Alternative sigma factors and their roles in bacterial virulence

Protein-DNA interactions that govern AAA+ activator-dependent bacterial transcription initiation

Transcriptional control at the promoter melting step is not yet well understood. In this study, a site-directed photo-cross-linking method was used to systematically analyse component protein-DNA interactions that govern promoter melting by the enhancer-dependent Escherichia coli RNA polymerase (RNAP) containing the sigma(54) promoter specificity factor (E sigma(54)) at a single base pair resolution in three functional states. The sigma(54)-factor imposes tight control upon the RNAP by creating a regulatory switch where promoter melting nucleates, approximately 12 bp upstream of the transcription start site. Promoter melting by E sigma(54) is only triggered upon remodelling of this regulatory switch by a specialised activator protein in an ATP-hydrolysing reaction. We demonstrate that prior to DNA melting, only the sigma(54)-factor directly interacts with the promoter in the regulatory switch within the initial closed E sigma(54)-promoter complex and one intermediate E sigma(54)-promoter complex. We establish that activator-induced conformational rearrangements in the regulatory switch are a prerequisite to allow the promoter to enter the catalytic cleft of the RNAP and hence establish the transcriptionally competent open complex, where full promoter melting occurs. These results significantly advance our current understanding of the structural transitions occurring at bacterial promoters, where regulation occurs at the DNA melting step.

Phenotypic and transcriptomic analyses demonstrate interactions between the transcriptional regulators CtsR and Sigma B in Listeria monocytogenes

Listeria monocytogenes sigma(B) positively regulates the transcription of class II stress response genes; CtsR negatively regulates class III stress response genes. To identify interactions between these two stress response systems, we constructed L. monocytogenes DeltactsR and DeltactsR DeltasigB strains, as well as a DeltactsR strain expressing ctsR in trans under the control of an IPTG (isopropyl-beta-d-thiogalactopyranoside)-inducible promoter. These strains, along with a parent and a DeltasigB strain, were assayed for motility, heat resistance, and invasion of human intestinal epithelial cells, as well as by whole-genome transcriptomic and quantitative real-time PCR analyses. Both DeltactsR and DeltactsR DeltasigB strains had significantly higher thermotolerances than the parent strain; however, full heat sensitivity was restored to the DeltactsR strain when ctsR was expressed in trans. Although log-phase DeltactsR was not reduced in its ability to infect human intestinal cells, the DeltactsR DeltasigB strain showed significantly lower invasion efficiency than either the parent strain or the DeltasigB strain, indicating that interactions between CtsR and sigma(B) contribute to invasiveness. Statistical analyses also confirmed interactions between the ctsR and the sigB null mutations in both heat resistance and invasion phenotypes. Microarray transcriptomic analyses and promoter searches identified (i) 42 CtsR-repressed genes, (ii) 22 genes with lower transcript levels in the DeltactsR strain, and (iii) at least 40 genes coregulated by both CtsR and sigma(B), including genes encoding proteins with confirmed or plausible roles in virulence and stress response. Our data demonstrate that interactions between CtsR and sigma(B) play an important role in L. monocytogenes stress resistance and virulence.

Identification of promoters recognized by RNA polymerase-sigmaE holoenzyme from Thermus thermophilus HB8

Thermus thermophilus sigma(E), an extracytoplasmic function sigma factor from the extremely thermophilic bacterium Thermus thermophilus HB8, bound to the RNA polymerase core enzyme and showed transcriptional activity. With the combination of in vitro transcription assay and GeneChip technology, we identified three promoters recognized by sigma(E). The predicted consensus promoter sequence for sigma(E) is 5'-CA(A/T)(A/C)C(A/C)-N(15)-CCGTA-3'.

The cyclic AMP receptor protein modulates quorum sensing, motility and multiple genes that affect intestinal colonization in Vibrio cholerae

Vibrio cholerae is the causative agent of cholera, which continues to be a major public health concern in Asia, Africa and Latin America. The bacterium can persist outside the human host and alternates between planktonic and biofilm community lifestyles. Transition between the different lifestyles is mediated by multiple signal transduction pathways including quorum sensing. Expression of the Zn-metalloprotease haemagglutinin (HA)/protease is subject to a dual regulation which involves the quorum-sensing regulator HapR and the cAMP receptor protein. In a previous study, we observed that a mutant defective in the cAMP-receptor protein (CRP) expressed lower levels of HapR. To further investigate the role of CRP in modulating HapR and other signal transduction pathways, we performed global gene expression profiling of a Deltacrp mutant of El Tor biotype V. cholerae. Here we show that CRP is required for the biosynthesis of cholera autoinducer 1 (CAI-1) and affects the expression of multiple HapR-regulated genes. As expected, the Deltacrp mutant produced more cholera toxin and enhanced biofilm. Expression of flagellar genes, reported to be affected in DeltahapR mutants, was diminished in the Deltacrp mutant. However, an epistasis analysis indicated that cAMP-CRP affects motility by a mechanism independent of HapR. Inactivation of crp inhibited the expression of multiple genes reported to be strongly induced in vivo and to affect the ability of V. cholerae to colonize the small intestine and cause disease. These genes included ompU, ompT and ompW encoding outer-membrane proteins, the alternative sigma factor sigma(E) required for intestinal colonization, and genes involved in anaerobic energy metabolism. Our results indicate that CRP plays a crucial role in the V. cholerae life cycle by affecting quorum sensing and multiple genes required for survival of V. cholerae in the human host and the environment.

Influence of Campylobacter jejuni fliA, rpoN and flgK genes on colonization of the chicken gut

Campylobacter jejuni, a commensal Gram-negative motile bacterium commonly found in chickens is a frequent cause of human gastrointestinal infections. The polar flagellum of C. jejuni is an important virulence and colonization factor, providing motility to the cell as well as a type III secretion function. The flagellar biosynthesis genes fliA (sigma28) and rpoN (sigma54) of C. jejuni regulate a large number of genes involved in motility, protein secretion and invasion, which have been shown to be important factors for the virulence of this organism. To understand the role of the flagellar sigma factors, sigma28 and sigma54, in regulating colonization of the chicken intestinal tract, we assessed fliA and rpoN mutants of C. jejuni NCTC11168 for their ability to secrete Cia proteins and to adhere to and invade Hela cells. The mutants were also tested for their in vivo colonization potential in a chicken model with two different challenge doses. The fliA mutant showed reduced motility (25% that of the wild type) but secreted Cia proteins, yet it did not colonize the chicken cecum. The rpoN mutant cells lacked the spiral shape of C. jejuni and motility was reduced to 10% of the wild-type. The rpoN mutant did not secrete any Cia proteins but RT-PCR analysis showed the presence of ciaB mRNA, indicating that ciaB gene expression was independent of sigma54. Not surprisingly, the colonization defects of both fliA and rpoN mutants were more severe than the flgK mutant. We also demonstrated that FlgK, the hook filament junction protein of C. jejuni, is required for assembly of the flagellar secretory apparatus and an flgK mutant of C. jejuni expressing only the hook showed diminished motility and was completely attenuated for cecal colonization in chickens.

Analysis of the RpoS regulon in Borrelia burgdorferi in response to mammalian host signals provides insight into RpoS function during the enzootic cycle

Borrelia burgdorferi (Bb) adapts to its arthropod and mammalian hosts by altering its transcriptional and antigenic profiles in response to environmental signals associated with each of these milieus. In studies presented here, we provide evidence to suggest that mammalian host signals are important for modulating and maintaining both the positive and negative aspects of mammalian host adaptation mediated by the alternative sigma factor RpoS in Bb. Although considerable overlap was observed between genes induced by RpoS during growth within the mammalian host and following temperature-shift, comparative microarray analyses demonstrated unequivocally that RpoS-mediated repression requires mammalian host-specific signals. A substantial portion of the in vivo RpoS regulon was uniquely upregulated within dialysis membrane chambers, further underscoring the importance of host-derived environmental stimuli for differential gene expression in Bb. Expression profiling of genes within the RpoS regulon by quantitative reverse transcription polymerase chain reaction (qRT-PCR) revealed a level of complexity to RpoS-dependent gene regulation beyond that observed by microarray, including a broad range of expression levels and the presence of genes whose expression is only partially dependent on RpoS. Analysis of Bb-infected ticks by qRT-PCR established that expression of rpoS is induced during the nymphal blood meal but not within unfed nymphs or engorged larvae. Together, these data have led us to postulate that RpoS acts as a gatekeeper for the reciprocal regulation of genes involved in the establishment of infection within the mammalian host and the maintenance of spirochetes within the arthropod vector.

Transcriptional regulation of the virR operon of the intracellular pathogen Rhodococcus equi

The virR operon, located on the virulence plasmid of the intracellular pathogen Rhodococcus equi, contains five genes, two of which (virR and orf8) encode transcriptional regulators. The first gene of the operon (virR), encoding a LysR-type transcriptional regulator, is transcribed at a constitutive low level, whereas the four downstream genes are induced by low pH and high growth temperature. Differential regulation of the virR operon genes could not be explained by differential mRNA stability, as there were no major differences in mRNA half-lives of the transcripts representing each of the five genes within the virR operon. Transcription of virR is driven by the P(virR) promoter, with a transcription start site 53 bp upstream of the virR initiation codon. The four genes downstream of virR are transcribed from P(virR) and from a second promoter, P(orf5), located 585 bp downstream of the virR initiation codon. VirR binds to a site overlapping the initiation codon of virR, resulting in negative autoregulation of the virR gene, explaining its low constitutive transcription level. The P(orf5) promoter is induced by high temperature and low pH, thus explaining the observed differential gene expression of the virR operon. VirR has a positive effect on P(orf5) activity, whereas the response regulator encoded by orf8 is not involved in regulating transcription of the virR operon. The P(virR) promoter is strikingly similar to those recognized by the principal sigma factors of Streptomyces and Mycobacterium, whereas the P(orf5) promoter does not share sequence similarity with P(virR). This suggests that P(orf5) is recognized by an alternative sigma factor.

Identification of the sigmaB regulon of Bacillus cereus and conservation of sigmaB-regulated genes in low-GC-content gram-positive bacteria

The alternative sigma factor sigma(B) has an important role in the acquisition of stress resistance in many gram-positive bacteria, including the food-borne pathogen Bacillus cereus. Here, we describe the identification of the set of sigma(B)-regulated genes in B. cereus by DNA microarray analysis of the transcriptome upon a mild heat shock. Twenty-four genes could be identified as being sigma(B) dependent as witnessed by (i) significantly lower expression levels of these genes in mutants with a deletion of sigB and rsbY (which encode the alternative sigma factor sigma(B) and a crucial positive regulator of sigma(B) activity, respectively) than in the parental strain B. cereus ATCC 14579 and (ii) increased expression of these genes upon a heat shock. Newly identified sigma(B)-dependent genes in B. cereus include a histidine kinase and two genes that have predicted functions in spore germination. This study shows that the sigma(B) regulon of B. cereus is considerably smaller than that of other gram-positive bacteria. This appears to be in line with phylogenetic analyses where sigma(B) of the B. cereus group was placed close to the ancestral form of sigma(B) in gram-positive bacteria. The data described in this study and previous studies in which the complete sigma(B) regulon of the gram-positive bacteria Bacillus subtilis, Listeria monocytogenes, and Staphylococcus aureus were determined enabled a comparison of the sets of sigma(B)-regulated genes in the different gram-positive bacteria. This showed that only three genes (rsbV, rsbW, and sigB) are conserved in their sigma(B) dependency in all four bacteria, suggesting that the sigma(B) regulon of the different gram-positive bacteria has evolved to perform niche-specific functions.

An extracytoplasmic function sigma factor acts as a general stress response regulator in Sinorhizobium meliloti

Sinorhizobium meliloti genes transcriptionally up-regulated after heat stress, as well as upon entry into stationary phase, were identified by microarray analyses. Sixty stress response genes were thus found to be up-regulated under both conditions. One of them, rpoE2 (smc01506), encodes a putative extracytoplasmic function (ECF) sigma factor. We showed that this sigma factor controls its own transcription and is activated by various stress conditions, including heat and salt, as well as entry into stationary phase after either carbon or nitrogen starvation. We also present evidence that the product of the gene cotranscribed with rpoE2 negatively regulates RpoE2 activity, and we therefore propose that it plays the function of anti-sigma factor. By combining transcriptomic, bioinformatic, and quantitative reverse transcription-PCR analyses, we identified 44 RpoE2-controlled genes and predicted the number of RpoE2 targets to be higher. Strikingly, more than one-third of the 60 stress response genes identified in this study are RpoE2 targets. Interestingly, two genes encoding proteins with known functions in stress responses, namely, katC and rpoH2, as well as a second ECF-encoding gene, rpoE5, were found to be RpoE2 regulated. Altogether, these data suggest that RpoE2 is a major global regulator of the general stress response in S. meliloti. Despite these observations, and although this sigma factor is well conserved among alphaproteobacteria, no in vitro nor in planta phenotypic difference from the wild-type strain could be detected for rpoE2 mutants. This therefore suggests that other important actors in the general stress response have still to be identified in S. meliloti.

Temperature-dependent expression of Listeria monocytogenes internalin and internalin-like genes suggests functional diversity of these proteins among the listeriae

The Listeria monocytogenes genome contains genes encoding several internalins and internalin-like proteins. As L. monocytogenes is present in many environments and can infect numerous, diverse host species, the environmental temperature was hypothesized to be a signal that might affect internalin gene transcription. A subgenomic microarray was used to investigate temperature-dependent transcription of 24 members of the internalin gene family in L. monocytogenes 10403S. The levels of internalin gene transcripts for cells grown at 37 degrees C were compared to the levels of transcripts for cells grown at 16, 30, and 42 degrees C using competitive microarray hybridization, and the results were confirmed by performing quantitative reverse transcriptase PCR for 14 internalin genes. Based on these studies, the internalin genes can be grouped into the following five temperature-dependent categories: (i) four sigma(B)-dependent internalin genes (inlC2, inlD, lmo0331, and lmo0610) with the highest levels of transcripts at 16 degrees C and generally the lowest levels of transcripts at 37 degrees C; (ii) three partially PrfA-dependent internalin genes (inlA, inlB, and inlC) with the lowest levels of transcripts at 16 degrees C and the highest levels of transcripts at 37 and 42 degrees C; (iii) four genes (inlG, inlJ, lmo0514, and lmo1290) with the lowest levels of transcripts at 16 degrees C and the highest levels of transcripts at 30 and/or 37 degrees C; (iv) one gene (lmo0327) with the highest levels of transcripts at 16 degrees C and low levels of transcripts at higher temperatures; and (v) 12 internalin genes with no differences in the levels of transcripts at the temperatures used in this study. The temperature-dependent transcription patterns suggest that the relative importance of different internalins varies by environment, which may provide insight into the specific functions of these proteins.

The HP0165-HP0166 two-component system (ArsRS) regulates acid-induced expression of HP1186 alpha-carbonic anhydrase in Helicobacter pylori by activating the pH-dependent promoter

The periplasmic alpha-carbonic anhydrase of Helicobacter pylori is essential for buffering the periplasm at acidic pH. This enzyme is an integral component of the acid acclimation response that allows this neutralophile to colonize the stomach. Transcription of the HP1186 alpha-carbonic anhydrase gene is upregulated in response to low environmental pH. A binding site for the HP0166 response regulator (ArsR) has been identified in the promoter region of the HP1186 gene. To investigate the mechanism that regulates the expression of HP1186 in response to low pH and the role of the HP0165-HP0166 two-component system (ArsRS) in this acid-inducible regulation, Northern blot analysis was performed with RNAs isolated from two different wild-type H. pylori strains (26695 and 43504) and mutants with HP0165 histidine kinase (ArsS) deletions, after exposure to either neutral pH or low pH (pH 4.5). ArsS-dependent upregulation of HP1186 alpha-carbonic anhydrase in response to low pH was found in both strains. Western blot analysis of H. pylori membrane proteins confirmed the regulatory role of ArsS in HP1186 expression in response to low pH. Analysis of the HP1186 promoter region revealed two possible transcription start points (TSP1 and TSP2) located 43 and 11 bp 5' of the ATG start codon, respectively, suggesting that there are two promoters transcribing the HP1186 gene. Quantitative primer extension analysis showed that the promoter from TSP1 (43 bp 5' of the ATG start codon) is a pH-dependent promoter and is regulated by ArsRS in combating environmental acidity, whereas the promoter from TSP2 may be responsible for control of the basal transcription of HP1186 alpha-carbonic anhydrase.

The alternative sigma factor sigmaH is required for toxin gene expression by Bacillus anthracis

Expression of the structural genes for the anthrax toxin proteins is coordinately controlled by host-related signals, such as elevated CO(2), and the trans-acting positive regulator AtxA. In addition to these requirements, toxin gene expression is under growth phase regulation. The transition state regulator AbrB represses atxA expression to influence toxin synthesis. During the late exponential phase of growth, when AbrB levels begin to decrease, toxin synthesis increases. Here we report that toxin gene expression also requires the presence of sigH, a gene encoding the RNA polymerase sigma factor associated with development in Bacillus subtilis. In the well-studied B. subtilis system, sigma(H) is required for sporulation and other post-exponential-phase processes and is part of a feedback control pathway for abrB expression. Our data indicate that a Bacillus anthracis sigH-null mutant is asporogenous and toxin deficient. Yet the sigma factor is required for toxin gene expression in a manner that is independent of the pathway leading to post-exponential-phase gene expression. Sigma(H) positively controls atxA in an AbrB-independent manner. These findings, combined with previous observations, suggest that the steady-state level of atxA expression is critical for optimal toxin gene transcription. We propose a model whereby, under toxin-inducing growth conditions, control of toxin gene expression is fine-tuned by the independent effects of sigma(H) and AbrB on the expression of atxA.

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.

Genome reduction in Leptospira borgpetersenii reflects limited transmission potential

Leptospirosis is one of the most common zoonotic diseases in the world, resulting in high morbidity and mortality in humans and affecting global livestock production. Most infections are caused by either Leptospira borgpetersenii or Leptospira interrogans, bacteria that vary in their distribution in nature and rely on different modes of transmission. We report the complete genomic sequences of two strains of L. borgpetersenii serovar Hardjo that have distinct phenotypes and virulence. These two strains have nearly identical genetic content, with subtle frameshift and point mutations being a common form of genetic variation. Starkly limited regions of synteny are shared between the large chromosomes of L. borgpetersenii and L. interrogans, probably the result of frequent recombination events between insertion sequences. The L. borgpetersenii genome is approximately 700 kb smaller and has a lower coding density than L. interrogans, indicating it is decaying through a process of insertion sequence-mediated genome reduction. Loss of gene function is not random but is centered on impairment of environmental sensing and metabolite transport and utilization. These features distinguish L. borgpetersenii from L. interrogans, a species with minimal genetic decay and that survives extended passage in aquatic environments encountering a mammalian host. We conclude that L. borgpetersenii is evolving toward dependence on a strict host-to-host transmission cycle.

Sigma X induces competence gene expression in Streptococcus pyogenes

Although not thought to become competent for DNA uptake, the bacterium Streptococcus pyogenes appears to encode within its genome the DNA uptake and recombination machinery required for competence. The promoters of these genes contain a conserved sequence, CIN-box, which is recognized by the S. pyogenes alternative RNA polymerase sigma factor X. Using microarray technology, we found that sigma X induced the expression of competence genes in S. pyogenes. Real-time RT-PCR was performed to confirm that the expression of these transcripts was induced 2-265-fold by sigma X. Of the eight CIN-box loci induced, femB, the ortholog a virulence factor in Staphylococcus aureus, was shown to be transcribed in vitro by RNA polymerase containing sigma X, indicating that sigma X directly activates expression of this CIN-box gene. Sigma X-dependent induction of genes encoding competence machinery in S. pyogenes raises the possibility that some strains of this human pathogen can develop competence for genetic transformation.

Extensive functional overlap between sigma factors in Escherichia coli

Bacterial core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Escherichia coli encodes seven sigma factors, each believed to be specific for a largely distinct subset of promoters. Using microarrays representing the entire E. coli genome, we identify 87 in vivo targets of sigma32, the heat-shock sigma factor, and estimate that there are 120-150 sigma32 promoters in total. Unexpectedly, 25% of these sigma32 targets are located within coding regions, suggesting novel regulatory roles for sigma32. The majority of sigma32 promoter targets overlap with those of sigma70, the housekeeping sigma factor. Furthermore, their DNA sequence motifs are often interdigitated, with RNAPsigma70 and RNAPsigma32 initiating transcription in vitro with similar efficiency and from identical positions. SigmaE-regulated promoters also overlap extensively with those for sigma70. These results suggest that extensive functional overlap between sigma factors is an important phenomenon.

Safe and efficacious probiotics: what are they?

Each year, >20 billion doses of probiotics are used by healthy people and by those diagnosed with a range of medical conditions. Compared to many pharmaceutical agents, probiotics are well tolerated and extremely safe, and serious adverse effects rarely occur. Nevertheless, as many new researchers enter the field and companies launch "probiotic" products, it is essential that standards are set for naming a product "probiotic" to show that it meets an acceptable level of safety and efficacy, and to understand the strengths and limitations of its activity. In this Opinion article, recommendations are made based upon the current understanding of scientific, clinical and regulatory issues, with a special focus on safety.

Contributions of Listeria monocytogenes σ B and PrfA to expression of virulence and stress response genes during extra- and intracellular growth

Listeria monocytogenes σ B and PrfA are pleiotropic regulators of stress response and virulence gene expression. Quantitative RT-PCR (qRT-PCR) was used to measure transcript levels of σ B- and PrfA-dependent genes in exponential-phase L. monocytogenes wild-type and ΔsigB strains as well as in bacteria exposed to environmental stresses (0.3 M NaCl or growth to stationary phase) or present in the vacuole or cytosol of human intestinal epithelial cells. Stationary-phase or NaCl-exposed L. monocytogenes showed σ B-dependent increases in opuCA (10- and 17-fold higher, respectively) and gadA transcript levels (77- and 14-fold higher, respectively) as compared to non-stressed, exponential-phase bacteria. While PrfA activity, as reflected by plcA transcript levels, was up to 95-fold higher in intracellular L. monocytogenes as compared to non-stressed bacteria, σ B activity was only slightly higher in intracellular than in non-stressed bacteria. Increased plcA transcript levels, which were similar in both host cell vacuole and cytosol, were associated with increases in both prfA expression and PrfA activity. qRT-PCR assays were designed to measure expression of prfA from each of its three promoter regions. Under all conditions, readthrough transcription from the upstream plcA promoter was very low. The relative contribution to total prfA transcription from the σ A-dependent P1prfA promoter ranged from ∼17 % to 30 %, while the contribution of the P2prfA region, which appears to be transcribed by both σ A and σ B, ranged from ∼70 % to 82 % of total prfA transcript levels. In summary (i) σ B is primarily activated during environmental stress and does not contribute to PrfA activation in intracellular L. monocytogenes and (ii) the partially σ B-dependent P2prfA promoter region contributes the majority of prfA transcripts in both intra- and extracellular bacteria.