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PubMed1985

Suppression of defective-sporulation phenotypes by mutations in the major sigma factor gene (rpoD) of Bacillus subtilis.

Mutations (crsA47 and crsA4) in the major sigma factor gene (rpoD) of Bacillus subtilis RNA polymerase have been found to be powerful intergenic suppressors of spoOB, spoOE, spoOF, spoOK and spoIIG mutations. The crsA47 suppressor restores sporulation of spoOE, spoOF, spoOK and spoIIG mutants to levels near those of wild type bacteria and substantially improves the sporulation of a spoOB strain. The crsA mutations are shown to prevent the induction by aliphatic alcohols of SpoO phenocopies in wild type B. subtilis cells.

Bacillus subtilis↗
PubMed1988

Multiple principal sigma factor homologs in eubacteria: identification of the "rpoD box".

Genes for the principal sigma factor (rpoD genes) of various eubacteria were identified with a synthetic oligonucleotide probe corresponding to a conserved sequence in rpoD gene products of Escherichia coli and Bacillus subtilis. Multiple rpoD homologs were found in the strains of Micrococcus, Pseudomonas, and Streptomyces, whereas single genes were detected in E. coli, B. subtilis, and Staphylococcus aureus. The four rpoD homologs of Streptomyces coelicolor A3(2) were cloned and sequenced. A homologous portion with 13 amino acids was found in the rpoD genes of S. coelicolor A3(2), E. coli, and B. subtilis and was named the "rpoD box."

Amino Acid Sequence↗
PubMed1995

Nucleotide sequence of a principal sigma factor gene (hrdB) of Streptomyces griseus.

The hrdB homologue was isolated from a streptomycin-producing Streptomyces griseus 2247 strain, which is independent of A-factor. The nucleotide sequence of the cloned DNA fragment revealed the presence of an open reading frame (ORF) of 1,542bp, which predicted a primary product of 514 amino acids and Mr 56,100. The N-terminal sequence of the purified HrdB protein of S. griseus was identical to the amino acid sequence deduced from the nucleotide sequence. The deduced amino acid sequence contains an "rpoD box" conserved in the principal sigma factors of eubacteria, and shows high similarity to the hrdB products of S. coelicolor A3(2)(89.9%) and S. aureofaciens (88.1%). The cloned gene encodes a principal sigma factor of S. griseus. The promoter region was identified by using a promoter-probe vector and by means of primer extensions experiments. The transcription start point is located 158-bp upstream of the initiation codon.

Amino Acid Sequence↗
PubMed2004

Crystal structure of the flagellar sigma/anti-sigma complex sigma(28)/FlgM reveals an intact sigma factor in an inactive conformation.

The key regulators of bacterial transcription initiation are the sigma factors, which direct promoter recognition and melting but only after binding to the core RNA polymerase to form the holoenzyme. X-ray crystal structures of the flagellar sigma, sigma(28), in complex with its anti-sigma, FlgM, explain the inhibition mechanism of FlgM, including its ability to attack and destabilize the sigma(28)-holoenzyme. The sigma domains (sigma(2), sigma(3), and sigma(4)) pack together in a compact unit with extensive interdomain interfaces that bury the promoter binding determinants, including the -35 element recognition helix of sigma(4), which fits in an acidic groove on the surface of sigma(3). The structure illustrates the large rearrangements that sigma(28) must undergo to form the holoenzyme and provides insights into the regulation of sigma(28) promoter binding activity that may extend, at least in principle, to other sigmas.

Amino Acid Sequence↗
PubMed2006

Solution structures of the putative anti-sigma-factor antagonist TM1442 from Thermotoga maritima in the free and phosphorylated states.

The NMR structures of the unphosphorylated Thermotoga maritima protein TM1442 at pH 4.8 and of the phosphorylated TM1442 (TM1442-P) at pH 7.0 are presented, and a functional interaction of TM1442 with TM0733 is characterized. Although the NMR spectra of TM1442-P at pH 7.0 are of high quality, detailed NMR studies of unphosphorylated TM1442 could be performed only at slightly acidic pH values and high salt concentration. TM1442 is a putative anti-sigma-factor antagonist related to the sigmaF and sigmaB regulation systems in Bacillus subtilis, which is the component in this system that can be phosphorylated. The kinase TM0733, which shows sequence similarity to the GHKL ATPase/kinase superfamily, was identified as the possible anti-sigma-factor of TM1442 using a bioinformatics analysis. Phosphorylation of TM1442 by TM0733 was confirmed by NMR, mass spectroscopy and native gel electrophoresis, and Ser59 was identified as the phosphorylation site using site-directed mutational analysis. The solution structure of TM1442-P at pH 7.0 has the same global fold as free TM1442 at pH 4.8, with an alpha/beta topology consisting of a central four-stranded beta sheet and three alpha helices, but the regular secondary structure elements wrapping the hydrophobic core of the protein undergo subtle conformational changes upon phosphorylation.

Amino Acid Sequence↗
PubMed2006

Growth-phase dependent differential gene expression in Synechocystis sp. strain PCC 6803 and regulation by a group 2 sigma factor.

Cyanobacteria must continually alter their physiological growth state in response to changes in light intensity and their nutritional and physical environment. Under typical laboratory batch growth conditions, cyanobacteria grow exponentially, then transition to a light-limited stage of linear growth before finally reaching a non-growth stationary phase. In this study, we utilized DNA microarrays to profile the expression of genes in the cyanobacterium Synechocystis sp. PCC 6803 to compare exponential and linear growth. We also studied the importance of SigB, a group 2 sigma factor in this cyanobacterium, during the different growth phases. The transcription of approximately 10% of the genes in the wild type were different in the linear, compared to the exponential phase, and our results showed that: (1) many photosynthesis and regulatory genes had lowered transcript levels; (2) individual genes, such as sigH, phrA, and isiA, which encode a group 4 sigma factor, a DNA photolyase, and a Chl-binding protein, respectively, were strongly induced; and, (3) the loss of SigB significantly impacted the differential expression of genes and modulated the changes seen in the wild type in regard to photosynthesis, regulatory and the unknown genes.

Bacterial Proteins↗
PubMed1999

Cloning and characterization in Escherichia coli of the gene encoding the principal sigma factor of an extreme thermophile, Thermus thermophilus.

The nucleotide sequence of the upstream region of the aspartate kinase genes of Thermus thermophilus HB27 revealed the presence of two open reading frames in the orientation opposite to that of the aspartate kinase genes. The upstream open reading frame termed ORF375 encodes a protein composed of 375 amino acid residues, possessing amino acid sequence motifs for methylases. Another open reading frame designated as sigA encodes a protein of 423 amino acid residues which shows significant identity in amino acid sequence to the principal sigma factor, a component of the DNA-dependent RNA polymerase holoenzyme. The close proximity of the open reading frames suggested that the two genes are transcribed in a polycistronic manner. By the use of an Escherichia coli expression system, SigA was produced in a soluble form. An in vitro transcription assay of purified SigA reconstituted with the core RNA polymerase of E. coli showed that Thermus SigA functioned as a sigma factor to initiate specific transcription.

Amino Acid Sequence↗
PubMed1994

Excretion of the anti-sigma factor through a flagellar substructure couples flagellar gene expression with flagellar assembly in Salmonella typhimurium.

More than 50 genes are required for flagellar formation and function in Salmonella typhimurium. According to the cascade model of the flagellar regulon, the flagellar operons are divided into three classes, 1, 2, and 3, with reference to their relative positions in the transcriptional hierarchy. This sequential transcription is coupled to the assembly process of the flagellar structure, that is, genes involved in formation of the hook-basal body complex belong to the class-2 operons, whereas those involved in formation of filament belong to the class-3 operons. The fliA gene encodes an alternative sigma factor specific for transcription of the class-3 operons. A negative regulatory gene, flgM, which is responsible for the coupling of expression of class-3 operons to flagellar assembly, encodes an anti-sigma factor that binds to FliA and prevents its association with RNA polymerase core enzyme. In the present study, we showed that the flgM gene is transcribed from two different promoters: one is its own class-3 promoter and the other is the class-2 promoter for the upstream gene, flgA. Furthermore, we showed that FlgM is excreted into culture medium from cells of the wild-type strain and of class-3 mutants that can produce complete hook-basal body structures. On the other hand, FlgM is not excreted from mutants defective in the hook-basal body genes. These results indicate that FlgM is excreted from the cells through the flagellar substructures that are formed by the function of the hook-basal body genes.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacterial Proteins↗
PubMed2004

RhuR, an extracytoplasmic function sigma factor activator, is essential for heme-dependent expression of the outer membrane heme and hemoprotein receptor of Bordetella avium.

Genes involved in iron (Fe) acquisition often are regulated in response to the local availability of Fe. In many bacteria, Fe-dependent responsiveness is mediated by Fur, a global Fe-dependent transcriptional repressor. Tighter regulatory control of Fur-responsive genes is afforded by incorporating additional regulators into Fur-dependent regulatory cascades. RhuI, a Fur-dependent extracytoplasmic function sigma factor of Bordetella avium, in response to the dual stimulation of Fe starvation and the presence of heme (or hemoproteins), regulates P(bhuR), a heme-responsive promoter which directs expression of the bhuRSTUV heme utilization operon. While BhuR, the outer membrane heme receptor, and RhuI have been shown to be indispensable for heme-dependent activation of P(bhuR), collateral components of the regulatory cascade have not been described. In this investigation, RhuR, an integral cytoplasmic membrane protein with homology to anti-sigma factors, is shown to be an essential activator of P(bhuR) expression. The functional domain of RhuR required for heme-dependent activation of P(bhuR) expression was mapped to the N-terminal 97 amino acids of the protein by use of a chimeric RhuR-BlaM fusion. Expression of the chimera in a rhuR mutant rendered P(bhuR) constitutive, thereby decoupling the promoter from heme dependency. Growth studies confirmed that B. avium requires RhuR for optimal utilization of hemoglobin, but not hemin, as a sole source of nutrient Fe. These data imply that B. avium expresses, in addition to the BhuR heme/hemoprotein utilization system, an alternative RhuR-independent heme utilization mechanism. A model is proposed in which RhuR is the functional bridge between BhuR and RhuI in a heme-dependent regulatory cascade.

Amino Acid Sequence↗
PubMed2001

An Arabidopsis sigma factor (SIG2)-dependent expression of plastid-encoded tRNAs in chloroplasts.

A eubacteria-type RNA polymerase (PEP) plays crucial roles for chloroplast development in higher plants. The core subunits are encoded on plastid DNA (rpo genes) while the regulatory sigma factors are encoded on the nuclear DNA (SIG genes). However, the definite gene specificity of each sigma factor is unknown. We recently identified an Arabidopsis recessive pale-green mutant abc1 in which T-DNA is inserted in SIG2 (sigB). In this mutant, almost normal etioplasts were developed under dark conditions while the small chloroplasts with poor thylakoid membranes and stacked lamellar were developed under light conditions. The sig2-1 mutant was deficient in accumulating enough photosynthetic and photosynthesis-related proteins as well as chlorophyll. However, mRNAs of their structural genes were not significantly reduced. Further analyses revealed that several plastid-encoded tRNAs including trnE-UUC that has dual function for protein and ALA biosyntheses were drastically reduced in the sig2-1 mutant. In contrast, nucleus-encoded T7 phage-type RNA polymerase (NEP)-dependent gene transcripts were steadily accumulated in the mutant. These results indicate that progress of chloroplast development requires SIG2-dependent expression of plastid genes, particularly some of the tRNA genes.

Arabidopsis↗
PubMed2003

Transient association of an alternative sigma factor, ComX, with RNA polymerase during the period of competence for genetic transformation in Streptococcus pneumoniae.

Natural transformation in Streptococcus pneumoniae is regulated by a quorum-sensing system that acts through accumulation and sensing of a peptide pheromone (competence-stimulating peptide [CSP]) to control many competence-specific genes acting in DNA uptake, processing, and integration. The period of competence induced by CSP lasts only 15 min (quarter-height peak width). The recently identified regulator ComX is required for the CSP-dependent expression of many competence-specific genes that share an unusual consensus sequence (TACGAATA) at their promoter regions. To test the hypothesis that this regulator acts as a transient alternative sigma factor, ComX was purified from an Escherichia coli overexpression strain and core RNA polymerase was purified from a comX-deficient S. pneumoniae strain. The reconstituted ComX-polymerase holoenzyme produced transcripts for the competence-specific genes ssbB, cinA, cglA, celA, and dalA and was inhibited by anti-ComX antibody, but not by anti-sigma(70) antibody. Western blotting using antibodies specific for ComX, sigma(70), and poly-His revealed a transient presence of ComX for a period of 15 to 20 min after CSP treatment, while RNA polymerase remained at a constant level and sigma(A) remained between 60 and 125% of its normal level. ComX reached a molar ratio to RNA polymerase of at least 1.5. We conclude that ComX is unstable and acts as a competence-specific sigma factor.

Amino Acid Sequence↗
PubMed2006

The ornibactin biosynthesis and transport genes of Burkholderia cenocepacia are regulated by an extracytoplasmic function sigma factor which is a part of the Fur regulon.

Burkholderia cenocepacia mutants that fail to produce the siderophore ornibactin were obtained following mutagenesis with mini-Tn5Tp. These mutants were shown to be growth restricted under conditions of iron depletion. In eight of the mutants, the transposon had integrated into one of two genes, orbI and orbJ, encoding nonribosomal peptide synthetases. In the other mutant, the transposon had inserted into an open reading frame, orbS, located upstream from orbI. The polypeptide product of orbS exhibits a high degree of similarity to the Pseudomonas aeruginosa extracytoplasmic function (ECF) sigma factor PvdS but possesses an N-terminal extension of approximately 29 amino acids that is not present in PvdS. Three predicted OrbS-dependent promoters were identified within the ornibactin gene cluster, based on their similarity to PvdS-dependent promoters. The iron-regulated activity of these promoters was shown to require OrbS. Transcription of the orbS gene was found to be under the control of an iron-regulated sigma(70)-dependent promoter. This promoter, but not the OrbS-dependent promoters, was shown to be a target for repression by the global regulator Fur. Our results demonstrate that production of ornibactin by B. cenocepacia in response to iron starvation requires transcription of an operon that is dependent on the Fur-regulated ECF sigma factor gene orbS. A mechanism is also proposed for the biosynthesis of ornibactin.

Base Sequence↗
PubMed2003

Regulation of the FecI-type ECF sigma factor by transmembrane signalling.

Induction of the ferric citrate transport genes of Escherichia coli K-12 involves a signalling cascade that starts at the cell surface and proceeds to the cytoplasm. Three specific proteins are involved: FecA in the outer membrane, FecR in the cytoplasmic membrane, and FecI in the cytoplasm. The binding of dinuclear ferric citrate to FecA causes substantial structural changes in FecA, triggering the signal cascade. The amino-proximal end of FecA interacts with the carboxy-proximal end of FecR in the periplasm. FecR then transmits the signal across the cytoplasmic membrane into the cytoplasm and activates the FecI sigma factor, which binds to the RNA polymerase core enzyme and directs the RNA polymerase to the promoter upstream of the fecABCDE transport genes to initiate transcription. Transcription of the fecIR regulatory genes and the fec transport genes is repressed by the Fur protein loaded with Fe(2+). Therefore, transcription of the fec transport genes is subjected to double control: cells first detect iron deficiency and respond by synthesis of the regulatory proteins FecI and FecR, which initiate transcription of the fec transport genes, provided ferric citrate is available. FecI belongs to the extracytoplasmic function sigma factors, which are widespread among bacteria. With the recent sequencing of complete microbial genomes, it has become apparent that the FecIRA cascade is now a paradigm for the regulatory control of FecI family sigmas in Gram-negative bacteria.

Amino Acid Sequence↗
PubMed1998

The fur-regulated gene encoding the alternative sigma factor PvdS is required for iron-dependent expression of the LysR-type regulator ptxR in Pseudomonas aeruginosa.

We previously identified a novel regulator of the exotoxin A gene (toxA) in Pseudomonas aeruginosa, PtxR, that belongs to the LysR family of prokaryotic regulatory proteins. Preliminary data also suggest that PtxR affects the expression of siderophores in P. aeruginosa. Because toxA expression and siderophore production in this organism are coordinately regulated by the ferric uptake regulator (Fur) and the Fur-regulated alternative sigma factor PvdS, regulation of ptxR itself in the context of these regulators was examined. RNase protection analyses of ptxR transcription revealed that there are two independent transcription initiation sites (T1 and T2). While transcription from the promoter of T1 is constitutive throughout the growth cycle of PAO1, transcription from the second promoter (P2) is negatively affected by iron. Transcription from the P2 promoter is constitutive in a fur mutant under microaerobic conditions but still iron regulated during aerobic growth. High concentrations (>100 nM) of the ferric uptake regulatory protein (Fur) failed to bind to either of the promoter regions of ptxR in either gel mobility shift assays or DNase I footprint experiments. These results indicate that Fur indirectly regulates the iron-dependent expression of ptxR. Iron-regulated transcription of ptxR from the P2 promoter, but not constitutive expression from the P1 promoter, was dependent on the Fur-regulated alternative sigma factor gene pvdS, even under aerobic conditions. Consequently, there are two levels of iron-regulated expression of ptxR. The iron-regulated expression of ptxR under microaerobic conditions from the P2 promoter of ptxR is mediated indirectly by Fur through the iron-regulated expression of pvdS. In contrast, pvdS-mediated iron regulation of ptxR under aerobic conditions is Fur independent.

Bacterial Proteins↗
PubMed2004

An extracytoplasmic-function sigma factor is involved in a pathway controlling beta-exotoxin I production in Bacillus thuringiensis subsp. thuringiensis strain 407-1.

Beta-exotoxin I is an insecticidal nucleotide analogue secreted by various Bacillus thuringiensis strains. In this report, we describe the characterization and transcriptional analysis of a gene cluster, designated sigW-ecfX-ecfY, that is essential for beta-exotoxin I production in B. thuringiensis subsp. thuringiensis strain 407-1. In this strain, the disruption of the sigW cluster resulted in nontoxic culture supernatants. sigW encodes a protein of 177 residues that is 97 and 94% identical to two putative RNA polymerase extracytoplasmic-function-type sigma factors from Bacillus anthracis strain Ames and Bacillus cereus strain ATCC 14579, respectively. It is also 50, 30, and 26% identical to SigW from Clostridium perfringens and SigW and SigX from Bacillus subtilis, respectively. EcfX, encoded by the gene following sigW, significantly repressed the expression of sigW when both genes were overtranscribed, suggesting that it could be the anti-sigma factor of SigW. Following the loss of its curable cry plasmid, strain 407 became unable to synthesize crystal toxins, in contrast to the mutant strain 407-1(Cry-)(Pig+), which overproduced this molecule in the absence of this plasmid. Transcriptional analysis of sigW indicated that this gene was expressed during the stationary phase and only in the 407-1(Cry-)(Pig+) mutant. This suggests that in the wild type-407(Cry+) strain, beta-exotoxin I was produced from determinants located on a cry gene-bearing plasmid and that sigW is able to induce beta-exotoxin I production in B. thuringiensis in the absence of cry gene-bearing plasmids. Although the signal responsible for this activation is unknown, these results indicate that beta-exotoxin I production in B. thuringiensis can be restored or induced via an alternative pathway that requires sigW expression.

Adenosine↗
PubMed1992

Characterization of the Agrobacterium tumefaciens heat shock response: evidence for a sigma 32-like sigma factor.

We have characterized the heat shock response of Agrobacterium tumefaciens and compared it with the well-characterized Escherichia coli heat shock response. Four major heat shock proteins with apparent molecular masses of 98, 75, 65, and 20 kDa were identified by pulse-labelling cultures after temperature upshift. The three largest proteins comigrated with proteins that were antigenically related to the E. coli heat shock proteins sigma 70, DnaK, and GroEL, respectively. The heat shock proteins were also strongly induced by ethanol and cadmium chloride and were mildly induced by mitomycin C. To determine whether the A. tumefaciens heat shock regulatory system was similar to that of E. coli, we introduced the E. coli dnaK gene into A. tumefaciens. The E. coli DnK protein was expressed in A. tumefaciens, and its synthesis was induced after heat shock. Primer extension analysis of the E. coli dnaK gene in A. tumefaciens indicated that transcription initiated from one or possibly both of the E. coli heat shock promoters. We conclude that A. tumefaciens has a heat shock response similar to that of E. coli, in that (i) similar proteins are induced by heat shock, (ii) synthesis of these proteins is induced in response to similar stimuli, and (iii) A. tumefaciens can recognize an E. coli heat shock promoter, suggesting that A. tumefaciens has a sigma factor similar to sigma 32.

Agrobacterium tumefaciens↗
PubMed1992

Physical interaction between heat shock proteins DnaK, DnaJ, and GrpE and the bacterial heat shock transcription factor sigma 32.

Genetic evidence indicates central roles for Hsp70 chaperones in the regulation of heat shock gene expression. This regulatory function has been postulated for Escherichia coli to rely on the direct association of DnaK (Hsp70) with the heat shock transcription factor sigma 32. This report presents evidence for the physical association of DnaK, DnaJ, and GrpE chaperones with sigma 32 in vivo. Surprisingly, an interaction of DnaJ with sigma 32 exists that is distinguishable from an interaction of DnaK and GrpE with sigma 32: addition of ATP disrupts the association of DnaK and GrpE with sigma 32, but not the association of DnaJ with sigma 32. Furthermore, DnaJ-sigma 32 and DnaK-sigma 32 associations occur independent of DnaK and DnaJ, respectively. These results suggest distinct regulatory functions of DnaJ and DnaK/GrpE.

Adenosine Triphosphatases↗
PubMed1990

Gene fliA encodes an alternative sigma factor specific for flagellar operons in Salmonella typhimurium.

Through genetic studies, the fliA gene product has been shown to regulate positively gene expression in late operons of the flagellar regulon in Salmonella typhimurium. In the present study, the fliA gene was cloned and sequenced. The fliA coding region consisted of 717 nucleotides beginning with the GTG initiation codon and the conserved sequence specific to promoters for flagellar operons was found to exist upstream of the coding region. The fliA gene product deduced from the nucleotide sequence was a protein with 239 amino acid residues and the calculated molecular mass was 27,470 dalton. The deduced amino acid sequence was homologous with that of sigma 28, a flagellar specific sigma factor of Bacillus subtilis. The fliA gene product was identified as a protein of molecular mass 29 kDa in the in vitro transcription-translation system, while three proteins of 29 kDa, 31 kDa and 32 kDa were found in the products programmed by the fliA gene in minicells and in maxicells. The 29 kDa FliA protein was purified from the FliA overproducing strain which carried the ptac-fliA fusion. This protein activated the in vitro synthesis of flagellin, the fliC gene product. RNA polymerase containing the purified FliA protein was shown to transcribe the fliC gene. These results indicate that FliA protein functions as an alternative sigma factor specific for S. typhimurium flagellar operons.

Amino Acid Sequence↗