FIELD OF THE INVENTION

The present invention relates to a method for transforming a strain of the Lactococcus genus through natural competence. The present invention further relates to strains obtained or obtainable by said method. The present invention also relates to a method for identifying a strain of the Lactococcus genus which is transformable through natural competence.

BACKGROUND TO THE INVENTION

Lactococcus lactis is one of the most important lactic acid bacteria used in the dairy industry, in particular as a main dairy starter species in various cheese preparations (e.g. gouda, cheddar, brie, parmesan, roquefort) and fermented milk products (e.g. buttermilk, sour cream). Other applications of L. lactis bacteria include as a host for heterologous protein production or as a delivery platform for therapeutic molecules. While the growth and fermentation properties of L. lactis have been gradually improved by selection and classical methods, there is great potential for further improvement through natural processes or by genetic engineering. Of particular interest are methods to naturally transform L. lactis without the use of genetic engineering, thereby generating new non-GMO strains with useful industrial properties.

Lactococcus raffinolactis is present in a wide range of environments, such as foods (meat, fish, milk, vegetable), animals, and plant materials. In the dairy environment, this species has been found in raw milks (cow, ewe, goat, and camel), natural dairy starter cultures, and a great variety of cheeses. The prevalence of this bacterium in foods even if with a "nondominant" status compared to other lactococci could make it a candidate for future development of starter cultures. DNA acquisition by natural transformation is widespread among prokaryotes and has been identified in over 80 species. Various functions are attributed to competence for natural transformation: genome plasticity, DNA repair, and/or nutrition. In Gram-positive bacteria, competence for natural transformation has been well-characterized in Bacillus subtilis and in various species of the genus Streptococcus (e.g. S. pneumoniae, S. mutans, and S. thermophilus).

In streptococci, competence for DNA transformation is induced in response to secreted signalling peptides referred to as competence pheromones/alarmones. The production of this class of cell-to-cell communication molecules is initiated in response to specific environmental stresses or conditions and allows the coordination of physiological functions (e.g. competence, predation, biofilm formation). Above a threshold concentration, competence pheromones activate the master regulator ComX (alternative sigma factor σ ), which ultimately leads to a transcriptional reprogramming of cells (globally known as late competence phase) including the induction of genes strictly required for DNA transformation. ComX binds to a specific DNA sequence named Corn-box or Cin-box, which is located at least in the vicinity of promoters of late competence (com) genes/operons responsible for DNA uptake (e.g.; comG, comF and comE operons), DNA protection (e.g. ssb) and DNA recombination (e.g. recA, dprA, coiA), and positively controls their expression.

The early steps leading to competence activation (early competence phase) differs among bacteria. In streptococci, two major peptide-based signaling pathways - i.e. ComCDE and ComRS - have been identified so far. In mitis and anginosus groups of streptococci (S. pneumoniae as paradigm), the competence signaling peptide (CSP, or mature ComC) triggers a phosphorylation cascade mediated by the two-component system ComD-ComE, leading to the transcriptional activation of comX. In salivarius, mutans, pyogenes, bovis and suis groups of streptococci, another regulation mechanism is operational (S. thermophilus as paradigm). This system involves the ComX-induction peptide (XI P, or mature ComS) which is internalized by the oligopeptide transporter Opp, binds to and activates the regulator ComR, and in turn induces comX transcription.

Orthologues of comX and of all late com genes essential for natural transformation have been identified in the genome of L. lactis, although some are present as putative pseudogenes in different strains {Wydau et al., 2006).

Specific growth conditions have been reported to activate com genes in Lactococcus lactis. For example, the promoter of comX was shown to be induced during cheese-making conditions in strain MG5267 (an MG1363 derivative) which belongs to the subspecies cremoris (Bachmann et al. 2010).

In the L. lactis subspecies (subsp.) lactis, carbon starvation was shown to activate six late com genes in strain IL1403 of dairy origin (i.e. comX, comEA, comGA, comGB, radA, and nucA) and most of the late essential com genes in strain KF147 of plant origin (i.e. comX, comC, coiA, and operons comG, comE, comF) (Ercan et al., 2015). However, when the authors attempted to validate functional natural transformation in KF147, they were unsuccessful.

Wydau et al. reported that all the well-established late genes/operons display an upstream and conserved Corn-box, suggesting that they are similarly controlled by ComX as reported in streptococci. However, the authors did not comment on whether comX over-expression in IL1403 induced natural competence. Indeed, the authors neither report any experiment evaluating natural competence in this strain nor suggest any experimental conditions appropriate for inducing natural competence. Thus, as noted in the recent literature (see Ercan et al., 2015) [i.e., 9 years after Wydau et al.], there is no experimental evidence for successful transformation of any species of the genus Lactococcus by natural competence, and even less of IL1403.

Accordingly, there remains a need for a method for naturally transforming Lactococcus strains using natural competence. In addition, since some strains of the Lactococcus genus may not encode a full set of functional late com genes, there is a need for a method for identifying Lactococcus strains which can be transformed by natural competence.

SUMMARY OF THE INVENTION

In a first aspect, the present invention provides a method for transforming a strain of the Lactococcus genus with an exogenous DNA polynucleotide comprising the steps of:

(a) providing a strain of the Lactococcus genus, wherein said strain is transformable through natural competence;

(b) modulating the production of a ComX protein in said strain;

(c) contacting said strain of step (b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome.

In one embodiment, the step of modulating the production of a ComX protein is performed by expressing a comX gene in said strain or increasing the expression of a comX gene in said strain.

In a further embodiment, the comXgene is an exogenous comX gene. Said exogenous comX gene may be transferred into said strain by conjugation, transduction, or transformation. Said exogenous com gene may be operably linked to transcription regulator(s).

In an alternative embodiment, said com gene is the endogenous comX gene of said strain. In one embodiment, when said comX gene is the endogenous comX gene of said strain, the method comprises:

(a) providing a strain of the Lactococcus genus, wherein said strain is transformable through natural competence; (b) modulating the production of a ComX protein, by expressing the endogenous comX gene or increasing the expression of the endegenous comX of said strain;

(c) contacting said strain of step (b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome,

wherein step (c) is carried out after step (b) or wherein step (b) and step (c) are carried out simultaneously.

In some embodiments, said ComX protein has the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, or has at least 90% identity or at least 90% similarity to the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20 or SEQ ID NO:22. In some embodiments, said ComX protein has the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, or has at least 90% identity or at least 90% similarity to the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4 or SEQ ID NO:6. In some embodiments, said comX gene has the nucleotide sequence of SEQ ID NO:1 , SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:1 1 , SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21 , or has at least 90% identity to the nucleotide sequence of SEQ ID NO:1 , SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:1 1 , SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19 or SEQ ID NO:21 .

In some embodiments, said comX gene has the nucleotide sequence of SEQ ID NO:1 , SEQ ID NO:3, SEQ ID NO:5, or has at least 90% identity to the nucleotide sequence of SEQ ID NO:1 , SEQ ID NO:3 or SEQ ID NO:5.

In some embodiments, the medium of step (c) is a chemically defined medium. In a preferred embodiment the chemically defined medium (CDM) comprises 0.5 g/L NH4CI, 9.0 g/L KH2PO4, 7.5 g/L K2HPO4, 0.2 g/L MgC , 5 mg/L FeCI ₂ , 50 mg/L CaCI ₂ , 5 mg/L ZnS0 ₄ , 2.5 mg/L C0CI2, 0.05 g/L tyrosine, 0.1 g/L asparagine, 0.1 g/L cysteine, 0.1 g/L glutamine, 0.1 g/L isoleucine, 0.1 g/L leucine, 0.1 g/L methionine, 0.1 g/L tryptophan, 0.1 g/L valine, 0.1 g/L histidine, 0.2 g/L arginine, 0.2 g/L glycine, 0.2 g/L lysine, 0.2 g/L phenylalanine, 0.2 g/L threonine, 0.3 g/L alanine, 0.3 g/L proline, 0.3 g/L serine, 10 mg/L paraaminobenzoic acid, 10 mg/L biotin, 1 mg/L folic acid, 1 mg/L nicotinic acid, 1 mg/L panthotenic acid, 1 mg/L riboflavin, 1 mg/L thiamine, 2 mg/L pyridoxine, 1 mg/L cyanocobalamin, 5 mg/L orotic acid, 5 mg/L 2-deoxythymidine, 5 mg/L inosine, 2.5 mg/L c//-6,8-thioctic acid, 5 mg/L pyridoxamine, 10 mg/L adenine, 10 mg/L guanine, 10 mg/L uracil, 10 mg/L xanthine, and 5 g/L glucose.

In some embodiments, prior to step (c) said strain is incubated in a pre-culture medium, preferably wherein the pre-culture medium is a complex medium, more preferably wherein the pre-culture medium is M17G or THBG.

In some embodiments of the present invention, said strain is incubated with the exogenous DNA polynucleotide for around 4 to 8 hours at around 30 °C and said medium of step (c) is supplemented with an osmo-stablizer, preferably wherein the osmo-stablizer is glycerol or mannitol, more preferably wherein the osmo-stabilizer is 5% [v/v] glycerol or 5% [w/v] mannitol.

In some embodiments, said exogenous DNA polynucleotide is from a strain of the Lactococcus lactis species. In some embodiments, said exogenous DNA polynucleotide is from a strain of the Lactococcus raffinolactis species.

In some embodiments, said strain of step (a) is a Lactoccocus lactis subsp. cremoris strain.

In another aspect, the present invention provides a strain of the Lactococcus genus obtained or obtainable by the method of the first aspect of the present invention. In one embodiment, said strain of the Lactococcus genus is a strain of the Lactococcus lactis or Lactococcus raffinolactis species.

In a further aspect, the present invention provides a method for identifying a strain of the Lactococcus genus which is transformable through natural competence comprising the steps of:

(a) providing a strain of the Lactococcus genus species;

(b) transforming said strain with a plasmid expressing a comX gene having at least 90% identity, preferably having 100% identity, to the endogenous comX gene of said strain;

(c) contacting said strain obtained in step (b) with an exogenous DNA polynucleotide encoding a marker gene in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) determining the rate of recombination events; wherein a rate of at least 1 x 10 ^"6 transformants per μg of DNA is indicative of a strain which is transformable through natural competence.

In a particular embodiment of method for transforming a strain of the Lactococcus genus of the present invention, said strain of step (a) is identified using the method for identifying a strain of the Lactococcus genus which is transformable through natural competence according to the present invention. In some embodiments of the present invention, said strain of step (a) is identified using Assay A.

DESCRIPTION OF THE DRAWINGS

Figure 1 : Table showing the status of genes involved in natural competence for L. lactis strains MG1363, SK11 , KW2, IL1403, SL12651 and SL12653.

Late com genes in the complete genomes of strains MG1363, SK1 1 , and KW2 of Lactococcus lactis subsp. cremoris and of strain IL1403, SL12651 and SL12653 of Lactococcus lactis subsp. lactis. Origin is indicated above strain names. Gene-associated function in DNA transformation is indicated on the left. Reg. denotes regulation. The complete and incomplete status of late genes is based on blastp and tblastn homology searches (https://blast.ncbi.nlm.nih.gov/Blast.cgi) using orthologues of S. pneumoniae TIGR4 and S. thermophilus LMD-9 and default parameters. + denotes the presence of a complete gene; ^* denotes the presence of an incomplete gene due to nucleotide(s) exchange, insertion or deletion resulting in a premature stop codon; and Tn denotes a disrupted gene by the insertion of at least one transposon.

Figure 2: Graphs displaying the results of luciferase assays which demonstrate the activation of a reporter construct comprising the late promoter PcomCA driven by constitutive comX overexpression

(A) Maximum specific luciferase (Lux) activity (RLU Ο βοο ^"1 ) emitted by eight independent clones (cl01 to cl08) of the KW2-derived reporter strain (BLD101 , P _C omGA[MG]-iuxAB) carrying plasmid pGhP32comXMG compared to the control strain (Ctl) carrying the empty vector pG ⁺ host9. (B) Kinetics of specific Lux activity (solid line) during growth (RLU/OD600; dotted line) for the control strain (Ctl; black lines) and three selected clones (BLD101 [pGhP32comXMG], cl02, cl04 and cl05; gray lines). (C) Kinetics of specific luciferase activity (closed symbols) during growth (RLU/OD600; open symbols) of the MG1363 + pGhP32comXMG-PcomG/vMGr/wc, grown in M17G at 30°C. (D) Kinetics of specific luciferase activity (closed symbols) during growth (RLU/OD600; open symbols) of IL1403 + pGhP32comXio-PcomG/v/or/wc strains, grown in M17G at 30°C. Figure 3: Graphs displaying the results of luciferase assays which demonstrate the impact of growth medium on ' comGA activation

Maximum specific Lux activity of BLD101 [pGhP32comXMG] cl02 grown in different final culture media (CDM, THBG, and M17G) according to preculture conditions (CDM, THBG, and M17G). Overnight precultures were 10-fold diluted in the pre-culture medium and grown for 2 hours. Then, cells were washed twice in distilled water and the Ο βοο was adjusted to 0.05 in the final growth medium before measuring growth and luciferase activity. One representative experiment of two independent replicates.

Figure 4: Results of a transformation assay implemented on a L. lactis subsp. cremoris KW2 constitutively expressing comX contacted with a DNA consisting of a mutated allele of the rpsL gene as exogenous DNA polynucleotide

(A) Alignment of the rpsL gene sequences of strain MG1363, a spontaneous streptomycin- resistant clone of strain MG1363, strain KW2 and a KW2-derived transformant obtained using the method of the invention (partial sequence). The arobase, pound and dollar signs below the alignment indicate the positions of nucleotide differences existing between the rpsL sequences. The dollar sign at position 167 indicates the point mutation (A->T; strA1 allele) responsible for the streptomycin-resistance phenotype; the pound sign at position 156 highlights a nucleotide that is naturally different between MG1363 and KW2 (T in KW2, A in MG1363); the arobase sign at position 39 indicates a silent nucleotide substitution (T->G) which is found in the streptomycin-resistant clone derived from MG1363. (B) DNA transformation with the strA1 allele was assessed for L. lactis strains constitutively expressing ComX. Transformation rate (white bars) and maximum specific luciferase (Lux) activity (black diamonds, RLU Οϋβοο ^"1 , as reported in Figure 2) of eight clones (cl01 to cl08) of the reporter strain (BLD101 , P _C omGA[MGrluxAB) carrying plasmid pGhP32comXMG compared to the negative control strain (Ctl-) carrying the empty vector (BLD101 [pG ⁺ host9]).

Figure 5: Graphs displaying the results of transformation rate of the KW2 derivative BLD101 [pGhP32comXMc] obtained with overlap PCR products (comEC, mecA, ciaRH, covRS and clpC) and strA1 {rpsL*)- donor DNA.

The threshold represents the theoretical transformation rate to obtain only one transformant.

Figure 6: Graphs depicting the results of transformation assays for a L. lactis subsp. cremoris deleted in its comEC gene and constitutively expressing comX.

DNA transformation with the strA1 allele was assessed for L. lactis strains constitutively expressing comX. Transformation rate (white bars) and maximum specific luciferase (Lux) activity (RLU Οϋβοο ^"1 ) of four clones (cl01 to cl04) of the ComEC-deficient reporter strain (BLD102, PcomGA[MGrluxAB) carrying plasmid pGhP32comXMG compared to the positive (Ctl ⁺ , BLD101 [pGhP32comX _MG ] cl02) and negative (Ctl-, BLD101 [pG ⁺ host9]) control strains. Transformability was assessed according to the standard protocol described in Materials and Methods using strA ^• /-carrying PCR products as donor DNA. ND denotes a transformation rate below the detection level of spontaneous Str ^r mutants (< 10 ^"7 ). One representative experiment of two independent replicates.

Figure 7: Graphs displaying natural competence in Lactococcus lactis subsp. lactis SL12651 and 12653 strains.

(A) Transformation rate of L. lactis subsp. lactis SL12651 and 12653 strains in M17G medium, with rpsL ^* donor DNA (+DNA) or without donor DNA (-DNA); (B) DNA transformation with increasing initial concentration of donor DNA assessed in SL12653 strain; (C) Comparison of transformation rates between wild-type (WT) SL12653 strain and a SL12653 strain deleted for the comX gene (ComX-); transformation rate of three clones of the ComX-deficient strain compared to the WT strain, in presence (+DNA) or in absence (-DNA) of donor DNA.

DETAILED DESCRIPTION

The present invention is based on the observation that overexpression of ComX in a strain of the Lactococcus genus allowed to transform this strain by natural competence. Using this approach a L. lactis strain was generated by natural transformation with an exogenous DNA polynucleotide. Importantly, these results are the first demonstration of transformation of a L. lactis strain by natural competence. Further, existence of natural competence in the Lactococcus genus has been confirmed in two strains of the Lactococcus raffinolactis species and two Lactococcus lactis species. The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, biochemistry, microbiology, bacteriology, and related fields, which are within the capabilities of a person of ordinary skill in the art. Such techniques are explained in the literature.

Thus, the present invention provides a method for transforming a strain of the Lactococcus genus with an exogenous DNA polynucleotide comprising the steps of:

(a) providing a strain of the Lactococcus genus, wherein said strain is transformable through natural competence;

(b) modulating the production of a ComX protein in said strain; (c) contacting said strain of step (b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome.

As detailed below, step (b) and step c) can be carried out sequentially [i.e., step (b) and then step (c)] or in another embodiment step (b) and step (c) can be carried out simultaneously.

Lactococcus genus

The present invention relates to a method for transforming a strain of the Lactococcus genus, a Gram-positive bacterium. Lactococcus strains are known as lactic acid bacteria (LAB) for their ability to convert carbohydrate to lactic acid. A strain of the Lactococcus genus and Lactococcus strain are used herein interchangeably.

The Lactococcus genus comprises, but is not limited to the following species: Lactococcus chungangensis, Lactococcus fujiensis, Lactococcus garvieae, Lactococcus lactis, Lactococcus piscium, Lactococcus plantarum and Lactococcus raffinolactis. Any strain of one of these species may be used in the current invention, provided that this strain is transformable through natural competence as defined herein.

In a particular embodiment, said strain of the Lactococcus genus of step a) is a strain of the Lactococcus lactis species or a strain of the Lactococcus raffinolactis species.

Lactococcus lactis

In a particular embodiment, said strain of the Lactococcus genus of step a) is a strain of the Lactococcus lactis species. The species Lactococcus lactis comprises several subspecies. Thus, when the strain of the Lactococcus genus of step a) is a strain of the Lactococcus lactis species, said strain is selected in the group consisting of Lactococcus lactis subsp. cremoris, Lactococcus lactis subsp. hordniae, Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. tructae. As used herein a strain of the Lactococcus lactis species is understood to be a genetic variant or subtype of any L. lactis species or subspecies. The different Lactococcus lactis subspecies disclosed here, and in particular the lactis and the cremoris subspecies, are defined herein based on DNA sequences coding for 16S ribosomal RNA [Ward et al., 1998].

In a particular aspect, the present invention provides a method for transforming a strain of the Lactococcus lactis species with an exogenous DNA polynucleotide comprising the steps of: (a) providing a strain of the Lactococcus lactis species, wherein said strain is transformable through natural competence;

(b) modulating the production of a ComX protein in said strain;

(c) contacting said strain of step (b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome.

In a preferred embodiment, the strain of step (a) is a Lactococcus lactis subsp. cremoris strain or a Lactococcus lactis subsp. lactis strain. Both subspecies have been identified and characterised with full genome sequences - see, e.g., Wegmann et al. (2007) J. Bacteriol. 189:3256-3270 and Bolotin et al. (2001 ) Genome Res. 1 1 :731-753. With regards to the dairy industry, L. lactis subsp. lactis (previously known as Streptococcus lactis) is preferred for making soft cheese while L. lactis subsp. cremoris (previously known as Streptococcus cremoris) is preferred for hard cheese production.

In a preferred embodiment, the strain of step (a) is Lactococcus lactis subsp. cremoris strain.

In another preferred embodiment, the strain of step (a) is Lactococcus lactis subsp. lactis strain.

Lactococcus raffinolactis

In a particular embodiment, said strain of the Lactococcus genus of step a) is a strain of the Lactococcus raffinolactis species.

In a particular aspect, the present invention provides a method for transforming a strain of the Lactococcus raffinolactis species with an exogenous DNA polynucleotide comprising the steps of:

(a) providing a strain of the Lactococcus raffinolactis species, wherein said strain is transformable through natural competence;

(b) modulating the production of a ComX protein in said strain;

(c) contacting said strain of step (b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome. Lactococcus plantarum

In a particular embodiment, said strain of the Lactococcus genus of step a) is a strain of the Lactococcus plantarum species.

In a particular aspect, the present invention provides a method for transforming a strain of the Lactococcus plantarum species with an exogenous DNA polynucleotide comprising the steps of:

(a) providing a strain of the Lactococcus plantarum species, wherein said strain is transformable through natural competence;

(b) modulating the production of a ComX protein in said strain;

(c) contacting said strain of step (b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome. Lactococcus piscium

In a particular embodiment, said strain of the Lactococcus genus of step a) is a strain of the Lactococcus piscium species.

In a particular aspect, the present invention provides a method for transforming a strain of the Lactococcus piscium species with an exogenous DNA polynucleotide comprising the steps of:

(a) providing a strain of the Lactococcus piscium species, wherein said strain is transformable through natural competence;

(b) modulating the production of a ComX protein in said strain;

(c) contacting said strain of step (b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome.

Lactococcus garvieae

In a particular embodiment, said strain of the Lactococcus genus of step a) is a strain of the Lactococcus garvieae species. In a particular aspect, the present invention provides a method for transforming a strain of the Lactococcus garvieae species with an exogenous DNA polynucleotide comprising the steps of:

(a) providing a strain of the Lactococcus garvieae species, wherein said strain is transformable through natural competence;

(b) modulating the production of a ComX protein in said strain;

(c) contacting said strain of step (b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome.

Lactococcus fujiensis

In a particular embodiment, said strain of the Lactococcus genus of step a) is a strain of the Lactococcus fujiensis species. In a particular aspect, the present invention provides a method for transforming a strain of the Lactococcus fujiensis species with an exogenous DNA polynucleotide comprising the steps of:

(a) providing a strain of the Lactococcus fujiensis species, wherein said strain is transformable through natural competence;

(b) modulating the production of a ComX protein in said strain;

(c) contacting said strain of step (b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome. Lactococcus chungangensis

In a particular embodiment, said strain of the Lactococcus genus of step a) is a strain of the Lactococcus chungangensis species.

In a particular aspect, the present invention provides a method for transforming a strain of the Lactococcus chunganensis species with an exogenous DNA polynucleotide comprising the steps of:

(a) providing a strain of the Lactococcus chungangensis species, wherein said strain is transformable through natural competence; (b) modulating the production of a ComX protein in said strain;

(c) contacting said strain of step (b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome.

DNA acquisition

Bacteria may naturally acquire exogenous DNA via one of three possible mechanisms: transformation, conjugation, or transduction.

As used herein the term "transformation" refers to the uptake of exogenous genetic material (e.g. a DNA polynucleotide) from the external medium. Since transformation requires that genetic material cross the bacterial cell wall and membrane and the uptake of exogenous genetic material is energetically costly, the process is tightly regulated. Accordingly, bacterial cells may only be transformed under certain conditions. Bacterial cells which are in a transformable state are said to be competent.

Competence may be artificially induced in the laboratory, e.g. by electroporation or exposure to divalent cations (e.g. CaC ) and heat shock. Alternatively, some species of bacteria express a proteinaceous machinery that provides natural competence; this system of natural competence has been widely studied in streptococci. As used herein the term "conjugation" refers to the transfer of genetic material between bacterial cells.

As used herein the term "transduction" refers to the transfer of genetic material from a virus (e.g. a bacteriophage) or a viral vector into bacterial cell.

ComX protein

The method of the present invention comprises the step of modulating the production of a ComX protein in said strain.

ComX protein is an alternative sigma factor, also known as o ^x , which acts as master regulator for the late com genes and is responsible for transcriptional reprogramming of cells including the induction of genes strictly required for DNA transformation (Lee et al., 1989; Petersen et al. 2004). ComX may bind to a specific target sequence (or box) termed the Corn-box (or Cin-box). Corn- boxes are located in the vicinity of the promoters of late competence (com) genes/operons responsible for DNA uptake (e.g., comG, comF, and comE operons), DNA protection (e.g. ssb) and DNA recombination (e.g. recA, dprA, coiA), and positively controls their expression [Campbell et ai, 1998; Luo and Morrison, 2003).

The production of the ComX protein in a strain of interest may be increased relatively to an appropriate control strain, i.e., the Lactococcus strain in which the production of the ComX protein has not been modulated. ComX protein may be produced (expressed) following modulation as compared to an appropriate control strain, i.e., the Lactococcus strain in which the ComX protein is not produced.

In some embodiments, the production of the ComX protein is constitutive or inducible.

The production of ComX protein may be monitored using any method known in the art. For example, by western blotting using an antibody specific for the ComX protein. Alternatively, comX gene mRNA transcript levels may be measured by qPCR. Alternatively, the ComX protein may be monitored using a reporter construct polynucleotide, e.g. as described in the Example 1 and Materials and Methods. The reporter construct polynucleotide may comprise genes encoding one or more reporter proteins, preferably the genes encoding the reporter proteins are operably linked to a promoter comprising a Corn-box sequence. The reporter proteins may be LuxAB or Luc. Accordingly, ComX expression (and activity) may be detected and measured using a luciferase assay (Fontaine et ai, 2010).

In some embodiments of the method of the present invention, the step of modulating the production of a ComX protein is performed by expressing a comX gene in said strain or increasing the expression of a comX gene in said strain. In a particular embodiment, the step of modulating the production of a ComX protein is performed by expressing a comX gene in said strain in some growth conditions, whereas said strain does not express the ComX protein outside of these growth conditions. In a particular embodiment, the step of modulating the production of a ComX protein is performed by increasing the expression of a comX gene in said strain in some growth conditions.

The comX gene may be an exogenous comX gene. As used herein an "exogenous comX gene" is understood to be a comXgene which is brought into the cytoplasm of the Lactococcus strain of step a), in order to be expressed. The exogenous comX gene may have the same sequence as the comX gene found in the genome of the Lactococcus strain of step a) or may have a different sequence from the com gene found in the genome of the Lactococcus strain of step a). When different, the comX gene may be derived from a strain of a different species, a different subspecies or a different strain of Lactococcus.

The exogenous comX gene may be integrated within the genome of said Lactococcus strain.

Alternatively, the exogenous comX gene may be located within a vector. The vector may be selected from a plasmid, a viral vector (e.g. a phage), a cosmid, or a bacterial artificial chromosome.

Said plasmid may be transferred into said Lactococcus strain by conjugation, transformation or transduction. Said plasmid may be auto-replicative in the transformed Lactococcus strain or not. The exogenous comX gene may be operably linked to transcription regulator(s). The exogenous comX gene may be located in a linear or circular polynucleotide.

Alternatively, in some embodiments of the method of the present invention, the comX gene is the endogenous comX gene of said Lactococcus strain. As used herein "the endogenous comX gene of said strain" is understood to be a comX gene that is naturally present in the genome of said strain.

In some embodiments, said comX gene is a Lactococcus comXgene. In an embodiment, said comX gene is a Lactococcus lactis comX gene. In a particular embodiment, said comX gene is a Lactococcus lactis subsp. lactis comX gene. In a particular embodiment, said comX gene is a Lactococcus lactis subsp. cremoris comX gene.

The comX gene may comprise or consist of a nucleotide sequence selected from the group consisting of:

- SEQ ID NO:1 , SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:1 1 , SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19; SEQ ID NO:21 ; - a nucleotide sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the nucleotide sequence of SEQ ID NO:1 , SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:1 1 , SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19; SEQ ID NO:21 ;

- a variant of SEQ ID NO:1 , SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:1 1 , SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21 encoding respectively a ComX protein of SEQ ID NO:2, SEQ I D NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID N0:14, SEQ ID N0:16, SEQ ID N0:18, SEQ ID NO:20 or SEQ ID NO:22; and

- a variant of SEQ ID NO:1 , SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:1 1 , SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21 encoding respectively a functional ComX protein having at least 90% identity or at least 90% similarity to a ComX protein of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20 or SEQ ID NO:22.

ATAACATATTACTTGGAAGAAGAGGATTTTGAAAATCTTTTTTCAGAAATGAAACCT ATAGTTATGAA ATTAATGAAACAAATTCGCATTAGAACATGGAAAATAGAGGATTATCTTCAAGAGGGGAT GATTATTT TACATCTTCTATTAGAAGAGCAGAACGATGGTCAAAAGCTGCATACAAAATTTAAGGTAA AGTATCAT CAAAGATTAATAGATGAATTAAGACGAAGTTATGCAAAGAAACGAAGCCATGACCATTTT ATAGGTTT AGATGTTTATGAATGCTCAGACTGGATAAATTCAGGTGATACTAGTCCAGATAATGAAGT GGTCTTCA ATCATTTGCTGGCAGAAGTATATGAAGGTTTGAGCGCACATTATCAAGACTTACTACTTC GACAAATG CGAGGAGAAGAACTAACTCGCATGCAACGGTATCGCCTTCGTGAAAAAATAAAGGCCATC TTATTTTC AGAAGACGAAGAGTGA [SEQ ID NO:l]

MTYYLEEEDFENLFSEMKPIVMKLMKQIRIRTWKIEDYLQEGMI ILHLLLEEQNDGQKLHTKFKVKYH QRLIDELRRSYAKKRSHDHFIGLDVYECSDWINSGDTSPDNEWFNHLLAEVYEGLSAHYQ DLLLRQM RGEELTRMQRYRLREKIKAILFSEDEE [SEQ ID NO : 2 ]

ATGACATATTACCTGGAAGAAAATGAATTCGAAGGTTTATTTTCTGGAATGAAACCA ATCATCAGAAA ATTGATGAAACAAATTCGAATCAAAGCATGGGACATAGAGGATTATTATCAAGAAGGAAT GATTATTT TGCATCACCTTTTAGAAGAAAATCACCCATCCACTAATATTTATACAAAGTTCAAAGTAA AATATCAT CAACATTTGATTGATGAACTACGCCATAGCTACGCCAAAAAACGGCTTCATGACCATTTT GTAGGTCT GGACATTTATGAATGTTCGGACTGGATAGATGCAGGAGGAAGTACCCCTGAAAGCGAGCT TGTGTTCA ATCATCTTTTAGCAGAAGTTTATGAAGGATTGAGCGCCCACTATCAGGAATTACTCGTGC GTCAAATG AGAGGAGAAGAACTCACGCGAATGGAACGCTATCGGCTAAGAGAAAAAATCAAAAATATA CTATTTTC TCGAGATGATGATTAA [SEQ ID NO: 3]

MTYYLEENEFEGLFSGMKPI IRKLMKQIRIKAWDIEDYYQEGMI ILHHLLEENHPSTNIYTKFKVKYH QHLIDELRHSYAKKRLHDHFVGLDIYECSDWI DAGGSTPESELVFNHLLAEVYEGLSAHYQELLVRQM RGEELTRMERYRLREKIKNILFSRDDD [SEQ ID NO : 4 ]

ATGGATGACATTCAAGAAAAATACGGTTTAGAATTCAACGAATTATTCTCTGAGATG CGGCCGATAAT TTATAAATTGATGAAGCAATTGCACATCAACACATGGGATTACGATGATTACTTCCAAGA GGGAATGA TTACACTACATGAATTGCTGCAGAAAATTACAAATTTAGATCATGTACATACGAAATTTA AAGTGGCT TACCATCAGCACTTAATTGACGAAATTCGCCATATTAAAGCACGAAAAAGAGGTTTTGAT CAGCTCCA TCCGATCAATGTTTATGACTGCGCAGATTGGATTGGCTCAAACCTTGCTACACCTGAAAG CGAGATAG TTTTCAACCATCTACTAGAAGAAGTTTATGATAAACTTTCAACACACTATAAAGAACTGT TGGTAAAG CAAATGCATGGGGAACATCTTACGAGAATGCAGAAGTATCGTTTAAAGGAAAAAATTAAA GCGATTTT ATTTGATGAAGACTAA [SEQ ID NO: 5]

MDDIQEKYGLEFNELFSEMRPI IYKLMKQLHI TWDYDDYFQEGMITLHELLQKITNLDHVHTKFKVA YHQHLIDEIRHIKARKRGFDQLHPINVYDCADWIGSNLATPESEIVFNHLLEEVYDKLST HYKELLVK QMHGEHLTRMQKYRLKEKIKAILFDED [SEQ ID NO: 6]

ATGGATAAAATTGAAACCATACTTAAAAGTATTGAACCGATTATTATGAACTGTCGGAAA AAAACTAA AATTCCTTCCTGGGAATTAGACGACTATATGCAGGAAGGGATGATTATTGCTTTAGAGAT GTACCATC AACTCTTATTAGATCCACCAGATGATGACTTTAACTTCTATGTCTATTTCAAAGTCAGGT ATTCTTGT TTCTTAATTGATCACTATCGCAAAGCTATGGCAGTCAAGAGAAAATTCGACCAGCTTGAC TATTGTGA ACTTTCTGAGTCTGTTAATCTTTTTGATCACAAACAAAATGTGTCTGAAAACGTCATGTA TAACTTGT TGTGTCAAGAAATACACTTGGTTTTATCCCCGGAGGAGCTCAAGCTTTTTGAGGCACTTA TTTGA

[SEQ ID NO: 7] MDKIETILKSIEPI IMNCRKKTKIPSWELDDYMQEGMI IALEMYHQLLLDPPDDDFNFYVYFKVRYSC FLIDHYRKAMAVKRKFDQLDYCELSESVNLFDHKQNVSENVMYNLLCQEIHLVLSPEELK LFEALI

[SEQ ID NO: 8]

ATGGATAGCATAGAAATGATGCTTCAAAATATTGAGCCAATTATTATGAATTGTAGT AAAACAACTAG GATTCCATCTTGGGAGCTAGATGATTACATGCAGGAGGGGATGATTATTGCACTGGAAAT GTATCAAA ATAGACATAACATCAATAACGGTAACGCGTTTAATTTCTATGTCTATTTTAAAGTCAGGT ATTCCTGT TACCTGATAGATAGTTTTAGAAAGGCTAACGCATATAAAAGAAAATTTGATCAACCATTA TATTGTGA AATATCTGAAGCCTTCAACCTTTATGATCACCACCAAAATGTTGCAGACAATGTCTGTTA TCAGCTAT TGCAAGTTGAAATTCTTGAGATATTAACACCAGATGAAGCTGATTTATTTATGACCTTGA AAAATGGT GGGAAAGTAGAGAGAAATAAAAAGTATAGATTAAAGAAAAAAATTATTGATTATCTTAAA GACATGTT ATGA [SEQ ID NO: 9]

MDSIEMMLQNIEPI IMNCSKTTRIPSWELDDYMQEGMI IALEMYQNRHNI NGNAFNFYVYFKVRYSC YLI DSFRKANAYKRKFDQPLYCEISEAFNLYDHHQNVADNVCYQLLQVEILEILTPDEADLFM TLKNG GKVERNKKYRLKKKI I DYLKDML [SEQ ID NO: 10]

ATGGAGACTTTAGAAGCCATGCTCAAAAACATTGAACCTATTATTATGAATTGTCAAAAG ATGGCAAA AATACCTTCCTGGGATATTGACGATTATATGCAGGAGGGGAGGATCATTGCATTAGACTT GTATAATC AGCTAGCAGAAAGAATGGAGACGGATGAGGTGAACTTTTACGTCTACTTCAAAGTCAGAT ATACCTGT TTCTTGATTGATACTTACCGTAAGACAAATGCCTTTAAAAGAAAATTTGACCAACCGATT TACTTAGA TGTATCCGAAGCATTTAATCTGTATGATCATAAGCAGAATGTCGCTGATAATGTCATGTA TACTTTAT TGCATCAGGAGATTCTAGACATCTTAACGCCTGTAGAAATTCAAACGCTAAACGCACTAA AAAGGGGA GAAAAGGTCGACCGCAATAAAAAATTTAGGATTAAAAAGAAGATTATCAACTATATTAAT CAGATTTT CTAG [SEQ ID NO: 11]

METLEAMLKNIEPI IMNCQKMAKIPSWDIDDYMQEGRI IALDLYNQLAERMETDEVNFYVYFKVRYTC FLI DTYRKTNAFKRKFDQPIYLDVSEAFNLYDHKQNVADNVMYTLLHQEILDILTPVEIQTLN ALKRG EKVDRNKKFRIKKKI INYINQI F [SEQ ID NO: 12]

ATGGAGCATAATTTAGATATGGAGCAGCTGGAAGAAATTTTTCATTCTGTCCAACATATT GTGTGGAA GAACAGTCGTTTGATTCCGATAAATTTTTGGACGTTTGATGACTATCAGCAGGAAGGGCG CTTGGTAT TATACGATTTGCTGGGAGATGGTGTGACGCAAAGGAACTTATTTTGCCATTTTAAGGTAC GCTATAAG CAGAGACTTATTGATATTAAAAGAAGGGAGCGGGCTTTTAAAAGGGGTTTTGATTGCGGG ACTGGCTT AGATATATACGAATATTCTGATGCTCTAAAGGGGAAAGCAGCCAGTCCAGAACATATCCT GATTTCTG GAAGTTTACTTGAAGAAGTTTTTGAAAACTTAAATTTACGCTACCGACGGCTCCTCAAAA GTTACCTC GCCGGCGATGAATTGCACCGTATGGAAAAGTATCGTTTGAAGGAAAAAATAACGAATATA TTATATGA ACAGCAGTGA [SEQ ID NO: 13]

MEHNLDMEQLEEI FHSVQHIVWKNSRLI PINFWTFDDYQQEGRLVLYDLLGDGVTQRNLFCHFKVRYK QRLIDIKRRERAFKRGFDCGTGLDIYEYSDALKGKAASPEHILI SGSLLEEVFENLNLRYRRLLKSYL AGDELHRMEKYRLKEKITNILYEQQ [SEQ ID NO: 14]

ATGGCAGAAAATAATTTAGATAAAGAACAGCTTGAAGAGTTATTCCATTCACTTCAACAT ATTGTTTG GAAGAACAGTCATTTAATTAAAATAAATTTTTGGACAATGGATGATTATCAGCAAGAAGG GCGACTGG TTTTATACCAGTTACTTGAAGATGGCGTGACACAGGAAAAACTATTTTGCCATTTTAAAG TGCGATAT AAGCAACGGTTGATTGATATAAAAAGACGAGAAAGAGCATTTAAGCGGGGTTTTGATTGT GGGGCTGG TTTAGATATATATGAGTATTCTGATGCCCTGAAAGGCAAAGCTACCAGTCCTGAATATAA CTTAATTT CAGTTACTTTACTTGAAGAGGTTCATCAAAGTTTGAGTTTGAGATACCGCAATTTATTGG AGAATCAT CTGTCAGGAGTGGAGTTGCATCGAATGGAAAAATACCGTTTAAAGGAAAAAATCAAGAGA ATACTCTA TGAAGAAGAATGA [SEQ ID NO: 15]

MAE NLDKEQLEELFHSLQHIVWKNSHLIKINFWTMDDYQQEGRLVLYQLLEDGVTQEKLFCHF KVRY KQRLI DIKRRERAFKRGFDCGAGLDIYEYSDALKGKATSPEYNLISVTLLEEVHQSLSLRYRNLL ENH LSGVELHRMEKYRLKEKIKRILYEEE [SEQ ID NO: 16]

ATGGAGCATAATTTAGATATGGAGCAGCTGGAAGAGATATTTCATTCTGTTCAACATATT GTATGGAA GAATAGTCGTTTGATTCCGATAAATTTTTGGACGATAGATGACTATCAGCAGGAAGGGCG TTTGGTAT TATATGATTTACTTGAGGATGGTGTGACACAAAGAAAACTTTTTTGCCATTTTAAAGTAC GTTATAAG CAGAGACTTATTGATATTAAAAGAAGGGAGCGGGCTTTTAAAAGGGGTTTTGACTGTGGG ACTGGGCT AGATATTTACGAATATTCAGATGCTTTAAAAGGAAAAGTAGCCAGTCCAGAACATACTCT GATTTCTG GCAGTTTGCTTGAAGAAGTTTTAGAAAACTTAAATTTACGCTACCGTGCTCTTCTTAAAA GTTACCTT GCTGGTGATGAACTGCATCGAATGGAAAAACATCGTTTGAAAGAAAAAATAATAAAAATA TTATATGA TGAACAGTGA [SEQ ID NO: 17]

MEHNLDMEQLEEI FHSVQHIVWKNSRLI PINFWTIDDYQQEGRLVLYDLLEDGVTQRKLFCHFKVRYK QRLIDIKRRERAFKRGFDCGTGLDIYEYSDALKGKVASPEHTLI SGSLLEEVLENLNLRYRALLKSYL AGDELHRMEKHRLKEKI IKILYDEQ [SEQ ID NO: 18]

TTGAAACCGATCGTTTCAAAATCTATGAGAACATTAAAAATCAATTTTTGGACTACA GAGGATTATCA TCAAGAGGGTCTAATTACATTAAATGAAATATTAAATTCAGGATGTAAGGAGTCACAACT ATACATTC ACTTTAAAGTCAAATATCGACAAAAGCTAATAGACGTGATTAGAAAATCACAGGCGCAAA AAAGAATC TGGGATAATGCAGAGAGTATTGATGTTTACGAATCTGAAAATCAAATTAATTCCAGTAAC TCAAACCC CGAAGACATAATAGTCTATGACAGTCTTGTAAAGGAAGTAATAACAAAATTAACACCTTC ATACCGGA AACTACTGAAACGACATCTAAGAGGTGAGGATGTGACAAGGATGGAAAAATACAGACTGA AGGAACGA ATCAAACAAATTTTATTTGATGGTGATTGA [SEQ ID NO: 19]

MKPIVSKSMRTLKINFWTTEDYHQEGLITLNEILNSGCKESQLYIHFKVKYRQKLIDVIR KSQAQKRI WDNAESI DVYESENQINSSNSNPEDI IVYDSLVKEVITKLTPSYRKLLKRHLRGEDVTRMEKYRLKER IKQILFDGD [SEQ ID NO:20]

ATGGATAAGATTGAAACCATACTTAAAAATATTGAACCGATTATCATGAACTGTCGAAAA AAAACTAA CATCCCTTCCTGGCAATTAGACGACTATCTCCAGGAAGGCATGATTATTGCTCTAGAGAT GTATCATC AACTTTTATTAGACCCACCAGATGATGACTTTAACTTCTATGTTTATTTCAAAGTGAGAT ATTCTTGT TTCTTGATTGATCAGTATCGGAGAAACATGGCTGTCAAAAGAAAATTCGACCAGATTGAC TATTGTGA ACTATCTGAGGCGTTTTATCTTTTTGATCAAAATCAAGATGTCTCTGAAAACGTCATGTA TAATTTGT TATGTCAAGAAATACACTTGCTTCTATCTCCTGAAGAACGAGAGCTTTTTGAGGCACTTA AAAATGGA CAGAAGATTGACCGTAATCAAAAGTTTCGTATCAAGAAGAAAATTATTGAATATATTAAG AGGTTTTG GTGA [SEQ ID NO: 21]

MDKIETILKNIEPI IMNCRKKTNI PSWQLDDYLQEGMI IALEMYHQLLLDPPDDDFNFYVYFKVRYSC FLI DQYRRNMAVKRKFDQI DYCELSEAFYLFDQNQDVSENVMYNLLCQEIHLLLSPEERELFEALKNG QKI DRNQKFRIKKKI IEYIKRFW [SEQ ID NO: 22] In some embodiments, said comX gene has the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:3 or SEQ ID NO:5 or has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:3 or SEQ ID NO:5 or is a variant of SEQ ID NO:1 or SEQ ID NO:3 or SEQ ID NO:5 encoding respectively the ComX protein of SEQ ID NO:2, SEQ ID NO:4 or SEQ ID NO:6 or is a variant of SEQ ID NO:1 or SEQ ID NO:3 or SEQ ID NO:5 encoding respectively a functional ComX protein having at least 90% identity or at least 90% similarity to a ComX protein of SEQ ID NO:2, SEQ ID NO:4 or SEQ ID NO:6. In a particular embodiment, said comX gene is used when the Lactococcus strain in step a) is a Lactococcus lactis strain.

In a particular embodiment, when the strain of step a) is a Lactococcus lactis subsp. lactis strain, the comX gene comprises the nucleotide sequence of SEQ ID NO:1 , any sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NO:1 , a variant of SEQ ID NO:1 encoding the ComX protein of SEQ ID NO:2 or a variant of SEQ ID NO:1 encoding a functional ComX protein having at least 90% identity or at least 90% similarity to a ComX protein of SEQ ID NO:2.

In a particular embodiment, when the strain of step a) is a Lactococcus lactis subsp. cremoris strain, the comX gene comprises the nucleotide sequence of SEQ ID NO:3 or SEQ ID NO:5, any sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NO:3 or SEQ ID NO:5 or a variant of SEQ ID NO:3 or SEQ ID NO:5 encoding respectively the ComX protein of SEQ ID NO:4 or SEQ ID NO:6 or a variant of SEQ ID NO:3 or SEQ ID NO:5 encoding respectively a functional ComX protein having at least 90% identity or at least 90% similarity to a ComX protein of SEQ ID NO:4 or SEQ ID NO:6.

In some embodiments, said comX gene has the nucleotide sequence of SEQ ID NO:7 or has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the nucleotide sequence of SEQ ID NO:7 or is a variant of SEQ ID NO:7 encoding the ComX protein of SEQ I D NO:8, or is a variant of SEQ ID NO:7 encoding a functional ComX protein having at least 90% identity or at least 90% similarity to a ComX protein of SEQ ID NO:8. In a particular embodiment, said comX gene is used when the Lactococcus strain in step a) is a Lactococcus raffinolactis strain.

In some embodiments, said comX gene has the nucleotide sequence of SEQ ID NO:9 or has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the nucleotide sequence of SEQ ID NO:9 or is a variant of SEQ ID NO:9 encoding the ComX protein of SEQ ID NO:10, or is a variant of SEQ ID NO:9 encoding a functional ComX protein having at least 90% identity or at least 90% similarity to a ComX protein of SEQ ID NO:10. In a particular embodiment, said comX gene is used when the Lactococcus strain in step a) is a Lactococcus plantarum strain.

In some embodiments, said comX gene has the nucleotide sequence of SEQ ID NO:1 1 or has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the nucleotide sequence of SEQ ID NO:1 1 or is a variant of SEQ ID NO:1 1 encoding the ComX protein of SEQ ID NO:12, or is a variant of SEQ ID NO:1 1 encoding a functional ComX protein having at least 90% identity or at least 90% similarity to a ComX protein of SEQ ID NO:12. In a particular embodiment, said comX gene is used when the Lactococcus strain in step a) is a Lactococcus piscium strain.

In a particular embodiment, said comX gene has the nucleotide sequence of SEQ ID NO:13 or SEQ ID NO:15 or SEQ ID NO:17, any sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NO:13 or SEQ ID NO:15 or SEQ ID NO:17 or a variant of SEQ ID NO:13 or SEQ ID NO:15 or SEQ ID NO:17 encoding respectively the ComX protein of SEQ ID NO:14 or SEQ ID NO:16 or SEQ ID NO:18 or a variant of SEQ ID NO:13 or SEQ ID NO:15 or SEQ ID NO: 17 encoding respectively a functional ComX protein having at least 90% identity or at least 90% similarity to a ComX protein of SEQ ID NO:14 or SEQ ID NO:16 or SEQ ID NO: 18. In a particular embodiment, said comX gene is used when the Lactococcus strain in step a) is a Lactococcus garvieae strain.

In some embodiments, said comX gene has the nucleotide sequence of SEQ ID NO:19 or has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the nucleotide sequence of SEQ ID NO:19 or is a variant of SEQ ID NO:19 encoding the ComX protein of SEQ ID NO:20, or is a variant of SEQ ID NO:19 encoding a functional ComX protein having at least 90% identity or at least 90% similarity to a ComX protein of SEQ ID NO:20. In a particular embodiment, said comX gene is used when the Lactococcus strain in step a) is a Lactococcus fujiensis strain.

In some embodiments, said comX gene has the nucleotide sequence of SEQ ID NO:21 or has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the nucleotide sequence of SEQ ID NO:21 or is a variant of SEQ ID NO:21 encoding the ComX protein of SEQ ID NO:22, or is a variant of SEQ ID NO:21 encoding a functional ComX protein having at least 90% identity or at least 90% similarity to a ComX protein of SEQ ID NO:22. In a particular embodiment, said comX gene is used when the Lactococcus strain in step a) is a Lactococcus chungangensis strain.

By way of example and for the avoidance of doubt, in particular embodiments, where a comX gene is specified as having a particular nucleotide sequence, it is understood that the comX gene comprises said nucleotide sequence. In particular other embodiments, where a comX gene is specified as having a particular nucleotide sequence, it is understood that the comX gene consists of said nucleotide sequence. In some embodiments, variants as defined herein of comX genes are selected from the list of

DNA sequences disclosed in Table 1 below:

Strain Accession number Position of comX, from start to stop

Lactococcus lactis AI06 CP009472.1 From 2260881 to 2261372 (reverse)

Lactococcus lactis Bpll JRFX01000055.1 From 34668 to 35159 (forward)

Lactococcus lactis LI1596 LDEK01000015.1 From 33401 to 33892 (forward)

Lactococcus lactis subsp. cremoris A17 JQIC01000009.1 From 6445 to 6936 (reverse)

Lactococcus lactis subsp. cremoris A76 CP003132.1 From 2293232 to 2293723 (reverse)

Lactococcus lactis subsp. cremoris AM2 UTE01000081.1 From 9954 to 10444 (forward)

Lactococcus lactis subsp. cremoris B40 UTC01000320.1 From 10186 to 10677 (forward)

Lactococcus lactis subsp. cremoris DPC6856 LAVW01000168.1 From 445 to 936 (reverse)

Lactococcus lactis subsp. cremoris GE214 AZSI01000020.1 From 186 to 677 (reverse)

Lactococcus lactis subsp. cremoris HP JAUH01000192.1 From 40 to 531 (reverse)

Lactococcus lactis subsp. cremoris IBB477 JMMZ01000035.1 From 92323 to 92814 (reverse)

Lactococcus lactis subsp. cremoris KW10 UYF01000023.1 From 40421 to 40912 (forward)

Lactococcus lactis subsp. cremoris KW2 CP004884.1 From 2276371 to 2276862 (reverse)

Lactococcus lactis subsp. cremoris LMG6897 USZ01000238.1 From 10034 to 10525 (forward)

Lactococcus lactis subsp. cremoris Mast36 JZUI01000076.1 From 310 to 801 (reverse)

Lactococcus lactis subsp. cremoris MG1363 AM406671.1 From 2376782 to 2377273 (reverse)

Lactococcus lactis subsp. cremoris NBRC 100676 BCVK01000073.1 From 9879 to 10370 (forward)

Lactococcus lactis subsp. cremoris NZ9000 CP002094.1 From 2377598 to 2378089 (reverse)

Lactococcus lactis subsp. cremoris SK11 CP000425.1 From 2283008 to 2283498 (reverse)

Lactococcus lactis subsp. cremoris TIFN1 ASXF01000005.1 From 5621 to 6112 (forward)

Lactococcus lactis subsp. cremoris TIFN3 ATBE01000400.1 From 431 to 922 (reverse)

Lactococcus lactis subsp. cremoris TIFN5 ATBC01000090.1 From 315 to 809 (reverse)

Lactococcus lactis subsp. cremoris TIFN6 ATBB01000278.1 From 265 to 756 (forward)

Lactococcus lactis subsp. cremoris TIFN7 ATBA01000081.1 From 5620 to 6111 (forward)

Lactococcus lactis subsp. cremoris UC509.9 CP003157.1 From 2107522 to 2108013 (reverse)

Lactococcus lactis subsp. cremoris V4 UYG01000005.1 From 8625 to 9116 (forward)

Lactococcus lactis subsp. hordniae NBRC 100931 BCVL01000030.1 From 70 to 561 (reverse)

Lactococcus lactis subsp. lactis 1AA59 AZQT01000035.1 From 118 to 609 (reverse)

Lactococcus lactis subsp. lactis 511 JNLP01000001.1 From 1703029 to 1703520 (reverse)

Lactococcus lactis subsp. lactis A12 LT599049.1 From 2415707 to 2416198 (reverse)

Lactococcus lactis subsp. lactis ATCC 19435 LKLC01000004.1 From 32310 to 32801 (forward)

Lactococcus lactis subsp. lactis bv. diacetylactis DRA4 UWD01000119.1 From 147 to 638 (reverse)

Lactococcus lactis subsp. lactis CV56 CP002365.1 From 2213300 to 2213791 (reverse)

Lactococcus lactis subsp. lactis DPC6853 LAVD01000101.1 From 544 to 1035 (reverse)

Lactococcus lactis subsp. lactis E34 LKLD01000014.1 From 197 to 688 (reverse)

Lactococcus lactis subsp. lactis 111403 AE005176.1 From 2223528 to 2224019 (reverse)

Lactococcus lactis subsp. lactis 10-1 DNA AP012281.1 From 2287126 to 2287617 (reverse)

Lactococcus lactis subsp. lactis JCM 7638 BBAP01000017.1 From 34164 to 34656 (forward)

Lactococcus lactis subsp. lactis K231 LKLE01000041.1 From 32159 to 32650 (forward)

Lactococcus lactis subsp. lactis K337 LKLF01000041.1 From 34909 to 35400 (forward)

Lactococcus lactis subsp. lactis KF134 LKU01000010.1 From 34939 to 35430 (forward)

Lactococcus lactis subsp. lactis KF147 CP001834.1 From 2446402 to 2446893 (reverse)

Lactococcus lactis subsp. lactis KF201 LKLM01000024.1 From 28747 to 29238 (forward)

Lactococcus lactis subsp. lactis KF24 LKLH01000011.1 From 34116 to 34607 (forward)

Lactococcus lactis subsp. lactis KF282 LKLN01000033.1 From 170 to 661 (reverse)

Lactococcus lactis subsp. lactis KLDS 4.0325 CP006766.1 From 2407603 to 2408094 (reverse)

Lactococcus lactis subsp. lactis LMG 7760 JQCM01000018.1 From 37736 to 38227 (forward)

Lactococcus lactis subsp. lactis LMG8526 LKLQ01000046.1 From 38499 to 38993 (forward)

Lactococcus lactis subsp. lactis NCDO 2118 CP009054.1 From 2402923 to 2403414 (reverse)

Lactococcus lactis subsp. lactis SO CP010050.1 From 2359456 to 2359947 (reverse)

Lactococcus lactis subsp. lactis UC317 LKLY01000004.1 From 36130 to 36621 (forward)

Lactococcus lactis WG2 LXWJ01000007.1 From 37921 to 38412 (forward)

Lactococcus raffinolactis NBRC 100932 BCVN01000102.1 From 139 to 617 (forward)

Lactococcus piscium CNCM 1-4031 FLZT01000001.1 From 149 to 628 (forward)

Lactococcus piscium MKFS47 LN774769.1 From 1708720 to 1709199 (forward)

Lactococcus garvieae 122061 AP017373.1 From 1356405 to 1356890 (forward)

Lactococcus garvieae 8831 AFCD01000005.1 From 510 to 995 (forward) Lactococcus garvieae Lg-ilsanpaik-gs201105 JPUJ01000002.1 From 180817 to 181302 (reverse)

Lactococcus garvieae LG9 AGQY01000137.1 From 5631 to 6116 (reverse)

Lactococcus garvieae M79 FOTJ01000023.1 From 3224 to 3709 (forward)

Lactococcus garvieae NBRC 100934 BBJW01000010.1 From 105946 to 106431 (reverse)

Lactococcus garvieae PAQ102015-99 LXWL01000009.1 From 238437 to 238922 (reverse)

Lactococcus garvieae TB25 AGQX01000090.1 From 28088 to 28573 (reverse)

Lactococcus garvieae lRFl AVFE01000015.1 From 42141 to 42626 (reverse)

Table 1

As used herein a comX gene is understood to be a gene that encodes a functional ComX protein in the strain where it is expressed. By "functional ComX protein" it is meant a protein which induces or is able to induce the expression of genes regulated by the Corn-box, and at least one of the late competence genes selected from comEA, comFA, comGA, dprA, coiA, ssbA, radA, radC, recA, and recX.

The ComX protein may have the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20 or SEQ ID NO:22, or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20 or SEQ ID NO:22, or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequence of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20 or SEQ ID NO:22.

In some embodiments, the ComX protein may have the amino acid sequence of SEQ ID NO:2, or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the amino acid sequence of SEQ ID NO:2 or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequence of SEQ ID NO:2. In a particular embodiment, said ComX protein is used when the Lactococcus strain in step a) is a Lactococcus lactis subsp. lactis strain.

In some embodiments, the ComX protein may have the amino acid sequence of SEQ ID NO:4 or SEQ ID NO:6, or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the amino acid sequence of SEQ ID NO:4 or SEQ ID NO:6 or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequence of SEQ ID NO:4 or SEQ ID NO:6. In a particular embodiment, said ComX protein is used when the Lactococcus strain in step a) is a Lactococcus lactis subsp. cremoris strain.

In some embodiments, the ComX protein may have the amino acid sequence of SEQ ID NO:8, or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the amino acid sequence of SEQ ID NO:8 or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequence of SEQ ID NO:8. In a particular embodiment, said ComX protein is used when the Lactococcus strain in step a) is a Lactococcus raffinolactis strain.

In some embodiments, the ComX protein may have the amino acid sequence of SEQ ID NO:10, or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the amino acid sequence of SEQ ID NO:10 or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequence of SEQ ID NO:10. In a particular embodiment, said ComX protein is used when the Lactococcus strain in step a) is a Lactococcus plantarum strain.

In some embodiments, the ComX protein may have the amino acid sequence of SEQ ID NO:12, or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the amino acid sequence of SEQ ID NO:12 or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequence of SEQ ID NO:12. In a particular embodiment, said ComX protein is used when the Lactococcus strain in step a) is a Lactococcus piscium strain.

In some embodiments, the ComX protein may have the amino acid sequence of SEQ ID NO:14, SEQ ID NO:16 or SEQ ID NO:18, or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the amino acid sequence of SEQ ID NO:14, SEQ ID NO:16 or SEQ ID NO:18 or an amino acid sequence having at least 90%, at Ieast 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequence of SEQ ID NO:14, SEQ ID NO:16 or SEQ ID NO:18. In a particular embodiment, said ComX protein is used when the Lactococcus strain in step a) is a Lactococcus garvieae strain.

In some embodiments, the ComX protein may have the amino acid sequence of SEQ ID NO:20, or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the amino acid sequence of SEQ ID NO:20 or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequence of SEQ ID NO:20. In a particular embodiment, said ComX protein is used when the Lactococcus strain in step a) is a Lactococcus fujiensis strain.

In some embodiments, the ComX protein may have the amino acid sequence of SEQ ID NO:22, or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the amino acid sequence of SEQ ID NO:22 or an amino acid sequence having at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequence of SEQ ID NO:22. In a particular embodiment, said ComX protein is used when the Lactococcus strain in step a) is a Lactococcus chungangensis strain.

According to the invention, when a ComX protein is defined by its amino acid sequence having a percentage of identity or percentage of similarity to a specific SEQ ID, said ComX protein is a functional ComX protein as defined herein.

By way of example and for the avoidance of doubt, in particular embodiments, where a ComX protein is specified as having a particular amino acid sequence, it is understood that the ComX protein comprises said amino acid sequence. In particular other embodiments, where a ComX protein is specified as having a particular amino acid sequence, it is understood that the ComX protein consists of said amino acid sequence.

In some embodiments, ComX proteins having percentage of identity or percentage of similarity as defined herein are selected from the list of protein sequences derived, after translation, from the list of DNA sequences disclosed in Table 1 above. Preferably, reference to a sequence which has a percentage identity or similarity to any one of the SEQ ID NOs detailed herein refers to a sequence which has the stated percent identity or similarity with the SEQ ID NO referred to, over the entire length of the two sequences. Percentage (%) sequence identity is defined as the percentage of amino acids or nucleotides in a candidate sequence that are identical to the amino acids or nucleotides in a reference sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Percentage (%) sequence similarity is defined as the percentage of amino acids in a candidate sequence that are similar to the amino acids in a reference sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence similarity. Similarity between amino acids is based on established amino acid substitution matrices such as the PAM series (Point Accepted Mutation; e.g. PAM30, PAM70, and PAM250) or the BLOSUM series (BLOck Substitution Matrix; e.g. BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, and BLOSUM90). Alignment for purposes of determining percent sequence identity or similarity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as CLUSTALW, CLUSTALX, CLUSTAL Omega, BLAST, BLAST-2, ALIGN, ALIGN-2 or Megalign (DNASTAR) software. In a particular embodiment, similarity between amino acids is determined using the BLASTp software with the BLOSUM62 matrix. Appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full-length of the sequences being compared, or gap penalties to be introduced, can be determined by known methods.

In a particular embodiment, when the modulation in step b) results from an exogenous comX gene, said exogenous comX gene is (obtained) from a strain of the same species, in particular of the same subspecies, as the strain provided in step a). In any case, the exogenous comX gene needs to be functional, in particular needs to encode a functional ComX protein, as defined herein in the strain provided in step a).

Exogenous DNA polynucleotide

The method of the present invention comprises the step of contacting the strain of step b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA into the genome of said strain [step c].

As used herein the term "exogenous DNA polynucleotide" refers to a DNA polynucleotide that is brought into the cytoplasm of said strain, in order to be integrated into the genome of said strain (target sequence).

In a particular embodiment, the method comprises carrying out step (b) [ComX modulation] and then carrying out step (c) [contact with the exogenous DNA polynucleotide] [i.e., that step (c) is carried out on a strain obtained following step (b)]. Thus, the method comprising the steps of: (a) providing a strain of the Lactococcus genus, wherein said strain is transformable through natural competence;

(b) modulating the production of a ComX protein in said strain;

(c) contacting said strain obtained in step (b) with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome.

In another embodiment, the method comprises carrying out simultaneously step (b) [ComX modulation] and step (c) [contact with the exogenous DNA polynucleotide]. This option is appropriate when the ComX modulation is the result of the expression of the endogenous comX gene or of the increase of the expression of the endogenous comX gene of said strain. Thus, the method comprising the steps of:

(a) providing a strain of the Lactococcus genus, wherein said strain is transformable through natural competence;

(b) modulating the production of a ComX protein in said strain;

(c) contacting said strain with an exogenous DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) selecting a strain which has integrated the exogenous DNA polynucleotide into its genome;

wherein step (b) and step (c) are carried out simultaneously.

In a particular embodiment, the sequence of the exogenous DNA polynucleotide used in step c) share some similarities or identities with the genome of the Lactococcus strain to be transformed (of step a). In a particular embodiment, the exogenous DNA polynucleotide used in step c) is designed such that its 5' part and its 3' part are identical or highly similar to parts of the genome of the Lactococcus strain to be transformed (of step a), while its central part can be different from the genome of the Lactococcus strain to be transformed (of step a). The high similarity of the arms with the regions surrounding the target sequence can be determined by the person skilled in the art using common general knowledge, in particular by reference to homologous recombination.

Thus, to replace a target sequence by a mutated sequence or a truncated sequence or a supplementary sequence in the genome of the Lactococcus strain to be transformed (of step a), the exogenous DNA polynucleotide used in step c) is designed such that: - its 5' part is identical or highly similar to the region of the genome of the Lactococcus strain to be transformed which is on one side of the target sequence;

- its central part contains the replacing sequence (i.e., the mutated sequence or the truncated sequence or the supplementary sequence); and

its 3' part is identical or highly similar to the region of the genome of the Lactococcus strain to be transformed which is on the other side of the target sequence.

The 5' part and 3' part are long enough to ensure efficient recombination. In a particular embodiment, each of the 5' part and 3' part is from 0.5 to 5 kb in length. The size of the arms can be determined by the person skilled in the art using common general knowledge, in particular by reference to homologous recombination.

In a particular embodiment, the exogenous DNA polynucleotide used in step c) is (obtained) from a strain of the Lactococcus genus.

In a particular embodiment, said exogenous DNA polynucleotide used in step (c) is (obtained) from a strain of the same species, in particular of the same subspecies, as the strain provided in step (a).

In a particular embodiment, the exogenous DNA polynucleotide used in step c) is from a strain of the Lactococcus lactis species. In a particular embodiment, the exogenous DNA polynucleotide used in step c) is from a strain of the same Lactococcus lactis subspecies as the strain provided in step a). In a particular embodiment, the exogenous DNA polynucleotide used in step c) is from a strain of a Lactococcus lactis subspecies which is different from the strain provided in step a).

In a particular embodiment, the exogenous DNA polynucleotide used in step c) is from a strain of the Lactococcus raffinolactis species

The exogenous DNA polynucleotide may encode part of a gene sequence, a gene sequence, or a plurality of gene sequences. The gene sequence may be operably linked to transcription regulator(s). In a particular embodiment, the exogenous DNA polynucleotide is linear. The exogenous DNA polynucleotide may be designed to facilitate its incorporation within the genome of the L. lactis strain by homologous recombination (e.g. the exogenous DNA polynucleotide may comprise one or more recombination arms). The exogenous DNA polynucleotide may be a single stranded linear DNA.

The exogenous DNA polynucleotide, when incorporated into the genome of said Lactococcus strain leads to genetic modification of the strain such as gene replacement (to add or to remove a mutation), gene addition (to add a new gene or to duplicate an existing gene), gene deletion (to remove part or the totality of a gene), modification of non-coding region (to modulate expression of a gene). Typically, the exogenous DNA polynucleotide, when incorporated into the genome of said Lactococcus strain confers an interesting or useful phenotype, e.g. modified kinetic of acidification, improved resistance to bacteriophage, modified capability to grow in milk, modified texturing properties, improved safety of the strain. For example, improved bacteriophage resistance could be achieved by incorporating genes coding for a restriction/modification system into the strain genome or by introducing a mutation or a deletion into the pip gene.

As an example, growth of a L. lactis strain in milk could be improved by inserting into the chromosome the prtP and prtM genes that allow casein hydrolysis and better nitrogen nutrition; alternatively, these genes could be inactivated to reduced milk proteolysis in cheese. hisDC and tyrDC are genes known to be responsible for biogenic amine production (histamine and tyramine, respectively) in a diversity of lactic acid bacteria; disruption or mutation of these genes could help to prevent safety issues related to cheese consumption.

In a particular embodiment, the exogenous DNA polynucleotide has a minimal size selected from the group consisting of 100 bp, 200 bp, 500 bp, 1 kb, 2 kb and 5 kb, and a maximal size selected from the group consisting of 500 bp, 1 kb, 2 kb, 5 kb, 10 kb, 20 kb and 50 kb. In a particular embodiment, the size of the exogenous DNA polynucleotide may be between 100 bp and 50 kb, more preferably between 500 bp to 20 kb, even more preferably between 1 kb to 10 kb.

The concentration of exogenous DNA polynucleotide in the medium of step (c) may be between 0.5 mg/L and 1 g/L, preferably between 1 mg/L and 500 mg/L, more preferably between 5 mg/L and 100 mg/L, even more preferably between 10 mg/L and 50 mg/L of medium. Selection of transformed strains

The method of the present invention comprises the step of selecting a strain which has integrated the exogenous DNA polynucleotide into its genome [step d)].

If needed, selection is carried out on some cells of colonies that have been previously obtained by multiplying, in the appropriate medium, cells obtained at the end of step c) (or at the end of the simultaneous steps b) and c), when appropriate).

Various methods for the selection of transformed bacteria are well known in the art (see, e.g. Sambrook et al.) and may be routinely applied by the person skilled in the art, such as PCR, DNA sequencing... For example, when the exogenous DNA polynucleotide used in step c) provides a particular phenotype that the Lactococcus strain of step a) does not display (either a new phenotype or restoring a lost phenotype), it is possible to select strains which have integrated the exogenous DNA polynucleotide into their genome by selecting strains expressing the phenotype. This is the case for a strain having integrated in its genome an exogenous DNA polynucleotide mutated for the pip gene (that provides resistance to some bacteriophages).

For example, when the exogenous DNA polynucleotide used in step c) leads once integrated to a loss of a phenotype initially displayed by the Lactococcus strain of step a), it is possible to select strains which have integrated the exogenous DNA polynucleotide into their genome by selecting strains which do not diplay the phenotype any more. This is the case for an exogenous DNA polynucleotide bearing a mutated hisDC or tyrDC gene, which suppresses or decreases the production of histamine or tyramine, respectively.

As a particular example, the exogenous DNA polynucleotide may bear an antibiotic resistance gene. Accordingly, a Lactococcus strain which has integrated the exogenous DNA polynucleotide into its genome may be selected by plating onto a medium comprising said antibiotic. Only strains that express the appropriate antibiotic resistance gene, as a result of a successful transformation with the exogenous DNA polynucleotide, will multiply.

Growth conditions

As described in Example 3, a positive effect on natural competence induction in L. lactis strains was observed when cells were pre-cultured in a complex medium before transferring the cells to a chemically defined medium (Figure 3).

Accordingly, in some embodiments the medium of step (c) is a chemically defined medium. As used herein, the term "chemically defined medium" (CDM) refers to a medium for which the exact chemical composition is known. Preferably, the CDM may have the composition of the CDM set out in Sissler et al. (1999, Proc Natl Acad Sci USA 96:8985-8990). Thus, in an embodiment, the chemically defined medium (CDM) comprises 0.5 g/L NH4CI, 9.0 g/L KH2PO4, 7.5 g/L K2HPO4, 0.2 g/L MgCI ₂ , 5 mg/L FeCI ₂ , 50 mg/L CaCI ₂ , 5 mg/L ZnS0 ₄ , 2.5 mg/L C0CI2, 0.05 g/L tyrosine, 0.1 g/L asparagine, 0.1 g/L cysteine, 0.1 g/L glutamine, 0.1 g/L isoleucine, 0.1 g/L leucine, 0.1 g/L methionine, 0.1 g/L tryptophan, 0.1 g/L valine, 0.1 g/L histidine, 0.2 g/L arginine, 0.2 g/L glycine, 0.2 g/L lysine, 0.2 g/L phenylalanine, 0.2 g/L threonine, 0.3 g/L alanine, 0.3 g/L proline, 0.3 g/L serine, 10 mg/L paraaminobenzoic acid, 10 mg/L biotin, 1 mg/L folic acid, 1 mg/L nicotinic acid, 1 mg/L panthotenic acid, 1 mg/L riboflavin, 1 mg/L thiamine, 2 mg/L pyridoxine, 1 mg/L cyanocobalamin, 5 mg/L orotic acid, 5 mg/L 2-deoxythymidine, 5 mg/L inosine, 2.5 mg/L c//-6,8-thioctic acid, 5 mg/L pyridoxamine, 10 mg/L adenine, 10 mg/L guanine, 10 mg/L uracil, 10 mg/L xanthine, and 5 g/L glucose..

In some embodiments, prior to step (c) said strain is incubated in a pre-culture medium, preferably wherein the pre-culture medium is a complex medium, more preferably wherein the pre-culture medium is M17G (i.e., the M17 medium supplemented with glucose) or THBG (i.e., the THB medium supplemented with glucose).

The complex medium may be Todd Hewitt broth (THB) (Todd and Hewitt, 1932; Updyke and Nickle, 1954) or M17 broth (Terzaghi and Sandine, 1975). THB may comprise 500 g/L beef heart infusion, 20 g/L peptic digest of animal tissue, 2 g/L dextrose, 2 g/L sodium chloride, 0.4 g/L sodium phosphate, 2.5 g/L sodium carbonate. M17 broth may comprise: 0.5 g/L ascorbic acid, 5 g/L lactose, 0.25 g/L magnesium sulfate, 5 g/L meat extract, 2.5 g/L meat peptone (peptic), 19 g/L sodium glycerophosphate, 5 g/L soya peptone (papainic), 2.5 g/L tryptone, 2.5 g/L yeast extract. Method for identifying strains transformable by natural competence

In another aspect, the present invention relates to a method for identifying a strain of the Lactococcus genus which is transformable through natural competence. Said method comprises the following steps:

(a) providing a strain of the Lactococcus genus;

(b) transforming said strain with a plasmid expressing a comX gene having at least 90% identity, preferably having 100% identity, to the endogenous comX gene of said strain;

(c) contacting said strain obtained in step (b) with an exogenous marker DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) determining the rate of recombination events;

wherein a rate of at least 1 x 10 ^"6 transformants per μg of DNA is indicative of a strain which is transformable through natural competence. The term "rate of recombination events" may be used interchangeably with the term "transformation rate". The rate of recombination events is calculated by determining the ratio of the number of cells having integrated the exogenous marker DNA polynucleotide over the total number of viable cells. A rate of at least 10 ^"6 was selected as a threshold, based on the observation that the level of spontaneous mutation in lactococci is less than 10 ^"6 , typically around 10 ^"7 mutants per μg of DNA [spontaneous means with no comX expression or overexpression].

By "at least 90% identity to the endogenous comXgene of said strain", it is meant - as particular embodiments of the method - at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity. In a particular embodiment, said comX gene has 100% identity to the endogenous comX gene of said strain.

In a particular embodiment, said method is implemented with a strain of the Lactococcus genus selected from the group consisting of Lactococcus lactis, Lactococcus raffinolactis, Lactococcus plantarum, Lactococcus piscium, Lactococcus garivieae, Lactococcus fujiensis and Lactococcus chungangensis.

In a particular embodiment, said method is implemented with a strain of the Lactococcus lactis species. Said method comprises the following steps:

(a) providing a strain of the Lactococcus lactis species;

(b) transforming said strain with a plasmid expressing a comX gene having at least 90% identity to the polynucleotide sequence of SEQ ID NO:1 , 3 or 5;

(c) contacting said strain obtained in step (b) with an exogenous marker DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) determining the rate of recombination events;

wherein a rate of at least 1 x 10 ^"6 transformants per μg of DNA is indicative of a strain of the Lactococcus lactis species which is transformable through natural competence.

In a particular embodiment, said method is implemented with a strain of the Lactococcus raffinolactis species. Said method comprises the following steps:

(a) providing a strain of the Lactococcus raffinolactis species;

(b) transforming said strain with a plasmid expressing a comX gene having at least

90% identity to the polynucleotide sequence of SEQ ID NO:7;

(c) contacting said strain obtained in step (b) with an exogenous marker DNA polynucleotide in a medium and incubating the resulting mixture for integration of the exogenous DNA polynucleotide into the genome of said strain; and

(d) determining the rate of recombination events; wherein a rate of at least 1 x 10 ^"6 transformants per μg of DNA is indicative of a strain of the Lactococcus lactis species which is transformable through natural competence.

In some embodiments, the comX gene is from a strain of the same species, in particular of the same subspecies, as the strain provided in step a). In some embodiments, the comX gene is identical (100% identity) to the polynucleotide sequence of the endogenous comX gene of the strain of step a).

In some embodiments, when the strain of step a) is a Lactococcus lactis subsp. lactis strain, the comX gene has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to the polynucleotide sequence of SEQ ID NO:1.

In some embodiments, when the strain of step a) is a Lactococcus lactis subsp. cremoris strain the comX gene has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to the polynucleotide sequence of SEQ ID NO:3 or SEQ ID NO:5. In some embodiments, when the strain of step a) is a Lactococcus raffinolactis strain the comX gene has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to the polynucleotide sequence of SEQ ID NO:7.

In some embodiments, when the strain of step a) is a Lactococcus plantarum strain the comX gene has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to the polynucleotide sequence of SEQ ID NO:9.

In some embodiments, when the strain of step a) is a Lactococcus piscium strain the comX gene has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to the polynucleotide sequence of SEQ ID NO:1 1.

In some embodiments, when the strain of step a) is a Lactococcus garvieae strain the comX gene has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to the polynucleotide sequence of SEQ ID NO:13, SEQ ID NO:15, or SEQ ID NO:17.

In some embodiments, when the strain of step a) is a Lactococcus fujiensis strain the comX gene has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to the polynucleotide sequence of SEQ ID NO:19.

In some embodiments, when the strain of step a) is a Lactococcus chungangensis strain the comX gene has at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to the polynucleotide sequence of SEQ ID NO:21 .

It is preferable to use, as an exogenous marker DNA polynucleotide, a polynucleotide bearing a gene which is initially not present in the Lactococcus strain of step a) [even as a mutated version]. This would avoid that during step c) the Lactococcus strain acquires a functional gene by other means than natural competence, e.g. by spontaneous mutation of its genome.

As an example, the exogenous marker DNA polynucleotide bears a gene encoding a luciferase gene. Accordingly, a Lactococcus strain which has integrated the exogenous DNA polynucleotide into its genome may be selected for expression of the luciferase. Only strains that express the luciferase gene (i.e., integrated) will be detectable by bioluminescence. As another example, the exogenous marker DNA polynucleotide bears an antibiotic resistance gene. Accordingly, a Lactococcus strain which has integrated the exogenous DNA polynucleotide into its genome may be selected by plating the cells onto a medium comprising said antibiotic.

An example of a method for identifying a strain of the Lactococcus genus which is transformable through natural competence according to the present invention (Assay A) may be performed using the following steps:

i) Providing a strain of the Lactococcus genus, in particular of the Lactococcus lactis species.

ii) Transforming said strain with a plasmid expressing a comX gene having at least 90% identity, preferably having 100% identity to the endogenous comX gene of said strain (e.g. the pGhP32comXMG plasmid of Materials and Methods).

iii) Pre-culturing the transformed strain overnight in a complex medium supplemented with glucose (e.g. M17G) at 30 °C.

iv) Diluting about 1.5 mL of the pre-culture in about 8.5 mL of fresh medium.

v) After about 2 hours further growth at 30 °C, washing the cells twice with distilled water and adjusting the Ο βοο to 0.05 in a chemically defined medium (e.g. CDM) containing 5 μg mL ^"1 erythromycin and an osmo-stabilizer (e.g. 5 % [v/v] glycerol or 5 % [w/v] mannitol). vi) Adding 5 μg of exogenous DNA polynucleotide bearing an antibiotic resistance gene to 300 μΙ of the culture medium (e.g. the 3.7 kb PCR product generated from the pGEMrpsL plasmid as described in Materials and Methods).

vii) Incubating the resulting culture for about 6 hours at 30 °C.

viii) Plating the cells onto agar plates comprising the complex medium supplemented with glucose (e.g. M17G) and appropriate antibiotic (i.e. corresponding to the antibiotic resistance gene of the exogenous DNA polynucleotide) and incubating for about 48 hours.

ix) Counting the colony forming units (CFU) and determining the transformation rate, wherein a transformation rate of at least 1 x 10 ^"6 transformants per μg of DNA is indicative of a strain which is transformable through natural competence.

The transformation rate may be calculated as the number of antibiotic-resistance CFU mL ^"1 divided by the total number of viable CFU mL ^"1 . Various preferred features and embodiments of the present invention will now be described by way of non-limiting examples.

EXAMPLES Example 1 : Induction of the comGA promoter by constitutive comX expression in various strains of the Lactococcus species a) in Lactococcus lactis subsp. cremoris strains (MG1363 and KW2)

To test the ability of ComX to induce the late competence genes in Lactococcus lactis subsp. cremoris strains, a constitutive comX expression plasmid (pGhP32comXMG) was created by cloning the comX gene from strain MG1363, under the control of the lactococcal P32 promoter on the thermosensitive plasmid pG ⁺ host9. The latter was introduced in strain KW2 that contains a chromosomally-encoded P _C omGA[MGrluxAB transcriptional fusion (BLD101 ). The promoter of the late competence gene comGA (PCO GA) contains a putative ComX-binding motif and is used here as proxy for competence activation in the ComX ⁺ strain.

As alternative for more resistant strains to electro-transformation, and subsequently to chromosome integration, a portable luminescent reporter system was also constructed. This replicative plasmid carries the luminescent reporter P _C omGA[MG]-luc with the P32-comXMG cassette. The pGhP32comXMG-PcomG/v/wGr/wc plasmid was transformed in strain MG1363. Specific P _CO mGA[MG]-luc/luxAB activities were monitored for the different strains constructed. The luminescent assays were performed in rich (M17G) and/or CDM media comparing the luciferase activity between the overexpressing comX strain and its related negative control (no additional comX copy). In the KW2 strain containing the P _CO mGA[MG _] -luxAB reporter as mono-copy in their chromosome, specific luciferase activity was observed for KW2 containing the P 32-comX cassette allowing the constitutive production of ComX. This confirms that comX expression can be carried out in various L. lactis subsp. cremoris strains using an exogenous comX gene obtained from the same strain or from a strain of the same subspecies. Eight recombinant clones of the KW2 ComX ⁺ reporter strain were randomly selected and their specific luciferase activity was monitored in CDM growth conditions. This medium was chosen because it was shown to be permissive for competence development in various streptococcal species. To ensure reproducibility of the assay, exponentially-growing cells in complex medium (M 17 conditions) were washed and inoculated in fresh CDM before starting the experiment. As expected, all tested ComX ⁺ clones (cl01 to cl08) displayed between 10 ¹ -and 10 ⁴ -fold higher specific luciferase (Lux) activity than the control strain carrying the empty vector (Figure 2A and 2B).

Similar results were obtained with the portable luminescent reporter systems in MG1363 (Figure 2C).

These results strongly suggest that, in the L. lactis subsp. cremoris strains MG1363 and KW2, ComX induces the comG operon. Additionally, these observations validate these reporter fusions (both chromosomal and plasmid-borne) as a tool to identify conditions capable to activate the comG-operon which is essential to natural transformation. b) in a L. lactis subsp. lactis strain (IL1403)

A constitutive comX expression plasmid (pGhP32comXio) was created by cloning the comX gene from strain 10-1 , under the control of the lactococcal P32 promoter on the thermosensitive plasmid pG ⁺ host9. A portable luminescent reporter system was also constructed; this replicative plasmid carries the luminescent reporter P _C omGA[io]-luc with the P32-comXio cassette. The promoter of the late competence gene comGA (PCO GA) contains a putative ComX-binding motif and is used here as proxy for competence activation in the ComX ⁺ strain. This replicative plasmid pGhP32comXio-PcomG/v/qr/wc was transformed in strain I L1403 and specific P _C omGA[io]-luc activities were monitored. One of the I L1403 transformants produced specific P _C omGA[io]-luc activities confirming that ComX induces the comG operon (Figure 2D). Example 2: Analysis of essential late com genes present in L. lactis genomes

Among L. lactis strains, genomic variability was previously investigated for comX and dprA alleles (Wydau et al., 2006). While all strains (31/31 ) display a complete version of comX, the dprA content is variable among subspecies: 50 % of the lactis strains (10/20) contain nonsense mutations in dprA while all cremoris strains (1 1/1 1 ) harbor an intact and potentially functional dprA gene.

Since dprA is hypothesized to be important in the natural competence mechanism, its integrity in L. lactis strains prompted us to further analyze the minimal set of late com genes (17 candidate genes including comX; Figure 1 ) in the genomes of 3 subsp. cremoris strains and 1 subsp. lactis strain which are publicly available (strains MG1363, SK1 1 , KW2 and IL1403). This in silico analysis reveals that the genome of SK1 1 contains a high number of pseudogenes in key competence genes (between 5 and 8 incomplete late com genes) due to transposon insertion or frameshifting events (nucleotide(s) insertion or deletion). In particular, the presence of transposable elements in comGA and/or comEC genes, which are respectively essential for pilus assembly and DNA transport, strongly suggests that natural transformation is no more functional in those strains. Although the set of full-length competence genes in the laboratory strain MG1363 is larger, mutations in comEC (nucleotide insertion) and coiA (nonsense mutation) probably impair its ability to transform DNA by competence (Wegmann et al., 2007). Those mutations were also found in the genome of its isogenic derivative NZ9000, which strongly suggests that they do not result from DNA sequencing errors. As far as the L. lactis subsp. lactis IL1403 strain is concerned, its dprA gene contains nonsense mutations probably impairing its ability to transform DNA by competence. In contrast, strain KW2 of plant origin (corn fermentation) contains the whole set of known essential late genes required to fulfil natural DNA transformation, making it the best candidate to further study the functionality of competence in the cremoris subspecies. Two other strains from our collection, L. lactis subsp. lactis SL12651 and SL12653, were also found to contain the whole set of known essential late genes (Figure 1 ). Example 3: Effect of growth conditions on ComX activation

We investigated the effect of pre-culturing and culturing conditions (M17G, THBG, and CDM) on the activation of the reporter fusion in the ComX ⁺ strain. For this purpose, clone 02 (Figure 2A) was selected since it exhibits the strongest Lux activity. Interestingly, more than a 20-fold variation in the maximum Lux activity was dependent on the pre- and culturing medium which was used (Figure 3). Particularly, a positive impact of the transition of pre-culture cells from a complex medium to a defined medium was observed. The highest specific Lux activity (-3 ^χ 10 ⁶ RLU ODeoo ^"1 ) was obtained for a switch from M 17G to CDM, followed by TH BG to CDM, while all other combinations gave lower activities (between ~ 1 .5 * and 5.5 ^χ 10 ⁵ RLU Ο βοο ^"1 ). This indicates that first a chemically defined medium is superior for maximizing activation of late com genes of L. lactis KW2 than complex rich media, but also that the switch from complex medium (e.g. M 17G or TH BG) to defined medium is critical.

Together, these results show that ComX is functional in strain KW2 when it is constitutively produced (i.e. expressed) and that growth conditions have a significant impact on the activation of late com genes.

Example 4: Constitutive comX expression induces natural transformation a) Acquisition of single mutations in the KW2 genome from exogenous DNA

We first tested the transfer of single point mutations in the chromosome of the ComX ⁺ KW2 strain. The transforming PCR fragments used encompass the mutated rpsL allele of a spontaneous streptomycin-resistant (Str ^r ) clone of L. lactis subsp. cremoris MG1363 (strA 1 allele, also called rpsL*). This mutated allele bears an A→T substitution at position 167 [resulting in the altered ribosomal protein S12 with mutation K56I] as compared to the sequence of the wild-type, streptomycin-sensitive MG1363. In addition to this mutation, the two rpsL alleles differ by a silent nucleotide substitution at position 39 (T→G). The sequence of the rpsL (wild-type) and rpsL* (conferring streptomycin resistance) alleles are disclosed respectively as SEQ ID NO:23 and NO:24 (Figure 4A). Independently of these two substitutions located at positions 39 and 167, the rpsL alleles of KW2 and MG1363 differ by a nucleotide substitution at position 156 (A in MG1363, T in KW2). The rpsL allele of KW2 is disclosed as SEQ ID NO:25 (Figure 4A). To ensure efficient recombination, the transforming PCR product also contains upstream and downstream recombination arms of -1 .85 kb surrounding the strA 1 mutation. Transformation assays were performed with the eight previously selected clones of the ComX ⁺ reporter strain (BLD101 [pGhP32comXMG]) and the control strain (BLD101 [pG ⁺ host9], empty vector) using the standard protocol reported in Material and Methods. Validation of natural transformation is made by sequencing the rpsL region covering the point mutations from the donor DNA conferring streptomycin resistance using primers RpsL Univ UP and RpsL Univ DN.

Remarkably, the ComX ⁺ clones 02 and 04 that displayed the highest PCO GA activation (≥ 7 ^χ 10 ⁵ RLU Ο βοο ^"1 ) yielded mutation frequencies ~15-fold higher than the background level of spontaneous mutation that was calculated in the absence of DNA (Figure 4B). After subtraction of the background, a transformation rate of up to 4 10 ^"5 transformants per μg of DNA (~10 ⁴ transformants ml ^"1 ) was obtained for clone 02 which displays the highest PCO GA activation. In contrast, the negative control strain had a spontaneous mutation rate of -1 x 10 ^{" 7} transformants per μg of DNA. The rpsL ORF of 10 Str -derivatives of cl02 was amplified by PCR and sequenced. In all cases, we observed the co-transfer of strA 1 (mutation A→T at position 167 of the rpsL gene) and the closely-located T→A mutation at position 156. In some cases, the T→G mutation at position 39 was also co-transferred with strA 1. The chimeric nature of rpsL in some Str ^r ComX ⁺ derivatives of KW2 (i.e. presence of both mutations at positions 156 and 167 without the mutation at position 39) ultimately demonstrates that a recombination process occurred between the exogenous and chromosomal DNA (Figure 4A). In contrast, this rearrangement was not observed in the rpsL gene of spontaneous Str ^r mutants obtained in the negative control experiments (i.e. assays performed in absence of exogenous DNA, or with the control strain carrying the empty vector in presence of exogenous DNA). These results show that exogenous DNA can enter KW2 cells and be integrated in their chromosome by homologous recombination when a certain threshold of comX expression is reached. b) Construction of deletion mutants by natural competence in L. lactis subsp. cremoris KW2 overexpressing comX

The previous result (Example 4, section a) strongly suggests that DNA transfer occurs in L. lactis KW2. The 3 mutations transferred by natural transformation are grouped on a 128-bp fragment. If a longer DNA fragment could be similarly integrated in the L. lactis chromosome remains to be determined.

We wondered if overlap PCR as donor DNA could equivalently allow gene insertions or gene deletions. The idea was to replace the target gene by an antibiotic resistance cassette, i.e. the chloramphenicol resistance cassette P32-cat. For this purpose, a DNA fragment was constructed by overlap PCR containing the P32-cat cassette flanked by two homologous arms (minimum ~ 1 .5kb) containing the upstream and downstream regions of the targeted gene.

To this end, exogenous DNA polynucleotides containing P32-cat surrounded by KW2-specific recombination arms (~ 1 .5 kb) were assembled in vitro by overlapping PCR to target the comEC, mecA, ciaRH, covRS or clpC gene (see Materials and Methods for details) and transferred by natural transformation in the ComX ⁺ strain (cl02). Validation of natural transformation is made by sequencing the targeted region (comEC, mecA, ciaRH, covRS or clpC, which should contain the chloramphenicol resistance cassette P32-cat) using primers listed in Table 3. The transformation rate observed for overlap PCR products was ~ 1 .2 x 10 ^"6 to 1 .1 x 10 ^"4 transformants per μg of DNA for the different overlap DNA fragments that were tested (see Figure 5). Compared to the transformation rate observed for the exchange of a homologous DNA fragment containing only three point mutations (rpsL* donor DNA; 8 x 10 ^"4 transformants per μg of DNA), these rates are relatively high for DNA double recombination deletion/replacement.

Example 5: A KW2 AcomEC mutant is unable of natural competence transformation To confirm that the observed horizontal DNA transfer in ComX ⁺ KW2 cells was indeed mediated by natural competence, and not by phage transduction or conjugation, we investigated the role of the ComEC protein, which is essential for the uptake of transforming DNA through the cell membrane (the comEA gene, together with the comFA, comGA, dprA, coiA, ssbA, radA, radC, recA and recX genes are preceded by a Corn-box and have been found to be activated in KW2 following constitutive comX expression; data not shown).

To create the AcomEC strain, clone 02 of the ComX ⁺ reporter strain, which was tested above, was grown in CDM conditions in presence of PCR products encompassing the comEC gene disrupted by the insertion of the chloramphenicol resistance cassette P32-cai (see Materials and Methods). Four mutants with disrupted comEC (BLD102 [pGhP32comX _M G] cl01 to cl04) were validated by PCR for P^-cat insertion in comEC. Transformation assays with the mutated rpsL allele showed that the frequencies of appearance for Str ^r clones in all tested AcomEC derivatives were similar to the background level of spontaneous rpsL mutation frequencies (< 10 ^"7 ) (Figure 6). Although heterogeneity in PCO GA activation was observed between clones as previously reported for the WT ComX ⁺ reporter strain, half of the AcomEC derivative clones (i.e. cl01 and cl03) displayed maximum specific Lux activity similar to the transformable WT strains (> 1 .0 x 10 ⁶ RLU Οϋβοο ^"1 ) (Figure 4B). This shows that the transformation defect in these AcomEC clones does not result from a too low production of ComX.

Taken together, these results demonstrate that natural DNA transformation could be activated by ComX overexpression in L. lactis subsp. lactis KW2. Moreover, to the best of our knowledge, these data provide the first ever experimental evidence of transformation of L. lactis by natural competence.

Example 6: Natural competence in two strains of the L. raffinolactis species Following the positive results obtained regarding natural competence in Lactococcus lactis strains, other strains of the Lactococcus genus were tested. Two strains of L. raffinolactis were able to capture plasmid pGhost-Core (15 μ9 / 300 μΙ) used as donor DNA: LMG13098 and LMG14164. These results suggest that these two strains of L. raffinolactis are naturally competent for plasmid transformation and that, in these strains, natural competence is independent of artificial comX-overexpression. The fact that another Lactococcus species could be transformed by competence opens additional possibilities for industrial applications.

Example 7: Transformation by natural competence in 2 Lactococcus lactis subsp. lactis strains

Two Lactococcus lactis subsp. lactis strains, SL12651 and SL12653, carrying all the essential late com genes (Figure 1 ) were tested. As donor DNA, PCR fragments which encompass the mutated rpsL allele (rpsL ^* ) of a spontaneous streptomycin-resistant (Str ^r ) clone of L. lactis subsp. lactis IL1403 was used. Cells were pre-cultured overnight in a complex medium supplemented with glucose (e.g. M17G) at 30°C. Cells were washed twice with distilled water and inoculated at an Ο βοο of 0.05 in 200 μΙ M17G containing 25 μg mL ^"1 donor DNA rpsL ^* . After 24 hours of culture at 30°C, cells incubated or not with donor DNA were spread onto agar plates comprising the complex medium supplemented with glucose (e.g. M17G) and appropriate antibiotic (i.e. streptomycin). CFUs were counted after 48 hours of incubation at 30°C. Remarkably, SL12651 and SL12653 yielded a transformation rate of up to 1 x 10 ^"6 of DNA when grown in M17G rich medium (Figure 7A; +DNA). In contrast, the negative control in absence of donor DNA had a spontaneous mutation rate of 6 x 10 ^"9 (Figure 7A; -DNA). The transformants were validated by sequencing the rpsL region covering the point mutation from the donor DNA conferring streptomycin resistance.

Then, the SL12653 strain was assayed in the same conditions with variable quantity of donor DNA (0.5, 2.5, 5 and 25 μg mL ^"1 ). It has been shown that the transformation rate obtained is directly correlated to the initial quantity of donor DNA, yielding up to a transformation rate of 5 x 10 ^"6 (Figure 7B).

Moreover, to confirm that the observed horizontal DNA transfer was mediated by natural competence, the comXgene of SL12653 was knocked-out (as described in example 5 above). Three mutants of SL12653 with disrupted comX gene were designed by inserting PCR products encompassing the comX gene disrupted by the insertion of the chloramphenicol resistance cassette P32-cai and validated by PCR for P^-cat insertion. Transformation assays with rpsL ^* as donor DNA in all AcomX clones (ComX ^" ) showed that the frequencies of appearance of Str ^r clones were similar to the background level of spontaneous mutation frequencies (Figure 7C). These results confirm that in SL12653, the transformation is dependent on the expression of the endogenous comX gene.

Finally, the transformability of the SL12653 strain was also assayed by overexpressing the comX gene. Thus, an inducible comX expression plasmid [pGhPxylTcomXio] was constructed by cloning the comX gene from strain L. lactis subsp. lactis 10-1 under the control of the P _xy ir promoter from strain 10-1 on the thermosensitive plasmid pG ⁺ host9. This plasmid is a variant of pGhPxylTcomXMG (pGIFPTOOI ) described in David et al., 2017. The transformation procedure described in David et al (2017) was followed. In presence of xylose (1 %), SL12653 [pGhPxylTcomXio] yielded a transformation rate at least 20-fold higher than in absence of xylose, confirming that the overexpression of comX in SL12653 increased its transformability by natural competence.

Materials and Methods

^■ Bacterial strains, plasmids, and growth conditions

The bacterial strains and plasmids used in this application are listed in Table 2.

Table 2: list of used bacterial strains and plasmids

a Em ^r , Ap ^r , Cm ^r and Ts: erythromycin, ampicillin, chloramphenicol resistance and thermo-sensitive RepA protein, respectively. Escherichia coli was grown with shaking at 37°C in Lysogeny-Broth (LB) broth. Plasmids derived from pMG36e and pG ⁺ host9 were constructed in E. coli strains TG1 and EC1000, respectively. L. lactis and L. raffinolactis were cultivated in M17 (Becton, Dickinson, and Company), Todd Hewitt broth (THB) (Becton, Dickinson, and Company) or CDM at 30°C without agitation. M17 and THB were supplemented with 0.5% (w/v) of glucose (M17G and THBG, respectively). Solid agar plates were prepared by adding 2% (w/v) agar to the medium. When required, 5 μg ml ^"1 of erythromycin, 1 mg ml ^"1 of streptomycin, and/or 10 μg ml ^"1 of chloramphenicol were added to the medium for L. lactis and L. raffinolactis; and 250 μg ml ^"1 of erythromycin, 250 μg ml ^"1 of ampicillin, 10 μg ml ^"1 of chloramphenicol for £. coli.

^■ Detection of absorbance and luminescence.

Growth (Ο βοο) and luciferase (Lux) activity were monitored at 10-minutes intervals in a Varioskan Flash multi-mode reader (ThermoFisher). The luciferase activity is expressed in relative light units (RLU) and the specific luciferase activity in RLU Ο βοο ^"1 .

^■ DNA techniques and electrotransformation

General molecular biology techniques were performed according to the instructions given by Sambrook et al. (1989). Electrotransformation of E. coli and L. lactis was performed as previously described. The electrotransformed cells of L. lactis were immediately resuspended in 1 ml of M17G and incubated for 6 hours at 30 °C. Chromosomal DNAs of L. lactis were prepared as previously described. PCRs were performed with Phusion DNA polymerase (NEB) in a GeneAmp PCR system 2400 (Applied Biosystems). The primers used in this application are listed in Table 3.

Primer name Sequence (5'-3')

Primers used for the construction of the constitutive comX expression plasmid pGhP32comXMG/io:

BID ComXSDLLCup AAAAGAGCTCAATTATGAAAAAGAGG

BID ComXSDLLCdown AAAACTGC AGTTAATCATCATCTCG

BID ComXSDLLLup AAAAGAGCTCATAAAAGGAGAACTTTCC

BID ComXSDLLLdown AAAACTGCAGTCACTCTTCGTCTTC

BID_pMGP32UpMfel ATATCAATTGGTCCTCGGGATATGATAAG

BID pMGTerDown GACTTTGAACCTCAACTCC

Primers used for the construction of the PcomGA[MG]-luxAB reporter strain BLD101 :

BID LuxLLCfl ATAGTCTCGAGTTTAAGCAATTGAATCGCTAG

BID LuxLLCM GCAAAAAGTTTCCAAATTTCATACTAGAATATACGCAATTTG

BID_LuxLLCf2 CAAATTGCGTATATTCTAGTATGAAATTTGGAAACTTTTTGC

BID_LuxLLCr2 GCGAAAGGATCCCTATTAGGTATATTCCATGTGG

BID_P3pseudoLLC GCTCCCTCGAGGGCGGCTCTGTTGGATTAATATATGG Primers used for the construction of portable luc reporter vectors:

BID LucLLCrl CTTTATGTTTTTGGCGGATCTCATACTAGAATATACGCAATTTG

BID_LucLLCf2 CAAATTGCGTATATTCTAGTATGAGATCCGCCAAAAACATAAAG

BID_LucLLCr2 GCGAAAGGATCCTTACAATTTGGGCTTTCCG

BID_PcomGALLCF1 * AAAACCCGGGTTTAAGCAATTGAATCGCTAG

BID_PcomGALLLF1 * 5' AAAACCCGGGAAATAAATGGCTACAAAATT

BIDJucRI * AAAACGGCCGTTACAATTTGGGCTTTCCG

BIDJuxLLL.f1 ATAGTCTCGAGAAATAAATGGCTACAAAATT

BID JucLLLrl CTTTATGTTTTTGGCGGATCTCATACTAGACTATACGCAAATAATC

BID JucLLLf2 GATTATTTGCGTATAGTCTAGTATGAGATCCGCCAAAAACATAAAG

BID JucLLLr2 GCGAAAGGATCCTTACAATTTGGGCTTTCCG

Primers used for the construction of pGhost-Core

DD-pGhost-CoreUp AGCTTCCTAATACAACACAATTAATATTGTGTTGTATTATTG

DD-pGhost-CoreDW AATTCAATAATACAACACAATATTAATTGTGTTGTATTAGGA

Primers used for rpsL sequencing:

RpsL Univ UP ATGCCTACAATTAACCAAT

RpsL Univ DN CACCGTATTTAGAACGG

LR RpsL Univ UP ATGCCTACTATTAACCAAT

LR RpsL Univ DN TACCGTATTTAGAACGG

Primers used for rpsL amplification:

BID LLcdacARpsL AGTAGTATCAGCACTGACAGC

BID LLIcfusARpsL ACACCTTTGTTCTTGAAGG

primers used for the construction of the comEC disruption mutant:

BID ComECLLCUp AAAGAGCTCAAAATAAAAATGAAATTATGG

BID ComECLLCDown AAAGCTAGCGGGAAAAAATTGTGAATTAC

BID CatUpSpel AAAAACTAGTGCAGTTTAAATTCGGTCCTCGG

BID CatDownSpel AAAAACTAGTGTACAGTCGGCATTATCTCAT

Primers used for the construction and validation of the mecA deletion mutant:

BID_fgt01 FmecArec CTTTAATGATGGAATGATTG

BID fgtOI RVmecArec CTATTAATCTTATCATATCCCGAGGATCCATATAACTATATGAAACC

BID_fgt02Fcat TCCTCGGGATATGATAAGATTAATAG

BID_fgt02RVcat TCTCATATTATAAAAGCCAGTCATTAG

BID_fgt03FmecArec CTAATGACTGGCTTTTATAATATGAGACTTAGAAAAATCTAAATATGGTTG

B 1 D_fgt03RVmecArec GAAGATTTTTAATTTCAAGTGTAG

BID mecAKOF TCAGTACCGAAAAACGAATG

BID mecAKORV ATTTACCAGTTCCGTTAGG

Primers used for the construction and validation of the ciaRH deletion mutant:

BID ciaRHUPF TAACAATGATACAGAAGATG

BID ciaRHUPRVRec CTATTAATCTTATCATATCCCGAGGATATTTTTGTCTTGTACTAGG

BID_fgt02Fcat TCCTCGGGATATGATAAGATTAATAG BID_fgt02RVcat TCTCATATTATAAAAGCCAGTCATTAG

B 1 D cia RH Down F Rec CTAATGACTGGCTTTTATAATATGAGAGAGAGAAAAAAATTACTGAC

BID ciaRHDownRV AAAATCTGTTAGAACTGTTG

BID ciaRHKODiagF AAGATAAGGCAGTTGAAATG

BID ciaRHKODiagRv TCACCATGTGAATAAAGTCC

Primers used for the construction and validation of the covRSdeletion mutant:

BID_covRSfgt01 F CAAAAATGTGAAGCTTATC

BID covRSfgtOI RVRec CTATTAATCTTATCATATCCCGAGGATGCATAATTCGATTTC

BID_fgt02Fcat TCCTCGGGATATGATAAGATTAATAG

BID_fgt02RVcat TCTCATATTATAAAAGCCAGTCATTAG

BID_covRSfgt03FRec TAATGACTGGCTTTTATAATATGAGACTATTTATCTGCTCATTTC

BID_covRSfgt03RV GAG CTTTTTTCAAATCTTC

BID covRSKOFdiag GAAGTGATGAATGAGATG

B 1 D covRS KO RVd iag CTTTCTCATCAATTGAGAC

Primers used for the construction and validation of the clpC deletion mutant:

BID clpCUPF CTTTGGGTTCTAATTTATC

BID clpCUPRVRec CTATTAATCTTATCATATCCCGAGGACGTTGGTGTATATTTTAC

BID_fgt02Fcat TCCTCGGGATATGATAAGATTAATAG

BID_fgt02RVcat TCTCATATTATAAAAGCCAGTCATTAG

BID clpCDownFRec CTAATGACTGGCTTTTATAATATGAGATAGAAATAAAGGAAAGGAC

BID clpCDownRV TTGCTTTAAGGATAGTTTC

BID clpCFdiag AG AAG CCAATAATG ACG ATG

BID clpCRVdiag AGAATTCTGATGATGCACAGTC

Primers used for the construction of the inducible comX expression piasmid pGhPxylTcomXio:

FT pGhPxylcomXIOsa

AGCGCCGCGGTGGGATCCTCTAGAGTC

cllrv

FT pGhPxylcomX CTGCAGGCATGCACATCATCAACTTGAAGGG

FT PxylTIOsacllfw CCCACCGCGGTGGAGATACGAACAAATTAG

FT PxylTIOrv GATAGTAACTCCTTAATTTTTATTTGC

GCAAATAAAAATTAAGGAGTTACTATCATGACATATTACTTGGAAGAAGAGGAT

FT comXIOrecfw

TTTG

FT comXIOrecrv CCTTCAAGTTGATGATGTGCATGCCTGCAGTCACTCTTCGTCTTC

Primers used for the construction and validation of the SL12653-comX deletion mutant

FT_comXlocusfw TGACCATGTTACACAAGCCTATATCCT

CGCCCTTATGGGATTTATCTTCCTTACTTCGTTTCTTTGCATAACTTCGTCTTA

FT comXrecrv

AT

Uplox66 TAAGGAAGATAAATCCCATAAGG

Dnlox71 TTCACGTTACTAAAGGGAATGTA

TCTACATTCCCTTTAGTAACGTGAACCATGACCATTTTATAGGTTTAGATGTTT

FT_comXrecfw

ATG

AR comxDNspecR CGGTGTTCCTCCATATATCTACGC

FT PxylcomXfw CGCTAAACTCAACAGGTGATCCGATTG

Table 3: list of primers ^■ Construction of plasmid pGhP32comXMG

As a representative of the cremoris subspecies, the comX gene from the laboratory strain MG1363 was initially chosen. ComX proteins of this subspecies are highly conserved with at least 98% of identity. The comX gene was amplified by PCR using primers BID_ComXSDLLCup/BID_ComXSDLLCdown and inserted into plasmid pMG36eT under the control of the constitutive P32 promoter by Sacl/Pstl cloning, yielding plasmid pMGP32comXMG. The P32-comXMG fusion from pMGP32comXMG was amplified by PCR with primers BID_pMGP32UpMfel/BID_pMGTerDown, digested by Mfel/Kpnl, and cloned in the EcoRI/Kpnl-digested thermosensitive pG ⁺ host9 vector. The resulting plasmid was named pGhP32comX _M G.

^■ Construction of plasmid pGhP32comXio

As a representative of the lactis subspecies, the comX gene from the 10-1 strain was chosen. The comX gene was amplified by PCR using primers BI D_ComXSDLLLup/BID_ComXSDLLLdown and inserted into plasmid pMG36eT under the control of the constitutive P32 promoter by Sacl/Pstl cloning, yielding plasmid pMGP32comXio. The P32-comXio fusion from pMGP32comXio was amplified by PCR with primers BID_pMGP32UpMfel/BID_pMGTerDown, digested by Mfel/Kpnl, and cloned in the EcoRI/Kpnl-digested thermosensitive pG ⁺ host9 vector. The resulting plasmid was named pGhP32comXio.

^■ Construction of plasmid pGhost-Core

The Core part of the resolution site (I RS) recognized by the Tnpl recombinase from Tn4430 was assembled by using the complementary primers DD-pGhost-CoreUp/DD-pGhost- CoreDW. The resulting DNA fragment was cloned between Hind 111 and EcoRI sites in plasmid pG ⁺ host9. The resulting plasmid, named pGhost-Core, was transformed in E. coli harbouring plasmid pGIV004 (Τηρ ) for obtaining multimeric forms (Vanhooff V, Galloy C, Agaisse H, Lereclus D, Revet B, Hallet B. Mol Microbiol. 2006 May;60(3):617-29). ■ Construction of PcomGA[MG]-luxAB reporter strain BLD101

The PcomGA[MG] promoter was amplified by PCR from chromosomal DNA of L. lactis MG1363 (identical nucleotide sequence between MG1363 and KW2) with primers BID_LuxLLCf1/BID_LuxLLCr1 (PCR1 product). The luxAB genes were amplified by PCR from plasmid pJI M4900 with primers BID_LuxLLCf2/BID_LuxLLCr2 (PCR2 product). The P _CO mGA[MGr luxAB fusion was created by overlapping PCR using PCR1 and PCR2 products and primers BID_LuxLLCf1 /BID_LuxLLCr2. The resulting fusion was cloned in plasmid pSEUDOPusp45GFP using restriction enzymes Xhol and BamHI, yielding plasmid pSEUDOPusp45PcomGAIuxAB. In order to remove the P _USP 45 promoter, the entire vector except the P _USP 45 promoter was amplified by inverse PCR with primers BID_P3pseudoLLC/BID_LuxLLCf1 and self-ligated after Xhol digestion, leading to plasmid pSEUDOPcomGAIuxAB. The insertion cassette llmg_pseudo_10: : P _C omGA _[ MGrluxAB was excised from plasmid pSEUDOPcomGAIuxAB and cloned into the pG ⁺ host9 thermosensitive vector using restriction enzymes Kpnl/Eagl. The resulting plasmid pGhPcomGAIuxAB was then electro-transformed in strain KW2 and used to integrate the P _CO mGA[MGrluxAB cassette at locus kw2_0563 (llmg_pseudo_10 in MG1363) by double homologous recombination, resulting in the reporter strain KW2 kw2_0563 ^m . : P _C omGA _[ MGrluxAB (strain BLD101 ).

^■ Construction of portable luc reporter systems

The PcomGA[MG] promoter was amplified by PCR from chromosomal DNA of L. lactis MG1363 with primers BID_LuxLLCf1/BID_LucLLCr1 (PCR1 product). The luc gene was amplified by PCR from plasmid pXL with primers BID_LucLLCf2/BID_LucLLCr2 (PCR2 product). The PcomGA[MG]~luc fusion was created by overlapping PCR using PCR1 and PCR2 products and primers BID_LuxLLCf1/BID_LucLLCr2. The resulting fusion was cloned in plasmid pSEUDOPusp45GFP using restriction enzymes Xhol and BamHI, yielding plasmid pSEUDOPusp45PcomGAIuc. In order to remove the P _USP 45 promoter, the entire vector except the Pus _P 45 promoter was amplified by inverse PCR with primers BID_P3pseudoLLC/BID_LuxLLCf1 and self-ligated after Xhol digestion, leading to plasmid pSEUDOPcomGAIuc. The reporter cassette P _C omGA[MG]-luc was amplified by PCR from pSEUDOPcomGAluc (primers BID_PcomGALLCF17 BIDJucRI ^* ) and cloned between Xmal and Eagl into the pGhP32comXMG plasmid. The resulting reporter plasmid was named pGh P32comXMG-P /uc. The PcomGA[io] promoter was amplified from the 10-1 chromosome (primers BIDJuxLLLfl/ BIDJucLLLrl ) and the luciferase gene (luc) was amplified from plasmid pXL (primers BIDJucLLLf2/BIDJucLLLr2). The cassette P _CO mGA[io]-luc was created by overlapping PCR with primers BIDJuxLLLfl /BIDJucLLLr2. The cassette P _CO mGA[io]-luc was then amplified from the overlapping PCR product with primers BID_PcomGALLLF17 BIDJucRI ^* for Xmal/Eagl cloning into pGhP32comXio. The resulting reporter plasmid was named pGhP32comXio-

~ com GA[IOrlUC.

' Isolation of a rpsL mutant conferring resistance to streptomycin

Spontaneous streptomycin-resistant MG1363 clones were isolated on 1 mg ml ^"1 streptomycin- containing plates. After the sequencing of the rpsL gene with primers RpsL Univ UP/RpsL Univ DN, one spontaneous mutant resulting in a mutation (K56I) into the ribosomal protein S12 that was previously shown to confer resistance to streptomycin was selected (Figure 6). A 3.7-kb fragment containing the rpsL mutated gene (strA1 allele) was amplified by PCR with primers BID_LLcdacARpsL/BID_LLIcfusARpsL and cloned into the pGEM®-T easy vector (Promega), yielding plasmid pGEMrpsL ^* . This plasmid was used as template to generate the 3.7-kb PCR product with primers BID_LLcdacARpsL/BID_LLIcfusARpsL that was used as donor DNA in natural transformation assays of strain KW2.

^■ Standard natural transformation assay

The BLD101 reporter strain carrying the pGhP32comX _M G plasmid (BLD101 [pGhP32comX _M G]) was grown overnight in M17G at 30°C. Then, 1 .5 ml of the pre-culture was diluted in 8.5 ml of fresh M17G medium to restart the culture. After 2 hours of growth, cells were washed twice in distilled water and Ο βοο was adjusted to 0.05 in CDM containing erythromycin (5 μg ml ^"1 ) and supplemented with either 5% (v/v) glycerol or 5% (w/v) mannitol used as potential osmo- stabilizers. Typically, 5 μg of DNA was added in 300 μΙ of inoculated medium and the culture was further incubated during 6 hours at 30°C. Cells were then spread on M17G agar plates supplemented with appropriate antibiotics and CFUs were counted after 48 hours of incubation. The transformation frequency was calculated as the number of antibiotic-resistant CFU ml ^"1 divided by the total number of viable CFU ml ^"1 . In the case of streptomycin-resistant transformants, antibiotic-resistant CFU ml ^"1 corresponds to the number of transformants obtained in presence of DNA less the number of spontaneous transformants obtained in conditions where no DNA is added in the culture. The transfer of the mutation conferring streptomycin resistance was confirmed by DNA sequencing of the rpsL gene after its amplification by PCR using primers RpsL Univ UP/RpsL Univ DN. ■ Disruption of comEC by natural transformation

A comEC-containing DNA fragment of -3.2 kb was amplified by PCR with primers BID_ComECLLCUp/BID_ComECLLCDown. Then, the PCR product was digested by Sacl/Nhel and cloned into the Sacl/Xbal-digested suicide plasmid pUC18Ery (van Kranenburg et al., 1997), yielding plasmid pUCcomEC. To generate a comEC disruption cassette that allows the selection of double crossing-over recombinants, the P32-cai fusion conferring resistance to chloramphenicol was cloned in the middle of the comEC gene. For this purpose, the P32-cai cassette was amplified by PCR from plasmid pNZ5319 (Lambert et al., 2007, Appl. Environ. Microbiol. 73:1 126-1 135) with primers BID_CatUpSpel/BID_CatDownSpel. The amplification product was digested by Spel and cloned into the Xbal-digested pUCcomEC, yielding plasmid pUCcomECcat. This suicide plasmid was used to generate high quantity of donor DNA by PCR amplification for comEC disruption by natural transformation. The insertion of the P32-cai cassette in the comEC gene of KW2 transformants was validated by PCR (primers in Table 3).

^■ Deletion of mecA, ciaRH, covRS, and clpC genes by natural transformation

The mecA, ciaRH, covRS, and clpC genes were similarly inactivated by the exchange of their ORFs by the Pwcat cassette using double crossing-over events. For this purpose, overlapping PCR products containing the P32-cai cassette flanked by two recombination arms of -1 .5 kb (upstream and downstream homologous regions) were generated as previously reported. Briefly, upstream, downstream, and P32-cai fragments were separately amplified by PCR, purified, mixed in equimolar concentration, and assembled by overlapping PCR by using the most external primers (see list of primers in Table 3). 5 μg of the obtained overlapping PCR product was used as donor DNA for natural transformation of strain BLD101 [pGhP32comXMG]. The correct insertion of the P32-cai cassette in each targeted locus of the KW2 transformants was validated by PCR (see list of primers in Table 3). To obtain the final mutant strains, the thermosensitive vector pGhP32comXMG was cured by growing the strains overnight at 37°C without erythromycin. The cultures were subsequently diluted and plated on M17G agar without erythromycin at 30°C. The resulting colonies were streaked in parallel on M17G plates with and without erythromycin. Absence of plasmid pGhP32comXMG in Ery ^s clones was validated by PCR.

^■ Induction of natural competence in Lactococcus raffinolactis

Wild-type Lactococcus raffinolactis (i.e., L. raffinolactis strains which have not been previously engineered for the overproduction of the comX gene) were grown overnight in M17G at 30°C. 1 .5 ml of the pre-culture was diluted in 8.5 ml of fresh M17G medium to restart the culture. After 2 hours of growth, cells were washed twice in distilled water and Ο βοο was adjusted to 0.05 in CDM supplemented with either 5% (v/v) glycerol or 5% (w/v) mannitol used as potential osmo-stabilizers. 15 μg of plasmid pGhost-Core was added in 300 μΙ of inoculated medium and the culture was further incubated during 6 hours at 30°C. Cells were then spread on M17G agar plates supplemented with appropriate antibiotics and CFUs were counted after 48 hours of incubation. The transformation frequency was calculated as the number of antibiotic- resistant CFU ml ^"1 divided by the total number of viable CFU ml ^"1 .

^■ Natural competence in Lactococcus lactis subsp lactis SL12651 and SL12653 strains The L. lactis subsp. lactis SL12653 and 12651 strains were grown overnight at 30°C. Cells were washed twice in distilled water and Ο βοο was adjusted to 0.05 in M17G. Typically, 5 μg of donor DNA was added in 200 μΙ of inoculated medium (25 μg ml) and the culture was further incubated during 24 hours at 30°C. Cells were then spread on M17G agar plates supplemented with appropriate antibiotics and CFUs were counted after 48 hours of incubation at 30°C. The transformation frequency calculated exactly as described above (see Standard natural transformation assay).

The same experiments were done in SL12653 with various concentrations of donor DNA (0.5, 2.5, 5 and 25 Mg/ml)

^■ Construction ofplasmid pGhPxylTcomXIO

As a representative of the lactis subspecies, the comX gene and the promoter of the xylT gene from the 10-1 strain were chosen. The comX gene was amplified by PCR using primers FT_comXIOrecfw and FT_comXIOrecrv (PCR1 ), both containing overlapping sequences. The xylT promoter region was amplified by PCR using primers FT_PxylTIOsacllfw and FT_PxylTIOrv (PCR2). The carrying vector was amplified from plasmid pGhP32comXMG and amplified by PCR using primers FT_pGhPxylcomXIOsacllrv and FT_pGhPxylcomX (PCR3). The three PCR products were purified, mixed in an equimolar concentration and assembled by overlapping PCR using the most external primers, containing a Sacll restriction site. The amplification product was digested by Sacll and self-ligated. The resulting plasmid was named pGhPxylTcomXio.

^■ Transformation assay in SL 12653 mutants deleted for the comX gene

The comX gene of SL12653 was inactivated by exchange of their ORF by the P32-cai cassette using double crossing-over events. For this purpose, overlapping PCR products containing the P32-cai cassette flanked by two recombination arms of -1.5 kb (upstream and downstream homologous regions) were generated as previously reported. Briefly, upstream, downstream, and the P32-cai fragments were separately amplified by PCR, purified and mixed in equimolar concentration, and assembled by overlapping PCR by using the most external primers (see primers in Table 3). 5 μg of the obtained PCR product was used as donor DNA for natural transformation of strain SL12653 [pGhPxylTcomXio] (ComX ⁺ ). The correct insertion of the P32-cai cassette in the targeted locus of SL12653 transformants was validated by PCR (see primers in Table 3). To obtain the final mutant strains, the thermosensitive vector pGhPxylTcomXio was cured by growing the strains overnight at 37°C without erythromycin. The cultures were subsequently diluted and plated on M17G agar without erythromycin at 30°C. The resulting colonies were streaked in parallel on M17G plates with and without erythromycin. Absence of plasmid pGhPxylTcomXio in Ery ^s clones was validated by PCR. Thus, 3 AcomX clones of SL12653 were obtained. ^■ Xylose-induced natural transformation in SL12653.

The L. lactis subsp. lactis SL12653 [pGhPxylTcomXio] was grown overnight at 30°C. Cells were washed twice in distilled water and OD600 was adjusted to 0.05 in M17 supplemented with 1 % (w/v) xylose. Typically, 5 μg of DNA was added in 200 μΙ of inoculated medium and the culture was further incubated during 24 hours at 30°C. Cells were then spread on M17G agar plates supplemented with appropriate antibiotics and CFUs were counted after 48 hours of incubation at 30°C. The transformation frequency was calculated exactly as described above (see Standard natural transformation assay). All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described present invention will be apparent to those skilled in the art without departing from the scope and spirit of the present invention. Although the present invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in molecular biology, biochemistry, microbiology, bacteriology, or related fields are intended to be within the scope of the following claims.

REFERENCES

Bachmann, H., W. L. de, M. Kleerebezem, and J. E. van Hylckama Vlieg. 2010. Time- resolved genetic responses of Lactococcus lactis to a dairy environment. Environ. Microbiol. 12:1260-1270.

Campbell, E. A., S. Y. Choi, and H. R. Masure. 1998. A competence regulon in

Streptococcus pneumoniae revealed by genomic analysis. Mol. Microbiol. 27:929-939

David, B., Radziejwoski, A., Toussaint, F., Fontaine, L, Henry de Frahan, M., Patout, C.,van Dillen, S., Boyaval, P., Horvath, P., Fremaux, C. and P. Hols. 2017. Natural DNA transformation is functional in Lactococcus lactis subsp. cremoris KW2. Appl. Environ. Microbiol. 83(16): 1-17

Ercan, O., M. Wels, E. J. Smid, and M. Kleerebezem. 2015. Genome-wide transcriptional responses to carbon starvation in nongrowing Lactococcus lactis. Appl. Environ. Microbiol. 81 :2554-2561 .

Fontaine, L, C. Boutry, M. H. de Frahan, B. Delplace, C. Fremaux, P. Horvath, P. Boyaval, and P. Hols. 2010. A novel pheromone quorum-sensing system controls the development of natural competence in Streptococcus thermophilus and Streptococcus salivarius. J. Bacteriol. 192:1444-1454. Lee, M. S. and D. A. Morrison. 1999. Identification of a new regulator in Streptococcus pneumoniae linking quorum sensing to competence for genetic transformation. J. Bacteriol. 181 :5004-5016.

Luo, P. and D. A. Morrison. 2003. Transient association of an alternative sigma factor, ComX, with RNA polymerase during the period of competence for genetic transformation in Streptococcus pneumoniae. J. Bacteriol. 185:349-358

Martin-Galiano and de la Campa 2003. High-Efficiency Generation of Antibiotic-Resistant Strains of Streptococcus pneumoniae by PCR and Transformation. Antimicrob Agents Chemother. 47(4):1257-1261

Peterson, S. N., C. K. Sung, R. Cline, B. V. Desai, E. C. Snesrud, P. Luo, J. Walling, H.

Li, M. Mintz, G. Tsegaye, P. C. Burr, Y. Do, S. Ahn, J. Gilbert, R. D. Fleischmann, and D. A. Morrison. 2004. Identification of competence pheromone responsive genes in Streptococcus pneumoniae by use of DNA microarrays. Mol. Microbiol. 51 :1051 -1070

Terzaghi and Sandine 1975. Improved Medium for Lactic Streptococci and Their Bacteriophages. Applied Microbiology 29(6): 807-813

Todd, E.W., and L.F. Hewitt. 1932. A new culture medium for the production of antigenic streptococcal haemolysin. J. Pathol. Bacteriol. 35:973-975

Updyke, E.L., and M.I. Nickle. 1954. A dehydrated medium for the preparation of type specific extracts of group A streptococci. Appl. Microbiol. 2:1 17-1 18

Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual.

Sissler, M., Delorme, C, Bond, J., Dusko Ehrlich, S., Renault, P. and C. Francklyn. 1999. An aminoacyl-tRNA synthetase paralog with a catalytic role in histidine biosynthesis. Proc. Natl. Acad. Sci. 96:8985-8990

van Kranenburg, R., J. D. Marugg, I. I. van Swam, N. J. Willem, and W. M. de Vos. 1997. Molecular characterization of the plasmid-encoded eps gene cluster essential for exopolysaccharide biosynthesis in Lactococcus lactis. Mol. Microbiol. 24:387-397.

Ward, L. J., J. C. Brown, and G. P. Davey. 1998. Two methods for the genetic differentiation of Lactococcus lactis ssp. lactis and cremoris based on differences in the 16S rRNA gene sequence. FEMS Microbiol Lett. 166:15-20

Wegmann, U., M. O'Connell-Motherway, A. Zomer, G. Buist, C. Shearman, C. Canchaya,

M. Ventura, A. Goesmann, M. J. Gasson, O. P. Kuipers, S. D. van, and J. Kok. 2007. Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J. Bacteriol. 189:3256-3270.

Wydau, S., R. Dervyn, J. Anba, E. S. Dusko, and E. Maguin. 2006. Conservation of key elements of natural competence in Lactococcus lactis ssp. FEMS Microbiol. Lett. 257:32-42.