Methods and Means for Regulating Gene Expression

The invention relates to the field of biochemistry, molecular biology and food production. More in particular, the invention relates to methods and means for regulating gene expression. Even more in particular, the invention relates to CodY target sequences.

The Gram-positive lactic acid bacterium Lactococcus lactis is an important microorganism in dairy food production. It is part of many starter cultures used in cheese manufacturing, where its function is to degrade the milk protein casein into small peptides and amino acids (Kok and Vos, 1993). L. lactis, like other lactic acid bacteria, is a multiple amino acid auxotroph. It has a complex proteolytic system to break down the major milk protein casein into small peptides and free amino acids that are necessary for growth in this medium (Kunji et al., 1996, Christensen et al., 1999). Initial breakdown of casein is carried out by the extracellular cell wall-bound serine proteinase PrtP. Several lactococcal prtP genes have been cloned and sequenced (Kok et al., 1985, Kok et al., 1988, de Vos et al., 1989, Kiwaki et al., 1989). Although they are over 98% identical on the amino. acid sequence level, the proteinases can have quite different caseinolytic specificities (Visser et al., 1986). For the production of an active proteinase, the product of prtM, a gene that is in a back-to-back orientation with prtP, is required. The so-called maturase PrtM plays a role as an extracellular chaperone, inducing the pro-proteinase to adopt a conformation in which it is able to autoproteolytically cleave off its pro-region (Kok, 1990, Haandrikman, 1990). Peptides that are produced by the proteinase can be internalized by either one of three different transport systems. Oligopeptides are taken up by Opp, while DtpT and DtpP transport di- and three-peptides respectively (Tynkkynen et al., 1993, Foucaud et al., 1995). Intracellularly, the peptides are further hydrolyzed into smaller peptides and amino acids by the action of over 15 different peptidases (Kunji et al., 1996, Christensen et al., 1999).

Proteinase and maturase production is inhibited in peptide-rich medium (e.g. containing casitone, a tryptic digest of casein) in a number of lactococcal strains (Exterkate, 1985, Laan et al., 1993, Marugg et al., 1995, Miladinov et al., 2001). As PrtP expression is not down-regulated in strains that lack the di- and tripeptide transporter DtpT, it was hypothesized that the internal concentration of small (di-tri) peptides, or amino acids derived thereof, are important in the regulation of proteinase production (Marugg et al., 1995). The genetic information for proteinase regulation was shown to be present on a 90-bp subfragment of the prtP/prtM intergenic region encompassing the transcription start sites of both genes (Marugg et al., 1996). Disruption of an inverted repeat that is present in this region resulted in derepression of the prtP and prtM promoters in medium with a high peptide concentration.

The expression of genes of other components of the proteolytic system of L. lactis is also affected by medium composition. The expression of OppA, DtpT and DtpP is increased when cells are grown in medium with a low peptide concentration (Detmers et al., 1998, Kunji et al., 1996, Foucaud et al., 1995). Moreover, the expression of the peptidases PepX and PepN in L. lactis MG1363 was shown to be regulated in a similar way (Meijer et al., 1996). Promoters of pepC, pepN, pepO1, and pepO2 were also reported to be more active in medium with amino acids than in peptide-rich medium (Guedon et al., 2001a). In the same study, the prtP promoter was shown to be subject of a similar regulatory circuit.

Recently, a pleiotropic regulator, CodY, has been identified in L. lactis MG1363 that represses several genes involved in the processes mentioned above (Guedon et al., 2001b). CodY, was first identified in the Gram-positive bacterium Bacillus subtilis, in which it also serves as a repressor of several genes involved in proteolysis (Serror and Sonenshein, 1996b; Serror and Sonenshein, 1996a). In B. subtilis, the activity of CodY is dependent on intracellular GTP levels, thereby sensing the energy state of the cell (Ratnayake-Lecamwasam et al., 2001). For L. lactis it was shown that the repression by CodY is relieved upon a decrease in the intracellular pool of the branched chain amino acids (BCAA's) Leu, Iso and Val (Guedon et al., 2001b).

Like its B. subtilis counterpart, CodY of L. lactis contains a C-terminal helix-turn-helix DNA binding motif. In B. subtilis it has been shown that the protein is able to bind to sequences overlapping the −35 and −10 sequences of its target promoters (Serror and Sonenshein, 1996b; Fisher, Rohrer, and Ferson, 1996).

Herein we show that CodY represses its target genes by binding to specific DNA sequences upstream of the respective genes. A conserved target site was identified by analyzing upstream sequences of derepressed genes in a delta codY L. lactis MG1363 derivative, as identified in a DNA micro-array study. The present application furthermore discloses CodY target sequences from other gram-positive bacteria, like B. subtilis and Streptococcus.

Hence, the invention provides CodY target sequences that may be used in different applications to repress or derepress gene expression.

In a first embodiment, the invention provides a method for regulating the expression of a gene of interest in a host cell that comprises a CodY-like protein comprising providing said cell with a gene of interest in operable linkage with a promoter and at least one CodY target sequence.

Regulation of gene expression is a very desirable characteristic of gene expression systems. For example, when one would like to express a protein that is toxic for the used host cell, preferably a gene encoding said protein is under the control of a regulator which can be switched on or off at will. Typically, for production of such a protein, expression of the corresponding gene is suppressed until enough biomass has been obtained and then expression of said gene is obtained for example by providing an inducer. However, also expression of non-toxic proteins is preferably regulated by an induction system. Examples of these kinds of expression systems are well known in the art and hence no further elaboration on this subject is necessary. In a method according to the invention a CodY-like protein and at least one CodY target sequence, control expression of a gene of interest. Binding of a CodY-like protein to said at least one CodY target sequence results in repression of expression of the gene of interest that is under control of said CodY target sequence. In the absence of (sufficient) CodY-like protein or in the presence of non-functional (i.e. non-binding) CodY-like protein, said gene of interest is expressed. Hence, the invention provides a way for regulating gene expression. As CodY-like proteins are typically found in gram-positive bacteria, for example lactic acid bacteria, the invention preferably provides a method for regulation gene expression in gram-positive bacteria. However, it is clear to the person skilled in the art that necessary components of the method according to the invention, i.e. a CodY-like protein and a CodY target sequence may easily be transferred to for example a gram-negative bacterium.

CodY proteins show a large amount of homology in gram-positive bacteria with a low G+C content. A Blast search with the CodY amino acid sequence of L. lactis shows homology with Bacillus subtilis, Bacillus anthracis, Bacillus halodurans, Bacillus stearothermophilus, Clostridium acetobutylicum, Clostridium difficile, Enterococcus faecalis, Staphylococcus aureus, Streptococcus mutans, Streptococcus pneumoniae and Streptococcus pyogenes. Moreover, these CodY proteins all comprise a DNA binding motif, preferably a helix-turn-helix DNA binding motif. It is furthermore shown that CodY proteins comprise putative GTP binding motifs as summarised in Table 1. Furthermore, binding of these CodY proteins to their target sequences is typically under the influence of the energy level of the cell (GTP) or the intracellular pool of branched chain amino acids or the nutritional value of the medium (nitrogen source like casitone).

A CodY-like protein is typically a CodY protein or a functional equivalent and/or a functional fragment thereof, obtained/derived from a gram-positive bacterium, which CodY protein comprises the above outlined characteristics, i.e. capable of binding to a (consensus) CodY target sequence and sensitive to a change in the energy level of the cell, the intracellular pool of branched amino acids or the medium composition. Examples of CodY proteins are the CodY proteins from Lactococcus lactis (Guedon et al, 2001b)) or Bacillus subtilis (Serror and Sonenshein, 1996b; Serror and Sonenshein, 1996a). It is clear that for example a CodY protein from L. lactis can be modified without significantly changing the above outlined characteristics, for example, by introducing point mutations or (small) deletions. Hence, a CodY-like protein is a Cod protein obtained from a gram-positive bacterium such as Bacillus subtilis, Bacillus anthracis, Bacillus halodurans, Bacillus stearothermophilus, Clostridium acetobutylicum, Clostridium difficile, Enterococcus faecalis, Staphylococcus aureus, Streptococcus mutans, Streptococcus pneumoniae, Streptococcus pyogenes, and Lactococcus lactis, possibly comprising mutations which do not interfere significantly with for example the binding of said CodY-like protein to a CodY target sequence and furthermore is sensitive to the energy state of a cell, the intracellular pool of branched amino acids or the medium composition.

The location of the CodY target sequence with regard to the promoter sequence is flexible. The CodY target sequence may be either located upstream, downstream or overlapping with regard to the −35 and −10 sequences. Furthermore, at least one CodY target sequence is used in a method according to the invention. As disclosed herein within the experimental part, an increase in the number of CodY target sequences results in a more pronounced regulation of expression and hence introduction of more than one CodY target sequence is useful depending on, for example, the characteristics of the gene of interest.

The promoter used in a method according to the invention is preferably a promoter that is functional in the used host cell. For example, a promoter that is functional in a gram-positive bacterium is used, in operable linkage with a CodY target sequence and a gene of interest, for regulating expression of said gene of interest in a gram-positive bacterium. The prior art provides a large amount of promoter sequences, both from gram-positive as well as gram-negative bacteria, and hence no further elaboration on this item is necessary.

In a preferred embodiment, said promoter and/or said CodY target sequence is heterologous with regard to said gene of interest. In yet another preferred embodiment, said CodY target sequence is heterologous with regard to said promoter. Hence, the invention preferably makes use of combinations in which at least one component (i.e. promoter sequence or gene of interest or CodY target sequence) is different when compared to wild type/natural situation. The gene of interest may be an endogenous gene or a heterologous gene. For an endogenous gene that is already in operable linkage with a promoter, only at least one CodY target sequence has to be introduced (in operable linkage with said promoter and said gene). After introduction of said at least one CodY target sequence, expression of said endogenous gene will, in the presence/absence of CodY-like protein, be repressed/derepressed and hence expression of said endogenous gene is regulated. Furthermore, it is within the scope of the present application to introduce an extra copy of an endogenous gene in operable linkage with its own promoter and/or at least one CodY target sequence or with another promoter and/or at least one CodY target sequence. Hence, at least two copies of said endogenous gene are then present. A heterologous gene in operable linkage with a promoter and at least one CodY sequence may for example be introduced via a plasmid. However, it also possible to only introduce said gene of interest and further provide said gene of interest with the necessary means for homologous recombination to an endogenous gene that is under control of a CodY target sequence. In this way an endogenous gene is replaced by another gene, which is, then under control of a CodY target sequence.

The introduction of new and/or extra genetic information into a host cell may be accomplished by methods known in the art, for example by electroporation, protoplast transformation, transfection, transduction or any other known method.

Any sequence can be used as sequence of interest. Preferably, said sequence enables the production of a protein of interest not present as such or present in a (too) low concentration, in said cell. For example, a sequence/open reading frame (ORF) specifying an enzyme (protease or peptidase), a vitamin or an anti-microbial peptide is used. Preferably, said gene of interest is a gene from a gram-positive bacterium. Even more preferably, said gene of interest is a gene from a lactic acid bacterium, like Lactococcus, Lactobacillus, Streptococcus, Leuconostoc, Pediococcus, Bifidobacterium, Carnobacterium or Propionibacterium. An example of a gene of interest is a gene that encodes a protease or a peptidase or an anti-microbial peptide or a vitamin. Other examples of gene products include, but is not limited to, hydrolytic enzymes selected from proteases such as chymosin, peptidases including endopeptidases, lipases, nucleases and carbohydrases; lytic enzymes such as lysozyme or phage lysins; flavour enhacing substances; bacteriocins including nisin, pediocin and bavaracin; amino acids; organic acids; and pharmacologically active substances. Further examples comprise genes of which the products make host cells more resistant to advere conditions, for instance conditions to which micro-organisms are confronted at various stages during industrial use, e.g. starvation, lactic acid accumulation, oxygen stress, drying-stress, temperature stress. For example probiotic formula's are made more robust during and/or after production, e.g. by optimising the survival of cells of probiotic strains. As another example, the re-growth of starter cultures is made more reliable.

In a preferred embodiment the invention provides a method for regulating the expression of a gene of interest in a host cell that comprises a CodY-like protein comprising providing said cell with a gene of interest in operable linkage with a promoter and at least one CodY target sequence, wherein said CodY target sequence comprises a sequence as depicted in the upper part of FIG. 6A, or a functional equivalent and/or a functional fragment thereof. The upper part of FIG. 6A discloses a consensus CodY target sequence. In another preferred embodiment the invention provides a method for regulating the expression of a gene of interest in a host cell that comprises a CodY-like protein comprising providing said cell with a gene of interest in operable linkage with a promoter and at least one CodY target sequence, wherein said CodY target sequence comprises a sequence as depicted in FIG. 6B, or a functional equivalent and/or a functional fragment thereof. Moreover, the invention provides in Table 4 and Table 4A multiple examples of L. lactis CodY target sequences that provide non-limiting examples of combinations of W, R, D and H as depicted in FIGS. 6A and 6B. Until the present patent application, no (consensus) sequence for CodY binding was disclosed. Now that the consensus sequence and some of its variants are disclosed herein (see upper part of FIG. 6A, Table 4 and Table 4A) a person skilled in the art is very well capable of obtaining a functional equivalent and/or a functional fragment of said consensus sequence. A functional equivalent and/or a functional fragment must still be capable of binding a CodY-like protein. A functional equivalent is for example obtained by screening other bacteria for the presence of the herein disclosed CodY target sequences. For example, the present inventors have identified CodY target sequences in Bacillus subtilis, Streptococcus pneumoniae and Streptococcus agalacticiae, as disclosed herein within FIG. 6A lower part, Table 5, 6, 7 or 8. The lower part of FIG. 6A discloses the CodY target consensus sequence in B. subtilis and Table 5 and 6 show multiple examples of the typical CodY target sequences. Table 7 and 8 disclose multiple examples of Streptococus CodY target sequences. It is clear that point mutation and deletion studies lead to further functional equivalents and/or functional fragments and hence these also within the scope of the present patent application.

One embodiment of the present invention provides a method for regulating the expression of a gene of interest in a host cell that comprises a CodY-like protein comprising providing said cell with a gene of interest in operable linkage with a promoter and at least one CodY target sequence, wherein said CodY target sequence comprises an ATGTTCA sequence and an inversely repeated ATGTTCA sequence. An example of such sequence is shown in FIG. 1. As is shown in the examples, said CodY target sequence is involved in CodY-mediated regulation of PoppD. Preferably, said nucleic acid sequence comprises a spacing of about 9 base pairs between said ATGTTCA sequence and said inversely repeated ATGTTCA sequence. More preferably, said nucleic acid sequence comprises the sequence ATGTTCAGAAAATTCATGAACAT.

Based on the herein disclosed (consensus) CodY target sequences it is furthermore possible to construct for example constructs comprising two or more (identical or different) CodY-like target sequences. In this way a more stringent regulation of expression is obtained. For example a gene of interest in operable linkage with a promoter and two (identical or different) CodY target sequence is used to obtain more stringent control of expression. However, it is also possible to introduce a construct that comprises multiple CodY target sequences (with or without a promoter and/or a gene of interest) in a cell that comprises CodY regulated genes and hence a competitive binding of CodY to said construct that comprises multiple CodY target sequences and binding to a CodY target sequence in operable linkage with a gene of interest and a promoter takes place. In this way a gene of interest is derepresses and said gene of interest is expressed.

The method according to the invention allows both active as well as inactive/passive regulation of gene expression of a gene of interest. Said regulation is preferably based on influencing the binding between a CodY-like protein and at least one CodY target sequence. An example of passive/indirect/inactive regulation is a gene of interest in operable linkage with a promoter and a CodY target sequence that is introduced into a host cell that comprises CodY-like protein. During exponential growth of said host cell said CodY-like protein binds to said CodY target sequence and hence expression of said gene of interest is repressed. After the exponential phase, said CodY-like protein will release from said CodY target sequence and hence expression of said gene of interest is induced. Such an approach is extremely useful in cases in which one would like to have expression of a gene of interest after exponential growth. Active regulation of gene expression of a gene in operable linkage with a promoter and a at least one CodY target sequence is for example obtained by regulating binding of a CodY-like protein and a CodY target sequence by subjecting said cell to a change in a growth condition, preferably to a growth limiting condition like a limited availability of a nitrogen source. In case, a CodY-like protein or a functional fragment and/or a functional derivative thereof of L. lactis is used, means that result in a decrease in the intracellular pool of the branched amino acids Leu, Iso and Val results in relief of CodY repression. The CodY protein of B. subtilis is for example actively regulated by a means that influence the level of GTP in a host cell. Hence, actively subjecting a CodY-like protein comprising host cell that further comprises a gene of interest in operable linkage with a promoter and at least one CodY target sequence to a medium with a limited availability of a nitrogen source results in derepression and hence expression of said gene of interest.

In a preferred embodiment, the invention provides a method for regulating the expression of a gene of interest in a host cell that comprises a CodY-like protein comprising providing said cell with a gene of interest in operable linkage with a promoter and at least one CodY target sequence, wherein said host cell is a cell from a food production species and even more preferably a dairy food production species. Preferably, said species is selected from the gram-positive species and even more preferably said species is a lactic acid bacterium such as Lactococcus or Lactobacillus or Streptococcus or Leuconostoc or Pediococcus or Bifidobacterium or Carnobacterium. An example of a gram-positive, non lactic acid bacterium is Propionibacterium. Amongst others, these species are used in the production of food, for example in a fermentation step for the production of a dairy product. Hence, by providing these species with a gene of interest under the control of a promoter and at least one CodY target sequence and either indirectly/passively or directly/actively influencing the binding between a CodY-like protein and its target sequence results in repression or derepression (i.e regulation) of gene expression of said gene of interest. This may be used for the metabolic engineering of various catabolic pathways by a rerouting strategy consisting of the controlled overproduction and/or disruption of genes. For example, genes of which the products, directly or indirectly, are involved in the production of compounds that are involved in the formation of off-flavours during exponential growth during a (dairy) food production, are repressed by providing said genes with a CodY target sequence. Food or dairy food production species in which said genes are under the control of a CodY target sequence, will produce less (or preferably no) off-flavours and hence these production processes are improved. It has for instance become possible to alter flavour formation in cheese, yoghurt and/or other fermented (dairy) products by altering the expression of enzymes that, when present in different quantities, give rise to re-routing of specific pathways. Examples of such enzymes are enzymes involved in e.g.

1) lactose, citrate and diacetyl metabolism, and alcohol metabolism,
2) lipid degradation, modification and synthesis,
3) polysaccharide synthesis,
4) amino acid degradation,
5) protein and carbohydrate utilisation and conversion,
6) cell lysis (e.g. bacteriophage and host cell-encoded cell wall hydrolases and DEAD-box helicase proteins) and cell wall synthesis.

In an analogous way it is also possible to induce expression of a gene of interest after the exponential growth and hence provide said species with altered flavour formation, altered cell lysis capabilities or induce production of antimicrobial substances and/or health promoting substances (such as vitamins) or provide said species with means to at least in part prevent acidification of the same or another species. For the latter possibilities, a gene of interest (for example a gene involved in cell lysis or flavour formation or a gene encoding a vitamin) is placed under the control of a promoter and at least one CodY target sequence and after the end of exponential growth, CodY-like protein will be released from said CodY target sequence and hence expression of said gene is induced. Furthermore, CodY-like proteins are released from their target sequences by providing cells with for example synthetic CodY targets. Said CodY target may be added to the medium, taken up by the cells (for example B. subtilis) and the CodY-like proteins are released from their targets and will bind to the synthetic CodY targets. With a method of the invention it has for instance become possible to induce the production of antimicrobial substances (for instance antimicrobial peptides) of which the production would be detrimental during the fermentation process but is benificial after exponential growth to prevent spoilage organisms in the fermented product. A method of the invention is for instance suitable for inducing bacteriocin (e.g. nisin) production in cheese, yoghurt and/or other fermented (dairy) products after exponential growth thereby preventing that the fermenting micro-organisms are affected during fermentation.

In another aspect a method of the invention is used in order to decrease the expression of a gene in a stationary phase culture or equivalent of said culture. This is for instance done by providing a host cell with an antisense nucleic acid sequence in operable linkage with a promoter and at least one codY target sequence. In the presence of CodY, expression of said antisense nucleic acid is repressed during exponential growth. Upon transcription of said antisense nucleic acid during the stationary phase, produced RNA will bind mRNA of said undesired gene, thereby preventing translation of said undesired gene. Said undesired gene for instance comprises a gene involved in post-acidification. Said gene for instance comprises a gene involved in carbon catabolism, glucose and lactose catabolism (such as for instance glycolytic enzymes/lactate dehydrogenase) and lactose uptake. It has also become possible to prevent undesired CO₂production by inhibiting citrate catabolism, to prevent off-flavour production or re-routing of specific pathways by inhibiting expression of a gene encoding undesired proteins/peptides, and/or to extend the shelf life of fermented (dairy) products by decreasing metabolism, ((post-)acidification, glycolysis, lipolysis, proteolysis, peptidolysis) and/or cell lysis.

Hence, with a method of the present invention expression of a gene can be regulated at any stage of growth, for instance during exponential growth and/or during the stationary phase. In a further aspect a method of the invention is used in order to decrease expression of a gene, wherein binding of a CodY-like protein to a CodY target sequence is regulated by subjecting said cell to a change in a growth condition. Preferably, said cell is subjected to a growth limiting condition. In a preferred embodiment said growth limiting condition is a limited availability of a nitrogen source.

Now that the invention discloses multiple (consensus) CodY target sequences it is furthermore part of the invention to modify endogenous CodY sequences, to for example increase or decrease (or more generally alter) binding of CodY to one of its endogenous target sequences and hence production of an endogenous gene that is under control of the CodY/CodY target sequence regulation may be altered. For example, proteins which expression is under the control of CodY (and hence are not or hardly not produced during the exponential growth phase) but whose product provides advantageous uses when present during exponential growth may now be amended such that binding of CodY to said CodY target sequence is not or hardly not possible under the exponential growth phase conditions. Hence, said protein is expressed during exponential growth and advantage is taken of the properties of said expressed protein.

In case a host cell does not comprise or does not comprise enough CodY-like protein or comprises non-functional (i.e. CodY protein that is not capable of binding to a CodY target sequence) CodY-like protein, the invention furthermore provides a method for regulating the expression of a gene of interest in a host cell that comprises a CodY-like protein comprising providing said cell with a gene of interest in operable linkage with a promoter and at least one CodY target sequence wherein said host cell is further provided with a nucleic acid encoding a CodY-like protein. Examples of CodY sequences are already outlined above and hence no further details are provided. In case a host cell does not comprise/express enough CodY-like protein said cell may be provided with either endogenous and/or heterologous CodY-like protein.

In yet another preferred embodiment, the invention provides an isolated or recombinant nucleic acid that comprises at least one CodY target sequence or a functional fragment and/or a functional equivalent thereof. It is clear from FIG. 6A (lower and upper part), FIG. 6B and Tables 4 to 8, that the length of said nucleic acid generally comprises about 15 to 30 nucleotides. A functional fragment and/or a functional equivalent thereof is defined as a fragment and/or equivalent that is capable of binding a CodY-like protein. A functional fragment is for example obtained by introducing an N-, C- or internal deletion. Examples of suitable CodY target sequences are provided herein (FIG. 6A, FIG. 6B and Tables 4 to 8). A nucleic acid that comprises multiple (either identical or different) CodY target sequences is also included herein. Furthermore, artificial or synthetic CodY target sequences are also included herein.

In a preferred embodiment said isolated or recombinant nucleic acid that comprises at least one CodY target sequence or a functional fragment and/or a functional equivalent thereof, further comprises a promoter sequence and/or a promoter sequence in operable linkage with a gene of interest.

In case a host cell does not comprise or does not comprise enough endogenous CodY-like or comprises non-functional CodY protein, the invention furthermore provides an isolated or recombinant nucleic acid that comprises at least one CodY target sequence or a functional fragment and/or a functional equivalent thereof wherein said nucleic acid further comprises a gene encoding a CodY-like protein or a functional fragment and/or a functional equivalent thereof.

In a preferred embodiment, said promoter and/or said at least one CodY target sequence is heterologous with regard to said gene of interest and in another preferred embodiment, said CodY target sequence is heterologous with regard to said promoter.

Again, as already outlined above, said gene of interest may either be an endogenous and/or a heterologous gene. Preferably, said gene of interest is a gene from a gram-positive bacterium, such as a gene from a lactic acid bacterium for example Lactococcus or Lactobacillus or Streptococcus or Leuconostoc or Pediococcus or Bifidobacterium or Carnobacterium. An example of a gram-positive, non lactic acid bacterium is Propionibacterium.

A gene of interest may be any gene, preferably said gene of interest encodes a protease or a peptidase or an anti-microbial peptide or a vitamin. Other suitable examples include hydrolytic enzymes selected from proteases such as chymosin, peptidases including endopeptidases, lipases, nucleases and carbohydrases; lytic enzymes such as lysozyme or phage lysins; flavour enhacing substances; bacteriocins including nisin, pediocin and bavaracin; amino acids; organic acids; and pharmacologically active substances.

In a preferred embodiment, the invention provides an isolated or recombinant nucleic acid that comprises at least one CodY target sequence or a functional fragment and/or a functional equivalent thereof, wherein said CodY target sequence comprises a sequence as depicted in FIG. 6A and/or FIG. 6B, or a functional equivalent and/or a functional fragment thereof. The upper part of FIG. 6A, and FIG. 6B disclose a consensus CodY target sequence. Moreover, the invention provides in Table 4 and Table 4A multiple examples of L. lactis CodY target sequences that provide non-limiting examples of combinations of W, R, D and H as depicted in FIG. 6A and FIG. 6B. Until the present patent application, no (consensus) sequence for CodY binding was disclosed.

In a further preferred embodiment, the invention provides an isolated or recombinant nucleic acid that comprises at least one CodY target sequence or a functional fragment and/or a functional equivalent thereof, wherein said CodY target sequence comprises a sequence as depicted in Table 4, Table 4A, Table 5, Table 6, Table 7 and/or Table 8, or a functional equivalent and/or a functional fragment thereof.

In another preferred embodiment the invention provides an isolated or recombinant nucleic acid that comprises at least one CodY target sequence or a functional fragment and/or a functional equivalent thereof, wherein said CodY target sequence comprises an ATGTTCA sequence and an inversely repeated ATGTTCA sequence. Preferably, said nucleic acid sequence comprises a spacing of about 9 base pairs between said ATGTTCA sequence and said inversely repeated ATGTTCA sequence. More preferably, said nucleic acid sequence comprises the sequence ATGTTCAGAAAATTCATGAACAT.

Now that a consensus sequence and some of its variants are disclosed herein (see FIG. 6B, upper part of FIG. 6A, Table 4 and Table 4A) a person skilled in the art is very well capable of obtaining a functional equivalent and/or a functional fragment of said consensus sequence. A functional equivalent and/or a functional fragment must still be capable of binding a CodY-like protein. A functional equivalent is for example obtained by screening other bacteria for the presence of the herein disclosed CodY target sequences. For example, the present inventors have identified CodY target sequences in Bacillus subtilis, Streptococcus pneumoniae and Streptococcus agalacticiae, as disclosed herein within FIG. 6A lower part, Table 5, 6, 7 or 8. The lower part of FIG. 6A discloses the CodY target consensus sequence in B. subtilis and Table 5 and 6 show multiple examples of the typical CodY target sequences. Table 7 and 8 disclose multiple examples of Streptococus CodY target sequences. It is clear that point mutation and deletion studies lead to further functional equivalents and/or functional fragments and hence these also within the scope of the present patent application.

Moreover, the present inventors have identified alternative sequences in the upstream region of CodY regulated genes that may also be included in a method for regulating the expression of a gene of interest in a host cell that comprises a CodY-like protein (FIG. 7). These sequences may also be used in a method and/or nucleic acid according to the invention.

In another embodiment the invention provides a vector comprising a nucleic acid as described above. Said vector may further be provided with means for homologous recombination. With these means said at least one CodY target sequence and/or a gene of interest and/or a promoter and/or a gene encoding CodY-like protein may be integrated into the genome of a cell and hence a more stable situation may be obtained. In yet another embodiment, the invention provides a gene delivery vehicle comprising a nucleic acid or a vector according to the invention. Gene delivery vehicles are well known in the art and hence no further details are provided on this subject matter.

In a further embodiment the invention provides a host cell that comprises a nucleic acid, a vector or a gene delivery vehicle according to the invention. Preferably, said host cell is a cell from a food production species and even more preferably said host cell is a cell from a dairy food production species. Non-limiting examples of said species are gram positive lactic acid bacteria such as Lactococcus or Lactobacillus or Streptococcus or Leuconostoc or Pediococcus or Bifidobacterium or Carnobacterium. An example of a gram positive, non lactic acid species is Propionibacterium.

In another embodiment, the invention provides use of at least one CodY target sequence for regulating the expression of a gene of interest. Preferably, said at least one CodY target sequence is selected from FIG. 6A. FIG. 6B or Tables 4 to 8. For example, the use of at least one CodY target sequence in operable linkage with a promoter and a gene of interest in a Cod-like protein comprising host cell result, for example under exponential growth in repression of expression of said gene of interest. After exponential growth, CodY protein will be released from its target, resulting in depression of expression of said gene of interest.

In yet another embodiment the invention provides a method for producing a food product comprising a nucleic acid or a vector or a gene delivery vehicle or a host cell as described above. Preferably said food product is a dairy food product. As a non-limiting example, the use of a host cell is described in more detail. A lot of (dairy) food production processes involve the use of a (fermenting) host cell. These host cells may now be manipulated with regard their protein products. For example, genes of which the products, directly or indirectly, are involved in the production of compounds that are involved in the formation of off-flavours during exponential growth during a (dairy) food production, are repressed by providing said genes with a CodY target sequence. Food or dairy food production species in which said genes are under the control of a CodY target sequence, will produce less (or preferably no (detectable)) off-flavours during exponential growth and hence these production processes are altered. In an analogous way it is also possible to induce expression of a gene of interest after the exponential growth of said host cell and hence provide said species with altered flavour formation, altered cell lysis capabilities or induce production of antimicrobial substances and/or health promoting substances (such as vitamins) or provide said species with means to prevent acidification of the same or another species. For the latter possibilities, a gene of interest (for example a gene involved in cell lysis or a gene involved in flavour formation or a gene encoding a vitamin) is placed under the control of a promoter and at least one CodY target sequence and after the end of exponential growth, CodY-like protein will be released from said CodY target sequence and hence expression of said gene is induced.

Furthermore expression of undesired genes during the stationary phase can be, at least in part, decreased.

With regard to a fluid dairy product a method to at least in part decrease lysis of bacteria and/or acidification after production of said fluid diary product, i.e. after exponential growth of the used bacteria, is very advantageous with regard to the shelf life of said fluid dairy product. First, genes that are capable of at least in part preventing lysis and/or acidification are identified. After identification, such genes are placed under the regulation of at least one CodY target sequence. Said genes are expressed and hence lysis and/or acidification is at least in part prevented (and more preferably completely inhibited) and hence the shelf life of said product is increased.

Moreover, in case integration of said nucleic acid or vector is desired, use may be made of food grade integration techniques (for example see Leenhouts, 1995, herein incorporated by reference).

Preferably, the invention provides a method for producing a (dairy) food product comprising a nucleic acid or a vector or a gene delivery vehicle or a host cell as described herein, wherein said dairy product is a cheese or a fermented milk product. The production of a lot of dairy products involves fermentation of lactic acid bacteria and hence the application of modified host cells as described herein are particularly advantageous. The term “dairy product” include but is not limited to cheese, fluid dairy products like milk and yoghurt, fermented milk product, ice cream, butter, buttermilk, margarine and milk powder.

In another embodiment the invention provides food or a dairy food, such as a cheese or a fermented milk product, obtainable by a method according to the invention. Such a product comprises for example a different or extra taste or comprises specific compounds/structures (such as health improving compounds as vitamins) not present in food or dairy food product not obtained according to a method of the invention. Food or dairy food products prepared by a method according to the invention may comprise different amounts or different kinds of enzymes, peptides, amino acids, flavour enhancing or pharmacologically active substances or organic acids.

In yet another embodiment, the invention provides a method for at least in part preventing the formation of off-flavours during a process for the production of a (dairy) food product, comprising providing at least one CodY target sequence in operable linkage with a gene which product is, directly or indirectly, involved in the formation of off-flavours.

Now that the present inventors have disclosed CodY target sequences, interesting leads are provided in the fight against food-spoilers and pathogens.

PpmA is a recently identified pneumococcal protein with significant sequence homology to the proteinase maturation protein (PrtM) of lactic acid bacteria. PrtM is a trans-acting protein involved in the processing of precursors of serine protease PrtP into active enzymes and belongs to the family of peptidyl-prolyl cis/trans isomerases. These enzymes are thought to assist in protein folding by catalyzing the cis/trans isomerization of the petidyl-prolyl bonds in peptides and proteins. The pneumococcal proteins(s) that is activated by PpmA is currently unknown. PpmA of Streptococcus pneumoniae was demonstrated to be involved in virulence. Inactivation of ppmA significantly reduced the virulence of strain D39 for mice as judged by the survival time after intranasal challenge. The present inventors identified a CodY target sequence upstream of ppmA (Table 7) indicating that the expression of this gene probably is under the control of CodY. Hence, the invention provides a method for regulating the expression of ppmA.

Spore-forming bacteria (e.g. Bacillus) can cause serious problems in industrial food fermentations as the spores can survive most processing conditions. In Bacillus subtilis it was shown that the target genes of CodY generally encode proteins useful to the cell in adapting to poor nutritional conditions, but also include several genes whose expression is critical to the acquisition of genetic competence and the initiation of sporulation. The present invention provides a method for influencing the expression of these genes.

In Clostridium difficile, the synthesis of two toxin proteins responsible for antibiotic-associated colitis and pseudomembranous colitis were shown to be dependent on a RNA polymerase sigma factor TxeR (Sonenshein, unpublished). Both TxeR and the toxin proteins were not synthesized in exponential phase cells, probably due to the action of CodY as it was shown to bind to the toxin regulatory region.

The invention will now be illustrated by means of the following, non-limiting examples.

EXPERIMENTAL PART
Materials and Methods

Bacterial Strains, Plasmids and Growth Conditions

The strains and plasmids used in this study are listed in Table 9. Escherichia coli was grown in TY medium at 37° C. with vigorous agitation or on TY medium solidified with 1.5% agar, containing 100 μg of erythromycin per ml when needed. 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal) was used at a final concentration of 40 μg/ml. L. lactis was grown at 30° C. in M17 broth or on M17 medium solidified with 1.5% agar, supplemented with 0.5% glucose. When needed, erythromycin, chloramphenicol and X-gal were added at final concentrations of 5 μg, 5 μg and 80 μg per ml, respectively. Chemically defined medium (CDM) was prepared according to Poolman and Koning (1988).

DNA Preparation, Molecular Cloning and Transformation

Routine DNA manipulations were performed as described by Sambrook et al.(1989). Total chromosomal DNA from L. lactis MG1363 was extracted as described previously. Plasmid DNA was isolated by the alkaline lysis procedure described by Sambrook et al (1989). Minipreparations of plasmid DNA from E. coli and L. lactis were made using the High Pure Plasmid isolation Kit from Roche, with minor modifications for L. lactis. Restriction enzymes and T4 DNA ligase were purchased from Roche. PCR amplifications were carried out using Pwo DNA polymerase for cloning fragments and Taq DNA polymerase for checking DNA insert sizes in plasmids from transformants. Electrotransformation of E. coli and L. lactis were performed with a Bio-Rad Gene Pulser (Bio-Rad Laboratories, Richmond, Calif.).

RNA Preparation and Primer Extension

The opp transcript was subjected to primer extension analysis using the oligonucleotide sto14 (CTTGCCATGGAATCACCCG) essentially as described previously (Buist et al, 1997). In the reactions, 30 μg of total RNA that was isolated from L. lactis MG1363 cells as described (van Asseldonk et al, 1993) was used as template. A DNA sequence ladder was obtained using the T7 sequencing kit (Amersham Pharmacia Biotech, Little Chalfont, United Kingdom) according to the manufacturers' descriptions.

Cloning of oppD Promoter Fragments

In order to study the regulation of promoter strength upstream of the oppD a deletion analysis of the respective promoters was carried out. Combinations of oligonucleotides oppl (5′ GCTCTAGACACTCACTTGTTTTGCTTCC 3′), opp2 (5′ AACTGCAGGAAAATTCATGAACATACC 3′), opp1-opp3 (5′ AACTGCAGTAAAACAATAATAAAAGCAG 3′), opp1-opp4 (5′ AACTGCAGGATAATAAAATTTGGACTG 3′), opp1-opp14 (5′ AACTGCAGCGTAATGTTCAGAAAATTC 3′), opp1-opp15 (a) (5′ AACTGCAGCGTAATATTTAGAAAATTCATGAACATACC 3′) and opp1-opp15 (b) (5′ AACTGCAGCGTACTGTGCCGAAAATTCATGAACATACC 3′) were used to amplify chromosomal DNA from L. lactis MG1363 in order to obtain fragments encompassing the oppD promoter. The PCR products were digested with XbaI and PstI and transcriptionally fused upstream of the promoterless lacZ gene in the integration vector pORI13 (Sanders et al., 1998), also digested with the same enzymes. The resulting plasmids were called pORIopp2, pORIopp3, pORIopp4, pORIopp14, pORIopp15 (a) and pORIopp15 (b). All pORI constructions were preformed in E. coli EC101 which contains a chromosomal copy of the lactococcal repA gene needed for replication. They were then transformed into L. lactis LL108 and/or LL302 which contain multiple and single chromosomal copies of repA, respectively.

Random Mutagenesis of oppD Promoter Region

PCR fragments encompassing the oppD promoter region containing randomly introduced base pair substitutions were obtained essentially as described (Spee, de Vos, and Kuipers, 1993). Chromosomal DNA isolated from L. lactis MG1363 cultures were used as a template in the amplification step. Subsequently, the obtained variants were cloned into plasmid pORI13 and introduced into L. lactis LL108 as described above. Mutants showing distorted blue coloring on plates containing X-gal were selected and analyzed in more detail as described in results.

Construction of a codY Deletion Strain.

A 1400 bp EcoRI/HinDIII chromosomal fragment of L. lactis MG1363, containing codY, was subcloned in pUC19. The resulting plasmid was digested with SnaBI and subsequently selfligated. In this way, 423 bp were deleted from codY The oligonucleotides cod280A (5′ GGGAATTCGGATTGTCTATCTGCCTCG 3′) and cod280B (5′ GGGGGATCCAGATCTGACCATGATTACGCCAAGCTT 3) were used to amplify the ΔcodY-containing fragment. PCR product was digested with EcoRI/BamHI (restriction sites are underlined in the oligonucleotide sequence) and ligated into corresponding sites in pORI280. The resulting plasmid, pORIΔcodY, was introduced together with pVE6007 into L. lactis MG1363. As this strain does not contain the repA gene, selection for growth in the presence of erythromycin and increased temperature (37° C.) forces pORIΔcodY to integrate into the chromosome by homologous recombination. A number of integrants were subsequently grown for about 30 generations under nonselective conditions allowing a second recombination event to occur, which results in either the deletion or the wild-type gene codY. The ΔCodY mutation was confirmed by PCR.

β-Galactosidase Activity Assay

In vivo β-galactosidase (β-gal) assays were carried out in a Tecan microplate reader. Overnight cultures of L. lactis grown in GM17 were washed twice in 0.9% NaCl before inoculation to 2.5% in 200 μl of the appropriate medium containing erythromycin (5 μg/ml) for maintenance of pORI13 in L. lactis LL108/LL302 and erythromycin and chloramphenicol (2.5 μg/ml each) (Leenhouts et al., 1996). The media also contained the β-gal substrate 2% β-triiluoromethylumbelliferyl β-D-galactopyranoside (Molecular probe T-657). Multilabelling experimental data (absorbance and fluorescence measurements) were processed using the Magellan software program. β-Gal production due to the transcription driven from the oppD upstream region was calculated as a function of light emission. β-Gal assays were performed throughout the growth of L. lactis grown in media in which growth rates differ significantly as a function of the nitrogen source i.e. CDM 0.2% casitone and CDM 2% casitone and measured of the culture. β-Galactosidase activities were determined in permeabilized cell suspensions as described previously (Israelsen et al, 1995). β-Galactosidase enzyme activities, calculated as an average of three independent experiments, were expressed in arbitrary units (Miller, 1972).

Overproduction and Purification of His₆-CodY.

The chromosomaly located codY of L. lactis MG1363 was amplified by PCR with the oligonucleotides HC-5 (5′ CTAGACCACCATGGGG CATCACCATCACCATCACGTGGCTACATTACTTGAAAAAACACG 3′), introducing the underlined NcoI restriction enzyme site upstream of the hexa-histidine tag (italic) and HC-6 (5′ CTAGTCTAGATTAGAAATTACGTCCAGCAAGTTTATC 3′), introducing the underlined XbaI restriction enzyme site downstream of the stop codon (italic) of codY. The purified 833-bp PCR product was digested with NcoI and XbaI and ligated into the corresponding sites of pNZ8048, downstream of the nisin-inducible P_nisA. The resulting plasmid, pNH6CodY, was introduced in L. lactis NZ9000 to enable nisin induction of his6-codY, as described (de Ruyter, Kuipers, and de Vos, 1996; Kuipers et al., 1998). His6-CodY was isolated by affinity chromatography in an FPLC procedure (Amersham Pharmacia Biotech) using Ni-NTA agarose (Qiagen GmbH, Hilden, Germany).

Electrophoretic Mobility Shift Assays (EMSA's)

Gel retardation experiments were carried out essentially as described by Ebbole and Zalkin (Ebbole et al., 1989). Purified PCR products (2 μg) were end-labelled with polynucleotide kinase (Amersham Pharmacia Biotech) for 1 h at 37° C. using 30 μCi [γ-³²P]-ATP (Amersham Pharmacia Biotech) in a volume of 20 μl. Reactions were stopped by incubating the mixtures for 10 min at 70° C. Binding studies were carried out in 20 μl reaction volumes containing 20 mM Tris-HCl (pH 8.0), 8.7% (v/v) glycerol, 1 mM EDTA (pH 8.0), 5 mM MgCl₂, 100 mM KCL, 0.5 mM DTT, labelled DNA fragment (3000 cpm), and purified His6-CodY protein (50-400 ng). BSA (1 μg) and poly(dI-dC) (Amersham Pharmacia Biotech) were added to the reaction mixtures in order to reduce non-specific interactions. After incubation for 15 min at 30° C., samples were loaded onto a 4% polyacrylamide gel. Electrophoresis was performed in the Protean II Minigel System (Bio Rad Laboratories B. V., Veenendaal, The Netherlands) using a gradient (0.5× to 2×) of TAE buffer (Sambrook, Fritsch, and Maniatis, 1989) at 150 V for 1.5 h. Gels were dried and used for autoradiography at −80° C. using Kodak XAR-5 films and intensifying screens.

Preparation of Cells for Transcriptome Analysis

Cells were grown at 30° C. in GM17 supplemented with 0.5% glucose. Cells were grown till mid-exponential phase (OD600˜1.0). Approximately 5×10⁹cells (50 ml culture) were harvested by centrifugation for 5 min at 10.000 rpm and 4° C. Cells were resuspended in 2 ml ice-cold growth media and divided over 4 screw-cap tubes with rubber seal. After the addition of 500 μl Phenol/Chloroform, 30 μl 10% SDS, 30 μl 3 M NaAc (pH5.2) and 500 mg glass-beads (diameter 75-150 μm), cells were frozen in liquid nitrogen and stored at −80° C. or immediately used for RNA isolation.

Transcriptome Analysis

The DNA micro array experiments were essentially performed as described earlier (Kuipers et al., 2002), with the following modifications.

RNA Isolation

For each RNA isolation, one aliquot of the stored cell samples was used. Cells were disrupted by mechanical force using the Savant FastPrep FP120 system (Omnilabo) for 40 seconds at setting 5.0. Subsequently, RNA was extracted using the Roche “High Pure RNA Isolation Kit” according to the provided protocol. RNA yield and quality were determined spectrophotometrically and by performing a RNA 6000 Nano Labchip assay (Caliper Inc.) on the Agilent 2100 Bioanalyzer (Agilent Technologies, Amstelveen, the Netherlands) according to the manufacturers description respectively.

cDNA Labeling

Single-strand reverse transcription (amplification) and indirect labeling of 25 μg of isolated total RNA with either Cy3- or Cy5-dye were done with the Amersham CyScribe Post Labelling Kit according to the manufacturers protocol and, subsequently, used for hybridization.

Hybridisation and Scanning

Sylilated slides (Cel Associates) on which 2145 amplicons of L. lactis strain IL1403 were spotted in duplicate were used in the hybridization procedure. In addition, the slides contained 96 amplicons from L. lactis strain MG1363. Slides were pre-hybridized in Ambion SlideHyb buffer for 15 min at 40° C. in a Genomic Solutions Hybstation. After removal of the pre-hybridization buffer, 10-25 μl of the Cy3/Cy5-labeled cDNA mix in 150 μl Ambion SlideHyb buffer I was added and incubated for 1 h at 42° C. and finally for 16 h at 40° C. Afterwards, the hybridized slides were washed for 1 min in 2×SSC, 0.5% SDS and 5 min in 1×SSC, 0.25% SDS. The slides were scanned using a confocal laser scanner GeneTAC LS IV).

Signal Analysis

After scanning of the slides with the GeneTAC LS IV, individual spot intensities were determined. The raw data, along with the scanning image were stored in the Molecular Genetics Information System (MolGenIS). A grid definition was made to enable the spot analysis software Array Pro (Phoretix) to produce tables containing gene names and signal intensities. Using the program Excel Microsoft corporation), signal intensities were corrected for background and the ratios in signal intensity between the different samples were determined.

DNaseI Footprinting Analysis

DNaseI footprinting was performed essentially according to the description supplied with the Sure Track Footprinting Kit (Amersham Pharmacia Biotech). The DNA fragments were prepared by PCR, using Expand DNA polymerase (Amersham Pharmacia Biotech) and the oligonucleotides opp1 and opp3, one of which was first end-labeled with T4 polynucleotide kinase (Amersham Pharmacia Biotech) and [γ-³²P]ATP as described by the manufacturer. Binding reactions were identical to those used in EMSAs, in a total volume of 40 μl and in the presence of approximately 150,000 cpm of DNA probe. DNAseI footprinting experiments were then performed as described previously (Hamoen et al, 1998)

In Vitro Protein Cross-linking 5

Cross-linking reactions were performed in 1× cross-linking buffer (100 mM KCl, 15 mM Tris-HCl pH 7.5) in a total volume of 40 μl, containing 300 ng of purified H6-CodY, and, where indicated, GMP (1 mM) or GTP (1 mM). Formaldehyde was used as the cross-linking agent at a final concentration of 1% (v/v), with a 10 min incubation step at room temperature. Cross-linking reactions were stopped by the addition of 20 μl of 2×SDS gel loading buffer [4% SDS, 10% 2-mercaptoethanol, 20% glycerol, 100 mM Tris-HCl (pH 6.0)]. Samples were boiled for 5 min before separation by SDS polyacrylamide (10%) gel electrophoresis (Laemmli, 1970). SDS polyacrylamide gels were stained with Coomassie Brilliant Blue (Bio-Rad).

EXPERIMENTAL PART
Results

Determination of the Transcription Start Site of oppD.

It has been demonstrated that the genes of the oligopeptide permease system, encoded in the oppDFBCA-pepO1 locus of L. lactis MG1363, are transcribed polycistronically. Upstream of both oppD and oppA regions are present that could serve as promoter elements. To determine the location of the promoter upstream of oppD, the transcription start site (TSS) was determined. The opp transcript was analyzed by primer extension, using RNA that was isolated from exponentially growing MG1363 cells. The mRNA 5′ end corresponds to an adenine residue located 35 bases upstream of the translation start codon AUG of oppD. The −35 sequence (TTGCAA) is separated by a consensus 17 bases from the −10 region (TATACT) and a proper lactococcal ribosome binding site; GAGG is also present. The sequence upstream of oppD contains two regions of dyad symmetry centered around position −135 (−14.0 kcal/mol) and −62 (−5.6 kcal/mol) relative to the oppD transcriptional start site, respectively.

CodY Specifically Binds to the oppD Upstream Region.

In order to examine whether L. lactis CodY directly interacts with upstream DNA sequences of its main target known so far, oppD, in vitro DNA binding studies were performed. For this purpose, histidine-tagged CodY was overexpressed using the nisin inducible gene expression system (Kuipers et al., 1998) and subsequently purified to apparent homogeneity. A radioactively labeled PCR fragment spanning the oppD upstream region (FIG. 1) was used as a probe. The electrophoretic mobility shift assays (EMSA's) clearly showed that purified H6-CodY is capable of binding directly to a region encompassing the oppD promoter (FIG. 2). Multiple retarded fragments were observed, indicating that, probably, multimerization of H6-CodY on the oppD promoter occurs.

Upon gradually increasing the amount of H6-CodY from 10 to 100 ng, four distinct bands can be observed, indicating a tetrameric state of the protein. In most of our DNA binding experiments, a band corresponding to single stranded probe (s.s. DNA) was observed irrespective of the presence of H6-CodY. The occurrence of this denatured DNA probably results from the high AT content of the opp promoter region. No H6-CodY binding occurred when DNA fragments, with similar AT contents, were used that were obtained from internal gene segments (e.g. from comg of B. subtilis), indicating that H6-CodY binding to PoppD is specific (data not shown).

CodY Regulates the Expression of oppD by Binding to a Specific Upstream Sequence.

The upstream oppD region contains a small sequence that is inversely repeated with a spacing of 9 base pairs in between (FIG. 1). This region of dyad symmetry is located just upstream of the −35 promoter sequence. To determine whether this region is important for the interaction with CodY, a stepwise deletion analysis of the oppD upstream region was performed. Radioactively labeled deletion fragments of the region, obtained by PCR, were incubated with H6-CodY. As shown in FIG. 3, the fragments with an extended deletion of part of the oppD upstream region showed altered binding of CodY. Two truncated fragments, shortened from the 5′-end of the oppD upstream region contained in opp162, were obtained by PCR and examined for H6-CodY binding (FIG. 3A and 3B). Probe 2, spanning the region from −111 to +75, was still bound by H6-CodY, suggesting that nucleotides that are critical for CodY binding must reside downstream of the 5′-end of this probe. When a 160-bp DNA fragment was used, of which the 5′-end coincides with the center of the inverted repeated closest to the RBS of oppD (FIG. 1B), no binding of H6-CodY was observed, irrespective of the amount of protein added (probe 1 in FIG. 3B).

As the fragments used in the EMSA's were also cloned upstream of the promoterless lacZ gene in plasmid pORI13, the in vivo regulation of a downstream reporter gene (lacZ) could be determined by performing β-galactosidase (β-gal) assays in a chemically defined medium (Poolman and Konings, 1988) containing 2% of casitone as a nitrogen source. It was shown that deletion of the sequence abolished medium dependent repression of lacZ expression. the fragments were fused upstream of the promoterless lacZ gene in plasmid pORI13 (Sanders et al, 1998) and introduced in L. lactis LL108. β-Galactosidase activities in exponential phase cells growing in CDM supplemented with 2% casitone, where strong CodY-mediated repression is ensured, correlated with the observed binding pattern (FIG. 3C), indicating that at least part of an operator site for CodY must rely in a region between positions −111 and −68 relative to the oppD TSS.

The introduction of base substitutions in the upstream half-site of the inverted repeat gave rise to both weaker binding of H6-CodY and resulted in derepression of the promoter as shown by gel retardation analysis and β-gal assays, respectively (FIG. 4).

H6-CodY Protects an Extended Region of the oppD Promoter.

Although the EMSA experiments using truncated PoppD DNA fragments pointed to a specific region that is important for CodY binding, the actual area facilitating binding was rather large (position −68 to −111). Moreover, the assays did not exclude the possibility that more downstream sequences could contribute to CodY binding. Therefore, complex formation of H6-CodY with the oppD promoter region was investigated by DNaseI footprinting experiments, using the labeled promoter fragment (opp162) and binding conditions as used for the EMSAs (FIG. 10). H6-CodY binding results in the protection of bases extending from the −80 to −20 and −80 to −10 positions relative to the transcription start site of the upper and lower strand, respectively. In addition to these protected regions, both DNA strands contained hypersensitive sites when they were incubated with DNaseI in the presence of H6-CodY. These results show that H6-CodY binds to a region encompassing the −35 to −10 sequences of the promoter of oppD.

A Region in the oppD Promoter Containing an Inverted Repeat is Important for CodY-mediated Regulation.

A closer inspection of the area in the oppD promoter to which CodY binds revealed the presence of a short sequence (ATGTTCA) that is inversely repeated (IR) with a spacing of 9 bp between the partners (FIG. 1). This region of dyad symmetry is located 18 bp upstream of the −35 sequence and is entirely present in probes 2 and 3 to which H6-CodY bound (FIG. 3). The fact that H6-CodY was unable to form a protein-DNA complex when a probe was used that lacks the upstream arm of this IR (probe 1 in FIG. 3) implies that this area might serve as an operator site for CodY on PoppD. To study this region in more detail, site directed mutations were introduced by PCR using combinations of oligonucleotide opp1 with oligonucleotides opp14 (WT), opp15(a), opp(15b) or opp2, respectively (FIG. 4A). The PCR products were ligated upstream of the promoterless lacZ reporter gene in pORI13 and introduced into L. lactis LL108. Introducing base substitutions in the upstream arm of the repeat (opp15(a) and opp15(b)) resulted in both weaker binding of H6-CodY (FIG. 4C) and in derepression of PoppD-driven lacZ expression (FIG. 4D). When the unchanged half-site was replaced by an unrelated sequence (an XbaI endonuclease site, present in opp2), repression was reduced approximately 30-fold (in cells growing exponentially in rich medium) and H6-CodY binding was completely abolished (as shown in FIG. 3). Converting both the C and G residues in this region to adenines resulted in a reduction of repression of about 7-fold (opp15(a)), whereas changing 3 out of 6 bases (opp15(b)) led to a derepression of expression of more than 20 times. These results were in accordance with those obtained from gel retardation analyses (FIG. 4C), where the order of affinity of H6-CodY for the probes proved to be: WTprobe>opp115(a)>opp15(b). In case of the latter probe, hardly any protein-DNA complexes were present and all intermediate complexes that were observed with the WT and opp15(a) fragments were absent.

Random Mutation analysis of the oppD Upstream Region.

In order to identify bindings sites of CodY in the oppD upstream region, random mutation was carried out on the smallest oppD promoter fragment that is still bound by CodY (see FIG. 3). By choosing PCR conditions that allow mismatches to occur during DNA amplification, DNA fragments spanning the oppD promoter region were obtained containing randomly introduced base pair substitutions. The fragments were restricted using the appropriate restriction enzymes, cloned upstream of the promoterless lacZ reporter gene in pORI13 and introduced in L. lactis LL108. Transformants that show a derepressed phenotype appear as white or light blue colonies on agarplates containing excess nitrogen sources (2.5% of casitone) and X-gal. Mutants that showed a distorted blue coloring on plates were tested for the ability to complex with CodY in a gel retardation experiment. The strength of binding was determined by comparing the amount of shifted mutated DNA fragment as compared to that of the corresponding wild type fragment (FIG. 5). Weaker binding to all of the mutated promoter fragments was observed. Strikingly, all the mutants obtained carried substitutions in one or both of the half-sites of the inverted repeat present in the oppD upstream region, indicating the importance of this sequence in CodY binding. Sequence analysesof the PoppD variants obtained in this study revealed that all of them carried one or more base pair substitution(s), of which at least one is located in the region from −82 to −56 relative to the TSS of oppD. This, again, is an indication of the importance of this region for CodY binding.

Identification of Additional CodY Targets.

In order to identify additional genes that are regulated by CodY, the transcriptional profile of wild-type (WT) L. lactis MG1363 was compared with that of a L. lactis MG1363 strain containing a 423 bps internal deletion in the codY gene using DNA micro arrays containing genes of L. latis IL1403. These studies revealed several differentially expressed genes in the delta codY strain. The genes of which the expression is increased most significantly in the delta codY strain are listed in Table 2. The genes of which the expression is decreased most significantly in the absence of a CodY-like protein are listed in Table 3. As this increased expression (Table 2) could be a direct effect of the absence of CodY (derepression), the upstream regions were examined- for the presence of conserved nucleotide sequences. It was found that many of these genes contain an upstream sequence that is homologous to the upstream half-site of the palindromic sequence found to be important in oppD regulation (FIG. 6A). Interestingly, the upstream region of the gene that shows the highest fold difference in expression when comparing the codY strain to WT L. lactis MG1363, optS, contains two copies of this sequence. The sequence identified is not in all instances part of an inverted repeat. At a later stage, the experiment was repeated. Results are listed in table 10.

The conserved sequence could not be discerned in the upstream regions of all the differentially expressed genes. This could mean that the altered expression in the delta codY strain is an indirect effect of the mutation or that other sequences or structural determinants also play a role in the recognition/regulation by CodY. As can be seen in FIG. 7 several other conserved motifs could be identified in the upstream regions of several differentially expressed genes. These sequences could play a role in CodY-regulated expression (e.g. in the case of prtP and prtM).

Using a weight matrix constructed from the sequences that comprise the putative CodY box, a search was performed in a data set containing the upstream regions of all IL1403 genes (Table 4). The presence of such an element could indicate that the downstream gene is under direct transcriptional control of CodY.

An Overrepresented Motif is Present in the Upstream Regions of a Number of the CodY-repressed Genes

In order to assess whether the lactococcal members of the CodY regulon share a sequence motif in their regulatory regions, an in silico sequence analysis was performed using the algorithm of the MEME software tool. Firstly, a dataset was created containing the upstream regions of the genes that were derepressed to the highest extent in the codY strain in our DNA microarray experiments, as we assumed that these genes are most likely to be under direct control of CodY and thus contain a CodY binding site. This dataset was supplemented with the upstream regions of genes of which it is known that they are under direct control of CodY (i.e. oppD, pepC, pepN) as is the case for the intergenic region of the divergently transcribed L. lactis subsp. cremoris SK11 plasmid-located prtP and prtM genes for which it has been shown that purified H6-CodY of the closely related lactococcal strain MG1363 is able to interact with DNA fragments spanning this region in in vitro DNA binding studies. Since operator sites of regulatory proteins in bacteria are usually located within close proximity of their target promoters, fragments of 200 bps were chosen such that they encompassed the known or predicted promoter sequences of their cognate genes. In cases were a complete operon was found to be up-regulated in the codY deletion strain, the upstream region of the first gene of the transcriptional unit was selected (i.e ilv, his, opp and dpp). Of the latter operon, the region preceding dppA was also included in the dataset, since a putative promoter sequence is present in this area that, thus, might contain a CodY binding site as well.

Subsequently, the dataset containing 14 sequences was examined for the occurrence of common elements using the MEME algorithm. As there is no prior knowledge about a possible CodY binding site, MEME was not restricted with respect to the motif width and number of repetitions and allowed to search on either of the given or the reverse DNA strand. Moreover, these settings did prevent that the common upstream elements (−35 and −10 sequences and the ribosome binding site) would conceal the presence of a CodY binding site. As can be seen from Table 4A and FIG. 6B, application of the pattern recognition program approach revealed the presence of a distinct over-represented motif in a number of the DNA sequences of the dataset. Derivates of this 15 bps AATTTTCWGAAAATT inversely repeated (IR) cis-element are present in the upstream regions of 11 out of the 14 co-regulated genes that constitute the input data for the program. In the upstream regions of udp, hisC, and pepN this over-represented box in CodY-co-regulated genes (C-box) seems to be absent.

Interestingly, the upstream region of the operons that show the highest fold difference in expression when comparing the codY strain to WT L. lactis MG1363, dpp and ilv, contain two copies of this C-box preceding both dppP, dpp and ilvD, encoding the peptide binding proteins of the uptake system and the three branched-chain amino acid biosynthesis genes, respectively, whereas in case of ctrA and in front of gltA, even 3 copies of the motif can be found.

Inter-species Analysis of the over Represented Motif

A multi-species string search was performed on several Gram-positive bacteria in order to assess whether the putative CodY box found upstream of the genes belonging to the CodY regulon is also present in other bacteria containing a CodY protein. Such a comparison could reveal subtle differences in the consensus sequence of this motif. As depicted in FIG. 7, the comparison indeed showed that derivatives of the motif are present in the upstream sequences of CodY regulated genes of B. subtilis (e.g. dppA and hutP). FIG. 6A shows a graphical representation of a species-specific “weight matrix” that was built using the aligned sequences of L. lactis or B. subtilis, respectively. These matrices indicate the importance of specific bases at each position in the motif and show that the motif detected in L. lactis seems to be highly similar to the one of B. subtilis. Both encompass the same “core” sequence, but the consensus of the L. lactis motif seems to be somewhat extended on both sides.

Recently, Molle et al. (2003) reported the genome wide expression analysis of a B. subtilis codY mutant strain. Using the upstream nucleotide sequences of the targets found in that study, we searched for the presence of the putative CodY box in these sequences. Although the similarity scores with the consensus where not very high, derivates of the motif could be identified in some instances in this set of sequences (Table 5). Analysis of the full genome sequence of B. subtilis resulted in the identification of additional promoters containing the putative CodY box (Table 6).

A similar search was performed using the genomes of several other Gram-positive bacteria (Tables 7 and 8). Currently, we are mining the genome of L. lactis strain MG1363 of which the genome sequence is nearly completed.

Regulation of prtP and prtM is Derepressed in the CodY-deficient Strain.

As prtP and prtM respond in a similar way to changes in the nitrogen content of the growth medium as CodY-regulated genes (Miladinov, Kuipers, and Topisirovic, 2001; Guedon et al., 2001 a), the role of CodY in prtP and prtM expression was studied. A fragment containing the prtP/prtM intergenic region of L. lactis BGMN1-5 was cloned in between the promoterless Escherichia coli β-galactosidase (lacZ) and the Cyamopsis tetragonoloba α-galactosidase (α-gal) genes of pGKH10. Thus, translational fusions of prtP and prtM with the two reporter genes were created, the AUG codons of prtP or prtM serving as a start codon for lacZ or α-gal. In the resulting plasmid pGKB11, lacZ is under the control of the prtP promoter of BGMN1-5. In this plasmid the prtM promoter directs the transcription of the α-gal gene. In the corresponding plasmid pGKB12, the fragment is present in the opposite orientation. Plasmids pGKB11 and pGKB12 were introduced in the CodY-deficient L. lactis MG1363 strain (L. lactis MG1363codYΔ1) and lacZ expression was analysed in CDM media containing different amounts of casitone, and in peptide-rich M17 medium. In the WT strain, the β-gal activities of the prtP::lacZ and prtM::lacZ fusions were 6- and 8-fold lower in CDM with 2% than in CDM with 0.2% casitone, respectively. In the codY mutant, β-gal activity in CDM with 2% casitone was less than twofold lower than that in CDM with 0.2% casitone. β-gal activities in M17 were similar to those in CDM with 2% casitone for both MG1363 and MG1363codYΔ1. These results show that repression of these two gene fusions by medium peptides was almost fully abolished in the codY mutant.

CodY Binds to the prtP/prtM Intergenic Region.

The prtP/prtM intergenic regions of the L. lactis strains BGMN1-5, E8, SK11 and Wg2 each contain an inverted repeat (FIG. 8), that is highly conserved on the sequential level (Marugg et al., 1996). To determine whether CodY is also able to recognize and bind to the prtP/prtM intergenic region, gel mobility shift assays were performed using purified H6-CodY. A 330-bp γ-³²P-labelled PCR fragment containing the prtP/prtM intergenic region derived from L. lactis BGMN1-5, E8, SK11 and Wg2, respectively, were used as probes. Addition of His6-CodY resulted in a markedly lower electrophoretic mobility of all four double stranded PCR products on a polyacrylamide gel as compared to the situation in which CodY was not added (FIG. 9). Moreover, multiple shifted bands are present suggesting that CodY migh act as a multimer. These results indicate that CodY directly binds to the prtP/prtM intergenic regions of all four lactococcal strains tested. Since the inverted repeats present in the prtP/prtM intergenic region overlaps the −10 sequence of both the prtP and prtM promoter, they could function as a binding site for CodY, thereby blocking transcription of both genes simultaneously.

H6-CodY Forms Multimers in the Absence of GTP.

In order to identify whether the active form of H6-CodY, a protein of 29 kDa, consists of mono- or multimers, cross-linking experiments were carried out on purified H6-CodY. Initial experiments, using glutaraldehyde as a cross-linking reagent proved to be unsuccessful (data not shown). The results using formaldehyde as a cross-linking agent are shown in FIG. 11 and show that oligomeric forms of H6-CodY are present. Covalently linked CodY complexes of sizes close to those expected for dimeric (58 kDa) and, less pronounced, tetrameric H6-CodY molecules (116 kDa) were obtained. Formation of cross-linked H6-CodY complexes was not significantly stimulated by the presence of GTP, a molecule that serves as a cofactor of B. subtilis CodY. These results indicate that the native form of CodY is a di- or tetramer.

BCAAs Affect H6-CodY Binding Properties. 22

Evidence has been presented that CodY senses the nitrogen supply of the cell as a function of the BCAA pool. Although BCAAs might act as direct effectors of CodY activity, the exact nature of this signal remains to be established. Therefore, in vitro DNA binding of H6-CodY was examined in the presence or absence of the three BCAAs Val, Leu and Ile (FIG. 12). The addition of any of the three BCAAs resulted in severely altered binding of H6-CodY to the PoppD probe 3 as compared to the situation in which no or another, aliphatic, amino acid (i.e. alanine) was present. All of the probe DNA was retarded in the presence of Ile at concentrations of both 0.6 and 2.5 mM, showing that this amino acid directly stimulates the binding of H6-CodY to its target. Strikingly, in the presence of Val and Leu, H6-CodY behaved rather differently. The addition of either of these BCAAs to a final concentration of 0.6 mM resulted in a reduction of the amount of shifted, H6-CodY-bound, probe DNA. Increasing the concentration of these two amino acids to 2.5 mM led to the formation of a protein-DNA complex of high molecular weight, whereas the capability of H6-CodY to form complexes of lower molecular weight seems to be lost.

Similarly, we also tested whether GTP could stimulate the binding of H6-CodY to lactococcal PoppD, since in B. subtilis GTP serves as an effector molecule that enhances binding of bacillus CodY to a number of its targets. However, no effect is seen on lactococcal CodY at a concentration of 2.5 mM GTP (right lane in FIG. 12) as well as at other concentrations (data not shown).

CodY Directly Complexes with the asnB and ctrA Upstream Regions

To distinguish whether repression by CodY occurs directly or indirectly, an electric mobility shift assay (EMSA) was performed in which purified H6-CodY was used. FIG. 13 shows that H6-CodY, like in the case of the well-studied oppD promoter, interacted with a radioactively labeled DNA probe spanning the asnB promoter in vitro.

This result, together with those of the in vivo transcription assays indicate that expression of asnB is probably under the direct control of CodY. Using EMSA's, direct interaction of H6-CodY was also shown for a probe encompassing the upstream region of ctrA. As is apparent from Table 2 and Table 10, the transcript level of ctrA, a gene encoding a putative transporter with homology to several cationic amino acid permeases is highly elevated in L. lactis MG1363Dcody).

DESCRIPTION OF FIGURES

FIG. 1 Overview of the opp-pepO1 operon.

Panel A shows a schematic overview of the opp-pepO1 operon. Panel B shows a detailed view of the upstream sequence encompassing the oppD promoter. The −35, −10 and ribosome binding site (RBS) sequences are underlined. The arrows show the positions of the two pairs of inverted repeats. The inverted repeat that is discussed in the text in more detail is indicated in bold.

FIG. 2 His6-CodY binds to the oppD promoter.

Gel retardation assay using His6-CodY and the oppD promoter fragment. A DNA fragment encompassing the oppD promoter was amplified by PCR, radioactively labelled and incubated with no (lane 2) or increasing amounts of purified H6-CodY (lanes 3 to 9). Lane 1 contains the same probe, but was boiled in a 95% formamide solution in order to obtain single stranded DNA fragments.

FIG. 3 Determination of the minimal region involved in CodY binding to the oppD upstream promoter region.

Different parts of the oppD promoter region were amplified by PCR (panel A), radioactively labelled and incubated with no (lanes 1), 20 ng (lanes 2) or 200 ng (lanes 3) of His6-CodY protein, respectively (panel B). FIG. 3C: In vivo activity of PoppD variants. L. lactis LL108 strains carrying lacZ reporter plasmids fused the opp fragments depicted in panel A were grown in CDM containing 2% casitone. Cells were harvested in the exponential phase of growth and β-galactosidase activity was measured (solid bars). The experiments were carried out in triplicate. Error bars indicate standard deviations.

FIG. 4 Effects of site-directed mutations in the area of inverted repeat in the oppD upstream region. Three constructs (panel A) were compared for both β-gal activity (panel B) and H6-CodY binding (panel C). WT fragments contain no substitutions, whereas fragments Opp15 (a) and Opp15 (b) contain 2 and 3 mutations, respectively (indicated in bold in panel A). In opp2 an XbaI endonuclease site (doubly underlined) preceded by two adenine residues replaced the complete left arm. Solid lines mark the inverted repeats. Panel B shows the effects of mutations on in vivo lacZ expression during growth using WT (▪), Opp15 (a) (×) and Opp15 (b) (•) lacZ fusion constructs. Activity is depicted as the change of fluorescence per unit time as function of the optical density.

FIG. 4D: Promoter activity of PoppD variants. L. lactis LL108 strains carrying the lacZ reporter plasmids were grown in GM17 medium. Cells were harvested in the exponential phase of growth and β-galactosidase activity was measured (solid bars). The experiments were carried out in triplicate. Error bars indicate standard deviations. Open bars indicate a quantitative representation of the DNA binding assay shown in panel C. The relative binding affinity of H6-CodY for the PoppD variants was calculated by comparing the intensity of the shifted, H6-CodY bound complexes with the total radioactive signal in each lane in the presence of 100 ng protein.

FIG. 5 H6-CodY binding to fragments of derepressed variants of lacZ fusion constructs.

Panel A shows the positions of the basepair substitutions (indicated in bold) of the mutants that showed distorted repression by CodY relative to the WT. Solid lines mark the inverted repeat. Panel B shows the relative binding of H6-CodY (compared to WT) to labelled PCR products encompassing the promoter region of the mutants in an in vitro binding assay. The relative affinity was calculated by comparing the amount of H6-CodY required to shift 50% of the labelled DNA in the binding assay.

FIG. 6A Weight matrices as deduced from the seperate motifs as observed in L. lactis intergenic (upper part) and B. subtilis (lower part). IUPAC codes of the derived consensus are indicated in bold.

FIG. 6B Weight matrix obtained by pattern recognition program approach.

FIG. 7 Several conserved motifs that can be discerned in the upstream regions of CodY-regulated genes. Motif 10 represents the consensus CodY target sequence as depicted in FIG. 6.

FIG. 8 Comparison of the prtP/prtM promoter regions of L. lactis strains Wg2, SK11, E8 and BGMN1-5. The regions between bp 201 and 296 are shown double stranded for each strain, the other (flanking) regions are single stranded. Differences in the nucleotide sequences between the strains are depicted in lower case. prtP and prtM start codons are indicated in bold and with a small arrow. The deletion in the sequence of L. lactis Wg2 is indicated by a dashed line. The major transcription start sites for prtP (*) and prtM (•) are indicated above and below the sequence, respectively. Minor sites are indicated in bold face. Putative ribosomal binding sites (RBS^P, RBS^M) and −10 (−10^P, −10^M) and −35 (−35^P, −35^M) promoter sequences are overlined. Dashed arrows represent inverted repeats overlapping the promoters.

FIG. 9 Binding of H6-CodY to the prtP/prtM intergenic regions of L. lactis strains BGMN1-5, E8, SK11 and Wg2. The respective labelled DNA fragments were incubated with increasing amounts of CodY protein (as indicated above the gels) and subjected to gel electrophoresis. The positions of single stranded DNA (ss DNA) and free probe are indicated in the left margin.

FIG. 10 . DNaseI footprinting analysis of H6-CodY binding to the oppD promoter region. The left and right panels show the footprint of the upper and lower strand, respectively. Footprints using radioactively labeled probe 3, obtained in the absence or presence of 25 or 100 ng of H6-CodY, are flanked by a Maxam and Gilbert A+G sequence ladder (AG) on the left. Numbers on the left indicate basepair positions relative to the transcriptional start site. Protected regions are marked with bars and horizontal arrows indicate the positions of hypersensitive bonds. The vertical arrows indicate the region of dyad symmetry closest to the −35 sequence (see FIG. 1B).

FIG. 11 Detection of cross-linked H6-CodY multimers. Samples containing H6-CodY were incubated at 30° C. in the presence (marked by an F) or absence of 1% formaldehyde. GMP was added to the samples in lanes 4 and 5; GTP was added to samples in lanes 6 and 7. Lane 1 contains a molecular weight marker of which the sizes, in kilodaltons, are indicated in the left margin. The positions of monomeric, dimeric and tetrameric forms of H6-CodY are indicated in the right margin by closed, open and dotted arrows, respectively.

FIG. 12 EMSA analysis of the effects of BCAAs and GTP on H6-CodY binding to PoppD. Radioactively labeled probe 3 (see FIG. 3A) was incubated alone or in the presence of 50 ng of purified H6-CodY (marked by − or + signs, respectively). Where indicated, samples were incubated in the presence of 0.6 or 2.5 mM of Val, Leu, Ile and GTP, respectively. The positions of free probe, single stranded DNA and CodY-probe complexes are indicated in the right margin.

FIG. 13 Binding of H6-CodY to radioactively labeled DNA probes spanning the oppD, asnB promoter and ctrA upstream region.

TABLE 1Comparison of putative GTP binding motifsin CodY homologsG1G3G4Small GTPasesGXXXXGXTDXXGNKXDConsensus sequencesA STQFtsZLGGGTGTGDAFGTSLDE. coliCodYGGERLGTLDRVGNKFLB. subtilisB. stearothermophilusGGERLGTLDRVGDKFLB. haloduransGGQRLGTLDRVGDKFLB. anthracisGGERLGTLNAaNAaC. difficileGGMRLGSLDRIGNEGIC. acetobutylicumNRERLGTLDRVGILNDS. pneumoniaeSGIRLGSLDRIGLISDE. faecalisAGKRLGTIDRVGNQQFS. mutansGGMRLGSLDRIGNEGIS. aureusGGERLGTLDRIGEKGIS. pyogenesGGMRLGSLDRIGNEGIL. lactisSGMRLGTFDKIGTGLF
^a(uit Ratnayake-Lecamwasam et al., 2001), NA; not available.

TABLE 2

Genes up in CodY strain

Genes

up in

dcodY
Fold
Annotation

optS
8.8
oligopeptide ABC transporter substrate binding protein

ctrA
6.3
cationic amino acid transporter

pepO
5.7
neutral endopeptidase

citB
5.6
aconitate hydratase (EC 4.2.1.3)

oppA
5.3
oligopeptide ABC trasporter substrate binding protein

gltD
5.2
glutamate synthase small subunit (EC 1.4.1.13)

ilvD
4.8
dihydroxy-acid dehydratase (EC 4.2.1.9)

ilvN
4.5
acetolactate synthase small subunit (EC 4.1.3.18)

asnB
4.4
asparagine synthetase B

ymdC
3.9
kanamycin kinase (EC 2.7.1.95)

hisA
3.8
phosphoribosylformimino-5-aminoimidazole isomerase

oppB
3.4
oligopeptide ABC trasporter permease protein

oppC
2.9
oligopeptide ABC trasporter permease protein

oppF
2.8
oligopeptide ABC trasporter ATP binding protein

llrH
2.7
two-component system regulator

hisB
2.7
imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19)

serC
2.6
phosphoserine aminotransferase (EC 2.6.1.52)

hisK
2.5
histidinol phosphatase

oppD
2.5
oligopeptide ABC trasporter ATP binding protein

yahD
2.4
HYPOTHETICAL PROTEIN

leuC
2.3
3-isopropylmalate dehydratase large subunit

(EC 4.2.1.33)

optD
2.3
oligopeptide ABC trasporter ATP binding protein

serB
2.2
phosphoserine phosphatase (EC 3.1.3.3)

hisH
2.1
amidotransferase (EC 2.4.2.—)

udp
2.1
uridine phosphorylase

aldB
2.0
alpha-acetolactate decarboxylase (EC 4.1.1.5)

hisI
2.0
phosphoribosyl-ATP pyrophosphohydrolase

(EC 3.6.1.31)

icd
1.9
isocitrate dehydrogenase (EC 1.1.1.42)

yafC
1.9
HYPOTHETICAL PROTEIN

arcD1
1.8
arginine/ornitine antiporter

ilvB
1.8
acetolactate synthase large subunit (EC 4.1.3.18)

optF
1.8
oligopeptide ABC trasporter ATP binding protein

lacR
1.8
lactose transport regulator

hisD
1.7
histidinol dehydrogenase (EC 1.1.1.23)

arcC2
1.7
carbamate kinase (EC 2.7.2.2)

optA
1.7
oligopeptide ABC transporter substrate binding protein

serA
1.7
D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

recD
1.7
exodeoxyribonuclease V alpha chain (EC 3.1.11.5)

ilvC
1.7
ketol-acid reductoisomerase (EC 1.1.1.86)

ywaD
1.7
UNKNOWN PROTEIN

ydbD
1.7
UNKNOWN PROTEIN

glgD
1.7
glucose-1-phosphate adenylyltransferase (EC 2.7.7.27)

lmrP
1.6
integral membrane protein LmrP

pdhC
1.6
component of PDH complex (EC 2.3.1.12)

mesJ
1.6
cell cycle protein MesJ

lcnD
1.6
lactococcin A ABC transporter permease protein

glgA
1.6
glycogen synthase (EC 2.4.1.21)

trxA
1.6
thioredoxin

gltA
1.6
citrate synthase (EC 4.1.3.7)

pepN
1.6
aminopeptidase N

arcA
1.6
arginine deiminase (EC 3.5.3.6)

glgC
1.6
glucose-1-phosphate adenylyltransferase (EC 2.7.7.27)

yohC
1.6
transcriptional regulator

ywiE
1.6
UNKNOWN PROTEIN

yohD
1.6
UNKNOWN PROTEIN

yfiD
1.5
UNKNOWN PROTEIN

ycaF
1.5
UNKNOWN PROTEIN

ybhE
1.5
HYPOTHETICAL PROTEIN

rmlA
1.5
glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24)

grpE
1.5
stress responce protein GrpE

yccE
1.5
UNKNOWN PROTEIN

hrcA
1.5
heat-inducible transcription repressor HrcA

pi336
1.5
prophage pi3 protein 36

dhaM
1.5
dihydroxyacetone kinase (EC 2.7.1.2)

ywjC
1.5
UNKNOWN PROTEIN

purC
1.5
phosphoribosylaminoimidazole synthetase

xynB
1.5
beta-1,4-xylosidase (EC 3.2.1.37)

lysA
1.5
diaminopimelate decarboxylase (EC 4.1.1.20)

yccF
1.5
HYPOTHETICAL PROTEIN

rmaB
1.4
transcriptional regulator

optC
1.4
oligopeptide ABC trasporter permease protein

araT
1.4
aromatic amino acid specific aminotransferase

yciA
1.4
amino acid amidohydrolase

pi235
1.4
prophage pi2 protein 35

yfgC
1.4
UNKNOWN PROTEIN

pepC
1.4
aminopeptidase C

yaiB
1.4
HYPOTHETICAL PROTEIN

ybhD
1.4
UNKNOWN PROTEIN

ribA
1.4
GTP cyclohydrolase II (EC 3.5.4.25)

pyrG
1.4
CTP synthetase

ps120
1.4
prophage ps1 protein 20

yidA
1.4
transcription regulator

yahC
1.4
UNKNOWN PROTEIN

ps305
1.4
prophage ps3 protein 05

yndG
1.4
metal ABC transporter substrate binding protein

yahG
1.4
ABC transporter ATP binding protein

uxuA
1.4
D-mannonate dehydratase (EC 4.2.1.8)

ps112
1.4
prophage ps1 protein 12

hisC
1.4
histidinol-phosphate aminotransferase (EC 2.6.1.9)

arcC1
1.4
carbamate kinase (EC 2.7.2.2)

xy1X
1.4
acetyltransferase HYPOTHETICAL PROTEIN

rodA
1.4
rod-shape determining protein

yafB
1.4
sulfate transporter

ps113
1.4
prophage ps1 protein 13

ruvA
1.4
DNA helicase RuvA

asd
1.4
aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)

sugE
1.4
SugE protein

groES
1.4
10 KD chaperonin

rpsO
1.4
30S ribosomal protein S15

ybdA
1.4
transcription regulator

bcaT
1.4
branched-chain amino acid aminotransferase

(EC 2.6.1.42)

ybiK
1.4
UNKNOWN PROTEIN

yafJ
1.4
HYPOTHETICAL PROTEIN

pi302
1.4
prophage pi3 protein 02

aldR
1.4
regulatory protein AldR

menX
1.4
protein in menaquinone biosynthesis pathway

dapB
1.4
dihydrodipicolinate reductase (EC 1.3.1.26)

yphI
1.4
UNKNOWN PROTEIN

ydcG
1.3
transcriptional regulator

amtB
1.3
ammonium transporter

TABLE 3

Genes down in CodY strain

Genes

down in

dcodY
Fold
Annotation

plpA
3.3
outer membrane lipoprotein precursor

cysK
3.2
cysteine synthase (EC 4.2.99.8)

metB2
2.9
cystathionine gamma-synthase (EC 4.2.99.9)

plpB
2.9
outer membrane lipoprotein precursor

cysD
2.6
O-acetylhomoserine sulfhydrylase

plpC
2.5
outer membrane lipoprotein precursor

plpD
2.3
outer membrane lipoprotein precursor

yndE
2.3
UNKNOWN PROTEIN

cysM
2.1
cysteine synthase (EC 4.2.99.8)

yrbB
2.0
HYPOTHETICAL PROTEIN

yjgC
2.0
amino acid ABC transporter substrate binding protein

argH
1.8
argininosuccinate lyase (EC 4.3.2.1)

lysP
1.8
lysine specific permease

gntK
1.8
gluconate kinase (EC 2.7.1.12)

codY
1.7
transcriptional regulator

yshA
1.7
amino acid permease

ymgI
1.6
UNKNOWN PROTEIN

ytaA
1.6
conserved hypopthetical protein

panE
1.6
ketopantoate reductase (EC 1.1.1.169)

yhcE
1.6
conserved hypothetical protein

ywdD
1.5
UNKNOWN PROTEIN

ymbC
1.5
UNKNOWN PROTEIN

rpmD
1.5
50S ribosomal protein L30

ywjA
1.5
UNKNOWN PROTEIN

ynfG
1.5
HYPOTHETICAL PROTEIN

ybiD
1.5
HYPOTHETICAL PROTEIN

ydcB
1.5
amino acid ABC transporter ATP binding protein

ypjC
1.5
UNKNOWN PROTEIN

ytjE
1.5
aminotransferase

pydA
1.5
dihydroorotate dehydrogenase A (EC 1.3.3.1)

ymgG
1.5
HYPOTHETICAL PROTEIN

nrdG
1.4
ribonucleoside-triphosphate reductase activating protein

yxeA
1.4
HYPOTHETICAL PROTEIN

yueD
1.4
conserved hypothetical protein

ymbK
1.4
UNKNOWN PROTEIN

ylfH
1.4
N-acetylglucosamine catabolic protein

yqcA
1.4
UNKNOWN PROTEIN

yudI
1.4
HYPOTHETICAL PROTEIN

yvdF
1.4
amino acid ABC transporter substrate binding protein

yxaF
1.4
HYPOTHETICAL PROTEIN

ymbJ
1.4
UNKNOWN PROTEIN

ynfH
1.4
UNKNOWN PROTEIN

yxbE
1.4
conserved hypothetical protein

dxsA
1.4
1-deoxyxylulose-5-phosphate synthase

murI
1.4
glutamate racemase (EC 5.1.1.3)

ytbC
1.4
UNKNOWN PROTEIN

yccB
1.4
UNKNOWN PROTEIN

yhcH
1.4
HYPOTHETICAL PROTEIN

TABLE 4

Whole genome search for the presence of the

putative CodY box in intergenic regions of

L. lactis IL1403.

Sequence
Gene
Despription

TAATTTTCTGATAATATAGTCAATTT
yreE
UNKNOWN PROTEIN

TAATTTACTGACAAGTCTGTCAGTAA
ctrA
cationic amino

acid transporter

TAATTTACTGACAAAATTATCAGAAC
yciC
HYPOTETICAL

PROTEIN

AAATTTTCTGACAATAATAAAAATTG
optA
oligopeptide ABC

transporter sub-

strate binding

protein

AAATTATCAGAAAAATACAACAATAT
optS
oligopeptide ABC

transporter sub-

strate binding

protein

TAATTTTCAGAATAATATGAAAATTC
optS
oligopeptide ABC

transporter sub-

strate binding

protein

TAATTTACTGATAGATTTGTCAGTAA
parA
chromosome

partitioning

protein

TAATTTACTGACAGTTCTGTCAGTAA
aroF
Tyr-sensitive

aldolase

AAATTTACTGACAAAAAAGATAATGG
vacB1
RIBONUCLEASE II

(RNB) FAMILY

TAATTTTCAGAAAACATAACCATTAT
optA
oligopeptide ABC

transporter sub-

strate binding

protein

GAATTTTATGAAAAAAATATTAATTG
ypaG
HYPOTHETICAL

PROTEIN

GAATTTACTGACGAATCTATCATTAA
yiaB
oxidoreductase

TCATTCTCTGACAAATCTGTCAGTAA
ysdC
HYPOTHETICAL

PROTEIN

AAATTTACTGACAAGCTTGTTAGTAT
hemK
protoporphyrinogen

oxidase

AAATTTAATGATAAAACAATTAGTTT
prfC
peptide chain

release factor 3

AAAGTTACTGACAAATCTGTCAGTAA
yugB
ORF

TTATTTACTGACAAGTCTGTCAGTAA
murD
PEPTIDOGLYCAN

BIOSYNTHESIS

TATTTTACTGACAAAAAAATAAGTTT
ywdG
HYPOTHETICAL

PROTEIN

TAATTTACTGACAGCTTTGTCAGTAA
parC
topoisomerase IV

subunit B

(EC 5.99.1.-)

AAATTTACTGACAGAGCTGTCAGTAA
pepC
aminopeptidase

AAATTTACTGACAGACTTGTTAGTAA
mutM
formamidopyrimi-

dine-DNA glyco-

sylase

(EC 3.2.2.23)

AAATTTACTGACAACTTTGTCAGAAG
rgpAB
rhamnosyltrans-

ferase

AAAATGTCTGATAAAATGATTAATAC
vacB1
RIBONUCLEASE II

(RNB) FAMILY

TAATTTACTGACAGAATTTTAAATTT
recN
DNA repair protein

AAAATTACTAACAAAACTGTTAGTAA
llrH
two-component

system regulator

Detected motifs are sorted according to their similarity to the consensus

TABLE 4A

Search of motif in L. lactis MG1363 genome

Position
Sequence
Score
Gene

352819
AATTTTCAGAAAATT
11.8
dppP

164084
AATTGTCAGAAAATT
11.3
codY

558564
AATTTTCTGATAATT
11.3
serC

1799629
AATTTTCAGATAATT
11.3
thrA

1860656
ATTTTTCAGAAAATT
11.3
ygjD

2150244
AATTTTCGGAAAAAT
11.3
ytjF

628910
AATTTTCAGAAAATA
11.2
gitA

191904
ACTTTTCAGAAAATT
11.1
feoA

636386
AATTTTCTGAATATT
11.1
yghD

1516191
ATTTTTCAGAAAAAT
11.1
nrdF

112095
AATTGTCAGACAATT
10.9
ctrA

351027
ATTTTTCTGACAATT
10.9
dppA

683034
AATTTTCTGAACATT
10.9
oppD

2150244
ATTTTTCCGAAAATT
10.9
ytjF

279800
TATTTTCAAAAAATT
10.8
ychG

351095
ATTATTCTGAAAATT
10.8
dppA

383134
TATTTTCAAAAAATT
10.8
lysS

1474895
AATTTTTTGAAAATT
10.8
ORF

1815549
AAATTTCTGAAAATT
10.8
rliC

353051
AATTTTCTGACAATA
10.7
dppP

416868
ATTTTTCTGAAAATA
10.7
yeaG

742665
ATTTTTCAGAAAATA
10.7
pip

884469
GTTTTTCTGAAAATT
10.7
yqcE

1809077
AATTTTCAGAAGAAT
10.7
menD

16128
AATTTTCTAAAAAGT
10.6
mfd

352983
AATTTTCAGAAAACA
10.6
dppP

547027
TATTTTCAAAAAAAT
10.6
yfhC

868871
CATCTTCAGAAAATT
10.6
arsC

876166
AATATTCAGAAAATA
10.6
amtB

939654
AATTTTCAAAAAACT
10.6
purL

1001446
AATTTTCAGAAAAGA
10.6
yojB

1251475
AATGTTCTGACAAAT
10.6
ilvD

1920664
AATTTTTTGAAAAAT
10.6
ysbD

1940975
AATTTTTTGAAAAAT
10.6
ysdE

2105722
AATTTTCTAAAAACT
10.6
ORF

100225
ATTTTACAGAAAATT
10.5
ybaB

126604
AATTATCAGAAAATG
10.5
ORF

419279
AATTATCAGAAAATC
10.5
yebA

479710
ATTTTTCTGAAAATG
10.5
ORF

501762
AATTTTCTGACGATT
10.5
cysM

TABLE 5

Presence of putative CodY box upstream of

CodY regulated genes identified by Molle

et al. 2003.

gene
sequence

yufN
ATTATCAGAAAATTT

citB
ATTGTGAGAAAATTG

dppA
TTTGTTAGAATATTC

hutP
GTTATCAGAATTTTT

yxbC
ATTATCAGAGGATTA

yurPQ
AATTTCAGAAAATAA

ycgM
ATTTTGAGGATATTG

yhjC
AATTTCAGACAATTC

ybgE
ATATTCTGAAATTTA

ykbA
TTTATCAAAAAAGTC

ggaA
ATTTTCAGCAAAAAA

ycgM
ATAATCAGAATCTTT

yoaD
TTTTTATGAAAAATA

guaB
GTTATCTAAATATTT

ilvD
ATTGTCAAAATAAAA

yxbBC
ATTGACAGAATTATC

rocA
TTTTTCAGCAAAAGA

yhdG
TTTTTCTAACAATTT

yusC
TTTTGCAGAAAAAAC

yusC
TTTCTTAGAATAGTG

Detected motifs are sorted according to their similarity to the consensus

TABLE 6

Whole genome search for the presence of the

putative CodY box in intergenic regions of

B. subtilis 168.

Sequence

motif
Gene
notation

ATTATCAGAAAATTT
yufN
similar to ABC transporter

(lipoprotein)

ATTTTCAGAAATTTA
ydjJ
function = “unknown &

similar to sugar

transporter

TTTTTCAGAAAAATG
ytkC
similar to autolytic

amidase

TTTTTCAGAAAAATC
lytE
alkaline phosphatase A &

cell wall lytic activity

ATTGTCTGAATATTA
yoaC
similar to phosphoglycerate

dehydrogenase

TTTTTCTGAATATTC
ytnA
similar to proline permease

ATTTTCGGAAAATTT
aldY
aldehyde dehydrogenase

ATTTTCAGAAAAGTT
glnQ
glutamine ABC transporter

ATTTTCAGAAAATAA
ykuW
function = “unknown

ATTTTCAGTATATTT
yndN

TTTATCAGAAAAATA
yheI

ATTTTCAGGAAATTC
ykuM
similar to transcriptional

regulator (LysR family)”

ATTTTCAGAACAATT
gbsA
similar to hypothetical

proteins

ATTTTCAGAAAATCA
ynaC
function = “unknown

ATTGTCAGAAAACTT
yqiQ
similar to phosphoenolpy-

ruvate mutase

ATTTTCAGAATTATA
ggaA
membrane-bound protein

TTTTTCGGAATATTC
yurY
similar to ABC transporter

(ATP-binding protein)”

TTTATCTGAAAATTT
ureA
urease (beta subunit)”

ATATTCAGAATATTC
leuS
leucyl-tRNA synthetase

ATTTTCTGAAATTTC
yurO
similar to multiple sugar-

binding protein

ATTTTCTGAAATTTA
ykrQ
similar to hypothetical

proteins

TTTTTCAGTATATTT
yvcC
similar to ABC transporter

(ATP-binding protein)”

TTTTTCAGCAAATTT
thiC
thiamine-phosphate pyro-

phosphorylase

TTTTTCAGACAATTG
yvaV
similar to hypothetical

proteins

ATTGTCAGCATATTT
fliR
required for flagellar

formation

TTTTTCATAAAATTT
yokA
assimilatory nitrate

reductase

TTTTTCATAAAATTC
ygeY
similar to hypothetical

proteins

ATTGTTAGAAAATTA
yjcL
function = “unknown”

ACTTTCAGAATATTT
rapE
response regulator

aspartate phosphatase”

TTTTTCTGAATAATT
bfmBB
ranched-chain alpha-keto

acid dehydrogenase E2

subunit

Detected motifs are sorted according to their similarity to the consensus

TABLE 7

Whole genome search for the presence of the putative CodY

box in intergenic regions of Streptococcus pneumoniae.

Sequence
Gene
Description

TGATTTTCAGAAAAATTTAAGAAAAA
ppmA
Proteinase maturation protein

ATATTTTCTGAAAATTTCTTCAGTAA
Leu-A
2-isopropylmalate synthase, truncation

TTATTATCAGATAATTTTATCAATCG
hsds
type I restriction enzyme

CAATTTTCTGATAATTCGGTATATTC
livJ
ABC transporter branched chain amino acid

GAATTTTCTGAAAATTACAAAATATA
ilvE
Branched-chain-amino-acid transaminase

TTATTTTCTGAAAATTTGGTAAAATA
gapN
NADP-dependent glyceraldehyde-3-phosphate

TCATTTTTTGAAAAAATGATTATTAC
mefE
ABC transporter - macrolide efflux

CATTTTTCAGAAAATTCTTTTATTTC
IS1381
Degenerate transposase

ACATTTTCTGAAATTAAAAATAATAT
ugd
UDP-glucose dehydrogenase

GAAATTTCTGAAAAATATGATATAAT
hemK
protoporphyrinogen oxidase

AAATTATTTGATAATTCTATAATTTC
spr1649
Putative transcriptional regulator (phoU like)

AATTTATCTGAAAAAACGAAAAATAT
spr1765
Hypothetical protein

CAATTTTTTGAAAAAATATTGATTTA
glgB
1,4-alpha-glucan branching enzyme

TATTTTTCTGAAAACTCTGATATAAA
spr2010
Probable member of DHH superfamily

TCATTTTCAGATAAGGATAAAAATTG
spr0128
Hypothetical protein

GAATTGACAGATGAATTTGTTAAGAA
ABC-NDB
ABC transporter ATP-binding protein - unknown

AAATTGAATGAAAAGTATAAAATTAA
spr1149
Probable oligosaccharide repeat unit transporter

AAATTGTCAGAATTATGAGAAAATAG
rgg/
transcriptional regulator of glucosyltransferase

spr1934

CATTTTACTGAAGAATACGATATTAT
gidA
Glucose inhibited division protein

AAATTTCTAGATAAGTTAATAATTAA
abc-n/p
ABC transporter - unknown substrate

ATATTCTGTGAAAAATAAAATAGTAT
spr0119
Hypothetical protein

GAATTTCCAGATAAACTAAAAAAATC
hsdS 2X
type I restriction enzyme

ACATTATCTGAAAAATTAAACTATAA
spr0607
Hypothetical protein

TAATTGTCAGAAAGTTAAATAAAGGA
rpmI
50S Ribosomal protein L35

AAATTATCTAATAACAAAAATATTAT
spnIM
DNA modification methyltransferase

TTATTTACAGAAAGAACAAAAAATGC
spnIM
DNA modification methyltransferase

GAATTTTCAGAAAATTCTATACGCAT
ilvD
Dihydroxyacid dehydratase

ATATTTTTTGAAAAATTTTTTAAAAA
arcA
Arginine deiminase, truncation

AAATTGACAAATAAAAATTTGAATAT
ABC-NBD
ABC transporter ATP-binding protein anion transport

TACTTTACAGAAGAATTACAGAATAG
mfd
Transcription-repair coupling factor

GAATTTTCAGAATAATCTGTATATGT
spr0157
Conserved hypothetical protein

GAATTTCCTGAAAATCTGGCTATTAT
murM
Serine/alanine adding enzyme

GATTTTTCGGAAAATTATGTTAGAAT
zwf
Glucose-6-phosphate 1-dehydrogenase

CAATATTTAGAAAAAAAAGAAATTAA
licD1
phosphorylcholine incorporation in teichoic acids

ATATTTTCTGAACAATTAATATATTC
spr1403
Hypothetical protein

CATTTTGCGGAAAATTGAGTAAATAT
relA
GTP pyrophosphokinase

TAATTTTCTGATTTTTTGTAAAATAA
spr1650
Hypothetical protein

TTATTTTCTAATAGATATAAAATTAT
pcpA
Choline-binding protein

TAAATTTCAGATTGATGAAAAAATAG
rsuA
Ribosomal small subunit pseudouridine synthase

AATTTTTTAGAAAAAAGTGTAATTTT
ptsG
PTS glucose-specific enzyme IIABC component

AAATTCACTGAAAGTTTAAATATGAC
hsdS
type I restriction enzyme

GAATTGCCAGACTATTTTAATACTAT
spr0803
Hypothetical protein

AGATTTTAAGTAAAATTTATTAGTAA
spr0826
Hypothetical protein

AAATTTTAGAAAAAATTAAAGAATAC
flaV
Flavodoxin

CAATTATCTGATCATCTGAAAAATAT
ABC-NP
ABC transporter - multidrug resistance

Detected motifs are sorted according to their similarity to the consensus

TABLE 8

Whole genome search for the presence of the

putative CodY box in intergenic regions of

Streptococcus agalacticiae.

Sequence

motif
Gene
Description

ATTATCAGAATATTG
gbs1632
similar to branched-chain

amino acid ABC transporter

ATTTTCAGAAAAATA
gbs1105
similar to unknown protein

TTTATCAGAAAATTT
gbs0662
similar to ABC transporter

(ATP-binding protein)

ATTTTCTGAATATTC
gbs2002
similar to glycerol

dehydrogenase

TTTTTCTGAATATTT
gbs1489
possible surface protein

ATTTTCAAAAAATTT
gbs0054
similar to alcohol

dehydrogenase

ATTTTCAAAAAATTG
gbs0008
similar to unknown protein

ATTGTCAGAATTTTC
gbs1406
Similar to ABC transporter

ATTATCTGAAAATTT
gbs0144
similar to oligopeptide

ABC transporter

ATTATCTGAATATTA
gbs0898
acetoin dehydrogenase E3

ATTTTCAGTATATTC
gbs2007
similar to C5A peptidase,

putative peptidoglycan

linked protein

ATTTTCAGAAAATGT
gbs0235
gene = “rRNA-16s

ATTATCAGAAGATTT
gbs0577
Similar to unknown

proteins

ATTTTCAGATAATTG
gbs0143
similar to oligopeptide

ABC transporter

ATTTTTAGAAAATTA
gbs0604
similar to negative regu-

lator of FtsZ ring forma-

tion protein EzrA

ATTTTCTGAATAATT
dnaG
DNA primase

ATTTTCTGAATAATT
ftsA
Similar to cell division

protein FtsA

ATTTTCAGGATATTT
gbs1259
Similar to ABC transporter

Detected motifs are sorted according to their similarity to the consensus

TABLE 9

Bacterial strains and plasmids used in this patent application

Strain or plasmid
Relevant phenotype or genotype
Source or reference

Strains

L. lactis subsp.

cremoris

MG1363
Lac⁻; Prt⁻; Plasmid-free derivative of NCDO712
(Gasson, 1983)

LL108
Cm^r, MG1363 derivative containing pWV01 repA
(Leenhouts et al.,

gene in the chromosome
1998)

LL302
RepA⁺ MG1363, carrying one copy of pWV01 repA
(Leenhouts et al.,

gene on the chromosome
1998)

NZ9000
MG1363 pepN::nisRK
(Kuipers et al.,

1998)

NZ9700
Nisin producing transconjugant containing the
(Kuipers et al.,

nisin-sucrose transposon Tn5276
1993)

SK11
Lac⁺; Prt⁺; harbours, a.o., proteinase plasmid
(de Vos et al., 1984)

pSK111

Wg2
Prt⁺; harbours, a.o., proteinase plasmid pWV05
(Otto et al., 1982)

E8
Lac⁺; Prt⁺
(Kok, 1990)

L. lactis subsp.

lactis

BGMN1-5
Wild type strain, PrtP⁺, Bac501⁺, Bac513⁺
(Gajic et al., 1999)

E. coli

EC101
Kan^r; JM101 with repA from pWV01 integrated
J.Law et al., 1995

in chromosome

Plasmids

pNZ8048
Cm^r, inducible expression vector carrying P_nisA
(Kuipers et al.,

1998)

pNH6CodY
his6-codY of L. lactis MG1363 behind P_nisA
Gajić, to be

submitted

pGKH11
Em^r, Cm^r, contains genes for α-gal and β-gal,
(Haandrikman,

controlled by P_prtMand P_prtPof Wg2, respectively
1990)

pGKB11
Em^r, Cm^r, contains genes for α-gal and β-gal,
Gajić, to be

controlled by P_prtMand P_prtPof BGMN1-5,
submitted

respectively

pGKE11
Em^r, Cm^r, contains genes for α-gal and β-gal,
Gajić, to be

controlled by P_prtMand P_prtPof E8, respectively
submitted

pGKS11
Em^r, Cm^r, contains genes for α-gal and β-gal,
Gajić, to be

controlled by P_prtMand P_prtPof SK11, respectively
submitted

pORI13
Em^r; integration vector, promoterless lacZ, Ori⁺,
J. Sanders et

RepA- derivative of pWV01
al., 1998

pORIopp14
Em^r; pORI13 carrying 154bp oppD promoter
Gajić, to be

fragment amplified with primers opp1 and opp14
submitted

pORIopp15 (a)
Em^r; pORI13 carrying 154bp oppD promoter
Gajić, to be

fragment amplified with primers opp1 and
submitted

opp 15 (a)

pORIopp15 (b)
Emr^r; pORI13 carrying 154bp oppD promoter
Gajić, to be

fragment amplified with primers opp1 and
submitted

opp15 (b)

Em^r, Cm^rAp^r, resistance to erythromycin, chloramphenicol and ampicilin, respectively. P_nisA—inducible nisA promoter, P_prtP—prtP promoter, P_prtM—prtM promoter, α-gal—α-galactosidase, β-gal—β-galactosidase.

TABLE 10

Differentially expressed genes found in microarray expression

analysis of L. lactis MG1363 codY vs. WT.

Average

regulation (fold in

Gene
codY vs. WT)
Significance (p-value)

optS
9.8
7.17E−05

gltD
7.3
2.18E−05

citB
7.1
3.76E−03

asnB
6.0
1.08E−05

ctrA
5.8
3.68E−05

ilvD
5.4
3.81E−05

pepO
5.0
1.93E−05

ymdC
4.9
5.29E−04

hisA
4.9
2.52E−06

ilvN
4.7
6.10E−03

oppA
4.6
1.13E−05

icd
3.1
1.25E−05

oppD
3.1
5.86E−05

hisB
3.0
1.12E−02

leuD
3.0
5.09E−01

udp
3.0
1.89E−03

oppB
2.8
1.69E−04

yahD
2.7
1.15E−01

oppC
2.7
1.67E−03

yohC
2.6
3.00E−02

yveA
2.6
NA

uxuA
2.5
NA

serC
2.5
2.49E−03

oppF
2.5
2.92E−06

trxA
2.4
NA

arcC2
2.3
5.03E−03

ilvC
2.3
9.65E−02

serA
2.3
2.86E−02

argG
2.3
2.29E−02

arcD1
2.3
1.80E−04

hisK
2.2
7.72E−02

yxbA
2.2
NA

ydgD
2.2
NA

serB
2.2
7.60E−04

leuC
2.1
NA

optA
2.1
NA

yjjA
2.1
4.31E−01

asnS
2.1
4.31E−02

hisI
2.1
8.82E−05

yxaC
2.1
9.81E−02

groES
2.1
2.40E−03

yjhC
2.0
1.75E−01

rmeC
2.0
1.49E−01

ytdB
2.0
2.31E−01

ysiC
2.0
NA

yndG
2.0
1.36E−01

optD
2.0
4.14E−02

amtB
2.0
1.67E−04

feoB
1.9
NA

hisH
1.9
2.25E−02

ykcC
1.9
NA

lysA
1.9
1.63E−03

pepN
1.9
1.29E−03

glgC
1.9
3.76E−02

aldB
1.9
5.52E−05

arcC1
1.8
NA

lcnD
1.8
NA

hrcA
1.8
1.48E−03

yfiG
1.8
1.27E−01

thrC
1.7
1.30E−02

ydiE
1.7
2.15E−01

ilvA
1.7
NA

yxdG
1.7
1.09E−02

ynaD
1.7
1.08E−03

yedE
1.7
2.28E−01

thrA
1.7
1.86E−02

rodA
1.7
1.18E−01

ydiG
1.7
1.29E−01

yfiD
1.7
2.82E−01

yhfE
1.7
7.89E−02

yahA
1.7
1.30E−01

ydcG
1.7
1.27E−04

gltA
1.6
6.48E−02

yviC
1.6
1.51E−01

ybaD
1.6
1.02E−01

ybjA
1.6
2.65E−01

hisD
1.6
2.76E−01

glk
1.6
7.18E−02

rgpE
1.6
2.74E−01

thrB
1.6
1.25E−01

clpB
1.6
NA

bcaT
1.6
3.87E−03

hisF
1.6
NA

yvcA
1.6
3.16E−01

ymgK
1.6
NA

yajH
1.6
3.50E−01

yccE
1.6
1.49E−01

yndA
1.6
4.79E−04

ybhE
1.6
1.43E−01

adhE
1.6
1.53E−02

grpE
1.6
4.25E−02

yqaB
1.5
2.78E−03

pgiA
1.5
1.19E−01

yrhH
1.5
NA

ybhC
1.5
2.97E−01

glgD
1.5
1.57E−02

yidA
1.5
1.13E−01

yabF
1.5
1.54E−02

rimM
1.5
1.44E−01

yacl
1.5
2.36E−01

asd
1.5
NA

yijE
1.5
2.02E−01

yccF
1.5
6.44E−02

agl
1.5
1.28E−01

optC
1.5
1.91E−02

malF
1.5
8.17E−02

yjhB
1.5
4.32E−01

yibG
1.5
4.78E−04

ribA
1.5
NA

yabE
1.5
3.23E−01

thiL
1.5
2.06E−01

ycaF
1.5
7.56E−02

optF
1.5
5.78E−02

arcC3
1.5
NA

ymfD
1.5
2.40E−01

ps309
1.5
2.41E−01

ycfl
1.5
1.68E−01

uvrC
1.5
5.04E−01

yphC
1.5
2.67E−01

ybeM
1.5
2.42E−01

ygfA
1.5
NA

yphJ
1.5
1.00E−01

ynaA
1.5
9.20E−02

ahpF
1.5
1.75E−01

aroB
1.5
1.47E−01

ybhD
1.5
1.85E−01

hisC
1.5
6.57E−02

yoaF
1.5
3.16E−01

dexC
1.5
2.59E−02

amyY
1.5
3.85E−02

yueF
1.5
5.47E−01

ydgH
1.5
4.84E−01

dapB
1.4
1.11E−03

ftsZ
1.4
1.35E−01

ynhA
1.4
1.07E−02

ygiJ
1.4
2.11E−01

ptcA
1.4
1.29E−01

yqeH
1.4
2.45E−02

yrgl
1.4
6.06E−01

pepC
1.4
2.97E−03

ycfH
1.4
4.66E−01

ybcH
1.4
4.45E−02

pi345
1.4
3.31E−01

ps112
1.4
5.32E−01

yteD
1.4
NA

ythB
1.4
9.95E−02

yneD
1.4
7.17E−02

pmsR
1.4
7.19E−02

rgpC
1.4
1.34E−01

yjbB
1.4
3.70E−01

ygdF
1.4
2.48E−01

yoaB
1.4
1.38E−01

yfhK
1.4
1.10E−02

yvaB
1.4
4.18E−01

yqjA
1.4
1.45E−01

pi120
1.4
1.27E−03

yliC
1.4
6.76E−02

ydgC
1.4
5.49E−04

rarA
1.4
1.18E−01

ywdG
1.4
1.11E−01

yfdD
1.4
2.09E−01

ftsW1
1.4
6.18E−03

ybeB
1.4
7.74E−02

yvdD
1.4
9.09E−03

ymeB
1.4
2.19E−02

yoiC
1.4
NA

yhcK
1.4
3.80E−01

groEL
1.4
NA

xylM
1.4
1.38E−01

ydgG
1.4
3.77E−01

sugE
1.4
1.86E−01

pi360
1.4
3.37E−01

yfhB
1.4
2.97E−01

metS
1.4
6.97E−02

yeaC
1.4
NA

coiA
1.4
1.76E−01

butA
1.4
5.62E−03

clpP
1.3
1.82E−01

arcA
1.3
1.20E−01

yacB
1.3
4.34E−02

kinC
1.3
2.34E−02

ps305
1.3
2.30E−01

glnB
1.3
2.92E−01

ybbC
1.3
3.99E−02

ykhJ
1.3
8.11E−02

dnaK
1.3
9.17E−02

dnaG
1.3
2.16E−03

ybdJ
1.3
3.38E−01

yohD
1.3
1.39E−04

pi130
1.3
NA

yugC
1.3
1.75E−03

ycjH
1.3
3.25E−01

yjaB
1.3
1.33E−01

glgP
1.3
7.93E−02

pi235
1.3
NA

acmB
1.3
1.78E−01

xylX
1.3
NA

ybeH
1.3
1.00E−01

arcD2
1.3
1.82E−03

rgpB
1.3
6.26E−02

asnH
1.3
2.29E−01

yedF
1.3
5.47E−02

accB
1.3
5.35E−02

fhuD
1.3
5.56E−02

yccG
1.3
1.56E−01

ypiH
1.3
2.11E−01

yacC
1.3
2.26E−01

ybeF
1.3
2.13E−01

ygaE
1.3
3.66E−01

ygaF
1.3
1.38E−01

ybeD
1.3
2.18E−01

pi302
1.3
NA

ps302
1.3
NA

ydgB
1.3
1.14E−03

hemK
1.3
6.48E−02

ychH
1.3
2.07E−03

yjhD
1.3
6.68E−03

yfjA
1.3
2.97E−02

ykhD
1.3
1.11E−02

accC
1.3
1.54E−01

ynaC
1.3
1.95E−02

cdsA
1.3
1.94E−01

mtsA
1.3
2.11E−02

murA2
1.3
1.46E−01

ps120
1.3
8.81E−02

yejJ
1.3
1.31E−01

ybhB
1.3
2.25E−01

ysaA
1.3
3.07E−01

yagA
1.3
2.96E−01

pi336
1.3
1.09E−01

yjjD
1.3
3.11E−01

yjcA
1.3
1.25E−02

llrA
1.3
2.06E−01

msmK
1.3
2.57E−01

ybdA
1.3
3.20E−01

yjhF
1.3
5.21E−04

yrbC
1.3
3.38E−01

yhfF
1.3
1.43E−02

yjdE
1.3
1.95E−02

yhcA
1.3
1.56E−01

yjiB
1.3
1.68E−01

yjjC
1.3
3.30E−02

ycfG
1.3
2.08E−01

ycdF
1.3
4.78E−01

ymhC
1.3
4.73E−01

yjcF
1.3
2.48E−01

ps122
1.3
4.37E−02

ywcC
1.3
3.77E−01

xylT
1.3
8.99E−02

araT
1.3
1.20E−02

ycjG
1.3
5.87E−02

yjgF
1.3
3.49E−01

clpE
1.3
2.05E−01

frdC
1.3
5.17E−03

gpdA
1.3
9.30E−02

ychD
1.3
1.91E−01

yniJ
1.3
1.91E−02

glnP
1.3
1.65E−01

butB
1.3
1.31E−01

pyrG
1.3
2.66E−01

ftsW2
1.3
1.21E−01

yhhC
1.3
NA

noxD
1.3
5.88E−03

dinP
1.3
NA

recQ
−1.3
1.59E−01

lplL
−1.3
9.88E−03

xynD
−1.3
1.04E−01

pi225
−1.3
3.54E−01

yjfG
−1.3
4.16E−02

rheB
−1.3
2.17E−01

pi140
−1.3
2.73E−01

rpmGC
−1.3
1.58E−01

yxbC
−1.3
1.51E−02

bglR
−1.3
2.45E−01

yqbl
−1.3
5.59E−01

yghB
−1.3
6.78E−02

yqcA
−1.3
4.10E−01

ynjE
−1.3
1.85E−02

ymbK
−1.3
1.67E−01

ysjD
−1.3
3.18E−01

yweC
−1.3
2.43E−02

galM
−1.3
3.24E−01

ywfC
−1.3
2.66E−01

ps201
−1.3
3.98E−01

pi216
−1.3
3.19E−01

ykbC
−1.3
1.31E−01

yeeB
−1.3
9.29E−03

ileS
−1.3
2.32E−01

yjfB
−1.3
NA

yxeA
−1.3
2.88E−03

yciF
−1.3
1.57E−02

dukA
−1.3
1.34E−02

ywjC
−1.3
NA

yvdA
−1.3
8.07E−02

alaS
−1.3
1.01E−01

ndrH
−1.3
3.45E−03

gadR
−1.3
2.05E−01

yohH
−1.3
8.77E−02

ps119
−1.3
1.74E−01

ycgJ
−1.3
3.16E−02

pi223
−1.3
1.94E−01

yveD
−1.3
3.95E−01

sunL
−1.3
4.87E−01

yjbE
−1.3
1.40E−02

ywbB
−1.3
5.42E−01

yteC
−1.3
1.24E−01

metE
−1.3
2.85E−01

ycbD
−1.3
5.14E−03

purN
−1.3
2.65E−01

pabB
−1.3
6.63E−02

yrgF
−1.3
1.22E−01

ycjM
−1.3
1.23E−01

yljC
−1.3
4.16E−01

yjeF
−1.3
1.21E−01

comGC
−1.3
2.23E−01

yvel
−1.3
6.03E−02

ylcD
−1.3
3.25E−01

dltD
−1.3
NA

pi343
−1.3
5.49E−01

yueD
−1.3
NA

ppiA
−1.3
1.43E−01

dut
−1.3
1.00E−01

purB
−1.3
6.79E−03

ypjC
−1.3
3.96E−01

ytaB
−1.3
NA

cbr
−1.3
2.49E−01

rpmC
−1.3
3.99E−01

ycgH
−1.3
4.57E−01

ybiE
−1.3
2.75E−04

yvdF
−1.3
1.24E−01

rpmD
−1.3
2.07E−03

pi124
−1.3
5.76E−01

pbp2B
−1.3
2.74E−01

ypjA
−1.3
1.21E−01

yscE
−1.3
4.69E−01

ymbC
−1.3
2.22E−02

birA1
−1.4
1.24E−02

hflX
−1.4
1.48E−02

ffh
−1.4
1.60E−01

yecE
−1.4
1.13E−01

ycjl
−1.4
1.31E−01

ps315
−1.4
6.96E−02

comX
−1.4
2.55E−01

pi215
−1.4
1.81E−01

dcdA
−1.4
2.51E−02

glyA
−1.4
1.19E−01

yueA
−1.4
1.22E−04

hsdM
−1.4
1.36E−01

ybiD
−1.4
6.02E−03

queA
−1.4
6.69E−03

ywaD
−1.4
4.66E−01

pi123
−1.4
NA

pi308
−1.4
1.56E−01

phnC
−1.4
1.79E−01

ycjA
−1.4
3.16E−02

ypjl
−1.4
1.99E−01

ykhG
−1.4
4.29E−02

dnaA
−1.4
8.81E−03

phnE
−1.4
7.20E−03

yudD
−1.4
5.29E−01

yrfA
−1.4
2.43E−01

yeiD
−1.4
2.64E−03

rpmF
−1.4
2.56E−02

ysfG
−1.4
2.86E−01

pi249
−1.4
1.60E−01

yuiB
−1.4
3.97E−01

yvaD
−1.4
9.44E−02

recD
−1.4
1.42E−01

yfcB
−1.4
1.72E−01

kdgR
−1.4
7.74E−01

ps304
−1.4
4.41E−02

yqfC
−1.4
NA

yxbF
−1.4
8.14E−05

citE
−1.4
5.93E−02

yfcC
−1.4
2.53E−01

folD
−1.4
9.71E−02

pdhD
−1.4
2.62E−03

ps118
−1.4
1.75E−01

yafF
−1.4
3.14E−02

nagB
−1.5
6.51E−04

ymcF
−1.5
5.55E−01

yveB
−1.5
NA

yxbD
−1.5
3.56E−02

pi319
−1.5
6.45E−02

yoaD
−1.5
3.74E−01

ywaH
−1.5
4.10E−01

gidC
−1.5
9.87E−03

yfbK
−1.5
6.66E−03

yrgA
−1.5
2.34E−01

mgtA
−1.5
1.06E−02

ynbE
−1.5
2.98E−01

yrbE
−1.5
6.75E−02

ynfH
−1.5
3.06E−02

purE
−1.5
4.33E−01

ytjE
−1.5
2.12E−01

ymgF
−1.5
NA

gltS
−1.5
1.23E−01

kdgK
−1.5
3.45E−01

yccH
−1.5
NA

kinB
−1.5
1.09E−01

yuiA
−1.5
6.52E−02

yxbE
−1.6
4.59E−04

yceE
−1.6
4.59E−02

yueE
−1.6
5.60E−03

ywdB
−1.6
3.02E−01

zitR
−1.6
2.11E−01

ypdB
−1.6
1.75E−01

yjgB
−1.6
3.73E−02

argD
−1.6
1.74E−01

ps113
−1.6
2.75E−01

purK
−1.6
NA

yrbB
−1.6
4.82E−02

yjgC
−1.7
8.92E−02

ykiC
−1.7
2.54E−01

purH
−1.7
1.66E−01

rmaB
−1.7
NA

cysD
−1.7
3.29E−01

nrdG
−1.7
5.10E−03

pi104
−1.7
1.19E−01

yscD
−1.7
3.63E−01

gntR
−1.7
1.82E−01

tra983L
−1.7
3.08E−01

gntK
−1.7
4.13E−03

dxsA
−1.7
NA

yjal
−1.7
1.15E−01

ynjB
−1.7
NA

rmaC
−1.7
1.79E−01

pi230
−1.8
2.01E−01

yriD
−1.8
2.06E−01

yhcE
−1.8
2.70E−03

yveF
−1.8
1.91E−01

ytbC
−1.8
2.96E−01

lmrA
−1.8
3.06E−01

yhhA
−1.8
NA

purM
−1.9
1.99E−01

codY
−1.9
1.04E−02

pi122
−1.9
NA

yiiD
−1.9
2.86E−01

argH
−1.9
8.77E−02

yhcH
−2.0
3.61E−01

panE
−2.0
9.68E−03

purF
−2.0
5.26E−03

ps206
−2.0
NA

metB2
−2.0
5.73E−02

guaC
−2.0
1.40E−01

cysM
−2.0
1.88E−02

yviH
−2.1
1.80E−01

uxaC
−2.1
2.96E−01

gmk
−2.1
NA

rpsU
−2.1
NA

ycgA
−2.2
NA

cysK
−2.2
7.17E−03

yshA
−2.3
1.71E−03

ymgH
−2.3
2.11E−01

llrG
−2.3
NA

ps111
−2.4
NA

pi353
−2.5
2.00E−02

yliG
−2.5
2.61E−01

ynjJ
−2.5
1.82E−01

yndE
−2.6
NA

hpt
−2.6
NA

yojC
−2.7
NA

plpC
−2.7
5.16E−03

plpD
−2.7
1.97E−03

ywdA
−2.8
2.03E−01

yviJ
−3.2
NA

purC
−3.3
NA

plpB
−3.4
1.53E−03

purL
−3.4
5.25E−02

plpA
−3.4
1.08E−03

(NA = not available)

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Methods and Means for Regulating Gene Expression

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