT/A, a BoNT/B, a BoNT/CI , a BoNT/D, a BoNT/E, a BoNT/F, a BoNT/G or a TeNT.

[048] In another embodiment, a Clostridial toxin comprises a BoNT/A. In an aspect of this embodiment, a BoNT/A comprises a BoNT/A enzymatic domain, a BoNT/A translocation domain and a BoNT/A binding domain. In another aspect of this embodiment, a BoNT/A comprises SEQ ID NO: 1. In another aspect of this embodiment, a BoNT/A comprises a naturally occurring BoNT/A variant, such as, e.g., a BoNT/A isoform or a BoNT/A subtype. In another aspect of this embodiment, a BoNT/A comprises a naturally occurring BoNT/A variant of SEQ ID NO: 1 , such as, e.g., a BoNT/A isoform of SEQ ID NO: 1 or a BoNT/A subtype of SEQ ID NO: 1. In still another aspect of this embodiment, a BoNT/A comprises a non-naturally occurring BoNT/A variant, such as, e.g., a conservative BoNT/A variant, a non-conservative BoNT/A variant or an active BoNT/A fragment, or any combination thereof. In still another aspect of this embodiment, a BoNT/A comprises a non-naturally occurring BoNT/A variant of SEQ ID NO: 1 , such as, e.g., a conservative BoNT/A variant of SEQ ID NO: 1 , a non-conservative BoNT/A variant of SEQ ID NO:

1 or an active BoNT/A fragment of SEQ ID NO: 1 , or any combination thereof. In yet another aspect of this embodiment, a BoNT/A comprises a BoNT/A enzymatic domain or an active fragment thereof, a BoNT/A translocation domain or an active fragment thereof, a BoNT/A binding domain or an active fragment thereof, or any combination thereof. In yet another aspect of this embodiment, a BoNT/A comprising a BoNT/A enzymatic domain of amino acids 1-448 from SEQ ID NO: 1 or an active fragment thereof, a BoNT/A translocation domain of amino acids 449-871 from SEQ ID NO: 1 or an active fragment thereof, a BoNT/A binding domain of amino acids 872-1296 from SEQ ID NO: 1 or an active fragment thereof, and any combination thereof.

[049] In other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 1 , at least 75% amino acid identity with the SEQ ID NO: 1 , at least 80% amino acid identity with SEQ ID NO: 1 , at least 85% amino acid identity with SEQ ID NO: 1 , at least 90% amino acid identity with SEQ ID NO: 1 or at least 95% amino acid identity with SEQ ID NO: 1. In yet other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 1 , at most 75% amino acid identity with the SEQ ID NO: 1 , at most 80% amino acid identity with SEQ ID NO: 1 , at most 85% amino acid identity with SEQ ID NO: 1 , at most 90% amino acid identity with SEQ ID NO: 1 or at most 95% amino acid identity with SEQ ID NO: 1.

[050] In other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 1. In other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 1. In yet other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 1. In other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 1. In still other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 1. In other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 1.

[051] In other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 1. In other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 1. In yet other aspects of this

embodiment, a BoNT/A comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 1. In other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 1. In still other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 1. In other aspects of this embodiment, a BoNT/A comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 1.

[052] In another embodiment, a Clostridial toxin comprises a BoNT/B. In an aspect of this embodiment, a BoNT/B comprises a BoNT/B enzymatic domain, a BoNT/B translocation domain and a BoNT/B binding domain. In another aspect of this embodiment, a BoNT/B comprises SEQ ID NO: 2. In another aspect of this embodiment, a BoNT/B comprises a naturally occurring BoNT/B variant, such as, e.g., a BoNT/B isoform or a BoNT/B subtype. In another aspect of this embodiment, a BoNT/B comprises a naturally occurring BoNT/B variant of SEQ ID NO: 2, such as, e.g., a BoNT/B isoform of SEQ ID NO: 2 or a BoNT/B subtype of SEQ ID NO: 2. In still another aspect of this embodiment, a BoNT/B comprises a non-naturally occurring BoNT/B variant, such as, e.g., a conservative BoNT/B variant, a non-conservative BoNT/B variant or an active BoNT/B fragment, or any combination thereof. In still another aspect of this embodiment, a BoNT/B comprises a non-naturally occurring BoNT/B variant of SEQ ID NO: 2, such as, e.g., a conservative BoNT/B variant of SEQ ID NO: 2, a non-conservative BoNT/B variant of SEQ ID NO: 2 or an active BoNT/B fragment of SEQ ID NO: 2, or any combination thereof. In yet another aspect of this embodiment, a BoNT/B comprising a BoNT/B enzymatic domain or an active fragment thereof, a BoNT/B translocation domain or active fragment thereof, a BoNT/B binding domain or active fragment thereof, and any combination thereof. In yet another aspect of this embodiment, a BoNT/B comprising a BoNT/B enzymatic domain of amino acids 1-441 from SEQ ID NO: 2 or active fragment thereof, a BoNT/B translocation domain of amino acids 442-858 from SEQ ID NO: 2 or active fragment thereof, a BoNT/B binding domain of amino acids 859-1291 from SEQ ID NO: 2 or active fragment thereof, and any combination thereof.

[053] In other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 2, at least 75% amino acid identity with the SEQ ID NO: 2, at least 80% amino acid identity with SEQ ID NO: 2, at least 85% amino acid identity with SEQ ID NO: 2, at least 90% amino acid identity with SEQ ID NO: 2 or at least 95% amino acid identity with SEQ ID NO: 2. In yet other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 2, at most 75% amino acid identity with the SEQ ID NO: 2, at most 80% amino acid identity with SEQ ID NO: 2, at most 85% amino acid identity with SEQ ID NO: 2, at most 90% amino acid identity with SEQ ID NO: 2 or at most 95% amino acid identity with SEQ ID NO: 2.

[054] In other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 2. In other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 2. In yet other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 2. In other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 2. In still other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 2. In other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 2.

[055] In other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 2. In other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 2. In yet other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 2. In other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 2. In still other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 2. In other aspects of this embodiment, a BoNT/B comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 2.

[056] In another embodiment, a Clostridial toxin comprises a BoNTVCI . In an aspect of this embodiment, a BoNTVCI comprises a BoNTVCI enzymatic domain, a BoNTVCI translocation domain and a BoNTVCI binding domain. In another aspect of this embodiment, a BoNTVCI comprises SEQ ID NO: 3. In another aspect of this embodiment, a BoNT/C1 comprises a naturally occurring BoNT/C1 variant, such as, e.g., a BoNT/C1 isoform or a BoNT/C1 subtype. In another aspect of this embodiment, a B0NT/CI comprises a naturally occurring B0NT/CI variant of SEQ ID NO: 3, such as, e.g., a BoNT/C1 isoform of

SEQ ID NO: 3 or a BoNT/C1 subtype of SEQ ID NO: 3. In still another aspect of this embodiment, a BoNT/C1 comprises a non-naturally occurring BoNT/C1 variant, such as, e.g., a conservative BoNT/C1 variant, a non-conservative BoNT/C1 variant or an active B0NT/CI fragment, or any combination thereof. In still another aspect of this embodiment, a BoNT/C1 comprises a non-naturally occurring BoNT/C1 variant of SEQ ID NO: 3, such as, e.g., a conservative BoNT/C1 variant of SEQ ID NO: 3, a non- conservative BoNT/C1 variant of SEQ ID NO: 3 or an active B0NT/CI fragment of SEQ ID NO: 3, or any combination thereof. In yet another aspect of this embodiment, a B0NT/CI comprises a BoNT/C1 enzymatic domain or active fragment thereof, a BoNT/C1 translocation domain or active fragment thereof, a BoNT/C1 binding domain or active fragment thereof, and any combination thereof. In yet another aspect of this embodiment, a BoNT/C1 comprises a BoNT/C1 enzymatic domain of amino acid 1-449 from SEQ ID NO: 3 or active fragment thereof, a BoNT/C1 translocation domain of amino acids 450-866 from SEQ ID NO: 3 or active fragment thereof, a BoNT/C1 binding domain of amino acids 867-1291 from SEQ ID NO: 3 or active fragment thereof, and any combination thereof.

[057] In other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 3, at least 75% amino acid identity with the SEQ ID NO: 3, at least 80% amino acid identity with SEQ ID NO: 3, at least 85% amino acid identity with SEQ ID NO: 3, at least 90% amino acid identity with SEQ ID NO: 3 or at least 95% amino acid identity with SEQ ID NO: 3. In yet other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 3, at most 75% amino acid identity with the SEQ ID NO: 3, at most 80% amino acid identity with SEQ ID NO: 3, at most 85% amino acid identity with SEQ ID NO: 3, at most 90% amino acid identity with SEQ ID NO: 3 or at most 95% amino acid identity with SEQ ID NO: 3.

[058] In other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 3. In other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 3. In yet other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 3. In other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 3. In still other aspects of this embodiment, a B0NT/CI comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 3. In other aspects of this embodiment, a B0NT/CI comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 3.

[059] In other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 3. In other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 3. In yet other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 3. In other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 3. In still other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 3. In other aspects of this embodiment, a BoNT/C1 comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 3.

[060] In another embodiment, a Clostridial toxin comprises a BoNT/D. In an aspect of this embodiment, a BoNT/D comprises a BoNT/D enzymatic domain, a BoNT/D translocation domain and a BoNT/D binding domain. In another aspect of this embodiment, a BoNT/D comprises SEQ ID NO: 4. In another aspect of this embodiment, a BoNT/D comprises a naturally occurring BoNT/D variant, such as, e.g., a BoNT/D isoform or a BoNT/D subtype. In another aspect of this embodiment, a BoNT/D comprises a naturally occurring BoNT/D variant of SEQ ID NO: 4, such as, e.g., a BoNT/D isoform of SEQ ID NO: 4 or a BoNT/D subtype of SEQ ID NO: 4. In still another aspect of this embodiment, a BoNT/D comprises a non-naturally occurring BoNT/D variant, such as, e.g., a conservative BoNT/D variant, a non-conservative BoNT/D variant or an active BoNT/D fragment, or any combination thereof. In still another aspect of this embodiment, a BoNT/D comprises a non-naturally occurring BoNT/D variant of SEQ ID NO: 4, such as, e.g., a conservative BoNT/D variant of SEQ ID NO: 4, a non-conservative BoNT/D variant of SEQ ID NO: 4 or an active BoNT/D fragment of SEQ ID NO: 4, or any combination thereof. In yet another aspect of this embodiment, a BoNT/D comprises a BoNT/D enzymatic domain or an active fragment thereof, a BoNT/D translocation domain or an active fragment thereof, a BoNT/D binding domain or an active fragment thereof, or any combination thereof. In yet another aspect of this embodiment, a BoNT/D comprising a BoNT/D enzymatic domain of amino acids 1-445 from SEQ ID NO: 4 or an active fragment thereof, a BoNT/D translocation domain of amino acids 446-862 from SEQ ID NO: 4 or an active fragment thereof, a BoNT/D binding domain of amino acids 863-1276 from SEQ ID NO: 4 or an active fragment thereof, and any combination thereof.

[061] In other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 4, at least 75% amino acid identity with the SEQ ID NO: 4, at least 80% amino acid identity with SEQ ID NO: 4, at least 85% amino acid identity with SEQ ID NO: 4, at

least 90% amino acid identity with SEQ ID NO: 4 or at least 95% amino acid identity with SEQ ID NO: 4. In yet other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 4, at most 75% amino acid identity with the SEQ ID NO: 4, at most 80% amino acid identity with SEQ ID NO: 4, at most 85% amino acid identity with SEQ ID NO: 4, at most 90% amino acid identity with SEQ ID NO: 4 or at most 95% amino acid identity with SEQ ID NO: 4.

[062] In other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 4. In other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 4. In yet other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 4. In other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 4. In still other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 4. In other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 4.

[063] In other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 4. In other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 4. In yet other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 4. In other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 4. In still other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 4. In other aspects of this embodiment, a BoNT/D comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 4.

[064] In another embodiment, a Clostridial toxin comprises a BoNT/E. In an aspect of this embodiment, a BoNT/E comprises a BoNT/E enzymatic domain, a BoNT/E translocation domain and a BoNT/E binding domain. In another aspect of this embodiment, a BoNT/E comprises SEQ ID NO: 5. In another aspect of this embodiment, a BoNT/E comprises a naturally occurring BoNT/E variant, such as, e.g., a BoNT/E isoform or a BoNT/E subtype. In another aspect of this embodiment, a BoNT/E comprises a naturally occurring BoNT/E variant of SEQ ID NO: 5, such as, e.g., a BoNT/E isoform of SEQ ID NO: 5 or a BoNT/E subtype of SEQ ID NO: 5. In still another aspect of this embodiment, a BoNT/E comprises a non-naturally occurring BoNT/E variant, such.as, e.g., a conservative BoNT/E variant, a non-conservative BoNT/E variant or an active BoNT/E fragment, or any combination thereof. In still another aspect of this embodiment, a BoNT/E comprises a non-naturally occurring BoNT/E variant of SEQ ID NO: 5, such as, e.g., a conservative BoNT/E variant of SEQ ID NO: 5, a non-conservative BoNT/E variant of SEQ ID NO: 5 or an active BoNT/E fragment of SEQ ID NO: 5, or any combination thereof. In yet another aspect of this embodiment, a BoNT/E comprising a BoNT/E enzymatic domain or an active fragment thereof, a BoNT/E translocation domain or active fragment thereof, a BoNT/E binding domain or active fragment thereof, and any combination thereof. In yet another aspect of this embodiment, a BoNT/E comprising a BoNT/E enzymatic domain of amino acids 1-422 from SEQ ID NO: 5 or active fragment thereof, a BoNT/E translocation domain of amino acids 423-845 from SEQ ID NO: 5 or active fragment thereof, a BoNT/E binding domain of amino acids 846-1252 from SEQ ID NO: 5 or active fragment thereof, and any combination thereof.

[065] In other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 5, at least 75% amino acid identity with the SEQ ID NO: 5, at least 80% amino acid identity with SEQ ID NO: 5, at least 85% amino acid identity with SEQ ID NO: 5, at least 90% amino acid identity with SEQ ID NO: 5 or at least 95% amino acid identity with SEQ ID NO: 5. In yet other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 5, at most 75% amino acid identity with the SEQ ID NO: 5, at most 80% amino acid identity with SEQ ID NO: 5, at most 85% amino acid identity with SEQ ID NO: 5, at most 90% amino acid identity with SEQ ID NO: 5 or at most 95% amino acid identity with SEQ ID NO: 5.

[066] In other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 5. In other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 5. In yet other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 5. In other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 5. In still other aspects of this embodiment,

a BoNT/E comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 5. In other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 5.

[067] In other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 5. In other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 5. In yet other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 5. In other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 5. In still other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 5. In other aspects of this embodiment, a BoNT/E comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 5.

[068] In another embodiment, a Clostridial toxin comprises a BoNT/F. In an aspect of this embodiment, a BoNT/F comprises a BoNT/F enzymatic domain, a BoNT/F translocation domain and a BoNT/F binding domain. In another aspect of this embodiment, a BoNT/F comprises SEQ ID NO: 6. In another aspect of this embodiment, a BoNT/F comprises a naturally occurring BoNT/F variant, such as, e.g., a BoNT/F isoform or a BoNT/F subtype. In another aspect of this embodiment, a BoNT/F comprises a naturally occurring BoNT/F variant of SEQ ID NO: 6, such as, e.g., a BoNT/F isoform of SEQ ID NO: 6 or a BoNT/F subtype of SEQ ID NO: 6. In still another aspect of this embodiment, a BoNT/F comprises a non- naturally occurring BoNT/F variant, such as, e.g., a conservative BoNT/F variant, a non-conservative BoNT/F variant or an active BoNT/F fragment, or any combination thereof. In still another aspect of this embodiment, a BoNT/F comprises a non-naturally occurring BoNT/F variant of SEQ ID NO: 6, such as, e.g., a conservative BoNT/F variant of SEQ ID NO: 6, a non-conservative BoNT/F variant of SEQ ID NO: 6 or an active BoNT/F fragment of SEQ ID NO: 6, or any combination thereof. In yet another aspect of this embodiment, a BoNT/F comprises a BoNT/F enzymatic domain or active fragment thereof, a BoNT/F translocation domain or active fragment thereof, a BoNT/F binding domain or active fragment thereof, and any combination thereof. In yet another aspect of this embodiment, a BoNT/F comprises a BoNT/F enzymatic domain of amino acid 1-439 from SEQ ID NO: 6 or active fragment thereof, a BoNT/F translocation domain of amino acids 440-864 from SEQ ID NO: 6 or active fragment thereof, a BoNT/F

binding domain of amino acids 865-1274 from SEQ ID NO: 6 or active fragment thereof, and any combination thereof.

[069] In other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 6, at least 75% amino acid identity with the SEQ ID NO: 6, at least 80% amino acid identity with SEQ ID NO: 6, at least 85% amino acid identity with SEQ ID NO: 6, at least 90% amino acid identity with SEQ ID NO: 6 or at least 95% amino acid identity with SEQ ID NO: 6. In yet other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 6, at most 75% amino acid identity with the SEQ ID NO: 6, at most 80% amino acid identity with SEQ ID NO: 6, at most 85% amino acid identity with SEQ ID NO: 6, at most 90% amino acid identity with SEQ ID NO: 6 or at most 95% amino acid identity with SEQ ID NO: 6.

[070] In other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 6. In other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 6. In yet other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 6. In other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 6. In still other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 6. In other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 6.

[071] In other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 6. In other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 6. In yet other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 6. In other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 6. In still other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50,

100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 6. In other aspects of this embodiment, a BoNT/F comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 6.

[072] In another embodiment, a Clostridial toxin comprises a BoNT/G. In an aspect of this embodiment, a BoNT/G comprises a BoNT/G enzymatic domain, a BoNT/G translocation domain and a BoNT/G binding domain. In another aspect of this embodiment, a BoNT/G comprises SEQ ID NO: 7. In another aspect of this embodiment, a BoNT/G comprises a naturally occurring BoNT/G variant, such as, e.g., a BoNT/G isoform or a BoNT/G subtype. In another aspect of this embodiment, a BoNT/G comprises a naturally occurring BoNT/G variant of SEQ ID NO: 7, such as, e.g., a BoNT/G isoform of SEQ ID NO: 7 or a BoNT/G subtype of SEQ ID NO: 7. In still another aspect of this embodiment, a BoNT/G comprises a non-naturally occurring BoNT/G variant, such as, e.g., a conservative BoNT/G variant, a non-conservative BoNT/G variant or an active BoNT/G fragment, or any combination thereof. In still another aspect of this embodiment, a BoNT/D comprises a non-naturally occurring BoNT/G variant of SEQ ID NO: 7, such as, e.g., a conservative BoNT/G variant of SEQ ID NO: 7, a non-conservative BoNT/G variant of SEQ ID NO: 7 or an active BoNT/G fragment of SEQ ID NO: 7, or any combination thereof. In yet another aspect of this embodiment, a BoNT/G comprises a BoNT/G enzymatic domain or an active fragment thereof, a BoNT/G translocation domain or an active fragment thereof, a BoNT/G binding domain or an active fragment thereof, or any combination thereof. In yet another aspect of this embodiment, a BoNT/G comprising a BoNT/G enzymatic domain of amino acids 1-446 from SEQ ID NO: 7 or an active fragment thereof, a BoNT/G translocation domain of amino acids 447-863 from SEQ ID NO: 7 or an active fragment thereof, a BoNT/G binding domain of amino acids 864-1297 from SEQ ID NO: 7 or an active fragment thereof, and any combination thereof.

[073] In other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 7, at least 75% amino acid identity with the SEQ ID NO: 7, at least 80% amino acid identity with SEQ ID NO: 7, at least 85% amino acid identity with SEQ ID NO: 7, at least 90% amino acid identity with SEQ ID NO: 7 or at least 95% amino acid identity with SEQ ID NO: 7. In yet other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 7, at most 75% amino acid identity with the SEQ ID NO: 7, at most 80% amino acid identity with SEQ ID NO: 7, at most 85% amino acid identity with SEQ ID NO: 7, at most 90% amino acid identity with SEQ ID NO: 7 or at most 95% amino acid identity with SEQ ID NO: 7.

[074] In other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 7. In other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 7. In yet other

aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 7. In other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 7. In still other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 7. In other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 7.

[075] In other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 7. In other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 7. In yet other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 7. In other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 7. In still other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 7. In other aspects of this embodiment, a BoNT/G comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 7.

[076] In another embodiment, a Clostridial toxin comprises a TeNT. In an aspect of this embodiment, a TeNT comprises a TeNT enzymatic domain, a TeNT translocation domain and a TeNT binding domain. In an aspect of this embodiment, a TeNT comprises SEQ ID NO: 8. In another aspect of this embodiment, a TeNT comprises a naturally occurring TeNT variant, such as, e.g., a TeNT isoform or a TeNT subtype. In another aspect of this embodiment, a TeNT comprises a naturally occurring TeNT variant of SEQ ID NO: 8, such as, e.g., a TeNT isoform of SEQ ID NO: 8 or a TeNT subtype of SEQ ID NO: 8. In still another aspect of this embodiment, a TeNT comprises a non-naturally occurring TeNT variant, such as, e.g., a conservative TeNT variant, a non-conservative TeNT variant or an active TeNT fragment, or any combination thereof. In still another aspect of this embodiment, a TeNT comprises a non-naturally occurring TeNT variant of SEQ ID NO: 8, such as, e.g., a conservative TeNT variant of SEQ ID NO: 8, a non-conservative TeNT variant of SEQ ID NO: 8 or an active TeNT fragment of SEQ ID NO: 8, or any combination thereof. In yet another aspect of this embodiment, a TeNT comprising a TeNT

enzymatic domain or an active fragment thereof, a TeNT translocation domain or active fragment thereof, a TeNT binding domain or active fragment thereof, and any combination thereof. In yet another aspect of this embodiment, a TeNT comprising a TeNT enzymatic domain of amino acids 1-457 from SEQ ID NO: 8 or active fragment thereof, a TeNT translocation domain of amino acids 458-879 from SEQ ID NO: 8 or active fragment thereof, a TeNT binding domain of amino acids 880-1315 from SEQ ID NO: 8 or active fragment thereof, and any combination thereof.

[077] In other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 8, at least 75% amino acid identity with the SEQ ID NO: 8, at least 80% amino acid identity with SEQ ID NO: 8, at least 85% amino acid identity with SEQ ID NO: 8, at least 90% amino acid identity with SEQ ID NO: 8 or at least 95% amino acid identity with SEQ ID NO: 8. In yet other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 8, at most 75% amino acid identity with the SEQ ID NO: 8, at most 80% amino acid identity with SEQ ID NO: 8, at most 85% amino acid identity with SEQ ID NO: 8, at most 90% amino acid identity with SEQ ID NO: 8 or at most 95% amino acid identity with SEQ ID NO: 8.

[078] In other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 8. In other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 8. In yet other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 8. In other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 noncontiguous amino acid deletions relative to SEQ ID NO: 8. In still other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 8. In other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 8.

[079] In other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 8. In other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 8. In yet other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 8.

In other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 8. In still other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 8. In other aspects of this embodiment, a TeNT comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 8.

[080] Aspects of the present invention provide, in part, a Clostridial toxin substrate cleavage site. As used herein, the term "Clostridial toxin substrate cleavage site" means a scissile bond together with adjacent or non-adjacent recognition elements, or both, sufficient for detectable proteolysis at the scissile bond by a Clostridial toxin under conditions suitable for Clostridial toxin protease activity. By definition, a Clostridial toxin substrate cleavage site is susceptible to cleavage by at least one Clostridial toxin under conditions suitable for Clostridial toxin protease activity. It is envisioned that a Clostridial toxin substrate cleavage site of any and all lengths can be useful in aspects of the present invention with the proviso that the Clostridial toxin substrate cleavage site is capable of being cleaved by a Clostridial toxin. Thus, in aspects of this embodiment, a Clostridial toxin substrate cleavage site can be, e.g., at least 6 amino acids in length, at least 7 amino acids in length, at least 8 amino acids in length, at least 9 amino acids in length, at least 10 amino acids in length, at least 15 amino acids in length, at least 20 amino acids in length, at least 25 amino acids in length, at least 30 amino acids in length, at least 40 amino acids in length, at least 50 amino acids in length or at least 60 amino acids in length. In other aspects of this embodiment, a Clostridial toxin substrate cleavage site can be, e.g., at most 6 amino acids in length, at most 7 amino acids in length, at most 8 amino acids in length, at most 9 amino acids in length, at most 10 amino acids in length, at most 15 amino acids in length, at most 20 amino acids in length, at most 25 amino acids in length, at most 30 amino acids in length, at most 40 amino acids in length, at most 50 amino acids in length or at most 60 amino acids in length.

[081] A Clostridial toxin substrate cleavage site useful in aspects of the invention includes, without limitation, naturally occurring Clostridial toxin substrate cleavage site; naturally occurring Clostridial toxin substrate cleavage site variants; and non-naturally-occurring Clostridial toxin substrate cleavage site variants, such as, e.g., conservative Clostridial toxin substrate cleavage site variants, non-conservative Clostridial toxin substrate cleavage site variants and Clostridial toxin substrate cleavage site peptidomimetics. As used herein, the term "Clostridial toxin substrate cleavage site variant," whether naturally-occurring or non-naturally-occurring, means a Clostridial toxin substrate cleavage site that has at least one amino acid change from the corresponding region of the disclosed reference sequences and can be described in percent identity to the corresponding region of that reference sequence. Any of a variety of sequence alignment methods can be used to determine percent identity, including, without limitation, global methods, local methods and hybrid methods, such as, e.g., segment approach methods.

Protocols to determine percent identity are routine procedures within the scope of one skilled in the art and from the teaching herein.

[082] As used herein, the term "naturally occurring Clostridial toxin substrate cleavage site variant" means any Clostridial toxin substrate cleavage site produced without the aid of any human manipulation, including, without limitation, Clostridial toxin substrate cleavage site isoforms produced from alternatively- spliced transcripts, Clostridial toxin substrate cleavage site isoforms produced by spontaneous mutation and Clostridial toxin substrate cleavage site subtypes.

[083] As used herein, the term "non-naturally occurring Clostridial toxin substrate cleavage site variant" means any Clostridial toxin substrate cleavage site produced with the aid of human manipulation, including, without limitation, Clostridial toxin substrate cleavage site variants produced by genetic engineering using random mutagenesis or rational design and Clostridial toxin substrate cleavage site variants produced by chemical synthesis. Non-limiting examples of non-naturally occurring Clostridial toxin substrate cleavage site variants include, e.g., conservative Clostridial toxin substrate cleavage site variants, non-conservative Clostridial toxin substrate cleavage site variants and Clostridial toxin substrate cleavage site peptidomimetics.

[084] As used herein, the term "conservative Clostridial toxin substrate cleavage site variant" means a Clostridial toxin substrate cleavage site that has at least one amino acid substituted by another amino acid or an amino acid analog that has at least one property similar to that of the original amino acid from the reference Clostridial toxin substrate cleavage site sequence. Examples of properties include, without limitation, similar size, topography, charge, hydrophobicity, hydrophilicity, lipophilicity, covalent-bonding capacity, hydrogen-bonding capacity, a physicochemical property, of the like, or any combination thereof. A conservative Clostridial toxin substrate cleavage site variant can function in substantially the same manner as the reference Clostridial toxin substrate cleavage site on which the conservative Clostridial toxin substrate cleavage site variant is based, and can be substituted for the reference Clostridial toxin substrate cleavage site in any aspect of the present invention. A conservative Clostridial toxin substrate cleavage site variant may substitute one or more amino acids, two or more amino acids, three or more amino acids, four or more amino acids or five or more amino acids from the reference Clostridial toxin substrate cleavage site on which the conservative Clostridial toxin substrate cleavage site variant is based. A conservative Clostridial toxin substrate cleavage site variant can also possess at least 50% amino acid identity, 65% amino acid identity, 75% amino acid identity, 85% amino acid identity or 95% amino acid identity to the reference Clostridial toxin substrate cleavage site on which the conservative Clostridial toxin substrate cleavage site variant is based. Non-limiting examples of a conservative Clostridial toxin substrate cleavage site variant include, e.g., conservative BoNT/A substrate cleavage site variants, conservative BoNT/B substrate cleavage site variants, conservative BoNTVCI substrate cleavage site variants, conservative BoNT/D substrate cleavage site variants, conservative BoNT/E substrate cleavage site variants, conservative BoNT/F substrate cleavage site variants, conservative

BoNT/G substrate cleavage site variants, conservative TeNT substrate cleavage site variants, conservative BaNT substrate cleavage site variants and conservative BuNT substrate cleavage site variants.

[085] As used herein, the term "non-conservative Clostridial toxin substrate cleavage site variant' means a Clostridial toxin substrate cleavage site in which 1) at least one amino acid is deleted from the reference Clostridial toxin substrate cleavage site on which the non-conservative Clostridial toxin substrate cleavage site variant is based; 2) at least one amino acid added to the reference Clostridial toxin substrate cleavage site on which the non-conservative Clostridial toxin substrate cleavage site is based; or 3) at least one amino acid is substituted by another amino acid or an amino acid analog that does not share any property similar to that of the original amino acid from the reference Clostridial toxin substrate cleavage site sequence (Table 3). A non-conservative Clostridial toxin substrate cleavage site variant can function in substantially the same manner as the reference Clostridial toxin substrate cleavage site on which the non-conservative Clostridial toxin substrate cleavage site is based, and can be substituted for the reference Clostridial toxin substrate cleavage site in any aspect of the present invention. A non-conservative Clostridial toxin substrate cleavage site variant can add one or more amino acids, two or more amino acids, three or more amino acids, four or more amino acids, five or more amino acids, and ten or more amino acids to the reference Clostridial toxin substrate cleavage site on which the non-conservative Clostridial toxin substrate cleavage site variant is based. A non-conservative Clostridial toxin substrate cleavage site may substitute one or more amino acids, two or more amino acids, three or more amino acids, four or more amino acids or five or more amino acids from the reference Clostridial toxin substrate cleavage site on which the non-conservative Clostridial toxin substrate cleavage site variant is based. A non-conservative Clostridial toxin substrate cleavage site variant can also possess at least 50% amino acid identity, 65% amino acid identity, 75% amino acid identity, 85% amino acid identity or 95% amino acid identity to the reference Clostridial toxin substrate cleavage site on which the non- conservative Clostridial toxin substrate cleavage site variant is based. Non-limiting examples of a non- conservative Clostridial toxin substrate cleavage site variant include, e.g., non-conservative BoNT/A substrate cleavage site variants, non-conservative BoNT/B substrate cleavage site variants, non- conservative BoNT/Ci substrate cleavage site variants, non-conservative BoNT/D substrate cleavage site variants, non-conservative BoNT/E substrate cleavage site variants, non-conservative BoNT/F substrate cleavage site variants, non-conservative BoNT/G substrate cleavage site variants, non- conservative TeNT substrate cleavage site variants, non-conservative BaNT substrate cleavage site variants and non-conservative BuNT substrate cleavage site variants.

[086] As used herein, the term "Clostridial toxin substrate cleavage site peptidomimetic" means a Clostridial toxin substrate cleavage site that has at least one amino acid substituted by a non-natural oligomer that has at least one property similar to that of the first amino acid. Examples of properties include, without limitation, topography of a peptide primary structural element, functionality of a peptide primary structural element, topology of a peptide secondary structural element, functionality of a peptide

secondary structural element, of the like, or any combination thereof. A Clostridial toxin substrate cleavage site peptidomimetic can function in substantially the same manner as the reference Clostridial toxin substrate cleavage site on which the Clostridial toxin substrate cleavage site peptidomimetic is based, and can be substituted for the reference Clostridial toxin substrate cleavage site in any aspect of the present invention. A Clostridial toxin substrate cleavage site peptidomimetic may substitute one or more amino acids, two or more amino acids, three or more amino acids, four or more amino acids or five or more amino acids from the reference Clostridial toxin substrate cleavage site on which the Clostridial toxin substrate cleavage site peptidomimetic is based. A Clostridial toxin substrate cleavage site peptidomimetic can also possess at least 50% amino acid identity, at least 65% amino acid identity, at least 75% amino acid identity, at least 85% amino acid identity or at least 95% amino acid identity to the reference Clostridial toxin substrate cleavage site on which the Clostridial toxin substrate cleavage site peptidomimetic is based. For examples of peptidomimetic methods see, e.g., Amy S. Ripka & Daniel H. Rich, Peptidomimetic design, 2(4) CURR. OPIN. CHEM. BIOL. 441-452 (1998); and M. Angels Estiarte & Daniel H. Rich, Peptidomimetics for Drug Design, 803-861 (BURGER'S MEDICINAL CHEMISTRY AND DRUG DISCOVERY Vol. 1 PRINCIPLE AND PRACTICE, Donald J. Abraham ed., Wiley-lnterscience, 6 ^th ed 2003). Non-limiting examples of a conservative Clostridial toxin substrate cleavage site variant include, e.g., BoNT/A substrate cleavage site peptidomimetics, BoNT/B substrate cleavage site peptidomimetics, BoNTVCI substrate cleavage site peptidomimetics, BoNT/D substrate cleavage site peptidomimetics, BoNT/E substrate cleavage site peptidomimetics, BoNT/F substrate cleavage site peptidomimetics, BoNT/G substrate cleavage site peptidomimetics, TeNT substrate cleavage site peptidomimetics, BaNT substrate cleavage site peptidomimetics and BuNT substrate cleavage site peptidomimetics.

[087] One type of Clostridial toxin substrate cleavage site is derived from in vivo substrate targets of Clostridial toxins, such as, e.g., the SNARE proteins. The natural SNARE targets of the Clostridial toxins include, without limitation, the SNAP-25 family, the VAMP family and the Syntaxin family. SNAP-25 and Syntaxin are associated with the plasma membrane, whereas VAMP is associated with the synaptic vesicle membrane (see FIG. 3). BoNT/A and BoNT/E recognize and specifically cleave SNAP-25 at two different sites in the carboxyl-terminal portion of the protein (Table 2). TeNT and BoNT/B, BoNT/D, BoNT/F, and BoNT/G specifically target the conserved central portion of VAMPs (also known as synaptobrevin) at distinct bonds, depending on the toxin (Table 3). BoNT/C1 cleaves Syntaxin at a single site near the cytosolic membrane surface in addition to SNAP-25 near the carboxyl-terminus (Tables 2 & 4). The three protein targets of these Clostridial toxins are conserved from yeast to humans although cleavage sites and toxin susceptibility are not necessarily conserved, see below; see, also, e.g., Humeau, supra, (2000); Heiner Niemann et al., Clostridial Neurotoxins: New Tools for Dissecting Exocytosis, 4(5) Trends Cell Biol. 179-185 (1994); and Rossella Pellizzari et al., Tetanus and Botulinum Neurotoxins: Mechanism of Action and Therapeutic Uses, 354(1381 ) Philos. Trans. R. Soc. Lond. B Biol. Sci. 259-268 (1999).

[088] Naturally occurring SNAP-25, a protein of about 206 residues lacking a transmembrane segment,

is associated with the cytosolic surface of the nerve plasmalemma (see FIG. 3). SNAP-25 is required for axonal growth during development and may be required for nerve terminal plasticity in the mature nervous system. SNAP-25 has been isolated from a variety of vertebrate and invertebrate species including, e.g., species belonging to the genera Homo, Macaca, Bos, Rattus, Mus, Gallus, Carassius, Danio, Torpedo, Xenopus, Strongylocentrotus, Drosophila, Hirudo, Loligo, Lymnaea and Caenorhabditis (Table 2). In humans, at least two isoforms are differentially expressed during development; isoform a is constitutively expressed during fetal development, while isoform b appears at birth and predominates in adult life. SNAP-25 analogues such as SNAP-23 also are expressed outside the nervous system, for example, in pancreatic cells.

Nonprovisional Patent Application 17852 (BOT) Steward, L E et al , Clostridial Toxin Activatable Clostridial Toxins

site (ND)

[089] Table 2 — Cleavage of SNAP-25 and related proteins. Primate: Human SNAP-25A residues 163-206 of SEQ ID NO: 9; Human SNAP-25B residues 163-206 of SEQ ID NO: 10; Human SNAP-23A residues 169-211 of SEQ ID NO: 11 ; Human SNAP-23B residues 116-158 of SEQ ID NO: 12; Monkey SNAP-25B residues 163-206 of SEQ ID NO: 13; Rodent: Rat SNAP-25A residues 163-206 of SEQ ID NO: 14; Rat SNAP-25B residues 163-206 of SEQ ID NO: 15; Mouse SNAP-25B residues 163-206 of SEQ ID NO: 16; Rat SNAP-23 residues 168-210 of SEQ ID NO: 17; Mouse SNAP-23 residues 168-210 of SEQ ID NO: 18; Bird: Chicken SNAP-25B residues 163-206 of SEQ ID NO: 19; Fish: Goldfish SNAP-25A residues 161-204 of SEQ ID NO: 20; Goldfish SNAP-25B residues 160-203 of SEQ ID NO: 21 ; Zebrafish SNAP-25A residues 161 -204 of SEQ ID NO: 22; Zebrafish SNAP-25B residues 160-203 of SEQ ID NO: 23; Zebrafish SNAP-23 residues 174-214 of SEQ ID NO: 24; Ray: marbled electric ray SNAP-25 residues 170-210 of SEQ ID NO: 25; Amphibian: Frog SNAP-25A residues 163-206 of SEQ ID NO: 26; Frog SNAP-25B residues 163-206 of SEQ ID NO: 27; Frog SNAP-23 residues 163-204 of SEQ ID NO: 28; Sea urchin SNAP-25 residues 169-212 of SEQ ID NO: 29; Insect: Fruit fly SNAP-25 residues 171-212 of SEQ ID NO: 30; Fruit fly SNAP-24 residues 170-212 of SEQ ID NO: 31 ; Segmented worm: Leech SNAP-25 residues 170-212 of SEQ ID NO: 32; Cephalopod: squid SNAP-25 residues 245-267 of SEQ ID NO: 33; Gastropod: Pond snail SNAP-25 residues 244-266 of SEQ ID NO: 34; Round worm: Nematode worm SNAP-25 residues 165-207 of SEQ ID NO: 35.

[090] Naturally occurring VAMP is a protein of about 120 residues, with the exact length depending on the species and isoform. As shown in FIG. 3, VAMP contains a short carboxyl-terminal segment inside the vesicle lumen while most of the molecule is exposed to the cytosol. The proline-rich amino-terminal thirty residues are divergent among species and isoforms while the central portion of VAMP, which is rich in charged and hydrophilic residues and includes known cleavage sites, is highly conserved (Table 3). VAMP colocalizes with synaptophysin on synaptic vesicle membranes. VAMP has been isolated from a variety of vertebrate and invertebrate species including, e.g., species belonging to the genera Homo, Macaca, Bos, Rattus, Mus, Gallus, Danio, Torpedo, Xenopus, Strongylocentrotus, Drosophila, Hirudo, Loligo, Lymnaea, Aplysia and Caenorhabditis. In addition, multiple isoforms of VAMP have been identified including VAMP-1 , VAMP-2 and VAMP-3/cellubrevin, and forms insensitive to toxin cleavage have been identified in non-neuronal cells. VAMP appears to be present in all vertebrate tissues although the distribution of VAMP-1 and VAMP-2 varies in different cell types. Chicken and rat VAMP-1 are not cleaved by TeNT or BoNT/B. These VAMP-1 orthologs have a valine in place of the glutamine present in human and mouse VAMP-1 at the TeNT or BoNT/B cleavage site. The substitution does not affect BoNT/D, /F or /G, which cleave both VAMP-1 and VAMP-2 with similar rates.

Nonprovisional Patent Application 17852 (BOT) Steward, L. E. et al., Clostridial Toxin Activatable Clostridial Toxins

Nonprovisional Patent Application 17852 (BOT) Steward, L. E. et al., Clostridial Toxin Activatable Clostridial Toxins

site (ND)

[091] Table 3 — Cleavage of VAMP and related proteins. Primate: Human VAMP-1-1 residues 49-92 of SEQ ID NO: 36; Human VAMP-1-2 residues 49 ^: 92 of SEQ ID NO: 37; Human VAMP-1 -3 residues 49- 92 of SEQ ID NO: 38; Human VAMP-2 residues 47-90 of SEQ ID NO: 39; Monkey VAMP-2 residues 47- 90 of SEQ ID NO: 40; Human VAMP-3/cellubrevin residues 30-73 of SEQ ID NO: 41 ; Bovine: Cow VAMP-2 residues 47-90 of SEQ ID NO: 42; Rodent: Rat VAMP-1 residues 49-92 of SEQ ID NO: 43; Rat VAMP-1-b residues 49-92 of SEQ ID NO: 44; Mouse VAMP-1 residues 49-92 of SEQ ID NO: 45; Rat VAMP-2 residues 47-90 of SEQ ID NO: 46; Rat VAMP-2-b residues 47-90 of SEQ ID NO: 47; Mouse VAMP-2 residues 47-90 of SEQ ID NO: 48; Rat VAMP-3/cellubrevin residues 34-77 of SEQ ID NO: 49; Mouse VAMP-3/cellubrevin residues 34-77 of SEQ ID NO: 50; Bird: Chicken VAMP-1 residues 190-233 of SEQ ID NO: 51 ; Chicken VAMP-2 residues 47-88 of SEQ ID NO: 52; Chicken VAMP-3/cellubrevin residues 34-77 of SEQ ID NO: 53; Fish: Zebrafish VAMP-1 residues 50-93 of SEQ ID NO: 54; Zebrafish VAMP-2 residues 41-84 of SEQ ID NO: 55; Zebrafish VAMP-3 residues 33-60 of SEQ ID NO: 56; Ray: marbled electric ray VAMP-1 residues 51-94 of SEQ ID NO: 57; Amphibian: Frog VAMP-2 residues 45-88 of SEQ ID NO: 58; Frog VAMP-3 residues 32-75 of SEQ ID NO: 59; Sea urchin VAMP residues 31-74 of SEQ ID NO: 60; Insect: Fruit fly SynA1 residues 40-83 of SEQ ID NO: 61 ; Fruit fly SynA2 residues 63-106 of SEQ ID NO: 62; Fruit fly SynB1 residues 63-106 of SEQ ID NO: 63; Fruit fly SynB2 residues 63-106 of SEQ ID NO: 64; Fruit fly SynC residues 57-100 of SEQ ID NO: 65; Fruit fly SynD residues 66-109 of SEQ ID NO: 66; Fruit fly SynE residues 57-100 of SEQ ID NO: 67; Segmented worm: Leech VAMP residues 45-88 of SEQ ID NO: 68; Cephalopod: squid VAMP residues 56-99 of SEQ ID NO: 69; Gastropod: Pond snail VAMP residues 49-92 of SEQ ID NO: 70; sea hare VAMP residues 37-80 of SEQ ID NO: 71 ; Round worm: Nematode worm SNB1 residues 72-115 of SEQ ID NO: 72; Nematode worm SNB-like residues 82- 115 of SEQ ID NO: 73.

[092] Naturally occurring Syntaxin is located on the cytosolic surface of the nerve plasmalemma and is membrane-anchored via a carboxyl-terminal segment, with most of the protein exposed to the cytosol (see FIG. 3). Syntaxin colocalizes with calcium channels at the active zones of the presynaptic membrane, where neurotransmitter release takes place. In addition, syntaxin interacts with synaptotagmin, a protein of the SSV membrane that forms a functional bridge between the plasmalemma and the vesicles. Syntaxin has been isolated from a variety of vertebrate and invertebrate species including, e.g., species belonging to the genera Homo, Bos, Rattus, Mus, Gallus, Danio, Strongylocentrotus, Drosophila, Hirudo, Loligo, Lymnaea and Aplysia (Table 4). Three isoforms of slightly different length (285 and 288 residues) have been identified in nerve cells (isoforms 1A, 1 B1 and 1 B2), with isoforms 2, 3, 4 and 5 expressed in other tissues. The different isoforms have varying sensitivities to BoNT/C1 , with the 1 A, 1 B1 , 1 B2, 2 and 3 syntaxin isoforms cleaved by this toxin.

Proteolytic cleavage not

[093] Table 4 — Cleavage of Syntaxin and related proteins. Primate: Human SyntaxiniA residues 242-264 of SEQ ID NO: 74; Human Syntaxin1 B1 residues 241-263 of SEQ ID NO: 75; Human Syntaxιn1 B2 residues 241-263 of SEQ ID NO: 76; Human Syntaxin2-1 residues 241-263 of SEQ ID NO: 77; Human Syntaxin2-2 residues 241-263 of SEQ ID NO: 78; Human Syntaxin2-3 residues 241-263 of SEQ ID NO: 79; Human Syntaxin3 residues 241-263 of SEQ ID NO: 80; Bovine: Cow SyntaxiniA residues 242-264 of SEQ ID NO: 81 ; Cow Syntaxin1 B2 residues 241-263 of SEQ ID NO: 82; Rodent: Rat SyntaxiniA residues 242-264 of SEQ ID NO: 83; Rat Syntaxin1 B2 residues 241-263 of SEQ ID NO: 84; Mouse SyntaxiniA residues 242-264 of SEQ ID NO: 85; Mouse Syntaxin1 B1 residues 241-263 of SEQ ID NO: 86; Mouse Syntaxin1 B2 residues 241-263 of SEQ ID NO: 87; Rat Syntaxin2 residues 243-265 of SEQ ID NO: 88; Mouse Syntaxin2 residues 242-264 of SEQ ID NO: 89; Rat Syntaxin3A residues 241-263 of SEQ ID NO: 90; Mouse Syntaxin3A residues 241-263 of SEQ ID NO: 91 ; Mouse Syntaxin3B residues 241-263 of SEQ ID NO: 92; Mouse Syntaxin3C residues 223-245 of SEQ ID NO: 93; Bird: Chicken Syntaxini B residues 235-257 of SEQ ID NO: 94; Chicken Syntaxιn2 residues 240-262 of SEQ ID NO: 95;

Fish: Zebrafish Syntaxini B residues 241-263 of SEQ ID NO: 96; Zebrafish Syntaxin3 residues 239-261 of SEQ ID NO: 97; sea urchin SyntaxiM B residues 241-263 of SEQ ID NO: 98; Insect: Fruit fly SyntaxiniA residues 245-267 of SEQ ID NO: 99; Segmented worm: leech SyntaxiniA residues 248-270 of SEQ ID NO: 100; Cephalopod: squid SyntaxiniA residues 245-267 of SEQ ID NO: 101 ; Gastropod: Pond snail SyntaxiniA residues 244-266 of SEQ ID NO: 102; sea hare SyntaxiniA residues 244-266 of SEQ ID NO: 103.

[094] A wide variety of Clostridial toxin substrate cleavage sites are useful in aspects of the invention and specific and distinct cleavage sites for different Clostridial toxins are well known in the art. As non- limiting examples, BoNT/A cleaves a Gln-Arg bond and a Lys-His bond; BoNT/B and TeNT cleave a GIn- Phe bond; BoNT/C1 cleaves a Lys-Ala or Arg-Ala bond; BoNT/D cleaves a Lys-Leu bond; BoNT/E cleaves an Arg-lle bond and a Lys-lle bond; BoNT/F cleaves a Gln-Lys bond; and BoNT/G cleaves an Ala-Ala bond (see Table 5). In standard nomenclature, the sequence surrounding a Clostridial toxin cleavage site is denoted P5-P4-P3-P2-Pi-Pi'-P2 ' ^p 3'" ^p 4'" ^p 5'' ^{witn P} 1" ^p i' representing the scissile bond. It is understood that a P- _| or P- ₎ ' site, or both, can be substituted with another amino acid or amino acid mimetic in place of the naturally occurring residue. As an example, BoNT/A substrates have been prepared in which the P- ₎ position (GIn) is modified to be an alanine, 2-aminobutyric acid or asparagine residue; these substrates were hydrolyzed by BoNT/A at the P- _| -Arg bond, see, e.g., James J. Schmidt &

Karen A Bostian, Endoproteinase Activity of Type A Botulinum Neurotoxin: Substrate Requirements and Activation by Serum Albumin, 16(1) J. Protein Chem. 19-26 (1997). While it is recognized that substitutions can be introduced at the P- _] position of the scissile bond, for example, a BoNT/A scissile bond, it is further recognized that conservation of the Pi' residue can be advantageous, see, e.g.,

Vadakkanchery V. Vaidyanathan et al., Proteolysis of SNAP-25 lsoforms by Botulinum Neurotoxin Types A, C, and E: Domains and Amino Acid Residues Controlling the Formation of Enzyme-Substrate Complexes and Cleavage, 72(1) J. Neurochem. 327-337 (1999).

[095] Thus, in an embodiment, a modified Clostridial toxin substrate comprises a Clostridial toxin substrate cleavage site in which the Pi' residue is not modified or substituted relative to the naturally occurring residue in a target protein cleaved by the Clostridial toxin. In aspects of this embodiment, a Clostridial toxin substrate cleavage site in which the Pi' residue is not modified or substituted relative to the naturally occurring residue in a target protein cleaved by the Clostridial toxin can be, e.g., a BoNT/A substrate cleavage site, a BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site, a BoNT/G substrate cleavage site, a TeNT substrate cleavage site, a BaNT substrate cleavage site or a BuNT substrate cleavage site.

[096] In another embodiment, a modified Clostridial toxin substrate comprises a Clostridial toxin substrate cleavage site in which the Pi residue is modified or substituted relative to the naturally occurring residue in a target protein cleaved by the Clostridial toxin; such a Clostridial toxin substrate retains susceptibility to peptide bond cleavage between the Pi and Pi' residues. In aspects of this embodiment, a Clostridial toxin substrate cleavage site in which the Pi' residue is modified or substituted relative to the naturally occurring residue in a target protein cleaved by the Clostridial toxin can be, e.g., a BoNT/A substrate cleavage site, a BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site, a

BoNT/G substrate cleavage site, a TeNT substrate cleavage site, a BaNT substrate cleavage site or a BuNT substrate cleavage site.

[097] In an aspect of the invention, a modified Clostridial toxin comprises a BoNT/A substrate cleavage site. As used herein, the term "botulinum toxin serotype A substrate cleavage site" is synonymous with "BoNT/A substrate cleavage site" and means a scissile bond together with adjacent or non-adjacent recognition elements, or both, sufficient for detectable proteolysis at the scissile bond by a BoNT/A under conditions suitable for Clostridial toxin protease activity. A scissile bond cleaved by BoNT/A can be, for example, Gln-Arg or Lys-His. It is envisioned that a BoNT/A substrate cleavage site of any and all lengths can be useful in aspects of the present invention with the proviso that the BoNT/A substrate cleavage site is capable of being cleaved by BoNT/A. Thus, in aspects of this embodiment, a BoNT/A substrate cleavage site can be, e.g., at least 6 amino acids in length, at least 7 amino acids in length, at least 8 amino acids in length, at least 9 amino acids in length, at least 10 amino acids in length, at least 15 amino acids in length, at least 20 amino acids in length, at least 25 amino acids in length, at least 30 amino acids in length, at least 40 amino acids in length, at least 50 amino acids in length or at least 60 amino acids in length. In other aspects of this embodiment, a BoNT/A substrate cleavage site can be, e.g., at most 6 amino acids in length, at most 7 amino acids in length, at most 8 amino acids in length, at most 9 amino acids in length, at most 10 amino acids in length, at most 15 amino acids in length, at most 20 amino acids in length, at most 25 amino acids in length, at most 30 amino acids in length, at most 40 amino acids in length, at most 50 amino acids in length or at most 60 amino acids in length.

[098] A BoNT/A substrate cleavage sites useful in aspects of the invention can correspond to a segment of a protein that is sensitive to cleavage by BoNT/A, or can be substantially similar to a segment of a BoNT/A-sensitive protein. As shown in Table 2, a variety of naturally occurring proteins sensitive to cleavage by BoNT/A are known in the art and include, for example, human, rat, mouse, Danio, Carassius, SNAP-25A and SNAP-25B; and Torpedo SNAP-25. Thus, a BoNT/A substrate cleavage site can correspond, for example, to a segment of human SNAP-25A or SNAP-25B; bovine SNAP-25A or SNAP- 25B; rat SNAP-25A or SNAP-25B; mouse SNAP-25A or SNAP-25B; Xenopus SNAP-25A or SNAP-25B; Danio SNAP-25A or SNAP-25B; Carassius SNAP-25A or SNAP-25B; Torpedo SNAP-25; Strongylocentrotus SNAP-25; Loligo SNAP-25; Lymnaea SNAP-25; Aplysia SNAP-25, isoforms thereof, or another naturally occurring protein sensitive to cleavage by BoNT/A. Furthermore, comparison of native SNAP-25 amino acid sequences cleaved by BoNT/A reveals that such sequences are not absolutely conserved (Table 2). This finding indicates that a variety of amino acid substitutions and modifications relative to a naturally occurring BoNT/A-sensitive SNAP-25 sequence can be tolerated in a BoNT/A substrate cleavage site useful in aspects of the present invention. It is understood that a similar BoNT/A recognition sequence can be prepared, if desired, from a corresponding (homologous) segment of another BoNT/A-sensitive SNAP-25 isoform, paralog or ortholog, such as, the BoNT/A substrate cleavage site contain in the SNAP-25 proteins identified in the organisms listed above and in Table 2.

[099] Furthermore, experimental manipulation of the amino acid sequence comprising a native BoNT/A substrate cleavage site cleaved by BoNT/A reveals that such sequences are not absolutely conserved. These results indicate that a variety of residues can be substituted in a BoNT/A toxin substrate cleavage site as compared to a naturally occurring toxin-sensitive sequence. As a non-limiting example, as compared to a 17-mer corresponding to residues 187 to 203 of human SNAP-25, substitution of Asp193 with Asparagine in the BoNT/A substrate resulted in a relative rate of proteolysis of 0.23; substitution of Glu194 with Glutamine resulted in a relative rate of 2.08; substitution of Ala195 with 2-aminobutyric acid resulted in a relative rate of 0.38; and substitution of Gln197 with Asparagine, 2-aminobutyric acid or Alanine resulted in a relative rate of 0.66, 0.25, or 0.19, respectively (see Table 6). Furthermore, substitution of Ala199 with 2-aminobutyric acid resulted in a relative rate of 0.79; substitution of Thr200 with Serine or 2-aminobutyric acid resulted in a relative rate of 0.26 or 1.20, respectively; substitution of Lys201 with Alanine resulted in a relative rate of 0.12; and substitution of Met202 with Alanine or norleucine resulted in a relative rate of 0.38 or 1.20, respectively, see, e.g., Schmidt & Bostian, supra, (1997). In a separate study, Gln197 of SNAP-25 could be substituted with Methionine, Serine, Threonine, Glutamine or Lysine and still be cleaved efficiently by BoNT/A, see, e.g., Vadakkanchery V. Vaidyanathan et al., Proteolysis of SNAP-25 lsoforms by Botulinum Neurotoxin Types A, C, and E: Domains and Amino Acid Residues Controlling the Formation of Enzyme-Substrate Complexes and Cleavage, 72 J. Neurochem. 327-337 (1999). These results indicate that residues including but not limited to Glu194,

Ala195, Gln197, Ala199, Thr200 and Met202, Leu203, Gly204, Ser205, and Gly206, as well as residues more distal from the Gln-Arg scissile bond, can be substituted or conjugated.

[0100] A variety of BoNT/A substrate cleavage sites are well known in the art or can be defined by routine methods. A BoNT/A substrate cleavage site can have, for example, residues 46-206, residues 134 to 206, residues 137 to 206 or 146-206 of human SNAP-25, see, e.g., Teresa A. Ekong et al., Recombinant SNAP-25 is an Effective Substrate for Clostridium botulinum Type A Toxin Endopeptidase Activity in vitro, 143 (Pt 10) Microbiology 3337-3347 (1997); Clifford C. Shone et al., Toxin Assays, ^' U.S. Patent No. 5,962,637 (Oct. 5, 1999); and Vaidyanathan et al., supra, (1999). A BoNT/A substrate cleavage site also can comprise, without limitation, the sequence Thr-Arg-lle-Asp-Glu-Ala-Asn-Gln-Arg- Ala-Thr-Lys-Met (SEQ ID NO: 133) or a peptidomimetic thereof, which corresponds to residues 190 to 202 of human SNAP-25; Ser-Asn-Lys-Thr-Arg-lle-Asp-Glu-Ala-Asn-Gln-Arg-Ala-Thr-Lys (SEQ ID NO: 134) or a peptidomimetic thereof, which corresponds to residues 187 to 201 of human SNAP-25; Ser- Asn-Lys-Thr-Arg-lle-Asp-Glu-Ala-Asn-Gln-Arg-Ala-Thr-Lys-Met (SEQ ID NO: 135) or a peptidomimetic thereof, which corresponds to residues 187 to 202 of human SNAP-25; Ser-Asn-Lys-Thr-Arg-lle-Asp-Glu- Ala-Asn-Gln-Arg-Ala-Thr-Lys-Met-Leu (SEQ ID NO: 136) or a peptidomimetic thereof, which corresponds to residues 187 to 203 of human SNAP-25; Asp-Ser-Asn-Lys-Thr-Arg-lle-Asp-Glu-Ala-Asn-Gln-Arg-Ala- Thr-Lys-Met (SEQ ID NO: 150) or a peptidomimetic thereof, which corresponds to residues 186 to 202 of human SNAP-25; or Asp-Ser-Asn-Lys-Thr-Arg-lle-Asp-Glu-Ala-Asn-Gln-Arg-Ala-Thr- Lys-Met-Leu (SEQ ID NO: 151) or a peptidomimetic thereof, which corresponds to residues 186 to 203 of human SNAP-25. See, for example, James J. Schmidt & Karen A Bostian, Proteolysis of Synthetic Peptides by Type A Botulinum Neurotoxin, 14(8) J. Protein Chem. 703-708 (1995); Schmidt & Bostian, supra, (1997); James J. Schmidt et al., Type A Botulinum Neurotoxin Proteolytic Activity: Development of Competitive Inhibitors and Implications For Substrate Specificity at the SV Binding Subsite, 435(1) FEBS Lett. 61-64 (1998); and James J. Schmidt & Karen A Bostian, Assay for the Proteolytic Activity of Serotype a From Clostridium botulinum, U.S. Patent No. 5,965,699 (Oct. 12, 1999).

[0101] Thus, in an embodiment, a modified Clostridial toxin comprises a BoNT/A substrate cleavage site. In an aspect of this embodiment, a BoNT/A substrate cleavage site comprises at least six consecutive residues of SNAP-25 including Gln-Arg. In another aspect of this embodiment, a BoNT/A substrate cleavage site comprises at least six consecutive residues of SNAP-25 including Lys-His. In other aspects of this embodiment, a BoNT/A substrate cleavage site comprises, e.g., the amino acid sequence GIu-AIa- Asn-Gln-Arg-Ala-Thr-Lys (SEQ ID NO: 104); the amino acid sequence Glu-Ala-Asn-Lys-His-Ala-Thr-Lys (SEQ ID NO: 105); the amino acid sequence Glu-Ala-Asn-Lys-His-Ala-Asn-Lys (SEQ ID NO: 106). In another aspect of this embodiment, a BoNT/A substrate cleavage site comprises a naturally occurring BoNT/A substrate cleavage site variant. In another aspect of this embodiment, a BoNT/A substrate cleavage site comprises a naturally occurring BoNT/A substrate cleavage site variant of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106, such as, e.g., a BoNT/A substrate cleavage site isoform of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106; or a BoNT/A substrate cleavage site subtype of SEQ ID

NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106. In still another aspect of this embodiment, a BoNT/A substrate cleavage site comprises a non-naturally occurring BoNT/A substrate cleavage site variant, such as, e.g., a conservative BoNT/A substrate cleavage site variant, a non-conservative BoNT/A substrate cleavage site variant or a BoNT/A substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a BoNT/A substrate cleavage site comprises a non-naturally occurring BoNT/A substrate cleavage site variant of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106; such as, e.g., a conservative BoNT/A substrate cleavage site variant of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106; a non-conservative BoNT/A substrate cleavage site variant of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106; a BoNT/A substrate cleavage site peptidomimetic of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106; or any combination thereof. In still other aspects of this embodiment, a BoNT/A substrate cleavage site comprises, e.g., SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO: 141 , SEQ ID NO: 148, SEQ ID NO: 150 or SEQ ID NO: 151.

[0102] In other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 104, at least 62.5% amino acid identity with the SEQ ID NO: 104, at least 75% amino acid identity with SEQ ID NO: 104 or at least 87.5% amino acid identity with SEQ ID NO: 104. In still other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 104, at most 62.5% amino acid identity with the SEQ ID NO: 104, at most 75% amino acid identity with SEQ ID NO: 104 or at most 87.5% amino acid identity with SEQ ID NO: 104.

[0103] In other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 104. In yet other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten noncontiguous amino acid additions relative to SEQ ID NO: 104. In yet other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 104.

[0104] In other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide

having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 104. In yet other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 104. In yet other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a BoNT/A substrate cleavage site comprises a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 104.

[0105] In an aspect of the invention, a modified Clostridial toxin comprises a BoNT/B substrate cleavage site. As used herein, the term "botulinum toxin serotype B substrate cleavage site" is synonymous with "BoNTVB substrate cleavage site" and means a scissile bond together with adjacent or non-adjacent recognition elements, or both, sufficient for detectable proteolysis at the scissile bond by a BoNT/B under conditions suitable for Clostridial toxin protease activity. A scissile bond cleaved by BoNT/B can be, for example, Gln-Phe. It is envisioned that a BoNT/B substrate cleavage site of any and all lengths can be useful in aspects of the present invention with the proviso that the BoNT/B substrate cleavage site is capable of being cleaved by BoNT/B. Thus, in aspects of this embodiment, a BoNT/B substrate cleavage site can be, e.g., at least 6 amino acids in length, at least 7 amino acids in length, at least 8 amino acids in length, at least 9 amino acids in length, at least 10 amino acids in length, at least 15 amino acids in length, at least 20 amino acids in length, at least 25 amino acids in length, at least 30 amino acids in length, at least 40 amino acids in length, at least 50 amino acids in length or at least 60 amino acids in length. In other aspects of this embodiment, a BoNT/B substrate cleavage site can be, e.g., at most 6 amino acids in length, at most 7 amino acids in length, at most 8 amino acids in length, at most 9 amino acids in length, at most 10 amino acids in length, at most 15 amino acids in length, at most 20 amino acids in length, at most 25 amino acids in length, at most 30 amino acids in length, at most 40 amino acids in length, at most 50 amino acids in length or at most 60 amino acids in length.

[0106] A BoNT/B substrate cleavage sites useful in aspects of the invention can correspond to a segment of a protein that is sensitive to cleavage by BoNT/B, or can be substantially similar to a segment of a BoNT/B-sensitive protein. As shown in Table 3, a variety of naturally occurring proteins sensitive to cleavage by BoNT/B are known in the art and include, for example, human and mouse VAMP-1 , VAMP-2 and VAMP-3/cellubrevin; bovine VAMP-2; rat VAMP-2 and VAMP-3; chicken VAMP-2; Torpedo VAMP-1 ; Strongylocentrotus VAMP; Drosophila sybA, synB, synC, synD and synE; Hirudo VAMP; and Caenorhabditis SNB1-like. Thus, a BoNT/B substrate cleavage site can correspond, for example, to a segment of human VAMP-1 , VAMP-2 or VAMP-3; bovine VAMP-2; rat VAMP-2 or VAMP-3; mouse VAMP-1 , VAMP-2 or VAMP-3; chicken VAMP-1 , VAMP-2 or VAMP-3; Xenopus VAMP-2 or VAMP-3; Danio VAMP-1 or VAMP-2; Torpedo VAMP-1 ; Strongylocentrotus VAMP; Drosophila sybA, synB, synC,

synD or synE; Hirudo VAMP; Loligo VAMP; Lymnaea VAMP; Aplysia VAMP; Caenorhabditis SNB1 , isoforms thereof, or another naturally occurring protein sensitive to cleavage by BoNT/B. Furthermore, comparison of native VAMP amino acid sequences cleaved by BoNT/B reveals that such sequences are not absolutely conserved (Table 3). This finding indicates that a variety of amino acid substitutions and modifications relative to a naturally occurring BoNT/B-sensitive VAMP sequence can be tolerated in a BoNT/B substrate cleavage site useful in aspects of the present invention. It is understood that a similar BoNT/B substrate cleavage site can be prepared, if desired, from a corresponding (homologous) segment of another BoNT/B-sensitive VAMP-1 or VAMP-2 isoform, paralog or ortholog, such as, the BoNT/B substrate cleavage site contain in the VAMP-1 and VAMP-2 proteins identified in the organisms listed above and in Table 3.

[0107] A variety of BoNT/B substrate cleavage sites are well known in the art or can be defined by routine methods. Such BoNT/B substrate cleavage sites can include, for example, a sequence corresponding to some or all of the hydrophilic core of a VAMP protein such as human VAMP-1 or human VAMP-2. A BoNT/B substrate cleavage sites can include, without limitation, residues 33 to 94, residues 45 to 94, residues 55 to 94, residues 60 to 94, residues 65 to 94, residues 60 to 88 or residues 65 to 88 of human VAMP-2 (SEQ ID NO: 39), or residues 60 to 94 of human VAMP-1 -1 (SEQ ID NO: 36), VAMP-1 -2 (SEQ ID NO: 37) and VAMP-1-3 (SEQ ID NO: 38), see, e.g., Shone et al., Eur. J. Biochem. 217: 965-971 (1993); and Shone et al., supra, (Oct. 5, 1999). A BoNT/B substrate cleavage sites also can include, without limitation, the sequence Leu-Ser-Glu-Leu-Asp-Asp-Arg-Ala-Asp-Ala-Leu-Gln-Ala-Gly-Ala- Ser-Gln- Phe-Glu-Thr-Ser-Ala-Ala-Lys-Leu-Lys-Arg-Lys-Tyr-Trp-Trp-Lys- Asn-Leu-Lys (SEQ ID NO: 152) or a peptidomimetic thereof, which corresponds to residues 60 to 94 of human VAMP-2, see, e.g., James J. Schmidt & Robert G. Stafford, High Throughput Assays for the Proteolytic Activities of Clostridial Neurotoxins, U.S. Patent No. 6,762,280 (JuI. 13, 2004) and the BoNT/B recognition sequence Leu-Ser- Glu-Leu-Asp-Asp-Arg-Ala-Asp-Ala-Leu-Gln-Ala-Gly-Ala-Ser-Gln- Phe-Glu-Ser-Ser-Ala-Ala-Lys-Leu-Lys- Arg-Lys-Tyr-Trp-Trp-Lys-Asn-Cys-Lys (SEQ ID NO: 153) or a peptidomimetic thereof, which corresponds to residues 62 to 96 of human VAMP-1.

[0108] Thus, in an embodiment, a modified Clostridial toxin comprises a BoNT/B substrate cleavage site. In an aspect of this embodiment, a BoNT/B substrate cleavage site comprises at least six consecutive residues of VAMP including Gln-Phe. In other aspects of this embodiment, a BoNT/B substrate cleavage site comprises, e.g., the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Thr-Ser (SEQ ID NO: 107); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Ser-Ser (SEQ ID NO: 108); the amino acid sequence GIy- Ala-Ser-Gln-Phe-Glu-Thr-Asn (SEQ ID NO: 109); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Gln- GIn (SEQ ID NO: 110); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Ala-Ser (SEQ ID NO: 111); or the amino acid sequence Gly-Ala-Ser-Gln-Phe-Gln-Gln-Ser (SEQ ID NO: 112). In another aspect of this embodiment, a BoNT/B substrate cleavage site comprises a naturally occurring BoNT/B substrate cleavage site variant. In another aspect of this embodiment, a BoNT/B substrate cleavage site comprises a naturally occurring BoNT/B substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ

ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112, such as, e.g., a BoNT/B substrate cleavage site isoform of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; or a BoNT/B substrate cleavage site subtype of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112. In still another aspect of this embodiment, a BoNT/B substrate cleavage site comprises a non-naturally occurring BoNT/B substrate cleavage site variant, such as, e.g., a conservative BoNT/B substrate cleavage site variant, a non-conservative BoNT/B substrate cleavage site variant or a BoNT/B substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a BoNT/B substrate cleavage site comprises a non-naturally occurring BoNT/B substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; such as, e.g., a conservative BoNT/B substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; a non-conservative BoNT/B substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; a BoNT/B substrate cleavage site peptidomimetic of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; or any combination thereof.

[0109] In other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 107, at least 62.5% amino acid identity with the SEQ ID NO: 107, at least 75% amino acid identity with SEQ ID NO: 107 or at least 87.5% amino acid identity with SEQ ID NO: 107. In still other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 107, at most 62.5% amino acid identity with the SEQ ID NO: 107, at most 75% amino acid identity with SEQ ID NO: 107 or at most 87.5% amino acid identity with SEQ ID NO: 107.

[0110] In other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten noncontiguous amino acid additions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 107.

[0111] In other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a BoNT/B substrate cleavage site comprises a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 107.

[0112] In an aspect of the invention, a modified Clostridial toxin comprises a BoNTVCI substrate cleavage site. As used herein, the term "botulinum toxin serotype C1 substrate cleavage site" is synonymous with "BoNTVCI substrate cleavage site" and means a scissile bond together with adjacent or non-adjacent recognition elements, or both, sufficient for detectable proteolysis at the scissile bond by a BoNT/C1 under appropriate conditions. A scissile bond cleaved by BoNT/C1 can be, for example, Lys-Ala or Arg-Ala. It is envisioned that a BoNT/C1 substrate cleavage site of any and all lengths can be useful in aspects of the present invention with the proviso that the BoNT/C1 substrate cleavage site is capable of being cleaved by BoNT/C1. Thus, in aspects of this embodiment, a BoNT/C1 substrate cleavage site can be, e.g., at least 6 amino acids in length, at least 7 amino acids in length, at least 8 amino acids in length, at least 9 amino acids in length, at least 10 amino acids in length, at least 15 amino acids in length, at least 20 amino acids in length, at least 25 amino acids in length, at least 30 amino acids in length, at least 40 amino acids in length, at least 50 amino acids in length or at least 60 amino acids in length. In other aspects of this embodiment, a BoNT/C1 substrate cleavage site can be, e.g., at most 6 amino acids in length, at most 7 amino acids in length, at most 8 amino acids in length, at most 9 amino acids in length, at most 10 amino acids in length, at most 15 amino acids in length, at most 20 amino acids in length, at most 25 amino acids in length, at most 30 amino acids in length, at most 40 amino acids in length, at most 50 amino acids in length or at most 60 amino acids in length.

[0113] A BoNT/C1 substrate cleavage sites useful in aspects of the invention can correspond to a segment of a protein that is sensitive to cleavage by BoNT/C1 , or can be substantially similar to a segment of a BoNT/C1 -sensitive protein. As further shown in Table 4, a variety of naturally occurring proteins sensitive to cleavage by BoNT/C1 are known in the art and include, for example, human and mouse Syntaxin 1A, Syntaxin 1B1 and Syntaxin 1B2; bovine and rat Syntaxin 1A and Syntaxin 1B2; rat Syntaxin 2 and Rat syntaxin 3; Strongylocentrotus Syntaxin; Drosophila Syntaxin 1A; Hirudo Syntaxini A; Loligo Syntaxin 1A; Aplysia Syntaxin 1A. Thus, a BoNT/C1 substrate cleavage site can correspond, for

example, to a segment of human Syntaxin 1A, Syntaxin 1 B1 , Syntaxin 1 B2, Syntaxin 2-1 , Syntaxin 2-2, Syntaxin 2-3 or Syntaxin 3A; bovine Syntaxin 1A, Syntaxin 1 B1 or Syntaxin 1 B2; rat Syntaxin 1A, Syntaxin 1 B1 , Syntaxin 1 B2, Syntaxin 2 or Syntaxin 3A; mouse Syntaxin 1A, Syntaxin 1 B1 , Syntaxin 1 B2, Syntaxin 2, Syntaxin 3A, Syntaxin 3B or Syntaxin 3C; chicken Syntaxin 1A or Syntaxin 2; Xenopus Syntaxin 1A or Syntaxin 1 B; Danio Syntaxin 1A, Syntaxin 1 B or Syntaxin 3; Torpedo Syntaxin 1A or Syntaxin 1 B; Strongylocentrotus Syntaxin 1A or Syntaxin 1 B; Drosophila Syntaxin 1A or Syntaxin 1 B; Hirudo Syntaxin 1A or Syntaxin 1 B; Loligo Syntaxin 1A or Syntaxin 1 B; Lymnaea Syntaxin 1A or Syntaxin 1 B ₁ isoforms thereof, or another naturally occurring protein sensitive to cleavage by BoNT/CL Furthermore, comparison of native syntaxin amino acid sequences cleaved by BoNTVCI reveals that such sequences are not absolutely conserved (see Table 4), indicating that a variety of amino acid substitutions and modifications relative to a naturally occurring BoNT/C1 -sensitive syntaxin sequence can be tolerated in a BoNT/C1 substrate cleavage site useful in aspects of the present invention. It is understood that a similar BoNT/C1 substrate cleavage site can be prepared, if desired, from a corresponding (homologous) segment of another BoNT/C1 -sensitive syntaxin isoform, paralog or ortholog, such as, the BoNT/C1 substrate cleavage site contain in the syntaxin proteins identified in the organisms listed above and in Table 4.

[0114] Although not extensively studied, a variety of BoNT/C1 substrate cleavage sites can be defined by routine methods. The minimum optimal fragment for BoNT/C1 substrate cleavage sites can include, without limitation, residues 93 to 202 of human SNAP-25A (SEQ ID NO: 9), or residues 93 to 202 of human SNAP-25B (SEQ ID NO: 10), see, e.g., Vaidyanathan et al., supra, (1999). However, as with substrates for other BoNTs, it is suspected that a much smaller substrate fragment can be effectively cleaved by BoNT/C1.

[0115] As further shown in Table 2, a variety of naturally occurring proteins sensitive to cleavage by BoNT/C1 are known in the art and include, for example, human, rat, mouse, Danio, Carassius SNAP-25A and SNAP-25B; and Drosophila SNAP-25. Thus, a BoNT/C1 substrate cleavage site can correspond, for example, to a segment of human SNAP-25A or SNAP-25B; bovine SNAP-25A or SNAP-25B; rat SNAP- 25A or SNAP-25B; mouse SNAP-25A or SNAP-25B; Xenopus SNAP-25A or SNAP-25B; Danio SNAP- 25A or SNAP-25B; Carassius SNAP-25A or SNAP-25B; Torpedo SNAP-25; Strongylocentrotus SNAP- 25; Drosophila SNAP-25 or SNAP-24; Hirudo SNAP-25; Loligo SNAP-25; Lymnaea SNAP-25, isoforms thereof, or another naturally occurring protein sensitive to cleavage by BoNT/C1. As discussed above in regard to variants of naturally occurring syntaxin sequences, comparison of native SNAP-25 amino acid sequences cleaved by BoNT/C1 reveals significant sequence variability (Table 2), indicating that a variety of amino acid substitutions and modifications relative to a naturally occurring BoNT/C1 -sensitive SNAP-25 sequence can be tolerated in a BoNT/C1 substrate cleavage site disclosed in the present specification. It is understood that a similar BoNT/C1 substrate cleavage site can be prepared, if desired, from a corresponding (homologous) segment of another BoNT/C1 -sensitive SNAP-25 isoform, paralog or ortholog, such as, the BoNT/A substrate cleavage site contain in the SNAP-25 proteins identified in the

organisms listed above and in Table 2.

[0116] Thus, in an embodiment, a modified Clostridial toxin comprises a BoNT/01 substrate cleavage site. In an aspect of this embodiment, a BoNT/C1 substrate cleavage site comprises at least six consecutive residues of Syntaxin including Lys-Ala. In another aspect of this embodiment, a BoNT/C1 substrate cleavage site comprises at least six consecutive residues of Syntaxin including Arg-Ala. In other aspects of this embodiment, a B0NT/CI substrate cleavage site comprises, e.g., the amino acid sequence Asp-Thr-Lys-Lys-Ala-Val-Lys-Tyr (SEQ ID NO: 113); the amino acid sequence Glu-Thr-Lys- Lys-Ala-lle-Lys-Tyr (SEQ ID NO: 114); the amino acid sequence Glu-Ser-Lys-Lys-Ala-Val-Lys-Tyr (SEQ ID NO: 115); the amino acid sequence Glu-Thr-Lys-Arg-Ala-Met-Lys-Tyr (SEQ ID NO: 116); the amino acid sequence Glu-Thr-Lys-Lys-Ala-Val-Lys-Tyr (SEQ ID NO: 117); the amino acid sequence Asp-Thr- Lys-Lys-Ala-Leu-Lys-Tyr (SEQ ID NO: 118); or the amino acid sequence Asp-Thr-Lys-Lys-Ala-Met-Lys- Tyr (SEQ ID NO: 119). In another aspect of this embodiment, a BoNT/C1 substrate cleavage site comprises a naturally occurring BoNT/C1 substrate cleavage site variant. In another aspect of this embodiment, a BoNT/C1 substrate cleavage site comprises a naturally occurring BoNT/C1 substrate cleavage site variant of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119, such as, e.g., a B0NT/CI substrate cleavage site isoform of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119; or a B0NT/CI substrate cleavage site subtype of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119. In still another aspect of this embodiment, a BoNT/C1 substrate cleavage site comprises a non-naturally occurring BoNT/C1 substrate cleavage site variant, such as, e.g., a conservative BoNT/C1 substrate cleavage site variant, a non-conservative BoNT/C1 substrate cleavage site variant or a BoNT/C1 substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a BoNT/C1 substrate cleavage site comprises a non-naturally occurring BoNT/C1 substrate cleavage site variant of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119; such as, e.g., a conservative BoNT/C1 substrate cleavage site variant of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119; a non-conservative BoNT/C1 substrate cleavage site variant of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119; a BoNT/C1 substrate cleavage site peptidomimetic of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119; or any combination thereof.

[0117] In other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 113, at least 62.5% amino acid identity with the SEQ ID NO: 113, at least 75% amino acid identity with SEQ ID NO: 113 or at least 87.5% amino acid identity with SEQ ID NO: 113. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO:

113, at most 62.5% amino acid identity with the SEQ ID NO: 113, at most 75% amino acid identity with SEQ ID NO: 113 or at most 87.5% amino acid identity with SEQ ID NO: 113.

[0118] In other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 113. In yet other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten noncontiguous amino acid additions relative to SEQ ID NO: 113. In yet other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 113.

[0119] In other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 113. In yet other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 113. In yet other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 113.

[0120] In another aspect of this embodiment, a BoNT/C1 substrate cleavage site comprises at least six consecutive residues of SNAP-25 including Arg-Ala. In other aspects of this embodiment, a BoNT/C1 toxin substrate cleavage site comprises, e.g., the amino acid sequence Ala-Asn-Gln-Arg-Ala-Thr-Lys-Met (SEQ ID NO: 120); or the amino acid sequence Ala-Asn-Gln-Arg-Ala-His-Gln-Leu (SEQ ID NO: 121). In another aspect of this embodiment, a BoNT/C1 substrate cleavage site comprises a naturally occurring BoNT/C1 substrate cleavage site variant. In another aspect of this embodiment, a B0NT/CI substrate cleavage site comprises a naturally occurring BoNT/C1 substrate cleavage site variant of SEQ ID NO: 120 or SEQ ID NO: 121 , such as, e.g., a B0NT/CI substrate cleavage site isoform of SEQ ID NO: 120 or

SEQ ID NO: 121 ; or a BoNT/C1 substrate cleavage site subtype of SEQ ID NO: 120 or SEQ ID NO: 121. In still another aspect of this embodiment, a BoNT/C1 substrate cleavage site comprises a non-naturally occurring BoNT/C1 substrate cleavage site variant, such as, e.g., a conservative B0NT/CI substrate cleavage site variant, a non-conservative BoNT/C1 substrate cleavage site variant or a BoNT/C1 substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a BoNT/C1 substrate cleavage site comprises a non-naturally occurring BoNT/C1 substrate cleavage site variant of SEQ ID NO: 120 or SEQ ID NO: 121 ; such as, e.g., a conservative BoNT/C1 substrate cleavage site variant of SEQ ID NO: 120 or SEQ ID NO: 121 ; a non-conservative B0NT/CI substrate cleavage site variant of SEQ ID NO: 120 or SEQ ID NO: 121 ; a BoNT/C1 substrate cleavage site peptidomimetic of SEQ ID NO: 120 or SEQ ID NO: 121 ; or any combination thereof.

[0121] In other aspects of this embodiment, a B0NT/CI substrate cleavage site comprises a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 120, at least 62.5% amino acid identity with the SEQ ID NO: 120, at least 75% amino acid identity with SEQ ID NO: 120 or at least 87.5% amino acid identity with SEQ ID NO: 120. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 120, at most 62.5% amino acid identity with the SEQ ID NO: 120, at most 75% amino acid identity with SEQ ID NO: 120 or at most 87.5% amino acid identity with SEQ ID NO: 120.

[0122] In other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 120. In yet other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten noncontiguous amino acid additions relative to SEQ ID NO: 120. In yet other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 120.

[0123] In other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 120. In yet other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions

relative to SEQ ID NO: 120. In yet other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a BoNT/C1 substrate cleavage site comprises a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 120.

[0124] In an aspect of the invention, a modified Clostridial toxin comprises a BoNT/D substrate cleavage site. As used herein, the term "botulinum toxin serotype D substrate cleavage site" is synonymous with "BoNT/D substrate cleavage site" and means a scissile bond together with adjacent or non-adjacent recognition elements, or both, sufficient for detectable proteolysis at the scissile bond by a BoNT/D under appropriate conditions. A scissile bond cleaved by BoNT/D can be, for example, Lys-Leu. It is envisioned that a BoNT/D substrate cleavage site of any and all lengths can be useful in aspects of the present invention with the proviso that the BoNT/D substrate cleavage site is capable of being cleaved by BoNT/D. Thus, in aspects of this embodiment, a BoNT/D substrate cleavage site can be, e.g., at least 6 amino acids in length, at least 7 amino acids in length, at least 8 amino acids in length, at least 9 amino acids in length, at least 10 amino acids in length, at least 15 amino acids in length, at least 20 amino acids in length, at least 25 amino acids in length, at least 30 amino acids in length, at least 40 amino acids in length, at least 50 amino acids in length or at least 60 amino acids in length. In other aspects of this embodiment, a BoNT/D substrate cleavage site can be, e.g., at most 6 amino acids in length, at most 7 amino acids in length, at most 8 amino acids in length, at most 9 amino acids in length, at most 10 amino acids in length, at most 15 amino acids in length, at most 20 amino acids in length, at most 25 amino acids in length, at most 30 amino acids in length, at most 40 amino acids in length, at most 50 amino acids in length or at most 60 amino acids in length.

[0125] A BoNT/D substrate cleavage sites useful in aspects of the invention can correspond to a segment of a protein that is sensitive to cleavage by BoNT/D, or can be substantially similar to a segment of a BoNT/D-sensitive protein. As shown in Table 3, a variety of naturally occurring proteins sensitive to cleavage by BoNT/D are known in the art and include, for example, human, rat and mouse VAMP-1 , VAMP-2 and VAMP-3/cellubrevin; bovine VAMP-2; chicken VAMP-1 , VAMP-2 and VAMP-3; Xenopus VAMP-2 or VAMP-3; Danio VAMP-1 or VAMP-2; Torpedo VAMP-1 ; Strongylocentrotus VAMP; Drosophila sybA, synB, synC, synD, synE; Hirudo VAMP; Loligo VAMP; Lymnaea VAMP; Aplysia VAMP; and Caenorhabditis SNB1. Thus, a BoNT/D substrate cleavage site can correspond, for example, to a segment of human VAMP-1 , VAMP-2 or VAMP-3; bovine VAMP-2; rat VAMP-1 , VAMP-2 or VAMP-3; mouse VAMP-1 , VAMP-2 or VAMP-3; chicken VAMP-1 , VAMP-2 or VAMP-3; Xenopus VAMP-2 or VAMP-3; Danio VAMP-1 or VAMP-2; Torpedo VAMP-1 ; Strongylocentrotus VAMP; Drosophila sybA, synB, synC, synD, synE; Hirudo VAMP; Loligo VAMP; Lymnaea VAMP; Aplysia VAMP; Caenorhabditis SNB1 , isoforms thereof, or another naturally occurring protein sensitive to cleavage by BoNT/D.

Furthermore, comparison of native VAMP amino acid sequences cleaved by BoNT/D reveals that such sequences are not absolutely conserved (Table 3). This finding indicates that a variety of amino acid substitutions and modifications relative to a naturally occurring BoNT/D-sensitive VAMP sequence can be tolerated in a BoNT/D substrate cleavage site useful in aspects of the present invention. It is understood that a similar BoNT/D substrate cleavage site can be prepared, if desired, from a corresponding (homologous) segment of another BoNT/D-sensitive VAMP-1 or VAMP-2 isoform, paralog or ortholog, such as, the BoNT/D substrate cleavage site contain in the VAMP-1 and VAMP-2 proteins identified in the organisms listed above and in Table 3.

[0126] A variety of BoNT/D substrate cleavage sites are well known in the art or can be defined by routine methods. A BoNT/D substrate cleavage site can include, for example, residues 27 to 116; residues 37 to 116; residues 1 to 86; residues 1 to 76; or residues 1 to 69 of rat VAMP-2 (SEQ ID NO: 46), see, e.g., Shinji Yamasaki et al., Cleavage of members of the synaptobrevin/VAMP family by types D and F botulinum neurotoxins and tetanus toxin, 269(17) J. Biol. Chem. 12764-12772 (1994). Thus, a BoNT/D substrate cleavage site can include, for example, residues 27 to 69 or residues 37 to 69 of rat VAMP-2. A BoNT/D substrate cleavage site also can include, without limitation, the sequence AIa-GIn- Val-Asp-Glu-Val-Val-Asp-lle-Met-Arg-Val-Asn-Val-Asp-Lys-Val- Leu-Glu-Arg-Asp-Gln-Lys-Leu-Ser-Glu- Leu-Asp-Asp-Arg-Ala-Asp-Ala-Leu-Gln-Ala-Gly-Ala-Ser (SEQ ID NO: 154) or a peptidomimetic thereof, which corresponds to residues 37 to 75 of human VAMP-2, see, e.g., Schmidt & Stafford, supra, (JuI. 13, 2004) and the BoNT/D recognition sequence Ala-Gln-Val-Glu-Glu-Val-Val-Asp-lle-lle-Arg-Val-Asn-Val- Asp-Lys-Val-Leu-Glu-Arg-Asp-Gln-Lys-Leu-Ser-Glu-Leu-Asp-Asp- Arg-Ala-Asp-Ala-Leu-Gln-Ala-G Iy-AIa- Ser (SEQ ID NO: 155) or a peptidomimetic thereof, which corresponds to residues 39 to 77 of the human VAMP-1 isoforms, VAMP-1 -1 , VAMP-1 -2 and VAMP-1 -3.

[0127] Thus, in an embodiment, a modified Clostridial toxin comprises a BoNT/D substrate cleavage site. In an aspect of this embodiment, a BoNT/D substrate cleavage site comprises at least six consecutive residues of VAMP including Lys-Leu. In other aspects of this embodiment, a BoNT/D substrate cleavage site comprises, e.g., the amino acid sequence Arg-Asp-Gln-Lys-Leu-Ser-Glu-Leu (SEQ ID NO: 122); or the amino acid sequence Lys-Asp-Gln-Lys-Leu-Ala-Glu-Leu (SEQ ID NO: 123). In another aspect of this embodiment, a BoNT/D substrate cleavage site comprises a naturally occurring BoNT/D substrate cleavage site variant. In another aspect of this embodiment, a BoNT/D substrate cleavage site comprises a naturally occurring BoNT/D substrate cleavage site variant of SEQ ID NO: 122 or SEQ ID NO: 123, such as, e.g., a BoNT/D substrate cleavage site isoform of SEQ ID NO: 122 or SEQ ID NO: 123; or a BoNT/D substrate cleavage site subtype of SEQ ID NO: 122 or SEQ ID NO: 123. In still another aspect of this embodiment, a BoNT/D substrate cleavage site comprises a non-naturally occurring BoNT/D substrate cleavage site variant, such as, e.g., a conservative BoNT/D substrate cleavage site variant, a non-conservative BoNT/D substrate cleavage site variant or a BoNT/D substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a BoNT/D substrate cleavage site comprises a non-naturally occurring BoNT/D substrate cleavage site

variant of SEQ ID NO: 122 or SEQ ID NO: 123; such as, e.g., a conservative BoNT/D substrate cleavage site variant of SEQ ID NO: 122 or SEQ ID NO: 123; a non-conservative BoNT/Ci substrate cleavage site variant of SEQ ID NO: 122 or SEQ ID NO: 123; a BoNT/D substrate cleavage site peptidomimetic of SEQ ID NO: 122 or SEQ ID NO: 123; or any combination thereof.

[0128] In other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 122, at least 62.5% amino acid identity with the SEQ ID NO: 122, at least 75% amino acid identity with SEQ ID NO: 122 or at least 87.5% amino acid identity with SEQ ID NO: 122. In still other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 122, at most 62.5% amino acid identity with the SEQ ID NO: 122, at most 75% amino acid identity with SEQ ID NO: 122 or at most 87.5% amino acid identity with SEQ ID NO: 122.

[0129] In other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 122. In yet other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten noncontiguous amino acid additions relative to SEQ ID NO: 122. In yet other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 122.

[0130] In other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 122. In yet other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 122. In yet other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a BoNT/D substrate cleavage site comprises a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a BoNT/D

substrate cleavage site comprises a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 122.

[0131] In an aspect of the invention, a modified Clostridial toxin comprises a BoNT/E substrate cleavage site. As used herein, the term "botulinum toxin serotype E substrate cleavage site" is synonymous with "BoNT/E substrate cleavage site" and means a scissile bond together with adjacent or non-adjacent recognition elements, or both, sufficient for detectable proteolysis at the scissile bond by a BoNT/E under appropriate conditions. A scissile bond cleaved by BoNT/E can be, for example, Arg-lle or Lys-lle. It is envisioned that a BoNT/E substrate cleavage site of any and all lengths can be useful in aspects of the present invention with the proviso that the BoNT/E substrate cleavage site is capable of being cleaved by BoNT/E. Thus, in aspects of this embodiment, a BoNT/E substrate cleavage site can be, e.g., at least 6 amino acids .in length, at least 7 amino acids in length, at least 8 amino acids in length, at least 9 amino acids in length, at least 10 amino acids in length, at least 15 amino acids in length, at least 20 amino acids in length, at least 25 amino acids in length, at least 30 amino acids in length, at least 40 amino acids in length, at least 50 amino acids in length or at least 60 amino acids in length. In other aspects of this embodiment, a BoNT/E substrate cleavage site can be, e.g., at most 6 amino acids in length, at most 7 amino acids in length, at most 8 amino acids in length, at most 9 amino acids in length, at most 10 amino acids in length, at most 15 amino acids in length, at most 20 amino acids in length, at most 25 amino acids in length, at most 30 amino acids in length, at most 40 amino acids in length, at most 50 amino acids in length or at most 60 amino acids in length.

[0132] A BoNT/E substrate cleavage sites useful in aspects of the invention can correspond to a segment of a protein that is sensitive to cleavage by BoNT/E, or can be substantially similar to a segment of a BoNT/E-sensitive protein. As shown in Table 2, a variety of naturally occurring proteins sensitive to cleavage by BoNT/E are known in the art and include, for example, human, chicken, Danio, Carassius SNAP-25A and SNAP-25B; rat and mouse SNAP-25A, SNAP-25B and SNAP-23; and Caenorhabditis SNAP-25. Thus, a BoNT/E substrate cleavage site can correspond, for example, to a segment of human SNAP-25A or SNAP-25B; bovine SNAP-25A or SNAP-25B; rat SNAP-25A, SNAP-25B or SNAP-23; mouse SNAP-25A, SNAP-25B or SNAP-23; Xenopus SNAP-25A or SNAP-25B; Danio SNAP-25A or SNAP-25B; Carassius SNAP-25A or SNAP-25B; Strongylocentrotus SNAP-25; Drosophila SNAP-24; Hirudo SNAP-25; Loligo SNAP-25; Lymnaea SNAP-25; Caenorhabditis SNAP-25, isoforms thereof, or another naturally occurring protein sensitive to cleavage by BoNT/CI . Furthermore, comparison of native SNAP-23 and SNAP-25 amino acid sequences cleaved by BoNT/E reveals that such sequences are not absolutely conserved (Table 2). This finding indicates that a variety of amino acid substitutions and modifications relative to a naturally occurring BoNT/E-sensitive SNAP-23 or SNAP-25 sequence can be tolerated in a BoNT/E substrate cleavage site useful in aspects of the present invention. It is understood that a similar BoNT/E substrate cleavage site can be prepared, if desired, from a corresponding (homologous) segment of another BoNT/E-sensitive SNAP-25 isoform, paralog or ortholog, such as, the BoNT/E recognition sequence contain in the SNAP-25 proteins identified in the organisms listed above

and in Table 2.

[0133] A variety of BoNT/E substrate cleavage sites are well known in the art or can be defined by routine methods. A BoNT/E substrate cleavage site can have, for example, residues 46-206, residues 92 to 206, residues, residues 134 to 206, residues, 137 to 206; 146-206, 156-206 or 146-186 of human SNAP-25A (SEQ ID NO: 9) and human SNAP-25B (SEQ ID NO: 10), see, e.g., Vaidyanathan et al., supra, (1999); and Schmidt & Stafford, supra, (JuI. 13, 2004).

[0134] Thus, in an embodiment, a modified Clostridial toxin comprises a BoNT/E substrate cleavage site. In an aspect of this embodiment, a BoNT/E substrate cleavage site comprises at least six consecutive residues of SNAP-25 including Arg-lle. In another aspect of this embodiment, a BoNT/E substrate cleavage site comprises at least six consecutive residues of SNAP-25 including Lys-lle. In other aspects of this embodiment, a BoNT/E substrate cleavage site comprises, e.g., the amino acid sequence GIn-IIe- Asp-Arg-lle-Met-Glu-Lys (SEQ ID NO: 124); the amino acid sequence Gln-lle-Gln-Lys-lle-Thr-Glu-Lys (SEQ ID NO: 125); the amino acid sequence Gln-lle-Asp-Arg-lle-Met-Asp-Met (SEQ ID NO: 126); the amino acid sequence Gln-Val-Asp-Arg-lle-Gln-Gln-Lys (SEQ ID NO: 127); or the amino acid sequence Gln-Leu-Asp-Arg-lle-His-Asp-Lys (SEQ ID NO: 128). In another aspect of this embodiment, a BoNT/E substrate cleavage site comprises a naturally occurring BoNT/E substrate cleavage site variant. In another aspect of this embodiment, a BoNT/E substrate cleavage site comprises a naturally occurring BoNT/E substrate cleavage site variant of SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128, such as, e.g., a BoNT/E substrate cleavage site isoform of SEQ ID NO:

124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128; or a BoNT/E substrate cleavage site subtype of SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128. In still another aspect of this embodiment, a BoNT/E substrate cleavage site comprises a non-naturally occurring BoNT/E substrate cleavage site variant, such as, e.g., a conservative BoNT/E substrate cleavage site variant, a non-conservative BoNT/E substrate cleavage site variant or a BoNT/E substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a BoNT/E substrate cleavage site comprises a non-naturally occurring BoNT/E substrate cleavage site variant of SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128; such as, e.g., a conservative BoNT/E substrate cleavage site variant of SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128; a non-conservative BoNT/E substrate cleavage site variant of SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128; a BoNT/E substrate cleavage site peptidomimetic of SEQ ID NO: 124, SEQ ID NO:

125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128 or SEQ ID NO: XX; or any combination thereof.

[0135] In other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 124, at least 62.5% amino acid identity with the SEQ ID NO: 124, at least 75% amino acid identity with SEQ ID NO: 124 or at least 87.5% amino

acid identity with SEQ ID NO: 124. In still other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 124, at most 62.5% amino acid identity with the SEQ ID NO: 124, at most 75% amino acid identity with SEQ ID NO: 124 or at most 87.5% amino acid identity with SEQ ID NO: 124.

[0136] In other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 124. In yet other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten noncontiguous amino acid additions relative to SEQ ID NO: 124. In yet other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 124.

[0137] In other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 124. In yet other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 124. In yet other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a BoNT/E substrate cleavage site comprises a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 124.

[0138] In an aspect of the invention, a modified Clostridial toxin comprises a BoNT/F substrate cleavage site. As used herein, the term "botulinum toxin serotype F substrate cleavage site" is synonymous with "BoNTVF substrate cleavage site" and means a scissile bond together with adjacent or non-adjacent recognition elements, or both, sufficient for detectable proteolysis at the scissile bond by a BoNT/F under appropriate conditions. A scissile bond cleaved by BoNT/F can be, for example, Gln-Lys. It is envisioned that a BoNT/F substrate cleavage site of any and all lengths can be useful in aspects of the present

invention with the proviso that the BoNT/F substrate cleavage site is capable of being cleaved by BoNT/F. Thus, in aspects of this embodiment, a BoNT/F substrate cleavage site can be, e.g., at least 6 amino acids in length, at least 7 amino acids in length, at least 8 amino acids in length, at least 9 amino acids in length, at least 10 amino acids in length, at least 15 amino acids in length, at least 20 amino acids in length, at least 25 amino acids in length, at least 30 amino acids in length, at least 40 amino acids in length, at least 50 amino acids in length or at least 60 amino acids in length. In other aspects of this embodiment, a BoNT/F substrate cleavage site can be, e.g., at most 6 amino acids in length, at most 7 amino acids in length, at most 8 amino acids in length, at most 9 amino acids in length, at most 10 amino acids in length, at most 15 amino acids in length, at most 20 amino acids in length, at most 25 amino acids in length, at most 30 amino acids in length, at most 40 amino acids in length, at most 50 amino acids in length or at most 60 amino acids in length.

[0139] A BoNT/F substrate cleavage sites useful in aspects of the invention can correspond to a segment of a protein that is sensitive to cleavage by BoNT/F, or can be substantially similar to a segment of a BoNT/F-sensitive protein. As shown in Table 3, a variety of naturally occurring proteins sensitive to cleavage by BoNT/F are known in the art and include, for example, human, rat and mouse VAMP-1 , VAMP-2 and VAMP-3/cellubrevin; bovine VAMP-2; chicken VAMP-1 and VAMP-2; Torpedo VAMP-1 ; and Drosophila sybA and synB. Thus, a BoNT/F substrate cleavage site can correspond, for example, to a segment of human VAMP-1 , VAMP-2 or VAMP-3; bovine VAMP-2; rat VAMP-1 , VAMP-2 or VAMP-3; mouse VAMP-1 , VAMP-2 or VAMP-3; chicken VAMP-1 , VAMP-2 or VAMP-3; Xenopus VAMP-2 or VAMP-3; Danio VAMP-1 or VAMP-2; Torpedo VAMP-1 ; Drosophila sybA and synB; Hirudo VAMP; Loligo VAMP; Lymnaea VAMP; Aplysia VAMP; Caenorhabditis SNB1 , isoforms thereof, or another naturally occurring protein sensitive to cleavage by BoNT/F. Thus, a BoNT/F substrate cleavage site can correspond, for example, to a segment of human VAMP-1 or VAMP-2, mouse VAMP-1 or VAMP-2, bovine VAMP-1 or VAMP-2, rat VAMP-1 or VAMP-2, rat cellubrevin, chicken VAMP-1 or VAMP-2, Torpedo VAMP-1 , Aplysia VAMP, Drosophila syb, leech VAMP, or another naturally occurring protein sensitive to cleavage by BoNT/F. Furthermore, comparison of native VAMP amino acid sequences cleaved by BoNT/F reveals that such sequences are not absolutely conserved (Table 3). This finding indicates that a variety of amino acid substitutions and modifications relative to a naturally occurring BoNT/F-sensitive VAMP sequence can be tolerated in a BoNT/F substrate cleavage site useful in aspects of the present invention. It is understood that a similar BoNT/F substrate cleavage site can be prepared, if desired, from a corresponding (homologous) segment of another BoNT/F-sensitive VAMP-1 or VAMP-2 isoform, paralog or ortholog, such as, the BoNT/F substrate cleavage site contain in the VAMP-1 and VAMP-2 identified in the organisms listed above and in Table 3.

[0140] A variety of BoNT/F recognition sequences are well known in the art or can be defined by routine methods. A BoNT/F recognition sequence can include, for example, residues 27 to 116; residues 37 to 116; residues 1 to 86; residues 1 to 76; or residues 1 to 69 of rat VAMP-2 (SEQ ID NO: 46), see, e.g., Yamasaki et al., supra, (1994). These a BoNT/F recognition sequence also can comprise, for example,

residues 27 to 69 or residues 37 to 69 of rat VAMP-2. It is understood that a similar BoNT/F recognition sequence can be prepared, if desired, from a corresponding (homologous) segment of another BoNT/F-sensitive VAMP isoform, paralog or ortholog, such as, e.g., human VAMP-1 or human VAMP-2. A BoNT/F recognition sequence also can include, without limitation, the sequence Ala-Gln-Val-Asp-Glu- Val-Val-Asp-lle-Met-Arg-Val-Asn-Val-Asp-Lys-Val-Leu-Glu-Arg- Asp-Gln-Lys-Leu-Ser-Glu-Leu-Asp-Asp- Arg-Ala-Asp-Ala-Leu-Gln-Ala-Gly-Ala-Ser (SEQ ID NO: 154) or a peptidomimetic thereof, which corresponds to residues 37 to 75 of human VAMP-2, see, e.g., Schmidt & Stafford, supra, (JuI. 13, 2004) and the BoNT/F recognition sequence Ala-Gln-Val-Glu-Glu-Val-Val-Asp-lle-lle-Arg-Val-Asn-Val-Asp- Lys- Val-Leu-Glu-Arg-Asp-Gln-Lys-Leu-Ser-Glu-Leu-Asp-Asp-Arg-Ala- Asp-Ala-Leu-Gln-Ala-Gly-Ala-Ser (SEQ ID NO: 155) or a peptidomimetic thereof, which corresponds to residues 39 to 77 of human VAMP-1.

[0141] Thus, in an embodiment, a modified Clostridial toxin comprises a BoNT/F substrate cleavage site. In an aspect of this embodiment, a BoNT/F substrate cleavage site comprises at least six consecutive residues of VAMP including Gln-Lys. In other aspects of this embodiment, a BoNT/F substrate cleavage site comprises, e.g., the amino acid sequence Glu-Arg-Asp-Gln-Lys-Leu-Ser-Glu (SEQ ID NO: 129); or the amino acid sequence Glu-Lys-Asp-Gln-Lys-Leu-Ala-Glu (SEQ ID NO: 130). In another aspect of this embodiment, a BoNT/F substrate cleavage site comprises a naturally occurring BoNT/F substrate cleavage site variant. In another aspect of this embodiment, a BoNT/F substrate cleavage site comprises a naturally occurring BoNT/F substrate cleavage site variant of SEQ ID NO: 129 or SEQ ID NO: 130, such as, e.g., a BoNT/F substrate cleavage site isoform of SEQ ID NO: 129 or SEQ ID NO: 130; or a BoNT/F substrate cleavage site subtype of SEQ ID NO: 129 or SEQ ID NO: 130. In still another aspect of this embodiment, a BoNT/F substrate cleavage site comprises a non-naturally occurring BoNT/F substrate cleavage site variant, such as, e.g., a conservative BoNT/F substrate cleavage site variant, a non-conservative BoNT/F substrate cleavage site variant or a BoNT/F substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a BoNT/F substrate cleavage site comprises a non-naturally occurring BoNT/F substrate cleavage site variant of SEQ ID NO: 129 or SEQ ID NO: 130; such as, e.g., a conservative BoNT/F substrate cleavage site variant of SEQ ID NO: 129 or SEQ ID NO: 130; a non-conservative BoNT/F substrate cleavage site variant of SEQ ID NO: 129 or SEQ ID NO: 130; a BoNT/F substrate cleavage site peptidomimetic of SEQ ID NO: 129 or SEQ ID NO: 130; or any combination thereof.

[0142] In other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 129, at least 62.5% amino acid identity with the SEQ ID NO: 129, at least 75% amino acid identity with SEQ ID NO: 129 or at least 87.5% amino acid identity with SEQ ID NO: 129. In still other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 129, at most 62.5% amino acid identity with the SEQ ID NO: 129, at most 75% amino acid identity with SEQ ID NO: 129 or at most 87.5% amino acid identity with SEQ ID NO: 129.

[0143] In other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 129. In yet other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten noncontiguous amino acid additions relative to SEQ ID NO: 129. In yet other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 129.

[0144] In other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 129. In yet other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 129. In yet other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a BoNT/F substrate cleavage site comprises a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 129.

[0145] In an aspect of the invention, a modified Clostridial toxin comprises a BoNT/G substrate cleavage site. As used herein, the term "botulinum toxin serotype G substrate cleavage site" is synonymous with "BoNTVG substrate cleavage site" and means a scissile bond together with adjacent or non-adjacent recognition elements, or both, sufficient for detectable proteolysis at the scissile bond by a BoNT/G under appropriate conditions. A scissile bond cleaved by BoNT/G can be, for example, Ala-Ala. It is envisioned that a BoNT/G substrate cleavage site of any and all lengths can be useful in aspects of the present invention with the proviso that the BoNT/G substrate cleavage site is capable of being cleaved by BoNT/G. Thus, in aspects of this embodiment, a BoNT/G substrate cleavage site can be, e.g., at least 6 amino acids in length, at least 7 amino acids in length, at least 8 amino acids in length, at least 9 amino acids in length, at least 10 amino acids in length, at least 15 amino acids in length, at least 20 amino acids in length, at least 25 amino acids in length, at least 30 amino acids in length, at least 40 amino

acids in length, at least 50 amino acids in length or at least 60 amino acids in length. In other aspects of this embodiment, a BoNT/G substrate cleavage site can be, e.g., at most 6 amino acids in length, at most 7 amino acids in length, at most 8 amino acids in length, at most 9 amino acids in length, at most 10 amino acids in length, at most 15 amino acids in length, at most 20 amino acids in length, at most 25 amino acids in length, at most 30 amino acids in length, at most 40 amino acids in length, at most 50 amino acids in length or at most 60 amino acids in length.

[0146] A BoNT/G substrate cleavage sites useful in aspects of the invention can correspond to a segment of a protein that is sensitive to cleavage by BoNT/G, or can be substantially similar to a segment of a BoNT/G-sensitive protein. As shown in Table 3, a variety of naturally occurring proteins sensitive to cleavage by BoNT/G are known in the art and include, for example, human, rat and mouse VAMP-1 , VAMP-2 and VAMP-3/cellubrevin; bovine VAMP-2; chicken VAMP-1 , and VAMP-2; and Torpedo VAMP- 1. Thus, a BoNT/G recognition sequence can correspond, for example, to a segment of human VAMP-1 , VAMP-2 or VAMP-3; bovine VAMP-2; rat VAMP-1 , VAMP-2 or VAMP-3; mouse VAMP-1 , VAMP-2 or VAMP-3; chicken VAMP-1 , VAMP-2 or VAMP-3; Xenopus VAMP-2 or VAMP-3; Danio VAMP-1 or VAMP- 2; Torpedo VAMP-1 ; Caenorhabditis SNB1 , isoforms thereof, or another naturally occurring protein sensitive to cleavage by BoNT/G. Furthermore, comparison of native VAMP amino acid sequences cleaved by BoNT/G reveals that such sequences are not absolutely conserved (Table 3). This finding indicates that a variety of amino acid substitutions and modifications relative to a naturally occurring BoNT/G-sensitive VAMP sequence can be tolerated in a BoNT/G substrate cleavage site useful in aspects of the present invention. It is understood that a similar BoNT/G recognition sequence can be prepared, if desired, from a corresponding (homologous) segment of another BoNT/G-sensitive VAMP-1 or VAMP-2 isoform, paralog or ortholog, such as, the BoNT/G recognition sequence contain in the VAMP- 1 and VAMP-2 identified in the organisms listed above and in Table 3.

[0147] Thus, in an embodiment, a modified Clostridial toxin comprises a BoNT/G substrate cleavage site. In an aspect of this embodiment, a BoNT/G substrate cleavage site comprises at least six consecutive residues of VAMP including Ala-Ala. In other aspects of this embodiment, a BoNT/G substrate cleavage site comprises, e.g., the amino acid sequence Glu-Thr-Ser-Ala-Ala-Lys-Leu-Lys (SEQ ID NO: 131); or the amino acid sequence Glu-Ser-Ser-Ala-Ala-Lys-Leu-Lys (SEQ ID NO: 132). In another aspect of this embodiment, a BoNT/G substrate cleavage site comprises a naturally occurring BoNT/G substrate cleavage site variant. In another aspect of this embodiment, a BoNT/G substrate cleavage site comprises a naturally occurring BoNT/G substrate cleavage site variant of SEQ ID NO: 131 or SEQ ID NO: 132, such as, e.g., a BoNT/G substrate cleavage site isoform of SEQ ID NO: 131 or SEQ ID NO: 132; or a BoNT/G substrate cleavage site subtype of SEQ ID NO: 131 or SEQ ID NO: 132. In still another aspect of this embodiment, a BoNT/G substrate cleavage site comprises a non-naturally occurring BoNT/F substrate cleavage site variant, such as, e.g., a conservative BoNT/G substrate cleavage site variant, a non-conservative BoNT/G substrate cleavage site variant or a BoNT/G substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a

BoNT/G substrate cleavage site comprises a non-naturally occurring BoNT/G substrate cleavage site variant of SEQ ID NO: 131 or SEQ ID NO: 132; such as, e.g., a conservative BoNT/G substrate cleavage site variant of SEQ ID NO: 131 or SEQ ID NO: 132; a non-conservative BoNT/G substrate cleavage site variant of SEQ ID NO: 131 or SEQ ID NO: 132; a BoNT/G substrate cleavage site peptidomimetic of SEQ ID NO: 131 or SEQ ID NO: 132; or any combination thereof.

[0148] In other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 131 , at least 62.5% amino acid identity with the SEQ ID NO: 131 , at least 75% amino acid identity with SEQ ID NO: 131 or at least 87.5% amino acid identity with SEQ ID NO: 131. In still other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 131, at most 62.5% amino acid identity with the SEQ ID NO: 131, at most 75% amino acid identity with SEQ ID NO: 131 or at most 87.5% amino acid identity with SEQ ID NO: 131.

[0149] In other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 131. In yet other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten noncontiguous amino acid additions relative to SEQ ID NO: 131. In yet other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a BoHlIG substrate cleavage site comprises a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 131.

[0150] In other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 131. In yet other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 131. In yet other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a BoNT/G substrate cleavage site comprises a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a BoNT/G

substrate cleavage site comprises a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 131.

[0151] In an aspect of the invention, a modified Clostridial toxin comprises a TeNT substrate cleavage site. As used herein, the term "tetanus toxin substrate cleavage site" is synonymous with 'TeNT substrate cleavage site" and means a scissile bond together with adjacent or non-adjacent recognition elements, or both, sufficient for detectable proteolysis at the scissile bond by a TeNT under appropriate conditions. A scissile bond cleaved by TeNT can be, for example, Gln-Phe. It is envisioned that a TeNT substrate cleavage site of any and all lengths can be useful in aspects of the present invention with the proviso that the TeNT substrate cleavage site is capable of being cleaved by TeNT. Thus, in aspects of this embodiment, a TeNT substrate cleavage site can be, e.g., at least 6 amino acids in length, at least 7 amino acids in length, at least 8 amino acids in length, at least 9 amino acids in length, at least 10 amino acids in length, at least 15 amino acids in length, at least 20 amino acids in length, at least 25 amino acids in length, at least 30 amino acids in length, at least 40 amino acids in length, at least 50 amino acids in length or at least 60 amino acids in length. In other aspects of this embodiment, a TeNT substrate cleavage site can be, e.g., at most 6 amino acids in length, at most 7 amino acids in length, at most 8 amino acids in length, at most 9 amino acids in length, at most 10 amino acids in length, at most 15 amino acids in length, at most 20 amino acids in length, at most 25 amino acids in length, at most 30 amino acids in length, at most 40 amino acids in length, at most 50 amino acids in length or at most 60 amino acids in length.

[0152] A TeNT substrate cleavage sites useful in aspects of the invention can correspond to a segment of a protein that is sensitive to cleavage by TeNT, or can be substantially similar to a segment of a TeNT- sensitive protein. As shown in Table 3, a variety of naturally occurring proteins sensitive to cleavage by TeNT are known in the art and include, for example, human and mouse VAMP-1 , VAMP-2 and VAMP- 3/cellubrevin; bovine VAMP-2; rat VAMP-2 and VAMP-3; chicken VAMP-2; Torpedo VAMP-1 ; Strongylocentrotus VAMP; Drosophila sybA, synB, synC, synD and synE; Hirudo VAMP; and Caenorhabditis SNB1-like. Thus, a TeNT substrate cleavage site can correspond, for example, to a segment of human VAMP-1 , VAMP-2 or VAMP-3; bovine VAMP-2; rat VAMP-2 or VAMP-3; mouse VAMP-1 , VAMP-2 or VAMP-3; chicken VAMP-1 , VAMP-2 or VAMP-3; Xenopus VAMP-2 or VAMP-3; Danio VAMP-1 or VAMP-2; Torpedo VAMP-1 ; Strongylocentrotus. V ¹ AMP; Drosophila sybA, synB, synC, synD or synE; Hirudo VAMP; Loligo VAMP; Lymnaea VAMP; Aplysia VAMP; Caenorhabditis SNB1 and SNB-like, isoforms thereof, or another naturally occurring protein sensitive to cleavage by TeNT. Furthermore, comparison of native VAMP amino acid sequences cleaved by TeNT reveals that such sequences are not absolutely conserved (Table 3). This finding indicates that a variety of amino acid substitutions and modifications relative to a naturally occurring TeNT-sensitive VAMP sequence can be tolerated in a TeNT substrate cleavage site useful in aspects of the present invention. It is understood that a similar TeNT substrate cleavage site can be prepared, if desired, from a corresponding (homologous) segment of another TeNT-sensitive VAMP-1 or VAMP-2 isoform, paralog or ortholog, such

as, the TeNT substrate cleavage site contain in the VAMP-1 and VAMP-2 identified in the organisms listed above and in Table 3.

[0153] A variety of TeNT recognition sequences are well known in the art or can be defined by routine methods and include sequences corresponding to some or all of the hydrophilic core of a VAMP protein such as human VAMP-1 or human VAMP-2. A TeNT recognition sequence can include, for example, residues 25 to 93 or residues 33 to 94 of human VAMP-2 (SEQ ID NO: 39); F. Cornille et al., Solid- Phase Synthesis, Conformational Analysis and In Vitro Cleavage Of Synthetic Human Synaptobrevin Il 1- 93 by Tetanus Toxin L chain, 222(1 ) Eur. J. Biochem. 173-181 (1994); Patrick Foran et al., Differences in the Protease Activities of Tetanus and Botulinum B Toxins Revealed By the Cleavage of Vesicle- Associated Membrane Protein and Various Sized Fragments, 33(51) Biochemistry 15365-15374 (1994); residues 51 to 93 or residues 1 to 86 of rat VAMP-2, see, e.g., Yamasaki et al., supra, (1994); or residues 33 to 94 of human VAMP-1 -1 (SEQ ID NO: 36), residues 33 to 94 of human VAMP-1 -2 (SEQ ID NO: 37) and residues 33 to 94 of human VAMP-1 -3 (SEQ ID NO: 38). A TeNT recognition sequence also can include, for example, residues 25 to 86, residues 33 to 86 or residues 51 to 86 of human VAMP-2 (SEQ ID NO: 39) or rat VAMP-2 (SEQ ID NO: 46). It is understood that a similar TeNT recognition sequence can be prepared, if desired, from a corresponding (homologous) segment of another TeNT-sensitive VAMP isoform or species homolog such as human VAMP-1 or sea urchin or Aplysia VAMP.

[0154] Thus, in an embodiment, a modified Clostridial toxin comprises a TeNT substrate cleavage site. In an aspect of this embodiment, a TeNT substrate cleavage site comprises at least six consecutive residues of VAMP including Gln-Phe. In other aspects of this embodiment, a TeNT substrate cleavage site comprises, e.g., the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Thr-Ser (SEQ ID NO: 107); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Ser-Ser (SEQ ID NO: 108); the amino acid sequence GIy- Ala-Ser-Gln-Phe-Glu-Thr-Asn (SEQ ID NO: 109); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Gln- GIn (SEQ ID NO: 110); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Ala-Ser (SEQ ID NO: 111); or the amino acid sequence Gly-Ala-Ser-Gln-Phe-Gln-Gln-Ser (SEQ ID NO: 112). In another aspect of this embodiment, a TeNT substrate cleavage site comprises a naturally occurring TeNT substrate cleavage site variant. In another aspect of this embodiment, a TeNT substrate cleavage site comprises a naturally occurring TeNT substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112, such as, e.g., a TeNT substrate cleavage site isoform of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; or a TeNT substrate cleavage site subtype of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112. In still another aspect of this embodiment, a TeNT substrate cleavage site comprises a non-naturally occurring TeNT substrate cleavage site variant, such as, e.g., a conservative TeNT substrate cleavage site variant, a non- conservative TeNT substrate cleavage site variant or a TeNT substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a TeNT substrate cleavage site comprises a non-naturally occurring TeNT substrate cleavage site variant of SEQ ID NO: 107, SEQ ID

NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; such as, e.g., a conservative TeNT substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; a non-conservative TeNT substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; a TeNT substrate cleavage site peptidomimetic of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; or any combination thereof.

[0155] In other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 107, at least 62.5% amino acid identity with the SEQ ID NO: 107, at least 75% amino acid identity with SEQ ID NO: 107 or at least 87.5% amino acid identity with SEQ ID NO: 107. In still other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 107, at most 62.5% amino acid identity with the SEQ ID NO: 107, at most 75% amino acid identity with SEQ ID NO: 107 or at most 87.5% amino acid identity with SEQ ID NO: 107.

[0156] In other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 107.

[0157] In other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a TeNT substrate

cleavage site comprises a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a TeNT substrate cleavage site comprises a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 107.

[0158] Another type of Clostridial toxin substrate cleavage site is derived from autocatalytic fragments of the Clostridial toxins themselves. It has been noted that a Clostridial toxin can undergo autocatalytic fragmentation resulting in the formation of two major polypeptide fragments. For example, peptide bonds susceptible to autocatalytic cleavage have been located in two regions of BoNT/A. The first region comprises amino acids 250-267 of SEQ ID NO: 1 , where bonds Tyr250-Tyr251 and Phe266-Gly267 are susceptible to cleaved. The second region comprises residues 419-439 of SEQ ID NO: 1 , where bonds Phe419-Thr420, Phe423-Glu424, Leu429-Cys430, Cys 430-Val431 , Arg432-Gly433 and Lys438-Thr439 are susceptible to autocatalytic cleavage. The BoNT/A region corresponding to amino acids 250-267 of SEQ ID NO: 1 is highly conserved among Clostridial toxins (Table 7).

[0159] Thus, in an embodiment, a modified Clostridial toxin comprises a Clostridial toxin autocatalytic substrate cleavage site. In aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises at least six consecutive residues of a Clostridial toxin including the BoNT/A residues 250Tyr-251Tyr, the BoNT/B residues 256Phe-257Phe, the BoNT/C1 residues 257Phe-258Tyr, the BoNT/D residues 257Phe-258Phe, the BoNT/E residues 239Pro-240Leu, the BoNT/F residues 254Pro-255Leu, the BoNT/G residues 256Phe-257Phe or the TeNT residues 259lle-260Tyr. In another

aspect of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises at least six consecutive residues of a Clostridial toxin including Phe-Gly. In other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises at least six consecutive residues of a Clostridial toxin including the BoNT/A residues Phe266-Gly267, the BoNT/B residues Phe272-Gly273, the BoNT/C1 residues Phe273-Gly274, the BoNT/D residues Phe273-Gly274, the BoNT/E residues Phe255- Gly256, the BoNT/F residues Phe270-Gly271 , the BoNT/G residues Phe272-Gly273 or the TeNT residues Phe275-Gly276.

[0160] In other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises, e.g., the BoNT/A residues 246-271 of SEQ ID NO: 1 ; the BoNT/B residues 252-277 of SEQ ID NO: 2; the BoNT/C1 residues 253-278 of SEQ ID NO: 3; the BoNT/D residues 253-278 of SEQ ID NO: 4; the BoNT/E residues 235-260 of SEQ ID NO: 5; the BoNT/F residues 250-275 of SEQ ID NO: 6; the BoNT/G residues 252-277 of SEQ ID NO: 7; or the TeNT residues 255-280 of SEQ ID NO: 8. In still other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises, e.g., the BoNT/A residues 247-254 of SEQ ID NO: 1 ; the BoNT/B residues 253-260 of SEQ ID NO: 2; the BoNT/CI residues 254-261 of SEQ ID NO: 3; the BoNT/D residues 254-261 of SEQ ID NO: 4; the BoNT/E residues 236-243 of SEQ ID NO: 5; the BoNT/F residues 251-258 of SEQ ID NO: 6; the BoNT/G residues 253-260 of SEQ ID NO: 7; or the TeNT residues 256-263 of SEQ ID NO: 8. In yet other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises, e.g., the BoNT/A residues 263-270 of SEQ ID NO: 1 ; the BoNT/B residues 269-276 of SEQ ID NO: 2; the BoNT/C1 residues 270-277 of SEQ ID NO: 3; the BoNT/D residues 270-277 of SEQ ID NO: 4; the BoNT/E residues 252-259 of SEQ ID NO: 5; the BoNT/F residues 267-274 of SEQ ID NO: 6; the BoNT/G residues 269-276 of SEQ ID NO: 7; or the TeNT residues 272-279 of SEQ ID NO: 8.

[0161] In other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at least 50% amino acid identity with the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8; at least 60% amino acid identity with the BoNT/A residues 246- 271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8; at least 70% amino acid identity with the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253- 278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8; at least 80% amino acid identity with the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/CI

residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8; at least 90% amino acid identity with the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/CI residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8; or at least 95% amino acid identity with the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8.

[0162] In still other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at most 50% amino acid identity with the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/CI residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO:

5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8; at most 60% amino acid identity with the BoNT/A residues 246- 271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8; at most 70% amino acid identity with the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253- 278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8; at most 80% amino acid identity with the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8; at most 90% amino acid identity with the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8; or at most 95% amino acid identity with the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/CI residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO:

6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8.

[0163] In other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNTVCI residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8. In still other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/CI residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8.

[0164] In yet other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten noncontiguous amino acid additions relative to the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/CI residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8. In yet other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to the BoNT/A residues 246-271 of SEQ ID NO:

1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8.

[0165] In still other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO:

2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8. In still other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8.

[0166] In other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/CI residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8. In still other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8.

[0167] In yet other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/CI residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8. In yet other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8.

[0168] In still other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to the BoNT/A residues 246-271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/CI residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8. In still other aspects of this embodiment, a Clostridial toxin autocatalytic substrate cleavage site comprises a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to the BoNT/A residues 246- 271 of SEQ ID NO: 1 , the BoNT/B residues 252-277 of SEQ ID NO: 2, the BoNT/C1 residues 253-278 of SEQ ID NO: 3, the BoNT/D residues 253-278 of SEQ ID NO: 4, the BoNT/E residues 235-260 of SEQ ID

NO: 5, the BoNT/F residues 250-275 of SEQ ID NO: 6, the BoNT/G residues 252-277 of SEQ ID NO: 7 or the TeNT residues 255-280 of SEQ ID NO: 8.

[0169] In an aspect of the invention, a Clostridial toxin substrate cleavage site is located within the di- chain loop region. As used herein, the term "di-chain loop region" means the amino acid sequence of a Clostridial toxin containing a protease cleavage site used to convert the single-chain form of a Clostridial toxin into the di-chain form. As non-limiting examples, the di-chain loop region of BoNT/A comprises amino acids 430-454 of SEQ ID NO: 1 ; the di-chain loop region of BoNT/B comprises amino acids 437- 446 of SEQ ID NO: 2; the di-chain loop region of BoNT/Ci comprises amino acids 437-453 of SEQ ID NO: 3; the di-chain loop region of BoNT/D comprises amino acids 437-450 of SEQ ID NO: 4; the di-chain loop region of BoNT/E comprises amino acids 412-426 of SEQ ID NO: 5; the di-chain loop region of BoNT/F comprises amino acids 429-445 of SEQ ID NO: 6; the di-chain loop region of BoNT/G comprises amino acids 436-450 of SEQ ID NO: 7; and the di-chain loop region of TeNT comprises amino acids 439- 467 of SEQ ID NO: 8.

[0170] As mentioned above, a Clostridial toxin is converted from a single polypeptide form into a di-chain molecule by proteolytic cleavage. While the identity of the naturally-occurring protease is currently unknown, the location of the di-chain loop protease cleavage site for many Clostridial toxins has been determined (Table 8). Cleavage within the di-chain loop does not appear to be confined to a single peptide bond. Thus, cleavage of a Clostridial toxin with a naturally-occurring di-chain loop protease results in the lost of several residues centered around the original cleavage site. This loss is limited to a few amino acids located between the two cysteine residues that form the disulfide bridge. As a non- limiting example, BoNT/A single-chain polypeptide cleavage ultimately results in the loss of a ten amino

acids within the di-chain loop. For BoNTs, cleavage at K448-A449 converts the single-chain form of BoNT/A into the di-chain form; cleavage at K441-A442 converts the single-chain form of BoNT/B into the di-chain form; cleavage at K449-T450 converts the single-chain form of BoNT/C1 into the di-chain form; cleavage at R445-D446 converts the single-chain form of BoNT/D into the di-chain form; cleavage at R422-K423 converts the single-chain form of BoNT/E into the di-chain form; cleavage at K439-A440 converts the single-chain form of BoNT/F into the di-chain form; and cleavage at K446-S447 converts the single-chain form of BoNT/G into the di-chain form. Proteolytic cleavage of the single-chain form of TeNT at of A457-S458 results in the di-chain form.

[0171] However, it should also be noted that additional cleavage sites within the di-chain loop also appear to be cleaved resulting in the generation of a small peptide fragment being lost. As a non-limiting example, BoNT/A single-chain polypeptide cleavage ultimately results in the loss of a ten amino acid fragment within the di-chain loop. Thus, cleavage at S441-L442 converts the single polypeptide form of BoNT/A into the di-chain form; cleavage at G444-I445 converts the single polypeptide form of BoNT/B into the di-chain form; cleavage at S445-L446 converts the single polypeptide form of BoNT/C1 into the di-chain form; cleavage at K442-N443 converts the single polypeptide form of BoNT/D into the di-chain form; cleavage at K419-G420 converts the single polypeptide form of BoNT/E into the di-chain form; cleavage at K423-S424 converts the single polypeptide form of BoNT/E into the di-chain form; cleavage at K436-G437 converts the single polypeptide form of BoNT/F into the di-chain form; cleavage at T444- G445 converts the single polypeptide form of BoNT/G into the di-chain form; and cleavage at E448-Q449 converts the single polypeptide form of BoNT/G into the di-chain form.

[0172] The di-chain loop region can be modified to include a Clostridial toxin substrate cleavage site in addition to the naturally-occurring di-chain loop protease cleavage site. In this type of modification, both cleavage site are operably-linked in-frame to a modified Clostridial toxin as a fusion protein and both sites can be cleaved by their respective proteases. As a non-limiting example, a modified BoNT/A that comprises a di-chain loop containing both the naturally-occurring di-chain loop protease cleavage site and a BoNT/A substrate cleavage site can be cleaved by either the endogenous di-chain loop protease found in C. botulinum serotype A or by BoNT/A. As another non-limiting example, a modified BoNT/A that comprises a di-chain loop containing both the naturally-occurring di-chain loop protease cleavage site and a BoNT/E substrate cleavage site can be cleaved by either the endogenous di-chain loop protease found in C. botulinum serotype A or by BoNT/E.

[0173] The di-chain loop region can also be modified to replace the naturally-occurring di-chain loop protease cleavage site with a Clostridial toxin substrate cleavage site. In this type of modification, the naturally-occurring protease cleavage site is made inoperable and thus can not be cleaved by its protease. Only the Clostridial toxin substrate cleavage site can be cleaved by its corresponding toxin. Such a Clostridial toxin substrate cleavage site is operably-linked in-frame to a modified Clostridial toxin as a fusion protein. As a non-limiting example, a single-chain modified BoNT/A that comprises a di-chain

loop containing only a BoNT/A substrate cleavage site can be cleaved BoNT/A, but not the endogenous di-chain loop protease found in C. botulinum serotype A. As another non-limiting example, a single-chain modified BoNT/A that comprises a di-chain loop containing only a BoNT/E substrate cleavage site can be cleaved BoNT/E, but not the endogenous di-chain loop protease found in C. botulinum serotype A.

[0174] The naturally-occurring di-chain loop protease cleavage site can be made inoperable by altering at least the one of the amino acids flanking the peptide bond cleaved by the naturally-occurring protease. More extensive alterations can be made, with the proviso that the two cysteine residues of the di-chain loop region remain intact and formation of the disulfide bridge can still be acheived. Non-limiting examples of an amino acid alteration include deletion of an amino acid or replacement of the original amino acid with a different amino acid. These alterations can be made using standard mutagenesis procedures known to a person skilled in the art. In addition, non-limiting examples of mutagensis procedures, as well as well-characterized reagents, conditions and protocols are readily available from commercial vendors that include, without limitation, BD Biosciences-Clontech, Palo Alto, CA; BD Biosciences Pharmingen, San Diego, CA; Invitrogen, Inc, Carlsbad, CA; QIAGEN, Inc., Valencia, CA; and Stratagene, La JoIIa, CA. These protocols are routine procedures within the scope of one skilled in the art and from the teaching herein.

[0175] Thus, in one embodiment, a naturally-occurring di-chain loop protease cleavage site is made inoperable by altering at least one of the amino acids flanking the peptide bond cleaved by a naturally- occurring protease. In aspects of this embodiment, the P ₁ amino acid of the di-chain loop protease cleavage site is altered or the P _r amino acid of the di-chain loop protease cleavage site is altered. In other aspects of this embodiment, either K448 or A449 of BoNT/A is altered; either S441 or L442 of BoNT/A is altered; either K441 or A442 of BoNT/B is altered; either G444 or I445 of BoNT/B is altered; either K449 or T450 of BoNT/C1 is altered; either S445 or L446 of BoNT/C1 is altered; either R445 or D446 of BoNT/D is altered; either K442 or N443 of BoNT/D is altered; either R422 or K423 of BoNT/E is altered; either K419 or G420 of BoNT/E is altered; either K423 or S424 of BoNT/E is altered; either K439 or A440 of BoNT/F is altered; either K436 or G437 of BoNT/F is altered; either K446 or S447 of BoNT/G is altered; either T444 or G445 of BoNT/G is altered; either E448 or Q449 of BoNT/G is altered; or either A457 or S458 of TeNT is altered.

[0176] In another embodiment, a naturally-occurring di-chain loop protease cleavage site is made inoperable by altering the two amino acids flanking the peptide bond cleaved by a naturally-occurring protease, i.e., P ₁ and Py. In other aspects of this embodiment, both K448 and A449 of BoNT/A are altered; both S441 and L442 of BoNT/A are altered; both K441 and A442 of BoNT/B are altered; both G444 and I445 of BoNT/B are altered; both K449 and T450 of BoNT/C1 are altered; both S445 and L446 of B0NT/CI are altered; both R445 and D446 of BoNT/D are altered; both K442 and N443 of BoNT/D are altered; both R422 and K423 of BoNT/E are altered; both K419 and G420 of BoNT/E are altered; both K423 and S424 of BoNT/E are altered; both K439 and A440 of BoNT/F are altered; both K436 and G437

of BoNT/F are altered; both K446 and S447 of BoNT/G are altered; both T444 and G445 of BoNT/G are altered; both E448 and Q449 of BoNT/G are altered; or both A457 and S458 of TeNT are altered.

[0177] In other aspects of this embodiment, a naturally-occurring di-chain loop protease cleavage site is made inoperable by altering, e.g., at least two amino acids within the dischain loop region; at least three amino acids within the dischain loop region; at least four amino acids within the dischain loop region; at least five amino acids within the dischain loop region; at least six amino acids within the dischain loop region; at least seven amino acids within the dischain loop region; at least eight amino acids within the dischain loop region; at least nine amino acids within the dischain loop region; at least ten amino acids within the dischain loop region; or at least 15 amino acids within the dischain loop region. In still other aspects of this embodiment, a naturally-occurring di-chain loop protease cleavage site is made inoperable by altering one of the amino acids flanking the peptide bond cleaved by a naturally-occurring protease and, e.g., at least one more amino acid within the dischain loop region; at least two more amino acids within the dischain loop region; at least three more amino acids within the dischain loop region; at least four more amino acids within the dischain loop region; at least five more amino acids within the dischain loop region; at least six more amino acids within the dischain loop region; at least seven more amino acids within the dischain loop region; at least eight more amino acids within the dischain loop region; at least nine more amino acids within the dischain loop region; at least ten more amino acids within the dischain loop region; at least 15 more amino acids within the dischain loop region. In yet other aspects of this embodiment, a naturally-occurring di-chain loop protease cleavage site is made inoperable by altering the two amino acids flanking the peptide bond cleaved by a naturally-occurring protease and, e.g., at least one more amino acid within the dischain loop region; at least two more amino acids within the dischain loop region; at least three more amino acids within the dischain loop region; at least four more amino acids within the dischain loop region; at least five more amino acids within the dischain loop region; at least six more amino acids within the dischain loop region; at least seven more amino acids within the dischain loop region; at least eight more amino acids within the dischain loop region; at least nine more amino acids within the dischain loop region; at least ten more amino acids within the dischain loop region; at least 15 more amino acids within the dischain loop region.

[0178] In other aspects of this embodiment, a naturally-occurring di-chain loop protease cleavage site is made inoperable by altering, e.g., at most two amino acids within the dischain loop region; at most three amino acids within the dischain loop region; at most four amino acids within the dischain loop region; at most five amino acids within the dischain loop region; at most six amino acids within the dischain loop region; at most seven amino acids within the dischain loop region; at most eight amino acids within the dischain loop region; at most nine amino acids within the dischain loop region; at most ten amino acids within the dischain loop region; or at most 15 amino acids within the dischain loop region. In still other aspects of this embodiment, a naturally-occurring di-chain loop protease cleavage site is made inoperable by altering one of the amino acids flanking the peptide bond cleaved by a naturally-occurring protease and, e.g., at most one more amino acid within the dischain loop region; at most two more amino acids

within the dischain loop region; at most three more amino acids within the dischain loop region; at most four more amino acids within the dischain loop region; at most five more amino acids within the dischain loop region; at most six more amino acids within the dischain loop region; at most seven more amino acids within the dischain loop region; at most eight more amino acids within the dischain loop region; at most nine more amino acids within the dischain loop region; at most ten more amino acids within the dischain loop region; at most 15 more amino acids within the dischain loop region. In yet other aspects of this embodiment, a naturally-occurring di-chain loop protease cleavage site is made inoperable by altering the two amino acids flanking the peptide bond cleaved by a naturally-occurring protease and, e.g., at most one more amino acid within the dischain loop region; at most two more amino acids within the dischain loop region; at most three more amino acids within the dischain loop region; at most four more amino acids within the dischain loop region; at most five more amino acids within the dischain loop region; at most six more amino acids within the dischain loop region; at most seven more amino acids within the dischain loop region; at most eight more amino acids within the dischain loop region; at most nine more amino acids within the dischain loop region; at most ten more amino acids within the dischain loop region; at most 15 more amino acids within the dischain loop region.

[0179] It is envisioned that the di-chain loop region of a Clostridial toxin can be modified to include any and all Clostridial toxin substrate cleavage sites. In aspects of this embodiment, a di-chain loop of a Clostridial toxin disclosed in the present specification can be modified to comprise, e.g., a BoNT/A substrate cleavage site, a BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site, a BoNT/G substrate cleavage site, a TeNT substrate cleavage site, a BaNT substrate cleavage site or a BuNT substrate cleavage site. In other aspects of this embodiment, a di-chain loop of a Clostridial toxin, in addition to the naturally-occurring protease cleavage site, can be modified to comprise, e.g., a BoNT/A substrate cleavage site, a BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site, a BoNT/G substrate cleavage site, or a TeNT substrate cleavage site. In still other aspects of this embodiment, a di- chain loop of a Clostridial toxin can be modified to replace a naturally-occurring protease cleavage site with, e.g., a BoNT/A substrate cleavage site, a BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site, a BoNT/G substrate cleavage site, a TeNT substrate cleavage site, a BaNT substrate cleavage site or a BuNT substrate cleavage site.

[0180] The location of the Clostridial toxin substrate cleavage site can be anywhere in the Clostridial toxin, with the proviso that cleavage of the site must occur between the two cysteine residues that form the single disulfide bridge of toxin. Thus, in aspects of this embodiment, location of a Clostridial toxin substrate cleavage site can be, e.g., anywhere in the BoNT/A of SEQ ID NO: 1 , with the proviso that cleavage occurs between cysteine 430 and cysteine 454; anywhere in the BoNT/B of SEQ ID NO: 2, with the proviso that cleavage occurs between cysteine 437 and cysteine 446; anywhere in the BoNT/C1 of

SEQ ID NO: 2, with the proviso that cleavage occurs between cysteine 437 and cysteine 453; anywhere in the BoNT/D of SEQ ID NO: 4, with the proviso that cleavage occurs between cysteine 437 and cysteine 450; anywhere in the BoNT/E of SEQ ID NO: 5, with the proviso that cleavage occurs between cysteine 412 and cysteine 426; anywhere in the BoNT/F of SEQ ID NO: 6, with the proviso that cleavage occurs between cysteine 429 and cysteine 445; anywhere in the BoNT/G of SEQ ID NO: 7, with the proviso that cleavage occurs between cysteine 436 and cysteine 450; or anywhere in the TeNT of SEQ ID NO: 8, with the proviso that cleavage occurs between cysteine 439 and cysteine 467.

[0181] It is understood that a modified Clostridial toxin disclosed in the present specification can optionally include one or more additional components. As a non-limiting example of an optional component, a modified Clostridial toxin can further comprise a flexible region comprising a flexible spacer. Non-limiting examples of a flexible spacer include, e.g., a G-spacer GGGGS (SEQ ID NO: 156) or an A- spacer EAAAK (SEQ ID NO: 157). A flexible region comprising flexible spacers can be used to adjust the length of a polypeptide region in order to optimize a characteristic, attribute or property of a polypeptide. Such a flexible region is operably-linked in-frame to the modified Clostridial toxin as a fusion protein. As a non-limiting example, a polypeptide region comprising one or more flexible spacers in tandem can be use to better expose a protease cleavage site thereby facilitating cleavage of that site by a protease. As another non-limiting example, a polypeptide region comprising one or more flexible spacers in tandem can be use to better present a ligand domain, thereby facilitating the binding of that ligand domain to its binding domain on a receptor.

[0182] Thus, in an embodiment, a modified Clostridial toxin disclosed in the present specification can further comprise a flexible region comprising a flexible spacer. In another embodiment, a modified Clostridial toxin disclosed in the present specification can further comprise flexible region comprising a plurality of flexible spacers in tandem. In aspects of this embodiment, a flexible region can comprise in tandem, e.g., at least 1 G-spacer, at least 2 G-spacers, at least 3 G-spacers, at least 4 G-spacers or at least 5 G-spacers. In other aspects of this embodiment, a flexible region can comprise in tandem, e.g., at most 1 G-spacer, at most 2 G-spacers, at most 3 G-spacers, at most 4 G-spacers or at most 5 G- spacers. In still other aspects of this embodiment, a flexible region can comprise in tandem, e.g., at least 1 A-spacer, at least 2 A-spacers, at least 3 A-spacers, at least 4 A-spacers or at least 5 A-spacers. In still other aspects of this embodiment, a flexible region can comprise in tandem, e.g., at most 1 A-spacer, at most 2 A-spacers, at most 3 A-spacers, at most 4 A-spacers or at most 5 A-spacers. In another aspect of this embodiment, a modified Clostridial toxin can comprise a flexible region comprising one or more copies of the same flexible spacers, one or more copies of different flexible-spacer regions, or any combination thereof.

[0183] As another non-limiting example of an optional component, a modified Clostridial toxin can further comprise an epitope-binding region. An epitope-binding region can be used in a wide variety of procedures involving, e.g., protein purification and protein visualization. Such an epitope-binding region

is operably-linked in-frame to a modified Clostridial toxin as a fusion protein. Non-limiting examples of an epitope-binding region include, e.g., FLAG, Express™ (SEQ ID NO: 158), human Influenza virus hemagluttinin (HA) (SEQ ID NO: 159), human p62 ^{c My0} protein (c-MYC) (SEQ ID NO: 160), Vesicular Stomatitis Virus Glycoprotein (VSV-G) (SEQ ID NO: 161), Substance P (SEQ ID NO: 162), glycoprotein- D precursor of Herpes simplex virus (HSV) (SEQ ID NO: 163), V5 (SEQ ID NO: 164), AU1 (SEQ ID NO: 165) and AU5 (SEQ ID NO: 166); affinity-binding , such as. e.g., polyhistidine (HIS) (SEQ ID NO: 167), streptavidin binding peptide (strep), and biotin or a biotinylation sequence; peptide-binding regions, such as. e.g., the glutathione binding domain of glutathione-S-transferase, the calmodulin binding domain of the calmodulin binding protein, and the maltose binding domain of the maltose binding protein. Non- limiting examples of specific protocols for selecting, making and using an appropriate binding peptide are described in, e.g., Epitope Tagging, pp. 17.90-17.93 (Sambrook and Russell, eds., MOLECULAR CLONING A LABORATORY MANUAL, Vol. 3, 3 ^rd ed. 2001); ANTIBODIES: A LABORATORY MANUAL (Edward Harlow & David Lane, eds., Cold Spring Harbor Laboratory Press, 2 ^nd ed. 1998); and USING ANTIBODIES: A LABORATORY MANUAL: PORTABLE PROTOCOL NO. I (Edward Harlow & David Lane, Cold Spring Harbor Laboratory Press, 1998). In addition, non-limiting examples of binding peptides as well as well-characterized reagents, conditions and protocols are readily available from commercial vendors that include, without limitation, BD Biosciences-Clontech, Palo Alto, CA; BD Biosciences Pharmingen, San Diego, CA; Invitrogen, Inc, Carlsbad, CA; QIAGEN, Inc., Valencia, CA; and Stratagene, La JoIIa, CA. These protocols are routine procedures well within the scope of one skilled in the art and from the teaching herein.

[0184] Thus, in an embodiment, a modified Clostridial toxin disclosed in the present specification can further comprise an epitope-binding region. In another embodiment, a modified Clostridial toxin disclosed in the present specification can further comprises a plurality of epitope-binding regions. In aspects of this embodiment, a modified Clostridial toxin can comprise, e.g., at least 1 epitope-binding region, at least 2 epitope-binding regions, at least 3 epitope-binding regions, at least 4 epitope-binding regions or at least 5 epitope-binding regions. In other aspects of this embodiment, a modified Clostridial toxin can comprise, e.g., at most 1 epitope-binding region, at most 2 epitope-binding regions, at most 3 epitope-binding regions, at most 4 epitope-binding regions or at most 5 epitope-binding regions. In another aspect of this embodiment, a modified Clostridial toxin can comprise one or more copies of the same epitope-binding region, one or more copies of different epitope-binding regions, or any combination thereof.

[0185] The location of an epitope-binding region can be in various positions, including, without limitation, at the amino terminus of a modified Clostridial toxin, within a modified Clostridial toxin, or at the carboxyl terminus of a modified Clostridial toxin. Thus, in an embodiment, an epitope-binding region is located at the amino-terminus of a modified Clostridial toxin. In such a location, a start methionine should be placed in front of the epitope-binding region. In addition, it is known in the art that when adding a polypeptide that is operationally-linked to the amino terminus of another polypeptide comprising the start methionine that the original methionine residue can be deleted. This is due to the fact that the added polypeptide will contain a new start methionine and that the original start methionine may reduce optimal expression of

the fusion protein. In aspects of this embodiment, an epitope-binding region located at the amino- terminus of a modified Clostridial toxin disclosed in the present specification can be, e.g., a FLAG, Express™ epitope-binding region, a human Influenza virus hemagluttinin (HA) epitope-binding region, a human p62 ^{c Myc} protein (c-MYC) epitope-binding region, a Vesicular Stomatitis Virus Glycoprotein (VSV- G) epitope-binding region, a Substance P epitope-binding region, a glycoprotein-D precursor of Herpes simplex virus (HSV) epitope-binding region, a V5 epitope-binding region, a AU1 epitope-binding region, a AU5 epitope-binding region, a polyhistidine epitope-binding region, a streptavidin binding peptide epitope- binding region, a biotin epitope-binding region, a biotinylation epitope-binding region, a glutathione binding domain of glutathione-S-transferase, a calmodulin binding domain of the calmodulin binding protein or a maltose binding domain of the maltose binding protein.

[0186] In another embodiment, an epitope-binding region is located at the carboxyl-terminus of a modified Clostridial toxin. In aspects of this embodiment, an epitope-binding region located at the carboxyl-terminus of a modified Clostridial toxin disclosed in the present specification can be, e.g., a FLAG, Express™ epitope-binding region, a human Influenza virus hemagluttinin (HA) epitope-binding region, a human p62 ^c"Myc protein (c-MYC) epitope-binding region, a Vesicular Stomatitis Virus Glycoprotein (VSV-G) epitope-binding region, a Substance P epitope-binding region, a glycoprotein-D precursor of Herpes simplex virus (HSV) epitope-binding region, a V5 epitope-binding region, a AU1 epitope-binding region, a AU5 epitope-binding region, a polyhistidine epitope-binding region, a streptavidin binding peptide epitope-binding region, a biotin epitope-binding region, a biotinylation epitope-binding region, a glutathione binding domain of glutathione-S-transferase, a calmodulin binding domain of the calmodulin binding protein or a maltose binding domain of the maltose binding protein.

[0187] As still another non-limiting example of an optional component, a modified Clostridial toxin can further comprise an exogenous protease cleavage site. An exogenous protease cleavage site can be used in a wide variety of procedures involving, e.g., removal of an epitope-binding region by proteolytic cleavage. Such an exogenous protease cleavage site is operably-linked in-frame to a modified Clostridial toxin as a fusion protein. Non-limiting examples of protease cleavage sites include, e.g., an enterokinase cleavage site (Table 9); a Thrombin cleavage site (Table 9); a Factor Xa cleavage site (Table 9); a human rhinovirus 3C protease cleavage site (Table 9); a tobacco etch virus (TEV) protease cleavage site (Table 9); a dipeptidyl aminopeptidase cleavage site and a small ubiquitin-like modifier (SUMO)/ubiquitin-like protein-1(ULP-1) protease cleavage site, such as, e.g., MADSEVNQEAKPEVKPEVKPETHINLKVSDGSS EIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHR EQIGG (SEQ ID. NO: 185).

182

indicated

[0188] Thus, in an embodiment, a modified Clostridial toxin disclosed in the present specification can further comprise an exogenous protease cleavage site. In another embodiment, a modified Clostridial toxin disclosed in the present specification can further comprises a plurality of exogenous protease cleavage sites. In aspects of this embodiment, a modified Clostridial toxin can comprise, e.g., at least 1 exogenous protease cleavage site, at least 2 exogenous protease cleavage sites, at least 3 exogenous protease cleavage sites, at least 4 exogenous protease cleavage sites or at least 5 exogenous protease cleavage sites. In other aspects of this embodiment, a modified Clostridial toxin can comprise, e.g., at most 1 exogenous protease cleavage site, at most 2 exogenous protease cleavage sites, at most 3

exogenous protease cleavage sites, at most 4 exogenous protease cleavage sites or at most 5 exogenous protease cleavage sites. In another aspect of this embodiment, a modified Clostridial toxin can comprise one or more copies of the same exogenous protease cleavage site, one or more copies of different exogenous protease cleavage sites, or any combination thereof.

[0189] The location of an exogenous protease cleavage site may be in a variety of positions, including, without limitation, between an epitope-binding region and a modified Clostridial toxin in order to facilitate removal of the epitope-binding region by proteolytic cleavage. It is envisioned that an exogenous protease cleavage site can be used to remove an epitope-binding region. As mentioned above, epitope binding regions can be used in protein purification procedures and it is often desirable to remove such epitope binding regions after the protein is purified. A common way of doing so is to have a protease cleavage site in between the protein of interest and the epitope binding region, whereby proteolytic cleavage of the protease cleavage site separates the protein of interest from the epitope binding region. Non-limiting examples of protease cleavage sites used for the removal of epitope-binding regions as well as well-characterized proteases, reagents, conditions and protocols are readily available from commercial vendors that include, without limitation, BD Biosciences-Clontech, Palo Alto, CA; BD Biosciences Pharmingen, San Diego, CA; Invitrogen, Inc, Carlsbad, CA; QIAGEN, Inc., Valencia, CA; and Stratagene, La JoIIa, CA. The selection, making and use of an appropriate protease cleavage site are routine procedures within the scope of one skilled in the art and from the teaching herein.

[0190] Thus, in an embodiment, an exogenous protease cleavage site is located between an epitope- binding peptide and a modified Clostridial toxin. In other aspects of this embodiment, a bovine enterokinase cleavage site is located between an epitope-binding region and a modified Clostridial toxin, a Tobacco Etch Virus protease cleavage site is located between an epitope-binding region and a modified Clostridial toxin, a Human Rhinovirus 3C protease cleavage site is located between an epitope-binding region and a modified Clostridial toxin, a SUMO/ULP-1 protease cleavage site is located between an epitope-binding region and a modified Clostridial toxin, a Thrombin protease cleavage site is located between an epitope-binding region and a modified Clostridial toxin, or a Coagulation Factor Xa protease cleavage site is located between an epitope-binding region and a modified Clostridial toxin. In other aspects of the embodiment, the bovine enterokinase protease cleavage site located between an epitope- binding region and a modified Clostridial toxin comprises SEQ ID NO: 168. In other aspects of the embodiment, the Tobacco Etch Virus protease cleavage site located between an epitope-binding region and a modified Clostridial toxin comprises SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171 , SEQ ID NO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177 or SEQ ID NO: 178. In still other aspects of the embodiment, the Human Rhinovirus 3C protease cleavage site located between an epitope-binding region and a modified Clostridial toxin comprises SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181 , SEQ ID NO: 182, SEQ ID NO: 183 or SEQ ID NO: 184. In yet other aspects of the embodiment, the SUMO/ULP-1 protease cleavage site located between an epitope- binding region and a modified Clostridial toxin comprises SEQ ID NO: 185. In further other aspects of the

embodiment, the Thrombin protease cleavage site located between an epitope-binding region and a modified Clostridial toxin comprises SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 191 , SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 196, SEQ ID NO: 197, SEQ ID NO: 198, SEQ ID NO: 199 or SEQ ID NO: 200. In other aspects of the embodiment, the Coagulation Factor Xa protease cleavage site located between an epitope-binding region and a modified Clostridial toxin comprises SEQ ID NO: 201 or SEQ ID NO: 202.

[0191] Aspects of the present invention provide, in part modified Clostridial toxins. As used herein, the term "modified Clostridial toxin" means any naturally-occurring Clostridial toxin or non-naturally-occurring Clostridial toxin comprising at least the replacement of a naturally-occurring di-chain protease cleavage site with a Clostridial toxin substrate cleavage site as disclosed in the present specification, or the addition of a Clostridial toxin substrate cleavage site as disclosed in the present specification into the di- chain loop region. Non-limiting examples of modified Clostridial toxins disclosed in the present specification include, e.g., a modified Clostridial toxin comprising a Clostridial toxin substrate cleavage site, where the substrate cleavage site replaced the naturally-occurring di-chain loop protease cleavage site; a modified Clostridial toxin comprising a Clostridial toxin substrate cleavage site, where the substrate cleavage site is added into the di-chain loop region; a modified Clostridial toxin comprising a Clostridial toxin substrate cleavage site and a cell binding domain having an enhanced cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell, where the substrate cleavage site replaced the naturally-occurring di-chain loop protease cleavage site; a modified Clostridial toxin comprising a Clostridial toxin substrate cleavage site and a cell binding domain having an enhanced cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell, where the substrate cleavage site is added into the di-chain loop region; a modified Clostridial toxin comprising a Clostridial toxin substrate cleavage site and a cell binding domain having an altered cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell, where the substrate cleavage site replaced the naturally-occurring di-chain loop protease cleavage site; a modified Clostridial toxin comprising a Clostridial toxin substrate cleavage site and a cell binding domain having an altered cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell, where the substrate cleavage site is added into the di-chain loop region; a modified Clostridial toxin comprising a Clostridial toxin substrate cleavage site and a cell binding domain having an altered cell binding activity capable of intoxicating a non-naturally occurring Clostridial toxin target cell, where the substrate cleavage site replaced the naturally-occurring di-chain loop protease cleavage site; and a modified Clostridial toxin comprising a Clostridial toxin substrate cleavage site and a cell binding domain having an altered cell binding activity capable of intoxicating a non-naturally occurring Clostridial toxin target cell, where the substrate cleavage site is added into the di-chain loop region.

[0192] Non-limiting examples of Clostridial toxin modifications disclosed in the present specification include, e.g., replacement of a naturally-occurring di-chain protease cleavage site with a Clostridial toxin substrate cleavage site, addition of a Clostridial toxin substrate cleavage site, addition of an exogenous

protease cleavage site, replacement of an endogenous cell binding domain with a cell binding domain having an enhanced cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell, addition of a cell binding domain having an enhanced cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell, replacement of an endogenous cell binding domain with a cell binding domain having an altered cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell, addition of a cell binding domain having an altered cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell, replacement of an endogenous cell binding domain with a cell binding domain having an altered cell binding activity capable of intoxicating a non-naturally occurring Clostridial toxin target cell, addition of a cell binding domain having an altered cell binding activity capable of intoxicating a non-naturally occurring Clostridial toxin target cell, addition of an exogenous protease cleavage site, rearrangement of the enzymatic, translocation and binding domains, addition of a spacer region and addition of an epitope-binding region.

[0193] It is understood that all such modifications do not substantially affect the ability of a Clostridial toxin to intoxicate a cell. As used herein, the term "do not substantially affect" means a Clostridial toxin can still execute the overall cellular mechanism whereby a Clostridial toxin enters a neuron and inhibits neurotransmitter release and encompasses the binding of a Clostridial toxin to a low or high affinity receptor complex, the internalization of the toxin/receptor complex, the translocation of the Clostridial toxin light chain into the cytoplasm and the enzymatic modification of a Clostridial toxin substrate. In aspects of this embodiment, the modified Clostridial toxin is, e.g., at least 10% as toxic as a naturally- occurring Clostridial toxin, at least 20% as toxic as a naturally-occurring Clostridial toxin, at least 30% as toxic as a naturally-occurring Clostridial toxin, at least 40% as toxic as a naturally-occurring Clostridial toxin, at least 50% as toxic as a naturally-occurring Clostridial toxin, at least 60% as toxic as a naturally- occurring Clostridial toxin, at least 70% as toxic as a naturally-occurring Clostridial toxin, at least 80% as toxic as a naturally-occurring Clostridial toxin, at least 90% as toxic as a naturally-occurring Clostridial toxin or at least 95% as toxic as a naturally-occurring Clostridial toxin. In aspects of this embodiment, the modified Clostridial toxin is, e.g., at most 10% as toxic as a naturally-occurring Clostridial toxin, at most 20% as toxic as a naturally-occurring Clostridial toxin, at most 30% as toxic as a naturally-occurring Clostridial toxin, at most 40% as toxic as a naturally-occurring Clostridial toxin, at most 50% as toxic as a naturally-occurring Clostridial toxin, at most 60% as toxic as a naturally-occurring Clostridial toxin, at most 70% as toxic as a naturally-occurring Clostridial toxin, at most 80% as toxic as a naturally-occurring Clostridial toxin, at most 90% as toxic as a naturally-occurring Clostridial toxin or at most 95% as toxic as a naturally-occurring Clostridial toxin.

[0194J Aspects of the present invention provide, in part, polynucleotide molecules. As used herein, the term "polynucleotide molecule" is synonymous with "nucleic acid molecule" and means a polymeric form of nucleotides, such as, e.g., ribonucleotides and deoxyribonucleotides, of any length. It is envisioned that any and all polynucleotide molecules that can encode a modified Clostridial toxin disclosed in the present specification can be useful, including, without limitation naturally-occurring and non-naturally-

occurring DNA molecules and naturally-occurring and non-naturally-occurring RNA molecules. Non- limiting examples of naturally-occurring and non-naturally-occurring DNA molecules include single- stranded DNA molecules, double-stranded DNA molecules, genomic DNA molecules, cDNA molecules, vector constructs, such as, e.g., plasmid constructs, phagmid constructs, bacteriophage constructs, retroviral constructs and artificial chromosome constructs. Non-limiting examples of naturally-occurring and non-naturally-occurring RNA molecules include single-stranded RNA, double stranded RNA and mRNA.

[0195] Thus, in an embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a Clostridial toxin enzymatic domain, a Clostridial toxin translocation domain and a Clostridial toxin binding domain. In an aspect of this embodiment, a polynucleotide molecule encodes a Clostridial toxin comprises a naturally occurring Clostridial toxin variant, such as, e.g., a Clostridial toxin isoform or a Clostridial toxin subtype. In another aspect of this embodiment, a polynucleotide molecule encodes a Clostridial toxin comprises a non-naturally occurring Clostridial toxin variant, such as, e.g., a conservative Clostridial toxin variant, a non-conservative Clostridial toxin variant or an active Clostridial toxin fragment, or any combination thereof. In another aspect of this embodiment, a polynucleotide molecule encodes a Clostridial toxin comprises a Clostridial toxin enzymatic domain or an active fragment thereof, a Clostridial toxin translocation domain or an active fragment thereof, a Clostridial toxin binding domain or an active fragment thereof, or any combination thereof. In other aspects of this embodiment, a Clostridial toxins comprises a BoNT/A, a BoNT/B, a BoNT/C1 , a BoNT/D, a BoNT/E, a BoNT/F, a BoNT/G or a TeNT.

[0196] In another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/A. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a BoNT/A enzymatic domain, a BoNT/A translocation domain and a BoNT/A binding domain. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising SEQ ID NO: 1. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a naturally occurring BoNT/A variant, such as, e.g., a BoNT/A isoform or a BoNT/A subtype. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a naturally occurring BoNT/A variant of SEQ ID NO: 1 , such as, e.g., a BoNT/A isoform of SEQ ID NO: 1 or a BoNT/A subtype of SEQ ID NO: 1. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a non-naturally occurring BoNT/A variant, such as, e.g., a conservative BoNT/A variant, a non-conservative BoNT/A variant or an active BoNT/A fragment, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a non-naturally occurring BoNT/A variant of SEQ ID NO: 1 , such as, e.g., a conservative BoNT/A variant of SEQ ID NO: 1 , a non-conservative BoNT/A variant of SEQ ID NO: 1 or an active BoNT/A fragment of SEQ ID NO: 1 , or any combination thereof. In yet another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a BoNT/A enzymatic domain or an active fragment thereof, a BoNT/A translocation domain or an active fragment thereof, a BoNT/A binding domain or an active fragment thereof, or any combination thereof. In yet another aspect of this

embodiment, a BoNT/A comprising a BoNT/A enzymatic domain of amino acids 1-448 from SEQ ID NO: 1 or an active fragment thereof, a BoNT/A translocation domain of amino acids 449-860 from SEQ ID NO: 1 or an active fragment thereof, a BoNT/A binding domain of amino acids 861-1296 from SEQ ID NO: 1 or an active fragment thereof, and any combination thereof.

[0197] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 1 , at least 75% amino acid identity with the SEQ ID NO: 1 , at least 80% amino acid identity with SEQ ID NO: 1 , at least 85% amino acid identity with SEQ ID NO: 1 , at least 90% amino acid identity with SEQ ID NO: 1 or at least 95% amino acid identity with SEQ ID NO: 1. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 1 , at most 75% amino acid identity with the SEQ ID NO: 1 , at most 80% amino acid identity with SEQ ID NO: 1 , at most 85% amino acid identity with SEQ ID NO: 1 , at most 90% amino acid identity with SEQ ID NO: 1 or at most 95% amino acid identity with SEQ ID NO: 1.

[0198] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 1. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 noncontiguous amino acid substitutions relative to SEQ ID NO: 1. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 1. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 1. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 1. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 1.

[0199] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 1. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 1. In yet other aspects of this embodiment, a

polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 1. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 1. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 1. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 1.

[0200] In another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/B. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a BoNT/B enzymatic domain, a BoNT/B translocation domain and a BoNT/B binding domain. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising SEQ ID NO: 2. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a naturally occurring BoNT/B variant, such as, e.g., a BoNT/B isoform or a BoNT/B subtype. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a naturally occurring BoNT/B variant of SEQ ID NO: 2, such as, e.g., a BoNT/B isoform of SEQ ID NO: 2 or a BoNT/B subtype of SEQ ID NO: 2. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a non-naturally occurring BoNT/B variant, such as, e.g., a conservative BoNT/B variant, a non-conservative BoNT/B variant or an active BoNT/B fragment, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a non-naturally occurring BoNT/B variant of SEQ ID NO: 2, such as, e.g., a conservative BoNT/B variant of SEQ ID NO: 2, a non-conservative BoNT/B variant of SEQ ID NO: 2 or an active BoNT/B fragment of SEQ ID NO: 2, or any combination thereof. In yet another aspect of this embodiment, a BoNT/B comprising a BoNT/B enzymatic domain or an active fragment thereof, a BoNT/B translocation domain or active fragment thereof, a BoNT/B binding domain or active fragment thereof, and any combination thereof. In yet another aspect of this embodiment, a BoNT/B comprising a BoNT/B enzymatic domain of amino acids 1-441 from SEQ ID NO: 2 or active fragment thereof, a BoNT/B translocation domain of amino acids 442-847 from SEQ ID NO: 2 or active fragment thereof, a BoNT/B binding domain of amino acids 848-1291 from SEQ ID NO: 2 or active fragment thereof, and any combination thereof.

[0201] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 2, at least 75% amino acid identity with the SEQ ID NO: 2, at least 80% amino acid identity with SEQ ID NO: 2, at least 85% amino acid identity with SEQ ID NO: 2, at least 90% amino acid identity with SEQ ID NO: 2 or at least 95%

amino acid identity with SEQ ID NO: 2. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 2, at most 75% amino acid identity with the SEQ ID NO: 2, at most 80% amino acid identity with SEQ ID NO: 2, at most 85% amino acid identity with SEQ ID NO: 2, at most 90% amino acid identity with SEQ ID NO: 2 or at most 95% amino acid identity with SEQ ID NO: 2.

[0202] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 2. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 noncontiguous amino acid substitutions relative to SEQ ID NO: 2. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 2. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 2. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 2. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 2.

[0203] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 2. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 2. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 2. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 2. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 2. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B comprising a polypeptide having, e.g., at

least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 2.

[0204] In another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNTVCI . In an aspect of this embodiment, a polynucleotide molecule encodes a BoNTVCI comprising a BoNTVCI enzymatic domain, a BoNTVCI translocation domain and a BoNTVCI binding domain. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNTVCI comprising SEQ ID NO: 3. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNTVCI comprising a naturally occurring BoNTVCI variant, such as, e.g., a BoNTVCI isoform or a BoNTVCI subtype. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNTVCI comprising a naturally occurring BoNTVCI variant of SEQ ID NO: 3, such as, e.g., a BoNTVCI isoform of SEQ ID NO: 3 or a BoNTVCI subtype of SEQ ID NO: 3. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNTVCI comprising a non-naturally occurring BoNTVCI variant, such as, e.g., a conservative BoNTVCI variant, a non-conservative BoNTVCI variant or an active BoNTVCI fragment, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNTVCI comprising a non-naturally occurring BoNTVCI variant of SEQ ID NO: 3, such as, e.g., a conservative BoNTVCI variant of SEQ ID NO: 3, a non-conservative BoNTVCI variant of SEQ ID NO: 3 or an active BoNTVCI fragment of SEQ ID NO: 3, or any combination thereof. In yet another aspect of this embodiment, a polynucleotide molecule encodes a BoNTVCI comprising a BoNTVCI enzymatic domain or active fragment thereof, a BoNTVCI translocation domain or active fragment thereof, a BoNTVCI binding domain or active fragment thereof, and any combination thereof. In yet another aspect of this embodiment, a polynucleotide molecule encodes a BoNTVCI comprising a BoNTVCI enzymatic domain of amino acid 1-449 from SEQ ID NO: 3 or active fragment thereof, a BoNTVCI translocation domain of amino acids 450-855 from SEQ ID NO: 3 or active fragment thereof, a BoNTVCI binding domain of amino acids 856-1291 from SEQ ID NO: 3 or active fragment thereof, and any combination thereof.

[0205] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNTVCI comprising a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 3, at least 75% amino acid identity with the SEQ ID NO: 3, at least 80% amino acid identity with SEQ ID NO: 3, at least 85% amino acid identity with SEQ ID NO: 3, at least 90% amino acid identity with SEQ ID NO: 3 or at least 95% amino acid identity with SEQ ID NO: 3. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNTVCI comprising a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 3, at most 75% amino acid identity with the SEQ ID NO: 3, at most 80% amino acid identity with SEQ ID NO: 3, at most 85% amino acid identity with SEQ ID NO: 3, at most 90% amino acid identity with SEQ ID NO: 3 or at most 95% amino acid identity with SEQ ID NO: 3.

[0206] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNTVCI comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50,

100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 3. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 noncontiguous amino acid substitutions relative to SEQ ID NO: 3. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 3. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 3. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 3. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 3.

[0207] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 3. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 3. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 3. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 3. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 3. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 3.

[0208] In another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/D. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a BoNT/D enzymatic domain, a BoNT/D translocation domain and a BoNT/D binding domain. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising SEQ ID NO: 4. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a

naturally occurring BoNT/D variant, such as, e.g., a BoNT/D isoform or a BoNT/D subtype. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a naturally occurring BoNT/D variant of SEQ ID NO: 4, such as, e.g., a BoNT/D isoform of SEQ ID NO: 4 or a BoNT/D subtype of SEQ ID NO: 4. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a non-naturally occurring BoNT/D variant, such as, e.g., a conservative BoNT/D variant, a non-conservative BoNT/D variant or an active BoNT/D fragment, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a non-naturally occurring BoNT/D variant of SEQ ID NO: 4, such as, e.g., a conservative BoNT/D variant of SEQ ID NO: 4, a non-conservative BoNT/D variant of SEQ ID NO: 4 or an active BoNT/D fragment of SEQ ID NO: 4, or any combination thereof. In yet another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a BoNT/D enzymatic domain or an active fragment thereof, a BoNT/D translocation domain or an active fragment thereof, a BoNT/D binding domain or an active fragment thereof, or any combination thereof. In yet another aspect of this embodiment, a BoNT/D comprising a BoNT/D enzymatic domain of amino acids 1-442 from SEQ ID NO: 4 or an active fragment thereof, a BoNT/D translocation domain of amino acids 443-851 from SEQ ID NO: 4 or an active fragment thereof, a BoNT/D binding domain of amino acids 852-1276 from SEQ ID NO: 4 or an active fragment thereof, and any combination thereof.

[0209] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 4, at least 75% amino acid identity with the SEQ ID NO: 4, at least 80% amino acid identity with SEQ ID NO: 4, at least 85% amino acid identity with SEQ ID NO: 4, at least 90% amino acid identity with SEQ ID NO: 4 or at least 95% amino acid identity with SEQ ID NO: 4. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 4, at most 75% amino acid identity with the SEQ ID NO: 4, at most 80% amino acid identity with SEQ ID NO: 4, at most 85% amino acid identity with SEQ ID NO: 4, at most 90% amino acid identity with SEQ ID NO: 4 or at most 95% amino acid identity with SEQ ID NO: 4.

[0210] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 4. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 noncontiguous amino acid substitutions relative to SEQ ID NO: 4. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 4. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID

NO: 4. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 4. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 4.

[0211] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 4. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 4. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 4. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 4. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 4. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 4.

[0212] In another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/E. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a BoNT/E enzymatic domain, a BoNT/E translocation domain and a BoNT/E binding domain. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising SEQ ID NO: 5. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a naturally occurring BoNT/E variant, such as, e.g., a BoNT/E isoform or a BoNT/E subtype. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a naturally occurring BoNT/E variant of SEQ ID NO: 5, such as, e.g., a BoNT/E isoform of SEQ ID NO: 5 or a BoNT/E subtype of SEQ ID NO: 5. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a non-naturally occurring BoNT/E variant, such as, e.g., a conservative BoNT/E variant, a non-conservative BoNT/E variant or an active BoNT/E fragment, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a non-naturally occurring BoNT/E variant of SEQ ID NO: 5, such as, e.g., a conservative BoNT/E variant of SEQ ID NO: 5, a non-conservative BoNT/E variant of SEQ ID NO: 5 or an active

BoNT/E fragment of SEQ ID NO: 5, or any combination thereof. In yet another aspect of this embodiment, a BoNT/E comprising a BoNT/E enzymatic domain or an active fragment thereof, a BoNT/E translocation domain or active fragment thereof, a BoNT/E binding domain or active fragment thereof, and any combination thereof. In yet another aspect of this embodiment, a BoNT/E comprising a BoNT/E enzymatic domain of amino acids 1-422 from SEQ ID NO: 5 or active fragment thereof, a BoNT/E translocation domain of amino acids 423-834 from SEQ ID NO: 5 or active fragment thereof, a BoNT/E binding domain of amino acids 835-1252 from SEQ ID NO: 5 or active fragment thereof, and any combination thereof.

[0213] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 5, at least 75% amino acid identity with the SEQ ID NO: 5, at least 80% amino acid identity with SEQ ID NO: 5, at least 85% amino acid identity with SEQ ID NO: 5, at least 90% amino acid identity with SEQ ID NO: 5 or at least 95% amino acid identity with SEQ ID NO: 5. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 5, at most 75% amino acid identity with the SEQ ID NO: 5, at most 80% amino acid identity with SEQ ID NO: 5, at most 85% amino acid identity with SEQ ID NO: 5, at most 90% amino acid identity with SEQ ID NO: 5 or at most 95% amino acid identity with SEQ ID NO: 5.

[0214] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 5. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 noncontiguous amino acid substitutions relative to SEQ ID NO: 5. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 5. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 5. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 5. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 5.

[0215] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50,

100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 5. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 5. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 5. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 5. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 5. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 5.

[0216] In another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/F. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a BoNT/F enzymatic domain, a BoNT/F translocation domain and a BoNT/F binding domain. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising SEQ ID NO: 6. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a naturally occurring BoNT/F variant, such as, e.g., a BoNT/F isoform or a BoNT/F subtype. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a naturally occurring BoNT/F variant of SEQ ID NO: 6, such as, e.g., a BoNT/F isoform of SEQ ID NO: 6 or a BoNT/F subtype of SEQ ID NO: 6. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a non-naturally occurring BoNT/F variant, such as, e.g., a conservative BoNT/F variant, a non-conservative BoNT/F variant or an active BoNT/F fragment, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a non- naturally occurring BoNT/F variant of SEQ ID NO: 6, such as, e.g., a conservative BoNT/F variant of SEQ ID NO: 6, a non-conservative BoNT/F variant of SEQ ID NO: 6 or an active BoNT/F fragment of SEQ ID NO: 6, or any combination thereof. In yet another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a BoNT/F enzymatic domain or active fragment thereof, a BoNT/F translocation domain or active fragment thereof, a BoNT/F binding domain or active fragment thereof, and any combination thereof. In yet another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a BoNT/F enzymatic domain of amino acid 1-436 from SEQ ID NO: 6 or active fragment thereof, a BoNT/F translocation domain of amino acids 437-852 from SEQ ID NO: 6 or active fragment thereof, a BoNT/F binding domain of amino acids 853-1274 from SEQ ID NO: 6 or active fragment thereof, and any combination thereof.

[0217] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 6, at least 75% amino acid identity with the SEQ ID NO: 6, at least 80% amino acid identity with SEQ ID NO: 6, at least 85% amino acid identity with SEQ ID NO: 6, at least 90% amino acid identity with SEQ ID NO: 6 or at least 95% amino acid identity with SEQ ID NO: 6. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 6, at most 75% amino acid identity with the SEQ ID NO: 6, at most 80% amino acid identity with SEQ ID NO: 6, at most 85% amino acid identity with SEQ ID NO: 6, at most 90% amino acid identity with SEQ ID NO: 6 or at most 95% amino acid identity with SEQ ID NO: 6.

[0218] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 6. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 noncontiguous amino acid substitutions relative to SEQ ID NO: 6. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 6. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 6. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 6. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 6.

[0219] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 6. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 6. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 6. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 6. In still other aspects of this

embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 6. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 6.

[0220] In another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/G. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a BoNT/G enzymatic domain, a BoNT/G translocation domain and a BoNT/G binding domain. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising SEQ ID NO: 7. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a naturally occurring BoNT/G variant, such as, e.g., a BoNT/G isoform or a BoNT/G subtype. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a naturally occurring BoNT/G variant of SEQ ID NO: 7, such as, e.g., a BoNT/G isoform of SEQ ID NO: 7 or a BoNT/G subtype of SEQ ID NO: 7. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a non-naturally occurring BoNT/G variant, such as, e.g., a conservative BoNT/G variant, a non-conservative BoNT/G variant or an active BoNT/G fragment, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D comprising a non-naturally occurring BoNT/G variant of SEQ ID NO: 7, such as, e.g., a conservative BoNT/G variant of SEQ ID NO: 7, a non-conservative BoNT/G variant of SEQ ID NO: 7 or an active BoNT/G fragment of SEQ ID NO: 7, or any combination thereof. In yet another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a BoNT/G enzymatic domain or an active fragment thereof, a BoNT/G translocation domain or an active fragment thereof, a BoNT/G binding domain or an active fragment- thereof, or any combination thereof. In yet another aspect of this embodiment, a BoNT/G comprising a BoNT/G enzymatic domain of amino acids 1-442 from SEQ ID NO: 7 or an active fragment thereof, a BoNT/G translocation domain of amino acids 443-852 from SEQ ID NO: 7 or an active fragment thereof, a BoNT/G binding domain of amino acids 853-1297 from SEQ ID NO: 7 or an active fragment thereof, and any combination thereof.

[0221] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 7, at least 75% amino acid identity with the SEQ ID NO: 7, at least 80% amino acid identity with SEQ ID NO: 7, at least 85% amino acid identity with SEQ ID NO: 7, at least 90% amino acid identity with SEQ ID NO: 7 or at least 95% amino acid identity with SEQ ID NO: 7. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 7, at most 75% amino acid identity with the SEQ ID NO: 7, at most 80% amino acid identity with SEQ ID NO: 7, at most 85% amino acid identity with SEQ ID NO: 7, at most 90% amino acid identity with SEQ ID NO: 7 or at most 95% amino acid identity with SEQ ID NO: 7.

[0222] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 7. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 noncontiguous amino acid substitutions relative to SEQ ID NO: 7. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 7. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 7. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 7. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 7.

[0223] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 7. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 7. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 7. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 7. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 7. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 7.

[0224] In another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a TeNT. In an aspect of this embodiment, a polynucleotide molecule encodes a TeNT

comprising a TeNT enzymatic domain, a TeNT translocation domain and a TeNT binding domain. In an aspect of this embodiment, a polynucleotide molecule encodes a TeNT comprising SEQ ID NO: 8. In another aspect of this embodiment, a polynucleotide molecule encodes a TeNT comprising a naturally occurring TeNT variant, such as, e.g., a TeNT isoform or a TeNT subtype. In another aspect of this embodiment, a polynucleotide molecule encodes a TeNT comprising a naturally occurring TeNT variant of SEQ ID NO: 8, such as, e.g., a TeNT isoform of SEQ ID NO: 8 or a TeNT subtype of SEQ ID NO: 8. In still another aspect of this embodiment, a polynucleotide molecule encodes a TeNT comprising a non- naturally occurring TeNT variant, such as, e.g., a conservative TeNT variant, a non-conservative TeNT variant or an active TeNT fragment, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a TeNT comprising a non-naturally occurring TeNT variant of SEQ ID NO: 8, such as, e.g., a conservative TeNT variant of SEQ ID NO: 8, a non-conservative TeNT variant of SEQ ID NO: 8 or an active TeNT fragment of SEQ ID NO: 8, or any combination thereof. In yet another aspect of this embodiment, a TeNT comprising a TeNT enzymatic domain or an active fragment thereof, a TeNT translocation domain or active fragment thereof, a TeNT binding domain or active fragment thereof, and any combination thereof. In yet another aspect of this embodiment, a TeNT comprising a TeNT enzymatic domain of amino acids 1-441 from SEQ ID NO: 8 or active fragment thereof, a TeNT translocation domain of amino acids 442-870 from SEQ ID NO: 8 or active fragment thereof, a TeNT binding domain of amino acids 871-1315 from SEQ ID NO: 8 or active fragment thereof, and any combination thereof.

[0225] In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at least 70% amino acid identity with SEQ ID NO: 8, at least 75% amino acid identity with the SEQ ID NO: 8, at least 80% amino acid identity with SEQ ID NO: 8, at least 85% amino acid identity with SEQ ID NO: 8, at least 90% amino acid identity with SEQ ID NO: 8 or at least 95% amino acid identity with SEQ ID NO: 8. In yet other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at most 70% amino acid identity with SEQ ID NO: 8, at most 75% amino acid identity with the SEQ ID NO: 8, at most 80% amino acid identity with SEQ ID NO: 8, at most 85% amino acid identity with SEQ ID NO: 8, at most 90% amino acid identity with SEQ ID NO: 8 or at most 95% amino acid identity with SEQ ID NO: 8.

[0226] In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid substitutions relative to SEQ ID NO: 8. In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 noncontiguous amino acid substitutions relative to SEQ ID NO: 8. In yet other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 8. In other aspects of this embodiment, a polynucleotide molecule encodes a

TeNT comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid deletions relative to SEQ ID NO: 8. In still other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 8. In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 non-contiguous amino acid additions relative to SEQ ID NO: 8.

[0227] In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 8. In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid substitutions relative to SEQ ID NO: 8. In yet other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 8. In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid deletions relative to SEQ ID NO: 8. In still other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 8. In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine, 10, 20, 30, 40 , 50, 100, 200 or 500 contiguous amino acid additions relative to SEQ ID NO: 8.

[0228] In still another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a Clostridial toxin substrate cleavage site. In aspects of this embodiment, a polynucleotide molecule encodes a Clostridial toxin substrate cleavage site comprising a naturally occurring Clostridial toxin substrate cleavage site variant, such as, e.g., a Clostridial toxin substrate cleavage site isoform or a Clostridial toxin substrate cleavage site subtype. In other aspects of this embodiment, a polynucleotide molecule encodes a Clostridial toxin substrate cleavage site comprising a non-naturally occurring Clostridial toxin substrate cleavage site variant, such as, e.g., a conservative Clostridial toxin substrate cleavage site variant, a non-conservative Clostridial toxin substrate cleavage site variant or a Clostridial toxin substrate cleavage site peptidomimetic, or any combination thereof.

[0229] In still other aspects of this embodiment, a polynucleotide molecule encodes a modified Clostridial toxin substrate comprising a Clostridial toxin substrate cleavage site in which the P- ₎ ' residue is not modified or substituted relative to the naturally occurring residue in a target protein cleaved by the

Clostridial toxin. In still other aspects of this embodiment, a polynucleotide molecule encodes a Clostridial toxin substrate cleavage site in which the P-\' residue is not modified or substituted relative to the naturally occurring residue in a target protein cleaved by the Clostridial toxin can be, e.g., a BoNT/A substrate cleavage site, a BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site, a BoNT/G substrate cleavage site, a TeNT substrate cleavage site, a BaNT substrate cleavage site or a BuNT substrate cleavage site.

[0230] In still other aspects of this embodiment, a polynucleotide molecule encodes a modified Clostridial toxin substrate comprises a Clostridial toxin substrate cleavage site in which the P- ₎ residue is modified or substituted relative to the naturally occurring residue in a target protein cleaved by the Clostridial toxin; such a Clostridial toxin substrate retains susceptibility to peptide bond cleavage between the Pi and P- _] ' residues. In still other aspects of this embodiment, a polynucleotide molecule encodes a

Clostridial toxin substrate cleavage site in which the Pi' residue is modified or substituted relative to the naturally occurring residue in a target protein cleaved by the Clostridial toxin can be, e.g., a BoNT/A substrate cleavage site, a BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site, a BoNT/G substrate cleavage site, a TeNT substrate cleavage site, a BaNT substrate cleavage site or a BuNT substrate cleavage site.

[0231] In still another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/A substrate cleavage site. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising at least six consecutive residues of SNAP-25 including Gln-Arg. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprises, e.g., the amino acid sequence Glu-Ala-Asn-Gln-Arg-Ala-Thr- Lys (SEQ ID NO: 104); the amino acid sequence Glu-Ala-Asn-Lys-His-Ala-Thr-Lys (SEQ ID NO: 105); the amino acid sequence Glu-Ala-Asn-Lys-His-Ala-Asn-Lys (SEQ ID NO: 106). In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a naturally occurring BoNT/A substrate cleavage site variant. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprises a naturally occurring BoNT/A substrate cleavage site variant of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106, such as, e.g., a BoNT/A substrate cleavage site isoform of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106; or a BoNT/A substrate cleavage site subtype of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a non-naturally occurring BoNT/A substrate cleavage site variant, such as, e.g., a conservative BoNT/A substrate cleavage site variant, a non-conservative BoNT/A substrate cleavage site variant or a BoNT/A substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a non-naturally occurring BoNT/A substrate cleavage site variant of SEQ ID NO: 104, SEQ ID

NO: 105 or SEQ ID NO: 106; such as, e.g., a conservative BoNT/A substrate cleavage site variant of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106; a non-conservative BoNT/A substrate cleavage site variant of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106; a BoNT/A substrate cleavage site peptidomimetic of SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106; or any combination thereof. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising, e.g., SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO: 141 , SEQ ID NO: 148, SEQ ID NO: 150 or SEQ ID NO: 151.

[0232] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 104, at least 62.5% amino acid identity with the SEQ ID NO: 104, at least 75% amino acid identity with SEQ ID NO: 104 or at least 87.5% amino acid identity with SEQ ID NO: 104. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 104, at most 62.5% amino acid identity with the SEQ ID NO: 104, at most 75% amino acid identity with SEQ ID NO: 104 or at most 87.5% amino acid identity with SEQ ID NO: 104.

[0233] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 104. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 104. In yet other aspects of this embodiment, a polynucleotide molecule encodes BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 104.

[0234] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 104. In yet other aspects of this

embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 104. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 104. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/A substrate cleavage site comprising a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 104.

[0235] In still another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/B substrate cleavage site. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising at least six consecutive residues of VAMP including Gln-Phe. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising, e.g., the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Thr- Ser (SEQ ID NO: 107); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Ser-Ser (SEQ ID NO: 108); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Thr-Asn (SEQ ID NO: 109); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Gln-Gln (SEQ ID NO: 110); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu- Ala-Ser (SEQ ID NO: 111); or the amino acid sequence Gly-Ala-Ser-Gln-Phe-Gln-Gln-Ser (SEQ ID NO: 112). In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a naturally occurring BoNT/B substrate cleavage site variant. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a naturally occurring BoNT/B substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112, such as, e.g., a BoNT/B substrate cleavage site isoform of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; or a BoNT/B substrate cleavage site subtype of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a non-naturally occurring BoNT/B substrate cleavage site variant, such as, e.g., a conservative BoNT/B substrate cleavage site variant, a non-conservative BoNT/B substrate cleavage site variant or a BoNT/B substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a non- naturally occurring BoNT/B substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; such as, e.g., a conservative BoNT/B substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; a non-conservative BoNT/B substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; a BoNT/B substrate cleavage site peptidomimetic of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109,

SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; or any combination thereof.

[0236] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 107, at least 62.5% amino acid identity with the SEQ ID NO: 107, at least 75% amino acid identity with SEQ ID NO: 107 or at least 87.5% amino acid identity with SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 107, at most 62.5% amino acid identity with the SEQ ID NO: 107, at most 75% amino acid identity with SEQ ID NO: 107 or at most 87.5% amino acid identity with SEQ ID NO: 107.

[0237] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a polynucleotide molecule encodes BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 107.

[0238] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site

comprising a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/B substrate cleavage site comprising a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 107.

[0239] In still another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/C1 substrate cleavage site. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising at least six consecutive residues of Syntaxin including Lys-Ala. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising, e.g., the amino acid sequence Asp-Thr-Lys-Lys-Ala-Val- Lys-Tyr (SEQ ID NO: 113); the amino acid sequence Glu-Thr-Lys-Lys-Ala-lle-Lys-Tyr (SEQ ID NO: 114); the amino acid sequence Glu-Ser-Lys-Lys-Ala-Val-Lys-Tyr (SEQ ID NO: 115); the amino acid sequence Glu-Thr-Lys-Arg-Ala-Met-Lys-Tyr (SEQ ID NO: 116); the amino acid sequence Glu-Thr-Lys-Lys-Ala-Val- Lys-Tyr (SEQ ID NO: 117); the amino acid sequence Asp-Thr-Lys-Lys-Ala-Leu-Lys-Tyr (SEQ ID NO: 118); or the amino acid sequence Asp-Thr-Lys-Lys-Ala-Met-Lys-Tyr (SEQ ID NO: 119). In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a naturally occurring BoNT/C1 substrate cleavage site variant. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a naturally occurring BoNT/C1 substrate cleavage site variant of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119, such as, e.g., a BoNT/Ci substrate cleavage site isoform of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119; or a BoNT/C1 substrate cleavage site subtype of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a non-naturally occurring BoNT/C1 substrate cleavage site variant, such as, e.g., a conservative BoNT/C1 substrate cleavage site variant, a non-conservative B0NT/CI substrate cleavage site variant or a BoNT/C1 substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a non-naturally occurring BoNT/C1 substrate cleavage site variant of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119; such as, e.g., a conservative BoNT/C1 substrate cleavage site variant of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119; a non-conservative BoNT/C1 substrate cleavage site variant of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119; a BoNT/C1 substrate cleavage site peptidomimetic of SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118 or SEQ ID NO: 119; or any combination thereof.

[0240] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 113, at least 62.5% amino acid identity with the SEQ ID NO: 113, at least 75% amino acid identity with SEQ ID NO: 113 or at least 87.5% amino acid identity with SEQ ID NO: 113. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 113, at most 62.5% amino acid identity with the SEQ ID NO: 113, at most 75% amino acid identity with SEQ ID NO: 113 or at most 87.5% amino acid identity with SEQ ID NO: 113.

[0241] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/CA substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 113. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 113. In yet other aspects of this embodiment, a polynucleotide molecule encodes BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a polynucleotide molecule encodes a B0NT/CI substrate cleavage site comprising a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 113.

[0242] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 113. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 113. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 113. In still other aspects of this embodiment, a polynucleotide molecule encodes a

BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 113.

[0243] In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising at least six consecutive residues of SNAP-25 including Arg-Ala. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 toxin substrate cleavage site comprising, e.g., the amino acid sequence Ala-Asn-Gln-Arg-Ala-Thr-Lys-Met (SEQ ID NO: 120); or the amino acid sequence Ala-Asn-Gln-Arg-Ala-His-Gln-Leu (SEQ ID NO: 121). In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a naturally occurring BoNT/C1 substrate cleavage site variant. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a naturally occurring BoNT/CI substrate cleavage site variant of SEQ ID NO: 120 or SEQ ID NO: 121 , such as, e.g., a BoNT/C1 substrate cleavage site isoform of SEQ ID NO: 120 or SEQ ID NO: 121 ; or a BoNT/C1 substrate cleavage site subtype of SEQ ID NO: 120 or SEQ ID NO: 121. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a non- naturally occurring BoNT/C1 substrate cleavage site variant, such as, e.g., a conservative BoNT/C1 substrate cleavage site variant, a non-conservative BoNT/C1 substrate cleavage site variant or a BoNT/C1 substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a non-naturally occurring BoNT/C1 substrate cleavage site variant of SEQ ID NO: 120 or SEQ ID NO: 121 ; such as, e.g., a conservative BoNT/CI substrate cleavage site variant of SEQ ID NO: 99 or SEQ ID NO: XX; a non-conservative BoNT/C1 substrate cleavage site variant of SEQ ID NO: 120 or SEQ ID NO: 121 ; a BoNT/C1 substrate cleavage site peptidomimetic of SEQ ID NO: 120 or SEQ ID NO: 121 ; or any combination thereof.

[0244] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 120, at least 62.5% amino acid identity with the SEQ ID NO: 120, at least 75% amino acid identity with SEQ ID NO: 120 or at least 87.5% amino acid identity with SEQ ID NO: 120. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 120, at most 62.5% amino acid identity with the SEQ ID NO: 120, at most 75% amino acid identity with SEQ ID NO: 120 or at most 87.5% amino acid identity with SEQ ID NO: 120.

[0245] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/CI substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 120. In yet other

aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 120. In yet other aspects of this embodiment, a polynucleotide molecule encodes BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 120.

[0246] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 120. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 120. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 120. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/C1 substrate cleavage site comprising a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 120.

[0247] In still another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/D substrate cleavage site. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising at least six consecutive residues of VAMP including Lys-Leu. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising, e.g., the amino acid sequence Arg-Asp-Gln-Lys-Leu-Ser- Glu-Leu (SEQ ID NO: 122); or the amino acid sequence Lys-Asp-Gln-Lys-Leu-Ala-Glu-Leu (SEQ ID NO: 123). In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a naturally occurring BoNT/D substrate cleavage site variant. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a naturally occurring BoNT/D substrate cleavage site variant of SEQ ID NO: 122 or SEQ ID NO: 123, such as, e.g., a BoNT/D substrate cleavage site isoform of SEQ ID NO: 122 or SEQ ID NO: 123; or a BoNT/D

substrate cleavage site subtype of SEQ ID NO: 122 or SEQ ID NO: 123. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a non- naturally occurring BoNT/D substrate cleavage site variant, such as, e.g., a conservative BoNT/D substrate cleavage site variant, a non-conservative BoNT/D substrate cleavage site variant or a BoNT/D substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a non- naturally occurring BoNT/D substrate cleavage site variant of SEQ ID NO: 122 or SEQ ID NO: 123; such as, e.g., a conservative BoNT/D substrate cleavage site variant of SEQ ID NO: 122 or SEQ ID NO: 123; a non-conservative BoNT/C1 substrate cleavage site variant of SEQ ID NO: 122 or SEQ ID NO: 123; a BoNT/D substrate cleavage site peptidomimetic of SEQ ID NO: 122 or SEQ ID NO: 123; or any combination thereof.

[0248] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 122, at least 62.5% amino acid identity with the SEQ ID NO: 122, at least 75% amino acid identity with SEQ ID NO: 122 or at least 87.5% amino acid identity with SEQ ID NO: 122. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 122, at most 62.5% amino acid identity with the SEQ ID NO: 122, at most 75% amino acid identity with SEQ ID NO: 122 or at most 87.5% amino acid identity with SEQ ID NO: 122.

[0249] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 122. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 122. In yet other aspects of this embodiment, a polynucleotide molecule encodes BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 122.

[0250] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 122. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 122. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 122. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/D substrate cleavage site comprising a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 122.

[0251] In still another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/E substrate cleavage site. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising at least six consecutive residues of VAMP including Arg-lle. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising, e.g., the amino acid sequence Gln-lle-Asp-Arg-lle-Met-Glu- Lys (SEQ ID NO: 124); the amino acid sequence Gln-lle-Gln-Lys-lle-Thr-Glu-Lys (SEQ ID NO: 125); the amino acid sequence Gln-lle-Asp-Arg-lle-Met-Asp-Met (SEQ ID NO: 126); the amino acid sequence GIn- Val-Asp-Arg-lle-Gln-Gln-Lys (SEQ ID NO: 127); or the amino acid sequence Gln-Leu-Asp-Arg-lle-His- Asp-Lys (SEQ ID NO: 128). In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a naturally occurring BoNT/E substrate cleavage site variant. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a naturally occurring BoNT/E substrate cleavage site variant of SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128, such as, e.g., a BoNT/E substrate cleavage site isoform of SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128; or a BoNT/E substrate cleavage site subtype of SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128. In still another aspect of this embodiment, a polynucleotide molecule encodes a BpNT/E substrate cleavage site comprising a non-naturally occurring BoNT/E substrate cleavage site variant, such as, e.g., a conservative BoNT/E substrate cleavage site variant, a non-conservative BoNT/E substrate cleavage site variant or a BoNT/E substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a non-naturally occurring BoNT/E substrate cleavage site variant of SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128; such as, e.g., a conservative BoNT/E substrate cleavage site variant of SEQ ID NO:

124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128; a non-conservative BoNT/E substrate cleavage site variant of SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128; a BoNT/E substrate cleavage site peptidomimetic of SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128; or any combination thereof.

[0252] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 124, at least 62.5% amino acid identity with the SEQ ID NO: 124, at least 75% amino acid identity with SEQ ID NO: 124 or at least 87.5% amino acid identity with SEQ ID NO: 124. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 124, at most 62.5% amino acid identity with the SEQ ID NO: 124, at most 75% amino acid identity with SEQ ID NO: 124 or at most 87.5% amino acid identity with SEQ ID NO: 124.

[0253] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 124. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 124. In yet other aspects of this embodiment, a polynucleotide molecule encodes BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 124.

[0254] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 124. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 124. In yet other aspects of this embodiment, a polynucleotide molecule

encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 124. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/E substrate cleavage site comprising a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 124.

[0255] In still another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/F substrate cleavage site. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising at least six consecutive residues of VAMP including Gln-Lys. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising, e.g., the amino acid sequence Glu-Arg-Asp-Gln-Lys-Leu-Ser- GIu (SEQ ID NO: 129); or the amino acid sequence Glu-Lys-Asp-Gln-Lys-Leu-Ala-Glu (SEQ ID NO: 130). In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a naturally occurring BoNT/F substrate cleavage site variant. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a naturally occurring BoNT/F substrate cleavage site variant of SEQ ID NO: 129 or SEQ ID NO: 130, such as, e.g., a BoNT/F substrate cleavage site isoform of SEQ ID NO: 129 or SEQ ID NO: 130; or a BoNT/F substrate cleavage site subtype of SEQ ID NO: 129 or SEQ ID NO: 130. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a non-naturally occurring BoNT/F substrate cleavage site variant, such as, e.g., a conservative BoNT/F substrate cleavage site variant, a non-conservative BoNT/F substrate cleavage site variant or a BoNT/F substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a non-naturally occurring BoNT/F substrate cleavage site variant of SEQ ID NO: 129 or SEQ ID NO: 130; such as, e.g., a conservative BoNT/F substrate cleavage site variant of SEQ ID NO: 129 or SEQ ID NO: 130; a non- conservative BoNT/F substrate cleavage site variant of SEQ ID NO: 129 or SEQ ID NO: 130; a BoNT/F substrate cleavage site peptidomimetic of SEQ ID NO: 129 or SEQ ID NO: 130; or any combination thereof.

[0256] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 129, at least 62.5% amino acid identity with the SEQ ID NO: 129, at least 75% amino acid identity with SEQ ID NO: 129 or at least 87.5% amino acid identity with SEQ ID NO: 129. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 129, at most 62.5% amino acid identity with the SEQ ID NO: 129, at most 75% amino acid identity with SEQ ID NO: 129 or at most 87.5% amino acid identity with SEQ ID NO: 129.

[0257] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 129. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 129. In yet other aspects of this embodiment, a polynucleotide molecule encodes BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 129.

[0258] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 129. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 129. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 129. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/F substrate cleavage site comprising a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 129.

[0259] In still another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a BoNT/G substrate cleavage site. In an aspect of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising at least six consecutive residues of VAMP including Ala-Ala. In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising, e.g., the amino acid sequence Glu-Thr-Ser-Ala-Ala-Lys-Leu-

Lys (SEQ ID NO: 131); or the amino acid sequence Glu-Ser-Ser-Ala-Ala-Lys-Leu-Lys (SEQ ID NO: 132). In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a naturally occurring BoNT/G substrate cleavage site variant. In another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a naturally occurring BoNT/G substrate cleavage site variant of SEQ ID NO: 131 or SEQ ID NO: 132, such as, e.g., a BoNT/G substrate cleavage site isoform of SEQ ID NO: 131 or SEQ ID NO: 132; or a BoNT/G substrate cleavage site subtype of SEQ ID NO: 131 or SEQ ID NO: 132. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a non- naturally occurring BoNT/F substrate cleavage site variant, such as, e.g., a conservative BoNT/G substrate cleavage site variant, a non-conservative BoNT/G substrate cleavage site variant or a BoNT/G substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a non- naturally occurring BoNT/G substrate cleavage site variant of SEQ ID NO: 131 or SEQ ID NO: 132; such as, e.g., a conservative BoNT/G substrate cleavage site variant of SEQ ID NO: 131 or SEQ ID NO: 132; a non-conservative BoNT/G substrate cleavage site variant of SEQ ID NO: 131 or SEQ ID NO: 132; a BoNT/G substrate cleavage site peptidomimetic of SEQ ID NO: 131 or SEQ ID NO: 132; or any combination thereof.

[0260] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 131 , at least 62.5% amino acid identity with the SEQ ID NO: 131 , at least 75% amino acid identity with SEQ ID NO: 131 or at least 87.5% amino acid identity with SEQ ID NO: 131. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 131 , at most 62.5% amino acid identity with the SEQ ID NO: 131 , at most 75% amino acid identity with SEQ ID NO: 131 or at most 87.5% amino acid identity with SEQ ID NO: 131.

[0261] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 131. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 131. In yet other aspects of this embodiment, a polynucleotide molecule encodes BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having,

e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 131.

[0262] In other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 131. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 131. In yet other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 131. In still other aspects of this embodiment, a polynucleotide molecule encodes a BoNT/G substrate cleavage site comprising a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 131.

[0263] In still another embodiment, a polynucleotide molecule encodes a modified Clostridial toxin comprising a TeNT substrate cleavage site. In an aspect of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising at least six consecutive residues of VAMP including Gln-Phe. In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising, e.g., the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Thr-Ser (SEQ ID NO: 107); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Ser-Ser (SEQ ID NO: 108); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Thr-Asn (SEQ ID NO: 109); the amino acid sequence Gly-Ala-Ser- Gln-Phe-Glu-Gln-Gln (SEQ ID NO: 110); the amino acid sequence Gly-Ala-Ser-Gln-Phe-Glu-Ala-Ser (SEQ ID NO: 111); or the amino acid sequence Gly-Ala-Ser-Gln-Phe-Gln-Gln-Ser (SEQ ID NO: 112). In another aspect of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a naturally occurring TeNT substrate cleavage site variant. In another aspect of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a naturally occurring TeNT substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112, such as, e.g., a BoNT/B substrate cleavage site isoform of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112, such as, e.g., a TeNT substrate cleavage site isoform of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112, such as, e.g., a BoNT/B substrate cleavage site isoform of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110,

SEQ ID NO: 111 or SEQ ID NO: 112; or a TeNT substrate cleavage site subtype of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112, such as, e.g., a BoNT/B substrate cleavage site isoform of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112. In still another aspect of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a non-naturally occurring TeNT substrate cleavage site variant, such as, e.g., a conservative TeNT substrate cleavage site variant, a non-conservative TeNT substrate cleavage site variant or a TeNT substrate cleavage site peptidomimetic, or any combination thereof. In still another aspect of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a non-naturally occurring TeNT substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112, such as, e.g., a BoNT/B substrate cleavage site isoform of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; such as, e.g., a conservative TeNT substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112, such as, e.g., a BoNT/B substrate cleavage site isoform of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; a non-conservative TeNT substrate cleavage site variant of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112, such as, e.g., a BoNT/B substrate cleavage site isoform of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; a TeNT substrate cleavage site peptidomimetic of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112, such as, e.g., a BoNT/B substrate cleavage site isoform of SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112; or any combination thereof.

[0264] In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at least 50% amino acid identity with SEQ ID NO: 107, at least 62.5% amino acid identity with the SEQ ID NO: 107, at least 75% amino acid identity with SEQ ID NO: 107 or at least 87.5% amino acid identity with SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at most 50% amino acid identity with SEQ ID NO: 107, at most 62.5% amino acid identity with the SEQ ID NO: 107, at most 75% amino acid identity with SEQ ID NO: 107 or at most 87.5% amino acid identity with SEQ ID NO: 107.

[0265] In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three or four non-contiguous amino acid substitutions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at most one, two, three, four, five, six, seven, eight, nine or ten

non-contiguous amino acid additions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a polynucleotide molecule encodes TeNT substrate cleavage site comprising a polypeptide having, e.g., at least one, two, three, four, five, six, seven, eight, nine or ten non-contiguous amino acid additions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at most one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at least one, two or three non-contiguous amino acid deletions relative to SEQ ID NO: 107.

[0266] In other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at most two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at least two, three or four contiguous amino acid substitutions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at most two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 107. In yet other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at least two, three, four, five, six, seven, eight, nine or ten contiguous amino acid additions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at most two or three contiguous amino acid deletions relative to SEQ ID NO: 107. In still other aspects of this embodiment, a polynucleotide molecule encodes a TeNT substrate cleavage site comprising a polypeptide having, e.g., at least two or three contiguous amino acid deletions relative to SEQ ID NO: 107.

[0267] In yet another embodiment, a polynucleotide molecule encoding a modified Clostridial toxin disclosed in the present specification can further comprise a polynucleotide molecule encoding a flexible region comprising a flexible spacer. In another embodiment, a polynucleotide molecule encoding a modified Clostridial toxin disclosed in the present specification can further comprise a polynucleotide molecule encoding a flexible region comprising a plurality of flexible spacers in tandem. In aspects of this embodiment, a polynucleotide molecule encoding a flexible region can comprise in tandem, e.g., at least 1 G-spacer, at least 2 G-spacers, at least 3 G-spacers, at least 4 G-spacers or at least 5 G-spacers. In other aspects of this embodiment, a polynucleotide molecule encoding a flexible region can comprise in tandem, e.g., at most 1 G-spacer, at most 2 G-spacers, at most 3 G-spacers, at most 4 G-spacers or at most 5 G-spacers. In still other aspects of this embodiment, a polynucleotide molecule encoding a flexible region can comprise in tandem, e.g., at least 1 A-spacer, at least 2 A-spacers, at least 3 A- spacers, at least 4 A-spacers or at least 5 A-spacers. In still other aspects of this embodiment, a polynucleotide molecule encoding a flexible region can comprise in tandem, e.g., at most 1 A-spacer, at

most 2 A-spacers, at most 3 A-spacers, at most 4 A-spacers or at most 5 A-spacers. In another aspect of this embodiment, a polynucleotide molecule encoding a modified Clostridial toxin can comprise a polynucleotide molecule encoding a flexible region comprising one or more copies of the same flexible spacers, one or more copies of different flexible-spacers region, or any combination thereof.

[0268] In yet another embodiment, a polynucleotide molecule encoding a modified Clostridial toxin disclosed in the present specification can further comprises a polynucleotide molecule encoding an epitope-binding region. In another embodiment, a polynucleotide molecule encoding a modified Clostridial toxin disclosed in the present specification can further comprises a polynucleotide molecule encoding a plurality of epitope-binding regions. In aspects of this embodiment, a polynucleotide molecule encoding a modified Clostridial toxin can comprise, e.g., at least 1 polynucleotide molecule encoding an epitope-binding region, at least 2 polynucleotide molecules encoding epitope-binding regions, at least 3 polynucleotide molecules encoding epitope-binding regions, at least 4 polynucleotide molecules encoding epitope-binding regions or at least 5 polynucleotide molecules encoding epitope-binding regions. In other aspects of this embodiment, a polynucleotide molecule encoding a modified Clostridial toxin can comprise, e.g., at most 1 polynucleotide molecule encoding an epitope-binding region, at most 2 polynucleotide molecules encoding epitope-binding regions, at most 3 polynucleotide molecules encoding epitope-binding regions, at most 4 polynucleotide molecules encoding epitope-binding regions or at most 5 polynucleotide molecules encoding epitope-binding regions. In another aspect of this embodiment, a polynucleotide molecule encoding a modified Clostridial toxin can comprise one or more copies of the same polynucleotide molecules encoding epitope-binding region, one or more copies of different polynucleotide molecules encoding epitope-binding region, or any combination thereof. The location of a polynucleotide molecule encoding an epitope-binding region can be in various positions, including, without limitation, at the amino terminus of a modified Clostridial toxin, within a modified Clostridial toxin, or at the carboxyl terminus of a modified Clostridial toxin.

[0269] In an aspect of this embodiment, a polynucleotide molecule encoding an epitope-binding region is located at the amino-terminus of a modified Clostridial toxin. In aspects of this embodiment, a polynucleotide molecule encoding an epitope-binding region located at the amino-terminus of a modified Clostridial toxin disclosed in the present specification can be, e.g., a FLAG, Express™ epitope-binding region, a human Influenza virus hemagluttinin (HA) epitope-binding region, a human p62 ^c'My0 protein (c-MYC) epitope-binding region, a Vesicular Stomatitis Virus Glycoprotein (VSV-G) epitope-binding region, a Substance P epitope-binding region, a glycoprotein-D precursor of Herpes simplex virus (HSV) epitope-binding region, a V5 epitope-binding region, a AU1 epitope-binding region, a AU5 epitope-binding region, a polyhistidine epitope-binding region, a streptavidin binding peptide epitope-binding region, a biotin epitope-binding region, a biotinylation epitope-binding region, a glutathione binding domain of glutathione-S-transferase, a calmodulin binding domain of the calmodulin binding protein or a maltose binding domain of the maltose binding protein.

[0270] In another aspect of this embodiment, a polynucleotide molecule encoding an epitope-binding region is located at the carboxyl-terminus of a modified Clostridial toxin. In aspects of this embodiment, a polynucleotide molecule encoding an epitope-binding region located at the carboxyl-terminus of a modified Clostridial toxin disclosed in the present specification can be, e.g., a FLAG, Express™ epitope- binding region, a human Influenza virus hemagluttinin (HA) epitope-binding region, a human p62 ^{c Myc} protein (c-MYC) epitope-binding region, a Vesicular Stomatitis Virus Glycoprotein (VSV-G) epitope- binding region, a Substance P epitope-binding region, a glycoprotein-D precursor of Herpes simplex virus (HSV) epitope-binding region, a V5 epitope-binding region, a AU1 epitope-binding region, a AU5 epitope- binding region, a polyhistidine epitope-binding region, a streptavidin binding peptide epitope-binding region, a biotin epitope-binding region, a biotinylation epitope-binding region, a glutathione binding domain of glutathione-S-transferase, a calmodulin binding domain of the calmodulin binding protein or a maltose binding domain of the maltose binding protein.

[0271] In yet another embodiment, polynucleotide molecules encoding a modified Clostridial toxin disclosed in the present specification can further comprise a polynucleotide molecule encoding an exogenous protease cleavage site. In another embodiment, a polynucleotide molecule encoding a modified Clostridial toxin disclosed in the present specification can further comprises a plurality of polynucleotide molecules encoding exogenous protease cleavage sites. In aspects of this embodiment, a polynucleotide molecule encoding a modified Clostridial toxin can comprise, e.g., at least 1 polynucleotide molecule encoding an exogenous protease cleavage site, at least 2 polynucleotide molecules encoding exogenous protease cleavage sites, at least 3 polynucleotide molecules encoding exogenous protease cleavage sites, at least 4 polynucleotide molecules encoding exogenous protease cleavage sites or at least 5 polynucleotide molecules encoding exogenous protease cleavage sites. In other aspects of this embodiment, polynucleotide molecules encoding a modified Clostridial toxin can comprise, e.g., at most 1 polynucleotide molecule encoding an exogenous protease cleavage site, at most 2 polynucleotide molecules encoding exogenous protease cleavage sites, at most 3 polynucleotide molecules encoding exogenous protease cleavage sites, at most 4 polynucleotide molecules encoding exogenous protease cleavage sites or at most 5 polynucleotide molecules encoding exogenous protease cleavage sites. In another aspect of this embodiment, a polynucleotide molecule encoding a modified Clostridial toxin can comprise one or more copies of the same exogenous protease cleavage site, one or more copies of different exogenous protease cleavage site, or any combination thereof.

[0272] In yet another embodiment, a polynucleotide molecule encoding an exogenous protease cleavage site is located between a polynucleotide molecule encoding an epitope-binding peptide and a polynucleotide molecule encoding a modified Clostridial toxin. In other aspects of this embodiment, a polynucleotide molecule encoding a bovine enterokinase cleavage site is located between a polynucleotide molecule encoding an epitope-binding region and a polynucleotide molecule encoding a modified Clostridial toxin, a polynucleotide molecule encoding a Tobacco Etch Virus protease cleavage site is located between a polynucleotide molecule encoding an epitope-binding region and a

polynucleotide molecule encoding a modified Clostridial toxin, a polynucleotide molecule encoding a Human Rhinovirus 3C protease cleavage site is located between a polynucleotide molecule encoding an epitope-binding region and a polynucleotide molecule encoding a modified Clostridial toxin, a polynucleotide molecule encoding a SUMO/ULP-1 protease cleavage site is located between a polynucleotide molecule encoding an epitope-binding region and a polynucleotide molecule encoding a modified Clostridial toxin, a polynucleotide molecule encoding a Thrombin protease cleavage site is located between a polynucleotide molecule encoding an epitope-binding region and a polynucleotide molecule encoding a modified Clostridial toxin, or a polynucleotide molecule encoding a Coagulation Factor Xa protease cleavage site is located between a polynucleotide molecule encoding an epitope- binding region and a polynucleotide molecule encoding a modified Clostridial toxin. In other aspects of the embodiment, a polynucleotide molecule encoding the bovine enterokinase protease cleavage site of SEQ ID NO: 168 is located between a polynucleotide molecule encoding an epitope-binding region and a polynucleotide molecule encoding a modified Clostridial toxin. In other aspects of the embodiment, a polynucleotide molecule encoding the Tobacco Etch Virus protease cleavage site of SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171 , SEQ ID NO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177 or SEQ ID NO: 178 is located between a polynucleotide molecule encoding an epitope-binding region and a polynucleotide molecule encoding a modified Clostridial toxin. In still other aspects of the embodiment, a polynucleotide molecule encoding the Human Rhinovirus 3C protease cleavage site of SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181 , SEQ ID NO: 182, SEQ ID NO: 183 or SEQ ID NO: 184 is located between a polynucleotide molecule encoding an epitope-binding region and a polynucleotide molecule encoding a modified Clostridial toxin. In yet other aspects of the embodiment, a polynucleotide molecule encoding the SUMO/ULP-1 protease cleavage site of SEQ ID NO: 185 is located between a polynucleotide molecule encoding an epitope-binding region and a polynucleotide molecule encoding a modified Clostridial toxin. In further other aspects of the embodiment, a polynucleotide molecule encoding the Thrombin protease cleavage site of SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 191 , SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 196, SEQ ID NO: 197, SEQ ID NO: 198, SEQ ID NO: 199 or SEQ ID NO: 200 is located between a polynucleotide molecule encoding an epitope-binding region and a polynucleotide molecule encoding a modified Clostridial toxin. In other aspects of the embodiment, a polynucleotide molecule encoding the Coagulation Factor Xa protease cleavage site of SEQ ID NO: 201 or SEQ ID NO: 202 is located between a polynucleotide molecule encoding an epitope-binding region and a polynucleotide molecule encoding a modified Clostridial toxin.

[0273] Another aspect of the present invention provides a method of producing a modified Clostridial toxin comprising Clostridial toxin substrate cleavage site, wherein the Clostridial toxin substrate cleavage site is located within the di-chain loop region, such method comprising the step of expressing a polynucleotide molecule encoding a modified Clostridial toxin in a cell. Another aspect of the present invention provides a method of producing a modified Clostridial toxin comprising Clostridial toxin substrate cleavage site, wherein the Clostridial toxin substrate cleavage site is located within the di-chain

loop region, such method comprising the steps of introducing an expression construct comprising a polynucleotide molecule encoding a modified Clostridial toxin into a cell and expressing the expression construct in the cell.

[0274] The methods disclosed in the present specification include, in part, a Clostridial toxin. It is envisioned that any and all Clostridial toxins disclosed in the present specification can be produced using the methods disclosed in the present specification. Thus, aspects of this embodiment include producing, without limitation, naturally occurring Clostridial toxins, naturally occurring Clostridial toxins variants, such as, e.g., Clostridial toxins isoforms and Clostridial toxins subtypes, non-naturally occurring Clostridial toxins variants, such as, e.g., conservative Clostridial toxins variants, non-conservative Clostridial toxins variants and Clostridial toxins fragments thereof, or any combination thereof.

[0275] The methods disclosed in the present specification include, in part, Clostridial toxin substrate cleavage site. It is envisioned that any and all Clostridial toxin substrate cleavage site disclosed in the present specification can be produced using the methods disclosed in the present specification. Thus, aspects of this embodiment include producing, without limitation, naturally occurring Clostridial toxin substrate cleavage sites, naturally occurring Clostridial toxin substrate cleavage site variants, such as, e.g., Clostridial toxin substrate cleavage site isoforms and Clostridial toxin substrate cleavage site subtypes, non-naturally occurring Clostridial toxin substrate cleavage site variants, such as, e.g., conservative Clostridial toxin substrate cleavage site variants, non-conservative Clostridial toxin substrate cleavage site variants and Clostridial toxin substrate cleavage site peptidomimetics thereof, or any combination thereof.

[0276] The methods disclosed in the present specification include, in part, a polynucleotide molecule. It is envisioned that any and all polynucleotide molecules disclosed in the present specification can be used. Thus, aspects of this embodiment include, without limitation, polynucleotide molecules encoding naturally occurring Clostridial toxins; polynucleotide molecules encoding naturally occurring Clostridial toxins variants, such as, e.g., Clostridial toxins isoforms and Clostridial toxins subtypes; polynucleotide molecules encoding non-naturally occurring Clostridial toxins variants, such as, e.g., conservative Clostridial toxins variants, non-conservative Clostridial toxins variants and Clostridial toxins fragments thereof, or any combination thereof.

[0277] The methods disclosed in the present specification include, in part, an expression construct. An expression construct comprises a polynucleotide molecule disclosed in the present specification operably-linked to an expression vector useful for expressing the polynucleotide molecule in a cell or cell- free extract. A wide variety of expression vectors can be employed for expressing a polynucleotide molecule encoding a modified Clostridial toxin, including, without limitation, a viral expression vector; a prokaryotic expression vector; eukaryotic expression vectors, such as, e.g., a yeast expression vector, an insect expression vector and a mammalian expression vector; and a cell-free extract expression vector. It

is further understood that expression vectors useful to practice aspects of these methods may include those which express a modified Clostridial toxin under control of a constitutive, tissue-specific, cell- specific or inducible promoter element, enhancer element or both. Non-limiting examples of expression vectors, along with well-established reagents and conditions for making and using an expression construct from such expression vectors are readily available from commercial vendors that include, without limitation, BD Biosciences-Clontech, Palo Alto, CA; BD Biosciences Pharmingen, San Diego, CA; Invitrogen, Inc, Carlsbad, CA; EMD Biosciences-Novagen, Madison, Wl; QIAGEN, Inc., Valencia, CA; and Stratagene, La JoIIa, CA. The selection, making and use of an appropriate expression vector are routine procedures well within the scope of one skilled in the art and from the teachings herein.

[0278] Thus, aspects of this embodiment include, without limitation, a viral expression vector operably- linked to a polynucleotide molecule encoding a modified Clostridial toxin; a prokaryotic expression vector operably-linked to a polynucleotide molecule encoding a modified Clostridial toxin; a yeast expression vector operably-linked to a polynucleotide molecule encoding a modified Clostridial toxin; an insect expression vector operably-linked to a polynucleotide molecule encoding a modified Clostridial toxin; and a mammalian expression vector operably-linked to a polynucleotide molecule encoding a modified Clostridial toxin. Other aspects of this embodiment include, without limitation, expression constructs suitable for expressing a modified Clostridial toxin disclosed in the present specification using a cell-free extract comprising a cell-free extract expression vector operably linked to a polynucleotide molecule encoding a modified Clostridial toxin. Other aspects of this embodiment include, without limitation, expression constructs comprising polynucleotide molecules comprising any one of SEQ ID NO: 109 through SEQ ID NO: 132 and SEQ ID NO: 136 through SEQ ID NO: 159. Other aspects of this embodiment include, without limitation, expression constructs comprising polynucleotide molecules encoding a modified Clostridial toxin comprising any one of SEQ ID NO: 85 through SEQ ID NO: 108.

[0279] The methods disclosed in the present specification include, in part, a cell. It is envisioned that any and all cells can be used. Thus, aspects of this embodiment include, without limitation, prokaryotic cells including, without limitation, strains of aerobic, microaerophilic, capnophilic, facultative, anaerobic, gram-negative and gram-positive bacterial cells such as those derived from, e.g., Escherichia coli, Bacillus subtilis, Bacillus licheniformis, Bacteroides fragilis, Clostridia perfringens, Clostridia difficile, Caulobacter crescentus, Lactococcus lactis, Methylobacterium extorquens, Neisseria meningirulls, Neisseria meningitidis, Pseudomonas fluorescens and Salmonella typhimurium; and eukaryotic cells including, without limitation, yeast strains, such as, e.g., those derived from Pichia pastoris, Pichia methanolica, Pichia angusta, Schizosaccharomyces pombe, Saccharomyces cerevisiae and Yarrowia lipolytica; insect cells and cell lines derived from insects, such as, e.g., those derived from Spodoptera frugiperda, Trichoplusia ni, Drosophila melanogaster and Manduca sexta; and mammalian cells and cell lines derived from mammalian cells, such as, e.g., those derived from mouse, rat, hamster, porcine, bovine, equine, primate and human. Cell lines may be obtained from the American Type Culture Collection (2004); European Collection of Cell Cultures (2204); and the German Collection of

Microorganisms and Cell Cultures (2004). Non-limiting examples of specific protocols for selecting, making and using an appropriate cell line are described in e.g., INSECT CELL CULTURE ENGINEERING (Mattheus F. A. Goosen et al. eds., Marcel Dekker, 1993); INSECT CELL CULTURES: FUNDAMENTAL AND APPLIED ASPECTS (J. M. Vlak et al. eds., Kluwer Academic Publishers, 1996); Maureen A. Harrison & Ian F. Rae, GENERAL TECHNIQUES OF CELL CULTURE (Cambridge University Press, 1997); CELL AND TISSUE CULTURE: LABORATORY PROCEDURES (Alan Doyle et al eds., John Wiley and Sons, 1998); R. Ian Freshney, CULTURE OF ANIMAL CELLS: A MANUAL OF BASIC TECHNIQUE (Wiley-Liss, 4 ^th ed. 2000); ANIMAL CELL CULTURE: A PRACTICAL APPROACH (John R. W. Masters ed., Oxford University Press, 3 ^rd ed. 2000); MOLECULAR CLONING A LABORATORY MANUAL, supra, (2001 ); BASIC CELL CULTURE: A PRACTICAL APPROACH (John M. Davis, Oxford Press, 2 ^nd ed. 2002); and CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, supra, (2004). These protocols are routine procedures within the scope of one skilled in the art and from the teaching herein.

[0280] The methods disclosed in the present specification include, in part, introducing into a cell a polynucleotide molecule. A polynucleotide molecule introduced into a cell can be transiently or stably maintained by that cell. Stably-maintained polynucleotide molecules may be extra-chromosomal and replicate autonomously, or they may be integrated into the chromosomal material of the cell and replicate non-autonomously. It is envisioned that any and all methods for introducing a polynucleotide molecule disclosed in the present specification into a cell can be used. Methods useful for introducing a nucleic acid molecule into a cell include, without limitation, chemical-mediated transfection such as, e.g., calcium phosphate-mediated, diethyl-aminoethyl (DEAE) dextran-mediated, lipid-mediated, polyethyleneimine (PEI)-mediated, polylysine-mediated and polybrene-mediated; physical-mediated tranfection, such as, e.g., biolistic particle delivery, microinjection, protoplast fusion and electroporation; and viral-mediated transfection, such as, e.g., retroviral-mediated transfection, see, e.g., Introducing Cloned Genes into Cultured Mammalian Cells, pp. 16.1-16.62 (Sambrook & Russell, eds., Molecular Cloning A Laboratory Manual, Vol. 3, 3 ^rd ed. 2001). One skilled in the art understands that selection of a specific method to introduce an expression construct into a cell will depend, in part, on whether the cell will transiently contain an expression construct or whether the cell will stably contain an expression construct. These protocols are routine procedures within the scope of one skilled in the art and from the teaching herein.

[0281] In an aspect of this embodiment, a chemical-mediated method, termed transfection, is used to introduce a polynucleotide molecule encoding a modified Clostridial toxin into a cell. In chemical- mediated methods of transfection the chemical reagent forms a complex with the nucleic acid that facilitates its uptake into the cells. Such chemical reagents include, without limitation, calcium phosphate- mediated, see, e.g., Martin Jordan & Florian Worm, Transfection of Adherent and Suspended Cells by Calcium Phosphate, 33(2) Methods 136-143 (2004); diethyl-aminoethyl (DEAE) dextran-mediated, lipid- mediated, cationic polymer-mediated like polyethyleneimine (PEI)-mediated and polylysine-mediated and polybrene-mediated, see, e.g., Chun Zhang et al., Polyethylenimine Strategies for Plasmid Delivery to Brain-Derived Cells, 33(2) Methods 144-150 (2004). Such chemical-mediated delivery systems can be

prepared by standard methods and are commercially available, see, e.g., CellPhect Transfection Kit (Amersham Biosciences, Piscataway, NJ); Mammalian Transfection Kit, Calcium phosphate and DEAE Dextran, (Stratagene, Inc., La JoIIa, CA); Lipofectamine™ Transfection Reagent (Invitrogen, Inc., Carlsbad, CA); ExGen 500 Transfection kit (Fermentas, Inc., Hanover, MD), and SuperFect and Effectene Transfection Kits (Qiagen, Inc., Valencia, CA).

[0282] In another aspect of this embodiment, a physical-mediated method is used to introduce a polynucleotide molecule encoding a modified Clostridial toxin into a cell. Physical techniques include, without limitation, electroporation, biolistic and microinjection. Biolistics and microinjection techniques perforate the cell wall in order to introduce the nucleic acid molecule into the cell, see, e.g., Jeike E. Biewenga et al., Plasmid-Mediated Gene Transfer in Neurons Using the Biolistics Technique, 71(1) J. Neurosci. Methods. 67-75 (1997); and John O'Brien & Sarah C. R. Lummis, Biolistic and Diolistic Transfection: Using the Gene Gun to Deliver DNA and Lipophilic Dyes into Mammalian Cells, 33(2) Methods 121-125 (2004). Electroporation, also termed electropermeabilization, uses brief, high-voltage, electrical pulses to create transient pores in the membrane through which the nucleic acid molecules enter and can be used effectively for stable and transient transfections of all cell types, see, e.g., M. Golzio et al., In vitro and in vivo Electric Field-Mediated Permeabilization, Gene Transfer, and Expression, 33(2) Methods 126-135 (2004); and Oliver Greschet al., New Non-Viral Method for Gene Transfer into Primary Cells, 33(2) Methods 151-163 (2004).

[0283] In another aspect of this embodiment, a viral-mediated method, termed transduction, is used to introduce a polynucleotide molecule encoding a modified Clostridial toxin into a cell. In viral-mediated methods of transient transduction, the process by which viral particles infect and replicate in a host cell has been manipulated in order to use this mechanism to introduce a nucleic acid molecule into the cell. Viral-mediated methods have been developed from a wide variety of viruses including, without limitation, retroviruses, adenoviruses, adeno-associated viruses, herpes simplex viruses, picornaviruses, alphaviruses and baculoviruses, see, e.g., Armin Blesch, Lentiviral and MLV based Retroviral Vectors for ex vivo and in vivo Gene Transfer, 33(2) Methods 164-172 (2004); and Maurizio Federico, From Lentiviruses to Lentivirus Vectors, 229 Methods MoI. Biol. 3-15 (2003); E. M. Poeschla, Non-Primate Lentiviral Vectors, 5(5) Curr. Opin. MoI. Ther. 529-540 (2003); Karim Benihoud et al, Adenovirus Vectors for Gene Delivery, 10(5) Curr. Opin. Biotechnol. 440-447 (1999); H. Bueler, Adeno-Associated Viral Vectors for Gene Transfer and Gene Therapy, 380(6) Biol. Chem. 613-622 (1999); Chooi M. Lai et al., Adenovirus and Adeno-Associated Virus Vectors, 21(12) DNA Cell Biol. 895-913 (2002); Edward A. Burton et al., Gene Delivery Using Herpes Simplex Virus Vectors, 21 (12) DNA Cell Biol. 915-936 (2002); Paola Grandi et al., Targeting HSV Amplicon Vectors, 33(2) Methods 179-186 (2004); llya Frolov et al., Alphavirus-Based Expression Vectors: Strategies and Applications, 93(21) Proc. Natl. Acad. Sci. U. S. A. 11371-11377 (1996); Markus U. Ehrengruber, Alphaviral Gene Transfer in Neurobiology, 59(1) Brain Res. Bull. 13-22 (2002); Thomas A. Kost & J. Patrick Condreay, Recombinant Baculoviruses as Mammalian Cell Gene-Delivery Vectors, 20(4) Trends Biotechnol. 173-180 (2002); and A. Huser & C. Hofmann,

Baculovirus Vectors: Novel Mammalian Cell Gene-Delivery Vehicles and Their Applications, 3(1) Am. J. Pharmacogenomics 53-63 (2003).

[0284] Adenoviruses, which are non-enveloped, double-stranded DNA viruses, are often selected for mammalian cell transduction because adenoviruses handle relatively large polynucleotide molecules of about 36 kb, are produced at high titer, and can efficiently infect a wide variety of both dividing and non- dividing cells, see, e.g., Wim T. J. M. C. Hermens et at., Transient Gene Transfer to Neurons and GHa: Analysis of Adenoviral Vector Performance in the CNS and PNS, 71(1) J. Neurosci. 'Methods 85-98 (1997); and Hiroyuki Mizuguchi et al., Approaches for Generating Recombinant Adenovirus Vectors, 52(3) Adv. Drug Deliv. Rev. 165-176 (2001). Transduction using adenoviral-based system do not support prolonged protein expression because the nucleic acid molecule is carried from an episome in the cell nucleus, rather than being integrated into the host cell chromosome. Adenoviral vector systems and specific protocols for how to use such vectors are disclosed in, e.g., ViraPower™ Adenoviral Expression System (Invitrogen, Inc., Carlsbad, CA) and ViraPower™ Adenoviral Expression System Instruction Manual 25-0543 version A, Invitrogen, Inc., (JuI. 15, 2002); and AdEasy™ Adenoviral Vector System (Stratagene, Inc., La JoIIa, CA) and AdEasy™ Adenoviral Vector System Instruction Manual 064004f, Stratagene, Inc..

[0285] Nucleic acid molecule delivery can also use single-stranded RNA retroviruses, such as, e.g., oncoretroviruses and Antiviruses. Retroviral-mediated transduction often produce transduction efficiencies close to 100%, can easily control the proviral copy number by varying the multiplicity of infection (MOI), and can be used to either transiently or stably transduce cells, see, e.g., Tiziana Tonini et al., Transient Production Of Retroviral- and Lentiviral-Based Vectors For the Transduction of Mammalian Cells, 285 Methods MoI. Biol. 141-148 (2004); Armin Blesch, Lentiviral and MLV Based Retroviral Vectors for ex vivo and in vivo Gene Transfer, 33(2) Methods 164-172 (2004); Felix Recillas-Targa, Gene Transfer and Expression in Mammalian Cell Lines and Transgenic Animals, 267 Methods MoI. Biol. 417- 433 (2004); and Roland Wolkowicz et al., Lentiviral Vectors for the Delivery of DNA into Mammalian Cells, 246 Methods MoI. Biol. 391-411 (2004). Retroviral particles consist of an RNA genome packaged in a protein capsid, surrounded by a lipid envelope. The retrovirus infects a host cell by injecting its RNA into the cytoplasm along with the reverse transcriptase enzyme. The RNA template is then reverse transcribed into a linear, double stranded cDNA that replicates itself by integrating into the host cell genome. Viral particles are spread both vertically (from parent cell to daughter cells via the provirus) as well as horizontally (from cell to cell via virions). This replication strategy enables long-term persistent expression since the nucleic acid molecules of interest are stably integrated into a chromosome of the host cell, thereby enabling long-term expression of the protein. For instance, animal studies have shown that lentiviral vectors injected into a variety of tissues produced sustained protein expression for more than 1 year, see, e.g., Luigi Naldini et al., In vivo Gene Delivery and Stable Transduction of Non-Dividing Cells By a Lentiviral Vector, 272(5259) Science 263-267 (1996). The Oncoretroviruses-derived vector systems, such as, e.g., Moloney murine leukemia virus (MoMLV), are widely used and infect many

different non-dividing cells. Lentiviruses can also infect many different cell types, including dividing and non-dividing cells and possess complex envelope proteins, which allows for highly specific cellular targeting.

[0286] Retroviral vectors and specific protocols for how to use such vectors are disclosed in, e.g., U.S. Patent Nos. Manfred Gossen & Hermann Bujard, Tight Control of Gene Expression in Eukaryotic Cells By Tetracycline-Responsive Promoters, U.S. Patent No. 5,464,758 (Nov. 7, 1995) and Hermann Bujard & Manfred Gossen, Methods for Regulating Gene Expression, U.S. Patent No. 5,814,618 (Sep. 29, 1998) David S. Hogness, Polynucleotides Encoding Insect Steroid Hormone Receptor Polypeptides and Cells Transformed With Same, U.S. Patent No. 5,514,578 (May 7, 1996) and David S. Hogness, Polynucleotide Encoding Insect Ecdysone Receptor, U.S. Patent 6,245,531 (Jun. 12, 2001); Elisabetta Vegeto et al., Progesterone Receptor Having C. Terminal Hormone Binding Domain Truncations, U.S. Patent No. 5,364,791 (Nov. 15, 1994), Elisabetta Vegeto et al., Mutated Steroid Hormone Receptors, Methods For Their Use and Molecular Switch For Gene Therapy, U.S. Patent No. 5,874,534 (Feb. 23, 1999) and Elisabetta Vegeto et al., Mutated Steroid Hormone Receptors, Methods For Their Use and Molecular Switch For Gene Therapy, U.S. Patent No. 5,935,934 (Aug. 10, 1999). Furthermore, such viral delivery systems can be prepared by standard methods and are commercially available, see, e.g., BD™ Tet-Off and Tet-On Gene Expression Systems (BD Biosciences-Clonetech, Palo Alto, CA) and BD™ Tet- Off and Tet-On Gene Expression Systems User Manual, PT3001-1 , BD Biosciences Clonetech, (Mar. 14, 2003), GeneSwitch™ System (Invitrogen, Inc., Carlsbad, CA) and GeneSwitch™ System A Mifepristone- Regulated Expression System for Mammalian Cells version D, 25-0313, Invitrogen, Inc., (Nov. 4, 2002); ViraPower™ Lentiviral Expression System (Invitrogen, Inc., Carlsbad, CA) and ViraPower™ Lentiviral Expression System Instruction Manual 25-0501 version E, Invitrogen, Inc., (Dec. 8, 2003); and Complete Control ^® Retroviral Inducible Mammalian Expression System (Stratagene, La JoIIa, CA) and Complete Control ^® Retroviral Inducible Mammalian Expression System Instruction Manual, 064005e.

[0287] The methods disclosed in the present specification include, in part, expressing a modified Clostridial toxin from a polynucleotide molecule. It is envisioned that any of a variety of expression systems may be useful for expressing a modified Clostridial toxin from a polynucleotide molecule disclosed in the present specification, including, without limitation, cell-based systems and cell-free expression systems. Cell-based systems include, without limitation, viral expression systems, prokaryotic expression systems, yeast expression systems, baculoviral expression systems, insect expression systems and mammalian expression systems. Cell-free systems include, without limitation, wheat germ extracts, rabbit reticulocyte extracts and E. coli extracts and generally are equivalent to the method disclosed herein. Expression of a polynucleotide molecule using an expression system can include any of a variety of characteristics including, without limitation, inducible expression, non-inducible expression, constitutive expression, viral-mediated expression, stably-integrated expression, and transient expression. Expression systems that include well-characterized vectors, reagents, conditions and cells are well-established and are readily available from commercial vendors that include, without limitation,

Ambion, Inc. Austin, TX; BD Biosciences-Clontech, Palo Alto, CA; BD Biosciences Pharmingen, San Diego, CA; Invitrogen, Inc. Carlsbad, CA; QIAGEN, Inc., Valencia, CA; Roche Applied Science, Indianapolis, IN; and Stratagene, La JoIIa, CA. Non-limiting examples on the selection and use of appropriate heterologous expression systems are described in e.g., PROTEIN EXPRESSION. A PRACTICAL APPROACH (S. J. Higgins and B. David Hames eds., Oxford University Press, 1999); Joseph M. Fernandez & James P. Hoeffler, GENE EXPRESSION SYSTEMS. USING NATURE FOR THE ART OF EXPRESSION (Academic Press, 1999); and Meena Rai & Harish Padh, Expression Systems for Production of Heterologous Proteins, 80(9) Curr. Sci. 1121-1128, (2001). These protocols are routine procedures well within the scope of one skilled in the art and from the teaching herein.

[0288] A variety of cell-based expression procedures are useful for expressing a modified Clostridial toxin encoded by polynucleotide molecule disclosed in the present specification. Examples included, without limitation, viral expression systems, prokaryotic expression systems, yeast expression systems, baculoviral expression systems, insect expression systems and mammalian expression systems. Viral expression systems include, without limitation, the ViraPower™ Lentiviral (Invitrogen, Inc., Carlsbad, CA), the Adenoviral Expression Systems (Invitrogen, Inc., Carlsbad, CA), the AdEasy™ XL Adenoviral Vector System (Stratagene, La JoIIa, CA) and the ViraPort® Retroviral Gene Expression System (Stratagene, La JoIIa, CA). Non-limiting examples of prokaryotic expression systems include the Champion™ pET Expression System (EMD Biosciences-Novagen, Madison, Wl), the TriEx™ Bacterial Expression Systems (EMD Biosciences-Novagen, Madison, Wl), the Q\Aexpress ^® Expression System (QIAGEN, Inc.), and the Affinity ^® Protein Expression and Purification System (Stratagene, La JoIIa, CA). Yeast expression systems include, without limitation, the EasySelect™ Pichia Expression Kit (Invitrogen, Inc., Carlsbad, CA), the YES-Echo™ Expression Vector Kits (Invitrogen, Inc., Carlsbad, CA ) and the SpECTRA™ S. pombe Expression System (Invitrogen, Inc., Carlsbad, CA). Non-limiting examples of baculoviral expression systems include the BaculoDirect™ (Invitrogen, Inc., Carlsbad, CA), the Bac-to- Bac ^® (Invitrogen, Inc., Carlsbad, CA), and the BD BaculoGold™ (BD Biosciences-Pharmigen, San Diego, CA). Insect expression systems include, without limitation, the Drosophila Expression System (DES ^® ) (Invitrogen, Inc., Carlsbad, CA), InsectSelect™ System (Invitrogen, Inc., Carlsbad, CA) and InsectDirect™ System (EMD Biosciences-Novagen, Madison, Wl). Non-limiting examples of mammalian expression systems include the T-REx™ (Tetracycline-Regulated Expression) System (Invitrogen, Inc., Carlsbad, CA), the Flp-ln™ T-REx™ System (Invitrogen, Inc., Carlsbad, CA), the pcDNA™ system (Invitrogen, Inc., Carlsbad, CA), the pSecTag2 system (Invitrogen, Inc., Carlsbad, CA), the Exchanger ^® System, InterPlay™ Mammalian TAP System (Stratagene, La JoIIa, CA), Complete Control ^® Inducible Mammalian Expression System (Stratagene, La JoIIa, CA) and LacSwitch ^® Il Inducible Mammalian Expression System (Stratagene, La JoIIa, CA).

[0289] Another procedure of expressing a modified Clostridial toxin encoded by polynucleotide molecule disclosed in the present specification employs a cell-free expression system such as, without limitation, prokaryotic extracts and eukaryotic extracts. Non-limiting examples of prokaryotic cell extracts include

the RTS 100 E. coli HY Kit (Roche Applied Science, Indianapolis, IN), the ActivePro In Vitro Translation Kit (Ambion, Inc., Austin, TX), the EcoPro™ System (EMD Biosciences-Novagen, Madison, Wl) and the Expressway™ Plus Expression System (Invitrogen, Inc., Carlsbad, CA). Eukaryotic cell extract include, without limitation, the RTS 100 Wheat Germ CECF Kit (Roche Applied Science, Indianapolis, IN), the TnT ^® Coupled Wheat Germ Extract Systems (Promega Corp., Madison, Wl), the Wheat Germ IVT™ Kit (Ambion, Inc., Austin, TX), the Retic Lysate IVT™ Kit (Ambion, Inc., Austin, TX), the PROTEINscript ^® Il System (Ambion, Inc., Austin, TX) and the TnT ^® Coupled Reticulocyte Lysate Systems (Promega Corp., Madison, Wl).

[0290] Aspects of the present invention can also be described as follows:

1. A modified Clostridial toxin comprising a Clostridial toxin substrate cleavage site, wherein the Clostridial toxin substrate cleavage site is located within a di-chain loop region.

2. The modified Clostridial toxin according to 1 , wherein the Clostridial toxin substrate cleavage site is a Botulinum toxin substrate cleavage site.

3. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site is selected from the group consisting of a BoNT/A substrate cleavage site, a BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site and a BoNT/G substrate cleavage site

4. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises a BoNT/A cleavage site.

5. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a SNAP-25, said six consecutive residues comprising Gln-Arg.

6. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a SNAP-25, said six consecutive residues comprising Lys-His.

7. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106.

8. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises a BoNT/B cleavage site.

9. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a VAMP, said six consecutive residues comprising Gln-Phe.

10. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112.

11. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises a BoNT/C1 cleavage site.

12. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a SNAP-25, said six consecutive residues comprising Arg-Ala.

13. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a Syntaxin, said six consecutive residues comprising Lys-Ala.

14. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a Syntaxin, said six consecutive residues comprising Arg-Ala.

15. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 120 or SEQ ID NO: 121.

16. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises a BoNT/D cleavage site.

17. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a VAMP, said six consecutive residues comprising Lys-Leu.

18. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises SEQ ID NO: 122 or SEQ ID NO: 123.

19. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises a BoNT/E cleavage site.

20. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a SNAP-25, said six consecutive residues comprising Arg-lle.

21. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a SNAP-25, said six consecutive residues comprising Lys-lle.

22. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128.

23. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises a BoNT/F cleavage site.

24. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a VAMP, said six consecutive residues comprising Gln-Lys.

25. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises SEQ ID NO: 129 or SEQ ID NO: 130.

26. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises a BoNT/G cleavage site.

27. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a VAMP, said six consecutive residues comprising Ala- Ala.

28. The modified Clostridial toxin according to 2, wherein the Botulinum toxin substrate cleavage site comprises SEQ ID NO: 131 or SEQ ID NO: 132.

29. The modified Clostridial toxin according to 1 , wherein the Clostridial toxin substrate cleavage site is a Tetanus toxin substrate cleavage site.

30. The modified Clostridial toxin according to 29, wherein the Tetanus toxin substrate cleavage site comprises at least six consecutive residues of a VAMP, said six consecutive residues comprising Gln-Phe.

31. The modified Clostridial toxin according to 1 , wherein the modified Clostridial toxin comprises a Botulinum toxin enzymatic domain, a Botulinum toxin translocation domain and a Botulinum toxin binding domain.

32. The modified Clostridial toxin according to 1 , wherein the modified Botulinum toxin comprises a BoNT/A enzymatic domain, a BoNT/A translocation domain and a BoNT/A binding domain.

33. The modified Clostridial toxin according to 1 , wherein the modified Botulinum toxin comprises a BoNT/B enzymatic domain, a BoNT/B translocation domain and a BoNT/B binding domain.

34. The modified Clostridial toxin according to 1 , wherein the modified Botulinum toxin comprises a BoNT/CI enzymatic domain, a BoNT/CI translocation domain and a BoNT/CI binding domain.

35. The modified Clostridial toxin according to 1 , wherein the modified Botulinum toxin comprises a BoNT/D enzymatic domain, a BoNT/D translocation domain and a BoNT/D binding domain.

36. The modified Clostridial toxin according to 1 , wherein the modified Botulinum toxin comprises a BoNT/E enzymatic domain, a BoNT/E translocation domain and a BoNT/E binding domain.

37. The modified Clostridial toxin according to 1 , wherein the modified Botulinum toxin comprises a BoNT/F enzymatic domain, a BoNT/F translocation domain and a BoNT/F binding domain.

38. The modified Clostridial toxin according to 1 , wherein the modified Botulinum toxin comprises a BoNT/G enzymatic domain, a BoNT/G translocation domain and a BoNT/G binding domain.

39. The modified Clostridial toxin according to 1 , wherein the modified Clostridial toxin comprises a Tetanus toxin enzymatic domain, a Tetanus toxin translocation domain and a Tetanus toxin binding domain.

40. A modified Clostridial toxin comprising:

a) a Clostridial toxin substrate cleavage site; b) a di-chain loop region c) a Clostridial toxin enzymatic domain; d) a Clostridial toxin translocation domain; and e) an enhanced cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell;

wherein the Clostridial toxin substrate cleavage site is located within the di-chain loop region.

41. A modified Clostridial toxin comprising:

a) a Clostridial toxin substrate cleavage site; b) a di-chain loop region c) a Clostridial toxin enzymatic domain; d) a Clostridial toxin translocation domain; and e) an altered cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell;

wherein the Clostridial toxin substrate cleavage site is located within the di-chain loop region.

42. A modified Clostridial toxin comprising:

a) a Clostridial toxin substrate cleavage site; b) a di-chain loop region c) a Clostridial toxin enzymatic domain; d) a Clostridial toxin translocation domain; and e) an altered cell binding activity capable of intoxicating a non-naturally occurring Clostridial toxin target cell;

wherein the Clostridial toxin substrate cleavage site is located within the di-chain loop region.

43. The modified Clostridial toxin according to any one of 40-42, wherein the Clostridial toxin substrate cleavage site is selected from the group consisting of a BoNT/A substrate cleavage site, a BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site, a BoNT/G substrate cleavage site, a TeNT substrate cleavage site, a BaNT substrate cleavage site and a BuNT substrate cleavage site.

44. The modified Clostridial toxin according to any one of 40-42, wherein the Clostridial toxin enzymatic domain is selected from the group consisting of a BoNT/A enzymatic domain, a BoNT/B enzymatic domain, a BoNT/C1 enzymatic domain, a BoNT/D enzymatic domain, a BoNT/E enzymatic domain, a BoNT/F enzymatic domain, a BoNT/G enzymatic domain and a TeNT enzymatic domain, a BaNT enzymatic domain and a BuNT enzymatic domain.

45. The modified Clostridial toxin according to any one of 40-42, wherein the Clostridial toxin translocation domain is selected from the group consisting of a BoNT/A translocation domain, a

BoNT/B translocation domain, a BoNT/C1 translocation domain, a BoNT/D translocation domain, a BoNT/E translocation domain, a BoNT/F translocation domain, a BoNT/G translocation domain and a TeNT translocation domain, a BaNT translocation domain and a BuNT translocation domain.

46. A polynucleotide molecule encoding a modified Clostridial toxin comprising:

a) a Clostridial toxin substrate cleavage site; b) a di-chain loop region c) a Clostridial toxin enzymatic domain; d) a Clostridial toxin translocation domain; and e) an enhanced cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell;

wherein the Clostridial toxin substrate cleavage site is located within the di-chain loop region.

47. A polynucleotide molecule encoding a modified Clostridial toxin comprising:

a) a Clostridial toxin substrate cleavage site; b) a di-chain loop region c) a Clostridial toxin enzymatic domain; d) a Clostridial toxin translocation domain; and e) an altered cell binding activity capable of intoxicating a naturally occurring Clostridial toxin target cell;

wherein the Clostridial toxin substrate cleavage site is located within the di-chain loop region.

48. A polynucleotide molecule encoding a modified Clostridial toxin comprising:

a) a Clostridial toxin substrate cleavage site; b) a di-chain loop region c) a Clostridial toxin enzymatic domain; d) a Clostridial toxin translocation domain; and e) an altered cell binding activity capable of intoxicating a non-naturally occurring Clostridial toxin target cell;

wherein the Clostridial toxin substrate cleavage site is located within the di-chain loop region.

49. The polynucleotide molecule according to any one of 46-48, wherein the polynucleotide molecule encoding the Clostridial toxin substrate cleavage site encodes a BoNT/A substrate cleavage site, a

BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site, a BoNT/G substrate cleavage site, a TeNT substrate cleavage site, a BaNT substrate cleavage site and a BuNT substrate cleavage site.

50. The polynucleotide molecule according to any one of 46-48, wherein the polynucleotide molecule encoding the Clostridial toxin enzymatic domain encodes a BoNT/A enzymatic domain, a BoNT/B enzymatic domain, a BoNT/C1 enzymatic domain, a BoNT/D enzymatic domain, a BoNT/E enzymatic domain, a BoNT/F enzymatic domain, a BoNT/G enzymatic domain, a TeNT enzymatic domain, a BaNT enzymatic domain or a BuNT enzymatic domain.

51. The polynucleotide molecule according to any one of 46-48, wherein the polynucleotide molecule encoding the Clostridial toxin translocation domain encodes a BoNT/A translocation domain, a BoNT/B translocation domain, a B0NT/CI translocation domain, a BoNT/D translocation domain, a BoNT/E translocation domain, a BoNT/F translocation domain, a BoNT/G translocation domain, a TeNT translocation domain, a BaNT translocation domain or a BuNT translocation domain.

52. A polynucleotide molecule encoding a modified Clostridial toxin comprising a Clostridial toxin substrate cleavage site, wherein the Clostridial toxin substrate cleavage site is located within the di- chain loop region.

53. The polynucleotide molecule according to 52, wherein the polynucleotide molecule encoding the Clostridial toxin substrate cleavage site is a Botulinum toxin substrate cleavage site.

54. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site is selected from the group consisting of a BoNT/A substrate cleavage site, a BoNT/B substrate cleavage site, a BoNT/C1 substrate cleavage site, a BoNT/D substrate cleavage site, a BoNT/E substrate cleavage site, a BoNT/F substrate cleavage site and a BoNT/G substrate cleavage site.

55. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises a BoNT/A cleavage site.

56. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a SNAP-25, said six consecutive residues comprising Gln-Arg.

57. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a SNAP-25, said six consecutive residues comprising Lys-His.

58. The polynucleotide molecule according to 53, wherein the polynucleotide molecule comprising the Botulinum toxin substrate cleavage site encodes SEQ ID NO: 104, SEQ ID NO: 105 or SEQ ID NO: 106.

59. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises a BoNT/B cleavage site.

60. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a VAMP, said six consecutive residues comprising Gln-Phe.

61. The polynucleotide molecule according to 53, wherein the polynucleotide molecule comprising the Botulinum toxin substrate cleavage site encodes SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111 or SEQ ID NO: 112.

62. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises a BoNT/C1 cleavage site.

63. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a SNAP-25, said six consecutive residues comprising Arg-Ala.

64. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a Syntaxin, said six consecutive residues comprising Lys-Ala.

65. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a Syntaxin, said six consecutive residues comprising Arg-Ala.

66. The polynucleotide molecule according to 53, wherein the polynucleotide molecule comprising the Botulinum toxin substrate cleavage site encodes SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 120 or SEQ ID NO: 121.

67. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises a BoNT/D cleavage site.

68. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a VAMP, said six consecutive residues comprising Lys-Leu.

69. The polynucleotide molecule according to 53, wherein the polynucleotide molecule comprising the Botulinum toxin substrate cleavage site encodes SEQ ID NO: 122 or SEQ ID NO: 123.

70. The polynucleotide molecule according to 53, wherein the Botulinum toxin substrate cleavage site comprises a BoNT/E cleavage site.

71. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a SNAP-25, said six consecutive residues comprising Arg-lle.

72. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a SNAP-25, said six consecutive residues comprising Lys-lle.

73. The polynucleotide molecule according to 53, wherein the polynucleotide molecule comprising the Botulinum toxin substrate cleavage site encodes SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127 or SEQ ID NO: 128.

74. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises a BoNT/F cleavage site.

75. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a VAMP, said six consecutive residues comprising Gln-Lys.

76. The polynucleotide molecule according to 53, wherein the polynucleotide molecule comprising the Botulinum toxin substrate cleavage site encodes SEQ ID NO: 129 or SEQ ID NO: 130.

77. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises a BoNT/G cleavage site.

78. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding the Botulinum toxin substrate cleavage site comprises at least six consecutive residues of a VAMP, said six consecutive residues comprising Ala-Ala.

79. The polynucleotide molecule according to 53, wherein the polynucleotide molecule comprising the Botulinum toxin substrate cleavage site encodes SEQ ID NO: 131 or SEQ ID NO: 132.

80. The polynucleotide molecule according to 52, wherein the polynucleotide molecule encoding the Clostridial toxin substrate cleavage site is a Tetanus toxin substrate cleavage site.

81. The polynucleotide molecule according to 80, wherein the polynucleotide molecule encoding the Tetanus toxin substrate cleavage site comprises at least six consecutive residues of a VAMP, said six consecutive residues comprising Gln-Phe.

82. The polynucleotide molecule according to 80, wherein the polynucleotide molecule encoding the modified Clostridial toxin comprises a polynucleotide molecule encoding a Botulinum toxin enzymatic domain, a polynucleotide molecule encoding a Botulinum toxin translocation domain and a polynucleotide molecule encoding a Botulinum toxin binding domain.

83. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding a modified Botulinum toxin comprises a polynucleotide molecule encoding a BoNT/A enzymatic domain, a polynucleotide molecule encoding a BoNT/A translocation domain and a polynucleotide molecule encoding a BoNT/A binding domain.

86. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding a modified Botulinum toxin comprises a polynucleotide molecule encoding a BoNT/B enzymatic domain, a polynucleotide molecule encoding a BoNT/B translocation domain and a polynucleotide molecule encoding a BoNT/B binding domain.

87. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding a modified Botulinum toxin comprises a polynucleotide molecule encoding a BoNT/C1 enzymatic domain, a polynucleotide molecule encoding a BoNT/C1 translocation domain and a polynucleotide molecule encoding a BoNT/C1 binding domain.

88. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding a modified Botulinum toxin comprises a polynucleotide molecule encoding a BoNT/D enzymatic domain, a polynucleotide molecule encoding a BoNT/D translocation domain and a polynucleotide molecule encoding a BoNT/D binding domain.

89. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding a modified Botulinum toxin comprises a polynucleotide molecule encoding a BoNT/E enzymatic domain, a polynucleotide molecule encoding a BoNT/E translocation domain and a polynucleotide molecule encoding a BoNT/E binding domain.

90. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding a modified Botulinum toxin comprises a polynucleotide molecule encoding a BoNT/F enzymatic domain, a polynucleotide molecule encoding a BoNT/F translocation domain and a polynucleotide molecule encoding a BoNT/F binding domain.

91. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding a modified Botulinum toxin comprises a polynucleotide molecule encoding a BoNT/G enzymatic domain, a polynucleotide molecule encoding a BoNT/G translocation domain and a polynucleotide molecule encoding a BoNT/G binding domain.

92. The polynucleotide molecule according to 53, wherein the polynucleotide molecule encoding a modified Clostridial toxin comprises a polynucleotide molecule encoding a Tetanus toxin enzymatic domain, a polynucleotide molecule encoding a Tetanus toxin translocation domain and a polynucleotide molecule encoding a Tetanus toxin binding domain.

93. A method of producing a modified Clostridial toxin comprising the step of expressing a modified Clostridial toxin encoded by a polynucleotide molecule in a cell, wherein the modified Clostridial toxin is defined by any one of 46-92.

94. A methods of producing a modified Clostridial toxin comprising the steps of a) introducing into a cell a polynucleotide molecule encoding a modified Clostridial toxin as defined in any one of 46-92; and b) expressing the modified Clostridial toxin encoded by the polynucleotide molecule.

95. A modified Clostridial toxin comprising:

a) a Clostridial toxin substrate cleavage site; b) a di-chain loop region c) a Clostridial toxin enzymatic domain; d) a Clostridial toxin translocation domain; and e) a Clostridial toxin cell binding domain;

wherein the Clostridial toxin substrate cleavage site is located within the di-chain loop region.

EXAMPLES

[0291] The following non-limiting examples are provided for illustrative purposes only in order to facilitate a more complete understanding of disclosed embodiments and are in no way intended to limit any of the embodiments disclosed in the present specification.

Example 1 Construction of modified Clostridial toxins comprising a BoNT/A substrate cleavage site

[0292] This example illustrates how to make a modified Clostridial toxin comprising a BoNT/A substrate cleavage site located in the di-chain loop region of the toxin.

[0293] A polynucleotide molecule (SEQ ID NO: 214) based on BoNT/A-A17 (SEQ ID NO: 203) is synthesized using standard procedures (BlueHeron ^® Biotechnology, Bothell, WA). BoNT/A-A17 is a BoNT/A modified to comprise a 17 amino acid Clostridial toxin substrate cleavage site that can be cleaved by BoNT/A. Oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate PUCBHB1/BONT/A-A17. The synthesized polynucleotide molecule is verified by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA).

[0294] If desired, an expression optimized polynucleotide molecule (SEQ ID NO: 225) based on BoNT/A-A17 (SEQ ID NO: 203) can be synthesized in order to improve expression in an Escherichia coli strain. The polynucleotide molecule encoding the BoNT/A-A17 can be modified to 1) contain synonymous codons typically present in native polynucleotide molecules of an Escherichia coli strain; 2) contain a G+C content that more closely matches the average G+C content of native polynucleotide molecules found in an Escherichia coli strain; 3) reduce polyribonucleotide regions found within the polynucleotide molecule; and/or 4) eliminate internal regulatory or structural sites found within the polynucleotide molecule, see, e.g., Lance E. Steward et al. Optimizing Expression of Active Botulinum Toxin Type E, International Patent Publication No. WO 2006/011966 (Feb. 2, 2006); Lance E. Steward et al. Optimizing Expression of Active Botulinum Toxin Type A, International Patent Publication No. WO 2006/017749 (Feb. 16, 2006), the contents of all of which are hereby incorporated by reference in their entirety. Once sequence optimization is complete, oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate pUCBHBI/BoNT/A-A^. The synthesized polynucleotide molecule is verified

by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA). If so desired, optimization to a different organism, such as, e.g., a yeast strain, an insect cell-line or a mammalian cell line, can be done, see, e.g., Steward, supra, International Patent Publication No. WO 2006/011966 (Feb. 2, 2006); and Steward, supra, International Patent Publication No. WO 2006/017749 (Feb. 16, 2006).

[0295] A similar cloning strategy is used to make pUCBHBI cloning constructs comprising the polynucleotide molecule of SEQ ID NO: 215 or SEQ ID NO: 226 encoding B0NT/A-A8 of SEQ ID NO: 204. B0NT/A-A8 is a BoNT/A modified to comprise an eight amino acid Clostridial toxin substrate cleavage site that can be cleaved by BoNT/A. In addition, one skilled in the art can modify Clostridial toxins, such as, e.g., BoNT/B, BoNT/C1 , BoNT/D. BoNT/E, BoNT/F, BoNT/G and TeNT, using similar cloning strategy described above so that these toxins possess a BoNT/A substrate cleavage site in the di- chain loop region of the toxin.

[0296] To construct pET29/BoNT/A-A17, a pUCBHB1/BoNT/A-A17 construct is digested with restriction endonucleases that 1) excise the insert comprising the open reading frame encoding BoNT/A-A17, such as, e.g., the polynucleotide molecule of SEQ ID NO: 225; and 2) enable this insert to be operably-linked to a pET29 vector (EMD Biosciences-Novagen, Madison, Wl). This insert is subcloned using a T4 DNA ligase procedure into a pET29 vector that is digested with appropriate restriction endonucleases to yield pET29/BoNT/A-A17. The ligation mixture is transformed into chemically competent E. coli DH5α cells (Invitrogen, Inc, Carlsbad, CA) using a heat shock method, plated on 1.5% Luria-Bertani agar plates (pH 7.0) containing 50 μg/mL of Kanamycin, and placed in a 37 ⁰ C incubator for overnight growth. Bacteria containing expression constructs are identified as Kanamycin resistant colonies. Candidate constructs are isolated using an alkaline lysis plasmid mini-preparation procedure and analyzed by restriction endonuclease digest mapping to determine the presence and orientation of the insert. This cloning strategy yielded a pET29 expression construct comprising the polynucleotide molecule of SEQ ID NO: 225 encoding the BoNT/A-A17 of SEQ ID NO: 203 operably-linked to a carboxyl terminal polyhistidine affinity binding peptide (FIG. 7).

[0297] A similar cloning strategy can be used to make pET29 expression constructs comprising the polynucleotide molecule of SEQ ID NO: 214 encoding BoNT/A-A17 of SEQ ID NO: 203; or the polynucleotide molecules of SEQ ID NO: 215 or SEQ ID NO: 226 encoding B0NT/A-A8 of SEQ ID NO: 204.

Example 2 Construction of modified Clostridial toxins comprising both a BoNT/B and a TeNT substrate cleavage site

[0298] This example illustrates how to make a modified Clostridial toxin comprising both a BoNT/B substrate cleavage site and a TeNT substrate cleavage site located in the di-chain loop region of the toxin.

[0299] A polynucleotide molecule (SEQ ID NO: 216) based on BoNT/A-BT35 (SEQ ID NO: 205) is synthesized using standard procedures (BlueHeron ^® Biotechnology, Bothell, WA). BoNT/A-BT35 is a BoNT/A modified to comprise a 35 amino acid Clostridial toxin substrate cleavage site that can be cleaved by either BoNT/B or TeNT. Oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate PUCBHB1/BONT/A-BT35. The synthesized polynucleotide molecule is verified by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA).

[0300] If desired, an expression optimized polynucleotide molecule (SEQ ID NO: 227) based on BoNT/A-BT35 (SEQ ID NO: 205) can be synthesized in order to improve expression in an Escherichia coli strain. The polynucleotide molecule encoding the BoNT/A-BT35 can be modified to 1) contain synonymous codons typically present in native polynucleotide molecules of an Escherichia coli strain; 2) contain a G+C content that more closely matches the average G+C content of native polynucleotide molecules found in an Escherichia coli strain; 3) reduce polyribonucleotide regions found within the polynucleotide molecule; and/or 4) eliminate internal regulatory or structural sites found within the polynucleotide molecule, see, e.g., Lance E. Steward ef a/. Optimizing Expression of Active Botulinum Toxin Type E, International Patent Publication No. WO 2006/011966 (Feb. 2, 2006); Lance E. Steward et al. Optimizing Expression of Active Botulinum Toxin Type A, International Patent Publication No. WO 2006/017749 (Feb. 16, 2006). Once sequence optimization is complete, oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate PUCBHB1/BONT/A-BT35. The synthesized polynucleotide molecule is verified by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA). If so desired, optimization to a different organism, such as, e.g., a yeast strain, an insect cell-line or a mammalian cell line, can be done, see, e.g., Steward, supra, International Patent Patent Publication No. WO 2006/011966 (Feb. 2, 2006); and Steward, supra, International Patent Publication No. WO 2006/017749 (Feb. 16, 2006).

[0301] A similar cloning strategy is used to make pUCBHBI cloning constructs comprising the polynucleotide molecule of SEQ ID NO: 217 or SEQ ID NO: 228 encoding B0NT/A-BT8 of SEQ ID NO:

206. BoNT/A-B8 is a BoNT/A modified to comprise an eight amino acid Clostridial toxin substrate cleavage site that can be cleaved by either BoNT/B or TeNT. In addition, one skilled in the art can modify Clostridial toxins, such as, e.g., BoNT/B, B0NT/CI , BoNT/D. BoNT/E, BoNT/F, BoNT/G and TeNT, using similar cloning strategy described above so that these toxins possess both a BoNT/B substrate cleavage site and a TeNT substrate cleavage site in the di-chain loop region of the toxin.

[0302] To construct pET29/BoNT/A-BT35, a pUCBHB1/BoNT/A-BT35 construct is digested with restriction endonucleases that 1) excise the insert comprising the open reading frame encoding BoNT/A- BT35, such as, e.g., the polynucleotide molecule of SEQ ID NO: 227; and 2) enable this insert to be operably-linked to a pET29 vector (EMD Biosciences-Novagen, Madison, Wl). This insert is subcloned using a T4 DNA ligase procedure into a pET29 vector that is digested with appropriate restriction endonucleases to yield pET29/BoNT/A-BT35. The ligation mixture is transformed into chemically competent E. coli DH5α cells (Invitrogen, Inc, Carlsbad, CA) using a heat shock method, plated on 1.5% Luria-Bertani agar plates (pH 7.0) containing 50 μg/mL of Kanamycin, and placed in a 37 ⁰ C incubator for overnight growth. Bacteria containing expression constructs are identified as Kanamycin resistant colonies. Candidate constructs are isolated using an alkaline lysis plasmid mini-preparation procedure and analyzed by restriction endonuclease digest mapping to determine the presence and orientation of the insert. This cloning strategy yielded a pET29 expression construct comprising the polynucleotide molecule of SEQ ID NO: 227 encoding the BoNT/A-BT35 of SEQ ID NO: 205 operably-linked to a carboxyl terminal polyhistidine affinity binding peptide (FIG. 8).

[0303] A similar cloning strategy can be used to make pET29 expression constructs comprising the polynucleotide molecule of SEQ ID NO: 216 encoding BoNT/A-BT35 of SEQ ID NO: 205; or the polynucleotide molecules of SEQ ID NO: 217 or SEQ ID NO: 228 encoding B0NT/A-BT8 of SEQ ID NO: 206.

Example 3 Construction of modified Clostridial toxins comprising a BoNT/C1 substrate cleavage site

[0304] This example illustrates how to make a modified Clostridial toxin comprising a BoNT/C1 substrate cleavage site located in the di-chain loop region of the toxin.

[0305] A polynucleotide molecule (SEQ ID NO: 218) based on BoNT/A-Csyn8 (SEQ ID NO: 207) is synthesized using standard procedures (BlueHeron ^® Biotechnology, Bothell, WA). BoNT/A-Csyn8 is a BoNT/A modified to comprise an eight amino acid Clostridial toxin substrate cleavage site that can be cleaved by BoNT/C1. Oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate

pUCBHBI/BoNT/A-Csynδ. The synthesized polynucleotide molecule is verified by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA).

[0306] If desired, an expression optimized polynucleotide molecule (SEQ ID NO: 229) based on BoNT/A-Csyn8 (SEQ ID NO: 207) can be synthesized in order to improve expression in an Escherichia co// strain. The polynucleotide molecule encoding the BoNT/A-Csyn8 can be modified to 1) contain synonymous codons typically present in native polynucleotide molecules of an Escherichia coli strain; 2) contain a G+C content that more closely matches the average G+C content of native polynucleotide molecules found in an Escherichia coli strain; 3) reduce polymononucleotide regions found within the polynucleotide molecule; and/or 4) eliminate internal regulatory or structural sites found within the polynucleotide molecule, see, e.g., Lance E. Steward et al. Optimizing Expression of Active Botulinum Toxin Type E, International Patent Publication No. WO 2006/011966 (Feb. 2, 2006); Lance E. Steward et al. Optimizing Expression of Active Botulinum Toxin Type A, International Patent Publication No. WO 2006/017749 (Feb. 16, 2006). Once sequence optimization is complete, oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate pUCBHBI/BoNT/A-Csynβ. The synthesized polynucleotide molecule is verified by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA). If so desired, optimization to a different organism, such as, e.g., a yeast strain, an insect cell-line or a mammalian cell line, can be done, see, e.g., Steward, supra, International Patent Publication No. WO 2006/011966 (Feb. 2, 2006); and Steward, supra, International Patent Publication No. WO 2006/017749 (Feb. 16, 2006).

[0307] A similar cloning strategy is used to make pUCBHBI cloning constructs comprising the polynucleotide molecule of SEQ ID NO: 219 or SEQ ID NO: 230 encoding BoNT/A-Csnp8 of SEQ ID NO: 208. BoNT/A-Csnp8 is a BoNT/A modified to comprise an eight amino acid Clostridial toxin substrate cleavage site that can be cleaved by BoNT/C1. In addition, one skilled in the art can modify Clostridial toxins, such as, e.g., BoNT/B, BoNT/C1 , BoNT/D. BoNT/E, BoNT/F, BoNT/G and TeNT, using similar cloning strategy described above so that these toxins possess a B0NT/CI substrate cleavage site in the di-chain loop region of the toxin.

[0308] To construct pET29/BoNT/A-Csyn8, a pUCBHBI /BoNT/A-Csyn8 construct is digested with restriction endonucleases that 1) excise the insert comprising the open reading frame encoding BoNT/A- Csynβ, such as, e.g., the polynucleotide molecule of SEQ ID NO: 229; and 2) enable this insert to be operably-linked to a pET29 vector (EMD Biosciences-Novagen, Madison, Wl). This insert is subcloned using a T4 DNA ligase procedure into a pET29 vector that is digested with appropriate restriction

endonucleases to yield pET29/BoNT/A-Csyn8. The ligation mixture is transformed into chemically competent E. coli DH5α cells (Invitrogen, Inc, Carlsbad, CA) using a heat shock method, plated on 1.5% Luria-Bertani agar plates (pH 7.0) containing 50 μg/mL of Kanamycin, and placed in a 37 ⁰ C incubator for overnight growth. Bacteria containing expression constructs are identified as Kanamycin resistant colonies. Candidate constructs are isolated using an alkaline lysis plasmid mini-preparation procedure and analyzed by restriction endonuclease digest mapping to determine the presence and orientation of the insert. This cloning strategy yielded a pET29 expression construct comprising the polynucleotide molecule of SEQ ID NO: 229 encoding the BoNT/A-Csyn8 of SEQ ID NO: 207 operably-linked to a carboxyl terminal polyhistidine affinity binding peptide (FIG. 9).

[0309] A similar cloning strategy can be used to make pET29 expression constructs comprising the polynucleotide molecule of SEQ ID NO: 218 encoding BoNT/A-A17 of SEQ ID NO: 207; or the polynucleotide molecules of SEQ ID NO: 219 or SEQ ID NO: 230 encoding BoNT/A-Csyn8 of SEQ ID NO: 208.

Example 4

Construction of modified Clostridial toxins comprising a BoNT/D substrate cleavage site, a BoNT/F substrate cleavage site or both a BoNT/D and a BoNT/F substrate cleavage site

[0310] This example illustrates how to make a modified Clostridial toxin comprising a BoNT/D substrate cleavage site located in the di-chain loop region of the toxin, a BoNT/F substrate cleavage site located in the di-chain loop region of the toxin or both a BoNT/D substrate cleavage site and a BoNT/F substrate cleavage site located in the di-chain loop region of the toxin.

[0311] A polynucleotide molecule (SEQ ID NO: 220) based on BoNT/A-DF39 (SEQ ID NO: 209) is synthesized using standard procedures (BlueHeron ^® Biotechnology, Bothell, WA). BoNT/A-DF39 is a BoNT/A modified to comprise a 39 amino acid Clostridial toxin substrate cleavage site that can be cleaved by either BoNT/D or BoNT/F. Oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate PUCBHB1/BONT/A-DF39. The synthesized polynucleotide molecule is verified by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA).

[0312] If desired, an expression optimized polynucleotide molecule (SEQ ID NO: 231) based on BoNT/A-DF39 (SEQ ID NO: 209) can be synthesized in order to improve expression in an Escherichia coli strain. The polynucleotide molecule encoding the BoNT/A-DF39 can be modified to 1) contain synonymous codons typically present in native polynucleotide molecules of an Escherichia coli strain; 2)

contain a G+C content that more closely matches the average G+C content of native polynucleotide molecules found in an Escherichia coli strain; 3) reduce polymononucleotide regions found within the polynucleotide molecule; and/or 4) eliminate internal regulatory or structural sites found within the polynucleotide molecule, see, e.g., Lance E. Steward ef a/. Optimizing Expression of Active Botulinum ^" Toxin Type E, International Patent Publication No. WO 2006/011966 (Feb. 2, 2006); Lance E. Steward et al. Optimizing Expression of Active Botulinum Toxin Type A ₁ International Patent Publication No. WO 2006/017749 (Feb. 16, 2006). Once sequence optimization is complete, oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate PUCBHB1/BONT/A-DF39. The synthesized polynucleotide molecule is verified by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA). If so desired, optimization to a different organism, such as, e.g., a yeast strain, an insect cell-line or a mammalian cell line, can be done, see, e.g., Steward, supra, International Patent Publication No. WO 2006/011966 (Feb. 2, 2006); and Steward, supra, International Patent Publication No. WO 2006/017749 (Feb. 16, 2006).

[0313] A similar cloning strategy is used to make pUCBHBI cloning constructs comprising the polynucleotide molecule of SEQ ID NO: 221 or SEQ ID NO: 232 encoding BoNT/A-Dδ of SEQ ID NO: 210; or constructs comprising the polynucleotide molecule of SEQ ID NO: 223 or SEQ ID NO: 234 encoding BoNT/A-Fδ of SEQ ID NO: 212 . BoNT/A-Dδ is a BoNT/A modified to comprise an eight amino acid Clostridial toxin substrate cleavage site that can be cleaved by BoNT/D. BoNT/A-Fβ is a BoNT/A modified to comprise an eight amino acid Clostridial toxin substrate cleavage site that can be cleaved by BoNT/F. In addition, one skilled in the art can modify Clostridial toxins, such as, e.g., BoNT/B, BoNT/CI , BoNT/D. BoNT/E, BoNT/F, BoNT/G and TeNT, using similar cloning strategy described above so that these toxins comprise a BoNT/D substrate cleavage site in the di-chain loop region of the toxin, comprise a BoNT/B substrate cleavage site in the di-chain loop region of the toxin or comprise both a BoNT/D substrate cleavage site and a BoNT/F substrate cleavage site in the di-chain loop region of the toxin.

[0314] To construct pET29/BoNT/A-DF39, a pUCBHBI /BoNT/A-DF39 construct is digested with restriction endonucleases that 1) excise the insert comprising the open reading frame encoding BoNT/A- DF39, such as, e.g., the polynucleotide molecule of SEQ ID NO: 231 ; and 2) enable this insert to be operably-linked to a pET29 vector (EMD Biosciences-Novagen, Madison, Wl). This insert is subcloned using a T4 DNA ligase procedure into a pET29 vector that is digested with appropriate restriction endonucleases to yield pET29/BoNT/A-DF39. The ligation mixture is transformed into chemically competent E. coli DH5α cells (Invitrogen, Inc, Carlsbad, CA) using a heat shock method, plated on 1.5% Luria-Bertani agar plates (pH 7.0) containing 50 μg/mL of Kanamycin, and placed in a 37 ⁰ C incubator for overnight growth. Bacteria containing expression constructs are identified as Kanamycin resistant

colonies. Candidate constructs are isolated using an alkaline lysis plasmid mini-preparation procedure and analyzed by restriction endonuclease digest mapping to determine the presence and orientation of the insert. This cloning strategy yielded a pET29 expression construct comprising the polynucleotide molecule of SEQ ID NO: 231 encoding the BoNT/A-DF39 of SEQ ID NO: 209 operably-linked to a carboxyl terminal polyhistidine affinity binding peptide (FIG. 10).

[0315] A similar cloning strategy can be used to make pET29 expression constructs comprising the polynucleotide molecule of SEQ ID NO: 220 encoding BoNT/A-DF39 of SEQ ID NO: 209; the polynucleotide molecules of SEQ ID NO: 221 or SEQ ID NO: 232 encoding BoNT/A-Dδ of SEQ ID NO: 210; or the polynucleotide molecules of SEQ ID NO: 223 or SEQ ID NO: 234 encoding BoNT/A-Fδ of SEQ ID NO: 212.

Example 5 Construction of modified Clostridial toxins comprising a BoNT/E substrate cleavage site

[0316] This example illustrates how to make a modified Clostridial toxin comprising a BoNT/E substrate cleavage site located in the di-chain loop region of the toxin.

[0317] A polynucleotide molecule (SEQ ID NO: 222) based on BoNT/A-Eδ (SEQ ID NO: 211) is synthesized using standard procedures (BlueHeron ^® Biotechnology, Bothell, WA). B0NT/A-E8 is a BoNT/A modified to comprise an eight amino acid Clostridial toxin substrate cleavage site that can be cleaved by BoNT/E. Oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate pUCBHBI/BoNT/A-Eδ. The synthesized polynucleotide molecule is verified by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA).

[0318] If desired, an expression optimized polynucleotide molecule (SEQ ID NO: 233) based on BoNT/A-Eδ (SEQ ID NO: 211) can be synthesized in order to improve expression in an Escherichia coli strain. The polynucleotide molecule encoding the BoNT/A-Eδ can be modified to 1) contain synonymous codons typically present in native polynucleotide molecules of an Escherichia coli strain; 2) contain a G+C content that more closely matches the average G+C content of native polynucleotide molecules found in an Escherichia coli strain; 3) reduce polymononucleotide regions found within the polynucleotide molecule; and/or 4) eliminate internal regulatory or structural sites found within the polynucleotide molecule, see, e.g., Lance E. Steward et al. Optimizing Expression of Active Botulinum Toxin Type E, International Patent Publication No. WO 2006/011966 (Feb. 2, 2006); Lance E. Steward et al. Optimizing Expression of Active Botulinum Toxin Type A, International Patent Publication No. WO 2006/017749

(Feb. 16, 2006). Once sequence optimization is complete, oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate pUCBHB1/BoNT/A-E8. The synthesized polynucleotide molecule is verified by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA). If so desired, optimization to a different organism, such as, e.g., a yeast strain, an insect cell-line or a mammalian cell line, can be done, see, e.g., Steward, supra, International Patent Publication No. WO 2006/011966 (Feb. 2, 2006); and Steward, supra, International Patent Publication No. WO 2006/017749 (Feb. 16, 2006).

[0319] One skilled in the art can modify Clostridial toxins, such as, e.g., BoNT/B, BoNT/C1 , BoNT/D. BoNT/E, BoNT/F, BoNT/G and TeNT, using similar cloning strategy described above so that these toxins possess a BoNT/E substrate cleavage site in the di-chain loop region of the toxin.

[0320] To construct pET29/BoNT/A-E8, a pUCBHB1/BoNT/A-E8 construct is digested with restriction endonucleases that 1) excise the insert comprising the open reading frame encoding B0NT/A-E8, such as, e.g., the polynucleotide molecule of SEQ ID NO: 233; and 2) enable this insert to be operably-linked to a pET29 vector (EMD Biosciences-Novagen, Madison, Wl). This insert is subcloned using a T4 DNA ligase procedure into a pET29 vector that is digested with appropriate restriction endonucleases to yield pET29/BoNT/A-E8. The ligation mixture is transformed into chemically competent E. coli DH5α cells (Invitrogen, Inc, Carlsbad, CA) using a heat shock method, plated on 1.5% Luria-Bertani agar plates (pH 7.0) containing 50 μg/mL of Kanamycin, and placed in a 37 ⁰ C incubator for overnight growth. Bacteria containing expression constructs are identified as Kanamycin resistant colonies. Candidate constructs are isolated using an alkaline lysis plasmid mini-preparation procedure and analyzed by restriction endonuclease digest mapping to determine the presence and orientation of the insert. This cloning strategy yielded a pET29 expression construct comprising the polynucleotide molecule of SEQ ID NO: 233 encoding the B0NT/A-E8 of SEQ ID NO: 211 operably-linked to a carboxyl terminal polyhistidine affinity binding peptide (FIG. 11).

Example 6 Construction of modified Clostridial toxins comprising a BoNT/G substrate cleavage site

[0321] This example illustrates how to make a modified Clostridial toxin comprising a BoNT/G substrate cleavage site located in the di-chain loop region of the toxin.

[0322] A polynucleotide molecule (SEQ ID NO: 224) based on B0NT/A-G8 (SEQ ID NO: 213) is synthesized using standard procedures (BlueHeron ^® Biotechnology, Bothell, WA). B0NT/A-G8 is a BoNT/A modified to comprise an eight amino acid Clostridial toxin substrate cleavage site that can be

cleaved by BoNT/G. Oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate pUCBHBI /B0NT/A-G8. The synthesized polynucleotide molecule is verified by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA).

[0323] If desired, an expression optimized polynucleotide molecule (SEQ ID NO: 235) based on BoNT/A-Eδ (SEQ ID NO: 213) can be synthesized in order to improve expression in an Escherichia coli strain. The polynucleotide molecule encoding the B0NT/A-D8 can be modified to 1) contain synonymous codons typically present in native polynucleotide molecules of an Escherichia coli strain; 2) contain a G+C content that more closely matches the average G+C content of native polynucleotide molecules found in an Escherichia coli strain; 3) reduce polymononucleotide regions found within the polynucleotide molecule; and/or 4) eliminate internal regulatory or structural sites found within the polynucleotide molecule, see, e.g., Lance E. Steward et at. Optimizing Expression of Active Botulinum Toxin Type E, International Patent Publication No. WO 2006/011966 (Feb. 2, 2006); Lance E. Steward et al. Optimizing Expression of Active Botulinum Toxin Type A, International Patent Publication No. WO 2006/017749 (Feb. 16, 2006). Once sequence optimization is complete, oligonucleotides of 20 to 50 bases in length are synthesized using standard phosphoramidite synthesis. These oligonucleotides are hybridized into double stranded duplexes that are ligated together to assemble the full-length polynucleotide molecule. This polynucleotide molecule is cloned using standard molecular biology methods into a pUCBHBI vector at the Sma\ site to generate pUCBHB1/BoNT/A-G8. The synthesized polynucleotide molecule is verified by sequencing using Big Dye Terminator™ Chemistry 3.1 (Applied Biosystems, Foster City, CA) and an ABI 3100 sequencer (Applied Biosystems, Foster City, CA). If so desired, optimization to a different organism, such as, e.g., a yeast strain, an insect cell-line or a mammalian cell line, can be done, see, e.g., Steward, supra, International Patent Publication No. WO 2006/011966 (Feb. 2, 2006); and Steward, supra, International Patent Publication No. WO 2006/017749 (Feb. 16, 2006).

[0324] One skilled in the art can modify Clostridial toxins, such as, e.g., BoNT/B, BoNT/C1 , BoNT/D. BoNT/E, BoNT/F, BoNT/G and TeNT, using similar cloning strategy described above so that these toxins possess a BoNT/G substrate cleavage site in the di-chain loop region of the toxin.

[0325] To construct pET29/BoNT/A-G8, a pUCBHBI /B0NT/A-G8 construct is digested with restriction endonucleases that 1) excise the insert comprising the open reading frame encoding B0NT/A-E8, such as, e.g., the polynucleotide molecule of SEQ ID NO: 235; and 2) enable this insert to be operably-linked to a pET29 vector (EMD Biosciences-Novagen, Madison, Wl). This insert is subcloned using a T4 DNA ligase procedure into a pET29 vector that is digested with appropriate restriction endonucleases to yield pET29/BoNT/A-G8. The ligation mixture is transformed into chemically competent E. coli DH5α cells

(Invitrogen, Inc, Carlsbad, CA) using a heat shock method, plated on 1.5% Luria-Bertani agar plates (pH 7.0) containing 50 μg/mL of Kanamycin, and placed in a 37 ⁰ C incubator for overnight growth. Bacteria containing expression constructs are identified as Kanamycin resistant colonies. Candidate constructs are isolated using an alkaline lysis plasm id mini-preparation procedure and analyzed by restriction endonuclease digest mapping to determine the presence and orientation of the insert. This cloning strategy yielded a pET29 expression construct comprising the polynucleotide molecule of SEQ ID NO: 235 encoding the BoNT/A-Gδ of SEQ ID NO: 213 operably-linked to a carboxyl terminal polyhistidine affinity binding peptide (FIG. 12).

Example 7 Expression of Modified Clostridial Toxins in a Bacterial Cell

[0326] The following example illustrates a procedure useful for expressing any of the modified Clostridial toxins disclosed in the present specification in a bacterial cell.

[0327] An expression construct, such as, e.g., pET29/BoNT/A-ED-PAR1Tb, pET29/BoNT/A-TD-PAR1Tb or pET29/BoNT/A-BD-PAR1Tb, see, e.g., Examples 1 , 2 and 3, is introduced into chemically competent E. coli BL21 (DE3) cells (Invitrogen, Inc, Carlsbad, CA) using a heat-shock transformation protocol. The heat-shock reaction is plated onto 1.5% Luria-Bertani agar plates (pH 7.0) containing 50 μg/mL of Kanamycin and is placed in a 37 ⁰ C incubator for overnight growth. Kanamycin-resistant colonies of transformed E. coli containing the expression construct, such as, e.g., pET29/BoNT/A-A17, pET29/BoNT/A-BT35, pET29/BoNT/A-Csyn8, pET29/BoNT/A-DF39, pET29/BoNT/A-E8 or pET29/BoNT/A-G8, are used to inoculate a baffled flask containing 3.0 mL of PA-0.5G media containing 50 μg/mL of Kanamycin which is then placed in a 37 ⁰ C incubator, shaking at 250 rpm, for overnight growth. The resulting overnight starter culture is in turn used to inoculate a 3 L baffled flask containing ZYP-5052 autoinducing media containing 50 μg/mL of Kanamycin at a dilution of 1 :1000. Culture volumes ranged from about 600 mL (20% flask volume) to about 750 mL (25% flask volume). These cultures are grown in a 37 ⁰ C incubator shaking at 250 rpm for approximately 5.5 hours and are then transferred to a 16 °C ^[ incubator shaking at 250 rpm for overnight expression. Cells are harvested by centrifugation (4,000 rpm at 4 ⁰ C for 20-30 minutes) and are used immediately, or stored dry at -80 ⁰ C until needed.

Example 8 Purification and Quantification of Modified Clostridial Toxins

[0328] The following example illustrates methods useful for purification and quantification of any modified Clostridial toxins disclosed in the present specification.

[0329] For immobilized metal affinity chromatography (IMAC) protein purification, E. coli BL21 (DE3) cell pellets used to express a modified Clostridial toxin, as described in Example 4, are resuspended in Column Binding Buffer (25 mM λ/-(2-hydroxyethyl) piperazine-λ/-(2-ethanesulfonic acid) (HEPES), pH 7.8; 500 mM sodium chloride; 10 mM imidazole; 2x Protease Inhibitor Cocktail Set III (EMD Biosciences- Calbiochem, San Diego CA); 5 units/mL of Benzonase (EMD Biosciences-Novagen, Madison, Wl); 0.1% (v/v) Triton-X ^® 100, 4-octylphenol polyethoxylate; 10% (v/v) glycerol), and then are transferred to a cold Oakridge centrifuge tube. The cell suspension is sonicated on ice (10-12 pulses of 10 seconds at 40% amplitude with 60 seconds cooling intervals on a Branson Digital Sonifier) in order to lyse the cells and then is centrifuged (16,000 rpm at 4 ⁰ C for 20 minutes) to clarify the lysate. An immobilized metal affinity chromatography column is prepared using a 20 mL Econo-Pac column support (Bio-Rad Laboratories, Hercules, CA) packed with 2.5-5.0 mL of TALON™ SuperFlow Co ²⁺ affinity resin (BD Biosciences- Clontech, Palo Alto, CA), which is then equilibrated by rinsing with 5 column volumes of deionized, distilled water, followed by 5 column volumes of Column Binding Buffer. The clarified lysate is applied slowly to the equilibrated column by gravity flow (approximately 0.25-0.3 mL/minute). The column is then washed with 5 column volumes of Column Wash Buffer (λ/-(2-hydroxyethyl) piperazine-λ/'-(2- ethanesulfonic acid) (HEPES), pH 7.8; 500 mM sodium chloride; 10 mM imidazole; 0.1% (v/v) Triton-X ^® 100, 4-octylphenol polyethoxylate; 10% (v/v) glycerol). The Clostridial toxin is eluted with 20-30 mL of Column Elution Buffer (25 mM λ/-(2-hydroxyethyl) piperazine-λ/'-(2-ethanesulfonic acid) (HEPES), pH 7.8; 500 mM sodium chloride; 500 mM imidazole; 0.1% (v/v) Triton-X ^® 100, 4-octylphenol polyethoxylate; 10% (v/v) glycerol) and is collected in approximately twelve 1 mL fractions. The amount of Clostridial toxin contained in each elution fraction is determined by a Bradford dye assay. In this procedure, 20 μL aliquots of each 1.0 mL fraction is combined with 200 μL of Bio-Rad Protein Reagent (Bio-Rad Laboratories, Hercules, CA), diluted 1 to 4 with deionized, distilled water, and then the intensity of the colorimetric signal is measured using a spectrophotometer. The five fractions with the strongest signal are considered the elution peak and are combined together. Total protein yield is determined by estimating the total protein concentration of the pooled peak elution fractions using bovine gamma globulin as a standard (Bio-Rad Laboratories, Hercules, CA).

[0330] For purification of a modified Clostridial toxin using a FPLC desalting column, a HiPrep™ 26/10 size exclusion column (Amersham Biosciences, Piscataway, NJ) is pre-equilibrated with 80 mL of 4 ^C C Column Buffer (50 mM sodium phosphate, pH 6.5). After the column is equilibrated, a Clostridial toxin sample is applied to the size exclusion column with an isocratic mobile phase of 4 ⁰ C Column Buffer and at a flow rate of 10 mL/minute using a BioLogic DuoFlow chromatography system (Bio-Rad Laboratories, Hercules, CA). The desalted modified Clostridial toxin sample is collected as a single fraction of approximately 7-12 mL.

[0331] For purification of a modified Clostridial toxin using a FPLC ion exchange column, a Clostridial toxin sample that has been desalted following elution from an IMAC column is applied to a 1 mL Q1™ anion exchange column (Bio-Rad Laboratories, Hercules, CA) using a BioLogic DuoFlow chromatography

system (Bio-Rad Laboratories, Hercules, CA). The sample is applied to the column in 4 ^C C Column Buffer (50 mM sodium phosphate, pH 6.5) and is eluted by linear gradient with 4 ⁰ C Elution Buffer (50 mM sodium phosphate, 1 M sodium chloride, pH 6.5) as follows: step 1 , 5.0 mL of 5% Elution Buffer at a flow rate of 1 mL/minute; step 2, 20.0 mL of 5-30% Elution Buffer at a flow rate of 1 mL/minute; step 3, 2.0 mL of 50% Elution Buffer at a flow rate of 1.0 mL/minute; step 4, 4.0 mL of 100% Elution Buffer at a flow rate of 1.0 mL/minute; and step 5, 5.0 mL of 0% Elution Buffer at a flow rate of 1.0 mL/minute. Elution of Clostridial toxin from the column is monitored at 280, 260, and 214 nm, and peaks absorbing above a minimum threshold (0.01 au) at 280 nm are collected. Most of the Clostridial toxin will elute at a sodium chloride concentration of approximately 100 to 200 mM. Average total yields of Clostridial toxin will be determined by a Bradford assay.

[0332] Expression of a modified Clostridial toxin is analyzed by polyacrylamide gel electrophoresis. Samples purified using the procedure described above are added to 2x LDS Sample Buffer (Invitrogen, Inc, Carlsbad, CA) and are separated by MOPS polyacrylamide gel electrophoresis using NuPAGE ^® Novex 4-12% Bis-Tris precast polyacrylamide gels (Invitrogen, Inc, Carlsbad, CA) under denaturing, reducing conditions. Gels are stained with SYPRO ^® Ruby (Bio-Rad Laboratories, Hercules, CA) and the separated polypeptides are imaged using a Fluor-S MAX Multilmager (Bio-Rad Laboratories, Hercules, CA) for quantification of Clostridial toxin expression levels. The size and amount of the Clostridial toxin is determined by comparison to MagicMark™ protein molecular weight standards (Invitrogen, Inc, Carlsbad, CA).

[0333] Expression of modified Clostridial toxin is also analyzed by Western blot analysis. Protein samples purified using the procedure described above are added to 2x LDS Sample Buffer (Invitrogen, Inc, Carlsbad, CA) and are separated by MOPS polyacrylamide gel electrophoresis using NuPAGE ^® Novex 4-12% Bis-Tris precast polyacrylamide gels (Invitrogen, Inc, Carlsbad, CA) under denaturing, reducing conditions. Separated polypeptides are transferred from the gel onto polyvinylidene fluoride (PVDF) membranes (Invitrogen, Inc, Carlsbad, CA) by Western blotting using a Trans-Blot ^® SD semi-dry electrophoretic transfer cell apparatus (Bio-Rad Laboratories, Hercules, CA). PVDF membranes are blocked by incubating at room temperature for 2 hours in a solution containing 25 mM Tris-Buffered Saline (25 mM 2-amino-2-hydroxymethyl-1 ,3-propanediol hydrochloric acid (Tris-HCI)(pH 7.4), 137 mM sodium chloride, 2.7 mM potassium chloride), 0.1% TWEEN-20 ^® , polyoxyethylene (20) sorbitan monolaureate, 2% bovine serum albumin, 5% nonfat dry milk. Blocked membranes are incubated at 4 ⁰ C for overnight in Tris-Buffered Saline TWEEN-20 ^® (25 mM Tris-Buffered Saline, 0.1% TWEEN-20 ^® , polyoxyethylene (20) sorbitan monolaureate) containing appropriate primary antibodies as a probe. Primary antibody probed blots are washed three times for 15 minutes each time in Tris-Buffered Saline TWEEN-20 ^® . Washed membranes are incubated at room temperature for 2 hours in Tris-Buffered Saline TWEEN-20 ^® containing an appropriate immunoglobulin G antibody conjugated to horseradish peroxidase as a secondary antibody. Secondary antibody-probed blots are washed three times for 15 minutes each time in Tris-Buffered Saline TWEEN-20 ^® . Signal detection of the labeled Clostridial toxin are visualized

using the ECL Plus™ Western Blot Detection System (Amersham Biosciences, Piscataway, NJ) and are imaged with a Typhoon 9410 Variable Mode Imager (Amersham Biosciences, Piscataway, NJ) for quantification of modified Clostridial toxin expression levels.

Example 9 Expression of Modified Clostridial Toxins in a Yeast Cell

[0334] The following example illustrates a procedure useful for expressing any of the modified Clostridial toxins disclosed in the present specification in a yeast cell.

[0335] To construct a suitable yeast expression construct encoding a modified Clostridial toxin, restriction endonuclease sites suitable for cloning an operably linked polynucleotide molecule into a pPIC A vector (Invitrogen, Inc, Carlsbad, CA) are incorporated into the 5'- and 3' ends of the polynucleotide molecule SEQ ID NO: 236 encoding BoNT/A-A17 of SEQ ID NO: 203. This polynucleotide molecule is synthesized and a pUCBHB1/BoNT/A-A17 construct is obtained as described in Example 1. This construct is digested with restriction enzymes that 1) excise the insert containing the open reading frame of SEQ ID NO: 236 encoding BoNT/A-A17; and 2) enable this insert to be operably-linked to a pPIC A vector. This insert is subcloned using a T4 DNA ligase procedure into a pPIC A vector that is digested with appropriate restriction endonucleases to yield pPIC A/BoNT/A-A17. The ligation mixture is transformed into chemically competent E. coli DH5α cells (Invitrogen, Inc, Carlsbad, CA) using a heat shock method, plated on 1.5% low salt Luria-Bertani agar plates (pH 7.5) containing 25 μg/mL of Zeocin™, and placed in a 37 ⁰ C incubator for overnight growth. Bacteria containing expression constructs are identified as Zeocin™ resistant colonies. Candidate constructs are isolated using an alkaline lysis plasmid mini-preparation procedure and analyzed by restriction endonuclease digest mapping to determine the presence and orientation of the insert. This cloning strategy yielded a pPIC A expression construct comprising the polynucleotide molecule of SEQ ID NO: 236 encoding the BoNT/A- A17 of SEQ ID NO: 203 operably-linked to a carboxyl-terminal c-myc and polyhistidine binding peptides (FIG. 13).

[0336] A similar cloning strategy is used to make pPIC A expression constructs encoding B0NT/A-A8 of SEQ ID NO: 204; BoNT/A-BT35 of SEQ ID NO: 205; B0NT/A-BT8 of SEQ ID NO: 206; BoNT/A-Csyn8 of SEQ ID NO: 207; BoNT/A-Csnp8 of SEQ ID NO: 208; BoNT/A-DF39 of SEQ ID NO: 209; B0NT/A-D8 of SEQ ID NO: 210; B0NT/A-E8 of SEQ ID NO: 211 ; B0NT/A-F8 of SEQ ID NO: 212; or B0NT/A-D8 of SEQ ID NO: 213.

[0337] To construct a yeast cell line expressing a modified Clostridial toxin, pPICZ A/BoNT/A-A17 is digested with a suitable restriction endonuclease {i.e., Sad, Pme\ or BsfK\) and the resulting linearized expression construct is transformed into an appropriate P. pastoris Mut ^s strain KM71 H using an electroporation method. The transformation mixture is plated on 1.5% YPDS agar plates (pH 7.5)

containing 100 μg/mL of Zeocin™ and placed in a 28-30 ⁰ C incubator for 1-3 days of growth. Selection of transformants integrating the pPICZ A/BoNT/A-A17 at the 5' A0X1 locus is determined by colony resistance to Zeocin™. Cell lines integrating a pPICZ A/BoNT/A-A17 construct is tested for BoNT/A-A17 expression using a small-scale expression test. Isolated colonies from test cell lines that have integrated pPICZ A/BoNT/A-A17 are used to inoculate 1.0 L baffled flasks containing 100 mL of MGYH media and grown at about 28-30 ⁰ C in a shaker incubator (250 rpm) until the culture reaches an OD ₆₀₀ =2-6 (approximately 16-18 hours). Cells are harvested by centrifugation (3,00Ox g at 22 °C for 5 minutes). To induce expression, the cell pellet is resuspended in 15 mL of MMH media and 100% methanol is added to a final concentration of 0.5%. Cultures are grown at about 28-30 ⁰ C in a shaker incubator (250 rpm) for six days. Additional 100% methanol is added to the culture every 24 hours to a final concentration of 0.5%. A 1.0 mL test aliquot is taken from the culture every 24 hours starting at time zero and ending at time 144 hours. Cells are harvested from the aliquots by microcentrifugation to pellet the cells and lysed using three freeze-thaw rounds consisting of -80 ⁰ C for 5 minutes, then 37 ⁰ C for 5 minutes. Lysis samples are added to 2x LDS Sample Buffer (Invitrogen, Inc. Carlsbad, CA) and expression from established cell lines is measured by Western blot analysis (as described in Example 8) using either anti- BoNT/A, anti-myc or anti-His antibodies in order to identify lines expressing BoNT/A-A17. The P. pastoris Mut ^s KM71 H cell line showing the highest expression level of BoNT/A-A17 is selected for large-scale expression using commercial fermentation procedures. Procedures for large-scale expression are as outlined above except the culture volume is approximately 2.5 L MGYH media grown in a 5 L BioFlo 3000 fermentor and concentrations of all reagents will be proportionally increased for this volume. A similar procedure can be used to express a pPICZ A construct encoding any of the modified Clostridial toxins of SEQ ID NO: 204 to SEQ ID NO: 213.

[0338] BoNT/A-A17 is purified using the IMAC procedure, as described in Example 8. Expression from each culture is evaluated by a Bradford dye assay, polyacrylamide gel electrophoresis and Western blot analysis (as described in Example 8) in order to determine the amounts of BoNT/A-A17 produced.

Example 10 Expression of Modified Clostridial Toxins in an Insect Cell

[0339] The following example illustrates a procedure useful for expressing any of the modified Clostridial toxins disclosed in the present specification in an insect cell.

[0340] To construct suitable an insect expression construct encoding a modified Clostridial toxin, restriction endonuclease sites suitable for cloning an operably linked polynucleotide molecule into a pBACgus3 vector (EMD Biosciences-Novagen, Madison, Wl) are incorporated into the 5 ¹ - and 3' ends of the polynucleotide molecule SEQ ID NO: 237 encoding BoNT/A-A17 of SEQ ID NO: 203. This polynucleotide molecule is synthesized and a pUCBHB1/BoNT/A-A17 construct is obtained as described in Example 1. This construct is digested with restriction enzymes that 1) excise the insert containing the

open reading frame of SEQ ID NO: 237 encoding BoNT/A-A17; and 2) enable this insert to be operably- linked to a pBACgus3 vector. This insert is subcloned using a T4 DNA ligase procedure into a pBACgus3 vector that is digested with appropriate restriction endonucleases to yield pBACgus3/BoNT/A-A17. The ligation mixture is transformed into chemically competent E. coli DH5α cells (Invitrogen, Inc, Carlsbad, CA) using a heat shock method, plated on 1.5% Luria-Bertani agar plates (pH 7.0) containing 100 μg/mL of Ampicillin, and placed in a 37 ⁰ C incubator for overnight growth. Bacteria containing expression constructs are identified as Ampicillin resistant colonies. Candidate constructs are isolated using an alkaline lysis plasm id mini-preparation procedure and analyzed by restriction endonuclease digest mapping to determine the presence and orientation of the insert. This cloning strategy yielded a pBACgus3 expression construct comprising the polynucleotide molecule of SEQ ID NO: 237 encoding the BoNT/A-A17 of SEQ ID NO: 203 operably linked to an amino-terminal gp64 signal peptide and a carboxyl-terminal, Thrombin cleavable, polyhistidine affinity binding peptide (FIG. 14).

[0341] A similar cloning strategy is used to make pBACgus3 expression constructs encoding BoNT/A-Aδ of SEQ ID NO: 204; BoNT/A-BT35 of SEQ ID NO: 205; B0NT/A-BT8 of SEQ ID NO: 206; BoNT/A-Csyn8 of SEQ ID NO: 207; BoNT/A-Csnp8 of SEQ ID NO: 208; BoNT/A-DF39 of SEQ ID NO: 209; B0NT/A-D8 of SEQ ID NO: 210; B0NT/A-E8 of SEQ ID NO: 211 ; B0NT/A-F8 of SEQ ID NO: 212; or B0NT/A-D8 of SEQ ID NO: 213.

[0342] To express a modified Clostridial toxin using a baculoviral expression system, about 2.5x10 ⁶ Sf9 cells are plated in four 60 mm culture dishes containing 2 mL of BacVector ^® Insect media (EMD Biosciences-Novagen, Madison, Wl) and incubated for approximately 20 minutes in a 28 ⁰ C incubator. For each transfection, a 50 μL transfection solution is prepared in a 6 mL polystyrene tube by adding 25 μl_ of BacVector ^® Insect media containing 100 ng of a pBACgus3 construct encoding a modified Clostridial toxin, such as, e.g., pBACgus3/BoNT/A-A17, and 500 ng TlowE transfer plasmid to 25 μL of diluted Insect GeneJuice ^® containing 5 μL Insect GeneJuice ^® (EMD Biosciences-Novagen, Madison, Wl) and 20 μL nuclease-free water and this solution is incubated for approximately 15 minutes. After the 15 minute incubation, add 450 μL BacVector ^® media to the transfection solution and mix gently. Using this stock transfection solution as the 1/10 dilution make additional transfection solutions of 1/50, 1/250 and 1/1250 dilutions. Add 100 μL of a transfection solution to the Sf9 cells from one of the four 60 mm culture dishes, twice washed with antibiotic-free, serum-free BacVector ^® Insect media and incubate at 22 ⁰ C. After one hour, add 6 mL of 1% BacPlaque agarose-BacVector ^® Insect media containing 5% bovine serum albumin. After the agarose is solidified, add 2 mL BacVector ^® Insect media containing 5% bovine serum albumin to the transfected cells and transfer the cells to a 28 ⁰ C incubator for 3-5 days until plaques are visible. After 3-5 days post-transfection, plaques in the monolayer will be stained for β- glucuronidase reporter gene activity to test for the presence of recombinant virus plaques containing pBACgus3/BoNT/A-A17 by incubating the washed monolayer with 2 mL of BacVector ^® Insect media containing 30 μL of 20 mg/mL X-Gluc Solution (EMD Biosciences-Novagen, Madison, Wl) for approximately 2 hours in a 28 °C incubator.

[0343] After identifying candidate recombinant virus plaques, several candidate virus plaques are eluted and plaque purified. To elute a recombinant virus, transfer a plug containing a recombinant virus plaque with a sterile Pasteur pipet to 1 mL BacVector ^® Insect media (EMD Biosciences-Novagen, Madison, Wl) in a sterile screw-cap vial. Incubate the vial for approximately 2 hours at 22 ⁰ C or for approximately 16 hours at 4 ⁰ C. For each recombinant virus plaque, 2.5x10 ⁵ Sf9 cells are plated in 35 mm culture dishes containing 2 mL of BacVector ^® Insect media (EMD Biosciences-Novagen, Madison, Wl) and incubated for approximately 20 minutes in a 28 ⁰ C incubator. Remove the media and add 200 μL of eluted recombinant virus. After one hour, add 2 mL of 1% BacPlaque agarose-BacVector ^® Insect media containing 5% bovine serum albumin. After the agarose is solidified, add 1 mL BacVector ^® Insect media containing 5% bovine serum albumin to the transfected cells and transfer the cells to a 28 ⁰ C incubator for 3-5 days until plaques are visible. After 3-5 days post-transfection, plaques in the monolayer will be stained for β-glucuronidase reporter gene activity to test for the presence of recombinant virus plaques containing pBACgus3/BoNT/A-A17 by incubating the washed monolayer with 2 mL of BacVector ^® Insect media containing 30 μL of 20 mg/mL X-Gluc Solution (EMD Biosciences-Novagen, Madison, Wl) for approximately 2 hours in a 28 ⁰ C incubator.

[0344] To prepare a seed stock of virus, elute a recombinant virus by transferring a plug containing a recombinant virus plaque with a sterile Pasteur pipet to 1 mL BacVector ^® Insect media (EMD Biosciences-Novagen, Madison, Wl) in a sterile screw-cap vial. Incubate the vial for approximately 16 hours at 4 ⁰ C. Approximately 5x10 ⁵ Sf9 cells are plated in T-25 flask containing 5 mL of BacVector ^® Insect media (EMD Biosciences-Novagen, Madison, Wl) and are incubated for approximately 20 minutes in a 28 ⁰ C incubator. Remove the media and add 300 μL of eluted recombinant virus. After one hour, add 5 mL BacVector ^® Insect media containing 5% bovine serum albumin to the transfected cells and transfer the cells to a 28 ⁰ C incubator for 3-5 days until the majority of cells become unattached and unhealthy. The virus is harvested by transferring the media to 15 mL snap-cap tubes and centrifuging tubes at 1000x g for 5 minutes to remove debris. The clarified supernatant is transferred to fresh 15 mL snap-cap tubes and are stored at 4 °C.

[0345] To prepare a high titer stock of virus, approximately 2x10 ⁷ Sf9 cells are plated in T-75 flask containing 10 mL of BacVector ^® Insect media (EMD Biosciences-Novagen, Madison, Wl) and are incubated for approximately 20 minutes in a 28 ⁰ C incubator. Remove the media and add 500 μL of virus seed stock. After one hour, add 10 mL BacVector ^® Insect media containing 5% bovine serum albumin to the transfected cells and transfer the cells to a 28 ^C C incubator for 3-5 days until the majority of cells become unattached and unhealthy. The virus is harvested by transferring the media to 15 mL snap-cap tubes and centrifuging tubes at 1000x g for 5 minutes to remove debris. The clarified supernatant is transferred to fresh 15 mL snap-cap tubes and are stored at 4 ⁰ C . High titer virus stocks should contain approximately 2x10 ⁸ to 3x10 ⁹ pfu of baculovirus.

[0346] To express gp64-BoNT/A-A17 using a baculoviral expression system, about 1.25x10 ⁸ Sf9 cells are seeded in a 1 L flask containing 250 mL of BacVector ^® Insect media and are grown in an orbital shaker (150 rpm) to a cell density of approximately 5x10 ⁸ . The culture is inoculated with approximately 2.5x10 ⁹ of high titer stock recombinant baculovirus and incubated for approximately 48 hours in a 28 ⁰ C orbital shaker (150 rpm). Media is harvested by transferring the media to tubes and centrifuging tubes at 50Ox g for 5 minutes to remove debris. Media samples are added to 2x LDS Sample Buffer (Invitrogen, Inc, Carlsbad, CA) and expression is measured by Western blot analysis (as described in Example 8) using either anti-BoNT/A or anti-His antibodies in order to identify baculoviral stocks expressing BoNT/A- A17. A similar procedure can be used to express a pBACgus3 construct encoding any of the modified Clostridial toxins of SEQ ID NO: 204 to SEQ ID NO: 213.

[0347] BoNT/A-A17 is purified using the IMAC procedure, as described in Example 8. Expression from each culture is evaluated by a Bradford dye assay, polyacrylamide gel electrophoresis and Western blot analysis (as described in Example 8) in order to determine the amounts of BoNT/A-A17 produced.

Example 11 Expression of Modified Clostridial Toxins in a Mammalian Cell

[0348] The following example illustrates a procedure useful for expressing any of the modified Clostridial toxins disclosed in the present specification in a mammalian cell.

[0349] To construct a suitable mammalian expression construct encoding a modified Clostridial toxin, restriction endonuclease sites suitable for cloning an operably linked polynucleotide molecule into a pSecTag2 vector (Invitrogen, Inc, Carlsbad, CA) are incorporated into the 5'- and 3' ends of the polynucleotide molecule SEQ ID NO: 238 encoding BoNT/A-A17 of SEQ ID NO: 203. This polynucleotide molecule is synthesized and a pUCBHB1/BoNT/A-A17 construct is obtained as described in Example 1. This construct is digested with restriction enzymes that 1) excise the insert containing the open reading frame of SEQ ID NO: 238 encoding BoNT/A-A17; and 2) enable this insert to be operably-linked to a pSecTag2 vector. This insert is subcloned using a T4 DNA ligase procedure into a pSecTag2 vector that is digested with appropriate restriction endonucleases to yield pSecTag2/BoNT/A-A17. The ligation mixture is transformed into chemically competent E. coli DH5α cells (Invitrogen, Inc, Carlsbad, CA) using a heat shock method, plated on 1.5% Luria-Bertani agar plates (pH 7.0) containing 100 μg/mL of Ampicillin, and placed in a 37 ⁰ C incubator for overnight growth. Bacteria containing expression constructs are identified as Ampicillin resistant colonies. Candidate constructs are isolated using an alkaline lysis plasmid mini-preparation procedure and analyzed by restriction endonuclease digest mapping to determine the presence and orientation of the insert. This cloning strategy yielded a pSecTag2 expression construct comprising the polynucleotide molecule of SEQ ID NO: 238 encoding the BoNT/A-A17 of SEQ ID NO: 203 operably-linked to a carboxyl-terminal c-myc and polyhistidine binding peptides (FIG. 15).

[0350] A similar cloning strategy is used to make pSecTag2 expression constructs encoding B0NT/A-A8 of SEQ ID NO: 204; BoNT/A-BT35 of SEQ ID NO: 205; B0NT/A-BT8 of SEQ ID NO: 206; BoNT/A-Csyn8 of SEQ ID NO: 207; BoNT/A-Csnp8 of SEQ ID NO: 208; BoNT/A-DF39 of SEQ ID NO: 209; B0NT/A-D8 of SEQ ID NO: 210; B0NT/A-E8 of SEQ ID NO: 211 ; B0NT/A-F8 of SEQ ID NO: 212; or B0NT/A-D8 of SEQ ID NO: 213.

[0351] To transiently express modified Clostridial toxin in a cell line, about 1.5x10 ⁵ SH-SY5Y cells are plated in a 35 mm tissue culture dish containing 3 ml_ of complete Dulbecco's Modified Eagle Media (DMEM), supplemented with 10% fetal bovine serum (FBS), 1x penicillin/streptomycin solution (Invitrogen, Inc, Carlsbad, CA) and 1x MEM non-essential amino acids solution (Invitrogen, Inc, Carlsbad, CA), and grown in a 37 ⁰ C incubator under 5% carbon dioxide until cells reach a density of about 5x10 ⁵ cells/ml (6-16 hours). A 500 μl_ transfection solution is prepared by adding 250 μl_ of OPTI-MEM Reduced Serum Medium containing 15 μL of LipofectAmine 2000 (Invitrogen, Carlsbad, CA) incubated at room temperature for 5 minutes to 250 μL of OPTI-MEM Reduced Serum Medium containing 5 μg of a pSecTag2 expression construct encoding a modified Clostridial toxin, such as, e.g., pSecTag2/BoNT/A- A17. This transfection is incubated at room temperature for approximately 20 minutes. The complete, supplemented DMEM media is replaced with 2 mL of OPTI-MEM Reduced Serum Medium and the 500 μL transfection solution is added to the SH-SY5Y cells and the cells are incubated in a 37 ⁰ C incubator under 5% carbon dioxide for approximately 6 to 18 hours. Transfection media is replaced with 3 mL of fresh complete, supplemented DMEM and the cells are incubated in a 37 °C incubator under 5% carbon dioxide for 48 hours. Both media and cells are collected for expression analysis of BoNT/A-A17. Media is harvested by transferring the media to 15 mL snap-cap tubes and centrifuging tubes at 50Ox g for 5 minutes to remove debris. Cells are harvested by rinsing cells once with 3.0 mL of 100 mM phosphate- buffered saline, pH 7.4 and lysing cells with a buffer containing 62.6 mM 2-amino-2-hydroxymethyl-1 ,3- propanediol hydrochloric acid (Tris-HCI), pH 6.8 and 2% sodium lauryl sulfate (SDS). Both media and cell samples are added to 2x LDS Sample Buffer (Invitrogen, Inc, Carlsbad, CA) and expression is measured by Western blot analysis (as described in Example 5) using either anti-BoNT/A, anti-c-myc or anti-His antibodies in order to identify pSecTag2 constructs expressing BoNT/A-A17. A similar procedure can be used to transiently express a pSecTag2 construct encoding any of the modified Clostridial toxins of SEQ ID NO: 204 to SEQ ID NO: 213.

[0352] To generate a stably-integrated cell line expressing a modified Clostridial toxin, approximately 1.5x10 ⁵ SH-SY5Y cells are plated in a 35 mm tissue culture dish containing 3 mL of complete DMEM, supplemented with 10% FBS, 1x penicillin/streptomycin solution (Invitrogen, Inc, Carlsbad, CA) and 1x MEM non-essential amino acids solution (Invitrogen, Inc, Carlsbad, CA), and grown in a 37 ⁰ C incubator under 5% carbon dioxide until cells reach a density of about 5x10 ⁵ cells/ml (6-16 hours). A 500 μL transfection solution is prepared by adding 250 μL of OPTI-MEM Reduced Serum Medium containing 15 μL of LipofectAmine 2000 (Invitrogen, Carlsbad, CA) incubated at room temperature for 5 minutes to 250

μl_ of OPTI-MEM Reduced Serum Medium containing 5 μg of a pSecTag2 expression construct encoding a modified Clostridial toxin, such as, e.g., pSecTag2/BoNT/A-A17. This transfection solution is incubated at room temperature for approximately 20 minutes. The complete, supplemented DMEM media is replaced with 2 ml_ of OPTI-MEM Reduced Serum Medium and the 500 μl_ transfection solution is added to the SH-SY5Y cells and the cells are incubated in a 37 ⁰ C incubator under 5% carbon dioxide for approximately 6 to 18 hours. Transfection media is replaced with 3 ml. of fresh complete, supplemented DMEM and cells are incubated in a 37 ⁰ C incubator under 5% carbon dioxide for approximately 48 hours. Media is replaced with 3 mL of fresh complete DMEM, containing approximately 5 μg/mL of Zeocin™, 10% FBS, 1x penicillin/streptomycin solution (Invitrogen, Inc, Carlsbad, CA) and 1x MEM non-essential amino acids solution (Invitrogen, Inc, Carlsbad, CA). Cells are incubated in a 37 ⁰ C incubator under 5% carbon dioxide for approximately 3-4 weeks, with old media being replaced with fresh Zeocin™-selective, complete, supplemented DMEM every 4 to 5 days. Once Zeocin™-resistant colonies are established, resistant clones are replated to new 35 mm culture plates containing fresh complete DMEM, supplemented with approximately 5 μg/mL of Zeocin™, 10% FBS, 1x penicillin/streptomycin solution (Invitrogen, Inc, Carlsbad, CA) and 1x MEM non-essential amino acids solution (Invitrogen, Inc, Carlsbad, CA), until these cells reach a density of 6 to 20x10 ⁵ cells/mL To test for expression of BoNT/A-A17 from SH-SY5Y cell lines that have stably-integrated a pSecTag2/BoNT/A-A17, approximately 1.5x10 ⁵ SH- SY5Y cells from each cell line are plated in a 35 mm tissue culture dish containing 3 mL of Zeocin™- selective, complete, supplemented DMEM and grown in a 37 ⁰ C incubator under 5% carbon dioxide until cells reach a density of about 5x10 ⁵ cells/ml (6-16 hours). Media is replaced with 3 mL of fresh Zeocin™- selective, complete, supplemented DMEM and cells are incubated in a 37 ⁰ C incubator under 5% carbon dioxide for 48 hours. Both media and cells are collected for expression analysis of BoNT/A-A17-c-myc- His. Media is harvested by transferring the media to 15 mL snap-cap tubes and centrifuging tubes at 50Ox g for 5 minutes to remove debris. Cells are harvest by rinsing cells once with 3.0 mL of 100 mM phosphate-buffered saline, pH 7.4 and lysing cells with a buffer containing 62.6 mM 2-amino-2- hydroxymethyl-1 ,3-propanediol hydrochloric acid (Tris-HCI), pH 6.8 and 2% sodium lauryl sulfate (SDS). Both media and cell samples are added to 2x LDS Sample Buffer (Invitrogen, Inc, Carlsbad, CA) and expression is measured by Western blot analysis (as described in Example 5) using either anti-BoNT/A, anti-c-myc or anti-His antibodies in order to identify SH-SY5Y cell lines expressing BoNT/A-A17. The established SH-SY5Y cell line showing the highest expression level of BoNT/A-A17 is selected for large- scale expression using 3 L flasks. Procedures for large-scale expression are as outlined above except the starting volume is approximately 800-1000 mL of complete DMEM and concentrations of all reagents are proportionally increased for this volume. A similar procedure can be used to stably express a pSecTag2 construct encoding any of the modified Clostridial toxin of SEQ ID NO: 204 to SEQ ID NO: 213.

[0353] BoNT/A-A17 is purified using the IMAC procedure, as described in Example 8. Expression from each culture is evaluated by a Bradford dye assay, polyacrylamide gel electrophoresis and Western blot

analysis (as described in Example 8) in order to determine whether the amounts of BoNT/A-A17 produced.

[0354] Although aspects of the present invention have been described with reference to the disclosed embodiments, one skilled in the art will readily appreciate that the specific examples disclosed are only illustrative of these aspects and in no way limit the present invention. Various modifications can be made without departing from the spirit of the present invention.