The pleiotropic response regulator DegU functions as a priming protein in competence development in Bacillus subtilis

Stochastic switching to competence

Distinct modes of gene expression enable isogenic populations of bacteria to maintain a diversity of phenotypes and to rapidly adapt to environmental changes. Competence development for DNA transformation in Bacillus subtilis has become a paradigm for a multimodal system which implements a genetic switch through a nonlinear positive feedback of a transcriptional master regulator. Recent advances in quantitative analysis at the single cell level in conjunction with mathematical modeling allowed a molecular level understanding of the switching probability between the noncompetent state and the competent state. It has been discovered that the genetic switching probability may be tuned by controlling noise in the transcription of the master regulator of competence, by timing of its expression, and by rewiring of the control circuit.

The Pta-AckA pathway controlling acetyl phosphate levels and the phosphorylation state of the DegU orphan response regulator both play a role in regulating Listeria monocytogenes motility and chemotaxis

DegU is considered to be an orphan response regulator in Listeria monocytogenes since the gene encoding the cognate histidine kinase DegS is absent from the genome. We have previously shown that DegU is involved in motility, chemotaxis and biofilm formation and contributes to L. monocytogenes virulence. Here, we have investigated the role of DegU phosphorylation in Listeria and shown that DegS of Bacillus subtilis can phosphorylate DegU of L. monocytogenes in vitro. We introduced the B. subtilis degS gene into L. monocytogenes, and showed that this leads to highly increased expression of motility and chemotaxis genes, in a DegU-dependent fashion. We inactivated the predicted phosphorylation site of DegU by replacing aspartate residue 55 with asparagine and showed that this modified protein (DegU(D55N)) is no longer phosphorylated by DegS in vitro. We show that although the unphosphorylated form of DegU retains much of its activity in vivo, expression of motility and chemotaxis genes is lowered in the degU(D55N) mutant. We also show that the small-molecular-weight metabolite acetyl phosphate is an efficient phosphodonor for DegU in vitro and our evidence suggests this is also true in vivo. Indeed, a L. monocytogenesDeltaptaDeltaackA mutant that can no longer synthesize acetyl phosphate was found to be strongly affected in chemotaxis and motility gene expression and biofilm formation. Our findings suggest that phosphorylation by acetyl phosphate could play an important role in modulating DegU activity in vivo, linking its phosphorylation state to the metabolic status of L. monocytogenes.

Involvement of nitrogen regulation in Bacillus subtilis degU expression

Bacillus subtilis DegS-DegU belongs to a bacterial two-component system that controls many processes, including the production of exocellular proteases and competence development. It was found that when the glutamine synthetase gene glnA, which is involved in nitrogen regulation, was disrupted, the expression of the response regulator degU gene was increased. Deletion analysis and 5'-end mapping of the degU transcripts showed that the increase was caused by induction of a promoter (P2) located before the degU gene. Disruption of tnrA, a global regulator of nitrogen regulation, eliminated the P2 promoter induction by the glnA mutation. The fact that the P2 promoter is under nitrogen regulation was demonstrated by an increase in P2 expression with nitrogen-limited growth. It was also found by primer extension analysis that degU was transcribed by another promoter, P3, that is located downstream of P2. Efficient expression of P3 was dependent on phosphorylated DegU, as inactivation of the sensor kinase gene, degS, resulted in the loss of degU expression, although less efficient stimulation of degU expression was also observed with an enhanced level of DegU in a degS-deficient mutant. The promoter located upstream of the degSU operon, designated the P1 promoter here, was insensitive to glnA and degU mutations. These results suggest that degU expression is controlled by the three promoters under different growth conditions.

Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis

The emerging field of synthetic genomics is expected to facilitate the generation of microorganisms with the potential to achieve a sustainable society. One approach towards this goal is the reduction of microbial genomes by rationally designed deletions to create simplified cells with predictable behavior that act as a platform to build in various genetic systems for specific purposes. We report a novel Bacillus subtilis strain, MBG874, depleted of 874 kb (20%) of the genomic sequence. When compared with wild-type cells, the regulatory network of gene expression of the mutant strain is reorganized after entry into the transition state due to the synergistic effect of multiple deletions, and productivity of extracellular cellulase and protease from transformed plasmids harboring the corresponding genes is remarkably enhanced. To our knowledge, this is the first report demonstrating that genome reduction actually contributes to the creation of bacterial cells with a practical application in industry. Further systematic analysis of changes in the transcriptional regulatory network of MGB874 cells in relation to protein productivity should facilitate the generation of improved B. subtilis cells as hosts of industrial protein production.

Promoter selectivity of the Bacillus subtilis response regulator DegU, a positive regulator of the fla/che operon and sacB

Background

The response regulator DegU and its cognate histidine kinase DegS constitute a two-component system in the Gram-positive soil bacterium Bacillus subtilis. Unphosphorylated and phosphorylated forms of DegU are known to activate target gene transcription in B. subtilis. Although phosphorylated DegU (DegU-P) regulates more than one hundred and twenty genes, the targets of unphosphorylated DegU are unknown, except for comK.

Results

We found that the fla/che (flagella and chemotaxis) operon is positively regulated by unphosphorylated DegU. The effect was most prominent in a strain bearing the functional swrAA gene, a positive regulator of fla/che. Unphosphorylated DegU bound to two regions in the fla/che regulatory region containing an inverted repeat-like sequence that resembles the inverted repeat (IR) in the comK promoter. Mutational analysis revealed that positive regulation of fla/che by SwrAA requires DegU-binding. An analysis of the DegU-P-regulated gene sacB (levansucrase gene) by footprint and mutational analyses revealed that DegU-P bound to a direct repeat (DR) of the DegU-recognition motifs, which has been shown to be functional in vivo, while unphosphorylated DegU did not. These results strongly suggest that the arrangement of the DegU-binding motifs determines whether unphosphorylated DegU or DegU-P binds to the sacB promoter. The hypothesis was confirmed by observing degS-independent expression when the DR in the sacB-lacZ fusion was changed to an IR, suggesting that unphosphorylated DegU regulates the sacB promoter through the newly created IR. This was confirmed by binding of unphosphorylated DegU to the IR in the sacB promoter.

Conclusion

This study demonstrated that DegU positively regulates flgB and sacB through its binding to the promoter regions. We demonstrated that DegU-P prefers binding to DR but not to IR in the sacB promoter.

Gradual activation of the response regulator DegU controls serial expression of genes for flagellum formation and biofilm formation inBacillus subtilis

In natural environments, bacteria fluctuate between growth as motile cells and growth as sessile, biofilm-forming cells. However, what controls the transition between these two-growth modes in Bacillus subtilis is not well understood yet. The degU mutation prevents both flagellum formation and biofilm formation, suggesting that one of the transition mechanisms may underlie regulation of the DegU activity. The expression profiles of DegU-regulated genes differed; flagellar genes and several unknown genes were expressed during the exponential phase, whereas other genes were induced in the stationary phase. The degS mutation did not affect transcription of the flgB-sigD operon, but reduced transcription of sigma(D)-dependent flagellar genes, degU and other DegU-regulated genes. In addition, the degQ mutation did not affect transcription of flagellar genes but reduce transcription of other DegU-regulated genes. Purified DegQ protein stimulated phosphotransfer from phospho-DegS to DegU in vitro. Moreover, DegU binds the promoter region of flgB with a high affinity, whereas DegU binds to the promoter regions of other DegU-regulated genes with a low affinity and in a DegS-dependent manner. Taken together, we propose that a gradual increase in DegU and phospho-DegU levels induces a transition from growth as motile cells to growth as sessile, biofilm-forming cells.

DegU and YczE positively regulate the synthesis of bacillomycin D by Bacillus amyloliquefaciens strain FZB42

Environmental strain Bacillus amyloliquefaciens FZB42 differs from the domesticated model organism of the same genus, Bacillus subtilis 168, in its ability to promote plant growth and suppress plant-pathogenic organisms present in the rhizosphere. This behavior is exerted mainly through the production of several nonribosomal cyclic lipopeptides and polyketides, which exhibit a broad range of action against phytopathogenic bacteria, fungi, and nematodes. Here, we provide evidence that the synthesis of the main antifungal agent of B. amyloliquefaciens FZB42, bacillomycin D, is regulated in multiple layers. Expression of the bacillomycin D operon (bmy) is dependent on a single sigma(A)-dependent promoter, P(bmy) and is favored in its natural host by the small regulatory protein DegQ. The global regulators DegU and ComA are required for the full transcriptional activation of bmy. DegU retains a key role since it binds directly to two sites located upstream of the bacillomycin D promoter. Moreover, both DegU and a transmembrane protein of unknown function, YczE, act on a later level of gene expression, exerting their posttranscriptional effects in a hitherto-unknown manner.

Basal expression rate of comK sets a 'switching-window' into the K-state of Bacillus subtilis

Bacillus subtilis cell population divides into a competent fraction and a non-competent fraction in the stationary phase. The transition from the non-competent state (with basal ComK concentration) to the K-state (with high ComK concentration) behaves like a bistable switch. To better understand the mechanism that sets the fraction of cells that switch into the K-state (K-fraction), we characterized the basal comK expression in individual non-competent cells and found a large cell-to-cell variation. Basal expression rate increased exponentially, reached a maximum and decreased towards zero in the stationary phase. Concomitantly, the intrinsic switching rate increased and decreased with a time lag. When switching was induced prematurely by reduction of ComK proteolysis, the K-fraction increased strongly. Our data support a model in which the average basal level of ComK raises during late exponential phase and due to noise in basal comK expression only those cells that are on the high end of comK expression trigger the autocatalytic feedback for ComK transcription. We show that a subsequent shut-down of basal expression rate sets a 'time-window' for switching and is thus involved in determining the K-fraction in the bimodal population.

DegU co-ordinates multicellular behaviour exhibited by Bacillus subtilis

Unicellular organisms use a variety of mechanisms to co-ordinate activity within a community and accomplish complex multicellular processes. Because some of the processes that are exhibited by one species can be physiologically incompatible, it raises the question of how entry into these different pathways is regulated. In the Gram-positive bacterium Bacillus subtilis, genetic competence, swarming motility, biofilm formation, complex colony architecture and protease production are all regulated by the response regulator DegU. DegU appears to integrate environmental signals and co-ordinate multicellular behaviours that are subsequently manifested at different levels of DegU phosphorylation. Data are presented which indicate that: (i) swarming motility is activated by very low levels of DegU approximately P that can be generated independently from its cognate sensor kinase DegS; (ii) complex colony architecture is activated by low levels of DegU approximately P that are produced in a DegS-dependent manner to activate transcription of yvcA, a novel gene required for complex colony architecture; and (iii) high levels of DegU approximately P inhibit complex colony architecture and swarming motility but are required prior to the activation of exoprotease production. A model is proposed to explain why such a system may have evolved within B. subtilis to control these multicellular processes through a single regulator.

Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein

Competence for genetic transformation in the bacterium Bacillus subtilis is a bistable differentiation process governed by the minor groove DNA binding protein ComK. No detectable comK transcription occurs in the absence of an intact comK gene, indicating that ComK has auto-activating properties. ComK auto-stimulation, which is dependent on ComK binding to the comK promoter, is a critical step in competence development, ensuring quick and high-level expression of the late-competence genes. Auto-stimulation is also essential for the bistable expression pattern of competence. Here, we demonstrate that ComK acts as an activator at its own promoter by antagonizing the action of two repressors, Rok and CodY. Importantly, antirepression occurs without preventing binding of the repressing proteins, suggesting that ComK and the repressors might bind at distinct surfaces of the DNA helix. DegU, a DNA binding protein known to increase the affinity of ComK for its own promoter, potentiates the antirepression activity of ComK. We postulate that antirepression is primarily achieved through modulation of DNA topology. Although to our knowledge ComK is the only DNA binding protein shown to act in this novel fashion, other minor groove binding proteins may act similarly.

A single, specific thymine mutation in the ComK-binding site severely decreases binding and transcription activation by the competence transcription factor ComK of Bacillus subtilis

The competence transcription factor ComK plays a central role in competence development in Bacillus subtilis by activating the transcription of the K regulon. ComK-activated genes are characterized by the presence of a specific sequence to which ComK binds, a K-box, in their upstream DNA region. Each K-box consists of two AT-boxes with the consensus sequence AAAA-(N)(5)-TTTT, which are separated by a flexible spacer resulting in either two, three, or four helical turns between the starting nucleotides of the repeating AT-box units. In this study, the effects of potential determinants of ComK regulation in K-boxes were investigated by testing ComK's transcription activation and DNA-binding affinity on altered K-boxes with mutations either in the spacer between the AT-boxes or in the consensus sequence of the AT-boxes. The most striking result demonstrates the importance of the second thymine base in the AT-boxes. Mutation of this T into a guanine resulted in a threefold reduction in transcription activation and DNA binding by ComK. Transcription activation, as well as DNA binding, was almost completely abolished when both AT-boxes contained a T(2)-to-G mutation. This result was corroborated by in silico analyses demonstrating that a combination of mutations at the T(2) positions of both AT-boxes is not found among any ComK-activated K-boxes, indicating that at least one consensus T(2) position is required to maintain a functional K-box. The results suggest an important structural role for T(2) in ComK binding, probably by its specific position in the minor groove of the DNA.

Induction of competence regulons as a general response to stress in gram-positive bacteria

Bacterial transformation, a programmed mechanism for genetic exchange originally discovered in Streptococcus pneumoniae, is widespread in bacteria. It is based on the uptake and integration of exogenous DNA into the recipient genome. This review examines whether induction of competence for genetic transformation is a general response to stress in gram-positive bacteria. It compares data obtained with bacteria chosen for their different lifestyles, the soil-dweller Bacillus subtilis and the major human pathogen S. pneumoniae. The review focuses on the relationship between competence and other global responses in B. subtilis, as well as on recent evidence for competence induction in response to DNA damage or antibiotics and for the ability of S. pneumoniae to use competence as a substitute for SOS. This comparison reveals that the two species use different fitness-enhancing strategies in response to stress conditions. Whereas B. subtilis combines competence and SOS induction, S. pneumoniae relies only on competence to generate genetic diversity through transformation.

Comparative evaluation of adhesion, surface properties, and surface protein composition of Listeria monocytogenes strains after cultivation at constant pH of 5 and 7

AIMS

To analyse the cellular mechanisms that influence Listeria monocytogenes adhesion onto inert surfaces under acidic growth conditions.

METHODS AND RESULTS

The adhesion capability of all the strains was significantly reduced after cultivation at constant pH 5 than at constant pH 7 and the cell surface was significantly less hydrophobic at pH 5 than at 7. At pH 5, the analyses of surface protein composition revealed that the flagellin was downregulated for all strains, which was confirmed by the absence of flagella and the P60 protein was upregulated for L. monocytogenes EGD-e, X-Li-mo 500 and 111. The use of L. monocytogenes EGD mutants revealed that flagellin could be involved in the adhesion process, but not P60 protein. It was also observed that the hydrophobic character was not linked to the presence or the absence of flagellin or P60 protein at the cell surface of L. monocytogenes.

CONCLUSIONS

The decrease of L. monocytogenes adhesion at pH 5 could be attributed to the downregulation of the flagellin synthesis under the acidic conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

Conservation of food product at pH 5 will delay bacterial adhesion and biofilm formation during food processing on inert surfaces when the product is contaminated with L. monocytogenes.

Bistability in bacteria

Gene expression in bacteria is traditionally studied from the average behaviour of cells in a population, which has led to the assumption that under a particular set of conditions all cells express genes in an approximately uniform manner. The advent of methods for visualizing gene expression in individual cells reveals, however, that populations of genetically identical bacteria are sometimes heterogeneous, with certain genes being expressed in a non-uniform manner across the population. In some cases, heterogeneity is manifested by the bifurcation into distinct subpopulations, and we adopt the common usage, referring to this phenomenon as bistability. Here we consider four cases of bistability, three from Bacillus subtilis and one from Escherichia coli, with an emphasis on random switching mechanisms that generate alternative cell states and the biological significance of phenotypic heterogeneity. A review describing additional examples of bistability in bacteria has been published recently.

Response regulator DegU of Listeria monocytogenes regulates the expression of flagella-specific genes

An isogenic mutant of Listeria monocytogenes EGD with a deletion of the response regulator gene degU showed a lack of motility due to the absence of flagella. In the present study, we used two-dimensional gel electrophoresis, mass-spectrometry and microarray analyses to identify the listerial genes that depend on DegU for expression. We found that the two L. monocytogenes operons encoding flagella-specific genes and the monocistronically transcribed flaA gene are positively regulated by DegU at 24 degrees C, but are not expressed at 37 degrees C.

Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop

High expression of the transcriptional activator ComK occurs in 10-20% of the cells in stationary phase cultures of Bacillus subtilis strain 168. ComK drives the expression of more than 100 genes constituting the semidormant K-state, distinct from sporulation and vegetative growth. Among the genes so activated are those that permit competence for genetic transformation. We have addressed the origin of bistability in expression of ComK. We show that bistability requires positive autoregulation at the promoter of comK, but not a potential toggle switch, in which ComK represses the promoter of rok and Rok represses the promoter of comK. We further address the source of the noise that results in the stochastic selection of cells that will express comK. A revised model for the regulation of comK expression is proposed that partially explains bistability.

Stripping Bacillus: ComK auto-stimulation is responsible for the bistable response in competence development

In Bacillus subtilis competence for genetic transformation develops only in a subpopulation of cells in an isogenic culture. The molecular mechanisms underlying this phenotypic heterogeneity are unknown. In this study, we stepwise simplify the signal transduction cascade leading to competence, yielding a strain devoid of all regulatory inputs for this process that have been identified so far. We demonstrate that auto-stimulation of ComK, the master regulator for competence development, is essential and in itself can be sufficient to generate a bistable expression pattern. We argue that transcriptional regulation determines the threshold of ComK to initiate the auto-stimulatory response, and that the basal level of ComK (in a wild-type strain governed by MecA-mediated proteolytic control) determines the fraction of cells that reach this threshold, and thus develop competence.

Construction and characterization of Listeria monocytogenes mutants with in-frame deletions in the response regulator genes identified in the genome sequence

Two-component systems are widely distributed in prokaryotes where they control gene expression in response to diverse stimuli. To study the role of the sixteen putative two-component systems of Listeria monocytogenes systematically, in frame deletions were introduced into 15 out of the 16 response regulator genes and the resulting mutants were characterized. With one exception the deletion of the individual response regulator genes has only minor effects on in vitro and in vivo growth of the bacteria. The mutant carrying a deletion in the ortholog of the Bacillus subtilis response regulator gene degU showed a clearly reduced virulence in mice, indicating that DegU is involved in the regulation of virulence-associated genes.

Characterization of DegU, a response regulator inListeria monocytogenes, involved in regulation of motility and contributes to virulence

The degU (lmo2515) gene encodes a putative response regulator in the food-borne pathogen Listeria monocytogenes. It has 63% amino acid identity to the DegU response regulator of Bacillus subtilis. We have characterized the degU gene product in L. monocytogenes EGD by generation of a deletion mutant. The DeltadegU mutant was found to be non-motile in motility plate assay and no flagellin was detected. The mutant was attenuated in challenge of mice. Northern blot analysis suggested that the degU gene product is a transcriptional activator of the flagellin gene, flaA, at 25 degrees C. However, the degU gene product had no influence on the transcription of prfA encoding the major virulence regulator, PrfA. The results indicate that the putative DegU response regulator is a pleiotropic regulator involved in expression of both motility at low temperature and in vivo virulence in mice.

DegU-P represses expression of the motility fla-che operon in Bacillus subtilis

Bacillus subtilis implements several adaptive strategies to cope with nutrient limitation experienced at the end of exponential growth. The DegS-DegU two-component system is part of the network involved in the regulation of postexponential responses, such as competence development, the production of exoenzymes, and motility. The degU32(Hy) mutation extends the half-life of the phosphorylated form of DegU (DegU-P); this in turn increases the production of alkaline protease, levan-sucrase, and other exoenzymes and inhibits motility and the production of flagella. The expression of the flagellum-specific sigma factor SigD, of the flagellin gene hag, and of the fla-che operon is strongly reduced in a degU32(Hy) genetic background. To investigate the mechanism of action of DegU-P on motility, we isolated mutants of degU32(Hy) that completely suppressed the motility deficiency. The mutations were genetically mapped and characterized by PCR and sequencing. Most of the mutations were found to delete a transcriptional termination signal upstream of the main flagellar operon, fla-che, thus allowing transcriptional readthrough from the cod operon. Two additional mutations improved the sigmaA-dependent promoter sequence of the fla-che operon. Using an electrophoretic mobility shift assay, we have demonstrated that purified DegU binds specifically to the PA promoter region of the fla-che operon. The data suggest that DegU represses transcription of the fla-che operon, and they indicate a central role of the operon in regulating the synthesis and assembly of flagella.

Binding of response regulator DegU to the aprE promoter is inhibited by RapG, which is counteracted by extracellular PhrG in Bacillus subtilis

We screened the putative rap-phr (response regulator aspartyl-phosphate phosphatase-phosphatase regulator) systems identified in the Bacillus subtilis genome for a rap gene that affects aprE (alkaline protease gene) expression by using a multicopy plasmid. We found that rapG was involved in the regulation of aprE, which belongs to the regulon of DegU, the response regulator of the DegS-DegU two-component system. Disruption of rapG and phrG resulted in enhancement and reduction of aprE-lacZ expression, respectively, suggesting that PhrG inhibits RapG activity. Addition of 1-30 nM of a synthetic pentapeptide (PhrG; NH2-EKMIG-COOH) to the phrG disruptant completely rescued aprE-lacZ expression, indicating that the PhrG peptide is indeed involved in aprE-lacZ expression. Surprisingly, either introduction of multicopy phrG or addition of the PhrG peptide at high concentrations (100-300 nM) to the phrG cells decreased aprE-lacZ expression. These results are reminiscent of the previous observation that at higher concentrations the PhrC peptide inhibits srfA-lacZ expression directed by ComA, the regulator of the ComP-ComA two-component system. Because the Rap proteins belong to a family of aspartyl protein phosphatases, we tried to investigate the possible influence of RapG on dephosphorylation of DegU-P (phosphorylated DegU) in vitro. RapG, however, did not affect dephosphorylation of DegU-P under the adopted experimental conditions. Therefore, we hypothesized that RapG might inhibit the binding activity of DegU to the target promoters. We analysed the interaction of DegU and RapG using the aprE promoter and another target, a comK promoter. Gel shift analysis revealed that RapG served as the inhibitor of DegU binding to the promoter regions of aprE and comK and that this inhibition was counteracted by the PhrG peptide.

The Bacillus subtilis transition state regulator AbrB binds to the -35 promoter region of comK

Genetic competence is a differentiation process initiated by Bacillus subtilis as a result of nutritional deprivation, and is controlled by a complex signal transduction cascade. The promoter of comK, encoding the competence transcription factor, is regulated by at least four different transcription factors: Rok, CodY, DegU and ComK itself. Genetic data have shown that comK expression is influenced by the transition state regulator AbrB as well. In this paper we show that AbrB binds specifically to the comK promoter and covers the RNA polymerase binding site, making it the fifth transcription factor regulating the activity of the comK promoter.

Adaptive, or stationary-phase, mutagenesis, a component of bacterial differentiation in Bacillus subtilis

Adaptive (stationary-phase) mutagenesis occurs in the gram-positive bacterium Bacillus subtilis. Furthermore, taking advantage of B. subtilis as a paradigm for the study of prokaryotic differentiation and development, we have shown that this type of mutagenesis is subject to regulation involving at least two of the genes that are involved in the regulation of post-exponential phase prokaryotic differentiation, i.e., comA and comK. On the other hand, a functional RecA protein was not required for this type of mutagenesis. The results seem to suggest that a small subpopulation(s) of the culture is involved in adaptive mutagenesis and that this subpopulation(s) is hypermutable. The existence of such a hypermutable subpopulation(s) raises important considerations with respect to evolution, the development of specific mutations, the nature of bacterial populations, and the level of communication among bacteria in an ecological niche.

A MecA paralog, YpbH, binds ClpC, affecting both competence and sporulation

ComK, the master regulator of competence, is degraded by the general stress-related protease ClpCP but must be targeted to this protease by binding to the adapter protein MecA. The genome of Bacillus subtilis contains a paralog of mecA, ypbH. We show in the present study that YpbH, like MecA, binds ClpC and that its elimination or overproduction affects competence and sporulation.

Rok (YkuW) regulates genetic competence in Bacillus subtilis by directly repressing comK

The Rok (YkuW) protein acts as a negative regulator of comK, which encodes the competence transcription factor of Bacillus subtilis. In the absence of Rok, ComK is overproduced, and when excess Rok is present comK transcription is inhibited. Rok acts transcriptionally to repress comK expression but does not affect ComK stability, which is controlled by the MecA switch. Gel-shift assays show that Rok binds directly to a DNA fragment that contains the comK promoter. SinR and AbrB act negatively on rok transcription, and the inactivation of rok bypasses the positive requirements for sinR and abrB for the expression of comK. Therefore, the dependence of comK expression on SinR and AbrB may be a result of their repression of rok transcription. It has also been shown in vivo that Rok and ComK can indivi-dually repress rok transcription, and that Rok and ComK bind to the rok promoter in vitro. These interactions establish feedback loops, and the roles of these circuits are discussed.

Loss-of-function mutations in yjbD result in ClpX- and ClpP-independent competence development of Bacillus subtilis

Mutations in clpP and clpX have pleiotropic effects on growth and developmentally regulated gene expression in Bacillus subtilis. ClpP and ClpX are needed for expression of comK, encoding the competence transcription factor required for the expression of genes within the competence regulon. ClpP, in combination with the ATPase ClpC, degrades the inhibitor of ComK, MecA. Proteolysis of MecA is stimulated by a small protein, ComS, which interacts with MecA. Suppressor mutations (cxs) were isolated that bypass the requirement for clpX for comK expression. These were found also to overcome the defect in comK expression conferred by a clpP mutation. These mutations were identified as missense mutations (cxs-5, -7 and -12) and a nonsense (UAG) codon substitution (cxs-10) in the yjbD coding sequence in a locus linked to mecA. That a yjbD disruption confers the cxs phenotype, together with its complementation by an ectopically expressed copy of yjbD, indicated that the suppressor alleles bear recessive, loss-of-function mutations of yjbD. ClpP- and ClpX-independent comK expression rendered by inactivation of yjbD was still medium-dependent and required ComS. MecA levels in a clpP-yjbD mutant were lower that those of clpP mutant cells and ComK protein concentration in the clpP mutant was restored to wild-type levels by the yjbD mutation. Consequently, the yjbD mutation bypasses the defect in competence development conferred by clpP and clpX. YjbD protein is barely detectable in wild-type cells, but is present in large amounts in the clpP mutant cells. The results suggest that the role of ClpP in competence development is to degrade YjbD protein so that ComS can productively interact with the MecA-ClpC-ComK complex. Alternatively, the result could suggest that YjbD has a negative effect on regulated proteolysis and that MecA is degraded independently of ClpP when YjbD is absent.

DNA microarray analysis of Bacillus subtilis DegU, ComA and PhoP regulons: an approach to comprehensive analysis of B.subtilis two-component regulatory systems

We have analyzed the regulons of the Bacillus subtilis two-component regulators DegU, ComA and PhoP by using whole genome DNA microarrays. For these experiments we took the strategy that the response regulator genes were cloned downstream of an isopropyl-beta-D-thiogalactopyranoside-inducible promoter on a multicopy plasmid and expressed in disruptants of the cognate sensor kinase genes, degS, comP and phoR, respectively. The feasibility of this experimental design to detect target genes was demonstrated by the following two results. First, expression of lacZ fusions of aprE, srfA and ydhF, the target genes of DegU, ComA and PhoP, respectively, was stimulated in their cognate sensor kinase-deficient mutants upon overproduction of the regulators. Secondly, by microarray analysis most of the known target genes for the regulators were detected and, where unknown genes were found, the regulator dependency of several of them was demonstrated. As the mutants used were deficient in the kinase genes, these results show that target candidates can be detected without signal transduction. Using this experimental design, we identified many genes whose dependency on the regulators for expression had not been known. These results suggest the applicability of the strategy to the comprehensive transcription analysis of the B.subtilis two-component systems.