Transcriptional activation by Bacillus subtilis ResD: tandem binding to target elements and phosphorylation-dependent and -independent transcriptional activation

Distinct Interaction Mechanism of RNAP and ResD and Distal Subsites for Transcription Activation of Nitrite Reductase in Bacillus subtilisψ

The ResD-ResE signal transduction system plays a pivotal role in anaerobic nitrate respiration in Bacillus subtilis. The nasD operon encoding nitrite reductase is essential for nitrate respiration and is tightly controlled by the ResD response regulator. To understand the mechanism of ResD-dependent transcription activation of the nasD operon, we explored ResD-RNA polymerase (RNAP), ResD-DNA, and RNAP-DNA interactions required for nasD transcription. Full transcriptional activation requires the upstream promoter region where five molecules of ResD bind. The distal ResD-binding subsite at -87 to -84 partially overlaps a sequence similar to the consensus distal subsite of the upstream (UP) element with which the Escherichia coli C-terminal domain of the α subunit (αCTD) of RNAP interacts to stimulate transcription. We propose that interaction between αCTD and ResD at the promoter-distal site is essential for stimulating nasD transcription. Although nasD has an extended -10 promoter, it lacks a reasonable -35 element. Genetic analysis and structural simulations predicted that the absence of the -35 element might be compensated by interactions between σ^A and αCTD, and between αCTD and ResD at the promoter-proximal ResD-binding subsite. Thus, our work suggested that ResD likely participates in nasD transcription activation by binding to two αCTD subunits at the proximal and distal promoter sites, representing a unique configuration for transcription activation. IMPORTANCE A significant number of ResD-controlled genes have been identified and transcription regulatory pathways in which ResD participates have emerged. Nevertheless, the mechanism of how ResD activates transcription of different genes in a nucleotide sequence-specific manner has been less explored. This study suggested that among the five ResD-binding subsites in the promoter of the nasD operon, the promoter-proximal and -distal ResD-binding subsites play important roles in nasD activation by adapting different modes of protein-protein and protein-DNA interactions. The finding of a new-type of protein-promoter architecture provides insight into the understanding of transcription activation mechanisms controlled by transcription factors including the ubiquitous response regulators of two-component regulatory systems particularly in Gram-positive bacteria.

Characterization of a two component system, Bas1213-1214, important for oxidative stress in Bacillus anthracis

Microbial colonization is an outcome of appropriate sensing and regulation of its gene expression. Bacillus anthracis adapts and thrives in its environment through complex regulatory mechanisms, among them, the two component systems (TCS). Many bacteria respond to the oxygen fluctuations via TCS. In the present work, a previously uncharacterized TCS, Bas1213-1214, of B. anthracis with a probable role in oxygen sensing has been characterized as a functional TCS. A substantial increase in the expression of Bas1213 was observed during the stationary growth phase, in presence of bicarbonate ions, and under oxidative stress thereby speculating the role of Bas1213 in toxin production and adaptive responses. Electrophoretic mobility shift assay (EMSA) and ANS assay highlighted autoregulation of the system. Identification of Bas1213 regulon further suggested its regulatory function in metabolism and adaptive responses. A marked reduction in sporulation was observed on overexpression of Bas1213 in B. anthracis which can be correlated with the augmented expression of sporulation kinase D. Additionally, Bas1213 was shown to regulate catalase, and ABC transporter (mntH) further implicating its essential role during oxidative stress. Finally, crucial residues involved in the DNA binding activity of Bas1213 were also identified. This study reports that the role of Bas1213-1214 in the regulation of metabolism and adaptive responses during oxidative stress. Both sporulation and response to environmental oxygen are important for the maintenance of B. anthracis lifecycle, therefore, characterization of Bas1213-1214 provides a step closer toward understanding the regulatory network governing in B. anthracis.

Genome-Wide Analysis of ResD, NsrR, and Fur Binding in Bacillus subtilis during Anaerobic Fermentative Growth by In Vivo Footprinting

Upon oxygen limitation, the Bacillus subtilis ResE sensor kinase and its cognate ResD response regulator play primary roles in the transcriptional activation of genes functioning in anaerobic respiration. The nitric oxide (NO)-sensitive NsrR repressor controls transcription to support nitrate respiration. In addition, the ferric uptake repressor (Fur) can modulate transcription under anaerobic conditions. However, whether these controls are direct or indirect has been investigated only in a gene-specific manner. To gain a genomic view of anaerobic gene regulation, we determined the genome-wide in vivo DNA binding of ResD, NsrR, and Fur transcription factors (TFs) using in situ DNase I footprinting combined with chromatin affinity precipitation sequencing (ChAP-seq; genome footprinting by high-throughput sequencing [GeF-seq]). A significant number of sites were targets of ResD and NsrR, and a majority of them were also bound by Fur. The binding of multiple TFs to overlapping targets affected each individual TF's binding, which led to combinatorial transcriptional control. ResD bound to both the promoters and the coding regions of genes under its positive control. Other genes showing enrichment of ResD at only the promoter regions are targets of direct ResD-dependent repression or antirepression. The results support previous findings of ResD as an RNA polymerase (RNAP)-binding protein and indicated that ResD can associate with the transcription elongation complex. The data set allowed us to reexamine consensus sequence motifs of Fur, ResD, and NsrR and uncovered evidence that multiple TGW (where W is A or T) sequences surrounded by an A- and T-rich sequence are often found at sites where all three TFs competitively bind.IMPORTANCE Bacteria encounter oxygen fluctuation in their natural environment as well as in host organisms. Hence, understanding how bacteria respond to oxygen limitation will impact environmental and human health. ResD, NsrR, and Fur control transcription under anaerobic conditions. This work using in situ DNase I footprinting uncovered the genome-wide binding profile of the three transcription factors (TFs). Binding of the TFs is often competitive or cooperative depending on the promoters and the presence of other TFs, indicating that transcriptional regulation by multiple TFs is much more complex than we originally thought. The results from this study provide a more complete picture of anaerobic gene regulation governed by ResD, NsrR, and Fur and contribute to our further understanding of anaerobic physiology.

A nitric oxide regulated small RNA controls expression of genes involved in redox homeostasis in Bacillus subtilis

RsaE is the only known trans-acting small regulatory RNA (sRNA) besides the ubiquitous 6S RNA that is conserved between the human pathogen Staphylococcus aureus and the soil-dwelling Firmicute Bacillus subtilis. Although a number of RsaE targets are known in S. aureus, neither the environmental signals that lead to its expression nor its physiological role are known. Here we show that expression of the B. subtilis homolog of RsaE is regulated by the presence of nitric oxide (NO) in the cellular milieu. Control of expression by NO is dependent on the ResDE two-component system in B. subtilis and we determined that the same is true in S. aureus. Transcriptome and proteome analyses revealed that many genes with functions related to oxidative stress and oxidation-reduction reactions were up-regulated in a B. subtilis strain lacking this sRNA. We have thus renamed it RoxS. The prediction of RoxS-dependent mRNA targets also suggested a significant enrichment for mRNAs related to respiration and electron transfer. Among the potential direct mRNA targets, we have validated the ppnKB mRNA, encoding an NAD⁺/NADH kinase, both in vivo and in vitro. RoxS controls both translation initiation and the stability of this transcript, in the latter case via two independent pathways implicating RNase Y and RNase III. Furthermore, RNase Y intervenes at an additional level by processing the 5′ end of the RoxS sRNA removing about 20 nucleotides. Processing of RoxS allows it to interact more efficiently with a second target, the sucCD mRNA, encoding succinyl-CoA synthase, thus expanding the repertoire of targets recognized by this sRNA.

Bacteria have evolved various strategies to continually monitor the redox state of the internal and external environments to prevent cell damage and/or to protect them from host defense mechanisms. These signals modify the expression of genes, allowing bacteria to adapt to altered redox environments and to maintain homeostasis. Studies in Enterobacteriaceae have shown that sRNAs play central roles in adaptation to oxidative stress. We show here that the conserved sRNA, RoxS is induced by the presence of nitric oxide (NO) in the medium, through the ResDE and SrrAB two-component systems of Bacillus subtilis and Staphylococcus aureus, respectively. B. subtilis RoxS regulates functions related to oxidation-reduction reactions and acts as an antisense RNA to control translation initiation and the degradation of ppnKB mRNA, encoding an NAD+/NADH kinase. Interestingly, RNase Y processes the 5′ end of the RoxS sRNA leading to a truncated sRNA that in turn interacts more efficiently with a second target, the sucCD mRNA, encoding succinyl-CoA synthase. Taken together this work shows that RoxS is part of a complex regulatory network that allows the cell to sense and respond to redox perturbations, and revealed a novel process that allows an expansion of the repertoire of sRNA targets.

Regulation of the anaerobic metabolism in Bacillus subtilis

The Gram-positive soil bacterium Bacillus subtilis encounters changing environmental conditions in its habitat. The access to oxygen determines the mode of energy generation. A complex regulatory network is employed to switch from oxygen respiration to nitrate respiration and various fermentative processes. During adaptation, oxygen depletion is sensed by the [4Fe-4S](2+) cluster containing Fnr and the two-component regulatory system ResDE consisting of the membrane-bound histidine kinase ResE and the cytoplasmic ResD regulator. Nitric oxide is the signal recognized by NsrR. Acetate formation and decreasing pH are measured via AlsR. Finally, Rex is responding to changes in the cellular NAD(+)/NADH ration. The fine-tuned interplay of these regulators at approximately 400 target gene promoters ensures efficient adaptation of the B. subtilis physiology.

Transcription Factor NsrR from Bacillus subtilis Senses Nitric Oxide with a 4Fe-4S Cluster (†)

In Bacillus subtilis, NsrR is required for the upregulation of ResDE-dependent genes in the presence of nitric oxide (NO). NsrR was shown to bind to the promoters of these genes and inhibit their transcription in vitro. NO relieves this inhibition by an unknown mechanism. Here, we use spectroscopic techniques (UV-vis, resonance Raman, and EPR) to show that anaerobically isolated NsrR from B. subtilis contains a [4Fe-4S](2+) cluster, which reacts with NO to form dinitrosyl iron complexes. This method of NO sensing is analogous to that of the FNR protein of Escherichia coli. The Fe-S cluster of NsrR is also reactive toward other exogenous ligands such as cyanide, dithiothreitol, and O(2). These results, together with the fact that there are only three cysteine residues in NsrR, suggest that the 4Fe-4S cluster contains a noncysteinyl labile ligand to one of the iron atoms, leading to high reactivity. Size exclusion chromatography and cross-linking experiments show that NsrR adopts a dimeric structure in its [4Fe-4S](2+) holo form as well as in the apo form. These findings provide a first stepping stone to investigate the mechanism of NO sensing in NsrR.

Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control

Under a shortage of oxygen, bacterial growth can be faced mainly by two ATP-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. This bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells can sense and respond to changes in oxygen tension and to the availability of other electron acceptors. Bacteria can sense oxygen by direct interaction of this molecule with a membrane protein receptor (e.g., FixL) or by interaction with a cytoplasmic transcriptional factor (e.g., Fnr). A third type of oxygen perception is based on sensing changes in redox state of molecules within the cell. Redox-responsive regulatory systems (e.g., ArcBA, RegBA/PrrBA, RoxSR, RegSR, ActSR, ResDE, and Rex) integrate the response to multiple signals (e.g., ubiquinone, menaquinone, redox active cysteine, electron transport to terminal oxidases, and NAD/NADH) and activate or repress target genes to coordinate the adaptation of bacterial respiration from oxic to anoxic conditions. Here, we provide a compilation of the current knowledge about proteins and regulatory networks involved in the redox control of the respiratory adaptation of different bacterial species to microxic and anoxic environments.

Nitric oxide-sensitive and -insensitive interaction of Bacillus subtilis NsrR with a ResDE-controlled promoter

NsrR is a nitric oxide (NO)-sensitive transcription repressor that controls NO metabolism in a wide range of bacteria. In Bacillus subtilis, NsrR represses transcription of the nitrite reductase (nasDEF) genes that are under positive control of the ResD-ResE two-component signal transduction system. Derepression is achieved by reaction of NO with NsrR. Unlike some NsrR orthologues that were shown to contain a NO-sensitive [2Fe-2S] cluster, B. subtilis NsrR, when purified anaerobically either from aerobic or from anaerobic Escherichia coli and B. subtilis cultures, contains a [4Fe-4S] cluster. [4Fe-4S]-NsrR binds around the -35 element of the nasD promoter with much higher affinity than apo-NsrR and binding of [4Fe-4S]-NsrR, but not apo-protein, is sensitive to NO. RNA polymerase and phosphorylated ResD make a ternary complex at the nasD promoter and NsrR dissociates the preformed ternary complex. In addition to the -35 region, NsrR binds to two distinct sites of the upstream regulatory region where ResD also binds. These interactions, unlike the high-affinity site binding, do not depend on the NsrR [4Fe-4S] cluster and binding is not sensitive to NO, suggesting a role for apo-NsrR in transcriptional regulation.

Regulation of respiratory genes by ResD-ResE signal transduction system in Bacillus subtilis

Successful respiration in Bacillus subtilis using oxygen or nitrate as the terminal electron acceptor requires the ResD-ResE signal transduction system. Although transcription of ResDE-controlled genes is induced at the stationary phase of aerobic growth, it is induced to a higher extent upon oxygen limitation. Furthermore, maximal transcriptional activation requires not only oxygen limitation, but also nitric oxide (NO). Oxygen limitation likely results in conversion of the ResE sensor kinase activity from a phosphatase-dominant to a kinase-dominant mode. In addition, low oxygen levels promote the production and maintenance of NO during nitrate respiration, which leads to elimination of the repression exerted by the NO-sensitive transcriptional regulator NsrR. ResD, after undergoing ResE-mediated phosphorylation, interacts with the C-terminal domain of the alpha subunit of RNA polymerase to activate transcription initiation at ResDE-controlled promoters.

Identification of the sequences recognized by the Bacillus subtilis response regulator YrkP

The Bacillus subtilis yrkP gene encodes a response regulator of a two-component regulatory system of unknown function. A previous DNA microarray experiment suggested that multicopy yrkP greatly enhanced the expression of yrkN, the ykcBC operon, and yrkO, which encodes a putative transporter. Here, lacZ fusion analysis confirmed these results and also revealed that YrkP autoregulates the putative yrkPQR operon, indicating that yrkPQR and yrkO form a divergon structure. In addition, real-time PCR analysis revealed that transcription of yrkO, yrkN, and ykcBC was significantly reduced in the yrkP strain. Hence, YrkP positively regulates the expression of these genes. Gel retardation analyses showed that YrkP bound to the promoter regions of yrkO, yrkN, and ykcB, albeit with lower binding affinities to the latter two promoters. The in vitro binding of YrkP to the promoter region of the yrkPQR and yrkO divergon was then analyzed by DNase I footprinting analysis. This revealed that YrkP recognizes three regions containing single-motifs or a direct repeat of the ten-base sequence [T/G]TCA[T/C]AAATT. lacZ fusion analysis of deleted and mutagenized promoter regions of yrkO and yrkPQR divergon confirmed that the three YrkP-binding regions are needed for the YrkP-mediated activation of yrkO and/or yrkPQR.

Phosphorylated AbsA2 negatively regulates antibiotic production in Streptomyces coelicolor through interactions with pathway-specific regulatory gene promoters

The AbsA two-component signal transduction system, comprised of the sensor kinase AbsA1 and the response regulator AbsA2, acts as a negative regulator of antibiotic production in Streptomyces coelicolor, for which the phosphorylated form of AbsA2 (AbsA2 approximately P) is the agent of repression. In this study, we used chromatin immunoprecipitation to show that AbsA2 binds the promoter regions of actII-ORF4, cdaR, and redZ, which encode pathway-specific activators for actinorhodin, calcium-dependent antibiotic, and undecylprodigiosin, respectively. We confirm that these interactions also occur in vitro and that the binding of AbsA2 to each gene is enhanced by phosphorylation. Induced expression of actII-ORF4 and redZ in the hyperrepressive absA1 mutant (C542) brought about pathway-specific restoration of actinorhodin and undecylprodigiosin production, respectively. Our results suggest that AbsA2 approximately P interacts with as many as four sites in the region that includes the actII-ORF4 promoter. These data suggest that AbsA2 approximately P inhibits antibiotic production by directly interfering with the expression of pathway-specific regulators of antibiotic biosynthetic gene clusters.

Regulators of the Bacillus subtilis cydABCD operon: identification of a negative regulator, CcpA, and a positive regulator, ResD

The cydABCD operon of Bacillus subtilis encodes products required for the production of cytochrome bd oxidase. Previous work has shown that one regulatory protein, YdiH (Rex), is involved in the repression of this operon. The work reported here confirms the role of Rex in the negative regulation of the cydABCD operon. Two additional regulatory proteins for the cydABCD operon were identified, namely, ResD, a response regulator involved in the regulation of respiration genes, and CcpA, the carbon catabolite regulator protein. ResD, but not ResE, was required for full expression of the cydA promoter in vivo. ResD binding to the cydA promoter between positions -58 and -107, a region which includes ResD consensus binding sequences, was not enhanced by phosphorylation. A ccpA mutant had increased expression from the full-length cydA promoter during stationary growth compared to the wild-type strain. Maximal expression in a ccpA mutant was observed from a 3'-deleted cydA promoter fusion that lacked the Rex binding region, suggesting that the effect of the two repressors, Rex and CcpA, was cumulative. CcpA binds directly to the cydA promoter, protecting the region from positions -4 to -33, which contains sequences similar to the CcpA consensus binding sequence, the cre box. CcpA binding was enhanced upon addition of glucose-6-phosphate, a putative cofactor for CcpA. Mutation of a conserved residue in the cre box reduced CcpA binding 10-fold in vitro and increased cydA expression in vivo. Thus, CcpA and ResD, along with the previously identified cydA regulator Rex (YdiH), affect the expression of the cydABCD operon. Low-level induction of the cydA promoter was observed in vivo in the absence of its regulatory proteins, Rex, CcpA, and ResD. This complex regulation suggests that the cydA promoter is tightly regulated to allow its expression only at the appropriate time and under the appropriate conditions.

Characterization of ResDE-dependent fnr transcription in Bacillus subtilis

The ResD-ResE signal transduction system is required for transcription of genes involved in aerobic and anaerobic respiration in Bacillus subtilis. Phosphorylated ResD (ResD approximately P) interacts with target DNA to activate transcription. A strong sequence similarity was detected in promoter regions of some ResD-controlled genes including fnr and resA. Single-base substitutions in the fnr and resA promoters were performed to determine a ResD-binding sequence. DNase I footprinting analysis indicated that ResD approximately P itself does not bind to fnr, but interaction of ResD approximately P with the C-terminal domain of the alpha subunit (alphaCTD) of RNA polymerase (RNAP) facilitates cooperative binding of ResD approximately P and RNAP, thereby increasing fnr transcription initiation. Consistent with this result, amino acid substitutions in alphaCTD, such as Y263A, K267A, A269I, or N290A, sharply reduced fnr transcription in vivo, and the K267A alphaCTD protein, unlike the wild-type protein, did not increase ResD approximately P binding to the fnr promoter. Amino acid residues of alphaCTD required for ResD-dependent fnr transcription, with the exception of N290, which may interact with DNA, constitute a distinct surface, suggesting that these residues likely interact with ResD approximately P.

The response regulator ResD modulates virulence gene expression in response to carbohydrates in Listeria monocytogenes

Listeria monocytogenes is a versatile bacterial pathogen that is able to accommodate to diverse environmental and host conditions. Presently, we have identified a L. monocytogenes two-component response regulator, ResD that is required for the repression of virulence gene expression known to occur in the presence of easily fermentable carbohydrates not found inside host organisms. Structurally and functionally, ResD resembles the respiration regulator ResD in Bacillus subtilis as deletion of the L. monocytogenes resD reduces respiration and expression of cydA, encoding a subunit of cytochrome bd. The resD mutation also reduces expression of mptA encoding the EIIABman component of a mannose/glucose-specific PTS system, indicating that ResD controls sugar uptake. This notion was supported by the poor growth of resD mutant cells that was alleviated by excess of selected carbohydrates. Despite the growth deficient phenotype of the mutant in vitro the mutation did not affect intracellular multiplication in epithelial or macrophage cell lines. When examining virulence gene expression we observed traditional induction by charcoal in both mutant and wild-type cells whereas the repression observed in wild-type cells by fermentable carbohydrates did not occur in resD mutant cells. Thus, ResD is a central regulator of L. monocytogenes when present in the external environment.

Mechanism of CcpA-mediated glucose repression of the resABCDE operon of Bacillus subtilis

The resABCDE operon of Bacillus subtilis encodes a three-protein complex involved in cytochrome c biogenesis as well as the ResE sensor kinase and the ResD response regulator that control electron transfer and other functions in response to oxygen availability. We have investigated the mechanism of CcpA-mediated control of res operon expression which occurs maximally in the stationary phase of growth. Two CcpA-binding (CRE) sites were found in the res operon, one (CRE1) in the control region in front of the resA promoter, the other (CRE2) in the resB structural gene. Both CRE sites proved to be essential for full CcpA-mediated glucose repression of res operon expression. We propose that both looping and road block mechanisms are involved in res operon control by CcpA.

Regulatory loop between redox sensing of the NADH/NAD(+) ratio by Rex (YdiH) and oxidation of NADH by NADH dehydrogenase Ndh in Bacillus subtilis

NADH dehydrogenase is a key component of the respiratory chain. It catalyzes the oxidation of NADH by transferring electrons to ubiquinone and establishes a proton motive force across the cell membrane. The yjlD (renamed ndh) gene of Bacillus subtilis is predicted to encode an enzyme similar to the NADH dehydrogenase II of Escherichia coli, encoded by the ndh gene. We have shown that the yjlC-ndh operon is negatively regulated by YdiH (renamed Rex), a homolog of Rex in Streptomyces coelicolor, and a redox-sensing transcriptional regulator that responds to the NADH/NAD(+) ratio. The ndh gene regulates expression of the yjlC-ndh operon, as indicated by the fact that mutation in ndh causes a higher NADH/NAD(+) ratio. An in vitro study showed that Rex binds to the downstream region of the yjlC-ndh promoter and that NAD(+) enhances the binding of Rex to the putative Rex-binding sites in the yjlC-ndh operon as well as in the cydABCD operon. These results indicated that Rex and Ndh together form a regulatory loop which functions to prevent a large fluctuation in the NADH/NAD(+) ratio in B. subtilis.

The nitric oxide-responsive regulator NsrR controls ResDE-dependent gene expression

The ResD-ResE signal transduction system is essential for aerobic and anaerobic respiration in Bacillus subtilis. ResDE-dependent gene expression is induced by oxygen limitation, but full induction under anaerobic conditions requires nitrite or nitric oxide (NO). Here we report that NsrR (formerly YhdE) is responsible for the NO-dependent up-regulation of the ResDE regulon. The null mutation of nsrR led to aerobic derepression of hmp (flavohemoglobin gene) partly in a ResDE-independent manner. In addition to its negative role in aerobic hmp expression, NsrR plays an important role under anaerobic conditions for regulation of ResDE-controlled genes, including hmp. ResDE-dependent gene expression was increased by the nsrR mutation in the absence of NO, but the expression was decreased by the mutation when NO was present. Consequently, B. subtilis cells lacking NsrR no longer sense and respond to NO (and nitrite) to up-regulate the ResDE regulon. Exposure to NO did not significantly change the cellular concentration of NsrR, suggesting that NO likely modulates the activity of NsrR. NsrR is similar to the recently described nitrite- or NO-sensitive transcription repressors present in various bacteria. NsrR likely has an Fe-S cluster, and interaction of NO with the Fe-S center is proposed to modulate NsrR activity.

Pheromone-induced expression of recombinant proteins in Streptococcus thermophilus

A locus encoding proteins with high homology to the pneumococcal BlpABCHR quorum-sensing system was identified in Streptococcus thermophilus LMG 18311. The BlpABCHR system regulates bacteriocin production in Streptococcus pneumoniae by monitoring the extracellular concentration of a peptide-pheromone encoded by blpC. The homologous system in S. thermophilus, termed StbABCHR, contains a corresponding gene (stbC) encoding a possible peptide-pheromone (STP) that presumably controls bacteriocin production in S. thermophilus. We synthesized this peptide and found that it activates transcription of a gusA reporter gene placed behind the promoter of the bacteriocin-like gene stbD. Furthermore, deletion mapping and mutational analysis of the stbD promoter region were used to identify a degenerated direct repeat motif required for STP induced GusA expression. Our findings provide strong evidence that STP regulates bacteriocin production in S. thermophilus LMG 18311, and show that the StbABCHR quorum-sensing system can be exploited for inducible expression of recombinant proteins in this bacterial species.

Coordinated patterns of cytochrome bd and lactate dehydrogenase expression in Bacillus subtilis

A variety of pathways for electron and carbon flow in the soil bacterium Bacillus subtilis are differentially expressed depending on whether oxygen is present in the cell environment. This study characterizes the regulation of the respiratory oxidase cytochrome bd and the NADH-linked fermentative lactate dehydrogenase (LDH). Transcription of the cydABCD operon, encoding cytochrome bd, is highly regulated and only becomes activated at low oxygen availability. This induction is not dependent on the gene encoding the redox regulator Fnr or the genes encoding the ResDE two-component regulatory system. The DNA-binding protein YdiH was found to be a principal regulator that controls cydABCD expression. Transcription from the cyd promoter is stimulated 15-fold by a region located upstream of the core promoter. The upstream region may constitute a binding site for an unidentified transcription activator that is likely to influence the level of transcription but not its timing, which is negatively controlled by YdiH. This report provides evidence that YdiH also functions as a repressor of the ldh gene encoding LDH and of a gene, ywcJ, which encodes a putative formate-nitrite transporter. Based on the similarity between YdiH and the Rex protein of Streptomyces coelicolor, it is proposed that YdiH serves as a redox sensor, the activity of which is regulated by cellular differences in the free levels of NAD+ and NADH. It is suggested that ydiH be renamed as rex.

Bacillus subtilis phosphorylated PhoP: direct activation of the E(sigma)A- and repression of the E(sigma)E-responsive phoB-PS+V promoters during pho response

The phoB gene of Bacillus subtilis encodes an alkaline phosphatase (PhoB, formerly alkaline phosphatase III) that is expressed from separate promoters during phosphate deprivation in a PhoP-PhoR-dependent manner and at stage two of sporulation under phosphate-sufficient conditions independent of PhoP-PhoR. Isogenic strains containing either the complete phoB promoter or individual phoB promoter fusions were used to assess expression from each promoter under both induction conditions. The phoB promoter responsible for expression during sporulation, phoB-P(S), was expressed in a wild-type strain during phosphate deprivation, but induction occurred >3 h later than induction of Pho regulon genes and the levels were approximately 50-fold lower than that observed for the PhoPR-dependent promoter, phoB-P(V). E(sigma)E was necessary and sufficient for P(S) expression in vitro. P(S) expression in a phoPR mutant strain was delayed 2 to 3 h compared to the expression in a wild-type strain, suggesting that expression or activation of sigma(E) is delayed in a phoPR mutant under phosphate-deficient conditions, an observation consistent with a role for PhoPR in spore development under these conditions. Phosphorylated PhoP (PhoP approximately P) repressed P(S) in vitro via direct binding to the promoter, the first example of an E(sigma)E-responsive promoter that is repressed by PhoP approximately P. Whereas either PhoP or PhoP approximately P in the presence of E(sigma)A was sufficient to stimulate transcription from the phoB-P(V) promoter in vitro, roughly 10- and 17-fold-higher concentrations of PhoP than of PhoP approximately P were required for P(V) promoter activation and maximal promoter activity, respectively. The promoter for a second gene in the Pho regulon, ykoL, was also activated by elevated concentrations of unphosphorylated PhoP in vitro. However, because no Pho regulon gene expression was observed in vivo during P(i)-replete growth and PhoP concentrations increased only threefold in vivo during phoPR autoinduction, a role for unphosphorylated PhoP in Pho regulon activation in vivo is not likely.

Bacillus subtilis ResD induces expression of the potential regulatory genes yclJK upon oxygen limitation

Transcription of the yclJK operon, which encodes a potential two-component regulatory system, is activated in response to oxygen limitation in Bacillus subtilis. Northern blot analysis and assays of yclJ-lacZ reporter gene fusion activity revealed that the anaerobic induction is dependent on another two-component signal transduction system encoded by resDE. ResDE was previously shown to be required for the induction of anaerobic energy metabolism. Electrophoretic mobility shift assays and DNase I footprinting experiments showed that the response regulator ResD binds specifically to the yclJK regulatory region upstream of the transcriptional start site. In vitro transcription experiments demonstrated that ResD is sufficient to activate yclJ transcription. The phosphorylation of ResD by its sensor kinase, ResE, highly stimulates its activity as a transcriptional activator. Multiple nucleotide substitutions in the ResD binding regions of the yclJ promoter abolished ResD binding in vitro and prevented the anaerobic induction of yclJK in vivo. A weight matrix for the ResD binding site was defined by a bioinformatic approach. The results obtained suggest the existence of a new branch of the complex regulatory system employed for the adaptation of B. subtilis to anaerobic growth conditions.