Reactivation of the Bacillus subtilis anti-sigma B antagonist, RsbV, by stress- or starvation-induced phosphatase activities

Distinct impacts of each anti-anti-sigma factor ortholog of the chlamydial Rsb partner switching mechanism on development in Chlamydia trachomatis

Partner switching mechanisms (PSMs) are signal transduction systems comprised of a sensor phosphatase (RsbU), an anti-sigma factor (RsbW, kinase), an anti-anti-sigma factor (RsbV, the RsbW substrate), and a target sigma factor. Chlamydia spp. are obligate intracellular bacterial pathogens of animals that undergo a developmental cycle transitioning between the infectious elementary body (EB) and replicative reticulate body (RB) within a host cell-derived vacuole (inclusion). Secondary differentiation events (RB to EB) are transcriptionally regulated, in part, by the housekeeping sigma factor (σ66) and two late-gene sigma factors (σ54 and σ28). Prior research supports that the PSM in Chlamydia trachomatis regulates availability of σ66. Pan-genome analysis revealed that PSM components are conserved across the phylum Chlamydiota, with Chlamydia spp. possessing an atypical arrangement of two anti-anti-sigma factors, RsbV1 and RsbV2. Bioinformatic analyses support RsbV2 as the homolog to the pan-genome-conserved RsbV with RsbV1 as an outlier. This, combined with in vitro data, indicates that RsbV1 and RsbV2 are structurally and biochemically distinct. Reduced levels or overexpression of RsbV1/RsbV2 did not significantly impact C. trachomatis growth or development. In contrast, overexpression of a non-phosphorylatable RsbV2 S55A mutant, but not overexpression of an RsbV1 S56A mutant, resulted in a 3 log reduction in infectious EB production without reduction in genomic DNA (total bacteria) or inclusion size, suggesting a block in secondary differentiation. The block was corroborated by reduced production of σ54/28-regulated late proteins and via transmission electron microscopy.IMPORTANCEChlamydia trachomatis is the leading cause of reportable bacterial sexually transmitted infections (STIs) and causes the eye infection trachoma, a neglected tropical disease. Broad-spectrum antibiotics used for treatment can lead to microbiome dysbiosis and increased antibiotic resistance development in other bacteria, and treatment failure for chlamydial STIs is a recognized clinical problem. Here, we show that disruption of a partner switching mechanism (PSM) significantly reduces infectious progeny production via blockage of reticulate body to elementary body differentiation. We also reveal a novel PSM expansion largely restricted to the species infecting animals, suggesting a role in pathogen evolution. Collectively, our results highlight the chlamydial PSM as a key regulator of development that could be a potential target for novel therapeutics.

The σB alternative sigma factor circuit modulates noise to generate different types of pulsing dynamics

Single-cell approaches are revealing a high degree of heterogeneity, or noise, in gene expression in isogenic bacteria. How gene circuits modulate this noise in gene expression to generate robust output dynamics is unclear. Here we use the Bacillus subtilis alternative sigma factor σB as a model system for understanding the role of noise in generating circuit output dynamics. σB controls the general stress response in B. subtilis and is activated by a range of energy and environmental stresses. Recent single-cell studies have revealed that the circuit can generate two distinct outputs, stochastic pulsing and a single pulse response, but the conditions under which each response is generated are under debate. We implement a stochastic mathematical model of the σB circuit to investigate this and find that the system's core circuit can generate both response types. This is despite one response (stochastic pulsing) being stochastic in nature, and the other (single response pulse) being deterministic. We demonstrate that the main determinant for whichever response is generated is the degree with which the input pathway activates the core circuit, although the noise properties of the input pathway also biases the system towards one or the other type of output. Thus, our work shows how stochastic modelling can reveal the mechanisms behind non-intuitive gene circuit output dynamics.

Computational and cellular exploration of the protein-protein interaction between Vibrio fischeri STAS domain protein SypA and serine kinase SypE

Anti-sigma factor antagonists SpoIIAA and RsbV from Bacillus subtilis are the archetypes for single-domain STAS proteins in bacteria. The structures and mechanisms of these proteins along with their cognate anti-sigma factors have been well studied. SpoIIAA and RsbV utilize a partner-switching mechanism to regulate gene expression through protein-protein interactions to control the activity of their downstream anti-sigma factor partners. The Vibrio fischeri STAS domain protein SypA is also proposed to employ a partner-switching mechanism with its partner SypE, a serine kinase/phosphatase that controls SypA's phosphorylation state. However, this regulation appears opposite to the canonical pathway, with SypA being the more downstream component rather than SypE. Here we explore the commonalities and differences between SypA and the canonical single-domain STAS proteins SpoIIAA and RsbV. We use a combination of AlphaFold 2 structure predictions and computational modeling to investigate the SypA-SypE binding interface. We then test a subset of our predictions in V.fischeri by generating and expressing SypA variants. Our findings suggest that, while SypA shares many sequence and structural traits with anti-sigma factor antagonist STAS domain proteins, there are significant differences that may account for SypA's distinct regulatory output.

A conserved arginine residue in a staphylococcal anti-sigma factor is required to preserve its kinase activity, structure, and stability

RsbW, σ^B, and RsbV, encoded by Staphylococcus aureus and related bacteria, act as an anti-sigma factor, an sigma factor, and an anti-anti-sigma factor, respectively. The interaction between RsbW and σ^B blocks the transcription initiation activity of the latter protein. RsbW also functions as a serine kinase and phosphorylates RsbV in the presence of ATP. Our modeling study indicates that the RsbW-RsbV complex is stabilized by twenty-four intermolecular non-covalent bonds. Of the bond-forming RsbW residues, Arg 23, and Glu 49 are conserved residues. To understand the roles of Arg 23 in RsbW, rRsbW[R23A], a recombinant S. aureus RsbW (rRsbW) harboring Arg to Ala change at position 23, was investigated using various probes. The results reveal that rRsbW[R23A], like rRsbW, exists as the dimers in the aqueous solution. However, rRsbW[R23A], unlike rRsbW, neither interacted with a chimeric RsbV (rRsbV) nor formed the phosphorylated rRsbV in the presence of ATP. Furthermore, the tertiary structure and hydrophobic surface area of rRsbW[R23A] matched little with those of rRsbW. Conversely, both rRsbW[R23A] and rRsbW showed interaction with a recombinant σ^B (rσ^B). rRsbW and rRsbW[R23A] were also unfolded via the formation of at least one intermediate in the presence of urea. However, the thermodynamic stability of rRsbW significantly differed from that of rRsbW[R23A]. Our molecular dynamics (MD) simulation study also reveals the substantial change of structure, dimension, and stability of RsbW due to the above mutation. The ways side chain of critical Arg 23 contributes to maintaining the tertiary structure, and stability of RsbW was elaborately discussed.Communicated by Ramaswamy H. Sarma.

The Partner Switching System of the SigF Sigma Factor in Mycobacterium smegmatis and Induction of the SigF Regulon Under Respiration-Inhibitory Conditions

The partner switching system (PSS) of the SigF regulatory pathway in Mycobacterium smegmatis has been previously demonstrated to include the anti-sigma factor RsbW (MSMEG_1803) and two anti-sigma factor antagonists RsfA and RsfB. In this study, we further characterized two additional RsbW homologs and revealed the distinct roles of three RsbW homologs [RsbW1 (MSMEG_1803), RsbW2 (MSMEG_6129), and RsbW3 (MSMEG_1787)] in the SigF PSS. RsbW1 and RsbW2 serve as the anti-sigma factor of SigF and the protein kinase phosphorylating RsfB, respectively, while RsbW3 functions as an anti-SigF antagonist through its protein interaction with RsbW1. Using relevant mutant strains, RsfB was demonstrated to be the major anti-SigF antagonist in M. smegmatis. The phosphorylation state of Ser-63 was shown to determine the functionality of RsfB as an anti-SigF antagonist. RsbW2 was demonstrated to be the only protein kinase that phosphorylates RsfB in M. smegmatis. Phosphorylation of Ser-63 inactivates RsfB to render it unable to interact with RsbW1. Our comparative RNA sequencing analysis of the wild-type strain of M. smegmatis and its isogenic Δaa₃ mutant strain lacking the aa₃ cytochrome c oxidase of the respiratory electron transport chain revealed that expression of the SigF regulon is strongly induced under respiration-inhibitory conditions in an RsfB-dependent way.

Structural insights into the regulation of SigB activity by RsbV and RsbW

Bacillus subtilis SigB is an alternative sigma factor that initiates the transcription of stress-responsive genes. The anti-sigma factor RsbW tightly binds SigB to suppress its activity under normal growth conditions and releases it when nonphosphorylated RsbV binds to RsbW in response to stress signals. To understand the regulation of SigB activity by RsbV and RsbW based on structural features, crystal structures and a small-angle X-ray scattering (SAXS) envelope structure of the RsbV-RsbW complex were determined. The crystal structures showed that RsbV and RsbW form a heterotetramer in a similar manner to a SpoIIAA-SpoIIAB tetramer. Multi-angle light scattering and SAXS revealed that the RsbV-RsbW complex is an octamer in solution. Superimposition of the crystal structure on the SAXS envelope structure showed that the unique dimeric interface of RsbW mediates the formation of an RsbV-RsbW octamer and does not prevent RsbV and SigB from binding to RsbW. These results provide structural insights into the molecular assembly of the RsbV-RsbW complex and the regulation of SigB activity.

Mild Stress Conditions during Laboratory Culture Promote the Proliferation of Mutations That Negatively Affect Sigma B Activity in Listeria monocytogenes

In Listeria monocytogenes, the full details of how stress signals are integrated into the σB regulatory pathway are not yet available. To help shed light on this question, we investigated a collection of transposon mutants that were predicted to have compromised activity of the alternative sigma factor B (σB). These mutants were tested for acid tolerance, a trait that is known to be under σB regulation, and they were found to display increased acid sensitivity, similar to a mutant lacking σB (ΔsigB). The transposon insertions were confirmed by whole-genome sequencing, but in each case, the strains were also found to carry a frameshift mutation in the sigB operon. The changes were predicted to result in premature stop codons, with negative consequences for σB activation, independently of the transposon location. Reduced σB activation in these mutants was confirmed. Growth measurements under conditions similar to those used during the construction of the transposon library revealed that the frameshifted sigB operon alleles conferred a growth advantage at higher temperatures, during late exponential phase. Mixed-culture experiments at 42°C demonstrated that the loss of σB activity allowed mutants to take over a population of parental bacteria. Together, our results suggest that mutations affecting σB activity can arise during laboratory culture because of the growth advantage conferred by these mutations under mild stress conditions. The data highlight the significant cost of stress protection in this foodborne pathogen and emphasize the need for whole-genome sequence analysis of newly constructed strains to confirm the expected genotype.IMPORTANCE In the present study, we investigated a collection of Listeria monocytogenes strains that all carried sigB operon mutations. The mutants all had reduced σB activity and were found to have a growth advantage under conditions of mild heat stress (42°C). In mixed cultures, these mutants outcompeted the wild type when mild heat stress was present but not at an optimal growth temperature. An analysis of 22,340 published L. monocytogenes genome sequences found a high rate of premature stop codons present in genes positively regulating σB activity. Together, these findings suggest that the occurrence of mutations that attenuate σB activity can be favored under conditions of mild stress, probably highlighting the burden on cellular resources that stems from deploying the general stress response.

Efficacy of Antimicrobial Peptide DP7, Designed by Machine-Learning Method, Against Methicillin-Resistant Staphylococcus aureus

Antimicrobial peptides (AMPs) provide a promising strategy against infections involving multidrug-resistant pathogens. In previous studies, we designed a short 12 amino acid AMP DP7, using a machine-learning method based on an amino acid activity contribution matrix. DP7 shows broad-spectrum antimicrobial activities both in vitro and in vivo. Here, we aim to investigate the efficacy of DP7 against multidrug resistant Staphylococcus aureus (S. aureus) and reveal the potential mechanisms. First, by measuring the killing kinetics of DP7 against S. aureus and comparing these results with antibiotics with different antimicrobial mechanisms, we hypothesize that DP7, in addition to its known ability to induce cell wall cation damage, can also exert a full killing effect. With FITC-conjugated or biotin-labeled DP7, we tracked DP7's attachment, membrane permeation and subsequent intracellular distribution in S. aureus. These results indicated that the possible targets of DP7 were within the bacterial cells. Transcriptome sequencing of S. aureus exposed to DP7 identified 333 differentially expressed genes (DEGs) influenced by DP7, involving nucleic acid metabolism, amino acid biosynthesis, cell wall destruction and pathogenesis, respectively, indicating the comprehensive killing efficacy of DP7. In addition, the genome sequencing results of the induced DP7 resistant strain S. aureus DP7-R revealed two-point mutations in the mprF and guaA gene. Moreover, in a murine model for MRSA blood stream infection, intravenously treating mice with DP7 showed a good protective effect on mice. In conclusion, DP7 is an effective bactericide for S. aureus, which deserves further study for clinical application and drug development.

Regulation of σ factors by conserved partner switches controlled by divergent signalling systems

Partner-Switching Systems (PSS) are widespread regulatory systems, each comprising a kinase-anti-σ, a phosphorylatable anti-σ antagonist and a phosphatase module. The anti-σ domain quickly sequesters or delivers the target σ factor according to the phosphorylation state of the anti-σ antagonist induced by environmental signals. The PSS components are proteins alone or merged to other domains probably to adapt to the input signals. PSS are involved in major cellular processes including stress response, sporulation, biofilm formation and pathogenesis. Surprisingly, the target σ factors are often unknown and the sensing modules acting upstream from the PSS diverge according to the bacterial species. Indeed, they belong to either two-component systems or complex pathways as the stressosome or Chemosensory Systems (CS). Based on a phylogenetic analysis, we propose that the sensing module in Gram-negative bacteria is often a CS.

Temporal regulation of σB by partner-switching mechanism at a distinct growth stage in Bacillus cereus

The alternative transcription factor σ^B in Bacillus cereus governs the transcription of a number of genes that confer protection against general stress. This transcription factor is regulated by protein-protein interactions among RsbV, RsbW, σ^B, RsbY, RsbM and RsbK, all encoded in the sigB cluster. Among these regulatory proteins, RsbV, RsbW and σ^B comprise a partner-switching mechanism. Under normal conditions, σ^B remains inactive by associating with anti-sigma factor RsbW, which prevents σ^B from binding to the core RNA polymerase. During environmental stress, RsbK activates RsbY to hydrolyze phosphorylated RsbV, and the dephosphorylated RsbV then sequesters RsbW to liberate σ^B from RsbW. Although the σ^B partner-switching module is thought to be the core mechanism for σ^B regulation, the actual protein-protein interactions among these three proteins in the cell remain to be investigated. In the current study, we show that RsbW and RsbV form a long-lived complex under transient stress treatment, resulting in high persistent expression of RsbV, RsbW and σ^B from mid-log phase to stationary phase. Full sequestration of RsbW by excess RsbV and increased RsbW:RsbV complex stability afforded by cellular ADP contribute to the prolonged activation of σ^B. Interestingly, the high expression levels of RsbV, RsbW and σ^B were dramatically decreased beginning from the transition stage to the stationary phase. Thus, protein interactions among σ^B partner-switching components are required for the continued induction of σ^B during environmental stress in the log phase and significant down-regulation of σ^B is observed in the stationary phase. Our data show that σ^B is temporally regulated in B. cereus.

Structure and Function of the Stressosome Signalling Hub

The stressosome is a multi-protein signal integration and transduction hub found in a wide range of bacterial species. The role that the stressosome plays in regulating the transcription of genes involved in the general stress response has been studied most extensively in the Gram-positive model organism Bacillus subtilis. The stressosome receives and relays the signal(s) that initiate a complex phosphorylation-dependent partner switching cascade, resulting in the activation of the alternative sigma factor σ^B. This sigma factor controls transcription of more than 150 genes involved in the general stress response. X-ray crystal structures of individual components of the stressosome and single-particle cryo-EM reconstructions of stressosome complexes, coupled with biochemical and single cell analyses, have permitted a detailed understanding of the dynamic signalling behaviour that arises from this multi-protein complex. Furthermore, bioinformatics analyses indicate that genetic modules encoding key stressosome proteins are found in a wide range of bacterial species, indicating an evolutionary advantage afforded by stressosome complexes. Interestingly, the genetic modules are associated with a variety of signalling modules encoding secondary messenger regulation systems, as well as classical two-component signal transduction systems, suggesting a diversification in function. In this chapter we review the current research into stressosome systems and discuss the functional implications of the unique structure of these signalling complexes.

Role of Autoregulation and Relative Synthesis of Operon Partners in Alternative Sigma Factor Networks

Despite the central role of alternative sigma factors in bacterial stress response and virulence their regulation remains incompletely understood. Here we investigate one of the best-studied examples of alternative sigma factors: the σ^B network that controls the general stress response of Bacillus subtilis to uncover widely relevant general design principles that describe the structure-function relationship of alternative sigma factor regulatory networks. We show that the relative stoichiometry of the synthesis rates of σ^B, its anti-sigma factor RsbW and the anti-anti-sigma factor RsbV plays a critical role in shaping the network behavior by forcing the σ^B network to function as an ultrasensitive negative feedback loop. We further demonstrate how this negative feedback regulation insulates alternative sigma factor activity from competition with the housekeeping sigma factor for RNA polymerase and allows multiple stress sigma factors to function simultaneously with little competitive interference.

Understanding the regulation of bacterial stress response holds the key to tackling the problems of emerging resistance to anti-bacteria’s and antibiotics. To this end, here we study one of the longest serving model systems of bacterial stress response: the σ^B pathway of Bacillus subtilis. The sigma factor σ^B controls the general stress response of Bacillus subtilis to a variety of stress conditions including starvation, antibiotics and harmful environmental perturbations. Recent studies have demonstrated that an increase in stress triggers pulsatile activation of σ^B. Using mathematical modeling we identify the core structural design feature of the network that are responsible for its pulsatile response. We further demonstrate how the same core design features are common to a variety of stress response pathways. As a result of these features, cells can respond to multiple simultaneous stresses without interference or competition between the different pathways.

Activation of the General Stress Response of Bacillus subtilis by Visible Light

A key challenge for microbiology is to understand how evolution has shaped the wiring of regulatory networks. This is amplified by the paucity of information of power-spectra of physicochemical stimuli to which microorganisms are exposed. Future studies of genome evolution, driven by altered stimulus regimes, will therefore require a versatile signal transduction system that allows accurate signal dosing. Here, we review the general stress response of Bacillus subtilis, and its upstream signal transduction network, as a candidate system. It can be activated by red and blue light, and by many additional stimuli. Signal integration therefore is an intricate function of this system. The blue-light response is elicited via the photoreceptor YtvA, which forms an integral part of stressosomes, to activate expression of the stress regulon of B. subtilis. Signal transfer through this network can be assayed with reporter enzymes, while intermediate steps can be studied with live-cell imaging of fluorescently tagged proteins. Different parts of this system have been studied in vitro, such that its computational modeling has made significant progress. One can directly relate the microscopic characteristics of YtvA with activation of the general stress regulon, making this system a very well-suited system for network evolution studies.

Analysis of the mechanism of action of potent antibacterial hetero-tri-organometallic compounds: a structurally new class of antibiotics

Two hetero-tri-organometallic compounds with potent activity against Gram-positive bacteria including multi-resistant Staphylococcus aureus (MRSA) were identified. The compounds consist of a peptide nucleic acid backbone with an alkyne side chain, substituted with a cymantrene, a (dipicolyl)Re(CO)3 moiety, and either a ferrocene (FcPNA) or a ruthenocene (RcPNA). Comparative proteomic analysis indicates the bacterial membrane as antibiotic target structure. FcPNA accumulation in the membrane was confirmed by manganese tracing with atomic absorption spectroscopy. Both organometallics disturbed several essential cellular processes taking place at the membrane such as respiration and cell wall biosynthesis, suggesting that the compounds affect membrane architecture. Correlating with enhanced antibacterial activity, oxidative stress was induced only by the ferrocene-substituted compound. The organometallics described here target the cytoplasmic membrane, a clinically proven antibacterial target structure, feature a bactericidal but non-bacteriolytic mode of action and limited cytotoxicity within the limits of solubility. Thus, FcPNA represents a promising lead structure for the development of a new synthetic class of antibiotics.

Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT

BACKGROUND

The stressosome is a bacterial signalling complex that responds to environmental changes by initiating a protein partner switching cascade, which leads to the release of the alternative sigma factor, σB. Stress perception increases the phosphorylation of the stressosome sensor protein, RsbR, and the scaffold protein, RsbS, by the protein kinase, RsbT. Subsequent dissociation of RsbT from the stressosome activates the σB cascade. However, the sequence of physical events that occur in the stressosome during signal transduction is insufficiently understood.

RESULTS

Here, we use computational modelling to correlate the structure of the stressosome with the efficiency of the phosphorylation reactions that occur upon activation by stress. In our model, the phosphorylation of any stressosome protein is dependent upon its nearest neighbours and their phosphorylation status. We compare different hypotheses about stressosome activation and find that only the model representing the allosteric activation of the kinase RsbT, by phosphorylated RsbR, qualitatively reproduces the experimental data.

CONCLUSIONS

Our simulations and the associated analysis of published data support the following hypotheses: (i) a simple Boolean model is capable of reproducing stressosome dynamics, (ii) different stressors induce identical stressosome activation patterns, and we also confirm that (i) phosphorylated RsbR activates RsbT, and (ii) the main purpose of RsbX is to dephosphorylate RsbS-P.

The response regulator SypE controls biofilm formation and colonization through phosphorylation of the syp-encoded regulator SypA in Vibrio fischeri

Bacteria utilize multiple regulatory systems to modulate gene expression in response to environmental changes, including two-component signalling systems and partner-switching networks. We recently identified a novel regulatory protein, SypE, that combines features of both signalling systems. SypE contains a central response regulator receiver domain flanked by putative kinase and phosphatase effector domains with similarity to partner-switching proteins. SypE was previously shown to exert dual control over biofilm formation through the opposing activities of its terminal effector domains. Here, we demonstrate that SypE controls biofilms in Vibrio fischeri by regulating the activity of SypA, a STAS (sulphate transporter and anti-sigma antagonist) domain protein. Using biochemical and genetic approaches, we determined that SypE both phosphorylates and dephosphorylates SypA, and that phosphorylation inhibits SypA's activity. Furthermore, we found that biofilm formation and symbiotic colonization required active, unphosphorylated SypA, and thus SypA phosphorylation corresponded with a loss of biofilms and impaired host colonization. Finally, expression of a non-phosphorylatable mutant of SypA suppressed both the biofilm and symbiosis defects of a constitutively inhibitory SypE mutant strain. This study demonstrates that regulation of SypA activity by SypE is a critical mechanism by which V. fischeri controls biofilm development and symbiotic colonization.

RsbV of Listeria monocytogenes contributes to regulation of environmental stress and virulence

SigmaB factor is an important regulatory factor for stress response in Gram-positive bacteria such as Listeria monocytogenes (L. monocytogenes), Staphylococcus aureus and Bacillus subtilis. However, the activity of SigmaB factor is regulated by RsbV factor. Currently, the functional studies of RsbV factor are mostly focused on non-pathogenic B. subtilis, but the roles of RsbV factor in pathogenic L. monocytogenes during the regulation of environmental stress and virulence are still unclear. In the study, a ∆RsbV mutant of L. monocytogenes was constructed to explore the regulatory role of RsbV in environmental stress and virulence. The environmental stress experiments indicated that the growth and survival capability of ∆RsbV mutant obviously decreased in stress of low temperature, osmotic pressure, alcohol and acid, compared with EGD strain. The macrophage infection experiment indicated that ∆RsbV mutant had weaker survival capability than EGD strain, and the expression of PrfA, actA, PlcA and LLO was down-regulated in infected cells. Animal inoculation experiments indicated that RsbV deletion significantly reduced the pathogenicity of L. monocytogenes. Our data demonstrate that, in addition to regulating tolerance under environmental stress conditions, RsbV also contributes to regulation of L. monocytogenes virulence.

Interplay of RsbM and RsbK controls the σ(B) activity of Bacillus cereus

The alternative transcription factor σ(B) of Bacillus cereus controls the expression of a number of genes that respond to environmental stress. Four proteins encoded in the sigB gene cluster, including RsbV, RsbW, RsbY (RsbU) and RsbK, are known to be essential in the σ(B)-mediated stress response. In the context of stress, the hybrid sensor kinase RsbK is thought to phosphorylate the response regulator RsbY, a PP2C serine phosphatase, leading to the dephosphorylation of the phosphorylated RsbV. The unphosphorylated RsbV then sequesters the σ(B) antagonist, RsbW, ultimately liberating σ(B). The gene arrangement reveals an open reading frame, bc1007, flanked immediately downstream by rsbK within the sigB gene cluster. However, little is known about the function of bc1007. In this study, the deletion of bc1007 resulted in high constitutive σ(B) expression independent of environmental stimuli, indicating that bc1007 plays a role in σ(B) regulation. A bacterial two-hybrid analysis demonstrated that BC1007 interacts directly with RsbK, and autoradiographic studies revealed a specific C(14)-methyl transfer from the radiolabelled S-adenosylmethionine to RsbK when RsbK was incubated with purified BC1007. Our data suggest that BC1007 (RsbM) negatively regulates σ(B) activity by methylating RsbK. Additionally, mutagenic substitution was employed to modify 12 predicted methylation residues in RsbK. Certain RsbK mutants were able to rescue σ(B) activation in a rsbK-deleted bacterial strain, but RsbK(E439A) failed to activate σ(B), and RsbK(E446A) only moderately induced σ(B). These results suggest that Glu439 is the preferred methylation site and that Glu446 is potentially a minor methylation site. Gene arrays of the rsbK orthologues and the neighbouring rsbM orthologues are found in a wide range of bacteria. The regulation of sigma factors through metylation of RsbK-like sensor kinases appears to be widespread in the microbial world.

Inactivation of a novel response regulator is necessary for biofilm formation and host colonization by Vibrio fischeri

The marine bacterium Vibrio fischeri uses a biofilm to promote colonization of its eukaryotic host Euprymna scolopes. This biofilm depends on the symbiosis polysaccharide (syp) locus, which is transcriptionally regulated by the RscS-SypG two-component regulatory system. An additional response regulator (RR), SypE, exerts both positive and negative control over biofilm formation. SypE is a novel RR protein, with its three putative domains arranged in a unique configuration: a central phosphorylation receiver (REC) domain flanked by two effector domains with putative enzymatic activities (serine kinase and serine phosphatase). To determine how SypE regulates biofilm formation and host colonization, we generated a library of SypE domain mutants. Our results indicate that the N-terminus inhibits biofilm formation, while the C-terminus plays a positive role. The phosphorylation state of SypE appears to regulate these opposing activities, as disruption of the putative site of phosphorylation results in a protein that constitutively inhibits biofilm formation. Furthermore, SypE restricts host colonization: (i) sypE mutants with constitutive inhibitory activity fail to efficiently initiate host colonization and (ii) loss of sypE partially alleviates the colonization defect of an rscS mutant. We conclude that SypE must be inactivated to promote symbiotic colonization by V. fischeri.

Structural characterization of the multidomain regulatory protein Rv1364c from Mycobacterium tuberculosis

The open reading frame rv1364c of Mycobacterium tuberculosis, which regulates the stress-dependent σ factor, σ(F), has been analyzed structurally and functionally. Rv1364c contains domains with sequence similarity to the RsbP/RsbW/RsbV regulatory system of the stress-response σ factor of Bacillus subtilis. Rv1364c contains, sequentially, a PAS domain (which shows sequence similarity to the PAS domain of the B. subtilis RsbP protein), an active phosphatase domain, a kinase (anti-σ(F) like) domain and a C-terminal anti-σ(F) antagonist like domain. The crystal structures of two PAS domain constructs (at 2.3 and 1.6 Å) and a phosphatase/kinase dual domain construct (at 2.6 Å) are described. The PAS domain is shown to bind palmitic acid but to have 100 times greater affinity for palmitoleic acid. The full-length protein can exist in solution as both monomer and dimer. We speculate that a switch between monomer and dimer, possibly resulting from fatty acid binding, affects the accessibility of the serine of the C-terminal, anti-σ(F) antagonist domain for dephosphorylation by the phosphatase domain thus indirectly altering the availability of σ(F).

Stressosomes formed in Bacillus subtilis from the RsbR protein of Listeria monocytogenes allow σ(B) activation following exposure to either physical or nutritional stress

The general stress regulon of Bacillus subtilis is controlled by σ(B), a transcription factor that is activated by physical or nutritional stress. In B. subtilis, each of these two stresses is communicated to the primary σ(B) regulators by distinct pathways. Physical stress activation of σ(B) involves a large-molecular-mass (>10(6)-Da) structure (stressosome) formed by one or more homologous proteins (RsbRA, -B, -C, and -D) onto which the pathway's principal regulators are bound. The RsbR proteins are thought to be potential receptors for stress signaling. Listeria monocytogenes encodes orthologs of σ(B) and its principal regulators; however, unlike B. subtilis, L. monocytogenes appears to use the stressosome pathway for both physical and nutritional stress activation of σ(B). In the current work, a B. subtilis strain that expressed L. monocytogenes rsbR (rsbR(Lm)) in lieu of B. subtilis rsbR (rsbR(Bs)) was created and was found to display the Listeria phenotype of σ(B) activation following exposure to either physical or nutritional stress. B. subtilis expressing either the RsbR paralog rsbRC or rsbRD, but not rsbRA or rsbRB, as the sole source of RsbR also allowed σ(B) induction following nutritional stress. It is unclear whether the nutritional stress induction seen in these strains is the result of a direct effect of nutritional stress on stressosome activity or a consequence of the background levels of σ(B) activation in these strains and the effects of diminished ATP on the downstream phosphorylation reaction needed to reinactivate σ(B).

From gene regulation to gene function: regulatory networks in bacillus subtilis

Bacillus subtilis is a sporulating Gram-positive bacterium that lives primarily in the soil and associated water sources. The publication of the B. subtilis genome sequence and subsequent systematic functional analysis and gene regulation programmes, together with an extensive understanding of its biochemistry and physiology, makes this micro-organism a prime candidate in which to model regulatory networks in silico. In this paper we discuss combined molecular biological and bioinformatical approaches that are being developed to model this organism’s responses to changes in its environment.

Control of biofilm formation and colonization in Vibrio fischeri: a role for partner switching?

Bacteria employ a variety of mechanisms to promote and control colonization of their respective hosts, including restricting the expression of genes necessary for colonization to distinct situations (i.e. encounter with a prospective host). In the symbiosis between the marine bacterium Vibrio fischeri and its host squid, Euprymna scolopes, colonization proceeds via a transient biofilm formed by the bacterium. The production of this bacterial biofilm depends on a complex regulatory network that controls transcription of the symbiosis polysaccharide (syp) gene locus. In addition to this transcriptional control, biofilm formation is regulated by two proteins, SypA and SypE, which may function in an unusual regulatory mechanism known as partner switching. Best characterized in Bacillus subtilis and other Gram-positive bacteria, partner switching is a signalling mechanism that provides dynamic regulatory control over bacterial gene expression. The involvement of putative partner-switching components within V. fischeri suggests that tight regulatory control over biofilm formation may be important for the lifestyle of this organism.

Expression of, and in vivo stressosome formation by, single members of the RsbR protein family in Bacillus subtilis

The Bacillus subtilis stressosome is a 1.8 MDa complex that is the focal point for activating the bacterium's general response to physical stress. In vitro studies demonstrated that the stressosome's core element can be formed from one or more of a family of paralogous proteins (RsbRA, -RB, -RC and -RD) onto which the system's activator protein (RsbT) and its principal inhibitor (RsbS) are bound. The RsbR components of the stressosome are envisioned to be the initial receptors of stress signalling with the stressosome structure itself serving as a device to integrate multiple stress signals for a coordinated response. In the current work, we examine several of the in vivo characteristics of the RsbR family members, including their expression and ability to form stressosomes to regulate sigma(B). Translational fusions of lacZ to each rsbR paralogue revealed that rsbRA, -RB and -RC are expressed at similar levels, which remain relatively constant during growth, ethanol stress and entry into stationary phase. rsbRD, in contrast, is expressed at a level that is only slightly above background during growth, but is induced to 30 % of the rsbRA expression level following ethanol stress. Velocity sedimentation analyses of B. subtilis extracts from strains expressing single rsbR paralogues demonstrated that each incorporates RsbS into fast-sedimenting complexes. However, consistent with rsbRD's lower expression, the RsbRD-dependent RsbS complexes were present at only 20 % of the level of the complexes seen in a wild-type strain. The lower stressosome level in the RsbRD strain is still able to hold RsbT's activity in check, implying that the RsbR/S component of stressosomes is normally in excess for the control of RsbT. Consistent with such a notion, reporter gene and Western blot assays demonstrate that although RsbT is synthesized at the same rate as RsbRA and RsbS, RsbT's ultimate level in growing B. subtilis is only 10 % that of RsbRA. Apparently, RsbT's inherent structure and/or its passage between the stressosome and its activation target compromises its persistence.

Bypass suppression analysis maps the signalling pathway within a multidomain protein: the RsbP energy stress phosphatase 2C from Bacillus subtilis

The network controlling the general stress response in Bacillus subtilis requires both the RsbP phosphatase and the RsbQ alpha/beta hydrolase to convey signals of energy stress. RsbP contains three domains: an N-terminal PAS, a central coiled-coil and a C-terminal PP2C phosphatase. We report here a genetic analysis that established the functional interactions of the domains and their relationship to RsbQ. Random mutagenesis of rsbP yielded 17 independent bypass suppressors that had activity in an rsbQ null strain background. The altered residues clustered in three regions of RsbP: the coiled-coil and two predicted helices of the phosphatase domain. One helix (alpha0) is unique to a subfamily of bacterial PP2C phosphatases that possess N-terminal sensing domains. The other (alpha1) is distinct from the active site in all solved PP2C structures. The phenotypes of the suppressors and directed deletions support a model in which the coiled-coil negatively controls phosphatase activity, perhaps via the alpha0-alpha1 helices, with RsbQ hydrolase activity and the PAS domain jointly comprising a positive sensing module that counters the coiled-coil. We propose that the alpha0 helix characterizes an extended PP2C domain in many bacterial signalling proteins, and suggest it provides a means to communicate information from diverse input domains.

Role of RsbU in controlling SigB activity in Staphylococcus aureus following alkaline stress

SigB is an alternative sigma factor that controls a large regulon in Staphylococcus aureus. Activation of SigB requires RsbU, a protein phosphatase 2C (PP2C)-type phosphatase. In a closely related organism, Bacillus subtilis, RsbU activity is stimulated upon interaction with RsbT, a kinase, which following an activating stimulus switches from a 25S high-molecular-weight complex, the stressosome, to the N-terminal domain of RsbU. Active RsbU dephosporylates RsbV and thereby triggers the release of SigB from its inhibitory complex with RsbW. While RsbU, RsbV, RsbW, and SigB are conserved in S. aureus, proteins similar to RsbT and the components of the stressosome are not, raising the question of how RsbU activity and hence SigB activity are controlled in S. aureus. We found that in contrast to the case in B. subtilis, the induced expression of RsbU was sufficient to stimulate SigB-dependent transcription in S. aureus. However, activation of SigB-dependent transcription following alkaline stress did not lead to a clear accumulation of SigB and its regulators RsbV and RsbW or to a change in the RsbV/RsbV-P ratio in S. aureus. When expressed in B. subtilis, the S. aureus RsbU displayed a high activity even in the absence of an inducing stimulus. This high activity could be transferred to the PP2C domain of the B. subtilis RsbU protein by a fusion to the N-terminal domain of the S. aureus RsbU. Collectively, the data suggest that the activity of the S. aureus RsbU and hence SigB may be subjected to different regulation in comparison to that in B. subtilis.

The growth-promoting and stress response activities of the Bacillus subtilis GTP binding protein Obg are separable by mutation

Bacillus subtilis Obg is a ribosome-associating GTP binding protein that is needed for growth, sporulation, and induction of the bacterium's general stress regulon (GSR). It is unclear whether the roles of Obg in sporulation and stress responsiveness are direct or a secondary effect of its growth-promoting functions. The present work addresses this question by an analysis of two obg alleles whose phenotypes argue for direct roles for Obg in each process. The first allele [obg(G92D)] encodes a missense change in the protein's highly conserved "obg fold" region. This mutation impairs cell growth and the ability of Obg to associate with ribosomes but fails to block sporulation or the induction of the GSR. The second obg mutation [obg(Delta22)] replaces the 22-amino-acid carboxy-terminal sequence of Obg with an alternative 26-amino-acid sequence. This Obg variant cofractionates with ribosomes and allows normal growth but blocks sporulation and impairs the induction of the GSR. Additional experiments revealed that the block on sporulation occurs early, preventing the activation of the essential sporulation transcription factor Spo0A, while inhibition of the GSR appears to involve a failure of the protein cascade that normally activates the GSR to effectively catalyze the reactions needed to activate the GSR transcription factor (sigma(B)).

Dynamics of protein phosphorylation on Ser/Thr/Tyr inBacillus subtilis

The Ser/Thr/Tyr phosphoproteome of Bacillus subtilis was analyzed by a 2-D gel-based approach combining Pro-Q Diamond staining and [(33)P]-labeling. In exponentially growing B. subtilis cells 27 proteins could be identified after staining with Pro-Q Diamond and/or [(33)P]-labeling and one additional protein was labeled solely by [(33)P] resulting in a total of 28 potentially phosphorylated proteins. These proteins are mainly involved in enzymatic reactions of basic carbon metabolism and the regulation of the alternative sigma factor sigma(B). We also found significant changes of the phosphoproteome including increased phosphorylation and dephosphorylation rates of some proteins as well as the detection of four newly phosphorylated proteins in response to stress or starvation. For nine proteins, phosphorylation sites at serine or threonine residues were determined by MS. These include the known phosphorylation sites of Crh, PtsH, and RsbV. Additionally, we were able to identify novel phosphorylation sites of AroA, Pyk, and YbbT. Interestingly, the phosphorylation of RsbRA, B, C, and D, four proteins of a multicomponent protein complex involved in environmental stress signaling, was found during exponential growth. For RsbRA, B, and D, phosphorylation of one of the conserved threonine residues in their C-termini were verified by MS (T171, T186, T181, respectively).

ClpP modulates the activity of the Bacillus subtilis stress response transcription factor, sigmaB

The general stress regulon of Bacillus subtilis is controlled by the activity state of sigmaB, a transcription factor that is switched on following exposure to either physical or nutritional stress. ClpP is the proteolytic component of an ATP-dependent protease that is essential for the proper regulation of multiple adaptive responses in B. subtilis. Among the proteins whose abundance increases in ClpP- B. subtilis are several known to depend on sigmaB for their expression. In the current work we examine the relationship of ClpP to the activity of sigmaB. The data reveal that the loss of ClpP in otherwise wild-type B. subtilis results in a small increase in sigmaB activity during growth and a marked enhancement of sigmaB activity following its induction by either physical or nutritional stress. It appears to be the persistence of sigmaB's activity rather than its induction that is principally affected by the loss of ClpP. sigmaB-dependent reporter gene activity rose in parallel in ClpP+ and ClpP- B. subtilis strains but failed to display its normal transience in the ClpP- strain. The putative ClpP targets are likely to be stress generated and novel. Enhanced sigmaB activity in ClpP- B. subtilis was triggered by physical stress but not by the induced synthesis of the physical stress pathway's positive regulator (RsbT). In addition, Western blot analyses failed to detect differences in the levels of the principal known sigmaB regulators in ClpP+ and ClpP- B. subtilis strains. The data suggest a model in which ClpP facilitates the turnover of stress-generated factors, which persist in ClpP's absence to stimulate ongoing sigmaB activity.

Isolation and characterization of dominant mutations in the Bacillus subtilis stressosome components RsbR and RsbS

The general stress response of Bacillus subtilis is controlled by the activity state of the sigma(B) transcription factor. Physical stress is communicated to sigma(B) via a large-molecular-mass (>10(6)-Da) structure (the stressosome) formed by one or more members of a family of homologous proteins (RsbR, YkoB, YojH, YqhA). The positive regulator (RsbT) of the sigma(B) stress induction pathway is incorporated into the complex bound to an inhibitor protein (RsbS). Exposure to stress empowers an RsbT-dependent phosphorylation of RsbR and RsbS, with the subsequent release of RsbT to activate downstream processes. The mechanism by which stress initiates these reactions is unknown. In an attempt to identify changes in stressosome components that could lead to sigma(B) activation, a DNA segment encoding these proteins was mutagenized and placed into B. subtilis to create a merodiploid strain for these genes. Eight mutations that allowed heightened sigma(B) activity in the presence of their wild-type counterparts were isolated. Two of the mutations are missense changes in rsbR, and six are amino acid changes in rsbS. Additional experiments suggested that both of the rsbR mutations and three of the rsbS mutations likely enhance sigma(B) activity by elevating the level of RsbS phosphorylation. All of the mutations were found to be dominant over wild-type alleles only when they are cotranscribed within an rsbR rsbS rsbT operon. The data suggest that changes in RsbR can initiate the downstream events that lead to sigma(B) activation and that RsbR, RsbS, and RsbT likely interact with each other concomitantly with their synthesis.

SigmaB activation under environmental and energy stress conditions in Listeria monocytogenes

To measure sigmaB activation in Listeria monocytogenes under environmental or energy stress conditions, quantitative reverse transcriptase PCR (TaqMan) was used to determine the levels of transcripts for the sigmaB -dependent opuCA and clpC genes in strains having null mutations in genes encoding regulator of sigma B proteins (rsbT and rsbV) and sigma B (sigB) and in the L. monocytogenes wild-type 10403S strain under different stress conditions. The DeltasigB, DeltarsbT, and DeltarsbV strains previously exhibited increased hemolytic activities compared to the hemolytic activity of the wild-type strain; therefore, transcript levels for hly were also determined. RsbT, RsbV, and sigmaB were all required for opuCA expression during growth under carbon-limiting conditions or following exposure to pH 4.5, salt, ethanol, or the protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP). Expression of clpC was RsbT, RsbV, and sigmaB dependent in the presence of CCCP but not under the other conditions. hly expression was not RsbT, RsbV, or sigmaB dependent in the presence of either CCCP or salt. opuCA transcript levels did not increase in the presence of rapidly lethal stresses (i.e., pH 2.5 or 13 mM cumene hydroperoxide) despite the enhanced survival of the wild type compared with the survival of the mutant strains under these conditions. These findings highlight the importance of complementing phenotypic characterizations with gene expression studies to identify direct and indirect effects of null mutations in regulatory genes, such as sigB. Overall, our data show that while sigmaB activation occurs through a single pathway under both environmental and energy stress conditions, regulation of expression of some stress response and virulence genes in the sigmaB regulon (e.g., clpC) appears to require networks involving multiple transcriptional regulators.

High-molecular-weight complexes of RsbR and paralogues in the environmental signaling pathway of Bacillus subtilis

Bacillus subtilis has developed an intricate signal transduction cascade to respond to the imposition of a variety of stresses on the cell. Reversible protein phosphorylation and the formation of alternative protein-protein complexes modulate the activity of sigma(B), the RNA polymerase sigma factor subunit responsible for the transcription of the general stress response genes. Some of the regulators of sigma(B), such as RsbR and RsbS, are known to associate in a 25S complex, called the stressosome, that can bind RsbT until RsbT phosphorylates target residues in RsbR and RsbS. To date, the RsbR-RsbS complex appears to be the most upstream component of the sigma(B) regulatory pathway. This large structure is thought to play an important role in sensing and/or integrating signals from different physical stresses. The roles of the paralogues of RsbR that are found in B. subtilis remain unclear. We describe here how the RsbR paralogues copurify with RsbR from B. subtilis cell lysates, and we demonstrate in vitro that the paralogues form large complexes either with RsbS or with a prepurified RsbR-RsbS binary complex. We conclude from these biochemical studies that stressosomes in B. subtilis cells contain minimally RsbS and all of the RsbT-phosphorylatable RsbR paralogues.

Core of the partner switching signalling mechanism is conserved in the obligate intracellular pathogen Chlamydia trachomatis

Chlamydia trachomatis is an obligate intracellular bacterial pathogen that can cause sexually transmitted and ocular diseases in humans. Its biphasic developmental cycle and ability to evade host-cell defences suggest that the organism responds to external signals, but its genome encodes few recognized signalling pathways. One such pathway is predicted to function by a partner switching mechanism, in which key protein interactions are controlled by serine phosphorylation. From genome analysis this mechanism is both ancient and widespread among eubacteria, but it has been experimentally characterized in only a few. C. trachomatis has no system of genetic exchange, so here an in vitro approach was used to establish the activities and interactions of the inferred partner switching components: the RsbW switch protein/kinase and its RsbV antagonists. The C. trachomatis genome encodes two RsbV paralogs, RsbV(1) and RsbV(2). We found that each RsbV protein was specifically phosphorylated by RsbW, and tandem mass spectrometry located the phosphoryl group on a conserved serine residue. Mutant RsbV(1) and RsbV(2) proteins in which this conserved serine was changed to alanine could activate the yeast two-hybrid system when paired with RsbW, whereas mutant proteins bearing a charged aspartate failed to activate. From this we infer that the phosphorylation state of RsbV(1) and RsbV(2) controls their interaction with RsbW in vivo. This experimental demonstration that the core of the partner switching mechanism is conserved in C. trachomatis indicates that its basic features are maintained over a large evolutionary span. Although the molecular target of the C. trachomatis switch remains to be identified, based on the predicted properties of its input phosphatases we propose that the pathway controls an important aspect of the developmental cycle within the host, in response to signals external to the C. trachomatis cytoplasmic membrane.

The sigmaB regulon in Staphylococcus aureus and its regulation

The Staphylococcus aureus genome codes for a sigma factor that shows close sequence similarity to the alternative sigma factor sigmaB of Bacillus subtilis. However, of the proteins controlling the activity of sigmaB in B. subtilis only RsbU, RsbV, and RsbW are encoded in the staphylococcal genome. Therefore, the regulation of the sigmaB activity must differ between these two bacterial species. The present study was designed (i) to describe the sigmaB regulon and (ii) to identify stimuli leading to an activation of sigmaB-dependent transcription. All conditions under which sigmaB was activated in S. aureus (heat shock, addition of MnCl2 or NaCl, alkaline shock) required the presence of RsbU, a positive regulator of sigmaB. In contrast to B. subtilis, a drop in the cellular ATP level caused by the addition of carbonyl cyanide m-chlorophenylhydrazone did not lead to an activation of sigmaB in S. aureus. Moreover, ethanol, a strong inductor of sigmaB activity in B. subtilis, also failed to induce sigmaB in S. aureus. Expression of sigB and sigmaB-dependent genes was enhanced following entry into stationary phase of cells grown in complex medium (LB medium). Our DNA microarray data indicated that 122 genes are positively regulated by sigmaB under alkaline stress conditions. Interestingly, only 12% of these genes have an orthologue in the B. subtilis sigmaB regulon, suggesting that the function of the sigmaB regulon in S. aureus is different from that in B. subtilis. We could show that sigmaB of S. aureus, in contrast to B. subtilis, may have a function in more basic cellular processes such as cell envelope composition, membrane transport processes and intermediary metabolism. sigmaB-dependent genes identified by the DNA microarray approach were subjected to detailed transcriptional analyses using primer extension and Northern blot techniques. These analyses confirmed our DNA microarray data and furthermore revealed different regulatory groups of sigmaB-dependent genes.

Coexpression patterns of sigma(B) regulators in Bacillus subtilis affect sigma(B) inducibility

RsbT is an essential component of the pathway that activates the Bacillus subtilis sigma(B) transcription factor in response to physical stress. rsbT is located within an operon that includes the genes for its principal negative regulator (RsbS) and the stress pathway component that it activates (RsbU), as immediate upstream and downstream neighbors. In the current work we demonstrate that RsbT's ability to function is strongly influenced by coexpression with these adjoining genes. When rsbT is expressed at a site displaced from rsbS and rsbU, RsbT accumulates but it is unable to activate sigma(B) following stress. RsbT activity is restored if rsbT is cotranscribed at the alternative site with the genes that normally abut it. Additionally, an rsbS allele whose product allows constitutively high RsbT-dependent sigma(B) activity displays this activity in rsbS merodiploid strains only when cotranscribed with rsbT and is recessive to a wild-type rsbS allele only if the wild-type rsbS gene is not cotranscribed with an rsbT gene of its own. The data suggest that RsbS and RsbT are synthesized in equivalent amounts and interact coincidently with their synthesis to form stable regulatory complexes that maintain RsbT in a state from which it can be stress activated.

Contributions of ATP, GTP, and redox state to nutritional stress activation of the Bacillus subtilis sigmaB transcription factor

The general stress regulon of Bacillus subtilis is induced by activation of the sigma(B) transcription factor. sigma(B) activation occurs when one of two phosphatases responds to physical or nutritional stress to activate a positive sigma(B) regulator by dephosphorylation. The signal that triggers the nutritional stress phosphatase (RsbP) is unknown; however, RsbP activation occurs under culture conditions (glucose/phosphate starvation, azide or decoyinine treatment) that reduce the cell's levels of ATP and/or GTP. Variances in nucleotide levels in these instances may be coincidental rather than causal. RsbP carries a domain (PAS) that in some regulatory systems can respond directly to changes in electron transport, proton motive force, or redox potential, changes that typically precede shifts in high-energy nucleotide levels. The current work uses Bacillus subtilis with mutations in the oxidative phosphorylation and purine nucleotide biosynthetic pathways in conjunction with metabolic inhibitors to better define the inducing signal for RsbP activation. The data argue that a drop in ATP, rather than changes in GTP, proton motive force, or redox state, is the key to triggering sigma(B) activation.

The RsbRST Stress Module in Bacteria: A Signalling System That May Interact with Different Output Modules

In the Gram-positive bacterium Bacillus subtilis, the activity of the alternative sigma factor sigma(B) is triggered upon exposure of the bacteria to environmental stress conditions or to nutrient limitation. sigma(B) activity is controlled by protein-phosphorylation-dependent interactions of anti-sigma with anti-anti-sigma factors. Under stress conditions, the phosphatase RsbU triggers release of sigma(B) and thus induces the expression of stress genes. RsbU activity is controlled by three proteins, RsbR, RsbS and RsbT which form a supramolecular complex called the stressosome. Here we review the occurrence of the genes encoding the stressosome proteins (called the RsbRST module) in a wide variety of bacteria. While this module is linked to the gene encoding sigma(B) and its direct regulators in B. subtilis and its close relatives, genes encoding two-component regulatory systems and more complex phosphorelays are clustered with the RsbRST module in bacteria as diverse as cyanobacteria, bacteroidetes, proteobacteria, and deinococci. The conservation of the RsbRST module and its clustering with different types of regulatory systems suggest that the stressosome proteins form a signal sensing and transduction unit that relays information to very different output modules.

Functional proteomics and correlated signaling pathway of the thermophilic bacterium Bacillus stearothermophilus TLS33 under cold-shock stress

The thermophilic bacterium Bacillus stearothermophilus TLS33 was examined under cold-shock stress by a proteomic approach to gain a better understanding of the protein synthesis and complex regulatory pathways of bacterial adaptation. After downshift in the temperature from 65 degrees C, the optimal growth temperature for this bacterium, to 37 degrees C and 25 degrees C for 2 h, we used the high-throughput techniques of proteomic analysis combining 2-DE and MS to identify 53 individual proteins including differentially expressed proteins. The bioinformatics database was used to search the biological functions of proteins and correlate these with gene homology and metabolic pathways in cell protection and adaptation. Eight cold-shock-induced proteins were shown to have markedly different protein expression: glucosyltransferase, anti-sigma B (sigma(B)) factor, Mrp protein homolog, dihydroorthase, hypothetical transcriptional regulator in FeuA-SigW intergenic region, RibT protein, phosphoadenosine phosphosulfate reductase and prespore-specific transcriptional activator RsfA. Interestingly, six of these cold-shock-induced proteins are correlated with the signal transduction pathway of bacterial sporulation. This study aims to provide a better understanding of the functional adaptation of this bacterium to environmental cold-shock stress.

From genomics via proteomics to cellular physiology of the Gram-positive model organism Bacillus subtilis

Complementing proteomic technologies enable an unbiased view of cellular adaptation and thus may provide a new understanding of cellular physiology, particularly for microorganisms because a major fraction of their proteome is accessible to currently available technology. In combination with transcriptional profiling expression proteomics provides access to interesting candidate genes and proteins that will then need to be validated and supplemented by traditional physiological, biochemical and genetic approaches. After a description of the current status of the technology, we display the potential of microbial proteomics using the model organism Bacillus subtilis as example. Starting from a proteome map a proteomic view of the metabolism will be provided. Furthermore, we demonstrate that proteomics complemented by transcriptomics is also useful for the study of stress and starvation responses and that integration of these data will lead to a comprehensive understanding of the adaptational network of bacterial cells. Thus, B. subtilis constitutes a highly versatile and tractable model organism for the study of generic stress responses and the expertise that has been gained can easily be transferred to the study of the cellular physiology of related Gram-positive pathogens and their pathophysiology.

RsbT and RsbV contribute to sigmaB-dependent survival under environmental, energy, and intracellular stress conditions in Listeria monocytogenes

Sigma B (sigma(B)) is a stress-responsive alternative sigma factor that has been identified in various gram-positive bacteria. Seven different regulators of sigma B (Rsbs) are located in the sigB operons of both Bacillus subtilis and Listeria monocytogenes. In B. subtilis, these proteins contribute to regulation of sigma(B) activity by conveying environmental and energy stress signals through two well-established branches of a signal transduction pathway. RsbT contributes to regulation of sigma(B) activity in response to environmental stresses, while RsbV contributes to sigma(B) activation under both environmental and energy stresses in B. subtilis. To probe L. monocytogenes Rsb roles in sigma(B)-mediated responses to various stresses, in-frame deletions were created in rsbT and rsbV. Phenotypic characterization of the L. monocytogenes rsbT and rsbV null mutants revealed that both mutants were similar to the DeltasigB strain in their abilities to survive under environmental stress conditions (exposure to synthetic gastric fluid, pH 2.5, acidified brain heart infusion broth [BHI], or oxidative stress [13 mM cumene hydroperoxide]). Under energy stress conditions (carbon starvation in defined media, entry into stationary phase, or reduced intracellular ATP), both DeltarsbT and DeltarsbV showed survival reductions similar to that of the DeltasigB strain. These observations suggest that the pathways for Rsb-dependent regulation of sigma(B) activity differ between L. monocytogenes and B. subtilis. As sigma(B) also activates transcription of the L. monocytogenes prfAP2 promoter, we evaluated virulence-associated characteristics of DeltaprfAP1rsbT and DeltaprfAP1rsbV double mutants in hemolysis and tissue culture assays. Both double mutants showed identical phenotypes to DeltaprfAP1P2 and DeltaprfAP1sigB double mutants, i.e., reduced hemolysis activity and reduced plaque size in mouse fibroblast cells. These findings indicate that RsbT and RsbV both contribute to sigma(B) activation in L. monocytogenes during exposure to environmental and energy stresses as well as during tissue culture infection.

Phosphorylation and RsbX-dependent dephosphorylation of RsbR in the RsbR-RsbS complex of Bacillus subtilis

In the pathway that controls sigmaB activity, the RsbR-RsbS complex plays an important role by trapping RsbT, a positive regulator of sigmaB of Bacillus subtilis. We have proposed that at the onset of stress, RsbR becomes phosphorylated, resulting in an enhanced activity of RsbT towards RsbS. RsbT is then free to interact with and activate RsbU, which in turn ultimately activates sigmaB. In this study with purified proteins, we used mutant RsbR proteins to analyze the role of its phosphorylatable threonine residues. The results show that the phosphorylation of either of the two RsbT-phosphorylatable threonine residues (T171 and T205) in RsbR enhanced the kinase activity of RsbT towards RsbS. However, it appeared that RsbT preferentially phosphorylates T171. We also present in vitro evidence that identifies RsbX as a potential phosphatase for RsbR T205.

RsbV-independent induction of the SigB-dependent general stress regulon of Bacillus subtilis during growth at high temperature

General stress proteins protect Bacillus subtilis cells against a variety of environmental insults. This adaptive response is particularly important for nongrowing cells, to which it confers a multiple, nonspecific, and preemptive stress resistance. Induction of the general stress response relies on the alternative transcription factor, SigB, whose activity is controlled by a partner switching mechanism that also involves the anti-sigma factor, RsbW, and the antagonist protein, RsbV. Recently, the SigB regulon has been shown to be continuously induced and functionally important in cells actively growing at low temperature. With the exception of this chill induction, all SigB-activating stimuli identified so far trigger a transient expression of the SigB regulon that depends on RsbV. Through a proteome analysis and Northern blot and gene fusion experiments, we now show that the SigB regulon is continuously induced in cells growing actively at 51 degrees C, close to the upper growth limit of B. subtilis. This heat induction of SigB-dependent genes requires the environmental stress-responsive phosphatase RsbU, but not the metabolic stress-responsive phosphatase RsbP. RsbU dependence of SigB activation by heat is overcome in mutants that lack RsbV. In addition, loss of RsbV alone or in combination with RsbU triggers a hyperactivation of the general stress regulon exclusively at high temperatures detrimental for cell growth. These new facets of heat induction of the SigB regulon indicate that the current view of the complex genetic and biochemical regulation of SigB activity is still incomplete and that SigB perceives signals independent of the RsbV-mediated signal transduction pathways under heat stress conditions.

In vivo phosphorylation of partner switching regulators correlates with stress transmission in the environmental signaling pathway of Bacillus subtilis

Exposure of bacteria to diverse growth-limiting stresses induces the synthesis of a common set of proteins which provide broad protection against future, potentially lethal stresses. Among Bacillus subtilis and its relatives, this general stress response is controlled by the sigmaB transcription factor. Signals of environmental and energy stress activate sigmaB through a multicomponent network that functions via a partner switching mechanism, in which protein-protein interactions are governed by serine and threonine phosphorylation. Here, we tested a central prediction of the current model for the environmental signaling branch of this network. We used isoelectric focusing and immunoblotting experiments to determine the in vivo phosphorylation states of the RsbRA and RsbS regulators, which act in concert to negatively control the RsbU environmental signaling phosphatase. As predicted by the model, the ratio of the phosphorylated to unphosphorylated forms of both RsbRA and RsbS increased in response to salt or ethanol stress. However, these two regulators differed substantially with regard to the extent of their phosphorylation under both steady-state and stress conditions, with RsbRA always the more highly modified. Mutant analysis showed that the RsbT kinase, which is required for environmental signaling, was also required for the in vivo phosphorylation of RsbRA and RsbS. Moreover, the T171A alteration of RsbRA, which blocks environmental signaling, also blocked in vivo phosphorylation of RsbRA and impeded phosphorylation of RsbS. These in vivo results corroborate previous genetic analyses and link the phosphorylated forms of RsbRA and RsbS to the active transmission of environmental stress signals.

RsbU-dependent regulation of Staphylococcus epidermidis biofilm formation is mediated via the alternative sigma factor sigmaB by repression of the negative regulator gene icaR

Transposon mutagenesis of rsbU leads to a biofilm-negative phenotype in Staphylococcus epidermidis. However, the pathway of this regulatory mechanism was unknown. To investigate the role of RsbU in the regulation of the alternative sigma factor sigma(B) and biofilm formation, we generated different mutants of the sigma(B) operon in S. epidermidis strains 1457 and 8400. The genes rsbU, rsbV, rsbW, and sigB, as well as the regulatory cascade rsbUVW and the entire sigma(B) operon, were deleted. Transcriptional analysis of sarA and the sigma(B)-dependent gene asp23 revealed the functions of RsbU and RsbV as positive regulators and of RsbW as a negative regulator of sigma(B) activity, indicating regulation of sigma(B) activity similar to that characterized for Bacillus subtilis and Staphylococcus aureus. Phenotypic characterization of the mutants revealed that the dramatic decrease of biofilm formation in rsbU mutants is mediated via sigma(B), indicating a crucial role for sigma(B) in S. epidermidis pathogenesis. However, biofilm formation in mutants defective in sigma(B) or its function could be restored in the presence of subinhibitory ethanol concentrations. Transcriptional analysis revealed that icaR is up-regulated in mutants lacking sigma(B) function but that icaA transcription is down-regulated in these mutants, indicating a sigma(B)-dependent regulatory intermediate negatively regulating IcaR. Supplementation of growth media with ethanol decreased icaR transcription, leading to increased icaA transcription and a biofilm-positive phenotype, indicating that the ethanol-dependent induction of biofilm formation is mediated by IcaR. This icaR-dependent regulation under ethanol induction is mediated in a sigma(B)-independent manner, suggesting at least one additional regulatory intermediate in the biofilm formation of S. epidermidis.

Mutational analysis of RsbT, an activator of the Bacillus subtilis stress response transcription factor, sigmaB

SigmaB, the stress-activated sigma factor of Bacillus subtilis, requires the RsbT protein as an essential positive regulator of its physical stress pathway. Stress triggers RsbT to both inactivate the principal negative regulator of the physical stress pathway (RsbS) by phosphorylation and activate a phosphatase (RsbU) required for sigmaB induction. Neither the regions of RsbT that are involved in responding to stress signaling nor those required for downstream events have been established. We used alanine scanning mutagenesis to examine the contributions of RsbT's charged amino acids to the protein's stability and activities. Eleven of eighteen rsbT mutations blocked sigmaB induction by stress. The carboxy terminus of RsbT proved to be particularly important for accumulation in Bacillus subtilis. Four of the five most carboxy-terminal mutations yielded rsbT alleles whose products were undetectable in B. subtilis extracts. Charged amino acids in the central region of RsbT were less critical, with four of the five substitutions in this region having no measurable effect on RsbT accumulation or activity. Only when the substitutions extended into a region of kinase homology was sigmaB induction affected. Six other RsbT variants, although present at levels adequate for activity, failed to activate sigmaB and displayed significant changes in their ability to interact with RsbT's normal binding partners in a yeast dihybrid assay. These changes either dramatically altered the proteins' tertiary structure without affecting their stability or defined regions of RsbT that are involved in multiple interactions.

RelA is a component of the nutritional stress activation pathway of the Bacillus subtilis transcription factor sigma B

The general stress regulon of Bacillus subtilis is induced by the activation of the sigma(B) transcription factor. Activation of sigma(B) occurs when one of two phosphatases (RsbU and RsbP), each responding to a unique type of stress, actuates a positive regulator of sigma(B) by dephosphorylation. Nutritional stress triggers the RsbP phosphatase. The mechanism by which RsbP becomes active is unknown; however, its activation coincides with culture conditions that are likely to reduce the cell's levels of high-energy nucleotides. We now present evidence that RelA, a (p)ppGpp synthetase and the key enzyme of the stringent response, plays a role in nutritional stress activation of sigma(B). An insertion mutation that disrupts relA blocks the activation of sigma(B) in response to PO(4) or glucose limitation and inhibits the drop in ATP/GTP levels that normally accompanies sigma(B) induction under these conditions. In contrast, the activation of sigma(B) by physical stress (e.g., ethanol treatment) is not affected by the loss of RelA. RelA's role in sigma(B) activation appears to be distinct from its participation in the stringent response. Amino acid analogs which induce the stringent response and RelA-dependent (p)ppGpp synthesis do not trigger sigma(B) activity. In addition, neither a missense mutation in relA (relA240GE) nor a null mutation in rplK (rplK54), either of which is sufficient to inhibit the stringent response and RelA-dependent (p)ppGpp synthesis, fails to block sigma(B) activation by PO(4) or glucose limitation.