Rapid isolation of RNA polymerase from sporulating cells of Bacillus subtilis

Two broadly conserved families of polyprenyl-phosphate transporters

Peptidoglycan and almost all surface glycopolymers in bacteria are built in the cytoplasm on the lipid carrier undecaprenyl phosphate (UndP)^1-4. These UndP-linked precursors are transported across the membrane and polymerized or directly transferred to surface polymers, lipids or proteins. UndP is then flipped to regenerate the pool of cytoplasmic-facing UndP. The identity of the flippase that catalyses transport has remained unknown. Here, using the antibiotic amphomycin that targets UndP^5-7, we identified two broadly conserved protein families that affect UndP recycling. One (UptA) is a member of the DedA superfamily⁸; the other (PopT) contains the domain DUF368. Genetic, cytological and syntenic analyses indicate that these proteins are UndP transporters. Notably, homologues from Gram-positive and Gram-negative bacteria promote UndP transport in Bacillus subtilis, indicating that recycling activity is broadly conserved among family members. Inhibitors of these flippases could potentiate the activity of antibiotics targeting the cell envelope.

Rapid preparation of 6S RNA-free B. subtilis σA-RNA polymerase and σA

The regulatory 6S-1 and 6S-2 RNAs of B. subtilis bind to the housekeeping RNA polymerase holoenzyme (σ^A-RNAP) with submicromolar affinity. We observed copurification of endogenous 6S RNAs from a published B. subtilis strain expressing a His-tagged RNAP. Such 6S RNA contaminations in σ^A-RNAP preparations reduce the fraction of enzymes that are accessible for binding to DNA promoters. In addition, this leads to background RNA synthesis by σ^A-RNAP utilizing copurified 6S RNA as template for the synthesis of short abortive transcripts termed product RNAs (pRNAs). To avoid this problem we constructed a B. subtilis strain expressing His-tagged RNAP but carrying deletions of the two 6S RNA genes. The His-tagged, 6S RNA-free σ^A-RNAP holoenzyme can be prepared with sufficient purity and activity by a single affinity step. We also report expression and separate purification of B. subtilis σ^A that can be added to the His-tagged RNAP to maximize the amount of holoenzyme and, by inference, in vitro transcription activity.

Transcriptional Regulation and Mechanism of SigN (ZpdN), a pBS32-Encoded Sigma Factor in Bacillus subtilis

Laboratory strains of Bacillus subtilis encode many alternative sigma factors, each dedicated to expressing a unique regulon such as those involved in stress resistance, sporulation, and motility. The ancestral strain of B. subtilis also encodes an additional sigma factor homolog, ZpdN, not found in lab strains due to being encoded on the large, low-copy-number plasmid pBS32, which was lost during domestication. DNA damage triggers pBS32 hyperreplication and cell death in a manner that depends on ZpdN, but how ZpdN mediates these effects is unknown. Here, we show that ZpdN is a bona fide sigma factor that can direct RNA polymerase to transcribe ZpdN-dependent genes, and we rename ZpdN SigN accordingly. Rend-seq (end-enriched transcriptome sequencing) analysis was used to determine the SigN regulon on pBS32, and the 5' ends of transcripts were used to predict the SigN consensus sequence. Finally, we characterize the regulation of SigN itself and show that it is transcribed by at least three promoters: P_sigN1 , a strong SigA-dependent LexA-repressed promoter; P_sigN2 , a weak SigA-dependent constitutive promoter; and P_sigN3 , a SigN-dependent promoter. Thus, in response to DNA damage SigN is derepressed and then experiences positive feedback. How cells die in a pBS32-dependent manner remains unknown, but we predict that death is the product of expressing one or more genes in the SigN regulon.IMPORTANCE Sigma factors are utilized by bacteria to control and regulate gene expression. Some sigma factors are activated during times of stress to ensure the survival of the bacterium. Here, we report the presence of a sigma factor that is encoded on a plasmid that leads to cellular death after DNA damage.

SweC and SweD are essential co-factors of the FtsEX-CwlO cell wall hydrolase complex in Bacillus subtilis

The peptidoglycan (PG) sacculus is composed of long glycan strands cross-linked together by short peptides forming a covalently closed meshwork that protects the bacterial cell from osmotic lysis and specifies its shape. PG hydrolases play essential roles in remodeling this three-dimensional network during growth and division but how these autolytic enzymes are regulated remains poorly understood. The FtsEX ABC transporter-like complex has emerged as a broadly conserved regulatory module in controlling cell wall hydrolases in diverse bacterial species. In most characterized examples, this complex regulates distinct PG hydrolases involved in cell division and is intimately associated with the cytokinetic machinery called the divisome. However, in the gram-positive bacterium Bacillus subtilis the FtsEX complex is required for cell wall elongation where it regulates the PG hydrolase CwlO that acts along the lateral cell wall. To investigate whether additional factors are required for FtsEX function outside the divisome, we performed a synthetic lethal screen taking advantage of the conditional essentiality of CwlO. This screen identified two uncharacterized factors (SweD and SweC) that are required for CwlO activity. We demonstrate that these proteins reside in a membrane complex with FtsX and that amino acid substitutions in residues adjacent to the ATPase domain of FtsE partially bypass the requirement for them. Collectively our data indicate that SweD and SweC function as essential co-factors of FtsEX in controlling CwlO during cell wall elongation. We propose that factors analogous to SweDC function to support FtsEX activity outside the divisome in other bacteria.

Evidence that regulation of intramembrane proteolysis is mediated by substrate gating during sporulation in Bacillus subtilis

During the morphological process of sporulation in Bacillus subtilis two adjacent daughter cells (called the mother cell and forespore) follow different programs of gene expression that are linked to each other by signal transduction pathways. At a late stage in development, a signaling pathway emanating from the forespore triggers the proteolytic activation of the mother cell transcription factor σ^K. Cleavage of pro-σ^K to its mature and active form is catalyzed by the intramembrane cleaving metalloprotease SpoIVFB (B), a Site-2 Protease (S2P) family member. B is held inactive by two mother-cell membrane proteins SpoIVFA (A) and BofA. Activation of pro-σ^K processing requires a site-1 signaling protease SpoIVB (IVB) that is secreted from the forespore into the space between the two cells. IVB cleaves the extracellular domain of A but how this cleavage activates intramembrane proteolysis has remained unclear. Structural studies of the Methanocaldococcus jannaschii S2P homolog identified closed (substrate-occluded) and open (substrate-accessible) conformations of the protease, but the biological relevance of these conformations has not been established. Here, using co-immunoprecipitation and fluorescence microscopy, we show that stable association between the membrane-embedded protease and its substrate requires IVB signaling. We further show that the cytoplasmic cystathionine-β-synthase (CBS) domain of the B protease is not critical for this interaction or for pro-σ^K processing, suggesting the IVB-dependent interaction site is in the membrane protease domain. Finally, we provide evidence that the B protease domain adopts both open and closed conformations in vivo. Collectively, our data support a substrate-gating model in which IVB-dependent cleavage of A on one side of the membrane triggers a conformational change in the membrane-embedded protease from a closed to an open state allowing pro-σ^K access to the caged interior of the protease.

Regulated Intramembrane Proteolysis is a broadly conserved mechanism for transducing information across lipid bilayers. In these signaling pathways a protease on one side of the membrane triggers the activation of a membrane-embedded protease that cleaves its substrate within or adjacent to the cytoplasmic face of the membrane. Site-2 metalloproteases (S2P) are the most commonly used intramembrane cleaving proteases in these pathways but the mechanism by which cleavage on one side of the membrane triggers intramembrane proteolysis remains poorly understood. Here, we provide evidence for a substrate-gating model in which an extracellular signaling protease triggers a conformational change in a S2P family member from a closed to an open conformation allowing its substrate access to the catalytic center of the enzyme.

X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway

Reiterative transcription is a noncanonical form of RNA synthesis in which a nucleotide specified by a single base in the DNA template is repetitively added to the nascent transcript. Here we determined the crystal structure of an RNA polymerase, the bacterial enzyme from Thermus thermophilus, engaged in reiterative transcription during transcription initiation at a promoter resembling the pyrG promoter of Bacillus subtilis The structure reveals that the reiterative transcript detours from the dedicated RNA exit channel and extends toward the main channel of the enzyme, thereby allowing RNA extension without displacement of the promoter recognition σ-factor. Nascent transcripts containing reiteratively added G residues are eventually extended by nonreiterative transcription, revealing an atypical pathway for the formation of a transcription elongation complex.

Salt-sensitivity of σ(H) and Spo0A prevents sporulation of Bacillus subtilis at high osmolarity avoiding death during cellular differentiation

The spore-forming bacterium Bacillus subtilis frequently experiences high osmolarity as a result of desiccation in the soil. The formation of a highly desiccation-resistant endospore might serve as a logical osmostress escape route when vegetative growth is no longer possible. However, sporulation efficiency drastically decreases concomitant with an increase in the external salinity. Fluorescence microscopy of sporulation-specific promoter fusions to gfp revealed that high salinity blocks entry into the sporulation pathway at a very early stage. Specifically, we show that both Spo0A- and SigH-dependent transcription are impaired. Furthermore, we demonstrate that the association of SigH with core RNA polymerase is reduced under these conditions. Suppressors that modestly increase sporulation efficiency at high salinity map to the coding region of sigH and in the regulatory region of kinA, encoding one the sensor kinases that activates Spo0A. These findings led us to discover that B. subtilis cells that overproduce KinA can bypass the salt-imposed block in sporulation. Importantly, these cells are impaired in the morphological process of engulfment and late forespore gene expression and frequently undergo lysis. Altogether our data indicate that B. subtilis blocks entry into sporulation in high-salinity environments preventing commitment to a developmental program that it cannot complete.

The interaction of ω2 with the RNA polymerase β' subunit functions as an activation to repression switch

The ω gene is encoded in broad-host range and low-copy plasmids. It is genetically linked to antibiotic resistance genes of the major human pathogens of phylum Firmicutes. The homodimeric forms of ω (ω₂) coordinate the plasmid copy number control, faithful partition (ω₂ and δ₂) and better-than-random segregation (ζϵ₂ζ) systems. The promoter (P) of the ωϵζ operon (P_ω) transiently interacts with ω₂. Adding δ₂ facilitates the formation of stable ω₂·P_ω complexes. Here we show that limiting ω₂ interacts with the N-terminal domain of the β’ subunit of the Bacillus subtilis RNA polymerase (RNAP-σ^A) vegetative holoenzyme. In this way ω₂ recruits RNAP-σ^A onto P_ω DNA. Partial P_ω occupancy by ω₂ increases the rate at which RNAP-σ^A complex shifts from its closed (RP_C) to open (RP_O) form. This shift increases transcription activation. Adding δ₂ further increases the rate of P_ω transcription initiation, perhaps by stabilizing the ω₂·P_ω complex. In contrast, full operator occupancy by ω₂ facilitates RP_C formation, but it blocks RP_O isomerization and represses P_ω utilization. The stimulation and inhibition of RP_O formation is the mechanism whereby ω₂ mediates copy number fluctuation and stable plasmid segregation. By this mechanism, ω₂ also indirectly influences the acquisition of antibiotic resistance genes.

CcpA-mediated catabolite activation of the Bacillus subtilis ilv-leu operon and its negation by either CodY- or TnrA-mediated negative regulation

The Bacillus subtilis ilv-leu operon functions in the biosynthesis of branched-chain amino acids. It undergoes catabolite activation involving a promoter-proximal cre which is mediated by the complex of CcpA and P-Ser-HPr. This activation of ilv-leu expression is negatively regulated through CodY binding to a high-affinity site in the promoter region under amino acid-rich growth conditions, and it is negatively regulated through TnrA binding to the TnrA box under nitrogen-limited growth conditions. The CcpA-mediated catabolite activation of ilv-leu required a helix face-dependent interaction of the complex of CcpA and P-Ser-HPr with RNA polymerase and needed a 19-nucleotide region upstream of cre for full activation. DNase I footprinting indicated that CodY binding to the high-affinity site competitively prevented the binding of the complex of CcpA and P-Ser-HPr to cre. This CodY binding not only negated catabolite activation but also likely inhibited transcription initiation from the ilv-leu promoter. The footprinting also indicated that TnrA and the complex of CcpA and P-Ser-HPr simultaneously bound to the TnrA box and the cre site, respectively, which are 112 nucleotides apart; TnrA binding to its box was likely to induce DNA bending. This implied that interaction of TnrA bound to its box with the complex of CcpA and P-Ser-HPr bound to cre might negate catabolite activation, but TnrA bound to its box did not inhibit transcription initiation from the ilv-leu promoter. Moreover, this negation of catabolite activation by TnrA required a 26-nucleotide region downstream of the TnrA box.

Two enzymes, TilS and HprT, can form a complex to function as a transcriptional activator for the cell division protease gene ftsH in Bacillus subtilis

The FtsH protein is an ATP-dependent cytoplasmic membrane protease involved in the control of membrane protein quality, cell division and heat shock response in Bacillus subtilis and many other bacteria. TilS, the tRNA(Ile2) lysidine synthetase, is a tRNA-binding protein that can modify pre-tRNA(Ile2). HprT, the hypoxanthine-guanine phosphoribosyltransferase, is implicated in purine salvage. Both tilS and hprT are essential for cell viability of B. subtilis. In this report, by co-purification experiments and gel filtration analyses, we show that there is complex formation between co-expressed TilS and HprT. Electrophoretic mobility shift assays and in vitro transcription analyses demonstrated that the TilS/HprT complex functions as a specific DNA-binding protein that can stimulate ftsH transcription in vitro. Two regions located upstream of the ftsH promoter have been identified as the TilS/HprT-binding sites and shown to be required for TilS/HprT-dependent ftsH transcription in vitro and in vivo. Results from gel supershift assays support the notion that the TilS/HprT complex likely employs its distinct segments for interaction with these two distinct TilS/HprT-binding sites, respectively. In conclusion, we present the first evidence that bi-functional TilS and HprT can form a complex to function as a transcriptional activator to stimulate ftsH transcription.

Organizational requirements of the SaeR binding sites for a functional P1 promoter of the sae operon in Staphylococcus aureus

In Staphylococcus aureus, the SaeRS two-component system controls the expression of multiple virulence factors. Of the two promoters in the sae operon, P1 is autoinduced and has two binding sites for the response regulator SaeR. In this study, we examined the organizational requirements of the SaeR binding sites in P1 for transcription activation. Mutational studies showed that both binding sites are essential for binding to phosphorylated SaeR (P-SaeR) and transcription activation. When the 21-bp distance between the centers of the two SaeR binding sites was altered to 26 bp, 31 bp, 36 bp, or 41 bp, only the 31-bp mutant retained approximately 40% of the original promoter activity. When the -1-bp spacing (i.e.,1-bp overlap) between the primary SaeR binding site and the -35 promoter region was altered, all mutant P1 promoters failed to initiate transcription; however, when the first nucleotide of the -35 region was changed from A to T, the mutants with 0-bp or 22-bp spacing showed detectable promoter activity. Although P-SaeR was essential for the binding of RNA polymerase to P1, it was not essential for the binding of the enzyme to the alpha-hemolysin promoter. When the nonoptimal spacing between promoter elements in P1 or the coagulase promoter was altered to the optimal spacing of 17 bp, both promoters failed to initiate transcription. These results suggest that SaeR binding sites are under rather strict organizational restrictions and provide clues for understanding the molecular mechanism of sae-mediated transcription activation.

Thermodynamic and molecular analysis of the AbrB-binding sites within the phyC-region of Bacillus amyloliquefaciens FZB45

AbrB is a global regulator of transition state that is known to repress more than 100 genes in Bacillus species. Although AbrB is involved in the regulation of most cellular processes, a conserved binding motif seems to be elusive. Thus, the mechanism of AbrB-mediated transcriptional control is still unclear. In our previous work we identified two separate AbrB-binding sites within phytase gene region (phyC) of Bacillus amyloliquefaciens FZB45, whose integrity is essential for repression. Comparable architecture of AbrB-binding sites is also described for tycA that encodes an antibiotic synthesis enzyme. Considering the size of the AbrB tetramer (56 kDa) and other AbrB binding motifs (~20 to 98 bp) we hypothesized preferred binding positions within both AbrB sites of phyC that exhibit higher affinities to AbrB. Thus, we used surface plasmon resonance (SPR) to study the binding kinetics between AbrB and 40-bp ds-oligonucleotides that were derived from both binding sites. Surface plasmon resonance sensorgrams revealed strong binding kinetics that showed nearly no dissociation and positive cooperativity of the AbrB-DNA interaction to the whole AbrB-binding site 2 and to a small part of AbrB-binding site 1. Using chemically modified DNA we found bases contacting AbrB mainly at one face of the DNA-helix within a core region separated by one helical turn each. High content of modified guanines presented in the control reaction of the KMnO(4) interference assay indicated distortion of the DNA-structure of phyC. In vitro transcription assays and base substitutions within the core region support this idea and the cooperativity of AbrB binding.

The transcriptional repressor CcpN from Bacillus subtilis uses different repression mechanisms at different promoters

CcpN, a transcriptional repressor from Bacillus subtilis that is responsible for the carbon catabolite repression of three genes, has been characterized in detail in the past 4 years. However, nothing is known about the actual repression mechanism as yet. Here, we present a detailed study on how CcpN exerts its repression effect at its three known target promoters of the genes sr1, pckA, and gapB. Using gel shift assays under non-repressive and repressive conditions, we showed that CcpN and RNA polymerase can bind simultaneously and that CcpN does not prevent RNA polymerase (RNAP) binding to the promoter. Furthermore, we investigated the effect of CcpN on open complex formation and demonstrate that CcpN also does not act at this step of transcription initiation at the sr1 and pckA and presumably at the gapB promoter. Investigation of abortive transcript synthesis revealed that CcpN acts differently at the three promoters: At the sr1 and pckA promoter, promoter clearance is impeded by CcpN, whereas synthesis of abortive transcripts is repressed at the gapB promoter. Eventually, we demonstrated with Far Western blots and co-elution experiments that CcpN is able to interact with the RNAP alpha-subunit, which completes the picture of the requirements for the repressive action of CcpN. On the basis of the presented results, we propose a new working model for CcpN action.

Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli

Background

Glucose is the preferred carbon and energy source for Bacillus subtilis and Escherichia coli. A complex regulatory network coordinates gene expression, transport and enzymatic activities, in response to the presence of this sugar. We present a comparison of the cellular response to glucose in these two model organisms, using an approach combining global transcriptome and regulatory network analyses.

Results

Transcriptome data from strains grown in Luria-Bertani medium (LB) or LB+glucose (LB+G) were analyzed, in order to identify differentially transcribed genes in B. subtilis. We detected 503 genes in B. subtilis that change their relative transcript levels in the presence of glucose. A similar previous study identified 380 genes in E. coli, which respond to glucose. Catabolic repression was detected in the case of transport and metabolic interconversion activities for both bacteria in LB+G. We detected an increased capacity for de novo synthesis of nucleotides, amino acids and proteins. A comparison between orthologous genes revealed that global regulatory functions such as transcription, translation, replication and genes relating to the central carbon metabolism, presented similar changes in their levels of expression. An analysis of the regulatory network of a subset of genes in both organisms revealed that the set of regulatory proteins responsible for similar physiological responses observed in the transcriptome analysis are not orthologous. An example of this observation is that of transcription factors mediating catabolic repression for most of the genes that displayed reduced transcript levels in the case of both organisms. In terms of topological functional units in both these bacteria, we found interconnected modules that cluster together genes relating to heat shock, respiratory functions, carbon and peroxide metabolism. Interestingly, B. subtilis functions not found in E. coli, such as sporulation and competence were shown to be interconnected, forming modules subject to catabolic repression at the level of transcription.

Conclusion

Our results demonstrate that the response to glucose is partially conserved in model organisms E. coli and B. subtilis, including genes encoding basic functions such as transcription, translation, replication and genes involved in the central carbon metabolism.

Different responses to Spo0A-mediated suppression of the related Bacillus subtilis phages Nf and phi29

The phi29 family of phages is divided in three groups. Members of groups 1 and 2 infect the spore-forming bacterium Bacillus subtilis. Previous studies showed that group 1 phage phi29 adapts its infection strategy to the physiological state of the host. Thus, the lytic cycle of phi29 is suppressed when cells are infected during the early stages of sporulation and the infecting genome becomes trapped into the spore. A major element of this adaptive strategy is a very sensitive response to the host-encoded Spo0A protein, the key regulator for sporulation activation, which is directly responsible for suppression of phi29 development. Here we analysed if this adaptation is conserved in phage Nf belonging to group 2. The results obtained show that although Nf also possesses the alternative infection strategy, it is clearly less sensitive to Spo0A-mediated suppression than phi29. Sequence determination of the Nf genome revealed striking differences in the number of Spo0A binding site sequences. The results provide evidence that the life style of two highly related phages is distinctly tuned by differences in binding sites for a host-encoded regulatory protein, being a good example of how viruses have evolved to optimally exploit features of their host.

Transition state regulator AbrB inhibits transcription of Bacillus amyloliquefaciens FZB45 phytase through binding at two distinct sites located within the extended phyC promoter region

We have previously identified the phyC gene of Bacillus amyloliquefaciens FZB45, encoding extracellular phytase, as a member of the PhoP regulon, which is expressed only during phosphate starvation. Its sigma(A)-dependent promoter is positively and negatively regulated by the phosphorylated PhoP response regulator in a phosphate-dependent manner (O. Makarewicz, S. Dubrac, T. Msadek, and R. Borriss, J. Bacteriol. 188:6953-6965, 2006). Here, we provide experimental evidence that the transcription of phyC underlies a second control mechanism exerted by the global transient-phase regulator protein, AbrB, which hinders its expression during exponential growth. Gel mobility shift and DNase I footprinting experiments demonstrated that AbrB binds to two different regions in the phyC promoter region that are separated by about 200 bp. One binding site is near the divergently orientated yodU gene, and the second site is located downstream of the phyC promoter and extends into the coding region of the phyC gene. Cooperative binding to the two distant binding regions is necessary for the AbrB-directed repression of phyC transcription. AbrB does not affect the transcription of the neighboring yodU gene.

Molecular mechanisms underlying the positive stringent response of the Bacillus subtilis ilv-leu operon, involved in the biosynthesis of branched-chain amino acids

Branched-chain amino acids are the most abundant amino acids in proteins. The Bacillus subtilis ilv-leu operon is involved in the biosynthesis of branched-chain amino acids. This operon exhibits a RelA-dependent positive stringent response to amino acid starvation. We investigated this positive stringent response upon lysine starvation as well as decoyinine treatment. Deletion analysis involving various lacZ fusions revealed two molecular mechanisms underlying the positive stringent response of ilv-leu, i.e., CodY-dependent and -independent mechanisms. The former is most likely triggered by the decrease in the in vivo concentration of GTP upon lysine starvation, GTP being a corepressor of the CodY protein. So, the GTP decrease derepressed ilv-leu expression through detachment of the CodY protein from its cis elements upstream of the ilv-leu promoter. By means of base substitution and in vitro transcription analyses, the latter (CodY-independent) mechanism was found to comprise the modulation of the transcription initiation frequency, which likely depends on fluctuation of the in vivo RNA polymerase substrate concentrations after stringent treatment, and to involve at least the base species of adenine at the 5' end of the ilv-leu transcript. As discussed, this mechanism is presumably distinct from that for B. subtilis rrn operons, which involves changes in the in vivo concentration of the initiating GTP.

Identification of ligands affecting the activity of the transcriptional repressor CcpN from Bacillus subtilis

Carbon catabolite repression in Bacillus subtilis is mediated primarily by the major regulator CcpA. However, sugar-dependent repression of three genes, sr1 encoding a small nontranslated RNA and two genes coding for gluconeogenic enzymes, gapB and pckA, is carried out by the transcriptional repressor CcpN (control catabolite protein of gluconeogenic genes). It has previously been shown that ccpN is constitutively expressed, which leads to a constant occupation of all operators with CcpN. Since this would not allow for specific regulation, a ligand that modulates CcpN activity is required. In vitro transcription assays demonstrated that CcpN is able to specifically repress transcription to a small extent at the three mentioned promoters in the absence of an activating ligand. Upon testing of several ligands, including nucleotides and glycolysis intermediates, it could be shown that ATP is able to specifically enhance the repressing activity of CcpN, and this effect was more pronounced at a slightly acidic pH. Furthermore, ADP was found to specifically counteract the repressive effect of ATP. Circular dichroism measurements demonstrated a significant alteration of CcpN structure in the presence of ATP at acidic pH and in the presence of ADP. Electrophoretic mobility shift assays revealed that neither ATP nor ADP altered the affinity of CcpN for its operators. Therefore, we hypothesise that the effect of ligand-bound CcpN on the RNA polymerase might be due to a conformational switch that alters the interaction between the two proteins. Based on these results, a working model for CcpN action is discussed.

Dual role of the PhoP approximately P response regulator: Bacillus amyloliquefaciens FZB45 phytase gene transcription is directed by positive and negative interactions with the phyC promoter

Several Bacillus strains secrete phytase, an enzyme catalyzing dephosphorylation of myo-inositol hexakisphosphate (phytate). We identified the phyC (phytase) gene from environmental Bacillus amyloliquefaciens FZB45 as a member of the phosphate starvation-inducible PhoPR regulon. In vivo and in vitro assays revealed that PhoP approximately P is essential for phyC transcription. The transcriptional start site was identified downstream of a sigmaA-like promoter region located 27 bp upstream of the probable translation ATG start codon. Inspection of the phyC promoter sequence revealed an unusual structure. The -35 and -10 regions are separated by a window of 21 bp. A pair of tandemly repeated PhoP TT(T/A/C)ACA binding boxes was located within and upstream of the -35 consensus promoter region. A single PhoP box was found within the -10 consensus promoter region. DNase I footprinting experiments performed with isolated PhoP confirmed that PhoP approximately P binds at two sites overlapping with the phyC -35 and -10 consensus promoter region. While binding of dimeric PhoP approximately P at -35 is essential for activation of the phyC promoter, binding of PhoP approximately P at -10 suppresses promoter activity. A sixfold enhancement of phyC gene expression was registered after T:G substitution of nucleotide -13 (mutant MUT13), which eliminates PhoP binding at the single PhoP box without impairing the -10 consensus sequence. Moreover, MUT13 also expressed phyC during phosphate-replete growth, suggesting that the repressing effect due to binding of PhoP approximately P at -10 was abolished. A model is presented in which transcription initiation of phyC is positively and negatively affected by the actual concentration of the PhoP approximately P response regulator.

Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs

Background

In bacteria, sigma factors and other transcriptional regulatory proteins recognize DNA patterns upstream of their target genes and interact with RNA polymerase to control transcription. As a consequence of evolution, DNA sequences recognized by transcription factors are thought to be enriched in intergenic regions (IRs) and depleted from coding regions of prokaryotic genomes.

Results

In this work, we report that genomic distribution of transcription factors binding sites is biased towards IRs, and that this bias is conserved amongst bacterial species. We further take advantage of this observation to develop an algorithm that can efficiently identify promoter boxes by a distribution-dependent approach rather than a direct sequence comparison approach. This strategy, which can easily be combined with other methodologies, allowed the identification of promoter sequences in ten species and can be used with any annotated bacterial genome, with results that rival with current methodologies. Experimental validations of predicted promoters also support our approach.

Conclusion

Considering that complete genomic sequences of over 1000 bacteria will soon be available and that little transcriptional information is available for most of them, our algorithm constitutes a promising tool for the prediction of promoter sequences. Importantly, our methodology could also be adapted to identify DNA sequences recognized by other regulatory proteins.

The mechanism of cell differentiation in Bacillus subtilis

Sporulation in Bacillus subtilis serves as a model for the development of two different cell types from a single cell. Although much information has been accumulated about the mechanisms that initiate the developmental programmes, important questions remain that can be answered only by quantitative analysis. Here we develop, with the help of existing and new experimental results, a mathematical model that reproduces published in vitro experiments and explains how the activation of the key transcription factor is regulated. The model identifies the difference in volume between the two cell types as the primary trigger for determining cell fate. It shows that this effect depends on the allosteric behaviour of a key protein kinase and on a low rate of dephosphorylation by the corresponding phosphatase; both predicted effects are confirmed experimentally.

Mechanism of transcription activation at the comG promoter by the competence transcription factor ComK of Bacillus subtilis

The development of genetic competence in Bacillus subtilis is regulated by a complex signal transduction cascade, which results in the synthesis of the competence transcription factor, encoded by comK. ComK is required for the transcription of the late competence genes that encode the DNA binding and uptake machinery and of genes required for homologous recombination. In vivo and in vitro experiments have shown that ComK is responsible for transcription activation at the comG promoter. In this study, we investigated the mechanism of this transcription activation. The intrinsic binding characteristics of RNA polymerase with and without ComK at the comG promoter were determined, demonstrating that ComK stabilizes the binding of RNA polymerase to the comG promoter. This stabilization probably occurs through interactions with the upstream DNA, since a deletion of the upstream DNA resulted in an almost complete abolishment of stabilization of RNA polymerase binding. Furthermore, a strong requirement for the presence of an extra AT box in addition to the common ComK-binding site was shown. In vitro transcription with B. subtilis RNA polymerase reconstituted with wild-type alpha-subunits and with C-terminal deletion mutants of the alpha-subunits was performed, demonstrating that these deletions do not abolish transcription activation by ComK. This indicates that ComK is not a type I activator. We also show that ComK is not required for open complex formation. A possible mechanism for transcription activation is proposed, implying that the major stimulatory effect of ComK is on binding of RNA polymerase.

RNA polymerase mutation activates the production of a dormant antibiotic 3,3'-neotrehalosadiamine via an autoinduction mechanism in Bacillus subtilis

Bacillus and Streptomyces species possess the ability to produce a variety of commercially important metabolites and extracellular enzymes. We previously demonstrated that antibiotic production in Streptomyces coeli-color A3(2) and Streptomyces lividans can be enhanced by RNA polymerase (RNAP) mutations selected for the rifampicin-resistant (Rif(r)) phenotype. Here, we have shown that the introduction of a certain Rif(r) rpoB mutation into a B. subtilis strain resulted in cells that overproduce an aminosugar antibiotic 3,3'-neotrehalosadiamine (NTD), the production of which is dormant in the wild-type strain. Mutational and recombinant gene expression analyses have revealed a polycistronic gene ntdABC (formally yhjLKJ) and a monocistronic gene ntdR (formally yhjM) as the NTD biosynthesis operon and a positive regulator for ntdABC, respectively. Analysis of transcriptional fusions to a lacZ reporter revealed that NTD acts as an autoinducer for its own biosynthesis genes via NtdR protein. Our results also showed that the Rif(r) rpoB mutation causes an increase in the activity of sigma(A)-dependent promoters including ntdABC promoter. Therefore, we propose that unlike the wild-type RNAP, the mutant RNAP efficiently recognized the sigma(A)-dependent promoters, resulting in the dramatic activation of the NTD biosynthesis pathway by an autoinduction mechanism.

A sporulation membrane protein tethers the pro-sigmaK processing enzyme to its inhibitor and dictates its subcellular localization

The developmental transcription factor sigmaK is derived from the inactive precursor protein pro-sigmaK by regulated proteolysis during the process of sporulation in the bacterium Bacillus subtilis. The putative pro-sigmaK processing enzyme SpoIVFB is a member of a family of membrane-embedded metalloproteases and is held inactive by two other integral membrane proteins, SpoIVFA and BofA. Herein we show that the processing enzyme and its two regulators exist in a multimeric complex that localizes to the membrane surrounding the developing spore (the forespore). We further show that one of the regulators, SpoIVFA, plays a central role in both the formation of this complex and its subcellular localization. Evidence is presented in support of a model in which SpoIVFA acts as a platform for bringing BofA and SpoIVFB together, whereby BofA inhibits pro-sigmaK processing until a signal has been received from the forespore.

Molecular organization of intrinsic restriction and modification genes BsuM of Bacillus subtilis Marburg

Transcriptional analysis and disruption of five open reading frames (ORFs), ydiO, ydiP, ydiR, ydiS, and ydjA, in the prophage 3 region of the chromosome of Bacillus subtilis Marburg revealed that they are component genes of the intrinsic BsuM restriction and modification system of this organism. The classical mutant strain RM125, which lacks the restriction and modification system of B. subtilis Marburg, lacks the prophage 3 region carrying these five ORFs. These ORFs constitute two operons, the ydiO-ydiP operon and the ydiR-ydiS-ydjA operon, both of which are expressed during the logarithmic phase of growth. The predicted gene products YdiO and YdiP are the orthologues of cytosine DNA methyltransferases. The predicted YdiS product is an orthologue of restriction nucleases, while the predicted YdiR and YdjA products have no apparent paralogues and orthologues whose functions are known. Disruption of the ydiR-ydiS-ydjA operon resulted in enhanced transformation by plasmid DNA carrying multiple BsuM target sequences. Disruption of ydiO or ydiP function requires disruption of at least one of the following genes on the chromosome: ydiR, ydiS, and ydjA. The degrees of methylation of the BsuM target sequences on chromosomal DNAs were estimated indirectly by determining the susceptibility to digestion with XhoI (an isoschizomer of BsuM) of DNAs extracted from the disruptant strains. Six XhoI (BsuM) sites were examined. XhoI digested at the XhoI sites in the DNAs from disruptants with disruptions in both operons, while XhoI did not digest at the XhoI sites in the DNAs from the wild-type strain or from the disruptants with disruptions in the ydiR-ydiS-ydjA operon. Therefore, the ydiO-ydiP operon and the ydiR-ydiS-ydjA operon are considered operons that are responsible for BsuM modification and BsuM restriction, respectively.

The ClpX protein of Bacillus subtilis indirectly influences RNA polymerase holoenzyme composition and directly stimulates sigma-dependent transcription

In Bacillus subtilis, several processes associated with the onset of stationary phase, including the initiation of sporulation, require the activity of the minor sigmaH form of RNA polymerase (RNAP). The induction of sigmaH-dependent gene transcription requires the regulatory ATPase, ClpX. The ClpX-dependent post-exponential increase in sigmaH activity is not dependent on the activator of sporulation gene expression, Spo0A. By determining the level of sigmaH and sigmaA in whole-cell extracts and RNAP preparations, evidence is presented that clpX does not influence the concentration of sigma subunits, but is required for the stationary phase reduction in sigmaA-RNAP holoenzyme. This is probably an indirect consequence of ClpX activity, because the ClpX-dependent decrease in sigmaA-RNAP concentration does not occur in a spo0A abrB mutant. The addition of ClpX to in vitro transcription reactions resulted in the stimulation of RNAP holoenzyme activity, but sigmaH-RNAP was observed to be more sensitive to ClpX-dependent stimulation than sigmaA-RNAP. No difference in transcriptional activity was observed in single-cycle in vitro transcription reactions, suggesting that ClpX acted at a step in transcription initiation after closed- and open-promoter complex formation. ClpX is proposed to function indirectly in the displacement of sigmaA from core RNAP and to act directly in the stimulation of sigmaH-dependent transcription in sporulating B. subtilis cells.

Rapid purification of His(6)-tagged Bacillus subtilis core RNA polymerase

Bacillus subtilis core RNA polymerase, containing a His(6)-fusion to the C-terminus of the beta' subunit, was isolated by Ni-NTA, Superdex 200 gel filtration, and Mono Q anion-exchange chromatography. The purified core enzyme was shown to be free of the major sigma factor(A) and the transcription factors NusA and GreA. The purification procedure can be completed within 1 working day, is scalable, and yields highly purified and active core RNA polymerase.

Temporal and selective association of multiple sigma factors with RNA polymerase during sporulation in Bacillus subtilis

BACKGROUND

During sporulation in Bacillus subtilis, an asymmetric division produces two cells, a forespore and mother cell, with which follow different developmental paths. The highly ordered programme of temporal and spatial gene activation during sporulation is governed by the principal RNA polymerase holoenzyme (EsigmaA) and alternative holoenzyme forms containing the developmental sigma factors sigmaH, sigmaF, sigmaE, sigmaG and sigmaK, which appear successively during development. The control mechanism(s) of temporal and selective association of multiple sigma factors with core RNA polymerase is unclear. As a first step to addressing these issues, this report quantifies the amount of each subunit of RNA polymerase that is present in the sporangium during sporulation, and analyses in vitro the relative affinities of each sigma subunit for core RNA polymerase.

RESULTS

Using quantitative immunoblot analysis, the amounts of EsigmaA, EsigmaH, EsigmaE and EsigmaK in relation to the total amount of RNA polymerase at appropriate time-points were found to be 15%, 1%, 6% and 2%, respectively. Therefore, the core RNA polymerase is predicted to be in excess. The level of core RNA polymerase and sigmaA remained constant during the transition from vegetative growth to sporulation, whereas the sporulation-specific sigma factors appeared successively, in the order sigmaH, sigmaE and sigmaK. Competition experiments between sigma factors in an in vitro transcription system revealed the dominance of sigmaA over sigmaH and sigmaE for open promoter complex formation. These results are inconsistent with the idea that late appearing sigma factors can displace earlier appearing sigmas from the core enzyme.

CONCLUSIONS

As the core RNA polymerase is in excess, the results suggest that successive sigma factors can bind to core RNA polymerase without having to displace earlier appearing sigma factors. Thus, the programme of gene expression during sporulation might not require mechanisms for the substitution of one sigma factor by another on the core RNA polymerase.

Identification of new sigma K-dependent promoters using an in vitro transcription system derived from Bacillus subtilis

In Bacillus subtilis, the genes that depend on sigma K-RNA polymerase for their transcription are expressed in the mother cell compartment at later stages of sporulation. More than a dozen genes belonging to the sigma K regulon have been identified. Here I describe the identification of two additional promoters under the control of sigma K-RNA polymerase. Using a set of histidine-tagged RNA polymerases prepared from cells harvested at various times during the course of growth and sporulation (Fujita, M., Sadaie, Y., 1998. Gene 221, 185-190), transcription initiated from putative promoter sequences on a number of DNA fragments, as inferred from genome sequencing, was examined in vitro. One of these showed sigma K-dependent transcription. For further characterization of transcription initiated from this site, in vitro transcription analysis was performed using RNA polymerase holoenzyme reconstituted from purified sigma K and core RNA polymerase. Two sigma K-dependent promoters, yfhP P1 and yfhP P2, separated by a distance of about 15 bp, were thereby identified. These promoters are located immediately upstream of the yfhP gene that encodes a protein of unknown function consisting of 327 amino acids residues. The promoter strength, the rate of open complex formation and the RNA polymerase binding affinity were examined for these two promoters in comparison with other known sigma K-dependent promoters, gerE and cotD. The promoter strength displayed was in the order of gerE > cotD > yfhP P2 > yfhP P1.

Sigma factor displacement from RNA polymerase during Bacillus subtilis sporulation

As Bacillus subtilis proceeds through sporulation, the principal vegetative cell sigma subunit (sigma(A)) persists in the cell but is replaced in the extractable RNA polymerase (RNAP) by sporulation-specific sigma factors. To explore how this holoenzyme changeover might occur, velocity centrifugation techniques were used in conjunction with Western blot analyses to monitor the associations of RNAP with sigma(A) and two mother cell sigma factors, sigma(E) and sigma(K), which successively replace sigma(A) on RNAP. Although the relative abundance of sigma(A) with respect to RNAP remained virtually unchanged during sporulation, the percentage of the detectable sigma(A) which cosedimented with RNAP fell from approximately 50% at the onset of sporulation (T(0)) to 2 to 8% by 3 h into the process (T(3)). In a strain that failed to synthesize sigma(E), the first of the mother cell-specific sigma factors, approximately 40% of the sigma(A) remained associated with RNAP at T(3). The level of sigma(A)-RNAP cosedimentation dropped to less than 10% in a strain which synthesized a sigma(E) variant (sigma(ECR119)) that could bind to RNAP but was unable to direct sigma(E)-dependent transcription. The E-sigma(E)-to-E-sigma(K) changeover was characterized by both the displacement of sigma(E) from RNAP and the disappearance of sigma(E) from the cell. Analyses of extracts from wild-type and mutant B. subtilis showed that the sigma(K) protein is required for the displacement of sigma(E) from RNAP and also confirmed that sigma(K) is needed for the loss of the sigma(E) protein. The results indicate that the successive appearance of mother cell sigma factors, but not necessarily their activities, is an important element in the displacement of preexisting sigma factors from RNAP. It suggests that competition for RNAP by consecutive sporulation sigma factors may be an important feature of the holoenzyme changeovers that occur during sporulation.

Identification of a new regulator in Streptococcus pneumoniae linking quorum sensing to competence for genetic transformation

Competence for genetic transformation in Streptococcus pneumoniae is regulated by a quorum-sensing system encoded by two genetic loci, comCDE and comAB. Additional competence-specific operons, cilA, cilB, cilC, cilD, cilE, cinA-recA, coiA, and cfl, involved in the DNA uptake process and recombination, share an unusual consensus sequence at -10 and -25 in the promoter, which is absent from the promoters of comAB and comCDE. This pattern suggests that a factor regulating transcription of these transformation machinery genes but not involved with comCDE and comAB expression might be an alternative sigma factor. A search for such a global transcriptional regulator was begun by purifying pneumococcal RNA polymerase holoenzyme. In preparations from competent pneumococcal cultures a protein which seemed to be responsible for cilA transcription in vitro was identified. The corresponding gene was identified and found to be present in two copies, designated comX1 and comX2, located adjacent to two of the repeated rRNA operons. Expression of transformation machinery operons, such as cilA, cilD, cilE, and cfl, but not that of the quorum-sensing operons comAB and comCDE, was shown to depend on comX, while comX expression depended on ComE but not on ComX itself. We conclude that the factor is a competence-specific global transcription modulator which links quorum-sensing information transduced to ComE to competence and propose that it acts as an alternate sigma factor. We also report that comAB and comCDE are not sufficient for shutoff of competence-stimulating peptide-induced gene expression nor for the subsequent refractory period, suggesting that these phenomena depend on one or more ComX-dependent genes.

Replacement of vegetative sigmaA by sporulation-specific sigmaF as a component of the RNA polymerase holoenzyme in sporulating Bacillus subtilis

Soon after asymmetric septation in sporulating Bacillus subtilis cells, sigmaF is liberated in the prespore from inhibition by SpoIIAB. To initiate transcription from its cognate promoters, sigmaF must compete with sigmaA, the housekeeping sigma factor in the predivisional cell, for binding to core RNA polymerase (E). To estimate the relative affinity of E for sigmaA and sigmaF, we made separate mixtures of E with each of the two sigma factors, allowed reconstitution of the holoenzyme, and measured the concentration of free E remaining in each mixture. The affinity of E for sigmaF was found to be about 25-fold lower than that for sigmaA. We used quantitative Western blotting to estimate the concentrations of E, sigmaA, and sigmaF in sporulating cells. The cellular concentrations of E and sigmaA were both about 7.5 microM, and neither changed significantly during the first 3 h of sporulation. The concentration of sigmaF was extremely low at the beginning of sporulation, but it rose rapidly to a peak after about 2 h. At its peak, the concentration of sigmaF was some twofold higher than that of sigmaA. This difference in concentration cannot adequately account for the replacement of sigmaA holoenzyme by sigmaF holoenzyme in the prespore, and it seems that some further mechanism-perhaps the synthesis or activation of an anti-sigmaA factor-must be responsible for this replacement.