Reference to a Sequence Listing

[0001] This application contains a Sequence Listing in computer readable form, which is incorporated herein by reference.

Background

[0002] Some bacteria contain genetic systems that may help the bacteria compete with other bacteria in the environment. One of these systems is called contact-dependent growth inhibition (CDI), in which one bacterium can inhibit growth of another bacterium after contact between the bacteria. These systems have been described in some Gram-negative genera (i.e., in some α, β and γ proteobacteria) and in a single Gram-positive species, Bacillus subtilis.

Summary

[0003] Disclosed herein are genetic systems from Bacillus amyloliquefaciens that may help the bacteria grow and compete with other bacteria. The disclosed CDI-like systems include WapA and Wapl proteins from Bacillus amyloliquefaciens subsp. plantarum and genes that encode the proteins. The systems encode a WapA protein that mediates growth inhibition of neighboring cells and a Wapl protein that confers protection against growth inhibition from cells producing WapA. Genes encoding WapA/WapI proteins were found in about 78% of tested Bacillus amyloliquefaciens subsp. plantarum strains, but not in subsp. amyloliquefaciens strains. The Bacillus amyloliquefaciens subsp. plantarum WapA and Wapl proteins clustered into 9 different "Wap Groups," based on identity between amino acid sequences. The data showed that a first Bacillus strain, that expressed a Bacillus amyloliquefaciens WapA protein, inhibited growth of a second Bacillus strain that did not express & Bacillus amyloliquefaciens Wapl protein. The data also showed that expression of a Bacillus amyloliquefaciens Wapl protein in the second Bacillus strain protected the second strain from the growth inhibition. In one example, the Wapl protein expressed in the second strain was from the same Wap Group as the WapA protein in the first strain. [0004] In one example, isolated polypeptides are disclosed that have amino acid sequences at least one of 90%, 95%, 97.5% 98.5%, 99.5% or 99% identical to the C-terminal 200 amino acids of a WapA (i.e., WapA-CT) protein. The WapA-CT polypeptides may be classified into at least Wap Groups 1, 2, 3, 4, 5, 6, 7, 8 or 9. The isolated polypeptides may be part of a WapA protein from Bacillus subtilis, Bacillus amyloliquefaciens or Bacillus amyloliquefaciens subsp.

plantarum, or part of other proteins. The isolated polypeptides, or other protein to which the WapA-CT polypeptides are a part, may be functional to inhibit growth of Bacillus organisms that do not express a Wapl protein, or do not express a Wapl protein from the same Wap Group as the WapA-CT polypeptide. The Bacillus organisms that may be growth inhibited may be at least Bacillus subtilis and/or Bacillus amyloliquefaciens. Nucleotide sequences encoding the isolated polypeptides are also disclosed and these may be part of/encoded by a vector. Also disclosed, in the Sequence Listing of this application, are amino acid sequences of complete WapA proteins (SEQ ID NOs: 93-113) and nucleotide sequences (SEQ ID NOs: 72-92) that encode the proteins.

[0005] In one example, isolated polypeptides are disclosed that have amino acid sequences at least one of 90%, 95%, 95.2%, 96%, 96.4%, 96.6%, 98.8% or 99% identical to a Wapl protein. The Wapl polypeptides may be classified into at least Wap Groups 1, 2, 3, 4, 5, 6, 7, 8 or 9. The isolated polypeptides may be functional to protect Bacillus organisms against growth inhibition mediated by a WapA protein or WapA-CT polypeptide, or against growth inhibition mediated by a WapA protein or WapA-CT polypeptide from the same Wap Group as the Wapl protein. The Bacillus organisms that may be protected may be Bacillus subtilis and/or Bacillus

amyloliquefaciens. Nucleotide sequences encoding the isolated peptides are also disclosed and these may be part of/encoded by a vector.

[0006] Also disclosed are vectors that include nucleotide sequences that encode the isolated WapA-CT polypeptides, which may be part of a WapA or other protein, and/or that encode the isolated Wapl polypeptides described above. The vectors may include nucleotide sequences that encode one or more Wapl polypeptides/proteins from separate Wap Groups. The vectors may include nucleotide sequences that encode a Wapl polypeptide/protein and a WapA

polypeptide/protein, both from the same Wap Group. Also disclosed are methods for

introducing the vectors into Bacillus subtilis or Bacillus amyloliquefaciens cells and bacteria expressing one or more of the vectors. [0007] Also disclosed are bacteria constructed to express at least one Wapl protein. The bacteria may be constructed to express 2, 3, 4, 5, 6, 7, 8, 9 or more Wapl proteins, generally from different Wap Groups. Bacteria may also be constructed to express at least one Wapl protein and at least one WapA protein, the Wapl and WapA proteins may be from the same Wap Group. Bacteria constructed to express multiple Wapl proteins, or one or more Wapl and one or more WapA proteins, may express at least some of the multiple proteins from one or more vectors, and/or from polycistronic mRNAs. Methods for supplying to an environment, bacteria constructed to express one or more of WapA and/or Wapl proteins are disclosed. The bacteria supplied may efficiently compete with other bacteria present in the environment. The bacteria supplied may inhibit growth of bacteria present in the environment.

[0008] Also disclosed are methods for obtaining a nucleotide sequence from at least part of a wapA or wapl nucleotide sequence from a Bacillus amyloliquefaciens organism, and classifying a WapA or Wapl polypeptide or protein encoded by the nucleotide sequence, into a Wap Group. The organism may be supplied to an environment based on the classifying, and may be capable of WapA-mediated growth inhibition of at least one organism present in the environment. In one example, two or more Wap-compatible Bacillus amyloliquefaciens organisms may be placed in proximity to one another based on classifying the organisms into a Wap Group.

[0009] Also disclosed are methods for ascertaining Wap-compatibility of at least two Bacillus amyloliquefaciens strains by determining whether the strains encode one or both of a wapA and a wapl nucleotide sequence in their genomes, comparing the nucleotide sequences or amino acids encoded by the nucleotide sequences, and designating the strains as Wap compatible or Wap non-compatible based on the determining (if the nucleotide sequences are not present in at least one genome) or based on the comparing (if the nucleotide sequences are present in the genomes). At least two strains may be placed in proximity to one another if determined to be Wap compatible. Two compatible strains may be supplied to a plant. Also disclosed are compositions of a mixture of at least two Bacillus amyloliquefaciens bacteria determined to be Wap compatible using the above method.

[0010] Also disclosed are methods for identifying an amino acid sequence and/or nucleotide sequence from a Bacillus amyloliquefaciens bacterium that has identity to a Wap query sequence and classifying the amino acid sequence and/or nucleotide sequence from Bacillus amyloliquefaciens into a Wap Group.

Brief Description of the Drawings

[0011] In the accompanying figures, which are incorporated in and constitute a part of the specification, disclosures related to Bacillus strains that have improved competitiveness, polypeptides and nucleic acids that encode the polypeptides for improved competitiveness, vectors encoding the polypeptides, bacteria that express the polypeptides, nucleic acids and vectors and methods of using the bacteria are disclosed. Changes, modifications and deviations from the disclosures illustrated in the figures may be made without departing from the spirit and scope of the invention, as disclosed below.

[0012] Fig. 1 illustrates an example sequence identity matrix for WapA-CT amino acid sequences from Bacillus amyloliquefaciens subsp. planetarium strains. The matrix was generated based on the ClustalW algorithm incorporated into the MegAlign program of

DNAStar® [version 7.2.1 (1), 410]. In this example matrix, sequences with high identity values and low divergence are closely related.

[0013] Fig. 2 illustrates an example phylogenetic tree/dendogram for Bacillus

amyloliquefaciens subsp. planetarium WapA-CT amino acid sequences. The numbers (1-9) denote Wap Group assignments as described in the specification. The tree was generated using the ClustalW algorithm incorporated into the MegAlign program of DNAStar® [version 7.2.1 (1), 410].

[0014] Fig. 3 illustrates an example sequence identity matrix for Wapl amino acid sequences from Bacillus amyloliquefaciens subsp. planetarium strains. The matrix was generated based on the ClustalW algorithm incorporated into the MegAlign program of DNAStar® [version 7.2.1 (1), 410]. In this example matrix, sequences with high identity values and low divergence are closely related.

[0015] Fig. 4 illustrates an example phylogenetic tree/dendogram for Bacillus

amyloliquefaciens subsp. planetarium Wapl amino acid sequences. The numbers (1-9) denote Wap Group assignments that correspond to those shown in Fig. 2. The tree was generated using the ClustalW algorithm incorporated into the MegAlign program of DNAStar® [version 7.2.1 (1), 410].

[0016] Fig. 5 illustrates an example phylogenetic tree for Bacillus amyloliquefaciens subsp. planetarium and Bacillus subtilis WapA-CT amino acid sequences. The numbers (1-9) and shading denote group assignments that correspond to those shown in Fig. 2. Groups 1-5 and 7-9 contain Bacillus amyloliquefaciens subsp. planetarium strains. Group 6 contains a Bacillus amyloliquefaciens subsp. planetarium strain and Bacillus subtilis strains. Unnumbered groups contain Bacillus subtilis strains. The tree was generated using the ClustalW algorithm

incorporated into the MegAlign program of DNAStar® [version 7.2.1 (1), 410].

[0017] Fig. 6 illustrates data from an example growth experiment using strains FZB24 (no WapA, no Wapl), SB3281 (contains WapA, contains Wapl), and BaC0202 (FZB24 strain transformed with plasmid expressing Wapl from SB3281). The x-axis indicates the strains used. The y-axis indicates CFU/ml (colony forming units/ml) for the strain indicated by the arrows at the top of the chart. Bars numbered 1-3 show growth of single strains (controls). Bars numbered 4-7 show co-culture of two strains.

Detailed Description

Definitions

[0018] The following includes definitions of selected terms and phrases that may be used in the disclosure. Both singular and plural forms of the terms and phrases fall within the definitions.

[0019] As used herein, "amino acid sequence" means a linear sequence of individual amino acids in a polypeptide or protein.

[0020] As used herein, "C-terminal region" generally refers to a portion of a polypeptide or protein that includes a terminal amino acid that has a free carboxyl group. The other end of a polypeptide or protein includes a terminal amino acid that has a free amine group, and is called an N-terminal region. WapA-CT is considered to be an example C-terminal region of WapA. [0021] As used herein, "classified" or "classifying," is related to designating a WapA or Wapl protein, or portion of a WapA or Wapl protein as a member of a specific Wap Group. Generally, classifying WapA/WapI proteins into a Wap Group is based on the amino acid sequence of all or part of a WapA/WapI protein or polypeptide, determination of pair-wise amino acid sequence identities between the specific WapA/WapI protein and other known WapA/WapI proteins, and grouping together those sequences that are substantially identical.

[0022] As used herein, "compatible" or "Wap compatible" generally refers to a situation where, when two bacteria, herein Bacillus amyloliquefaciens or Bacillus subtilis, are placed together, growth of neither bacterium is inhibited by a WapA protein expressed by the other bacterium. Herein, under these conditions, the two bacteria are said to be compatible or Wap compatible. Generally, a compatible situation may occur between two of these bacteria when: i) neither of the two bacteria expresses a WapA protein, or ii) when one of the bacteria expresses a WapA protein and the other bacterium expresses a Wapl protein, the Wapl protein generally being from the same Wap Group as the WapA protein (i.e., the Wapl protein expressed in one bacterium is a cognate pair of the WapA protein expressed in the other bacterium). In these situations, both bacteria retain viability (e.g., are not growth inhibited) when in proximity to one another (e.g., when they are capable of contacting one another). Generally, when bacteria are classified into a Wap Group, and two or more of the bacteria that are compatible are placed in proximity to one another, both bacteria are capable of surviving and/or growing/dividing.

[0023] As used herein, "constructed to express," refers to a bacterium that, at one point in time, did not express a specific polypeptide or protein, but which has been modified or manipulated to express the polypeptide or protein, and now does express, or is capable of expressing, the polypeptide or protein. Generally, a bacterium is constructed to express a specific protein by introducing a gene encoding the specific protein into the bacterium. In one example, a gene may be introduced into a bacterium using transformation by a vector encoding the specific protein to be expressed (e.g., the gene encoding the specific protein to be expressed may be said to be "part of the vector).

[0024] As used herein, "encoding" or "encode" refers to a nucleotide sequence, generally DNA, that is capable of being transcribed into mRNA, and the mRNA translated, to yield a specific polypeptide or protein (i.e., the DNA sequence encodes the protein). For example, a DNA molecule that encodes a Wapl protein will contain consecutive nucleotide codons in the DNA that, after transcription and translation, yield the Wapl protein.

[0025] As used herein, "environment" means a particular physical location and/or set of conditions. In one example, an environment may be a closed or artificial environment. Closed or artificial environments may include an environment where microbes are grown. One type of closed or artificial environment may be a fermenter. In one example, an environment may be an open or natural environment. Open or natural environments may include a plot of land where crops are planted (e.g., soil), for example. Other environments may include plant seeds, roots, stems, leaves, etc. Other environments may include microbiomes, for example, of humans, animals or various environments animals. Other types of environments may exist.

[0026] Herein, "express" or "expressed" refers to production of a specific protein by a bacterium. For example, the phrase "bacterium X expresses a Wapl protein" means that bacterium X produces a Wapl protein. Bacterium X generally contains a gene that encodes the specific Wapl protein (i.e., a wapl gene). The wapl gene would be transcribed into mRNA and the mRNA would then be translated into Wapl protein in the bacterium.

[0027] As used herein, "functional to inhibit growth" generally refers to the ability of a WapA protein that is expressed by a bacterium, to inhibit growth of another bacterium that does not express a cognate Wapl protein. A WapA protein that is functional to inhibit growth, as above, generally may also be said to mediate WapA growth inhibition. Herein, "inhibit growth," when referring to growth inhibition mediated by WapA, may include cells whose growth is inhibited are killed. In various examples, the growth inhibition may be complete or partial. In various examples, the growth inhibition may be at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%), 90%), or even 100%> or at other levels, compared to growth of cells that are not growth inhibited.

[0028] As used herein, "functional to protect" generally refers to the ability of a Wapl protein that is expressed by a bacterium, to protect that bacterium against WapA-mediated growth inhibition by a bacterium expressing a cognate WapA protein. In various examples, the protection against growth inhibition may be complete or partial. In various examples, the protection against growth inhibition may be 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%) or at other levels, compared to cells that are growth inhibited.

[0029] As used herein, "introducing," when referring to a vector, means that the vector is caused to enter into a bacterial cell. In one example, a vector may be introduced into a cell by the process of bacterial transformation. A variety of other methods may be used.

[0030] As used herein, "is part of," when referring, for example, to a WapA-CT sequence that is part of a WapA or other protein, means that the amino acid sequence of the WapA-CT polypeptide is connected to or linked to another amino acid sequence, via peptide bonding, to form a WapA or other protein.

[0031] As used herein, "isolated," generally in reference to a molecule like a polypeptide, protein or nucleic acid, means that the molecule is not in close proximity to at least some substances normally found in close proximity to the molecule when the molecule is present in its natural environment. Molecules may be isolated from the natural environment, away from at least some of the substances normally found with the molecules, by purification methods.

[0032] As used herein, "mRNA" means messenger RNA.

[0033] As used herein, "non-compatible" or "Wap non-compatible" generally refers to a situation where, when two bacteria, herein Bacillus amyloliquefaciens or Bacillus subtilis, are placed together, growth of one or both of the bacteria is inhibited by a WapA protein expressed by the other bacteria. Herein, under these conditions, the two bacteria are said to be non- compatible or Wap non-compatible. Generally, a non-compatible situation may occur between two of these bacteria when: i) one bacterium expresses a WapA protein and the other bacterium does not express a Wapl protein, or does not express a Wapl protein from the same Wap Group as the WapA protein (i.e., the Wapl protein expressed in one bacterium is not cognate to the WapA protein expressed in the other bacterium), or ii) when both bacteria express a WapA protein and neither expresses a Wapl protein that is cognate to the WapA protein expressed by the other bacterium (i.e., the Wapl protein expressed in each bacterium is not cognate to the WapA protein expressed by the other bacterium). In these situations, one or both of the bacteria will be growth inhibited (or may not retain viability) when in proximity to the other (e.g., when they are capable of contacting one another). Generally, when bacteria are classified into Wap Groups, and two or more of the bacteria that are non-compatible are placed in proximity to one another, one or both bacteria fail to survive/grow/divide.

[0034] As used herein, "nucleic acid" generally refers to a DNA or RNA molecule.

[0035] As used herein, "nucleotide sequence" means the linear sequence of individual nucleotides in a nucleic acid molecule.

[0036] As used herein, "obtaining a nucleotide sequence," generally of a DNA molecule, means to acquire a nucleotide sequence, as may be done when a nucleotide sequence is obtained from a database, or to determine the nucleotide sequence using various sequencing methods known in the art.

[0037] As used herein, "orthologue" refers to similar nucleotide sequences in two different species of organisms.

[0038] As used herein, "polycistronic mRNA" means an mRNA that encodes two or more polypeptides or proteins.

[0039] As used herein, "polypeptide" means a linear polymer of amino acids, of a length longer than a few amino acids, where the amino acids are connected to or linked to one another by peptide bonds. Polypeptide may refer to a protein.

[0040] As used herein, "protein" generally refers to the full length of a polypeptide or complete sequence of amino acids for a protein encoded by a gene.

[0041] As used herein, "sequence identity," is a term used to describe the relatedness of two amino acid or nucleotide sequences, when the sequences are compared to one another (i.e., pair- wise comparison). Sequence identity between two sequences is generally determined after the two sequences are aligned. After alignment, the identity of the amino acids (if

polypeptide/protein) or nucleotides (if nucleic acid) at the same positions within the aligned sequences is determined. Generally, sequence identity is set forth as a percentage of amino acids or nucleotides within the two sequences being compared, that are identical at the same position within the aligned sequences. There are a variety of methods for determining sequence identity between two sequences which may, within limits, yield different determinations of percent sequence identity. In one example, different methods for determining sequence identity may use different techniques for aligning two sequences. Different alignment techniques may determine different sequence gaps. A sequence gap between sequences may occur when, for example, there are regions between two related sequences that do not align. In one example, gaps may occur because of deletions or insertions of consecutive amino acids or nucleotides within one of the two sequences being compared. The methods used herein for determination of sequence identity are described in this disclosure.

[0042] As used herein, "strain" refers to a species of bacteria. When two or more bacterial strains of the same species of bacteria are referenced, the separate strains generally have differences in the nucleotide sequences of their genomes between one another.

[0043] As used herein, "supplying" or "supplying to," as in reference to supplying a bacterium to an environment, means placing the bacterium in the particular environment. In this context, "placing" is a physical/mechanical act that results in the bacteria being located in the particular environment.

[0044] As used herein, "vector" refers to a nucleic acid molecule, generally DNA that encodes at least one polypeptide or protein, and is capable of being introduced into a bacterium such that the bacterium expresses the polypeptide or protein encoded by the nucleic acid molecule. Minimal vectors may include not much more than a nucleotide sequence encoding all or part of the polypeptide or protein that is to be expressed (e.g., synthetic genes). Other vectors may include the nucleotide sequence encoding the polypeptide or protein to be expressed, in addition to sequences directing transcription (e.g., transcriptional promoters and/or terminators), DNA replication in a bacterial cell (e.g., plasmids) and/or sequences encoding a virus (e.g., bacteriophage). A vector may encode multiple polypeptides or proteins. For example, a vector may encode multiple Wapl proteins, a WapA protein and a cognate Wapl protein, multiple cognate pairs of WapA and Wapl proteins, and other combinations.

[0045] As used herein, "WapA" refers to proteins from the group that is generally exemplified by sequences referred to as WapA herein. Generally, the WapA proteins disclosed herein are from Bacillus amyloliquefaciens . WapA proteins are generally capable of functioning to inhibit growth of one or both of Bacillus subtilis and/or Bacillus amyloliquefaciens bacteria that do not express a Wapl protein from the same Wap Group as the WapA protein.

[0046] As used herein, "wapA" refers to a nucleotide sequence (e.g., a gene) that encodes a WapA protein.

[0047] As used herein, "WapA-CT" generally refers to the 200 C-terminal amino acids of a WapA protein.

[0048] As used herein, "Wapl" refers to a protein from the group that is generally

exemplified by sequences referred to as Wapl herein. Generally, the WapA proteins disclosed herein are from Bacillus amyloliquefaciens. Wapl proteins generally are capable of functioning to protect one or both of Bacillus subtilis and Bacillus amyloliquefaciens bacteria against growth inhibition mediated by a WapA protein from the same Wap Group as the Wapl protein.

[0049] As used herein, "wapF refers to a nucleotide sequence (e.g., a gene) that encodes a Wapl protein.

[0050] As used herein, "Wap Group" means a group of WapA molecules, generally from Bacillus amyloliquefaciens, that have high amino acid sequence identity between one another. Wap Group may also refer to a group of Wapl molecules, from Bacillus amyloliquefaciens, that have high amino acid sequence identity between one another. Herein, the amino acid sequence identity between either WapA or Wapl molecules that are part of the same Wap Group is normally at least about 90%, but may be at least 95% or greater. Generally, a Wapl protein from a specific Wap Group is capable of protecting a Bacillus subtilis or Bacillus amyloliquefaciens bacterium from growth inhibition mediated by a WapA protein from the same Wap Group.

WapA and Wapl proteins from the same Wap Group may be referred to as "cognate" or "cognate pairs" and, therefore, Wapl protects from growth inhibition mediated by cognate WapA. Herein, 9 Bacillus amyloliquefaciens Wap Groups are disclosed. It is likely that additional groups will be found as WapA/WapI proteins from more strains of Bacillus amyloliquefaciens are analyzed, and these additional groups are meant to be encompassed by this disclosure.

[0051] As used herein, "Wap query sequence" refers to a known Wap sequence or part of a Wap sequence (e.g., amino acid or nucleotide; e.g., WapA, Wap-CT, wapA, Wapl, wapl), generally from Bacillus amyloliquefaciens or Bacillus subtilis, used for querying a database for related Bacillus amyloliquefaciens sequences.

Polypeptides and Nucleic Acids

[0052] The polypeptides and nucleic acids disclosed herein are generally identified using computer-based methods where a sequence is used to query databases that include amino acid sequence/nucleotide sequences from various Bacillus amyloliquefaciens strains. Currently undiscovered Bacillus amyloliquefaciens wapAlwapI and/or WapA/WapI sequences, which are encompassed by this disclosure, may be found using one or more of the sequences disclosed herein to query various sequence-containing databases, and detect the sequences after they have been entered into the databases. For the work described here, the query sequences were obtained from Bacillus subtilis.

[0053] In Bacillus subtilis, 4 different wapA sequences and 4 different wapl sequences were found in a study of multiple Bacillus subtilis strains (Koskiniemi, et al., 2013, Rhs proteins from diverse bacteria mediate intercellular competition, Proc. Natl. Acad. Sci. USA 110:7032-7037). In each of the Bacillus subtilis strains examined, a specific wapA sequence was found together with a specific wapl sequence. Therefore, specific wapA alleles co-segregated (e.g., the specific wapA and wapl alleles were found together) with specific wapl alleles in Bacillus subtilis.

[0054] Herein, to find wapA or WapA sequences in Bacillus amyloliquefaciens, wop nucleotide and/or Wap amino acid sequences from Bacillus subtilis were used to query Bacillus amyloliquefaciens sequences and/or databases containing Bacillus amyloliquefaciens sequences, for sequences with identity to the query sequence (i.e., Bacillus amyloliquefaciens orthologues of Bacillus subtilis sequences are queried; Examples 2 and 3). In one example, the query sequences can be one or more of the wap or Wap sequences from Bacillus amyloliquefaciens disclosed herein.

[0055] The databases queried may contain whole-genome nucleotide sequences of various Bacillus amyloliquefaciens strains. In one example, the Bacillus amyloliquefaciens genome sequences may be obtained from public databases. In one example, Bacillus amyloliquefaciens genome sequences may be determined by sequencing the genomes in the laboratory, using conventional methods. In the studies described herein, sequences were obtained using both methods (Example 1).

[0056] In one example of a query, a WapA sequence from Bacillus subtilis subsp. subtilis strain 168 (Genbank accession P 391802) is used to query proteins from Bacillus amyloliquefaciens using a BlastP search, as described in Example 2. Table 1 shows the nucleotide sequences encoding the 200 C-terminal amino acids of the full-length WapA amino acid sequences. The encoded amino acid sequences are shown in Table 4.

[0057] From the analysis of the Bacillus amyloliquefaciens genome regions encoding WapA proteins, these regions appeared syntenic with the WapA-encoding genome regions of Bacillus subtilis. In Bacillus subtilis, wapl genes are co-linear with, and downstream of wapA

(Koskiniemi, et al., 2013, Rhs proteins from diverse bacteria mediate intercellular competition, Proc. Natl. Acad. Sci. USA 110:7032-7037). Putative Bacillus amyloliquefaciens Wapl- encoding regions were assigned based on their location downstream (3') of Wap A-encoding regions (Example 3). The Bacillus amyloliquefaciens Wapl amino acid sequences are shown in Table 2. The nucleotide sequences encoding these amino acid sequences are shown in Table 3.

[0058] Although the disclosed Wapl-encoding regions were identified based on their location in the genomes with respect to wapA (Example 3), the Wapl-encoding sequences may also be identified using query sequences, similar to the methods used to identify Bacillus

amyloliquefaciens WapA sequences, described above.

[0059] Once it is determined that a Bacillus amyloliquefaciens strain contains wapA and or wapl genes in their genomes and/or encodes WapA and/or Wapl proteins, sequences from different strains may be compared to determine their relative sequence identities. In order to compare two sequences, the sequences generally are aligned and sequence identity calculated. There are a variety of methods to align multiple sequences. The methods generally differ in how "gaps" between the sequences are handled. There are a variety of such methods. In one example, the ClustalW method was used (Thompson et al., 2002, Multiple sequence alignment using ClustalW and ClustalX, Curr. Protoc. Bioinformatics 2:2.3.1-2.3.22). The ClustalW algorithm used was incorporated into the MegAlign program of DNAStar® [version 7.2.1 (1), 410].

[0060] To compare relative sequence identities of WapA proteins, the 200 C-terminal acids of the full-length WapA amino acid sequences shown in Table 4 were used.

[0061] Pair-wise amino acid identity comparisons of the Bacillus amyloliquefaciens WapA-

CT sequences, the sequences shown in Table 4, were determined as described in Example 2. Pair-wise sequence identities for the sequences are shown in Fig. 1. WapA-CT sequences with significant identity to one another were grouped or classified into the same "Wap Group." WapA-CT sequences that lacked significant identity with other WapA-CT sequences were classified into their own Wap Group. The sequence comparisons and results of classifying WapA-CT and are shown in Fig. 2.

[0062] A similar comparing and classifying for Bacillus amyloliquefaciens Wapl polypeptide sequences, as shown in Table 2, was performed as described in Example 3. Pair-wise sequence identities for the sequences are shown in Fig. 3. The sequence comparisons and results of classifying WapA-CT and are shown in Fig. 4. As shown in Figs. 2 and 4, both WapA-CT and Wapl sequences were classified into 9 Wap Groups.

[0063] Due to their co-linear arrangement within the bacterial genome, WapA-CT and Wapl from the same Bacillus amyloliquefaciens strains co-segregated. Co-segregating WapA-CT and Wapl were classified into the same Wap Groups, based on their amino acid identities. Within Wap Groups that contained multiple members (i.e., Wap Groups 1-5, 8 and 9), the amino acid identities of WapA-CT polypeptides were not less than 97.5% (Table 5). For WapA-CT polypeptides classified into different Wap Groups, the polypeptides were no greater than 71.8% identical, and as low as 32.3% identical. Within Wap Groups that contained multiple members, the amino acid identities of Wapl polypeptides were not less than 95.2%. For Wapl polypeptides classified into different Wap Groups, the polypeptides were no greater than 21.0% identical, and as low as 5.5% identical.

[0064] In addition, the data showed that, at the level of amino acid sequence identity, the Wap sequences from Bacillus amyloliquefaciens were largely different from Wap sequences from Bacillus subtilis (Example 3). When the 8 WapA-CT amino acid sequences from Bacillus subtilis were included along with WapA-CT amino acid sequences from Bacillus

amyloliquefaciens, and were used to determine a phylogenetic tree/dendogram of the sequences, the arrangement shown in Fig. 5 was obtained. The data showed that 2 of the 8 Bacillus subtilis WapA-CT sequences grouped together with a single Bacillus amyloliquefaciens Wap-CT sequence in Wap Group 6. The other 6 Bacillus subtilis WapA-CT amino acid sequences grouped into 3 different Wap Groups, all 3 of these Wap Groups containing only Bacillus subtilis sequences, and all 3 Wap Groups distinct from the 9 Bacillus amyloliquefaciens Wap Groups. Therefore, the Bacillus subtilis Wap sequences are largely distinct from the Bacillus

amyloliquefaciens Wap sequences. In one example, the Bacillus amyloliquefaciens sequences claimed herein do not include one or more of Wap A, WapA-CT and Wapl sequences from Bacillus subtilis (i.e., the Bacillus subtilis sequences are excluded). In one example, the Bacillus amyloliquefaciens sequences claimed herein do not include one or more of Wap A, WapA-CT and Wapl sequences from Bacillus subtilis that could be classified into Wap Group 6 based on sequence identity (e.g., sequences from at least Bacillus subtilis strains RO-NN and TU-B-10 are excluded).

[0065] Although the Bacillus subtilis study discussed earlier reported no strains of Bacillus subtilis that did not contain wapA/wapI genes (Koskiniemi, et al., 2013, Rhs proteins from diverse bacteria mediate intercellular competition, Proc. Natl. Acad. Sci. USA 110:7032-7037), this was not the case for Bacillus amyloliquefaciens. The studies disclosed herein showed no wapA or wapl nucleotide sequences in 8 out of 8 tested Bacillus amyloliquefaciens subsp.

amyloliquefaciens strains. The studies herein also showed that wapA and wapl nucleotide sequences were present in Bacillus amyloliquefaciens subsp. plantarum strains, but only in about 78% of those strains (32 examined). Therefore, the situation in Bacillus amyloliquefaciens is different than in Bacillus subtilis. Functions of Wap Proteins/Pol ypeptides

[0066] The Bacillis subtilis work (Koskiniemi, et al., 2013, Rhs proteins from diverse bacteria mediate intercellular competition, Proc. Natl. Acad. Sci. USA 110:7032-7037) showed that expression of a WapA-CT polypeptide (the C-terminal 200 amino acids of WapA) inhibited growth of/was toxic to the bacterial cell in which it was expressed. Co-expression of Wapl in the same cell protected against the growth suppression/toxicity when the wapl encoding the Wapl was the same allele that co-segregated with the wapA allele that encoded the WapA in the cell (i.e., when the WapA-CT and Wapl were "cognate" pairs; from the same Wap Group). In addition, biochemical studies showed that expression of WapA-CT polypeptides in cells caused cleavage of tRNA molecules within the cells, suggesting a mechanism for this particular WapA- mediated growth inhibition. The tRNAase activity of WapA-CT polypeptides was blocked by co-expression in the cells of its cognate Wapl protein, but not by co-expression of non-cognate Wapl proteins. These data, therefore, showed that the 4 co-segregating wapA/wapI alleles represented 4 functional, cognate growth inhibiting (wapA)/protection from growth inhibition (wapl) gene/protein pairs in Bacillus subtilis.

[0067] In one example, a bacterium expressing a Bacillus amyloliquefaciens WapA protein or WapA-CT polypeptide may inhibit growth of a second bacterium when the second bacterium does not express a Wapl protein, or expresses a Wapl protein that is not functional to protect against growth inhibition. Generally, contact between the first and second bacterium may occur in order for growth inhibition to occur. If the second bacterium expresses a Wapl protein, the second bacterium may be protected from growth inhibition by the WapA-expressing bacterium. In one example, the first and/or second bacterium may be a Bacillus organism. In one example, the first and/or second bacterium may be a Bacillus subtilis organism. In one example, the first and/or second bacterium may be a Bacillus amyloliquefaciens organism.

[0068] In light of the Bacillus subtilis work, the Bacillus amyloliquefaciens Wap Groups disclosed herein may be considered functional groups. In one example, a bacterium expressing a Bacillus amyloliquefaciens WapA protein or WapA-CT polypeptide may inhibit growth of a second bacterium, if the second bacterium does not express a Wapl protein, expresses a Wapl protein that is not functional to protect against growth inhibition, or if the second bacterium expresses a Wapl protein from a Wap Group other than the Wap Group from which the WapA protein has been classified. Generally, contact between the first and second bacterium may occur in order for growth inhibition to occur. If the second bacterium expresses a Wapl protein that is classified into the same Wap Group into which the WapA protein has been classified, the second bacterium is at least partially protected from growth inhibition by the WapA-expressing bacterium. In one example, the first and/or second bacterium may be a. Bacillus organism. In one example, the first and/or second bacterium may be a Bacillus subtilis organism. In one example, the first and/or second bacterium may be & Bacillus amyloliquefaciens organism.

Vectors and Bacteria Expressing the Vectors

[0069] Herein, vectors are considered to be nucleic acid molecules that encode one or more polypeptides or proteins that are capable of being introduced into bacterial cells so that the encoded polypeptides/proteins are expressed in the bacterial cell. In one example, a vector may include minimal nucleotide sequences other than those that actually encode the one or more polypeptides or proteins. One such system may include nucleotide sequences that encode the polypeptides/proteins intended to be expressed, plus other nucleotide sequences that may facilitate recombination and/or incorporation into the genome of a bacterial cell into which the vector is introduced. In one example, a vector may include substantial nucleotide sequences other than those that actually encode the one or more polypeptides or proteins. One such system may include one or more plasmid vectors, bacteriophage vectors, and the like, that also encode the one or more polypeptides or proteins that are intended to be expressed in the bacterial cell. Vectors generally may encode nucleotide sequences that facilitate expression of encoded polypeptides/proteins (e.g., sequences that facilitate transcription and translation). In one example, introduction of single vectors into bacterial cells may be performed. In one example, introduction of two or more vectors into bacterial cells may be performed. In one example, the vector or vectors may encode at least one polycistronic mRNA. In one example, the vector or vectors may encode an operon under the control of a single transcriptional promoter.

[0070] Generally, the vectors include one or more nucleotide sequences that encode one or more of WapA-CT, WapA and Wapl. In various examples, a vector may encode a Wapl polypeptide or protein, may encode a WapA-CT or WapA polypeptide or protein, or may encode a WapA-CT/W apA polypeptide or protein and a Wapl polypeptide or protein. In one example, multiple vectors may encode a combination of the above polypeptides or proteins. The multiple vectors may be designed to be introduced into bacterial cells such that the cells simultaneously express the combination of the polypeptides or proteins.

[0071] Single or multiple vectors may also include nucleotide sequences that encode more than one of the Wapl, WapA-CT and/or WapA polypeptides/proteins. In one example, single or multiple vectors are designed to express 2, 3, 4, 5, 6, 7, 8, 9, or more, Wapl proteins in a bacterial cell. In one example, the Wapl proteins expressed are from different Wap Groups. In one example, single or multiple vectors may encode one or more WapA-CT and/or WapA polypeptides or proteins, and encode one or more cognate Wapl proteins. The vector(s) may be designed to express 1, 2, 3, 4, 5, 6, 7, 8, 9, or more, such cognate pairs. The multiple vectors may be designed to be introduced into bacterial cells such that the cells simultaneously express the combination of the polypeptides or proteins.

[0072] In one example, the bacterial cells into which the vectors may be

introduced/expressed (e.g., host cells) may be Bacillus bacterial cells. In one example, the bacterial cells into which the vectors may be introduced/expressed may be Bacillus subtilis bacterial cells. In one example, the bacterial cells into which the vectors may be

introduced/expressed may be Bacillus amyloliquefaciens bacterial cells. A number of systems for introducing genes into these cells are known in the art. A number of vector and

transcriptional promoter systems for use with such genes are known in the art. Generally, these systems facilitate so-called stable expression of the introduced polypeptides/proteins in the bacterial cells (e.g., self-replicating plasmids, integration of nucleotide sequences into the bacterial chromosome), although systems for transient expression of the introduced

polypeptides/proteins in the bacterial cells may be used.

[0073] In various examples, the host cells for the vectors may include strains of Bacillus amyloliquefaciens or Bacillus subtilis known in the art, and may include mutants or variants of those strains. In one example, Bacillus amyloliquefaciens host strains for the vectors disclosed herein could include FZB24 (Taegro ^® product), BSlb (Biostart TripleX™ product), QST713 (Bayer CropScience Serenade ^® product), FZB42 (ABiTEP GMBH RhizoVital ^® product), and others.

[0074] In various examples, the host cells for the vectors may include the following strains of Bacillus amyloliquefaciens, and mutants or variants thereof: Bacillus amyloliquefaciens strain BS27, Bacillus amyloliquefaciens strain BS2084, Bacillus amyloliquefaciens strain 15AP4, Bacillus amyloliquefaciens strain 3AP4, Bacillus amyloliquefaciens strain LSSA01, Bacillus amyloliquefaciens strain ABP278, Bacillus amyloliquefaciens strain 1013, Bacillus

amyloliquefaciens strain 918, Bacillus amyloliquefaciens strain 22CP1, Bacillus

amyloliquefaciens strain BS18, Bacillus amyloliquefaciens strain BA842, Bacillus

amyloliquefaciens strain BL21, Bacillus amyloliquefaciens strain IN937a, Bacillus

amyloliquefaciens strain B3, Bacillus amyloliquefaciens strain D747, and others.

[0075] In various examples, the host cells for the vectors may include the following strains of Bacillus subtilis, and mutants or variants thereof: Bacillus subtilis strain 3BP5, GB03 (Growth Products Companion ^® product), and others.

[0076] Other bacteria that may be host cells for the vectors disclosed herein may include Bacillus chitinosporus strain AQ746, Bacillus mycoides strain AQ726, Bacillus pumilus strain AQ717, Bacillus sp. AQ175, Bacillus sp. AQ177, Bacillus sp. AQ178, Bacillus subtilis strain AQ743, Bacillus subtilis strain AQ713, Bacillus subtilis strain AQ153, Bacillus thuringiensis strain BD#32, Bacillus thuringiensis strain AQ52, Bacillus thuringiensis subspec. kurstaki BMP 123, and mutants or variants of these bacteria.

Methods

[0077] Also disclosed herein are methods. In one example, methods for introducing into Bacillus cells, any of the vectors described herein are disclosed. The cells resulting from these methods have been constructed to express the Wap polypeptides/proteins that are generally encoded by the vectors. Generally, Bacillus cells can be constructed to express one or more Wapl polypeptides/proteins, independent of whether the cells express WapA. Bacillus cells constructed to express WapA, generally are simultaneously constructed to express a Wapl that is functional to protect the cells against growth inhibition mediated by the WapA. [0078] Bacterial cells constructed to express Wap polypeptides/proteins, by introducing vectors into the cells or otherwise, may be supplied to an environment. In one example, bacterial cells supplied to an environment may possess a phenotype that is advantageous for a purpose. Expression of one or both of WapA/WapI polypeptides/proteins in the cells may make the bacterial cells better suited for the purpose. In one example, the Bacillus amyloliquefaciens subsp. plantarum strain FZB24, which is present in the Taegro ^® product from Novozymes is, in part, a biofungicide/bactericide useful for suppressing certain soil-borne and/or foliar diseases on agricultural crops. As described in Example 6 herein, FZB24 does not express WapA or Wapl. Lacking Wapl expression, FZB24 that is supplied to the soil, may be susceptible to growth inhibition by bacteria in the soil that express WapA. Construction of an FZB24 to express one or more Wapl proteins, for example, may provide the bacterium with protection against growth inhibition by bacteria in the soil that may express WapA. The Wapl-expressing FZB24 bacterium may be more competitive than the parent FZB24 in the soil environment.

[0079] In one example of bacterial cells constructed to express Wap polypeptides/proteins that are supplied to an environment, expression of the Wap polypeptides/proteins may provide an additional phenotype to the cells that is advantageous for a purpose. For example, construction of FZB24 to express one or more WapA proteins (the cells would be constructed to also express cognate Wapl proteins), may provide the bacterium with the capability to inhibit growth of bacteria in a soil environment, where at least some of the bacteria in the soil may not express one or more Wapl proteins that are cognate to WapA proteins expressed in the constructed FZB24 strain. The WapA- and Wapl-expressing FZB24 may be more competitive in the soil environment than the parent FZB24 strain.

[0080] In one example of a method disclosed herein, a nucleotide sequence is obtained from one or both of a wapA and wapl nucleic acid found in a Bacillus amyloliquefaciens bacterium, and the bacterium is classified into a Wap Group, generally based on sequence identities of the proteins encoded by the wapA and wapl nucleic acids. Sequences that possess substantial sequence identity with one another may be classified into the same Wap Groups. Sequences that do not possess substantial identity to known Bacillus amyloliquefaciens WapA/WapI sequences may be placed into a new Wap Group. Organisms classified into Wap Groups may be determined to be advantageous for a purpose, based on the classifying, and supplied to an environment, similar to what has already been discussed above.

[0081] Two or more Bacillus amyloliquefaciens organisms, containing wapA and/or wapl sequences, that have been classified into a Wap Group, may be determined to be Wap compatible or Wap non-compatible, and placed in proximity to one another based on the compatibility. In one example, where it is desired that two organisms survive/function/grow when they are placed together, organisms that are Wap compatible will be placed in proximity to one another. In one example, where it is desired that at least one of two organisms does not survive/function/grow when they are placed together, organisms that are Wap non-compatible will be placed in proximity to one another.

[0082] In one example of a method disclosed herein, a determination is made as to whether two strains of Bacillus amyloliquefaciens strains encode one or both of a wapA and wapl nucleotide sequences in their genomes. The wapA/wapI nucleic acids, or WapA/WapI proteins encoded by the nucleic acids, if present in the genomes, are compared to each other or to known sequences. The two strains are designated as Wap compatible or Wap non-compatible, based on presence/absence of the sequences, or based on comparing the sequences. Similar to what has already been described, the strains may be placed in proximity to one another, or may be supplied to an environment (e.g., a plant environment), based on the method. Compositions of two or more Bacillus amyloliquefaciens strains (e.g., two strains are Wap compatible) may be made, based on the method.

Examples

[0083] The following examples are for the purpose of illustrating various embodiments and are not to be construed as limitations.

Example 1. Bacillus amyloliquefaciens strains, genome sequencing, and sequence assembly

[0084] Bacillus amyloliquefaciens subsp. plantarum strains were either internal Novozymes strains or were strains obtained from products purchased commercially, as indicated in Table 6. Genome sequences were determined internally for some of the strains, as described below. Genome sequences not determined internally were obtained from GenBank (NCBI), as indicated in Table 6, and included in the analyses.

[0085] For sequences that were determined internally, genomic DNA samples were purified from the bacteria using a previously described method (Pitcher et al., 1989, Rapid extraction of bacterial genomic DNA with guanidinium thiocyanate, Lett. Appl. Microbiol. 8: 151-156). The purified DNA was sheared to an average size of 300 base pairs by sonication with a Covaris M220 focused ultrasonicator (Covaris, Inc., Woburn, Massachusetts, USA). Sequencing libraries were prepared using the Apollo 324™ System (IntegenX, Inc., Pleasanton, California, USA). DNA sequencing was done on an Illumina MiSeq instrument (Illumina, Inc., San Diego, California, USA) as prescribed by the manufacturer. Illumina sequencing reads were trimmed using CLC Genomics Workbench 5 (CLCbio, Inc., Arhus, Denmark). The trimmed reads were assembled with a de novo assembly algorithm implemented in the CLC Genomics Workbench 5 software. GAPfiller (Boetzer and Pirovano, 2012, Toward almost closed genomes with

GapFiller, Genome Biol. Γ3 :R56) was used to reduce the number of undefined nucleotides in the genome assemblies using paired-reads to fill in the gapped regions within scaffolds. The sequences were assembled, annotated and made available for viewing with RAST (Aziz et al., 2008, The RAST server: rapid annotations using subsystems technology, BMC Genomics 9:75).

Example 2. Analysis and grouping of Bacillus amyloliquefaciens WapA-CT sequences

[0086] For analysis of the genomic sequences, proteins encoded by wapA orthologues were identified using Blastp (Altschul et al., 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402) and Bacillus subtilis Wap A (Genbank accession NP 391802) as the query sequence. For classification purposes, the C-terminal (WapA-CT) domains of the identified proteins, comprising 200 amino acids, were aligned using CLUSTALW (Thompson et al., 2002, Multiple sequence alignment using ClustalW and ClustalX, Curr. Protoc. Bioinformatics 2:2.3.1-2.3.22) included in the DNASTAR

Lasergene™ Suite, version 7.2.1 (DNASTAR, Inc., Madison, Wisconsin, USA). A sequence identity matrix was calculated for the WapA-CT sequences from the various strains (Fig. 1) and a phylogenetic tree was generated from these CLUSTALW alignments (Chenna et al., 2003, Multiple sequence alignment with the Clustal series of programs, Nucleic Acids Res. 31 :3497- 3500) (Fig. 2). From these analyses, WapA-CT amino acid sequences were classified into 9 discrete Wap Groups based on their sequence relatedness to one another, as shown in Fig. 2. The data showed that WapA-CT sequences within each of the 9 Wap Groups were no less than 97.5% identical, while percent identity between WapA-CT sequences from different Wap Groups ranged from a low of 32.3 to a high of 71.8 (Fig. 1).

Example 3. Analysis and grouping of Bacillus amyloliquefaciens Wapl sequences

[0087] From the initial sequence analyses, it was found that the chromosomal regions in which the wapA genes of Bacillus amyloliquefaciens were located appeared largely syntenic with the chromosomal regions of Bacillus subtilis. Since, in Bacillus subtilis, the wapA and wapl genes are immediately adjacent on the chromosome (i.e., wapl is immediately 3' of wapA)(Kumt et al., 1997, The complete genome sequence of the gram-positive bacterium Bacillus subtilis, Nature 390:249-256; Koskiniemi, et al., 2013, Rhs proteins from diverse bacteria mediate intercellular competition, Proc. Natl. Acad. Sci. USA 110:7032-7037), putative wapl genes in Bacillus amyloliquefaciens were assigned based on their location downstream (3') of the wapA coding sequences determined as described in Example 2. As already described for WapA-CT in Example 2, a sequence identity matrix was calculated for Wapl (Fig. 3) and a phylogenetic tree was generated from the CLUSTALW alignments (Fig. 4). From these analyses, Wapl amino acid sequences were classified based on their sequence relatedness to one another. Nine Wap Groups emerged for Wapl, just as for WapA-CT. The Wap Groupings for both WapA-CT and for Wapl appeared to be the same (i.e., WapA-CT sequences from the Bacillus amyloliquefaciens strains grouped together, based on sequence identity, the same as did Wapl sequences from the strains) (Fig. 2 and Table 3). Wapl sequences within each of the 9 Wap Groups were no less than 95.2% identical, while percent identity between Wapl sequences from distinct Wap Groups ranged from a low of 5.5 to a high of 21.0 (Fig. 3).

Example 4. Comparison of WapA-CT sequences from Bacillus amyloliquefaciens and Bacillus subtilis

[0088] The WapA-CT sequences from Bacillus amyloliquefaciens that have been analyzed and grouped (Fig. 2 and Table 3) were compared to WapA-CT sequences from a number of Bacillus subtilis organisms (Table 7). The genome sequences of these organisms were obtained from GenBank.

[0089] Using WapA-CT sequences from the Bacillus amyloliquefaciens strains indicated in Table 4, and from the Bacillus subtilis strains indicated in Table 7, a phylogenetic tree was generated, as shown in Fig. 5. The Wap Group numbers shown in Fig. 5 indicate the same Wap Groupings as determined in Example 2 (Fig. 2 and Table 4).

[0090] The data showed that, in the majority of cases, WapA-CT sequences from Bacillus subtilis were distinct from those from Bacillus amyloliquefaciens (Fig. 5). Six of the eight Bacillus subtilis strains formed groups containing only Bacillus subtilis WapA-CT sequences (these groups labelled as "B. sub" in Fig. 5). Two of the Bacillus subtilis WapA-CT sequences, however (RO-NN-1 and TU-B-10), were grouped with Bacillus amyloliquefaciens strain SB3297 in Wap Group 6 (the group labelled as "Mixed" in Fig. 5). These data indicated that Bacillus amyloliquefaciens WapA, and likely Wapl sequences (24 out of 25), were largely distinct from Bacillus subtilis WapA sequences.

Example 5. Construction of a plasmid expressing Wapl from Bacillus amyloliquefaciens strain SB3281

[0091] A plasmid called pBM347, expressing the Wapl protein from Bacillus

amyloliquefaciens strain SB3281, was constructed using a three-step process. In the first step, the plasmid vector, pBM346a, was constructed. As described below, pBM346a contained wap sequences from Bacillus subtilis strain 168. In the second step, the wapl coding sequence from Bacillus amyloliquefaciens strain SB3281 was prepared. In the third step, the insert from the second step was constructed into the vector from the first step to yield the Wapl-expressing plasmid, called pBM347.

[0092] In the first step, the plasmid vector, pBM346a was constructed as follows. The primers below were used to amplify the wapl gene from Bacillus subtilis strain 168.

[0093] Primer 1205397

[0095] Primer 1205398

[0097] Primer 1205397 contained a recognition sequence for HindSl (underlined) and a ribosome binding site (italics). Primer 1205398 contained a recognition sequence for Xbal (underlined) and a transcriptional termination signal. Both primers contained wapl sequences (bold). [0098] PCR was performed using the primers and Bacillus subtilis strain 168 DNA as template under standard conditions to obtain a 504 base-pair amplified fragment, which was purified by agarose gel electrophoresis. The fragment was cloned into plasmid pCR2.1-TOPO (Invitrogen, Carlsbad, California, USA) to yield a plasmid called pBM345.

[0099] pBM345 and another plasmid, called pBD2528 (described in PCT publication no. WO2008/079895) were both digested with Hindlll and Xbal restriction endonucleases. A 498 base pair fragment was purified from pBM345. A 6935 base pair fragment was purified from pBD2528. These two fragments were ligated and used to transform Escherichia coli cells. Plasmids from transformants were screened. A plasmid identified as having the expected restriction endonuclease pattern on agarose gels was designated pBM346a.

[00100] The primers below were then used to amplify the vector sequences from pBM346a.

[00101] Primer 1206817

[00103] Primer 1206818

[00105] Both primers contained wapl sequences (bold).

[00106] PCR was performed using the primers and pBM346a plasmid under standard conditions to obtain a 7001 base-pair amplified fragment, which was purified by gel electrophoresis.

[00107] In step 2, the primers below were used to amplify the wapl gene from Bacillus amyloliquefaciens strain SB3281. [00108] Primer 1206815

[00110] Primer 1206816

[00112] Both primers contained wapl sequences (bold). Primer 1206815 was complementary to primer 1206818. Primer 1206816 was complementary to primer 1206817.

[00113] PCR was performed using the primers and Bacillus amyloliquefaciens strain SB3281 DNA as template under standard conditions to obtain an 868 base-pair amplified fragment, which was purified by agarose gel electrophoresis.

[00114] In step 3, the 7001 base-pair fragment from pBM346a was joined to the 868 base-pair wapl fragment from Bacillus amyloliquefaciens strain SB3281 using an In-Fusion PCR Cloning Kit (Clonetech, Mountain View, California, USA) and a portion of the reaction mixture was used to transform Escherichia coli cells. Plasmids from transformants were screened. A plasmid identified as having the expected restriction endonuclease pattern on agarose gels was designated as pBM347.

Example 6. Protection from growth inhibition after expression of Wapl

[00115] Although many strains of Bacillus amyloliquefaciens were found to contain wapA/wap! genes (Examples 2 and 3), strains of Bacillus amyloliquefaciens were also found that did not contain wapAJwapI genes (about 78% of tested Bacillus amyloliquefaciens subsp.

plantarum strains contained wap sequences; no wap sequences were found in 8 tested strains of Bacillus amyloliquefaciens subsp. amyloliquefaciens). One strain of Bacillus amyloliquefaciens subsp. plantarum found not to contain wapAJwapI genes was Bacillus amyloliquefaciens strain FZB24. FZB24 is the strain used in Novozymes' Taegro ^® product. [00116] The ability of the FZB24 strain to grow in co-cultures with Bacillus

amyloliquefaciens strains that contain wapAJwapl genes was tested. FZB24 was co-cultured with the SB3281 strain of Bacillus amyloliquefaciens. The SB3281 strain was shown to contain wapA/wapI genes and was previously placed into Wap Group 5 (Tables 2 and 4 and Figs. 2 and 4). To perform the co-culturing experiment, both the FZB24 and SB3281 strains were separately grown to the mid-exponential phase of growth. The cultures were then mixed together and grown over night. Control cultures, containing cultures of FZB24 and SB3281, that were not mixed together, were also included. After the overnight incubation, both the control and co- cultured cultures were diluted and plated on agar plates, so colonies could be enumerated.

FZB24 colonies have a distinctive colony morphology that allowed them to be differentiated from colonies formed by the SB3281 strain.

[00117] The data from the example experiment are shown in Fig. 6. Cultures of individual strains (bars labeled 1-3) and co-cultures of two strains (bars labeled 4-7) are indicated on the x- axis of Fig. 6. Colony counts from the various cultures/co-cultures were expressed on the y-axis of Fig. 6 as colony-forming-units (CFU) per ml of culture. For the co-cultures (bars labeled 4-7), the strain whose CFU counts are represented by the bar is indicated on the top of the chart by the arrows.

[00118] The results indicated that both of the control cultures, FZB24 (Fig. 6, bar labeled 1) and SB3281 (Fig. 6, bar 2) grew well, with a titer of CFU of 10 ⁸ -10 ⁹ per ml of culture. However, when FZB24 was co-cultured with SB3281, CFU per ml for FZB24 were reduced at least 10 ⁴ - fold (Fig. 6, bar 4), while SB3281 grew well in the co-culture, with a CFU of about 10 ⁷ per ml of culture (Fig. 6, bar 5).

[00119] If the reduction in FZB24 growth in co-cultures with SB3281 was caused by WapA produced by the SB3281 strain, expression of SB3281 Wapl in FZB24 would be expected to increase FZB24 growth. To test this, pBM347 (from Example 5), encoding Wapl from SB3281, was transformed into FZB24. The pBM347-transformed FZB24 strain was designated BaC0202.

[00120] When the Wapl-expressing FZB24 strain, BaC0202, was co-cultured with SB3281, BaC0202 growth was increased (Fig. 6, bar 6) and actually grew to similar levels as SB3281 (compare Fig. 6, bar 6 with bar 5). Therefore, Wapl from strain SB3281 protected FZB24 from WapA-induced growth inhibition by strain SB3281. Interesting was that SB3281 growth was reduced in co-cultures with BaC0202 (Fig. 6, bar 7). Our data suggest that a set of genes distinct from wapAJwapl may be responsible for decreased growth of the SB3281 strain.

Example 7. Wapl expression protects against WapA-growth inhibition when Wapl and WapA are from the same Wap Group

[00121] In the experiment described in Example 6, the Wapl protein expressed in FZB24 (i.e., in the BaC0202 strain) was from strain SB3281, and protected FZB24 from growth inhibition by strain SB3281, which expressed WapA protein. In this experiment, both Wapl and WapA were from Group 5 (Figs. 4 and 2, respectively, and Tables 2 and 4). If the 9 Wap Groups into which the Bacillus amyloliquefaciens WapA/WapI proteins have been classified are functional groups, Wapl proteins from one of the 9 groups would be expected to protect against growth inhibition by WapA from the same Wap Group (i.e., cognate pairs) but not against growth inhibition by a WapA from a different Wap Group.

[00122] To test this, co-culture experiments similar to those shown in Example 6 will be performed. In a first experiment, FZB24 is co-cultured with SB3755. SB3755 contains wapAlwapI genes, but these genes have been placed into Wap Group 7, not Wap Group 5 as for SB3281. When the experiment is performed, the data are that SB3755 grows well in co-culture, but that there is a reduction in growth of FZB24, which does not contain wapAJwapl genes. SB3755, therefore, is expected to reduce FZB24 growth in co-cultures in the same way that SB3281 reduced growth of FZB24 in co-cultures, as shown in Example 6.

[00123] In a second experiment, the BaC0202 strain (FZB24 expressing Wapl from Wap Group 5, as described in Example 6) is co-cultured with SB3755. The data are that there is a reduction in growth of BaC0202, which expresses Wapl from Wap Group 5, but no WapA protein, while SB3755 grows well. Again, SB3755 expresses both WapA and Wapl proteins from Wap Group 7. Therefore, SB3755 (because it expresses WapA) is expected to reduce BaC0202 growth in co-cultures (because, although BaC0202 expresses Wapl, the Wapl is not cognate with WapA from SB3755). The conclusion is that the Group 5 Wapl protein that is expressed in the BaC0202 strain is not protective against growth inhibition mediated by the Group 7 WapA protein of SB3755. Example 8. Simultaneous expression of Wapl proteins from different Wap Groups protects against growth inhibition by multiple WapA proteins

[00124] An experiment is performed to test whether cells expressing Wapl proteins from multiple Wap Groups are resistant to growth inhibition by the multiple WapA proteins from those Wap Groups.

[00125] A gene sequence is synthesized that includes the complete coding regions of the wapl genes from strains SB3281 and SB3755. The coding sequences are synthesized, in tandem, such that a single polycistronic mRNA will be transcribed from the synthesized gene sequence, when placed downstream from a transcriptional promoter. The polycistronic mRNA will encode a Shine-Dai garno sequence upstream of the coding region nearest the 5' end of the mRNA. The separate SB3281 and SB3755 sequences within the polycistronic mRNA will each have their own start and stop codons. The synthesized sequence is constructed into a plasmid vector, downsteam of a transcriptional promoter. The plasmid is used to transform FZB24 cells.

[00126] The FZB24 cells constructed to express Wapl proteins from both strains SB3281 (Wap Group 5) and SB3755 (Wap Group 7), are co-cultured with strain SB3755 (Wap Group 7) and, separately, co-cultured with strain SB3281 (Wap Group 5), using the co-culturing method described in Example 6. The data are that the FZB24 cells expressing both the SB3281 and SB3755 Wapl proteins, grow well, both in co-culture with strain SB3281, and in co-culture with strain SB3755, without indication that either SB3281 or SB3755 decreases growth of the FBZ24 dual Wapl-expressing cells. Control FZB24 cells, not expressing any Wapl protein, will be growth inhibited by WapA from both SB3755 and SB3281.

[00127] The conclusion is that multiple wapl genes, from different of Wap Groups, are expressed in the same cells. The conclusion also is that cells expressing Wapl from different of the Wap Groups are protected from growth inhibition by the multiple WapA proteins, when the Wapl proteins are from the same groups (i.e., cognate) as are the WapA proteins.

[00128] While example compositions, methods, and so on have been illustrated by

description, and while the descriptions are in considerable detail, it is not the intention of the applicants to restrict or in any way limit the scope of the application. It is, of course, not possible to describe every conceivable combination of components or methodologies for purposes of describing the compositions, methods, and so on described herein. Additional advantages and modifications will readily appear to those skilled in the art. Therefore, the invention is not limited to the specific details and illustrative examples shown and described. Thus, this application is intended to embrace alterations, modifications, and variations that fall within the scope of the application. Furthermore, the preceding description is not meant to limit the scope of the invention.

[00129] To the extent that the term "includes" or "including" is employed in the detailed description or the claims, it is intended to be inclusive in a manner similar to the term

"comprising" as that term is interpreted when employed as a transitional word in a claim.

Furthermore, to the extent that the term "or" is employed in the detailed description or claims (e.g., A or B) it is intended to mean "A or B or both". When the applicants intend to indicate "only A or B but not both" then the term "only A or B but not both" will be employed. Thus, use of the term "or" herein is the inclusive, and not the exclusive use. See, Bryan A. Garner, A Dictionary of Modern Legal Usage 624 (2d. Ed. 1995). Also, to the extent that the terms "in" or "into" are used in the specification or the claims, it is intended to additionally mean "on" or "onto." Furthermore, to the extent the term "connect" is used in the specification or claims, it is intended to mean not only "directly connected to," but also "indirectly connected to" such as connected through another component or components.