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PubMed2006

Identification of promoters recognized by RNA polymerase containing Mycobacterium tuberculosis stress-response sigma factor sigma(F).

A previously optimized Escherichia coli two-plasmid system was used to identify Mycobacterium tuberculosis promoters recognized by RNA polymerase containing the M. tuberculosis stress response sigma factor sigma(F). The method allowed the identification of five new sigma(F)-dependent promoters. Transcriptional start points of the promoters were determined by high-resolution S1-nuclease mapping using RNA prepared from E. coli containing the two-plasmid system. The promoters were confirmed by an in vitro transcription assay. The Mycobacterium smegmatis and Mycobacterium tuberculosis core RNA polymerases, after complementation with sigma(F), were able to recognize all the five promoters. All the promoters contained sequences highly similar to the sequence of the previously identified M. tuberculosis sigma(F)-dependent promoter, usfXp1. Comparison of the promoters revealed a sigma(F) consensus sequence GtTtga-N(14-18)-GGGTAT. The sigma(F)-dependent promoters may govern expression of genes encoding a transcription regulator homologous to the response regulators of bacterial two-component signal transduction systems and proteins with unknown function.

DNA-Directed RNA Polymerases↗
PubMed1996

Function of E. coli RNA polymerase sigma factor sigma 70 in promoter-proximal pausing.

The sigma factor sigma 70 of E. coli RNA polymerase acts not only in initiation, but also at an early stage of elongation to induce a transcription pause, and simultaneously to allow the phage lambda gene Q transcription antiterminator to act. We identify the signal in DNA that induces early pausing to be a version of the sigma 70 -10 promoter consensus, and we show that sigma 70 is both necessary for pausing and present in the paused transcription complex. Regions 2 and 3 of sigma 70 suffice to induce pausing. Since pausing is induced by the nontemplate DNA strand of the open transcription bubble, we conclude that RNA polymerase containing sigma 70 carries out base-specific recognition of the nontemplate strand as single stranded DNA. We suggest that sigma 70 remains bound to core RNA polymerase when the -10 promoter contacts are broken, and then moves to the pause-inducing sequence.

Bacteriophage lambda↗
PubMed2002

Stress-response sigma factor sigma(H) directs expression of the gltB gene encoding glutamate synthase in Streptomyces coelicolor A3(2).

Using the previously established Escherichia coli two-plasmid system, we identified a promoter recognized by the Streptomyces coelicolor stress-response sigma factor sigma(H). The promoter directed expression of the gltB gene, encoding a protein with considerable homology with large subunit of glutamate synthases. S1-nuclease mapping using RNA prepared from S. coelicolor identified an identical transcription start point corresponding to the promoter. The level of the transcript from this promoter was substantially reduced in a S. coelicolor sigH mutant. In addition to this sigH-dependent gltBp2 promoter, expression of the S. coelicolor gltB gene was directed by two other promoters, gltBp1 and gltBp3, independent upon sigH. S. coelicolor core RNA polymerase, after complementation with sigma(H), was able to recognize the gltBp2 promoter in vitro. These results suggested that the S. coelicolor gltB gene is under the control of stress-response sigma(H).

Bacterial Proteins↗
PubMed2003

Transcriptional analysis of the rpoE gene encoding extracytoplasmic stress response sigma factor sigmaE in Salmonella enterica serovar Typhimurium.

The rpoE gene of Salmonella enterica serovar Typhimurium (S. Typhimurium), which encodes the extracytoplasmic stress response sigma factor sigmaE, is critically important for the virulence of S. Typhimurium. We analysed expression of rpoE by wild-type and mutant bacteria grown in different conditions by S1-nuclease mapping using RNA, and using in vivo reporter gene fusions. Three promoters, rpoEp1, rpoEp2 and rpoEp3, were located upstream of the S. Typhimurium rpoE gene. The promoters were differentially expressed during growth and under several stress conditions including cold shock. Expression from the rpoEp3 promoter was absent in an S. Typhimurium rpoE mutant, demonstrating its dependence upon sigmaE. The level of mRNA corresponding to rpoEp3 was also higher in a cpxR mutant, indicating a negative regulation of the promoter by the Cpx system. Using this rpoE-dependent promoter, we optimised a two-plasmid system for identification of promoters recognised by S. Typhimurium sigmaE. The rpoEp3 promoter was active in the Escherichia coli two-plasmid system and has an identical transcription start point as in S. Typhimurium but only after induction of S. Typhimurium rpoE expression.

Artificial Gene Fusion↗
PubMed1996

The RpoN-box motif of the RNA polymerase sigma factor sigma N plays a role in promoter recognition.

The RNA polymerase sigma factor sigma N (sigma 54) is characterized by the presence, near the C-terminal end of the protein, of a highly conserved sequence of 10 amino acids (ARRTVAKYRE) that has been termed the RpoN box. In order to examine the function of this motif, which is predicted to adopt an alpha-helical structure, we have isolated a number of mutations that alter residues within the box and examined the properties of the sigma N derivatives encoded by them. Certain mutations that alter charged and potentially exposed residues within the motif result in transcriptionally inactive proteins with impaired promoter recognition but no impairment in core RNA polymerase binding. We therefore suggest that the RpoN box could play a direct or indirect role in recognition of the -24, -12 promoter consensus that is characteristic of sigma N-dependent genes.

Amino Acid Sequence↗
PubMed1996

Rickettsia prowazekii sigma factor sigma 73 can be overexpressed in Escherichia coli and promotes RNA polymerase binding and transcription.

The sigma factor sigma 73 of the obligate intracytoplasmic bacterium Rickettsia prowazekii was overexpressed and purified from Escherichia coli. The rickettsial rpoD gene encoding sigma 73 was cloned into a Ndel-BamHI-cleaved pET-15b vector under control of T7 transcription and translation signals. The recombinant plasmid encoded a 75 kDa fusion protein that was overproduced in E. coli BL21(DE3) and purified from inclusion bodies after solubilization with guanidine hydrochloride and using His. Bind metal chelation resin. The N-terminal His. Tag sequence of the 75 kDa fusion protein was removed by thrombin treatment to obtain R. prowazekii sigma 73T. The R. prowazekii sigma 73T as well as the 75 kDa fusion protein had the ability to bind to core DNA-dependent RNA polymerase of both R. prowazekii and E. coli and to stimulate their interaction with a rickettsial promoter.

Base Sequence↗
PubMed1994

Molecular analysis of the operon which encodes the RNA polymerase sigma factor sigma 54 of Escherichia coli.

The rpoN gene (encoding the sigma factor sigma 54) of Escherichia coli was cloned and its nucleotide sequence determined. Promoter probe analysis confirmed the presence of a promoter in a 350 bp fragment covering the start of rpoN. The likely promoter was identified. The nucleotide sequence of the region extending 2.1 kb downstream of rpoN was also determined. This region contained four open reading frames encoding potential polypeptides of 10750, 17959, 32492 and 9810 Da; maxicell and T7 promoter studies showed that four polypeptides of similar molecular masses were expressed from this region. The amino acid sequence of the 17959 Da polypeptide showed homology to the enzyme IIA domains of several proteins of the bacterial sugar phosphotransferase system (PTS), and the 9810 Da polypeptide showed homology to the HPr proteins of the bacterial PTS. The proteins encoded downstream of rpoN are known to negatively regulate sigma 54 activity. The homologies therefore suggest that this effect on sigma 54 may be mediated by sequential protein phosphorylation and suggest that there is a link between signal transduction and transcription of sigma 54-dependent genes.

Amino Acid Sequence↗
PubMed1991

Cassette mutagenesis implicates a helix-turn-helix motif in promoter recognition by the novel RNA polymerase sigma factor sigma 54.

Cassette mutagenesis has been used to study the role of a helix-turn-helix (HTH) motif in the novel RNA polymerase sigma factor sigma 54 of Klebsiella pneumoniae. Of the four residues which are predicted to be solvent-exposed in the second helix, the first (Glu-378) tolerated all substitutions, and some mutations of this residue increased expression from sigma 54-dependent promoters. Certain substitutions in the third exposed residue (Ser-382) produced a promoter-specific phenotype and all substitutions in the fourth residue (Arg-383) inactivated the protein, identifying this residue as being likely to be involved in base-specific interactions with the promoter. In vivo footprinting indicated that the inactive HTH mutants of sigma 54 were defective in interaction with both the -24 and -12 regions of the glnAp2 promoter.

Amino Acid Sequence↗
PubMed1995

The stationary-phase sigma factor sigma S (RpoS) is required for a sustained acid tolerance response in virulent Salmonella typhimurium.

The acid tolerance response (ATR) of log-phase Salmonella typhimurium is induced by acid exposures below pH 4.5 and will protect cells against more extreme acid. Two systems are evident: a transiently induced system dependent on the iron regulator Fur that provides a moderate degree of acid tolerance and a more effective sustained ATR that requires the alternate sigma factor sigma S encoded by rpoS. Differences between the acid responses of virulent S. typhimurium and the attenuated laboratory strain LT2 were attributed to disparate levels of RpoS caused by different translational starts. The sustained ATR includes seven newly identified acid shock proteins (ASPs) that are dependent upon sigma S for their synthesis. It is predicted that one or more of these ASPs is essential for the sustained system. The sustained ATR also provided cross-protection to a variety of other environmental stresses (heat, H2O2 and osmolarity); however, adaptation to the other stresses did not provide significant acid tolerance. Therefore, in addition to starvation, acid shock serves as an important signal for inducing general stress resistance. Consistent with this model, sigma S proved to be induced by acid shock. Our results also revealed a connection between the transient and sustained ATR systems. Mutations in the regulator atbR are known to cause the overproduction of ten proteins, of which one or more can suppress the acid tolerance defect of an rpoS mutant. One member of the AtbR regulon, designated atrB, was found to be co-regulated by sigma S and AtbR. Both regulators had a negative effect on atrB expression. The results suggest AtrB serves as a link between the sustained and transient ATR systems. When sigma S concentrations are low, a compensatory increase in AtrB is required to engage the transiently induced, RpoS-independent system of acid tolerance. Results also suggest different acid-sensitive targets occur in log-phase versus stationary-phase cells.

Acids↗
PubMed2005

The alternative sigma factor sigma is required for resistance of Salmonella enterica serovar Typhimurium to anti-microbial peptides.

The enteric pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) encounters a variety of anti-microbial peptides during the course of infection. We report here that the extracytoplasmic sigma factor sigma(E) (RpoE) is required for Salmonella resistance to killing by the bactericidal/permeability-increasing protein (BPI)-derived peptide P2 and the murine alpha-defensin cryptdin-4 (Crp4). Moreover, sigma(E)-deficient S. Typhimurium is attenuated for virulence after oral infection of immunocompromised gp91phox(-/-) mice that lack a functional NADPH phagocyte oxidase, suggesting that sigma(E) plays an important role in resistance to non-oxidative mucosal host defences such as anti-microbial peptides. Although both P2 and Crp4 target the cell envelope, bacterial killing by these peptides appears to occur by distinct mechanisms. Formate enhances bacterial resistance to P2, as previously demonstrated, but not to Crp4. Both sigma(E) and cytoplasmic membrane-associated formate dehydrogenase are required for the protective effect of formate against P2. In contrast to P2, Crp4 does not inhibit bacterial respiration at lethal concentrations. However, both peptides induce expression of rpoE, suggesting that they trigger a common mechanism for sensing extracytoplasmic stress.

Administration, Oral↗
PubMed2004

Identification of sigma factor sigma B-controlled genes and their impact on acid stress, high hydrostatic pressure, and freeze survival in Listeria monocytogenes EGD-e.

The gene encoding the alternative sigma factor sigma(B) in Listeria monocytogenes is induced upon exposure of cells to several stresses. In this study, we investigated the impact of a sigB null mutation on the survival of L. monocytogenes EGD-e at low pH, during high-hydrostatic-pressure treatment, and during freezing. The survival of Delta sigB mutant exponential-phase cells at pH 2.5 was 10,000-fold lower than the survival of EGD-e wild-type cells. Moreover, the Delta sigB mutant failed to show an acid tolerance response. Upon preexposure for 1 h to pH 4.5, the survival at pH 2.5 was 100,000-fold lower for the Delta sigB mutant than for the wild type. The glutamate decarboxylase (GAD) acid resistance system is important in survival and adaptation of L. monocytogenes in acidic conditions. The sigma(B) dependence of the gad genes (gadA, gadB, gadC, gadD, and gadE) was analyzed in silico. Putative sigma(B)-dependent promoter sites were found upstream of the gadCB operon (encoding a glutamate/gamma-aminobutyrate antiporter and a glutamate decarboxylase, respectively) and the lmo2434 gene (gadD, encoding a putative glutamate decarboxylase). Reverse transcriptase PCR revealed that expression of the gadCB operon and expression of gadD are indeed sigma(B) dependent. In addition, a proteomics approach was used to analyze the protein expression profiles upon acid exposure. Although the GAD proteins were not recovered, nine proteins accumulated in the wild type but not in the Delta sigB strain. These proteins included Pfk, GalE, ClpP, and Lmo1580. Exposure to pH 4.5, in order to preload cells with active sigma(B) and consequently with sigma (B)-dependent general stress proteins, also provided considerable protection against high-hydrostatic-pressure treatment and freezing. The combined data argue that the expression of sigma(B)-dependent genes provides L. monocytogenes with nonspecific multiple-stress resistance that may be relevant for survival in the natural environment as well as during food processing.

Bacterial Proteins↗
PubMed2002

The alternative sigma factor sigma(E) plays an important role in intestinal survival and virulence in Vibrio cholerae.

The alternative sigma factor sigma(E) (RpoE) is involved in the response to extracytoplasmic stress and plays a role in the virulence of a variety of different bacteria. To assess the role of sigma(E) in Vibrio cholerae pathogenesis, a DeltarpoE mutant was constructed and analyzed using the infant mouse model. The results here show that sigma(E) contributes significantly to the virulence of V. cholerae. The DeltarpoE mutant was highly attenuated with a 50% lethal dose more than 3 logs higher than that for the parental strain, and its ability to colonize the intestine was reduced approximately 30-fold. A time course of infection revealed that the number of CFU of the DeltarpoE mutant was approximately 1 log lower than that of the parental strain by 12 h postinoculation and decreased further by 24 h. The defect in virulence in the DeltarpoE mutant thus appears to be a diminished ability to survive within the intestinal environment. The results here also show that sigma(E) is not required for growth and survival of V. cholerae in vitro at high temperatures but is required under other stressful conditions, such as in the presence of 3% ethanol. As in Escherichia coli, the expression of rpoE in V. cholerae is dependent upon two promoters located upstream of the gene, P1 and P2. P1 appears to be sigma(70) dependent, whereas the downstream promoter, P2, is positively autoregulated by sigma(E).

Animals↗
PubMed1991

Expression of ClpB, an analog of the ATP-dependent protease regulatory subunit in Escherichia coli, is controlled by a heat shock sigma factor (sigma 32).

Escherichia coli K-12 produces at least two ATP-dependent proteases, Lon (La) and Clp (Ti), the latter consisting of a regulatory subunit (ClpA) and a proteolytic subunit (ClpP). The gene clpB encoding an analog of ClpA had been found at 57 min on the E. coli chromosome. Cloning and examination of novel heat shock promoters led us to identify a major clpB promoter specifically controlled by a heat shock sigma factor, sigma 32 (the rpoH [= htpR] gene product). beta-Galactosidase synthesis from a PclpB-lacZ operon fusion was transiently induced upon temperature shift from 30 to 42 degrees C, and the induction depended on the rpoH function. Chromosomal clpB transcripts also increased upon temperature upshift and were totally absent in the rpoH deletion strain. In the in vitro transcription experiments, the clpB promoter was specifically recognized and transcribed by RNA polymerase-sigma 32. Nucleotide sequencing and determination of mRNA start sites permitted us to identify a major heat shock promoter located upstream of the clpB coding sequence. The results clearly indicate that clpB expression is under direct control of sigma 32. Since ClpP was recently shown to be a sigma 32-dependent heat shock protein, the present finding suggests the possibility that a potential ATP-dependent protease, ClpB-ClpP complex, plays an important role against thermal stress in E. coli.

ATP-Dependent Proteases↗
PubMed1991

Growth phase-regulated expression of bolA and morphology of stationary-phase Escherichia coli cells are controlled by the novel sigma factor sigma S.

The novel sigma factor (sigma S) encoded by rpoS (katF) is required for induction of many growth phase-regulated genes and expression of a variety of stationary-phase phenotypes in Escherichia coli. Here we demonstrate that wild-type cells exhibit spherical morphology in stationary phase, whereas rpoS mutant cells remain rod shaped and are generally larger. Size reduction of E. coli cells along the growth curve is a continuous and at least biphasic process, the second phase of which is absent in rpoS-deficient cells and correlates with induction of the morphogene bolA in wild-type cells. Stationary-phase induction of bolA is dependent on sigma S. The "gearbox" a characteristic sequence motif present in the sigma S-dependent growth phase- and growth rate-regulated bolAp1 promoter, is not recognized by sigma S, since stationary-phase induction of the mcbA promoter, which also contains a gearbox, does not require sigma S, and other sigma S-controlled promoters do not contain gearboxes. However, good homology to the potential -35 and -10 consensus sequences for sigma S regulation is found in the bolAp1 promoter.

Bacterial Proteins↗
PubMed1998

The general stress sigma factor sigmaS of Escherichia coli is induced during diauxic shift from glucose to lactose.

The general stress sigma factor sigmaS (RpoS) of Escherichia coli is strongly induced in response to glucose starvation. This increase in the cellular sigmaS level is due to stabilization of sigmaS, which under non-stress conditions is subject to rapid proteolysis. In the present study, it is demonstrated that sigmaS is also induced during the diauxic shift from glucose to lactose, i.e., under conditions of glucose exhaustion in the presence of another, less-preferred carbon source that eventually gets utilized. This sigmaS induction, which is due to stabilization, is transient and precedes the induction of beta-galactosidase. In parallel, sigmaS-dependent genes are transiently activated, as was shown here for osmY. Although sigmaS can mediate transcription of lacZ in vitro, sigmaS does not contribute to the induction of beta-galactosidase during the diauxic lag phase. Rather, the induction of sigmaS and the general stress response during the diauxic shift plays the role of a rapidly activated emergency system, which is shut off again as soon as the cells are able to cope with the stress situation by utilizing a more specific and more economical system.

Bacterial Proteins↗
PubMed1998

The two-component regulators GacS and GacA influence accumulation of the stationary-phase sigma factor sigmaS and the stress response in Pseudomonas fluorescens Pf-5.

Three global regulators are known to control antibiotic production by Pseudomonas fluorescens. A two-component regulatory system comprised of the sensor kinase GacS (previously called ApdA or LemA) and GacA, a member of the FixJ family of response regulators, is required for antibiotic production. A mutation in rpoS, which encodes the stationary-phase sigma factor sigmaS, differentially affects antibiotic production and reduces the capacity of stationary-phase cells of P. fluorescens to survive exposure to oxidative stress. The gacA gene of P. fluorescens Pf-5 was isolated, and the influence of gacS and gacA on rpoS transcription, sigmaS levels, and oxidative stress response of Pf-5 was determined. We selected a gacA mutant of Pf-5 that contained a single nucleotide substitution within a predicted alpha-helical region, which is highly conserved among the FixJ family of response regulators. At the entrance to stationary phase, sigmaS content in gacS and gacA mutants of Pf-5 was less than 20% of the wild-type level. Transcription of rpoS, assessed with an rpoS-lacZ transcriptional fusion, was positively influenced by GacS and GacA, an effect that was most evident at the transition between exponential growth and stationary phase. Mutations in gacS and gacA compromised the capacity of stationary-phase cells of Pf-5 to survive exposure to oxidative stress. The results of this study provide evidence for the predominant roles of GacS and GacA in the regulatory cascade controlling stress response and antifungal metabolite production in P. fluorescens.

Alleles↗
PubMed1999

Role of the alternative sigma factor sigmaS in expression of the AlkS regulator of the Pseudomonas oleovorans alkane degradation pathway.

The AlkS protein activates transcription from the PalkB promoter, allowing the expression of a number of genes required for the assimilation of alkanes in Pseudomonas oleovorans. We have identified the promoter from which the alkS gene is transcribed, PalkS, and analyzed its expression under different conditions and genetic backgrounds. Transcription from PalkS was very low during the exponential phase of growth and increased considerably when cells reached the stationary phase. The PalkS -10 region was similar to the consensus described for promoters recognized by Escherichia coli RNA polymerase bound to the alternative sigma factor sigmaS, which directs the expression of many stationary-phase genes. Reporter strains containing PalkS-lacZ transcriptional fusions showed that PalkS promoter is very weakly expressed in a Pseudomonas putida strain bearing an inactivated allele of the gene coding for sigmaS, rpoS. When PalkS was transferred to E. coli, transcription started at the same site and expression was higher in stationary phase only if sigmaS-RNA polymerase was present. The low levels of AlkS protein generated in the absence of sigmaS were enough to support a partial induction of the PalkB promoter. The -10 and -35 regions of PalkS promoter also show some similarity to the consensus recognized by sigmaD-RNA polymerase, the primary form of RNA polymerase. We propose that in exponential phase PalkS is probably recognized both by sigmaD-RNA polymerase (inefficiently) and by sigmaS-RNA polymerase (present at low levels), leading to low-level expression of the alkS gene. sigmaS-RNA polymerase would be responsible for the high level of activity of PalkS observed in stationary phase.

Alkanes↗
PubMed1991

Purification of the alternative sigma factor, sigma 54, from Salmonella typhimurium and characterization of sigma 54-holoenzyme.

The alternative sigma factor sigma 54 of enteric bacteria, or its homologue in other purple bacteria, is required for transcription of genes whose products have diverse physiological roles. Previous studies have indicated that sigma 54 confers on core RNA polymerase the ability to recognize a specific class of promoters but not the ability to isomerize from closed to open complexes. Isomerization requires ATP and one member of a family of activator proteins, it being different activator proteins that allow this form of polymerase to respond to different physiological signals. We have developed a strategy for overproducing and purifying sigma 54 from Salmonella typhimurium and have studied several biochemical properties of reconstituted sigma 54-holoenzyme. The initial binding constant KB for the formation of closed complexes between this holoenzyme and the ginA promoter in our transcription buffer is approximately 3 x 10(8) M-1, which was determined from DNaseI protection assays at 37 degrees C. After the formation of open complexes, several properties of sigma 54-holoenzyme appear to be similar to those of sigma 70-holoenzyme. We have determined the complete nucleotide sequence of the gene encoding sigma 54 (ntrA) in Salmonella.

Amino Acid Sequence↗