RpoS controls the Vibrio cholerae mucosal escape response

Vibrio cholerae causes a severe diarrhoeal disease by secreting a toxin during colonization of the epithelium in the small intestine. Whereas the initial steps of the infectious process have been intensively studied, the last phases have received little attention. Confocal microscopy of V. cholerae O1-infected rabbit ileal loops captured a distinctive stage in the infectious process: 12 h post-inoculation, bacteria detach from the epithelial surface and move into the fluid-filled lumen. Designated the “mucosal escape response,” this phenomenon requires RpoS, the stationary phase alternative sigma factor. Quantitative in vivo localization assays corroborated the rpoS phenotype and showed that it also requires HapR. Expression profiling of bacteria isolated from ileal loop fluid and mucus demonstrated a significant RpoS-dependent upregulation of many chemotaxis and motility genes coincident with the emigration of bacteria from the epithelial surface. In stationary phase cultures, RpoS was also required for upregulation of chemotaxis and motility genes, for production of flagella, and for movement of bacteria across low nutrient swarm plates. The hapR mutant produced near-normal numbers of flagellated cells, but was significantly less motile than the wild-type parent. During in vitro growth under virulence-inducing conditions, the rpoS mutant produced 10- to 100-fold more cholera toxin than the wild-type parent. Although the rpoS mutant caused only a small over-expression of the genes encoding cholera toxin in the ileal loop, it resulted in a 30% increase in fluid accumulation compared to the wild-type. Together, these results show that the mucosal escape response is orchestrated by an RpoS-dependent genetic program that activates chemotaxis and motility functions. This may furthermore coincide with reduced virulence gene expression, thus preparing the organism for the next stage in its life cycle.

Vibrio cholerae, a pathogenic microbe, causes a severe diarrhoeal disease mainly in Third World countries. Although the pathogenicity of this organism has been intensively studied for more than a century, most research has focused on the initial stages of the infection, especially colonization of the intestine and virulence gene expression. However, the last stages of the infectious process have received very little attention. In the present manuscript, the authors use the rabbit ileal loop model of cholera to show how this organism, late in the infection, detaches from the epithelial surface and migrates into the luminal fluid, a process the authors termed the “mucosal escape response.” This study identifies, for the first time, how the alternative starvation sigma factor RpoS regulates this process. Features of this genetic program include the dramatic induction of genes involved in motility and chemotaxis functions. This study furthermore identifies RpoS as an important regulator of virulence gene expression and shows that the mucosal escape response may coincide with diminished virulence gene expression. This work is essential for understanding a key and under-appreciated step in the life cycle of this important human pathogen: its exit from the intestine and how this serves to prepare it for transmission into environmental reservoirs or to new human hosts.

Role of RpoS in fine-tuning the synthesis of Vi capsular polysaccharide in Salmonella enterica serotype Typhi

Regulation of the synthesis of Vi polysaccharide, a major virulence determinant in Salmonella enterica serotype Typhi, is under the control of two regulatory systems, ompR-envZ and rscB-rscC, which respond to changes in osmolarity. Some serotype Typhi strains exhibit overexpression of Vi polysaccharide, which masks clinical detection of lipopolysaccharide O antigen. This variation in Vi polysaccharide and O antigen display (VW variation) has been observed since the initial studies of serotype Typhi. In this study, we report that rpoS plays a role in this increased expression in Vi polysaccharide. We constructed a variety of isogenic serotype Typhi mutants that differed in their expression levels of RpoS and examined the role of the rpoS product in synthesis of Vi polysaccharide under different osmolarity conditions. Vi polysaccharide synthesis was also examined in serotype Typhi mutants in which the native promoter of the rpoS was replaced by an araCP(BAD) cassette, so that the expression of rpoS was arabinose dependent. The RpoS(-) strains showed increased syntheses of Vi polysaccharide, which at low and medium osmolarities masked O antigen detection. In contrast, RpoS(+) strains showed lower syntheses of Vi polysaccharide, and an increased detection of O antigen was observed. During exponential growth, when rpoS is unstable or present at low levels, serotype Typhi RpoS(+) strains overexpress the Vi polysaccharide at levels comparable to those for RpoS(-) strains. Our results show that RpoS is another regulator of Vi polysaccharide synthesis and contributes to VW variation in serotype Typhi, which has implications for the development of recombinant attenuated Salmonella vaccines in humans.

A suppressor of cell death caused by the loss of sigmaE downregulates extracytoplasmic stress responses and outer membrane vesicle production in Escherichia coli

When envelope biogenesis is compromised or damage to envelope components occurs, bacteria trigger signaling cascades, which lead to the production of proteins that combat such extracytoplasmic stresses. In Escherichia coli, there are three pathways known to deal with envelope stresses: the Bae, Cpx, and sigma(E) responses. Although the effectors of the Bae and Cpx responses are not essential in E. coli, the effector of the sigma(E) response, the sigma factor RpoE (sigma(E)), is essential for viability. However, mutations that suppress the lethality of an rpoE-null allele can be easily obtained, and here we describe how we have isolated at least four classes of these suppressors. We present the first description of one such suppressor class, loss-of-function mutations in ydcQ, a gene encoding a putative DNA-binding protein. In wild-type rpoE(+) strains, ydcQ mutants have two distinct phenotypes: extracytoplasmic stress responses are significantly downregulated, and the production of outer membrane vesicles is severely reduced. We present a model in which sigma(E) is not essential per se but, rather, we propose that rpoE mutant cells die, possibly because they overreact to the absence of this sigma factor by triggering a cell death signal.

Altered levels of Salmonella DNA adenine methylase are associated with defects in gene expression, motility, flagellar synthesis, and bile resistance in the pathogenic strain 14028 but not in the laboratory strain LT2

Comparative genomic analysis has revealed limited strain diversity between Salmonella pathogenic and nonpathogenic isolates. Thus, some of the relative virulence and host-immune response disparities may be credited to differential gene regulation rather than gross differences in genomic content. Here we show that altered levels of Salmonella DNA adenine methylase (Dam) resulted in acute defects in virulence-associated gene expression, motility, flagellin synthesis, and bile resistance in the Salmonella pathogenic strain 14028 but not in avirulent laboratory strain LT2. The defects in motility exhibited by 14028 in response to altered Dam levels was not dependent on the presence of the regulatory protein, RpoS. The transitioning between flagellar types (phase variation) was also differentially regulated in 14028 versus LT2 in response to dam levels, resulting in distinct differences in flagellin expression states. These data suggest that differential gene regulation may contribute to the relative virulence disparities observed between Salmonella serovars that are closely related at the DNA level.

Nucleus-encoded plastid sigma factor SIG3 transcribes specifically the psbN gene in plastids

We have investigated the function of one of the six plastid sigma-like transcription factors, sigma 3 (SIG3), by analysing two different Arabidopsis T-DNA insertion lines having disrupted SIG3 genes. Hybridization of wild-type and sig3 plant RNA to a plastid specific microarray revealed a strong reduction of the plastid psbN mRNA. The microarray result has been confirmed by northern blot analysis. The SIG3-specific promoter region has been localized on the DNA by primer extension and mRNA capping experiments. Results suggest tight regulation of psbN gene expression by a SIG3-PEP holoenzyme. The psbN gene is localized on the opposite strand of the psbB operon, between the psbT and psbH genes, and the SIG3-dependent psbN transcription produces antisense RNA to the psbT-psbH intergenic region. We show that this antisense RNA is not limited to the intergenic region, i.e. it does not terminate at the end of the psbN gene but extends as antisense transcript to cover the whole psbT coding region. Thus, by specific transcription initiation at the psbN gene promoter, SIG3-PEP holoenzyme could also influence the expression of the psbB operon by producing psbT antisense RNA.

Origin of mutations under selection: the adaptive mutation controversy

Growth under selection causes new genotypes to predominate in a population. It is difficult to determine whether selection stimulates formation of new mutations or merely allows faster growth of mutants that arise independent of selection. In the practice of microbial genetics, selection is used to detect and enumerate pre-existing mutants; stringent conditions prevent growth of the parent and allow only the pre-existing mutants to grow. Used in this way, selection detects rare mutations that cause large, easily observable phenotypic changes. In natural populations, selection is imposed on growing cells and can detect the more common mutations that cause small growth improvements. As slightly improved clones expand, they can acquire additional mutational improvements. Selected sequential clonal expansions have huge power to produce new genotypes and have been suggested to underlie tumor progression. We suggest that the adaptive mutation controversy has persisted because the distinction between these two uses of selection has not been appreciated.

Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli

Hfq, a chaperone for small noncoding RNAs, regulates many processes in Escherichia coli, including the sigma(S)-mediated general stress response. Here we used microarray analysis to identify the changes in gene expression resulting from lack of Hfq. We identify several potential new targets for Hfq regulation, including genes encoding outer membrane proteins, enzymes, factors, and transporters. Many of these genes are involved in amino acid uptake and biosynthesis, sugar uptake and metabolism, and cell energetics. In addition, we find altered regulation of the sigma(E)- and sigma(32)-mediated stress responses, which we analyze further. We show that cells lacking Hfq induce the sigma(E)-mediated envelope stress response and are defective in sigma(E)-mediated repression of outer membrane proteins. We also show that the sigma(32)-mediated cytoplasmic stress response is repressed in cells lacking Hfq due to increased expression of DnaK. Furthermore, we show that cells lacking Hfq are defective in the "long-term adaptation" of sigma(32) to chronic chaperone overexpression. Together, our results indicate that Hfq may play a general role in stress response regulation in E. coli.

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.

[Effects of sigma38 subunit deletion of RNA polymerase on antibiotics biosynthesis in pseudomonas]

With the designed primers, PCR was carried out using the genomic DNA of Pseudomonas sp. M18 as a template and a 378bp DNA fragment of the rpoS gene was amplified. Then, a 3. 1kb EcoR I -Xho I fragment containing the rpoS gene and its flanking sequence was obtained by screening the genomic DNA library of Pseudomonas sp. M18.A sigma38-subunit-deficient mutant M18S was constructed with insertional gentamycin gene cassette. In PPM medium, the mutant M18S produced 20.4 microg/mL of PCA and 75 microg/mL of Plt. In KMB medium, the mutant M18S produced no PCA and 185.6 microg/mL of Pit. It is obvious that the deficiency of sigma38 subunit in the mutant M18S leads less or no PCA production and much more Plt production than those in the wild type strain M18. PCA and Plt production were restored to the levels in wild type strain after complementation with rpoS gene in trans in strain M18S. Moreover, beta-galactosidase activities of the translational fusions phzA'-'lacZ and pltA'-'lacZ in strain M18S confirmed the effects of sigma38 subunit on PCA and Plt biosynthetic operons. With these results, it is suggested that sigma38 subunit gives a differential impacts on PCA and Plt biosynthesis, i. e, PCA production is positively regulated but Plt production is negatively influenced by sigma38 subunit in Pseudomonas sp. M18.

Initial characterization of a bolA homologue from Pseudomonas fluorescens indicates different roles for BolA-like proteins in P. fluorescens and Escherichia coli

The RpoS-regulated bolA gene in Escherichia coli is important for the decrease in cell size during stationary phase or sudden carbon starvation. A Pseudomonas fluorescens strain mutated in a gene with homology to bolA reduced its cell size upon carbon starvation, and RpoS had little effect on bolA expression. The mutant grew slower than the wild-type strain in minimal medium with L-serine as the sole nitrogen source, while growth rates were similar on a mixture of L-serine and L-cysteine. Reverse transcriptase polymerase chain reaction analysis indicated that the bolA homologue is the second gene in an operon where the two next ORFs encode putative proteins with homology to sulphurtransferases and protein disulphide isomerases. Complementation of the mutant phenotypes was only obtained by plasmids encoding BolA as well as the above two proteins. Growth phenotypes and gene homologies suggest that BolA-like proteins have different functions in E. coli and Pseudomonas.

The single extracytoplasmic-function sigma factor of Xylella fastidiosa is involved in the heat shock response and presents an unusual regulatory mechanism

Genome sequence analysis of the bacterium Xylella fastidiosa revealed the presence of two genes, named rpoE and rseA, predicted to encode an extracytoplasmic function (ECF) sigma factor and an anti-sigma factor, respectively. In this work, an rpoE null mutant was constructed in the citrus strain J1a12 and shown to be sensitive to exposure to heat shock and ethanol. To identify the X. fastidiosa sigma(E) regulon, global gene expression profiles were obtained by DNA microarray analysis of bacterial cells under heat shock, identifying 21 sigma(E)-dependent genes. These genes encode proteins belonging to different functional categories, such as enzymes involved in protein folding and degradation, signal transduction, and DNA restriction modification and hypothetical proteins. Several putative sigma(E)-dependent promoters were mapped by primer extension, and alignment of the mapped promoters revealed a consensus sequence similar to those of ECF sigma factor promoters of other bacteria. Like other ECF sigma factors, rpoE and rseA were shown to comprise an operon in X. fastidiosa, together with a third open reading frame (XF2241). However, upon heat shock, rpoE expression was not induced, while rseA and XF2241 were highly induced at a newly identified sigma(E)-dependent promoter internal to the operon. Therefore, unlike many other ECF sigma factors, rpoE is not autoregulated but instead positively regulates the gene encoding its putative anti-sigma factor.

The sigma(E) cell envelope stress response of Streptomyces coelicolor is influenced by a novel lipoprotein, CseA

We have investigated the role of CseA in the sigma(E) cell envelope stress response of the gram-positive bacterium Streptomyces coelicolor. sigma(E) is an extracytoplasmic function RNA polymerase sigma factor required for normal cell envelope integrity in S. coelicolor. sigma(E) is encoded within a four-gene operon that also encodes CseA, a protein of unknown function, CseB, a response regulator and CseC, a transmembrane sensor histidine kinase (Cse represents control of sigma E). Previous work has shown that transcription of the sigE gene is completely dependent on the CseBC two-component system and that the CseBC-sigma(E) signal transduction system is induced by a wide variety of cell-wall-damaging agents. Here we address the role of CseA, a protein with no homologues outside the streptomycetes. We show that CseA is a novel lipoprotein localized to the extracytoplasmic face of the cell membrane and that loss of CseA results in upregulation of the sigE promoter.

Blocking chromosome translocation during sporulation of Bacillus subtilis can result in prespore-specific activation of sigmaG that is independent of sigmaE and of engulfment

Formation of spores by Bacillus subtilis is characterized by cell compartment-specific gene expression directed by four RNA polymerase sigma factors, which are activated in the order sigma(F)-sigma(E)-sigma(G)-sigma(K). Of these, sigma(G) becomes active in the prespore upon completion of engulfment of the prespore by the mother cell. Transcription of the gene encoding sigma(G), spoIIIG, is directed in the prespore by RNA polymerase containing sigma(F) but also requires the activity of sigma(E) in the mother cell. When first formed, sigma(G) is not active. Its activation requires expression of additional sigma(E)-directed genes, including the genes required for completion of engulfment. Here we report conditions in which sigma(G) becomes active in the prespore in the absence of sigma(E) activity and of completion of engulfment. The conditions are (i) having an spoIIIE mutation, so that only the origin-proximal 30% of the chromosome is translocated into the prespore, and (ii) placing spoIIIG in an origin-proximal location on the chromosome. The main function of the sigma(E)-directed regulation appears to be to coordinate sigma(G) activation with the completion of engulfment, not to control the level of sigma(G) activity. It seems plausible that the role of sigma(E) in sigma(G) activation is to reverse some inhibitory signal (or signals) in the engulfed prespore, a signal that is not present in the spoIIIE mutant background. It is not clear what the direct activator of sigma(G) in the prespore is. Competition for core RNA polymerase between sigma(F) and sigma(G) is unlikely to be of major importance.

Sporulation-specific expression of the yvgW (cadA) gene and the effect of blockage on spore properties in Bacillus subtilis

The yvgW gene of Bacillus subtilis has been reported to encode a product which resembles CPx-type ATPase having a function related to Cd2+ and Zn2+ resistance through efflux of this metal. We recently showed that yvgW gene product is also important for sporulation in B. subtilis. The present study was focused on the functional characterization of yvgW in the sporulation process of B. subtilis. The analysis of yvgW expression showed that a significant expression took place during the late stage of sporulation (T5-T8). The deletion of spoIIAC and spoIIGB genes, encoding for sigmaF and sigmaE, respectively, resulted in the complete elimination of yvgW-lacZ expression while the deletion of the spoIIIG coding for sigmaG decreased the yvgW-lacZ expression to only 37% that of the wild type level. In contrast, the deletion of spoIVCB gene coding for sigmaK had no significant effects on the yvgW-lacZ expression. Transcription initiation site of yvgW during sporulation was determined by 5'-RACE-PCR, indicating that -10 and -35 sequences exhibited very good homology with the consensus sequences recognized by RNA polymerase containing sigmaE. Moreover, through the construction of yvgWDelta537-1351::spc, yvgW mutant cells were investigated for their spore properties, such as their resistance profiles against heat, chloroform and lysozyme, pointing out that spores of the mutant cells showed high sensitivity to heat and chloroform, but resistance to lysozyme. The level of dipicolinic acid was also significantly reduced to approximately 63% in yvgW spores as compared to wild type spores. Furthermore, the analyses of the nutrition-specific germination and outgrowth characteristics of the null mutant and the wild type cells revealed no defect in the initiation of yvgW spore germination but they returned to vegetative state more slowly than the wild type spores in minimal medium.

Leaving on the lights: host-specific derepression of Mycobacterium tuberculosis gene expression by anti-sigma factor gene mutations

Regulation of transcription by alternative sigma factors is a strategy widely used by bacteria to adapt to changes in environmental conditions. For several pathogenic bacteria, alternative sigma factor-regulated gene expression is critical for virulence. The activity of many alternative sigma factors is in turn controlled by regulatory proteins that transduce and integrate environmental signals. In this issue of Molecular Microbiology, Said-Salim et al. demonstrate high-level expression of genes encoding major protein antigens in the bovine subspecies of Mycobacterium tuberculosis, in contrast to low-level expression in the human subspecies. Having previously suggested that SigK regulates the expression of these genes, the authors found that the high-expressers have point mutations in Rv0444c, a gene adjacent to sigK, and provided evidence that this gene encodes an anti-sigma factor whose function is abrogated by these mutations. These findings not only demonstrate an adaptive mechanism of potential importance in tuberculosis immunity and pathogenesis, but also raise interesting questions regarding the origin of these mutations and their effects on anti-sigma factor function.

The AlgT-dependent transcriptional regulator AmrZ (AlgZ) inhibits flagellum biosynthesis in mucoid, nonmotile Pseudomonas aeruginosa cystic fibrosis isolates

Pseudomonas aeruginosa is a microorganism associated with the disease cystic fibrosis. While environmental P. aeruginosa strains are generally nonmucoid and motile, isolates recovered from the cystic fibrosis lung frequently display a mucoid, nonmotile phenotype. This phenotypic conversion is mediated by the alternative sigma factor AlgT. Previous work has shown that repression of fleQ by AlgT accounts for the loss of flagellum biosynthesis in these strains. Here, we elucidate the mechanism involved in the AlgT-mediated control of fleQ. Electrophoretic mobility shift assays using purified AlgT and extracts derived from isogenic AlgT(+) and AlgT(-) strains revealed that AlgT inhibits fleQ indirectly. We observed that the AlgT-dependent transcriptional regulator AmrZ interacts directly with the fleQ promoter. To determine whether AmrZ functions as a repressor of fleQ, we mutated amrZ in the mucoid, nonmotile P. aeruginosa strain FRD1. Unlike the parental strain, the amrZ mutant was nonmucoid and motile. Complementation of the mutant with amrZ restored the mucoid, nonmotile phenotype. Thus, our data show that AlgT inhibits flagellum biosynthesis in mucoid, nonmotile P. aeruginosa cystic fibrosis isolates by promoting expression of AmrZ, which subsequently represses fleQ. Since fleQ directly or indirectly controls the expression of almost all flagellar genes, its repression ultimately leads to the loss of flagellum biosynthesis.

Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability

Nitrogen (N) often limits biological productivity in the oceanic gyres where Prochlorococcus is the most abundant photosynthetic organism. The Prochlorococcus community is composed of strains, such as MED4 and MIT9313, that have different N utilization capabilities and that belong to ecotypes with different depth distributions. An interstrain comparison of how Prochlorococcus responds to changes in ambient nitrogen is thus central to understanding its ecology. We quantified changes in MED4 and MIT9313 global mRNA expression, chlorophyll fluorescence, and photosystem II photochemical efficiency (Fv/Fm) along a time series of increasing N starvation. In addition, the global expression of both strains growing in ammonium-replete medium was compared to expression during growth on alternative N sources. There were interstrain similarities in N regulation such as the activation of a putative NtcA regulon during N stress. There were also important differences between the strains such as in the expression patterns of carbon metabolism genes, suggesting that the two strains integrate N and C metabolism in fundamentally different ways.

Signalling network with a bistable hysteretic switch controls developmental activation of the sigma transcription factor in Bacillus subtilis

The sporulation process of the bacterium Bacillus subtilis unfolds by means of separate but co-ordinated programmes of gene expression within two unequal cell compartments, the mother cell and the smaller forespore. sigmaF is the first compartment-specific transcription factor activated during this process, and it is controlled at the post-translational level by a partner-switching mechanism that restricts sigmaF activity to the forespore. The crux of this mechanism lies in the ability of the anti-sigma factor SpoIIAB (AB) to form alternative complexes either with sigmaF, holding it in an inactive form, or with the anti-anti-sigma factor SpoIIAA (AA) and a nucleotide, either ATP or ADP. In the complex with AB and ATP, AA is phosphorylated on a serine residue and released, making AB available to capture sigmaF in an inactive complex. Subsequent activation of sigmaF requires the intervention of the SpoIIE serine phosphatase to dephosphorylate AA, which can then attack the AB-sigmaF complex to induce the release of sigmaF. By incorporating biochemical, biophysical and genetic data from the literature we have constructed an integrative mathematical model of this partner-switching network. The model predicts that the self-enhancing formation of a long-lived complex of AA, AB and ADP transforms the network into an essentially irreversible hysteretic switch, thereby explaining the sharp, robust and irreversible activation of sigmaF in the forespore compartment. The model also clarifies the contributions of the partly redundant mechanisms that ensure correct spatial and temporal activation of sigmaF, reproduces the behaviour of various mutants and makes strong, testable predictions.

Regulation of the homologous two-component systems KvgAS and KvhAS in Klebsiella pneumoniae CG43

In Klebsiella pneumoniae CG43, deletion of the sensor gene kvgS reduced the kvgAS expression in M9 medium with 0.2 mM paraquat, 0.2 mM 2,2-dihydropyridyl, or 300 mM NaCl. This result shows an autoregulatory role of KvgS and a stress-responsive expression of the two-component system (2CS). The kvgS deletion also appeared to decrease the expression of kvhAS, paralogous genes of kvgAS. Additionally, measurements of the promoter activity in kvgA(-) mutant revealed that KvgA is probably an activator for the expression of kvgAS and kvhAS. The subsequent electrophoretic mobility shift assay, indicating a specific binding of the recombinant KvgA to the putative promoters P(kvgAS) and P(kvhAS), also supported an interacting regulation between the 2CSs. In P(kvgAS) and P(kvhAS), the presence of RpoS binding elements suggested an RpoS-dependent regulation. Nevertheless, the rpoS deletion reduced the expression of kvgAS but increased that of kvhAS. Moreover, the kvgA deletion reduced the expression of katG and sodC. The overexpression of KvhA altered the susceptibility to fosfomycin and an increasing activity of UDP-N-acetylglucosamine enolpyruvyl transferase, the target protein of fosfomycin, which suggesting a regulation by KvhA. Taken together, these indicated that the two 2CSs probably belong to different regulatory circuits of the RpoS regulon.

Cell wall-inhibitory antibiotics activate the alginate biosynthesis operon inPseudomonas aeruginosa: roles of σ22(AlgT) and the AlgW and Prc proteases

A bioassay was developed to identify stimuli that promote the transcriptional induction of the algD operon for alginate biosynthesis in Pseudomonas aeruginosa. Strain PAO1 carried the algD promoter fused to a chloramphenicol acetyl-transferase cartridge (PalgD-cat), and > 50 compounds were tested for promoting chloramphenicol resistance. Most compounds showing PalgD-cat induction were cell wall-active antibiotics that blocked peptidoglycan synthesis. PalgD-cat induction was blocked by mutations in the genes for sigma22 (algT/algU) or regulators AlgB and AlgR. Anti-sigma factor MucA was the primary regulator of sigma22 activity. A transcriptome analysis using microarrays verified that the algD operon undergoes high induction by D-cycloserine. A similar sigma(E)-RseAB complex in Escherichia coli responds to envelope stress, which requires DegS protease in a regulated intramembrane proteolysis (RIP) cascade to derepress the sigma. Mutant phenotypic studies in P. aeruginosa showed that AlgW (PA4446) is likely to be the DegS functional homologue. A mutation in algW resulted in a complete lack of PalgD-cat induction by D-cycloserine. Overexpression of algW in PAO1 resulted in a mucoid phenotype and alginate production, even in the absence of cell wall stress, suggesting that AlgW protease plays a role in sigma22 activation. In addition, a mutation in gene PA3257 (prc), encoding a Prc-like protease, resulted in poor induction of PalgD-cat by D-cycloserine, suggesting that it also plays a role in the response to cell wall stress.

Genome-wide gene expression analysis of Pseudomonas syringae pv. tomato DC3000 reveals overlapping and distinct pathways regulated by hrpL and hrpRS

Pseudomonas syringae pv. tomato DC3000 is a model pathogen infecting tomato and Arabidopsis plants. Genes encoding the type III secretion system and substrate proteins (collectively called TTSS genes) of this bacterium are induced in plants and in minimal medium (MM). The induction of TTSS genes is mediated by HrpL, an alternative sigma factor recognizing the hrp box in the promoter of TTSS genes. The transcription of hrpL is activated by HrpR and HrpS, two homologous DNA-binding proteins encoded by the hrpRS operon. Microarray analysis was conducted to evaluate the DC3000 genes regulated by hrpL and hrpRS in MM. The analysis identified a number of novel hrpL-activated genes with a putative TTSS-independent function. Genes regulated by hrpL were mostly regulated by hrpRS in the same manner, but a large number of genes regulated by hrpRS were hrpL-independent, indicating that hrpL represents one branch of the regulatory pathways downstream of hrpRS. The induction of the TTSS genes was associated with downregulation of the housekeeping genes, indicating that the activation of the TTSS has a cost on the basic cellular activities. The novel genes and pathways identified by the microarray provide new insight into the bacterial functions coordinating with the TTSS.

An RpoH-like heat shock sigma factor is involved in stress response and virulence in Brucella melitensis 16M

B. melitensis 16M genome analysis revealed the presence of six putative sigma factor-encoding genes: rpoD, rpoH1, rpoH2, rpoE1, rpoE2, and rpoN. We mutated all these genes except rpoD. Phenotypic analysis of the mutants reveals that a strain carrying an rpoH2 null mutation (DeltarpoH2) is impaired for growth at 21 and 42 degrees C and shows increased sensitivity to hydrogen peroxide. Compared to the wild-type strain, the DeltarpoH2 mutant is attenuated in all virulence models tested. Three other null mutants (DeltarpoH1, DeltarpoE1, and DeltarpoE2 mutants) are also defective for survival in mice at 4 weeks postinfection. We also demonstrated that rpoH2 deletion strongly reduces the expression of two major virulence factors in B. melitensis, the type IV secretion system and the flagellum.

Role of sigma E-regulated genes in Escherichia coli uropathogenesis

The sigma E regulon encodes proteins for maintenance and repair of the Escherichia coli cell envelope. Previously, we observed that an antirepressor of sigma E, DegS, is essential for uropathogenic E. coli virulence. Here we use a mouse urinary tract infection model to assay the virulence of mutants of E. coli genes described as sigma E dependent. Deletion mutants of candidate genes were made in the uropathogenic E. coli strain CFT073. Swiss Webster female mice were inoculated with a mixture of mutant and wild-type strains. Bladder and kidney homogenates were cultured 2 days after infection, and CFU of the wild type and mutant were compared. Eleven mutants were assayed, and two, CFT073 degP and CFT073 skp, showed significantly diminished survival compared to wild type. DegP is a chaperone and degradase active in the periplasm. Skp is also a periplasmic chaperone. The virulence of the skp deletion mutant could not be restored by complementation with skp. The virulence of the degP deletion mutant, in contrast, could be restored. However, complementation with a degP allele encoding a serine-to-alanine (S210A) mutation at the protease active site fails to restore virulence. Unlike degP mutants in other bacteria, the E. coli degP mutant is tolerant of oxidative stress. It disappears abruptly from bladder and kidney cultures between 6 and 12 hours after inoculation. A mutant of degQ, a close homolog of degP, was not attenuated in mice. This is the first report that the DegP degradase is an E. coli virulence factor in an animal infection model.

A branched pathway governing the activation of a developmental transcription factor by regulated intramembrane proteolysis

The proteolytic activation of the membrane-associated transcription factor pro-sigma(K) is controlled by a signal transduction pathway during sporulation in the bacterium Bacillus subtilis. The pro-sigma(K) processing enzyme SpoIVFB, a membrane-embedded metalloprotease, is held inactive by two other integral-membrane proteins, SpoIVFA and BofA. We demonstrate that the signaling protease SpoIVB (IVB) triggers pro-sigma(K) processing by cleaving the extracellular domain of the SpoIVFA regulator at multiple sites. In vitro, these cleavages do not disrupt the interactions between SpoIVFA, SpoIVFB, and BofA, suggesting that IVB-dependent activation of the processing enzyme results from a conformational change in this complex. Our data further suggest that when IVB is unable to cleave SpoIVFA, it can still activate pro-sigma(K) processing through a second protease, CtpB. Finally, we demonstrate that CtpB, like IVB, triggers pro-sigma(K) processing by cleaving SpoIVFA. We propose that IVB regulates intramembrane proteolysis through two proteolytic pathways, both of which converge on the same regulator.

Cascade of sigma factors in streptomycetes: identification of a new extracytoplasmic function sigma factor sigmaJ that is under the control of the stress-response sigma factor sigmaH in Streptomyces coelicolor A3(2)

By using the previously established Escherichia coli two-plasmid system, we identified a promoter recognized by the Streptomyces coelicolor A3(2) stress-response sigma factor sigmaH. The promoter directed expression of the sigJ gene encoding an extracytoplasmic function (ECF) sigma factor. S1-nuclease mapping using RNA prepared from E. coli containing the two-plasmid system, and S. coelicolor A3(2) from various developmental stages identified an identical transcription start point in both strains, corresponding to the sigJp promoter. The sigJp promoter was induced during sporulation of aerial hyphae. The level of the transcript from sigJp was dramatically reduced in a S. coelicolor A3(2) sigH mutant and unaffected in a sigF mutant. The S. coelicolor A3(2) core RNA polymerase, after complementation with sigmaH, was able to recognize the sigJp promoter in vitro. A sigJ mutation had no obvious effect on growth, stress response, differentiation, and production of antibiotics. The results suggested that the S. coelicolor A3(2) sigJ gene is under the control of stress-response sigmaH, thus indicating a cascade of sigma factors in Streptomyces stress response and development. Considering the expression of sigJ and its direct dependence upon developmentally-regulated sigmaH, we assume that sigmaJ may play a role in the later stages of development of S. coelicolor A3(2).