IMPROVEMENTS IN OR RELATING TO ORGANIC COMPOUNDS

The present invention relates to a method for producing heterologous or exogenous proteins in plant cell material such as transformed plant cells in culture or in plant tissue derived from transformed plant cells. In particular, the method relates to a method for producing proteins in plastids comprised in plant cell material, the genetic material required therefor, such as DNA and RNA, vectors, host cells, methods of introduction of genetic material into plant cells, and uses thereof.

A US Patent application to Biesgen C. (publication number 2006/0253916) relates to methods for the generation of transgenic plants possessing genetically modified plastids. The technical teaching behind the methods described therein does not rely on the use of an intron-derived RNA vehicle that makes use of endogenous cellular processes for the transfer of RNA from the cytoplasm of the cell into the plastid.

A disadvantage of prior art plastid transformation methods is that the transformation efficiency in terms of numbers of transformed plastids per cell tends to be low, and hence the amount of exogenous protein produced per cell tends also to be low. A further disadvantage of prior art methods is that the delivery of genetic information into the plastid is patchy. Prior art methods do not rely on endogenous cellular processes for transfer of RNA into the plastid genome, and as such, prior art processes for genetically modifying plastids are generally inefficient. These and other disadvantages of prior art plastid transformation technology will become apparent from the foregoing description.

The present inventors have found that by using or adapting endogenous cellular processes for the transfer of polynucleotides, such as RNAs, from the cytoplasm to plastids in the plant cell, polynucleotide sequences derived from nuclear transformation of the nucleus of a plant cell can be efficiently transferred to the plastid genome, within a plant cell that is so transformed, and expressed in the plastid of interest as described herein. For the purposes of the present invention the terms "plastid" and "plastids" and "plastid population" are used interchangeably, unless context demands otherwise. Also, for the purposes of the present invention the terms "plant cell" and "plant cells" are used interchangeably, unless context demands otherwise. By employing or adapting endogenous cellular processes for the transfer of RNA to the plastid genome as described herein, the method of the invention is

considered to be unique over prior art methods for the generation of plants possessing genetically modified plastids : the plastid population of the cell or of cells comprising plant tissue transformed according to the present invention is constantly bombarded by RNA that is derived from the nucleus of the cell, which is carried over from the plastid membrane and into the plastid genome where it is reverse transcribed, integrated and then expressed, resulting in the generation of proteins of interest.

There exists a need for an alternative plastid transformation method for the transformation of plant cells over those of the prior art.

The basis for the present invention, which does not appear to have been realised in the prior art, is to insert at least one polynucleotide sequence of interest into a suitable site of a domain of an intron, or into suitable sites within the domains of several introns, of either bacterial or plastid origin, or of both bacterial and plastid origin, such as a group I intron or a group II intron, and to engineer the insertion of the modified intron into the nucleus of a plant host cell where it is expressed as RNA. The nucleotide sequence of introns of interest in the invention may be further modified to eliminate cryptic splicing sites, thus improving expression in the plant cell. The expressed RNA is then transferred to the cytoplasm where it binds with a multifunctional protein that carries it over to the membrane of the plastid, where the RNA sequence is reverse transcribed into DNA which then inserts into the plastid genome where the polynucleotide sequence of interest under the control of a plastid specific promoter is then expressed, giving rise to a polypeptide or of polypeptides of interest, depending on design.

The present invention also relates to the production of transgenic plant cells and transgenic plants comprising plastids that are genetically modified with intron-derived polynucleotide sequences carrying polynucleotide sequences of interest under operational control of a plant plastid promoter.

According to the present invention there is provided a method of producing at least a heterologous or exogenous polypeptide in a plant cell that comprises :

1) introducing into the said plant cell a plant nuclear promoter that drives expression in a plant nucleus operably linked to an intron that

comprises a first isolated nucleic acid sequence wherein the said first isolated nucleic acid sequence comprises a plant plastid promoter that drives expression in a plant plastid operably linked to a second nucleic acid sequence that encodes at least an heterologous or exogenous polypeptide;

2) growing said plant cell of (1) under conditions wherein said plant nuclear promoter drives expression of said intron;

3) selecting a plant cell of (2) wherein said first isolated nucleic acid sequence is integrated into the plastid genome;

4) growing the plant cell of (3) under conditions wherein said plant plastid promoter expresses said heterologous or exogenous protein from said second nucleic acid sequence therefrom.

In a further embodiment of the invention there is provided a method of producing at least a heterologous or exogenous polypeptide in a plant that comprises :

1) introducing into a regenerable plant cell a plant nuclear promoter that drives expression in a plant nucleus operably linked to an intron that comprises a first isolated nucleic acid sequence wherein the said first isolated nucleic acid sequence comprises a plant plastid promoter that drives expression in a plant plastid operably linked to a second nucleic acid sequence that encodes at least an heterologous or exogenous polypeptide;

2) growing said plant cell of (1) under conditions wherein said plant nuclear promoter drives expression of said intron;

3) selecting a plant cell of (2) wherein said first isolated nucleic acid sequence is integrated into the plastid genome;

4) regenerating a plant from the plant cell of (3) ; and

5) growing the plant of (4) under conditions wherein said plant plastid promoter expresses said heterologous or exogenous protein from said second nucleic acid sequence therefrom.

The intron of 1) is derived from a bacterium, a fungus or a plastid from a plant and may be selected or derived from group I and group II introns or modified versions thereof in which cryptic splicing sites have been eliminated. Preferably, the intron is a group II intron, such as the Lactococcus lactis Ll.ltrB intron or a modified version of it in which cryptic splicing sites have been eliminated as outlined herein. Group II introns are widely represented in the organelles of plants (eg 25 introns in the tobacco plastid genome) and fungi, and in bacteria. Group II introns useful in the method of the invention are mobile, highly

structural retroelements that encode multifunctional protein (intron encoded protein or IEP) which possesses reverse transcriptase (RT) activity. The IEP facilitates splicing of intron RNA by stabilization of the catalytically active RNA structure, performs reverse transcription and insertion of the intron into specific DNA target sites of the bacterial genome at high frequency (Moran et al . (1995) MoI Cell Biol 15:2828-2838; Cousineau et al . (1998) Cell 94:451-462).

Group II introns of bacterial origin, such as those derived from Lactococcus that comprise a modified LtrA gene, are preferably used in the method of the invention. The LtrA polynucleotide sequence of a Lactococcus bacterium, such as Lactococcus lactis may be modified for optimum expression in plants by inserting into it at least one polynucleotide sequence comprising one or more introns from at least one plant nucleic acid sequence, such as from one or more plant genes and by substituting certain selected codons having a low frequency of usage in native plants with codons that occur with a higher frequency in such plants . Typically, the bacterial LtrA sequence of interest is analysed with reference to plant codon usage using in silico comparisons such as those found at the website www.kazusa.or.jp/codon for bacterial codons that occur with low frequency in plants . Such codons may then be substituted with codons that have a high frequency of occurrence in plants, and an in silico-derived modified polynucleotide sequence is generated. From this optimised LtrA sequence a synthetic LtrA polynucleotide sequence corresponding to the in silico generated sequence is made using standard polynucleotide synthesis procedures known in the art, and may then be used in the preparation of constructs of use in the present invention as outlined herein. It is thought that by using a modified sequence that comprises plant codon substitutions as outlined above more plant cell environment stable polynucleotide RNA sequences are generated.

Other introns that may be used in the method of the invention are those which naturally occur in the plastids of higher plants, especially group II introns, such as in the trnK genes of the plastid genome. Suitable trnk introns are found in plastids of Arabidopsis, maize and tobacco.

Other types of introns that may be used in the method of the invention include, for example, the group I intron from Tetrahymena (GenBank Ace. No.: X54512; Kruger K et al. (1982) Cell 31:147-157; Roman J and Woodson S A (1998) Proc Natl Acad Sci USA 95:2134-2139), the group II rll intron

from Scenedesmus obliquus (GenBank Ace No.: X17375.2 nucleotides 28831 to 29438; Hollander V and Kuck U (1999) Nucl Acids Res 27: 2339-2344;

Herdenberger F et al . (1994) Nucl Acids Res 22: 2869-2875; Kuck U et al . (1990) Nucl Acids Res 18:2691-2697), the Ll.LtrB intron (GenBank Ace.

No.: U50902 nucleotides 2854 to 5345), the Arabidopsis trnK intron (GenBank Ace. No.: AP000423, complementary nucleotides 1752 to 4310) [0222], the maize trnK intron (GenBank Ace. No.: X86563, complementary nucleotides 1421 to 3909), and the tobacco trnK intron (GenBank Ace. No.:

Z00044, complementary nucleotides 1752 to 4310) .

Aside from heterologous introns described herein, endogenous introns that occur naturally in the plastids of the plant cells of the plant of interest may be used in the method of the invention. However, it is thought that heterologous introns, such as trnk introns, are preferred since they may be used to avoid potential instabilities brought about by sequence duplication. Introns which occur naturally in the plastids of the plant of interest may be modified such that they have a sequence homology of about 50%, 60%, 70%, 75%, 80%, 85%, 90% or 95%, or of any percentage sequence homology therebetween, with the sequence of the starting intron, while retaining functionality, may also be employed in the method of the invention.

A plant nuclear promoter (for example, an exogenous nucleus specific promoter) is one that denotes a promoter that is introduced in front of a nucleic acid sequence of interest and is operably associated therewith. Thus a plant nuclear promoter is one that has been placed in front of a selected polynucleotide component, such as an introduced group I or group II intron. Thus a promoter may be native to a plant cell of interest but may not be operably associated with the group I or group II intron of the invention in a wild-type plant cell. Typically, a plant nuclear promoter, such as an exogenous nucleus specific promoter, is one that is transferred to a host cell or host plant from a source other than the host cell or host plant.

The cDNA' s encoding a polynucleotide of the invention, such as a group I or a group II intron, contain at least one type of promoter that is operable in a plant cell, for example, an inducible or a constitutive promoter operatively linked to a first and/or second nucleic acid sequence or nucleic acid sequence component as herein defined and as provided by the present invention. As discussed, this enables control of expression of the polynucleotide of the invention. The invention also

provides plants transformed with polynucleotide sequences or constructs and methods including introduction of such polynucleotide nucleic acid sequences or constructs into a plant cell and/or induction of expression of said first or second nucleic acid sequence or construct within a plant cell, e.g. by application of a suitable stimulus, such as an effective exogenous inducer .

The term "inducible" as applied to a promoter is well understood by those skilled in the art. In essence, expression under the control of an inducible promoter is "switched on" or increased in response to an applied stimulus (which may be generated within a cell or provided exogenously) . The nature of the stimulus varies between promoters. Some inducible promoters cause little or undetectable levels of expression (or no expression) in the absence of the appropriate stimulus. Other inducible promoters cause detectable constitutive expression in the absence of the stimulus. Whatever the level of expression is in the absence of the stimulus, expression from any inducible promoter is increased in the presence of the correct stimulus. The preferable situation is where the level of expression increases upon application of the relevant stimulus by an amount effective to alter a phenotypic characteristic. Thus an inducible (or "switchable") promoter may be used which causes a basic level of expression in the absence of the stimulus which level is too low to bring about a desired phenotype (and may in fact be zero) . Upon application of the stimulus, expression is increased (or switched on) to a level, which brings about the desired phenotype. One example of an inducible promoter is the ethanol inducible gene switch disclosed in Caddick et al (1998) Nature Biotechnology 16: 177-180. A number of inducible promoters are known in the art .

Chemically regulated promoters can be used to modulate the expression of a gene or a polynucleotide sequence of the invention in a plant through the application of an exogenous chemical regulator. Depending upon the objective, the promoter may be a chemically inducible promoter, where application of the chemical induces gene expression, or a chemical- repressible promoter, where application of the chemical represses gene expression. Chemically inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR-la promoter, which is activated by salicylic acid. Other chemically regulated

promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 83:10421-10425 and McNellis et al. (1998) Plant J. 14 (2) :247-257) and tetracycline-inducible and tetracycline- repressible promoters (see, for example, Gatz et al. (1991) MoI. Gen. Genet. 227:229-237 , and U.S. Patent Nos. 5,814,618 and 5,789,156), herein incorporated by reference .

Where enhanced expression in particular tissues is desired, tissue- specific promoters can be utilized. Tissue-specific promoters include those described by Yamamoto et al. (1997) Plant J. 12 (2)255-265; Kawamata et al. (1997) Plant Cell Physiol. 38 (7) :792-803 ; Hansen et al. (1997) MoI. Gen Genet. 254 (3) :337-343 ; Russell et al. (1997) Transgenic Res. 6 (2) -.157-168; Rinehart et al. (1996) Plant Physiol. 112 (3) -.1331-1341; Van Camp et al . (1996) Plant Physiol. 112 (2) -.525-535; Canevascini et al. (1996) Plant Physiol. 112 (2) -.513-524 ; Yamamoto et al. (1994) Plant Cell Physiol. 35 (5) :773-778; Lam (1994) Results Probl . Cell Differ. 20:181- 196; Orozco et al . (1993) Plant MoI Biol. 23 (6) : 1129-1138; Matsuoka et al. (1993) Proc Natl. Acad. Sci. USA 90 (20) -.9586-9590 ; and Guevara-Garcia et al. (1993) Plant J. 4 (3) : 495-505.

So-called constitutive promoters may also be used in the methods of the present invention. Constitutive promoters include, for example, CaMV 35S promoter (Odell et al. (1985) Nature 323:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant MoI. Biol. 12:619-632 and Christensen et al. (1992) Plant MoI. Biol. 18:675-689) ; pEMU (Last et al . (1991) Theor. Appl . Genet. 81:581- 588); MAS (Velten et al . (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Application Serial No. 08/409,297), and the like. Other constitutive promoters include those in U.S. Patent Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; and 5,608,142.

The expression in plastids is effected by employing a plant plastid promoter such as plastid specific promoters and/or transcription regulation elements . Examples include the RNA polymerase promoter (WO 97/06250) and other promoters described in the art, eg in WO 00/07431, U.S. Pat. No. 5,877,402, WO 97/06250, WO 98/55595, WO 99/46394, WO 01/42441 and WO 01/07590,- the rpo B promoter element, the atpB promoter element, the clpP promoter element (see also WO 99/46394) and the 16S rDNA promoter element . The plastid specific promoter may also have a polycistronic "operon" assigned to it (EP-A 1 076 095,- WO 00/20611) .

Further promoters that may be used in the method of the invention also include the PrbcL promoter, the Prpslδ promoter, and the Prrnl6 promoter described in US Patent application 2006/0253916, the plastid specific promoters Prrn-62, Pycf2-1577, PatpB-289, Prps2-152, Prpsl6-107, Pycfl- 41, PatpI-207, PclpP-511, PclpP-173 and PaccD-129 (WO 97/06250; Hajdukiewicz P T J et al. (1997) EMBO J 16:4041-4048), the PaccD-129 promoter of the tobacco accD gene (WO 97/06250) , the PclpP-53 promoter of the clpP gene as highly active NEP promoter in chloroplasts (WO 97/06250) , the Prrn-62 promoter of the rrn gene, the Prpsl6-107 promoter of the rpsl6 gene, the PatpB/E-290 promoter of the tobacco atpB/E gene (Kapoor S et al . (1997) Plant J 11:327-337), and the PrpoB-345 promoter of the rpoB gene (Liere K & Maliga P (1999) EMBO J 18: 249-257) . Furthermore, all those promoters which belong to class III (Hajdukiewicz P T J et al. (1997) EMBO J 16:4041-4048) and all fragments of the class II promoters which control the initiation of transcription by NEP may be utilized in the method of the invention. Such promoters or promoter moieties are not generally known to be highly conserved. ATAGAATAAA is given as consensus near the transcription initiation site of NEP promoters (Hajdukiewicz P T J et al (1997) EMBO J 16:4041-4048).

Naturally, the man skilled in the art will appreciate that terminator DNA sequences will be present in constructs used in the invention. A terminator is contemplated as a DNA sequence at the end of a transcriptional unit which signals termination of transcription. These elements are 3 ' -non-translated sequences containing polyadenylation signals, which act to cause the addition of polyadenylate sequences to the 3' end of primary transcripts. For expression in plant cells the nopaline synthase transcriptional terminator (A. Depicker et al . , 1982, J. of MoI. & Applied Gen. 1:561-573) sequence serves as a transcriptional termination signal.

Those skilled in the art are well able to construct vectors and design protocols for recombinant nucleic acid sequences or gene expression. Suitable vectors can be chosen or constructed, containing appropriate regulatory sequences, including promoter sequences, terminator fragments, polyadenylation sequences, enhancer sequences, marker genes and other sequences as appropriate. For further details see, for example, Molecular Cloning: a Laboratory Manual: 2nd edition, Sambrook et al, 1989, Cold Spring Harbor Laboratory Press. Many known techniques and protocols for manipulation of nucleic acid, for example in preparation of nucleic acid constructs, mutagenesis, sequencing, introduction of DNA

into cells and gene expression, and analysis of proteins, are described in detail in Current Protocols in Molecular Biology, Second Edition, Ausubel et al . eds . , John Wiley & Sons, 1992. The disclosures of Sambrook et al . and Ausubel et al . are incorporated herein by reference . Specific procedures and vectors previously used with wide success upon plants are described by Bevan (Nucl. Acids Res. 12, 8711-8721 (1984)) and Guerineau and Mullineaux (1993) (Plant transformation and expression vectors. In: Plant Molecular Biology Labfax (Croy RRD ed.) Oxford, BIOS Scientific Publishers, pp 121-148) .

Naturally, the skilled addressee will appreciate that each introduced group I and/or group II intron will be under regulatory control of its own exogenous promoter and terminator. When two or more target proteins are destined to be produced from a single carrier RNA it is preferable if they are able to be readily separated, for example by binding to different protein-specific antibodies (monoclonal or polyclonal) in the harvesting phase of the plant cell culture system.

Selectable genetic markers may facilitate the selection of transgenic plants and these may consist of chimaeric genes that confer selectable phenotypes such as resistance to antibiotics such as spectinomycin, streptomycin, kanamycin, neomycin, hygromycin, puramycin, phosphinotricin, chlorsulfuron, methotrexate, gentamycin, spectinomycin, imidazolinones and glyphosate.

When introducing selected nucleic acid sequences according to the present invention into a cell, certain considerations must be taken into account, well known to those skilled in the art. The nucleic acid to be inserted should be assembled within a construct, which contains effective regulatory elements, which will drive transcription. There must be available a method of transporting the construct into the cell . Once the construct is within the cell membrane, integration into the endogenous chromosomal material either will or will not occur. Finally, as far as plants are concerned the target cell type must be such that cells can be regenerated into whole plants .

Plants transformed with DNA segments containing sequences of interest as provided herein may be produced by standard techniques, which are already known for the genetic manipulation of plants. DNA can be transformed into plant cells using any suitable technology, such as a disarmed Ti- plasmid vector carried by Agrobacterium exploiting its natural gene

transfer ability (EP-A-270355, EP-A-0116718, NAR 12(22) 8711 -87215 1984) , particle or micro projectile bombardment (US 5100792, EP-A-444882, ξP-A-434616) microinjection (WO 92/09696, WO 94/00583, EP 331083, EP 175966, Green et al . (1987) Plant Tissue and Cell Culture, Academic Press), electroporation (EP 290395, WO 8706614) other forms of direct DNA uptake (DE 4005152, WO 9012096, US 4684611), liposome mediated DNA uptake (e.g. Freeman et al. Plant Cell Physiol. 29: 1353 (1984)), or the vortexing method (e.g. Kindle, PNAS U.S.A. 87: 1228 (1990d) Physical methods for the transformation of plant cells are reviewed in Oard, 1991, Biotech. Adv. 9: 1-11.

Thus once a nucleic acid sequence or gene has been identified, it may be reintroduced into plant cells using techniques well known to those skilled in the art to produce transgenic plants of the appropriate phenotype .

Agrobacterium transformation is widely used by those skilled in the art to transform dicotyledonous species. Production of stable, fertile transgenic plants in almost all economically relevant monocot plants is also now routine : (Toriyama, et al . (1988) Bio/Technology 6, 1072-1074; Zhang, et al . (1988) Plant Cell Rep. 7, 379-384; Zhang, et al . (1988) Theor. Appl. Genet 76, 835-840; Shimamoto, et al . (1989) Nature 338, 274- 276; Datta, et al . (1990) Bio/Technology 8, 736-740; Christou, et al .

(1991) Bio/Technology 9, 957-962; Peng, et al . (1991) International Rice Research Institute, Manila, Philippines 563-574; Cao, et al . (1992) Plant Cell Rep. 11, 585-591; Li, et al . (1993) Plant Cell Rep. 12, 250-255; Rathore, et al . (1993) Plant Molecular Biology 21, 871-884; Fromm, et al .

(1990) Bio/Technology 8, 833-839; Gordon-Kamm, et al . (1990) Plant Cell 2, 603-618; D'Halluin, et al . (1992) Plant Cell 4, 1495-1505; Walters, et al. (1992) Plant Molecular Biology 18, 189-200; Koziel, et al . (1993) Biotechnology 11, 194-200; Vasil, I. K. (1994) Plant Molecular Biology 25, 925-937; Weeks, et al . (1993) Plant Physiology 102, 1077-1084; Somers, et al . (1992) Bio/Technology 10 , 1589-1594; WO92/14828) . In particular, Agrobacterium mediated transformation is now a highly efficient alternative transformation method in monocots (Hiei et al .

(1994) The Plant Journal 6, 271-282) .

The generation of fertile transgenic plants has been achieved in the cereals rice, maize, wheat, oat, and barley (reviewed in Shimamoto, K. (1994) Current Opinion in Biotechnology 5, 158-162.; Vasil, et al . (1992) Bio/Technology 10, 667-674; Vain et al . , 1995, Biotechnology Advances 13

(4) : 653-671; Vasil, 1996, Nature Biotechnology 14 page 702) . Wan and Lemaux (1994) Plant Physiol- 104: 37-48 describe techniques for generation of large numbers of independently transformed fertile barley plants .

Micro projectile bombardment, electroporation and direct DNA uptake are preferred where Agrobacterium is inefficient or ineffective. Alternatively, a combination of different techniques may be employed to enhance the efficiency of the transformation process, e.g. bombardment with Agrobacterium coated micro particles (EP-A-486234) or micro projectile bombardment to induce wounding followed by co-cultivation with Agrobacterium (EP-A-486233) .

Following transformation, a plant may be regenerated, e.g. from single cells, callus tissue or leaf discs, as is standard in the art. Almost any plant can be entirely regenerated from cells, tissues and organs of the plant. Available techniques are reviewed in Vasil et al . , Cell Culture and Somatic Cell Genetics of Plants, Vol. I, II and III, Laboratory Procedures and Their Applications, Academic Press, 1984, and Weiss Bach and Weiss Bach, Methods for Plant Molecular Biology, Academic Press, 1989.

The particular choice of a transformation technology will be determined by its efficiency to transform certain plant species as well as the experience and preference of the person practising the invention with a particular methodology of choice. It will be apparent to the skilled person that the particular choice of a transformation system to introduce nucleic acid into plant cells is not essential to or a limitation of the invention, nor is the choice of technique for plant regeneration.

The invention further encompasses a host cell transformed with vectors or constructs as set forth above, especially a plant or a microbial cell. Thus, a host cell, such as a plant cell, including nucleotide sequences of the invention as herein indicated is provided. Within the cell, the nucleotide sequence may be incorporated within the chromosome.

Also according to the invention there is provided a plant cell having incorporated into its genome at least a nucleotide sequence, particularly heterologous nucleotide sequences, as provided by the present invention under operative control of regulatory sequences for control of expression as herein described. The coding sequence may be operably linked to one

or more regulatory -sequences which may be heterologous or foreign to the nucleic acid sequences employed in the invention, such as those not naturally associated with the nucleic acid sequence (s) for its (their) expression. The nucleotide sequence according to the invention may be placed under the control of an externally inducible promoter to place expression under the control of the user. A further aspect of the present invention provides a method of making such a plant cell involving introduction of nucleic acid sequence (s) contemplated for use in the invention or a suitable vector including the sequence (s) contemplated for use in the invention into a plant cell and causing or allowing recombination between the vector and the plant cell genome to introduce the said sequences into the genome. The invention extends to plant cells containing a nucleotide sequence according to the invention as a result of introduction of the nucleotide sequence into an ancestor cell .

The term "heterologous" may be used to indicate that the gene/sequence of nucleotides in question have been introduced into said cells of the plant or an ancestor thereof, using genetic engineering, ie by human intervention. A transgenic plant cell, i.e. transgenic for the nucleotide sequence in question, may be provided. The transgene may be on an extra-genomic vector or incorporated, preferably stably, into the genome. A heterologous gene may replace an endogenous equivalent gene, ie one that normally performs the same or a similar function, or the inserted sequence may be additional to the endogenous gene or other sequence. An advantage of introduction of a heterologous gene is the ability to place expression of a sequence under the control of a promoter of choice, in order to be able to influence expression according to preference. Furthermore, mutants, variants and derivatives of the wild- type gene, e.g. with higher activity than wild type, may be used in place of the endogenous gene. Nucleotide sequences heterologous, or exogenous or foreign, to a plant cell may be non-naturally occurring in cells of that type, variety or species. Thus, a nucleotide sequence may include a coding sequence of or derived from a particular type of plant cell or species or variety of plant, placed within the context of a plant cell of a different type or species or variety of plant. A further possibility is for a nucleotide sequence to be placed within a cell in which it or a homologue is found naturally, but wherein the nucleotide sequence is linked and/or adjacent to nucleic acid which does not occur naturally within the cell, or cells of that type or species or variety of plant, such as operably linked to one or more regulatory sequences, such as a promoter sequence, for control of expression. A sequence within a plant

or other host cell may be identifiably heterologous, exogenous or foreign.

Plants which include a plant cell according to the invention are also provided, along with any part or propagule thereof, seed, selfed or hybrid progeny and descendants. Particularly provided are transgenic crop plants, which have been engineered to carry genes identified as stated above. Examples of suitable plants include tobacco (Nicotiana tabacum) and other Nicotiana species, carrot, vegetable and oilseed Brassica' s , melons, Capsicums, grape vines, lettuce, strawberry, sugar beet, wheat, barley, (corn)maize, rice, soyabean, peas, sorghum, sunflower, tomato, cotton, and potato. Especially preferred transgenic plants of the invention include cotton, rice, oilseed Brassica species such as canola, corn (maize) and soyabean.

In addition to a plant, the present invention provides any clone of such a plant, seed, selfed or hybrid progeny and descendants, and any part of any of these, such as cuttings, seed. The invention provides any plant propagule, that is any part which may be used in reproduction or propagation, sexual or asexual, including cuttings, seed and so on. Also encompassed by the invention is a plant which is a sexually or asexually propagated offspring, clone or descendant of such a plant, or any part or propagule of said plant, offspring, clone or descendant.

The present invention also encompasses the polypeptide expression product of a nucleic acid molecule according to the invention as disclosed herein or obtainable in accordance with the information and suggestions herein. Also provided are methods of making such an expression product by expression from a nucleotide sequence encoding therefore under suitable conditions in suitable host cells e.g. E.coli. Those skilled in the art are well able to construct vectors and design protocols and systems for expression and recovery of products of recombinant gene expression.

The heterologous or exogenous target protein is contemplated to be any protein of interest that may be produced by the method of the invention. Types of target proteins that are contemplated for production in a method of the present invention include plant proteins and pharmaceutical proteins for use in mammals, including man, such as insulin, preproinsulin, proinsulin, glucagon, interferons such as α-interferon, β- interferon, γ-interferon, blood-clotting factors selected from Factor VII, VIII, IX, X, XI, and XII, fertility hormones including luteinising

hormone, follicle stimulating hormone growth factors including epidermal growth factor, platelet-derived growth factor, granulocyte colony- stimulating factor and the like, prolactin, oxytocin, thyroid stimulating hormone, adrenocorticotropic hormone, calcitonin, parathyroid hormone, somatostatin, erythropoietin (EPO) , enzymes such as β-glucocerebrosidase, haemoglobin, serum albumin, collagen, insect toxic protein from Bacillus thuringiensis; herbicide resistance protein (glyphosate) ; salt-tolerance proteins; nutritional enhancement proteins involved in the biosynthesis of phenolics, starches, sugars, alkaloids, vitamins, and edible vaccines, and the like. Furthermore, the method of the invention can be used for the production of specific monoclonal antibodies or active fragments thereof and of industrial enzymes.

All proteins mentioned hereinabove are of the plant and human type. Other proteins that are contemplated for production in the present invention include proteins for use in veterinary care and may correspond to animal homologues of human proteins, such as the human proteins mentioned hereinabove .

A polypeptide according to the present invention may be an allele, variant, fragment, derivative, mutant or homologue of the (a) polypeptides as mentioned herein. The allele, variant, fragment, derivative, mutant or homologue may have substantially the same function of the polypeptides alluded to above and as shown herein or may be a functional mutant thereof .

"Homology" in relation to an amino acid sequence or polypeptide sequence produced by the method of the invention may be used to refer to identity or similarity, preferably identity. As noted already above, high level of amino acid identity may be limited to functionally significant domains or regions .

In certain embodiments, an allele, variant, derivative, mutant derivative, mutant or homologue of the specific sequence may show little overall homology, say about 20%, or about 25%, or about 30%, or about 35%, or about 40% or about 45%, with the specific sequence. However, in functionally significant domains or regions, the amino acid homology may be much higher. Putative functionally significant domains or regions can be identified using processes of bioinformatics, including comparison of the sequences of homologues .

Functionally significant domains or regions of different polypeptides may be combined for expression from encoding nucleic acid as a fusion protein. For example, particularly advantageous or desirable properties of different homologues may be combined in a hybrid protein, such that the resultant expression product, may include fragments of various parent proteins, if appropriate.

Similarity of amino acid sequences may be as defined and determined by the TBLASTN program, of Altschul et al . (1990) J. MoI. Biol. 215: 403-10, which is in standard use in the art. In particular, TBLASTN 2.0 may be used with Matrix BLOSUM62 and GAP penalties: existence: 11, extension: 1. Another standard program that may be used is BestFit, which is part of the Wisconsin Package, Version 8, September 1994, (Genetics Computer Group, 575 Science Drive, Madison, Wisconsin, USA, Wisconsin 53711) . BestFit makes an optimal alignment of the best segment of similarity between two sequences. Optimal alignments are found by inserting gaps to maximize the number of matches using the local homology algorithm of Smith and Waterman (Adv. Appl. Math. (1981) 2: 482-489). Other algorithms include GAP, which uses the Needleman and Wunsch algorithm to align two complete sequences that maximizes the number of matches and minimizes the number of gaps. As with any algorithm, generally the default parameters are used, which for GAP are a gap creation penalty = 12 and gap extension penalty = 4. Alternatively, a gap creation penalty of 3 and gap extension penalty of 0.1 may be used. The algorithm FASTA (which uses the method of Pearson and Lipman (1988) PNAS USA 85: 2444- 2448) is a further alternative.

Use of either of the terms "homology" and "homologous" herein does not imply any necessary evolutionary relationship between compared sequences, in keeping for example with standard use of terms such as "homologous recombination" which merely requires that two nucleotide sequences are sufficiently similar to recombine under the appropriate conditions. Further discussion of polypeptides according to the present invention, which may be encoded by nucleic acid according to the present invention, is found below.

The teaching of all references cited herein is incorporated in its entirety into the present description.

There now follow non-limiting examples and figures illustrating the invention.

Figure 1: Set of constructs for Arabidopsis chloroplast transformation.

Figure 2: Set of constructs for tobacco chloroplast transformation.

Figure 3: Set of constructs for tomato chloroplast transformation.

Figure 4: Set of constructs for rice chloroplast transformation.

Figure 5: Optimised chloroplast transformation cassette which includes introns in aadA and mGFP gene to stabilise transcript. trnl-LFS and trnA RFS- trnl and trnA flanking sequence; Prrn- chloroplast promoter from rrnl6 gene; intl-intδ- introns from the Arabidopsis genome introduced into coding sequences of aadA and mGFP4 genes in order to stabilise the transcript; psbA ter- chloroplast terminator from the chloroplast psbA gene; PBS - primer binding site for induction of the reverse transcriptase reaction.

Figure 6: Optimised cassette of LtrASi gene for expression in plants. Ubiq3At- ubiquitine 3 gene promoter from Arabidopsis; cTP- chloroplast transit peptide; LtrASi- synthetic LtrA gene synthesised for optimal expression in plants; ADH2-Intl, ADH2-Int2, intron 3- intron from Arabidopsis genome introduce to stabilise transcript of sLtrA in plants,- ags ter- plant polyadenylation sequence.

Figure 7: Tntl reverse transcriptase (RT) -RNase H (RH) (RT-RH) gene cassette facilitating reverse transcription of the chloroplast transgene cassette in the chloroplasts .

Figure 8: Vector constructs used for optimisation of chloroplast transformation using group II intron transformation vector. (A) ALG241 vector carrying chloroplast transgene cassette and LtrASi gene in pGreenOO29 binary vector (Hellens et al (2000) Plant MoI. Biol 42: 819- 832; www.pgreen.ac.uk). (B) ALG231 vector carrying Tntl RT-RH in pSOUP- 0179 binary vector (Hellens, supra) . Both plasmids were co-transformed into the Agrobacterium strain AGLl which was used for tobacco transformation.

Examples

Transgene delivery to the chloroplasts using group II intron vectors.

Concept

We have exploited the functional features of the intron to target and insert polynucleotide sequences of interest into the plastid, for example, the chloroplast genome. Group II introns have a conserved secondary structure and comprise six functional domains . Domain IV has not been shown to play any role in the splicing reaction, but it may contain an open reading frame (ORF) encoding a multifunctional protein (IEP) that is involved in splicing and intron mobility. We have removed this ORF from intron Domain IV and replaced it with a nucleotide sequence of interest for insertion into the chloroplast genome. The native ORF of the intron was fused to an organelle transit peptide and co-expressed separately.

We utilised the LtrB intron from Lactococcus lactis (amplified from Lactococcus lactis strain MG1363, Genoscope, FranceJ and the native chloroplast trnK intron from tobacco (amplified by PCR from tobacco genomic DNA of variety Petite Gerard) , both of which contain an ORF in Domain IV. The native maize atpF and petD introns (amplified from maize genomic DNA) , which do not have any ORF in Domain IV, were also used. Briefly, the chloroplast transgene cassette was inserted into Domain IV of the above-mentioned introns and it was expected that intron encoded ORF co-expressed in trans or in the case of the native maize atpF and petD introns that have no ORF in Domain IV, that native protein (s) expressed from the nuclear genome would be involved in intron splicing and targeting into the chloroplasts . The chloroplast transgene cassette contains a chloroplast Prrn promoter from tobacco, aadA-GFP4 fusion sequence, psbA 3'UTR terminator sequence from the tobacco chloroplast genome and two flanking regions homologous to the region of tobacco chloroplast genome between rbcL and accD genes .

Technology Rationale

The process of chloroplast transformation comprises two steps.

(1) Targeting of RNA-protein complex to the chloroplasts.

After delivery of the intron construct into the plant cell a strong expression of the intron RNA which contains the chloroplast targeted cassette is achieved from the nuclear-specific promoter. The intron encoded protein (IEP) fused to a chloroplast transit peptide, will be also over-expressed on co-delivery from the same or a different vector and then will bind to the intron RNA and facilitate folding and intron splicing from mRNA. Since the IEP is fused to a chloroplast transit

peptide it will then preferentially transfer the intron RWA into the chloroplasts . For introns such as atpF and petD which do not have any ORF for IEP in Domain IV it is expected that a native nuclear-encoded protein will perform similar functions as those of the introduced IEP with the LtrB and trnk introns. Once the intron cassette is presented in the plant cell via nuclear transformation, the chloroplast will then be permanently bombarded by the expressed IEP-intron RNA complex. Such stable and continuous pumping of the complex into the targeted organelle is a prerequisite for achieving a high efficiency of organelle transformation. The technology exploits the finding that the chloroplast transit sequence is sufficient to permit the whole IEP-intron RNA complex to be then taken up by the chloroplast .

(2) Reverse transcription of the transgene cassette and insertion into the chloroplast genome.

Once inside the organelle, the over-expression of the reverse transcriptase (RT-RH) from the tobacco tntl retrotransposon fused to the Rubisco small subunit chloroplast transit peptide facilitates reverse transcription of RNA from the transgene cassette. RT-RH recognises a primer binding site (PBS) and initiates reverse transcription using chloroplast encoded tRNA-Met as primer. RT-RH will catalyse reverse transcription of the transgene cassette, and insertion of the reverse transcribed cassette into the chloroplast genome will be induced due to homologous recombination between flanking sequences of the cassette and the homologous region in the chloroplast genome .

Once the population of organelle genomes has been transformed in the initial plant line, the nuclear encoded transgenes are no longer required and they can then be removed through segregation in subsequent plant generations, leaving a clean organelle transformed plant line.

Materials and Methods .

Preparation of group II intron based vector.

The LtrB intron, not containing the intron-encoded LtrA gene in Domain IV, was amplified using standard procedures known in the art (e.g. Molecular Cloning: a Laboratory Manual: 2nd edition, Sambrook et al, 1989, Cold Spring Harbor Laboratory Press) from Lactococcus lactis strain MG1364 using the following primers:

for 5 ' -prime part of the intron

IMlO 5

INT5-F (Xhol) TGTCTCGAGTGTGATTQCAACCCACGTCGAT (SEQ ID NO.l)

IMl06

INT5-R (ASCI) TGTGGCGCGCCACGCGTCGCCACGTAATAAATA (SEQ ID NO.2);

for 3 ' -prime part of the intron

IMl07

INT3-F (NotI) TGTGCGGCCGCTGGGAAATGGCAATGATAGCGA (SEQ ID NO . 3)

IMl08

INT3-R (EcoRI) TGTGAATTCCAGTCAAATTGTTTGCCAGTATAAAG (SEQ ID NO. 4)

LtrB 5' -intron

GTACGGAGTACTCGTAGTAGTCTGAGAAGGGTAACGCCCTTTACATGGCAAAGGGGT ACAGTTATTGTGTACT

AAATTCACAAGAAAATATAGACGAAGTTTTTACAAGACTTTATCGTTATCTTTTACG TCCAGATATTTATTAC GTGGCGACGCGTGGCGCGC (SEQ ID NO. 5)

LtrB 3 '-intron

CGGTTCCCGAAGAGGGTGGTGCAAACCAGTCACAGTAATGTGAACAAGGCGGTACCT CCCTACTTCACCATAT CATTTTTAATTCTACGAATCTTTATACTGGCAAACAATTTGACTGGAATTC (SEQ ID NO .6)

Intron encoded gene for LtrA protein was amplified separately from genomic DNA of L. lactis strain MG1363 using the following pair of primers :

_2Q

AS384 -F (SphI) GGCATGCATGAAACCAACAATGGCAATTTTA (SEQ ID NO . 7 )

AS187 -R (Spel ) GACTAGTTCACTTGTGTTTATGAATCACGTG (SEQ ID NO . 8 )

LtrA ORF

ACCACGTTACACTCATTGGACTCATCAATCTTAAAATCAAAGATATGAAAATGAGCC AATTGATTTATAAATT

CAAGAAGTTGGAGGGTGAAGAAAAAGCTAAAGTTCTTTTAGAATATCAAGAAAAACG TAAAAGATTACCCACA

GTTTCCAGTTCACAGGAAATATCTTATTCGTTCAACAGACTTΆGAAATCATCACAA TTTATAΆTTCTGAATTA AGAGGGATTTGTAATTACTACGGTCTAGCAAGTAATTTTAACCAGCTCAATTATTTTGCT TATCTTATGGAAT

TGTAAΆTCCCCTTATCAATTTACGGATGAGATAΆGTCAAGCTCCTGTATTGTATG GCTATGCCCGGAATACTC

ACTCTTGTTGTATGCTTTCATTGTCATCGTCACGTGATTCATAAACACAΆGTGAAC TAGT (SEQ ID

No.9)

The LtrA gene was translationally fused to chloroplast transit peptide using methods commonly employed in the art (e.g. Maniatis et al, supra) from pea chloroplast heat shock protein (Accession No. L03299) . The sequence for the transit peptide was amplified using the following primers :

AS293 - F (Xhol )

TCTCGAGTTGATGGCTTCTTCTGCTCAAATA (SEQ ID NO.10)

AS294-R (SphI)

GGCATGCAACTCTCAAAGTGAAACCCTTC (SEQ ID NO.11)

cTP

CGCATTCCCTAAGTTAAGTAGCAAAACCTTTAAGAAGGGTTTCACTTTGAGAGTTGC ATGC (SEQ ID NO.12)

The trnK intron was amplified from tobacco genomic DNA of variety Petite Gerard using primers

for 5' end of intron:

AS402 (Xhol)

GCTCGAGGTTGCTAACTCAACGGTAGAGTAC (SEQ ID NO. 13)

AS521 (ASCI)

GCACGCGTGGCGCGCCATTTCTATTTAAACCATGATCA (SEQ ID NO.14)

for 3' end of intron:

AS568 (Notl)

CACGCGTGCGGCCGCTTCTTCTAGTTTGTGGGGAGTA (SEQ ID NO.15)

AS405 (BamHI)

GGGATCCGATATGCTAGTGGGTTGCCCGGGA (SEQ ID NO. 16)

trnK intron 5 ' end

GTGCGGCTAGTCTCTTTTACACΆTΆTGGATGAAGTGAGGGΆTTCGTCCATACTC TCGGTAAAGTTTGGAAGAC CACGΆCTGATCCTGΆAAGGGAATGAATGGTAAAΆATAGCΆTGTCGTATCAACGGAA AGTTCTGAGAΆTATTTC ATTGTTCCTAGATGGGTATAAAACCGTGTTAGAATTCTTGGAACGGAACAAAATAAAGTT GGGTCGAATGAAT AAATGGATAGGGCTGCGGCTTCAATTAAATTATAGGGAAAGAAAGAAAAAGCAACGAGCT TTTGTTCTTAATT TGAATGATTCCCGATCTAATTAGACGTTAAAAATTTATTAGTGCCTGATGCGGGAAGGGT TTCTTGTCCCATG AGTGGATTCTCCATTTTTTTAATGAATCCTAACTATTACCATTTTCTATTACGGAGATGT GTGTGTAGAΆGAA ACAGTATΆTTGATAAΆGΆAAGTTTTTTCCGAAGTCAAAAGAGCGATTAGGTTGAΆA AAATAAAGGATTTCTAA

CCATCTTATTATCCTATAACACTATAACATAGACCAATTAAACGAAACGAAAAAAAA AAGAGATGATAGAGAA TCCGTTGAGAAGTTTACCTGTATCCΆAGGTATCTATTCTTACTAΆAΆTACTTTGTTT TAACTGTATCGCACTA

TTGCTCATGATCATGGTTTAAATAGAAATGCGCC(SEQ ID NO.17)

trnK intron 3' end

TCTAATTTCTATAAGAAAGGAACTGATGTATACATAGGGAAAGCCGTGTGCAATGAA AAATGCAAGCACGGCT

CCAT(SEQ ID NO. 18)

trnK intron encoded protein MatK was amplified from tobacco genomic DNA of variety Petite Gerard with primers

AS442 (Sphl)

GGCATGCCAAATGGAAGAAATCCAAAGATA (SEQ ID NO.19)

AS443 (SStI)

GGAGCTCTCATTGATAATTCGCCAGATCA (SEQ ID NO.20)

MatK

TTTTCAGGTTACCCTATGGTTATTCAAGGATCCTTTCATGCATTATGTTAGGTATCA AGGAAAATCCATTCTG GCTTCAAAAGGGACGTTTCTTTTGATGAATAAATGGAAATTTTACCTTGTCAATTTTTGG CAATGTCATTGTT CTCTGTGCTTTCACACAGGAAGGATCCATATAAACCAATTATCCAΆTCATTCCCGTGAC TTTATGGGCTATCT TTCΆAGTGTGCGACTAAΆTCCTTCAATGGTACGTAGTCAAATGTTAGAAAATTCATTT CTAΆTCAΆTAATGCΆ ATTAAGAAGTTCGATACCCTTGTTCCAATTATTCCTTTGATTGGATCATTAGCTAAAGCA AACTTTTGTACCG

TATTAGGGCATCCCATTAGTAAACCGGTTTGGTCCGATTTATCAGATTCTGATATTA TTGACCGATTTGGGCG

TATATGCAGAAATCTTTTTCATTATTATΆGCGGΆTCTTCCAAAAAAAAGACTTTA TATCGAATAAAGTATATA CTTCGACTTTCTTGTGCTAGAACTTTAGCTCGGAAACACAAΆΆGTACTGTACGCACTT TTTTGΆAAAGATCGG GCTCGGAATTATTGGAAGAATTCTTAACGTCGGAAGAACAAGTTCTTTCTTTGACCTTCC CACGAGCTTCTTC TAGTTTGTGGGGAGTATATAGAAGTCGGATTTGGTATTTGGATATTTTTTGTATCAATGA TCTGGCGAATTAT CAATGAGAGCTC (SEQ ID NO. 21)

Mat K was fused to chloroplast transit peptide sequence from pea HSP70 gene (see sequence above) .

The atpF intron was amplified from maize genomic DNA using primers

AS409 (Xhol)for 5' end of intron

GCTCGAGACTGTAGTGGTTGGTGTATTG (SEQ ID NO.22)

AS410 (ASCI)

GGGCGCGCCTTCTTTTTTGTTATGTATTATGGCT (SEQ ID NO.23)

for 3 ' end of intron

AS411 (Notl)

GGCGGCCGCAAAAAGGAGCGGGAGAGCCAAA (SEQ ID NO.24)

AS412 (Spel)

GACTAGTGAATAGTACTTAAAATCCTCTG (SEQ ID NO.25)

atpF intron 5' end

CTCGACGAATTACTTCTGAATAACTTCAGAAATCATATGGAΆGAACCATAGCΆTT TCGCGΆTTCATTGGTAAA

TTTTTCCAΆTGCCAAATCGACGACCTATGTATAΆAAAAAAGAGΆAATTTTTTGG ATTTGAAGΆAAAAATAΆAA GGΆATTCTΆTCAΆTTTTTATTTTCCATTTATTTΆGTTAGTTTTTCTTAATGAAATT GAAATTATTAACTAΆCΆ GAGCAAACACAAATAAAGAAACAACTTTGCTGACCATGATAGATTTTTATCTAGTTGGAA GAGTCCTCTTAAT ATTCATCTAGTCTTATATAAGTTTGGGTATATAGAAATACAAACAGAAAAGAGAGGATAG AGGATAGGCTCAT TACATAAAAAAAAGATATGGAAATAGCCATAATACATAACAAAAAAGAAGGCGCGCC (SEQ ID NO.26)

atpF intron 3' end

GCGGCCGCAAAAAGGAGCGGGAGAGCCAAATGAATCGAAAGATTCATGTTTGGTTCG GGAAGAGATCATAAAA ATTGTAAACTTAATAGCAAGATAATCTACTTTCATTAAAAGATTTATTAGATAATCGAAA ACAGAGGATTTTA AGTACTATTCACTAGT (SEQ ID NO.27)

petD intron was amplified from maize genomic DNA using primers

for 5' end of intron:

AS413 (Sail)

GGTCGACGGATACTTCTCTTCAACTTCGAAGT (SEQ ID NO.28)

AS414 (Spel)

GACTAGTACGCGGGTTCCCCATAATAATTATG (SEQ ID NO.29)

for 3' end of intron:

AS415 (Ascl)

GGGCGCGCCATAATGACTCAATGACTCAAGGTA (SEQ ID NO.30)

AS416 (Notl)

GGCGGCCGCATACCCCTATTCTATTGTGGATC (SEQ ID NO. 31)

petD intron 5' end

TCACTCGAGGAGAATATTTTCTATGATCATACCCCACCAACCATGTCATCCATGAAC AGGCTCCGTAAGATCC

TATGGAAATGCATTCATTTTCTTTGCATCGATTTTGATCCGCAATACTATCGGAGTA AAAGAAGGGATCTAAG

GAAAAGATAATTTGATAAAGTTTTTCTTACCTTGAGTCATTGAGTCATTATGGCGCG CC (SEO ID NO. 32)

petD intron 3 ' end

CTGACTTAAATGATCCTGTATTAAGAGCAAAATTAGCTAAAGGGATGGGACATAATT ATTATGGGGAACCCGC GTACTAGT (SEQ ID NO.33)

The chloroplast transformation cassette contains:

Prrn promoter tobacco

CTCGAGTTTGCTCCCCCGCCGTCGTTCAATGAGAATGGATAAGAGGCTCGTGGGATT GACGTGAGGGGGCAGG GATGGCTATATTTCTGGGAGCGAACTCCGGGCGAATACGAAGCGCTTGGATACAGTTGTA GGGAGGGATTTCC CGGG (SEQ ID NO.34)

Prrn was amplified from tobacco DNA with the primers

AS134-F (XhOl) TCTCGAGTTTGCTCCCCCGCCGTCGTTC (SEQ ID NO.35)

AS135-R (Smal) CCCCGGGCCCTCCCTGGAGTTCGCTCCCAGAAATAT (SEQ ID NO.36)

Prpsl6 promoter wheat

CCGCGGCATTCATATGATAGAATATGGGTTTAAATAAATTGGCTCTTTGCGGAGTCT TTCCCGATAAATACTT

AT (SEQ ID NO. 37)

Prpslδ was amplified from wheat genomic DNA cv. Pavon using primers

AS425 (SstII)

GCCGCGGCATTCATATGATAGAATATGGGT (SEQ ID NO.38)

AS518 (CIaI)

TATCGATAACATTCCTCTAATTTCATTGCA (SEQ ID NO.39)

aadA gene

CCCGGGATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTT GGCGTCATCGAGCGCC ATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGA AGCCACACAGTGA

GAΆΆCTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCA TTGTTGTGCACGACGACA TCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATG ACATTCTTGCAGG

TTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTT GAGGCGCTAAATGAAA

TTGGTACΆGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGG CAATGGAGCGCCTGCCG

GCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAA GATCGCTTGGCCTCGC

GCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAG TCGGCAAATCAGGATC C (SEQ ID NO.40)

aadA gene was amplified from E. coli carrying pCNl plasmid (Chinault et al (1986) Plasmid 15:119-131) using primers:

AS130 (Sma I)

GCCCGGGATGAGGGAAGCGGTGATCGCCGA (SEQ ID NO.41)

AS131 (Bam HI) GGGATCCTGATTTGCCGACTACCTTGGT (SEQ ID NO.42)

mGPP4 gene

(SEQ ID NO.43)

mGFP4 gene was synthesised based on NCBI data bank (http://www.ncbi.nlm.nih.gov/) Ac. No. U87624 and amplified using primers:

AS132 (Bam HI) GGGATCCATGAGTAAAGGAGAAGAACT (SEQ ID NO.44)

AS133 (Xba I)

TTCTAGATTATTTGTATAGTTCATCCA (SEQ ID NO.45)

The aadA and mGFP4 were then fused into one sequence to generate aadA- mGFP4 fusion

aadA-mGFP4 fusion sequence

CCCGGGATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTT GGCGTCATCGAGCGCC

TATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTT GATCAACGACCTTTTG GAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTT GTGCACGACGACA TCATTCCGTGGCGTTATCCAGCTAAGCGCGAΆCTGCΆATTTGGAGΆATGGCAGCGCA ATGACATTCTTGCAGG TATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGA ACATAGCGTTGCC TTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAG GCGCTAAATGAAA CCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTA CGTTGTCCCGCAT TTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAAT GGAGCGCCTGCCG

GCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAG TCGGCAAATCAGGATC

GGATCGAGCTTAAGGGAATCGATTTCAAGGAGGACGGAAACATCCTCGGCCACAAGT TGGAATACAACTACAA

CCTTCTTGAGTTTGTAACAGCTGCTGGGATTACACATGGCATGGATGAACTATACAA ATAATCTAGA (SEQ ID NO.46)

psbA terminator from tobacco

GTGCTATTGCTCCTTTCTTTTTTTCTTTTTATTTATTTACTAGTATTTTACTTACAT AGACTTTTTTGTTTAC

ATTGAAATAAGAAAGAAGAGCTATATTCGACCGCGG (SEQ ID NO.47)

psbA terminator was amplified from tobacco genomic DNA of variety Petite Gerard with primers :

AS136 (Xba I)

GTCTAGAGATCTTGGCCTAGTCTATAGGA (SEQ ID NO.48)

AS137 (Sac II) GCCGCGGTCGAATATAGCTCTTCTTTCTTA (SEQ ID NO.49)

atpA terminator from wheat

ACTAGTCAAATAAATTTTGCATGTCTACTCTTGTTAGTAGAATAGGAATCGTTGAGA AAGATTTTTCATTTGA

ATCΆTGCΆΆAAAAGTTTTCTTTGTTTTTAGTTTAGTATAGTTATTTΆAAGAAT AGATAGAAATAAGATTGCGT

CCAΆTAGGΆTTTGAACCTATACCΆAAGGTTTΆGΆAGACCTCTGTCCTATCCA TTAGACAATGGACGCTTTTCT

AΆATCAAAAΆATCCAGATACAAATGCATGATGTATATATTATATCΆTGCΆTΆ TATCATAAΆGAAGGAGTATGG AAGCTT (SEQ ID NO.50)

was amplified from wheat genomic DNA cv Pavon using primers

AS427 (Spel)

GACTAGTCAAATAAATTTTGCATGTCTACTC (SEQ ID NO.51)

AS428 (HinduI) GAAGCTTTCCATACTCCTTCTTTATGATATATG (SEQ ID NO.52)

Arabidopsis atpB Flanking Sequence

AGCCTTTGTTTTATCTAGCGAATTCGAAACGGAACTTTAGTTATGATTCATTATTTC GATCTCATTAGCCTTT TTTTTCGTATTTTCATTTTAGCATATCCGGTTCTCGAG (SE ID NO .53 )

was amplified from genomic DNA of Arabidopsis thaliana (CoI-O) with the primers :

Clf-f (Hind III) CCCAAGCTTTCTCATAATAAAAAAAATATGTTA (SEQ ID NO.54)

CIf-r (Xho I)

CCGCTCGAGAACCGGATATGCTAAAATGAAAATA (SEQ ID NO.55)

Arabidopsis rbcL Flanking Sequence

CATATGAAAGAATATACAATAATGATGTATTTGGCGAATCAAATATCATGGTCTAAT AAAGAATAATTCTGAT TAGTTGATAΆTTTTGTGAAAGΆTTCCTGTGAAAAAGGTTΆATTAAATCTATTCCTAA TTTATGTCGAGTAGAC CTTGTTGTTTTGTTTTATTGCAAGAATTCTAAATTCATGACTTGTAGGGAGGGACTTATG TCTAGA (SEQ

ID NO.56)

was amplified from genomic DNA of Arabidopsis thaliana (CoI-O) using primers :

Crf-f (Sac II) TCCCCGCGGATGCGTCCCATTTATTCATCCCT (SEQ ID NO.57)

Crf-r (Xba I)

GCTCTAGACATAAGTCCCTCCCTACAAGT (SEQ ID NO.58)

Tobacco rbcL Flanking Sequence

CTTGTGAΆGTATGGAΆAGAGATCGTΆTTTAATTTTGCAGCΆGTGGACGTTTTG GATAAGTAAAAACAGTAGAC

CATATATTTTGACTAAGTATATACTTACCTAGATATACAAGATTTGAAATACAAAAT CTAGCCGCGG (SEQ ID NO.59)

was amplified from tobacco genomic DNA of variety Petite Gerard with primers :

AS395 (Ascl)

GGGCGCGCCGAGACATAACTTTGGGCTTTGTTGA (SEQ ID NO.60)

AS397 (SacII)

GGCCGCGGCTAGATTTTGTATTTCAAATCTTGT (SEQ ID NO.61)

Tobacco accD Flanking Sequence

TCCTTAGGATTGGTATATTCTTTTCTATCCTGTAGTTTGTAGTTTCCCTGAATCAAG CCAAGTATCACACCTC

TCTTTATAGGAGAGGACAAATCTCTTTTTTCGATGCGAATTTGACACGACATAGGAG AAGCCGCCCTTTATTA

ATAGGAΆATAΆGATATTCAAATAAATAATTTTATAGCGAATGACTATTCATCTAT TGTATTTTCATGCAAATA

T(SEQ ID NO.62)

was amplified from tobacco genomic DNA of variety Petite Gerard with primers :

AS396 (Spel))

GGACTAGTGCGTTCGAACTCCTTCTTAAACAAC (SEQ ID NO.63)

AS398 (XhOl)

GGCTCGAGAACTAAATCAAAATCTAAGACTCA (SEQ ID NO.64)

Tomato atpB Flanking Sequence (tmLFS)

GGCGCGCCGTCCGCTAGCACGTCGATCGGTTAATTCAAAAAAATCGGAATTAGCACT CGATTTCGTTGGCACC

TTTTCTTTGCGTTTTTCTTTCTTTTTTATACCTTTCATΆGATTCATAGAGGAATTC CΆTΆTΆTTTTCACATCT AGGATTTACATATACAACATATACCACTGTCAAGGGGGAAGTTCCCGCGG (SEQ ID NO.65)

was amplified from tomato genomic DNA (Lycopersicon esculentum var. Moneymaker) with primers

AS417 (Ascl)

GGGCGCGCCGTCCGCTAGCACGTCGATCGGT (SEQ ID NO.66)

AS418 (SStII)

GCCGCGGGAACTTCCCCCTTGACAGTGGTAT (SEQ ID NO.67)

Tomato rbcL Flanking Sequence (tmRFS)

GAGTTCCACCTGAAGAAGCAGGGGCCGCGGTAGCTGCCGAATCTTCTACTGGTACAT GGACAACTGTATGGAG CATGC (SEQ ID NO.68)

was amplified from tomato genomic DNA (Lycopersicon esculentum var. Moneymaker) with primers :

AS419 (Sail)

GGTCGACAGGGGGAAGTTCTTATTATTTAGGT (SEQ ID NO.69)

AS420 (Sphl)

GGCATGCTCCATACAGTTGTCCATGTACCAGT (SEQ ID NO.70)

Rice atpB Flanking Sequence (rLFS)

GGCGCGCCCTTGTTGAATAATGCCAAATCAACACCAAAAAAATATCCAAAAATCCAA AAGTCAAAAGGAAATG

ATCAAATCCATGGTTTAATAACGAAGCATGTTAACTTACCATAACAACAACAAGCTT (SEQ ID NO.71)

was amplified from rice genomic DNA (Oryza sativa) , var. Nippon bare with primers :

AS421 (Ascl)

GGGCGCGCCCTTGTTGAATAATGCCAAATCAA (SEQ ID NO.72)

AS422 (Hindlll) GAAGCTTGTTGTTGTTATGGTAAGTTAACA (SEQ ID NO.73)

Rice Right rbcL Sequence (rRFS)

GTTGATATTAATTGAATATCTTTTTTTTAAGATTTTTGCAAAGGTTTCATTTACGCC TAATCCATATCGAGTA GACCCTGTCGTTGTGAGAATTCTTAATTCATGAGTTGTAGGGAGGGACGTATGTCACCAC AAACAGAAACTAA AGCAAGTGTTGGATTTAAAGCTGGTGTTAAGGATTATAAATTGACTTACTACACCCCGGA GTACGAΆACCAΆG GACACTGATATCTTGGCAGCATTCCGAGTAACTCCTCAGCCGGGGGTTCCGCCCGAAGAA GCAGGGGCTGCAG TAGCTGCCGAATCTTCTACTGGTACATGGACAACTGTTTGGACTGATGGACTTACCAGTC TTGAGCATGC

(SEQ ID NO.74)

was amplified from rice genomic DNA (Oryza sativa) , var. Nippon bare with primers

AS423 (SStII) GCCGCGGTCAATTCCTATCGAATTCCTATAGTA (SEQ ID NO.75)

AS424 (Sphl)

GGCATGCTCAAGACTGGTAAGTCCATCAGTCC (SEQ ID NO.76)

35S Promoter was synthesized based on NCBI data bank Ac. No. NC_001497 (http://www.ncbi.nlm.nih.gov/) was used for expression of intron containing the chloroplast transgene cassette.

35S Promoter

CCGAGTAACAATCTCCAGGAGATCAAATACCTTCCCAAGAAGGTTAAAGATGCAGTC AAAAGATTCAGGACTA ATTGCATCAAGAACACAGAGAΆAGACATATTTCTCAAGATCAGAAGTACTATTCCAGTA TGGACGATTCAAGG CTTGCTTCATAAACCAAGGCAAGTAATAGAGATTGGAGTCTCTAΆAAΆGGTAGTTCCT ACTGAATCTΆAGGCC ATGCATGGAGTCTAAGATTCAAATCGAGGATCTAACAGAACTCGCCGTGAAGACTGGCGA ACAGTTCATACAG

AAATGCCATCATTGCGATAAAGGAAAGGCTATCATTCAAGATCTCTCTGCCGACAGT GGTCCCAAAGATGGAC

CATCTCCACTGACGTAAGGGATGACGCACAATCCCACTATCCTTCGCAAGACCCTTC CTCTATATAAGGAAGT TCATTTCATTTGGAGAGGACΆCGCTCGAG (SEQ ID NO.77)

Arabidopsis TAF2 promoter was used to drive expression of intron encoded proteins (IEP) . It was amplified from genomic DNA of Arabidopsis thaliana (CoI-O) using the following primers:

TAF2-F GGTACCATGATCGCTTCATGTTTTTATC (SEQ ID NO. 153) TAF2-R CTCGAGGTTCCTTTTTTGCCGATATGTT (SEQ ID NO. 154)

Arabidopsis TAF2 promoter

GGTACCΆTGATCGCTTCATGTTTTTATCTAATTTGTTAGCΆTATTGΆATGATTG ATTTTCTTTTAΆTTTGGAT

TCGACAATCGATGCGTATGTGTACACAATTACCAAAACAATTATTTGAΆTATTCAG ACATGGGTTGACATCAC

TTTCATAGTTCATACATCACTAATACTAAAAGATGCATCATTTCACTAGGGTCTCAT GAAATAGGAGTTGACA TTTTTTTTTGTAACGACAGAΆGTTGACATGTTAAGCΆTCAATTTTTTTAAGAGTGGΆ TTATACTAGTTTTTTT TTTTTTTTTTAATGTATGGTATGATACAACAACAAΆΆACTATAAAATAGAAAAAGTCA GTGAAACCTCAAATT GAAGGAAAAACTTTTGCACAAAAAGAGAGAGAGAGAGAAAGAATGTAAATCCAAATAAAT GGGCCTAATTGAG AATGCTTTAACTTTTTTTTTTTGGCTAAAAGAGAATGCTTTAACTAAGCCCATAAAATGA ACATCAAACTCAΆ AGGGTAAGATTAATACATTTAGAAAACAATAGCCGAATATTTAATAAGTTTAAGACATAG AGGAGTTTTATGT AATTTAGGAACCGATCCATCGTTGGCTGTATAAAAAGGTTACATCTCCGGCTAACATATC GGCAAAAAAGGAA

CCTCGAG (SEQ ID NO.78)

Plant Transformation

Transformation of Arabidopsis Plants

Transformation of Arabidopsis plants was performed as described by Clough & Bent (Clough & Bent (1998) Plant Journal 16:735-743). Agrobacterium tumefacience strain GV3101 (Koncz & Schell (1986) MoI Gen Genet 204:383- 396) was used for transformation. Transformation of plants was carried out with three different constructs ALG4-1, ALG4-2 and ALG8-1 (Figure 1) based on the pGreen 0029 binary vector (Hellens et al (2000) Plant MoI. Biol 42: 819-832). In brief, a chloroplast transformation cassette containing atpB flank, Prrn promoter, aadA-mGFP4 fusion, psbA 3' UTR, rbcL flank was inserted into domain IV of the LtrB or trnK introns using Ascl-Notl enzymes. The introns containing the transformation cassette were fused to the 35S promoter and nos terminator and introduced into the pGreenOO29 binary vector (Figure 1) . The LtrB intron encoded protein LtrA was fused to a chloroplast transit peptide and inserted into pGreen 0029 together with the cassette from ALG4-1, resulting in ALG4-2. Transgenic lines were recovered on selection medium supplemented with 50mg/l of kanamycin.

Transformation of tobacco plants

Tobacco plants were transformed as described by Horschet (Horschet al(1985) Science 227: 1229-1231) using Agrobacterium strain AGLl (see protocol, below) .

Five constructs comprising four different introns, the LtrB intron from Lactococcus lactis, trnK intron from tobacco, and the atpF and petD introns from maize were used for vector construction (Figure 2) . A chloroplast transgene cassette carrying rbcL flank, Prrn promoter, aadA-

mGPP4 fusion, psbA 3' UTR, accD flank was inserted into domain IV of each of the said introns . The intron containing the transgene cassette was placed under control of the 35S promoter and nos terminator, and then inserted into the binary vector pGreenOO29, resulting in constructs ALG6, ALG8, ALG9, ALGlO. The LtrB intron encoded gene for LtrA was fused to a chloroplast transit peptide and Arabidopsis TAF2 promoter was added to the ALG6 construct resulting in ALG7 vector. The trnK intron encoded gene for matK proteins was also fused with chloroplast transit peptide and added to ALG8 resulting in ALG8-1 vector.

Transgenic tobacco plants were regenerated on selection medium supplemented with 300 mg/1 of kanamycin.

Transformation of tomato plants

Transgenic tomato plants were generated as described by Fillatti et al . (Fillatti et al (1987) Bio/Technology 5, 726-730) using Agrobacterium strain AGLl (see protocol, below) . Two constructs were prepared based on ALG7 and ALG8-2 vectors, wherein tobacco flanking sequences were replaced by tomato specific atpB and rbcL flanking sequences resulting in ALG7-1 and ALG8-3 vectors (Figure 3) .

Transformation of rice plants

Rice transformation was performed using particle bombardment as described by Christou et al (Christou et al (1991) Bio/Technology 9:957-962). The japonica rice cultivar Nipponbare was used for transformation. A chloroplast transgene cassette containing rice atpB flanking region, wheat 16S promoter, aadA-mGFP4 fusion, wheat atpA ternminator, and rice rbcL flanking sequences was prepared. This transgene cassette was inserted into the LtrB intron cassette, atpF intron cassette and petD intron cassette in the pGreen 0179 vector containing hygromycin encoded resistance, resulting in vectors ALG7-2, ALG9-1 and ALGlO-I (Figure 4). Transgenic plants were recovered on medium supplemented with 50 mg/1 of hygromycin.

Molecular-biological analysis

DNA from transgenic plants was isolated using the procedure described by Puchooa (Puchooa (2004) African J Biotech 3:253-255) or by using Invitrogen DNeasy plant mini kit following the manufacturer's instructions. RNA was isolated using TRI REAGENT™ (Sigma) .

PCR reactions were performed using GoTaq Flexi DNA Polymerase (Promega) , following the manufacturer's instructions. The following primers were used:

Arabidopsis

MS7 CCCTCTGTCGCACTCATAGCTACAG (SEQ ID NO.79)

MS18 GGAGATGTTGTGCGAGTATCGACAGG(SEQ ID NO.80)

IM68 CAACCATTACCTGTCCACACAATCTGCC(SEQ ID NO.81)

IM69 GCTGGGATTACACATGGCATGGATGAAC(SEQ ID NO.82)

IM70 ATAGGTGAAAGTAGTGACAAGTGTTGGC(SEQ ID NO.83)

IM71 CGTATGTTGCATCACCTTCACCCTCTC(SEQ ID NO.84)

Tobacco

AS457 AGAGAATTGGGCGTTCCGATCGTAA (SEQ ID NO.85) AS458 GGATTCACCGCAAATACTAGCTTG (SEQ ID NO.86) AS459 GAAATTCCGAATGTCTTTAACGCCGA(SEQ ID NO.87) AS460 TGGAATAACTGTCTCCATTCCTATCACT(SEQ ID NO.88) IM68 CAACCATTACCTGTCCACACAATCTGCC(SEQ ID NO.81) IM69 GCTGGGATTACACATGGCATGGATGAAC(SEQ ID NO.82) IM70 ATAGGTGAAAGTAGTGACAAGTGTTGGC(SEQ ID NO.83) IM71 CGTATGTTGCATCACCTTCACCCTCTC(SEQ ID NO.84)

Tomato

TMl AAAGGCTACATCTAGTACCGGAC (SEQ ID NO.89)

TM2 CCAGAAGTAGTAGGATTGATTCTCA(SEQ ID NO.90)

TM3 CGATCAAGACTGGTAAGTCCAT(SEQ ID NO.91)

TM4 ACAATGGAAGTAAGCATATTGGTAA(SEQ ID NO.92)

Rice

RCl GGGTCCAATAATTTGATCGATA(SEQ ID NO.93)

RC2 CGAGAAGTAGTAGGATTGGTTCTC(SEQ ID NO.94)

RC3 GTCTAATGGATAAGCTACATAAGCGA(SEQ ID NO.95)

RC4 CCCACAATGGAAGTAAACATGT(SEQ ID NO.96)

Amplified fragments were cloned into the pGEM t-easy vector and sequenced to confirm correct insertion site. Non-radioactive Southern and Northern analyses were performed using DIG High Prime DNA Labeling and Detection Kit and DIG Northern Kit (Roche) following manufacturer's instructions.

Results and Discussion

The transformation of Arabidopsis, tobacco, tomato and rice was performed with group II-based intron vectors containing transgene cassettes for chloroplast transformation. Vectors with intron encoded proteins (IEP) such as LtrA and matK or without introduced IEP were used. In all cases we were able to detect insertion of the transgene cassette into the chloroplast genome using PCR amplification of junction regions. Five independent transgenic lines were analysed for all constructs and we could amplify correct size DNA fragment for insertion junctions in all lines. The amplified fragments were seguenced and correct insertion sites were confirmed. The same data was generated with PCR amplification of insertion flanks in tobacco for lines with tobacco trnK intron based vector (ALG8) and maize atpF and petD based vectors. Northern analysis was also performed to confirm presence of sense chloroplast transcripts . All transformation vectors had the transgene cassette inserted in the antisense orientation and as a result, the transcript generated from the nucleus will also be in the antisense orientation. Only the transgene cassette which is inserted into the chloroplast genome can generate a sense transcript of the transgene. We have prepared DIG-labeled antisense probes using T3 RNA polymerase and used them in Northern hybridisation. Indeed, we could detect sense transcripts on total RNA in all lines transformed with ALG6,ALG7 and ALG8 vectors. No signal was detected on the mRNA sample indicating that the transcript was of chloroplast origin (chloroplast transcripts are mainly not polyadenylated) or in the negative control where total RNA of wild type tobacco was used.

We have learned that over-expression of the IEP improves the efficiency of transformation, however, endogenous proteins expressed from the nucleus may also perform the same functions due to the conserved structure of the intron. Putative proteins related to group II reverse transcriptase/maturases were identified using sequence alignments in Arabidopsis and rice genomes (Mohr & Lambowitz (2003) Nucleic Acids Research 31:647-652) . It has also been shown that a number of proteins expressed from the nucleus (CRSl, CRS2 , CAFl, HCF-152) are participating in splicing of organellar introns (Jenkins et al (1997) Plant Cell 9:283- 296; Vogel et al (1999) Nucleic Acids Research 27:3866-3874; Fisk et al (1999) EMBO J 18: 2621-2630; Meierhoff et al (2003) Plant Cell 15: 1480- 1495; Ostheimer et al (2003) EMBO J 22: 3919-3929). These proteins bind to intron RNA and are thought to serve as a vessel for targeting of RNA of intron-based vectors into the organelles. The chloroplast genome of plants contains only one ORF matK which is similar to the LtrA gene from

L.lactis and is encoded by the trnK intron. It has been shown that this protein has intron RNA-binding activity and may be responsible for reverse transcription in the chloroplasts (Liere & Link (1995) Nucleic Acids Research 23: 917-921). The presence of this protein in chloroplasts is the major prerequisite for insertion of intron-based vectors as they could be reverse transcribed by matK after targeting into the chloroplasts by nuclear- encoded proteins involved in splicing.

2. Chloroplast Transformation Optimisation

The following improvements were introduced to optimise efficiency of chloroplast transformation:

1. The Ll.LtrB intron of Lactococcus lactis was optimised in silico by eliminating cryptic splicing sites and optimising its expression in plants using the web-based programme found at http : //www. cbs .dtu.dk/services/NetPGene/ .

2. The chloroplast transgene cassette was modified by insertion of introns from the Arabidopsis genes At2g29890 (introns 1, 2, 3, 5, 6) and Atlg67090 (intron 4)

(http: //www. arabidopsis . org/servlets/Search?type=general&action=new __search) which stabilises the transcript in plant cells, and by addition of a primer binding site (PBS) to the 3' end of the cassette to better facilitate reverse transcription of the cassette;

3. A synthetic LtrA gene was synthesised with optimal plant codon usage for expression in plants, and selected introns from the Arabidopsis At5g43940 gene were introduced to improve stability of the RNA transcript;

4. Over-expression of the reverse transcriptase (RT-RH) from the tobacco tntl retrotransposon (Accession No. X13777) fused to the Rubisco small subunit chloroplast transit peptide (Accession No. X02353, position 1048-1218) from tobacco was generated to facilitate reverse transcription of RNA from the transgene cassette. RT-RH recognises the primer binding site (PBS) and so initiates reverse transcription using the chloroplast tRNA-Met as a primer.

Optimised Ll.LtrB intron

ACACATCCATAACGTGCGCCCAGATAGGGTGTTAAGTCAAGTAGTTTAAGGTACTAC TCAGTAAGATAACACT GAAAACΆGCCAACCTAACCGAAAAGCGAAAGCTGATACGGGAACAGAGCACGGTTGGAA AGCGATGAGTTAGC TAAAGACAATCGGCTACGACTGAGTCGCAATGTTAATCAGATATAAGCTATAAGTTGTGT TTACTGAACGCAA GTTTCTAATTTCGGTTATGTGTCGATAGAGGAAΆGTGTCTGAAACCTCTAGTACAΆAG AAAGCTAAGTTATGG

GCGAGAATCTGAATTTACCAAGACTTAACACTAACTGGGGATAGCCTAAACAAGAAT GCCTAATAGAAAGGAG GAAAAAGGCTATAGCACTAGAGCTTGAAAATCTTGCAAGGCTACGGAGTAGTCGTAGTAG TCTGAGAAGGCTA

GGGTGGTGCAAACCAGTCACAGTAATGTGAACAAGGCGGTACCTCCCTACTTCAC (SEQ ID NO. 97)

Synthetic LtrA gene optimised for plant transformation (LtrASi)

TTCTACAAAGGGAATCCTCGATGATACAGCTGATGGATTCTCTGAGGAGAAGATCAA GAAGATCATCCAATCT

AAGACTTACAGCGGAACACCTCAGGGCGGAΆTCCTCTCTCCTCTCCTCGCTAACAT CTATCTTCATGAATTGG ACAAGTTCGTTCTCCAACTCAAGATGAAGTTCGACCGAGAGAGTCCAGAGAGAATCACAC CTGAATACCGGGA GCTTCACAACGAGATCAAAAGAATCTCTCACCGTCTCAAGAAGTTGGAGGGCGAGGAGAA GGCTAAGGTTCTC TTGGAATACCAGGAGAAGAGGAAGAGGTTGCCTACACTCCCTTGTACATCACAAACAAAC AAGGTTCGTTCTC TCCATTTTCΆTTCGTTTGAGTCTGATTTAGTGTTTTGTGGTTGATCTGAΆTCGATTTA TTGTTGATTAGTGAA TCAATTTGAGGCTGTGTCCTAATGTTTTGACTTTTGATTACAGGTCTTGAAGTACGTCCG ATACGCTGACGAC TTCATCΆTCTCTGTTAAGGGΆΆGCAAGGΆGGACTGTCAΆTGGATCAAGGAGCAAT TGAΆGCTCTTCATCCΆTA ACAAGCTCAAGATGGAATTGAGTGAGGAGAAGACACTCATCACACATAGCAGTCAGCCTG CTCGTTTCCTCGG ATACGACATCCGAGTCAGGAGAAGTGGAACTATCAAGCGATCTGGAAAGGTCAAGAAGAG AACACTCAACGGG AGTGTGGAGCTTCTCATCCCTCTCCAΆGACAAGATCCGTCAATTCATCTTCGACAAGΆ AGATCGCTATCCAGA AGAAGGATAGCTCATGGTTCCCAGTTCACAGGAAGTACCTTATCCGTTCAACAGACTTGG AGATCATCACAAT CTACAACTCTGAATTGAGAGGTΆAGCTGCTACCTCAAACTTTCTAGTGCTTCCATATTT CCTTTCTTCTGCAA GGCAGAGAACCATTGTGGTTAAGTGTTTTAAATTGTGAATGTATAGGTATCTGCAACTAC TACGGTCTCGCAA GTAACTTCAACCAGCTCAACTACTTCGCTTACCTTATGGAATACTCTTGCTTGAAGACTA TCGCATCTAAGCA TAAGGGAΆCACTCTCΆAAGACCATCTCTATGTTCΆAGGATGGAΆGTGGTTCTTGGG GAΆTCCCTTACGAGΆTC

AAGCAGGGGAAGCAGAGGAGATACTTCGCCAACTTCAGTGAATGCAAATCTCCTTAC CAATTCACTGATGAGA TCAGTCAAGCTCCTGTGCTTTACGGATACGCTCGGAACACTCTTGΆGAACAGΆCTTAA GGCTAAGTGTTGTGA GCTTTGTGGAACATCTGATGAGAACACATCTTACGAGATCCACCACGTCAACAAGGTCAA GAACCTTAAGGGA AAGGAGAAGTGGGAGATGGCAATGATCGCTAAGCAGCGGAAGACTCTTGTTGTTTGCTTC CATTGTCATCGTC ACGTGATCCATAAGCACAAGTGA (SEQ ID NO. 98)

The LtrASi (LtrASi : LtrA Synthetic + Introns) sequence was designed in silico and then chemically synthesised using introns that were introduced into the synthetic sequence using overlapping primers. The introns were amplified from Arabidopsis genomic DNA using the following primers :

IM333 ATCTACAAGTTCCTCAAGGCAGGTACCTTTATCCTCGATCCTCG (SEQ ID NO. 99) IM334 TACTGCCAGTTTTCGAGGTAACCTATGTGAATCGGCGTCAAAAT (SEQ ID NO. 100) for intron 1;

IM337 TTGTACATCACAAACAAACAAGGTTCGTTCTCTCCATTTTCATT (SEQ ID NO. 101) IM338 CGTATCGGACGTACTTCAAGACCTGTAATCAAAAGTCAAAACAT (SEQ ID NO. 102) for intron 2.

IM341 ATCTACAACTCTGAATTGAGAGGTAAGCTGCTACCTCAAACTTT (SEQ ID NO. 103) IM342 AGACCGTAGTAGTTGCAGATACCTATACATTCACAATTTAAAAC (SEQ ID NO. 104) for intron 3.

The LtrAS coding region was amplified using standard procedures employed in the art (e.g. Maniatis et al supra) using the following primers:

LTRA-F21 GCATGCATGAAGCCAACAATGG (SEQ ID NO.105)

IM332 CGAGGATCGAGGATAAAGGTACCTGCCTTGAGGAACTTGTAGAT (SEQ ID NO.106) for fragment 1 ;

IM335 ATTTTGACGCCGATTCACATAGGTTACCTCGAAAACTGGCAGTA (SEQ ID NO. 107) IM336 AATGAAAATGGAGAGAACGAACCTTGTTTGTTTGTGATGTACAA (SEQ ID NO. 108) for fragment 2 ;

IM339 ATGTTTTGACTTTTGATTACAGGTCTTGAAGTACGTCCGATACG (SEQ ID NO. 109) IM340 AAAGTTTGAGGTAGCAGCTTACCTCTCAATTCAGAGTTGTAGAT (SEQ ID NO.110) for fragment 3 ;

IM343 GTTTTAAATTGTGAATGTATAGGTATCTGCAACTACTACGGTCT (SEQ ID NO. Ill) LTRA-R21 TTACTAGTTCACTTGTGCTTATGG (SEQ ID NO. 112)

for fragment 4.

The intron and coding sequence fragments were pooled together and PCR amplification using methods commonly employed in the art (Maniatis et al, supra) of the whole LtrASi sequence was performed with LTRA-F21 and LTRA- R21 primers.

aadA-mGFP fusion optimised for transformation

ATTTCTTCGTTTCCGTCTGCAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGAC GTTGCTGGCCGTACAT

GGCTTGATGAAACAΆCGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCT TCCCCTGGAGAGAGCGA

CGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATG GCAGCGCAATGACATT CTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAA GCAAGAGAACATA GCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATC TATTTGAGGCGCT AAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCAGGTAAGAAATCTTTTCC CATCTTGAAGTCA

TATACTTTCACTAATAATATGCGTGGAAACATTGCAGGTGATGAGCGAAATGTAGTG CTTACGTTGTCCCGCA TTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAA TGGAGCGCCTGCC GGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAΆG ATCGCTTGGCCTCG

CCATGGCTAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAAT TAGATGGTGATGTTAA TGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAΆGGTAATTAAACAAAATTTAAACATC TATATAAACTAGCT

TTCAAAGATGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTAAGTAA ATATTGGTAATATAAC ATTTTTACATGACTTTGGTGTCTTAATTTGTCGTTTCGCATGTGTTTCATTTAGTTTCTG CCAGAGCATCTGA

AGGAΆTCGACTTCAAGGAAGATGGAAACATCCTCGGACACAAGCTGGAGTACAACTACA ACTCACACAACGTG TACATCACCGCAGACAAACAGAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCACAAC ATTGAAGATGGTT CCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATAGGTACGCAGGCTATATAGG CTTTGACATTTTT TTGTTTTCATATTTTTC _TT TGTTCCACTATGAACTTCATTCTGTTTTTTGACTTCΆTTGCAGGTGATGGCCCT GTCCTTTTACCAGACAΆCCATTACCTGTCGACACAATCTGCCCTTTCGAAAGATCCCAA CGAAAAGCGAGACC

ACATGGTCCTTCTTGΆGTTTGTAACAGCTGCTGGGATTΆCACATGGCATGGΆTG AGCTCTACAAATAA (SEQ

ID NO. 113)

The introns were inserted into aadA-mGFP4 fusion sequence by PCR with overlapping primers . Introns were amplified by PCR from Arabidopsis genomic DNA using the following primers: aadAP2 actatcagaggtaagtaacttttagctctca (SEQ ID No. 114) aadAR2 cgccaactacctgcagacggaaacgaagaa (SEQ ID No. 115) for intron 1 ; aadAF4 cgctgtagaggtaattttcatctttgtttggcct (SEQ ID NO. 116) aadAR4 caatggtgacctgcaatctcataagtacaatg (SEQ ID NO. 117) for intron 2 ; aadAP6 gactgggcaggtaagaaatcttttcccatcttga (SEQ ID NO. 118) aadARβ cgctcatcacctgcaatgtttccacgcatat (SEQ ID NO. 119) for intron 3 ; mGFP2F gagggtgaaggtaatttattcttctttgttttc (SEQ ID NO. 120) mGFP2R gtagcatcacctgtttaagaagaaaatcaaaat (SEQ ID NO. 121) for intron 4 ; mGFP4F aagtttgaaggtaagtaaatattggtaatataac (SEQ ID NO. 122) mGFP4R agggtatcacctagagcaaagcaacatcatatc (SEQ ID NO. 123) for intron 5 ; mGFP6F tactccaataggtacgcaggctatataggctttg (SEQ ID NO. 124) mGFP6R agggccatcacctgcaatgaagtcaaaaaacag (SEQ ID No. 125) for intron 6 (Fig. 5) .

The PCR for aadA fragments was performed with the following primers :

AS756 atacaagtgagttgtagggagggaatcatggcagaagcggtgatcgccga (SEQ ID

NO.126) aadARl aagttacttacctctgatagttgagtcgata (SEQ ID NO. 127) for fragment 1; aadAF3 ccgtctgcaggtagttggcgtcatcgagcgcca (SEQ ID NO. 128) aadAR3 gatgaaaattacctctacagcgcggagaatct (SEQ ID NO. 129) for fragment 2 ; aadAF5 gagattgcaggtcaccattgttgtgcacgac (SEQ ID NO. 130) aadAR5 agatttcttacctgcccagtcgggcggcga (SEQ ID NO. 131) for fragment 3 ; aadAF7 aaacattgcaggtgatgagcgaaatgtagtgct (SEQ ID NO. 132)

AS131 tcctgatttgccgactaccttggt (SEQ ID NO. 133) for fragment 4.

The fragments amplified with primers for introns 1, 2 and 3 were mixed with the fragments 1, 2, 3 and 4 amplified from the aadA gene and PCR was

performed with AS756 and AS131 primers to generate aadA sequence with introns .

mGFP gene fragments were amplified with the following primers :

AS132 gggatccatgagtaaaggagaagaact (SEQ ID NO. 134) πiGFPRl aaaatttagaacagatattgaccttcaccctctccactgacagaa (SEQ ID NO.135) for fragment 1 ; mGFPF3 ttcttaaacaggtgatgctacatacggaaaac (SEQ ID NO. 136) mGFPR3 atttacttaccttcaaacttgacttcagcac (SEQ IS NO. 137) for fragment 2 ; mGFPF5 ctttgctctaggtgatacccttgttaatcgta (SEQ ID NO. 138) mGFPR5 agcctgcgtacctattggagtattttgttgataat (SEQ ID NO. 139) for fragment 3 ; nιGFPF7 ttcattgcaggtgatggccctgtccttttacca (SEQ ID NO. 140)

AS133 ttctagattatttgtatagttcatcca (SEQ ID NO. 141) for fragment 4.

The intron 4, 5 and 6 fragments were mixed with mGFP fragments 1, 2, 3 and 4, and PCR was performed with the primers AS132 and AS133 to generate mGFP sequence with introns .

The generated aadA and mGFP sequences with introns were fused by digestion of aadA fragment with Xmal-BamHI enzymes, mGFP fragment with

BamHI-Xbal enzymes and ligation in BlueScript SK digested with Xmal-Xbal enzymes . The resulting fusion fragment was then subsequently inserted in chloroplast cassette (Fig. 5) .

Tntl-RT-RH sequence (RT-RH)

ATGTCAGAAAAGGTGAAGAATGGTATAATTCCTAACTTTGTTACTATTCCTTCTACT TCTAACAATCCCACAA GTGCAGAΆAGTACGACCGACGAGGTTTCCGAGCAGGGGGAGCAACCTGGTGAGGTTATT GAGCAGGGGGAGCA ACTTGATGAAGGTGTCGAGGAAGTGGAGCACCCCACTCAGGGAGAAGAACAACATCAACC TCTGAGGAGATCA GAGAGGCCAAGGGTAGAGTCACGCAGGTACCCTTCCACAGAGTATGTCCTCATCAGTGAT GAGGGGGAGCCAG AAAGTCTTAAGGAGGTGTTGTCCCATCCAGAAAAGAACCAGTGGATGAAAGCTATGCAAG AAGAGATGGAATC TCTCCAGAAAAATGGCACATACAAGCTGGTTGAACTTCCAAAGGGTAΆAAGACCACTCA AATGCAAATGGGTC TTTAAACTCAAGAAAGATGGAGATGGCAAGCTGGTCAGATACAAAGCTCGATTGGTGGTT AAAGGCTTCGAAC AGAAGAAAGGTATTGATTTTGACGAAATTTTCTCCCCCGTTGTTAAAATGACTTCTATTC GAACAATTTTGAG CTTAGCAGCTAGCCTAGATCTTGAAGTGGAGCAGTTGGATGTGAAAACTGCATTTCTTCA TGGAGATTTGGAA GAGGAGATTTATATGGAGCAACCAGAAGGATTTGAAGTAGCTGGAAAGAΆACACATGGT GTGCΆAATTGAATA AGΆGTCTTTATGGATTGAAGCAGGCΆCCAAGGCAGTGGTACATGAAGTTTGATTCATT CATGAAAAGTCAAΆC ATACCTAAΆGACCTATTCTGATCCATGTGTATACTTCAAAΆGATTTTCTGAGAATAAC TTTATTATATTGTTG TTGTATGTGGATGACATGCTAATTGTAGGAAAAGACAAGGGGTTGATAGCAAAGTTGAAA GGAGATCTGTCCA AGTCATTTGATATGAAGGACTTGGGCCCAGCACAACAAATTCTAGGGATGAAGATAGTTC GAGAGAGAACAAG

TAGAAAGTTGTGGCTATCTCAGGAGAAGTACATTGAACGTGTACTAGAACGCTTCAA CATGAAGAATGCTAAG

CCAGTCΆGCACACCTCTTGCTGGTCATCTAAAGTTGAGTAAAAAGATGTGTCCTAC AACAGTGGAAGΆGAAΆG GGAACATGGCTAAAGTTCCTTATTCTTCAGCAGTCGGAΆGCTTGATGTATGCAATGGTA TGTACTAGACCTGΆ TATTGCTCACGCAGTTGGTGTTGTCAGCAGGTTTCTTGAΆAATCCTGGAAAGGAACATT GGGAAGCΆGTCAAG TGGATACTCAGGTACCTGAGAGGTACCACGGGAGATTGTTTGTGCTTTGGAGGATCTGAT CCAATCTTGAAGG

TCGGAATGCATTCAAACTAG (SEQ ID NO. 142)

The RT-RH fragment was amplified from tobacco genomic DMA following standard procedures using the following primers :

AS774 ggcatgcatgtcagaaaaggtga (SEQ ID NO. 143)

AS775 gactagtctagtttgaatgcattccgacaagttct (SEQ ID NO. 144)

Rubisco small subunit transit peptide sequence

ATGGCTTCCTCAGTTCTTTCCTCTGCAGCAGTTGCCACCCGCAGCAATGTTGCTCAA GCTAACATGGTTGCAC

CAGCAATGGTGGAAGAGTGCAATGTATGCAGGTA (SEQ ID NO. 145)

Rubisco small subunit transit peptide sequence was amplified from tobacco genomic DNA using the following primers:

AS794 gctcgagacaatggcttcctcagttctttcctct (SEQ ID NO. 146)

AS639 cgcatgctacctgcatacattgcactcttccaccat (SEQ ID NO. 147)

The transit peptide was then fused to RT-RH (Fig. 7)

Primer Binding Site (PBS) sequence

TTGGTACCTACT (SEQ ID NO. 148)

Primer binding site was introduced to trnA RFS by primer:

RFS-PBS-R gccgcagtaggtaccaattgcccttctccgaccctgac (SEQ ID NO. 149) .

Arabidopsis ubiquitin promoter (Ubiq3At)

CGGTACCTACCGGATTTGGAGCCAAGTCTCATAAACGCCATTGTGGAAGAAAGTCTT GAGTTGGTGGTAATGT AACAGAGTAGTAAGAACAGAGAAGAGAGAGAGTGTGAGATACATGAATTGTCGGGCAACA AAAATCCTGAACA TCTTATTTTAGCAAAGAGAAAGAGTTCCGAGTCTGTAGCAGAAGAGTGAGGAGAAATTTA AGCTCTTGGACTT GTGAATTGTTCCGCCTCTTGAATΆCTTCTTCAΆTCCTCΆTATATTCTTCTTCTATGT TACCTGAAAACCGGCΆ TTTAATCTCGCGGGTTTATTCCGGTTCAACΆTTTTTTTTGTTTTGAGTTATTATCTGGG CTTAATAΆCGCAGG

CCTGAAATAAATTCAAGGCCCAACTGTTTTTTTTTTTAAGAAGTTGCTGTTAAAAAA AAAAAAAGGGAATTAΆ CAACAΆCAACAAΆAAAAGATAAΆGAAAATAATAACAATTACTTTAΆTTGTΆGΆC TAAΆAAAACATAGATTTTA TCATGAAAAAAAGAGAAAAGAΆATAAAAACTTGGATCAAAAAAAAAACATACAGΆTCT TCTAATTATTAACTT TTCTTAAAAATTAGGTCCTTTTTCCCAACAATTAGGTTTAGΆGTTTTGGΆATTΆAAC CAΆAAAGATTGTTCTA AAAAATACTCAAATTTGGTAGATAAGTTTCCTTATTTTAΆTTAGTCAATGGTAGΆTAC TTTTTTTTCTTTTCT

ACATGAAATTAAAAGAAAAATCTCATATATAGTATTAGTATTCTCTATATATATTAT GATTGCTTATTCTTAA TTCTATAGAAAAGAAAGAAΆTTATTTGAGGAAAAGTATATACAAAAAGAAAAATAGAAA AATGTCAGTGAAGC

GGTGGAAAATATGACACGTATCATATGATTCCTTCCTTTAGTTTCGTGATAATAATC CTCAACTGATATCTTC CTTTTTTTGTTTTGGCTAAAGATATTTTATTCTCATTAATAGAAAAGACGGTTTTGGGCT TTTGGTTTGCGAT ATAAAGAAGACCTTCGTGTGGAAGATAATAATTCATCCTTTCGTCTTTTTCTGACTCTTC AATCTCTCCCAAA

TAATTTCTTGCTTGATTGTGAAATTAGGATTTTCAAGGACGATCTATTCAATTTTTG TGTTTTCTTTGTTCGA TGATTTGGTATΆTGTTCGCTGATTGGTTTCTACTTGTTCTATTGTTTTATTTCAGGTCA CCAAACACTCGAG

(SEQ ID. NO. 150)

Promoter was amplified from Arabidopsis genomic DNA (CoI-O) using the following primers :

AS724 CGGTACCTACCGGATTTGGAGCCAAGTC (SEQ ID NO . 151)

AS726 GCTCGΆGTGTTTGGTGACCTGAAATAAAACAATΆGAACAAGT (SEQ ID NO. 152)

In conclusion we present an efficient system for chloroplast transformation using groupll intron-based vectors . Both bacterial and native introns could be utilised for delivery and insertion of transgene of interest into the chloroplasts .

Transformation of tobacco leaf explants with Agrobacterium strain AGLl

All items are autoclave-sterilised prior to use.

Filter sterilize antibiotics to prevent fungal growth and keep antibiotics for plant tissue culture in separate box.

Sterilize plant material: Take plants of about 9cm high; they should not have started to flower. Cut leaves with cuticle (4-6 leaves per construct, enough to cut 100 explants) , dip in 70% Ethanol and immediately dip in 1% Na- hypochlorite (cat. No 01032500; use bottle of bleach that is no more than 3 months old because the chlorine gas evaporates) , hold leaves with forceps and stir in for 20 min. Avoid damaging the cuticle, otherwise bleach will enter the vascular system. Rinse briefly in sterile water 5-6 times and leave in water until ready to be cut .

Co-cultivation of agro with tobacco explants: Grow AGLl in LB or L broth with appropriate antibiotics overnight at 28-30 °C and the next day re-suspend agro

in co-cultivation solution so that the final concentration is around 0.4-0.6 OD _600n -, . Place tobacco leaves in co-culture broth and cut squares of 1-1.5cm x 1-1.5cm with a rounded sterile scalpel using a rolling action. Dip the leaf explants in the agro solution with sterile forceps (stored in 100% ethanol, flamed and let cool prior to touching the leaf tissue) blot on sterile Whatman paper and transfer onto non-selective TSM plates (6 explants per plate), preparing about 15 plates per construct. Repeat this procedure for each construct, making sure that the scalpel and forceps are dipped in ethanol and flamed between each construct to prevent cross-contamination. Leave for 2 days only for AGLl (3-4 days for other agro strains) .

Transfer onto selective TSM plates: Use sterile flamed forceps to pick up and wash explants in 100 mis co-cultivation broth supplemented with timentin 320mg/l (one pot per construct), shake well, blot on sterile whatman paper and place the washed explants on selective TSM plates supplemented with appropriate selective antibiotics and timentin 320mg/l to kill agrobacterium.

Shoot regeneration: Takes around 1 month to see shoots appear, explants should be transferred on fresh plates every 10-14 days. Watch for AGLl recurrent growth; if Timentin is not enough to kill agro, add cefotaxime at 250mg/l.

Root regeneration: Takes around 1 week. Shoots are cut from the explants; place in growth boxes containing TRM supplemented with the appropriate selective antibiotics and timentin 320mg/l + cefotaxime 250mg/l to prevent agrobacterium recurrent growth.

Maintain plants in TRM boxes : Sub them every two weeks until ready to be transferred into glasshouse

Adaptation to glasshouse conditions: Soak peat pellets in sterile water until they swell to normal size and carefully place one plant per pellet, incubate the plants under 100% humidity conditions in a propagator, gradually opening the little windows until plants adapt to normal atmosphere over several days.

Recipes :

Co-culture: MS with vitamins and MES + O.lmg/1 NAA + lτng/1 BA + 3% sucrose, pH 5.7

TSM: MS with vitamins and MES + O.lmg/1 NAA + lmg/1 BA + 3% sucrose, pH5.7 ,

0.2% gelrite

TRM: y ₂ MS salts with vitamins and MES + 0.5% sucrose, pH5.7, 0.2% gelrite.

Autoclave .

Antibiotics concentration

For agrobacterium LB or L cultures:

To grow AGLl carrying pGreen/pSOUP : Carbenicillin lOOmg/1, Tetracycline 5mg/ml, Rifampicin 50mg/ml, Kanamycin 50mg/ml

AGLl carrying pSOUP: Carbenicilin lOOmg/1, Tetracycline 5mg/ml, Rifampicin 50mg/ml.

AGLl empty: Carbenicillin lOOmg/1, Rifampicin 50mg/ml.

For plant culture:

Kanamycin: 300mg/l (lOOmg/1 if using benthamiana)

Hygromycin: 30mg/l (lOmg/1 if using benthamiana)

PPT: 20mg/l (2mg/l if using benthamiana)

Timentin: 320mg/l. It is used to kill agro, but it is rather unstable. Make up small amount of stock and store in freezer for up to 1 month; after that the antibiotic is no longer efficient.

Cefotaxime: 250mg/l. Also used to kill agro, add to TS

Tomato Transformation Protocol

Seed Germination

Surface Sterilisation

Give tomato seeds a 70% EtOH treatment for 2 minutes to loosen gelatinous seed coat .

Remove EtOH and rinse once with sterile water.

(At this stage you can include a 20 minute trisodium phosphate treatment to eliminate seed transmission of TMV) . Rinse.

Add 10% Domestos/Vortex for 3 hours, shaking.

Wash 4 times with water. Leave in final change of water and shake at 25 ⁰ C overnight .

(The long bleach treatment and overnight imbibition are to encourage more even germination) . Seeds may be left for up to 3 months at 4 ⁰ C. Indeed after 3 weeks in a refrigerator, nearly all the seeds will germinate at the same time.

20-30 seeds are placed in tubs containing germination medium and left at 25°C in culture room (16 hour photoperiod, supplemented with Gro-Lux or incandescent light, which is especially important for regeneration) .

Seedlings are grown for 7-10 days. For transformation ideally cotyledons are young and still expanding, no true leaf formation is visible.

Transformation procedure Day 1

Morning; set up Agrobacterium tumefaciens culture

Inoculate lOmls of minimal A medium containing the appropriate antibiotics with LBA4404 strain. Grow shaking at 28 °C.

Afternoon; set up feeder layers

Put ImI of fine tobacco suspension culture onto plates containing the cell suspension medium solidified with 0.6% agarose or MS medium with 0.5mg/L 2,4-D, 0.6% agarose. Spread around to give an even layer. Place plates unsealed and stacked in the culture room in low light.

Day 2

Morning;

Incubation of Explants .

Place a Whatman no.l filter paper on top of the feeder plates. Take care to exclude any air bubbles and make sure the paper is completely wetted.

Cutting up plant material .

Cotyledons are used-hypocotyls give rise to a high number of tetraploids . Always cut under water and with a rolling action of a rounded scalpel blade to minimise damage to the tissue. In a petri dish cut off the tip of the cotyledon and then make two more transverse cuts to give two explants of about 0.5 cm long. Transfer the explants to a new petri dish of water to prevent any damage during further cutting. Always handle pieces with great care . The use of rounded forceps to scoop up the cut cotyledons helps prevent puncture with sharp tips .

Once a number of explants are collected in the pool, blot them on sterile filter paper and place about 30-40 on a feeder plate, abaxil surface uppermost (upside down) . Place petri dishes unsealed and stacked at 25 ⁰ C under low light intensity. Leave preincubating for 8 hours .

Afternoon; co-cultivation

Spin down Agrobacterium culture and resuspend pellet in MS medium 3% sucrose to an OD ₆₀₀ of 0.4-0.5.

Put bacterial suspension in a petri dish and immerse the explants from one feeder plate. Remove them and blot on sterile filter paper before returning to the original feeder plate, again taking care not to damage the tissue. No particular period of time is required in the bacteria, but ensure that the pieces have been completely immersed. Return the plates to the same conditions as used in the preincubation phase . Co-cultivate for 40 hours.

Day 4

Morning; apply selection

Take the pieces from the feeder layers and place on tomato regeneration plates containing Augmentin or carbenicillin at 500ug/ml and the appropriate antibiotic to select for the T-DNA transformation marker, e.g. kanamycin at lOOug/ml or preferably Augmentin since it may have a slight stimulatory effecton regeneration. Place the cotyledons right side upwards so that they curl into the medium ensuring good contact between the cut edges of the leaf with the nutrients and antibiotics .

Using Agar gel as the setting agent produces a soft medium into which the pieces can be pushed gently. Place 12 pieces per petri dish. Plates are left unsealed and returned to the culture room.

Week 2 or 3

Explants are transferred to fresh medium every 2-3 weeks. When regenerating material is too large for petri dishes it is placed on larger screw-capped glass jars, a petri dish lid replacing the plastic cap to allow better light penetration and better gas exchange.

Shoots are cut from the explants and placed in rooting medium with reduced antibiotic concentrations, Augmentin at 200ug/ml and kanamycin at 50ug/ml. If they do not root at first, re-cut and place in fresh medium. If they still fail to produce roots they are probably escapes. If using the kanamycin resistance gene as the selectable marker a simple npt II assay can be carried out to confirm the identity of true transformants .

To transfer to soil, remove as much of the medium as possible by washing the roots gently under running water. Plant carefully in hydrated,

autoclaved Jiffy pots (peat pots) and keep enclosed to keep humidity high while in the growth room. Gradually decrease humidity. Once roots can be seen growing through the Jiffy-pots the plants are ready to go to the glasshouse .

N. B. 1 This protocol is used with the Moneymaker variety of tomato. Transformation efficiencies with other varieties may be lower using these conditions and alterations in preincubation period, density of the Agrobacterium suspension and the length of the period of co-cultivation may be necessary to optimise the protocol for any particular variety. N. B. 2 One difficulty that may arise, especially if the transgenic plants are required for seed production, is that of tetraploidy. It seems that a significant proportion of regenerants may have a doubled chromosome number. This can be assessed, either by chloroplast number in guard cells or by chromosome counts .

REGENERATION

/Litre

MS salts Ix myo-inositol lOOmg

Nitsch's vitamins ImI of IOOOX stock Sucrose 2Og

Agargel 4g

pH 6.0 (KOH)

Autoclave

Zeatin Riboside (trans isomer) 2mg

(Filter sterilise and add after autoclaving )

Nitsch's Vitamins

Final cone . mg/1 100Ox stock (mg/100ml)

Thiamine 0.5 50 Glycine 2.0 200

Nicotinic acid 5.0 500 Pyridoxine HCl 0.5 50 Folic acid 0.5 50

Biotin 0.05 5

At 100Ox not all vitamins go into solution. Keep at 4°C and shake before using.

Rooting g/Litre

MS medium 0.5X

Sucrose 5g

Gelrite 2.25g

pH 6.0 (KOH)

Media

Seed Germination

/Litre

MS medium Ix

Glucose 1Og

Agarose 6g pH 5.8

Pour into round Sigma ¹ margarine' tubs

Minimal A /Litre

K ₂ HPO ₄ 10.5g

KH ₂ PO ₄ 4.5g

(NH ₄ J ₂ SO ₄ 1.Og

Na citrate.2H ₂ O 0.5g

Autoclave in 990ml

Before use add; 1.0ml of IM MgSO ₄ -H ₂ O

10ml of 20% Glucose

For plates;

Make the above in 500ml and autoclave. Separately autoclave 15g Bactoagar in 490 ml H ₂ O Add MgSO ₄ and glucose and combine .

Transformation of Rice Immature Embryos.

Immature Embryo Excision

Day 1:

Remove milky/post-milky stage immature seeds from panicles (immature embryos 1-2 mm in size are desired) .

Sterilize immature seeds: 50% sodium hypochlorite (12%) + 1 drop of tween 20. Shake 10 min.

Rinse 3-5x in sterile deionised water. Drain off surplus water. Aliquot seeds (around 40) in sterile Petri dishes.

Set up a 60 x 15 mm Petri dish containing a 50% sodium hypochlorite solution and next to this a sterile beaker on its side with a sterile filter paper in it. Use sterile forceps to aseptically remove glumes from the first seed. Immerse this seed in the 50% sodium hypochlorite. Remove glumes from a second seed and immerse the second seed into the sodium hypochlorite solution whilst removing the first seed and storing this dehusked/sterilized seed on the filter paper in the beaker. Continue.

After all the glumes are removed:

Sterilize dehusked seeds: 50% sodium hypochlorite: 5 min. with agitation.

Rinse: 5-7 x in sterile deionized water, drain.

Place all seeds in a large sterile Petri dish. Aliquot for embryo excision (to keep seeds from drying out, work with only 50-100 in the plate at a time leaving the rest in the master plate) .

Remove the embryo from each seed and place embryo, scutellum up, in a 90 x 15 mm Petri dish containing proliferation medium (40-50 embryos / plate) . Culture at 28 ⁰ C in the dark for 2 days prior to bombardment

Day 3 :

Check each embryo for contamination before blasting

Remove the embryos from the proliferation medium. Distribute 35-40 embryos scutellum upwards in an area 1 cm ² in the centre of a 60 x 15 mm target plate containing 10 ml of proliferation medium + osmoticum (0.6M) .

Check each target plate so that the scutellum is straight. Allow enough room so the scutella do not shade each other out.

Bombardment :

Gun 14 kV

Vacuum : 25 inches of Hg

1 ^st bombardment 4 hours after osmoticum treatment 2 ^nd bombardment 4 hours after 1 ^st bombardment

Day 4 :

4-16 hours after the 2nd blast transfer immature embryos to proliferation medium without osmoticum. Culture in the dark at 28°C for 2 days.

Selection:

Day 5 :

Aseptically cut out with scissors the germinating shoot. Transfer 16 - 20 immature embryos to fresh proliferation medium containing 30-50 mg/1 Hygromycin (depending on the genotype) ; culture in the dark at 28°C; record total number of embryos .

After 10 days carefully remove the callus from the scutellum by breaking it up into 2-10 small pieces; subculture onto fresh proliferation medium + hygromycin. Do not subculture brown tissue and remaining immature embryo which could inhibit further growth of healthy callus .

Subculture every 10 days by selecting healthy tissue: (embryogenic if present) and transfer it to fresh proliferation medium + hygromycin. Remove brown callus as it could be inhibiting to embryogenic callus.

30 to 40 days after bombardment change selection procedure. Instead of eliminating bad-looking tissue keep embryogenic tissue only (eliminate healthy non-embryogenic tissue)

Regeneration:

After 40 to 60 days, transfer established embryogenic callus showing differential growth on proliferation medium + hygromycin to regeneration medium + hygromycin. Culture at 28 °C under low light for 10 days then under high light for 10 additional days. Check plates periodically in

the light for the development of embryos and green shoots. As shoots develop it is sometimes beneficial to gently move the developing shoot away from the callus it originated from and remove any dead tissue from the shoot itself to prevent inhibition of growth.

Germination:

Transfer white compact embryos and green shoots initiating roots to the germination medium under high light at 28°C for 1 to 2 weeks. Check plates periodically. Remove necrotic tissue and divide germinating embryos if necessary.