Sequence-specific interactions between promoter DNA and the RNA polymerase sigma factor E

Genome-wide analysis of cell type-specific gene transcription during spore formation in Clostridium difficile

Clostridium difficile, a Gram positive, anaerobic, spore-forming bacterium is an emergent pathogen and the most common cause of nosocomial diarrhea. Although transmission of C. difficile is mediated by contamination of the gut by spores, the regulatory cascade controlling spore formation remains poorly characterized. During Bacillus subtilis sporulation, a cascade of four sigma factors, σ(F) and σ(G) in the forespore and σ(E) and σ(K) in the mother cell governs compartment-specific gene expression. In this work, we combined genome wide transcriptional analyses and promoter mapping to define the C. difficile σ(F), σ(E), σ(G) and σ(K) regulons. We identified about 225 genes under the control of these sigma factors: 25 in the σ(F) regulon, 97 σ(E)-dependent genes, 50 σ(G)-governed genes and 56 genes under σ(K) control. A significant fraction of genes in each regulon is of unknown function but new candidates for spore coat proteins could be proposed as being synthesized under σ(E) or σ(K) control and detected in a previously published spore proteome. SpoIIID of C. difficile also plays a pivotal role in the mother cell line of expression repressing the transcription of many members of the σ(E) regulon and activating sigK expression. Global analysis of developmental gene expression under the control of these sigma factors revealed deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We showed that the expression of the σ(E) regulon in the mother cell was not strictly under the control of σ(F) despite the fact that the forespore product SpoIIR was required for the processing of pro-σ(E). In addition, the σ(K) regulon was not controlled by σ(G) in C. difficile in agreement with the lack of pro-σ(K) processing. This work is one key step to obtain new insights about the diversity and evolution of the sporulation process among Firmicutes.

Staphylococcus aureus methicillin-resistance factor fmtA is regulated by the global regulator SarA

fmtA encodes a low-affinity penicillin binding protein in Staphylococcus aureus. It is part of the core cell wall stimulon and is involved in methicillin resistance in S. aureus. Here, we report that the transcription factor, SarA, a pleiotropic regulator of virulence genes in S. aureus, regulates the expression of fmtA. In vitro binding studies with purified SarA revealed that it binds to specific sites within the 541-bp promoter region of fmtA. Mutation of a key residue of the regulatory activity of SarA (Arg90) abolished binding of SarA to the fmtA promoter, suggesting that SarA binds specifically to the fmtA promoter region. In vivo analysis of the fmtA promoter using a lux operon reporter fusion show high level expression following oxacillin induction, which was abrogated in a sarA mutant strain. These data suggest that SarA is essential for the induction of fmtA expression by cell wall-specific antibiotics. Further, in vitro transcription studies show that SarA enhances fmtA transcription and suggest that regulation of fmtA could be via a SigA-dependent mechanism. Overall, our results show that SarA plays a direct role in the regulation of fmtA expression via binding to the fmtA promoter.

Mutational analysis of an extracytoplasmic-function sigma factor to investigate its interactions with RNA polymerase and DNA

The extracytoplasmic-function (ECF) family of sigma factors comprises a large group of proteins required for synthesis of a wide variety of extracytoplasmic products by bacteria. Residues important for core RNA polymerase (RNAP) binding, DNA melting, and promoter recognition have been identified in conserved regions 2 and 4.2 of primary sigma factors. Seventeen residues in region 2 and eight residues in region 4.2 of an ECF sigma factor, PvdS from Pseudomonas aeruginosa, were selected for alanine-scanning mutagenesis on the basis of sequence alignments with other sigma factors. Fourteen of the mutations in region 2 had a significant effect on protein function in an in vivo assay. Four proteins with alterations in regions 2.1 and 2.2 were purified as His-tagged fusions, and all showed a reduced affinity for core RNAP in vitro, consistent with a role in core binding. Region 2.3 and 2.4 mutant proteins retained the ability to bind core RNAP, but four mutants had reduced or no ability to cause core RNA polymerase to bind promoter DNA in a band-shift assay, identifying residues important for DNA binding. All mutations in region 4.2 reduced the activity of PvdS in vivo. Two of the region 4.2 mutant proteins were purified, and each showed a reduced ability to cause core RNA polymerase to bind to promoter DNA. The results show that some residues in PvdS have functions equivalent to those of corresponding residues in primary sigma factors; however, they also show that several residues not shared with primary sigma factors contribute to protein function.

The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis

Asymmetric division during sporulation by Bacillus subtilis generates a mother cell that undergoes a 5-h program of differentiation. The program is governed by a hierarchical cascade consisting of the transcription factors: σ^E, σ^K, GerE, GerR, and SpoIIID. The program consists of the activation and repression of 383 genes. The σ^E factor turns on 262 genes, including those for GerR and SpoIIID. These DNA-binding proteins downregulate almost half of the genes in the σ^E regulon. In addition, SpoIIID turns on ten genes, including genes involved in the appearance of σ^K_. Next, σ^K activates 75 additional genes, including that for GerE. This DNA-binding protein, in turn, represses half of the genes that had been activated by σ^K while switching on a final set of 36 genes. Evidence is presented that repression and activation contribute to proper morphogenesis. The program of gene expression is driven forward by its hierarchical organization and by the repressive effects of the DNA-binding proteins. The logic of the program is that of a linked series of feed-forward loops, which generate successive pulses of gene transcription. Similar regulatory circuits could be a common feature of other systems of cellular differentiation.

A comprehensive genomic analysis of sporulation in Bacillus subtilis reveals a coordinated program of gene activation and repression, which involves 383 genes

Autoinduction of Bacillus subtilis phoPR operon transcription results from enhanced transcription from EsigmaA- and EsigmaE-responsive promoters by phosphorylated PhoP

The phoPR operon encodes a response regulator, PhoP, and a histidine kinase, PhoR, which activate or repress genes of the Bacillus subtilis Pho regulon in response to an extracellular phosphate deficiency. Induction of phoPR upon phosphate starvation required activity of both PhoP and PhoR, suggesting autoregulation of the operon, a suggestion that is supported here by PhoP footprinting on the phoPR promoter. Primer extension analyses, using RNA from JH642 or isogenic sigE or sigB mutants isolated at different stages of growth and/or under different growth conditions, suggested that expression of the phoPR operon represents the sum of five promoters, each responding to a specific growth phase and environmental controls. The temporal expression of the phoPR promoters was investigated using in vitro transcription assays with RNA polymerase holoenzyme isolated at different stages of Pho induction, from JH642 or isogenic sigE or sigB mutants. In vitro transcription studies using reconstituted EsigmaA, EsigmaB, and EsigmaE holoenzymes identified PA4 and PA3 as EsigmaA promoters and PE2 as an EsigmaE promoter. Phosphorylated PhoP (PhoP approximately P) enhanced transcription from each of these promoters. EsigmaB was sufficient for in vitro transcription of the PB1 promoter. P5 was active only in a sigB mutant strain. These studies are the first to report a role for PhoP approximately P in activation of promoters that also have activity in the absence of Pho regulon induction and an activation role for PhoP approximately P at an EsigmaE promoter. Information concerning PB1 and P5 creates a basis for further exploration of the regulatory coordination or overlap of the PhoPR and SigB regulons during phosphate starvation.

Identification of a DNA binding region in GerE from Bacillus subtilis

Proteins that have a structure similar to those of LuxR and FixJ comprise a large subfamily of transcriptional activator proteins. Most members of the LuxR-FixJ family contain a similar amino-terminal receiver domain linked by a small region to a carboxy-terminal domain that contains an amino acid sequence similar to the helix-turn-helix (HTH) motif found in other DNA-binding proteins. GerE from Bacillus subtilis is the smallest member of the LuxR-FixJ family. Its 74-amino-acid sequence is similar over its entire length to the DNA binding region of this protein family, including the HTH motif. Therefore, GerE provides a simple model for studies of the role of this HTH domain in DNA binding. Toward this aim, we sought to identify the amino acids within this motif that are important for the specificity of binding to DNA. We examined the effects of single base pair substitutions in the high-affinity GerE binding site on the sigK promoter and found that nucleotides at positions +2, +3, and +4 relative to the transcription start site on the sigK promoter are important for a high-affinity interaction with GerE. We next examined the effects of single alanine substitutions at two positions in the HTH region of GerE on binding to wild-type or mutant target sites. We found that the substitution of an alanine for the threonine at position 42 of GerE produced a protein that binds with equal affinity to two sites that differ by 1 bp, whereas wild-type GerE binds with different affinities to these two sites. These results provide evidence that the amino acyl residues in or near the putative HTH region of GerE and potentially other members of the LuxR-FixJ family determine the specificity of DNA binding.

Characterization of an ECF sigma factor protein from Pseudomonas aeruginosa

The PvdS protein is essential for synthesis of the siderophore pyoverdine by Pseudomonas aeruginosa. PvdS has some sequence similarity to a family of alternative sigma factor proteins (the ECF [extracytoplasmic factor] family) that direct bacterial RNA polymerases to transcribe genes encoding extracytoplasmic factors. PvdS was purified as a His-tagged protein (hPvdS) and this was used to test the hypothesis that PvdS is a sigma factor protein. The purified protein caused core RNA polymerase from Escherichia coli to bind specifically to the promoters of pyoverdine synthesis genes and enabled transcription from these promoters in vitro. In addition, PvdS was found to co-purify with RNA polymerase from P. aeruginosa, indicating that PvdS associates with RNA polymerase inside the bacteria. These results show that PvdS is a sigma factor protein.

Structure and assembly of the bacterial endospore coat

Many biological processes are mediated through the action of multiprotein complexes, often assembled at specific cellular locations. Bacterial endospores for example, are encased in a proteinaceous coat, which confers resistance to lysozyme and harsh chemicals and influences the spore response to germinants. In Bacillus subtilis, the coat is composed of more than 20 polypeptides, organized into three main layers: an amorphous undercoat; a lamellar, lightly staining inner structure; and closely apposed to it, a striated electron-dense outer coat. Synthesis of the coat proteins is temporally and spatially governed by a cascade of four mother cell-specific transcription factors. However, the order of assembly and final destination of the coat structural components may rely mainly on specific protein-protein interactions, as well as on the action of accessory morphogenetic proteins. Proteolytic events, protein-protein crosslinking, and protein glycosylation also play a role in the assembly process. These modifications are carried out by enzymes that may themselves be targeted to the coat layers. Coat genes have been identified by reverse genetics or, more recently, by screens for mother cell-specific promoters or for peptide sequences able to interact with certain bait proteins. A role for a given locus in coat assembly is established by a combination of regulatory, functional, morphological, and topological criteria. Because of the amenability of B. subtilis to genetic analysis (now facilitated by the knowledge of its genome sequence), coat formation has become an attractive model for the assembly of complex macromolecular structures during development.

Activation of the Bacillus subtilis spoIIG promoter requires interaction of Spo0A and the sigma subunit of RNA polymerase

Bacillus subtilis Spo0A activates transcription from both sigmaA- and sigmaH-dependent promoters. Baldus et al. (2) identified two amino acid substitutions in the carboxyl terminus of sigmaA, K356E and H359R, that specifically impaired Spo0A-activated transcription in vivo. To test the model in which the K356E and H359R substitutions in sigmaA interfere with the interaction of Spo0A and sigmaA, we examined the effects of alanine substitutions at these positions in sigmaA on sigmaA's ability to direct transcription in vivo and in vitro. We found that alanine substitutions at these positions specifically reduced expression from the sigmaA-dependent, Spo0A-dependent promoters, spoIIG and spoIIE, in vivo. Furthermore, we found that stimulation of spoIIG promoter activity by Spo0A in vitro was reduced by the single substitutions H359A and H359R in sigmaA.

cse15, cse60, and csk22 are new members of mother-cell-specific sporulation regulons in Bacillus subtilis

We report on the characterization of three new transcription units expressed during sporulation in Bacillus subtilis. Two of the units, cse15 and cse60, were mapped at about 123 degrees and 62 degrees on the genetic map, respectively. Their transcription commenced around h 2 of sporulation and showed an absolute requirement for sigmaE. Maximal expression of both cse15 and cse60 further depended on the DNA-binding protein SpoIIID. Primer extension results revealed -10 and -35 sequences upstream of the cse15 and cse60 coding sequences very similar to those utilized by sigmaE-containing RNA polymerase. Alignment of these and other regulatory regions led to a revised consensus sequence for sigmaE-dependent promoters. A third transcriptional unit, designated csk22, was localized at approximately 173 degrees on the chromosome. Transcription of csk22 was activated at h 4 of sporulation, required the late mother-cell regulator sigmaK, and was repressed by the GerE protein. Sequences in the csk22 promoter region were similar to those of other sigmaK-dependent promoters. The cse60 locus was deduced to encode an acidic product of only 60 residues. A 37.6-kDa protein apparently encoded by cse15 was weakly related to the heavy chain of myosins, as well as to other myosin-like proteins, and is predicted to contain a central, 100 residue-long coiled-coil domain. Finally, csk22 is inferred to encode a 18.2-kDa hydrophobic product with five possible membrane-spanning helices, which could function as a transporter.

Potassium permanganate susceptibility of sigma E-RNA polymerase-promoter complexes

We used potassium permanganate (KMnO4) to identify unpaired thymidine (T) residues in promoter complexes formed by RNA polymerase (RNAP) associated with sigma E (sigma E-RNAP) from Bacillus subtilis. We found that a region of the spoIIID promoter from at least -10 to +1 becomes melted in the presence of this polymerase. In promoter complexes formed by RNAP associated with a mutant sigma E that melts promoter DNA inefficiently, we noted additional KMnO4 sensitivity at the -11 position of the spoIIID promoter. We suggest that the base pair at -11 is unpaired in both mutant and wild type (wt) complexes; however, close proximity of wt sigma E-RNAP with the T at -11 may protect it from KMnO4 attack. The absence of a close contact between the mutant sigma E-RNAP and the base at -11 may explain why this polymerase uses promoters less efficiently than wt sigma E-RNAP.

sigma E changed to sigma B specificity by amino acid substitutions in its -10 binding region

The association of a sigma factor (sigma) with RNA polymerase in bacteria determines its specificity of promoter utilization. To identify amino acid residues in sigma E from Bacillus subtilis that determine the specificity of its interaction with the nucleotides at the -10 region of its cognate promoters, we tested whether base pair substitutions in the -10 region of a sigma B-dependent promoter could signal its utilization by sigma E-RNA polymerase. We found that a combination of base pair substitutions at positions -15 and -14 of the sigma B-dependent ctc promoter resulted in its utilization by sigma E-RNA polymerase in vivo. We also found that the combination of two amino acid substitutions at positions 119 and 120 in sigma E changed its specificity for promoter utilization, resulting in a sigma factor that directed transcription from the sigma B-dependent ctc promoter, but not from sigma E-dependent promoters. These results suggest that amino acid residues at positions 119 and 120 determine, at least in part, the specificity of interactions between sigma E and the nucleotides in the -10 region of its cognate promoters.