AbrB is a regulator of the sigma(W) regulon in Bacillus subtilis

Analyzing AbrB-Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2

As an industrial bacterium, Bacillus licheniformis DW2 produces bacitracin which is an important antibiotic for many pathogenic microorganisms. Our previous study showed AbrB-knockout could significantly increase the production of bacitracin. Accordingly, it was meaningful to understand its genome features, expression differences between wild and AbrB-knockout (ΔAbrB) strains, and the regulation of bacitracin biosynthesis. Here, we sequenced, de novo assembled and annotated its genome, and also sequenced the transcriptomes in three growth phases. The genome of DW2 contained a DNA molecule of 4,468,952 bp with 45.93% GC content and 4,717 protein coding genes. The transcriptome reads were mapped to the assembled genome, and obtained 4,102∼4,536 expressed genes from different samples. We investigated transcription changes in B. licheniformis DW2 and showed that ΔAbrB caused hundreds of genes up-regulation and down-regulation in different growth phases. We identified a complete bacitracin synthetase gene cluster, including the location and length of bacABC, bcrABC, and bacT, as well as their arrangement. The gene cluster bcrABC were significantly up-regulated in ΔAbrB strain, which supported the hypothesis in previous study of bcrABC transporting bacitracin out of the cell to avoid self-intoxication, and was consistent with the previous experimental result that ΔAbrB could yield more bacitracin. This study provided a high quality reference genome for B. licheniformis DW2, and the transcriptome data depicted global alterations across two strains and three phases offered an understanding of AbrB regulation and bacitracin biosynthesis through gene expression.

Substitutional analysis of the C-terminal domain of AbrB revealed its essential role in DNA-binding activity

The global transition state regulator AbrB controls more than 100 genes of the Bacillus relatives and is known to interact with varying DNA-sequences. The DNA-binding domain of the AbrB-like proteins was proposed to be located exclusively within the amino-terminal ends. However, the recognition of DNA, and specificity of the binding mechanism, remains elusive still in view of highly differing recognition sites. Here we present a substitutional analysis to examine the role of the carboxy-terminal domain of AbrB from Bacillus subtilis and Bacillus amyloliquefaciens. Our results demonstrate that the carboxy-terminal domains of AbrB affect the DNA-binding properties of the tetrameric AbrB. Most likely, the C-termini are responsible for the cooperative character observed for AbrB interaction with some DNA targets like tycA and phyC.

Thermodynamic and molecular analysis of the AbrB-binding sites within the phyC-region of Bacillus amyloliquefaciens FZB45

AbrB is a global regulator of transition state that is known to repress more than 100 genes in Bacillus species. Although AbrB is involved in the regulation of most cellular processes, a conserved binding motif seems to be elusive. Thus, the mechanism of AbrB-mediated transcriptional control is still unclear. In our previous work we identified two separate AbrB-binding sites within phytase gene region (phyC) of Bacillus amyloliquefaciens FZB45, whose integrity is essential for repression. Comparable architecture of AbrB-binding sites is also described for tycA that encodes an antibiotic synthesis enzyme. Considering the size of the AbrB tetramer (56 kDa) and other AbrB binding motifs (~20 to 98 bp) we hypothesized preferred binding positions within both AbrB sites of phyC that exhibit higher affinities to AbrB. Thus, we used surface plasmon resonance (SPR) to study the binding kinetics between AbrB and 40-bp ds-oligonucleotides that were derived from both binding sites. Surface plasmon resonance sensorgrams revealed strong binding kinetics that showed nearly no dissociation and positive cooperativity of the AbrB-DNA interaction to the whole AbrB-binding site 2 and to a small part of AbrB-binding site 1. Using chemically modified DNA we found bases contacting AbrB mainly at one face of the DNA-helix within a core region separated by one helical turn each. High content of modified guanines presented in the control reaction of the KMnO(4) interference assay indicated distortion of the DNA-structure of phyC. In vitro transcription assays and base substitutions within the core region support this idea and the cooperativity of AbrB binding.

Extracytoplasmic function sigma factors with overlapping promoter specificity regulate sublancin production in Bacillus subtilis

Bacillus subtilis harbors seven extracytoplasmic function (ECF) sigma factors. At least three ECF sigma factors (sigma(M), sigma(W), and sigma(X)) are induced by, and provide resistance to, antibiotics and other agents eliciting cell envelope stress. Here, we report that ECF sigma factors also contribute to antibiotic production. B. subtilis 168 strains that are lysogenic for the SPbeta bacteriophage produce sublancin, which inhibits the growth of other, nonlysogenic strains. Genetic studies demonstrate that synthesis of sublancin is largely dependent on sigma(X), with a smaller contribution from sigma(M). A sigM sigX double mutant is unable to produce sublancin. This defect is primarily due to the fact that the sublancin biosynthesis is positively activated by the transition state regulator and AbrB paralog Abh, which counteracts transcriptional repression of the sublancin biosynthesis operon by AbrB. Ectopic expression of abh bypasses the requirement for sigma(M) or sigma(X) in sublancin synthesis, as does an abrB mutation. In addition to their major role in regulating sublancin expression by activating abh transcription, sigma(X) and sigma(M) also have a second role as positive regulators of sublancin expression that is independent of AbrB and Abh. Since sublancin resistance in nonlysogens is largely dependent on sigma(W), ECF sigma factors control both sublancin production and resistance.

Parallel pathways of repression and antirepression governing the transition to stationary phase in Bacillus subtilis

The AbrB protein of the spore-forming bacterium Bacillus subtilis is a repressor of numerous genes that are switched on during the transition from the exponential to the stationary phase of growth. The gene for AbrB is under the negative control of the master regulator for entry into sporulation, Spo0A-P. It has generally been assumed that derepression of genes under the negative control of AbrB is achieved by Spo0A-P-mediated repression of abrB followed by rapid degradation of the AbrB protein. Here, we report that AbrB levels do decrease during the transition to stationary phase, but that this decrease is not the entire basis by which AbrB-controlled genes are derepressed. Instead, AbrB is inactivated by the product of a uncharacterized gene, abbA (formerly ykzF), whose transcription is switched on by Spo0A-P. The abbA gene encodes an antirepressor that binds to AbrB and prevents it from binding to DNA. Combining our results with previous findings, we conclude that Spo0A-P sets in motion two parallel pathways of repression and antirepression to trigger the expression of diverse categories of genes during the transition to stationary phase.

Analysis of a growth-phase-regulated two-component regulatory system in the periodontal pathogen Treponema denticola

Nothing is currently known regarding the global regulatory networks of Treponema denticola and other oral spirochetes. In this report, we assess the properties and potential phosphotransfer capability of a putative two-component regulatory system (TCS) of T. denticola that is formed by the products of open reading frames tde0032 (a sensor kinase) and tde0033 (a response regulator), henceforth designated AtcS and AtcR, respectively. Using PCR and DNA sequence analyses, atcS and atcR were demonstrated to be widely distributed and conserved among T. denticola isolates. Reverse transcription-PCR (RT-PCR) analyses revealed that these genes are cotranscribed and may also be expressed as part of a larger operon that includes several flanking genes. Analyses using 5' rapid amplification of cDNA ends identified the transcriptional start sites for these operons and provided evidence that some of these genes may be independently transcribed from internal promoters. Real-time RT-PCR and Western blot analysis revealed significant upregulation of atcRS during late-stage growth, indicating growth-phase-dependent expression. Lastly, the phosphorelay capability of the AtcRS system was assessed and demonstrated using recombinant proteins. AtcS was found to undergo autophosphorylation and to transfer phosphate to AtcR. These analyses represent the first description of a functional TCS in an oral spirochetes and provide insight into the transcriptional regulatory mechanisms of these important bacteria.

Abh and AbrB control of Bacillus subtilis antimicrobial gene expression

The Bacillus subtilis abh gene encodes a protein whose N-terminal domain has 74% identity to the DNA-binding domain of the global regulatory protein AbrB. Strains with a mutation in abh showed alterations in the production of antimicrobial compounds directed against some other Bacillus species and gram-positive microbes. Relative to its wild-type parental strain, the abh mutant was found deficient, enhanced, or unaffected for the production of antimicrobial activity. Using lacZ fusions, we examined the effects of abh upon the expression of 10 promoters known to be regulated by AbrB, including five that transcribe well-characterized antimicrobial functions (SdpC, SkfA, TasA, sublancin, and subtilosin). For an otherwise wild-type background, the results show that Abh plays a negative regulatory role in the expression of four of the promoters, a positive role for the expression of three, and no apparent regulatory role in the expression of the other three promoters. Binding of AbrB and Abh to the promoter regions was examined using DNase I footprinting, and the results revealed significant differences. The transcription of abh is not autoregulated, but it is subject to a degree of AbrB-afforded negative regulation. The results indicate that Abh is part of the complex interconnected regulatory system that controls gene expression during the transition from active growth to stationary phase.

Evidence for a novel protease governing regulated intramembrane proteolysis and resistance to antimicrobial peptides in Bacillus subtilis

Evidence is presented that the activation of the RNA polymerase sigma factor sigma(W) in Bacillus subtilis by regulated intramembrane proteolysis is governed by a novel, membrane-embedded protease. The sigma(W) factor is activated by proteolytic destruction of the membrane-bound anti-sigma(W) factor RsiW in response to antimicrobial peptides and other agents that damage the cell envelope. RsiW is destroyed by successive proteolytic events known as Site-1 and Site-2 cleavage. Site-2 cleavage is mediated by a member of the SpoIVFB-S2P family of intramembrane-acting metalloproteases, but the protease responsible for Site-1 cleavage was unknown. We have identified a previously uncharacterized, multipass membrane protein called PrsW (annotated YpdC) that is both necessary and sufficient (when artificially produced in an unrelated host bacterium) for Site-1 cleavage of RsiW. PrsW is a member of a widespread family of membrane proteins that includes at least one previously known protease. We identify residues important for proteolysis and a cluster of acidic residues involved in sensing antimicrobial peptides and cell envelope stress.

The absence of FtsH metalloprotease activity causes overexpression of the sigmaW-controlled pbpE gene, resulting in filamentous growth of Bacillus subtilis

FtsH is a membrane-bound and energy-dependent metalloprotease in bacteria which is involved in the posttranslational control of the activity of a variety of important transcription factors and in the degradation of uncomplexed integral membrane proteins. For Bacillus subtilis, little is known about the target proteins of FtsH protease. Its gene is not essential, but knockout strains display a pleiotropic phenotype including sensitivity toward salt and heat stress, defects in sporulation and competence, and largely filamentous growth. Comparison of the intracellular proteomes of wild-type and ftsH knockout strains revealed that at least nine proteins accumulated in the absence of ftsH, four of which could be identified. Two of these proteins turned out to be members of the sigma(W) regulon. Accumulation of one of these sigma(W)-controlled proteins, the penicillin-binding protein PBP4*, was analyzed in more detail. We could show that PBP4* is not a proteolytic substrate of FtsH and that its overproduction is due to the enhanced transcription of its gene (pbpE) in ftsH null mutants. The filamentous growth phenotype of DeltaftsH strains was abolished in a DeltaftsH DeltapbpE double knockout. In ftsH wild-type strains with the pbpE gene under regulatable control, pbpE overexpression caused filamentation of the cells. DNA macroarray analysis revealed that most genes of the sigma(W) regulon are transcribed at elevated levels in an ftsH mutant. The influence of FtsH on sigma(W)-controlled genes is discussed.