Biomedical subjects

Mitsuo Ogura

Publications and source records attributed to Mitsuo Ogura.

12 recordsLinked to original sources

PubMed2007

Bacillus subtilis rapD, a direct target of transcription repression by RghR, negatively regulates srfA expression.

The Bacillus subtilis genome encodes eleven Rap proteins, which are conserved tetratricopeptide-containing regulatory proteins. Of those characterized to date, all except RapI negatively regulate response regulators, including Spo0F, ComA and DegU, via protein-protein interactions. RapD has not yet been fully characterized. It was examined whether RapD inhibits the expression of spoIIE, srfA and aprE, which are Spo0F-, ComA- and DegU-regulated genes, respectively. It was observed that multicopy rapD inhibited srfA expression, which suggests that RapD inhibits ComA. This was reinforced by the fact that multicopy rapD also blocked the expression of rapC and rapF, which belong to the ComA regulon. The expression of rapD was reported to depend on the extracytoplasmic function sigma factor SigX. DNA microarray analysis and gel retardation assays revealed that rapD expression is directly repressed by RghR. Thus, the ComA regulon is regulated by rapD in a SigX- and RghR-dependent manner.

Bacillus subtilis↗

PubMed2006

Superoxide stress decreases expression of srfA through inhibition of transcription of the comQXP quorum-sensing locus in Bacillus subtilis.

During the course of screening for competence-deficient mutants in the mutant collection constructed by the Japan Consortium of Bacillus Functional Genomics, a disruption mutant of sodA encoding superoxide dismutase was identified as a mutant with decreased transformation efficiency. In fact, in the sodA mutant we observed a severe decrease in the expression of srfA required for the development of genetic competence. Northern and primer extension analyses revealed inhibition of the transcription of the comQXP quorum-sensing locus in the sodA mutant, thereby preventing srfA expression. Furthermore, an excess amount of superoxide anion induced by the addition of paraquat also resulted in a decrease in comQXP transcription. Thus, it was concluded that high levels of superoxide are able to inhibit specifically the transcription of the comQXP operon. In support of this conclusion, the effect of added paraquat was significantly alleviated in a comX-independent srfA expression system.

Bacillus subtilis↗

PubMed2006

Bacillus subtilis RghR (YvaN) represses rapG and rapH, which encode inhibitors of expression of the srfA operon.

Rap proteins regulate the activity of response regulators including Spo0F, DegU and ComA. We found that overexpression of either RapG or RapH severely downregulated the expression of srfA, which belongs to the ComA regulon. Disruption of those genes, however, showed small effects on srfA expression. These observations suggested that Bacillus subtilis cells possess a repressor for rapG and rapH. To identify candidate repressors we developed a novel transcription factor array (TF array) assay, in which disruptions of 287 genes encoding regulatory proteins were independently transformed into a strain carrying rapH-lacZ and the resultant transformants were grown on agar plates containing Xgal to detect beta-galactosidase activity. We identified a yvaN disruptant which showed a rapH-overproducing phenotype. DNA microarray analysis of the yvaN mutant suggested that both rapG and rapH were overproduced, leading to inhibition of srfA expression. In a gel retardation assay, purified His-tagged YvaN specifically bound to promoter sequences of rapG and rapH. Further footprint and gel retardation analyses using various deleted probes uncovered critical sequences for YvaN binding. In addition, a lacZ fusion analysis confirmed the significance of YvaN binding for transcription regulation of rapG and rapH. Thus, YvaN was renamed RghR (rapG and rapH repressor). As the rapH gene is activated by ComK and RapH inhibits comK indirectly, this constitutes an autoregulatory loop modulated by RghR.

Bacillus subtilis↗

PubMed2005

The H2O2 stress-responsive regulator PerR positively regulates srfA expression in Bacillus subtilis.

srfA is an operon required for the synthesis of surfactin and the development of genetic competence in Bacillus subtilis. We observed that the expression of srfA is downregulated upon treatment with H2O2. Thus, we examined the involvement of several oxidative stress-responsive transcription factors in srfA expression. Our DNA microarray analysis revealed that the H2O2 stress-responsive regulator PerR is required for srfA expression. This was confirmed by lacZ fusion analysis. A ComX feeding assay and epistatic analyses revealed that the role of PerR in srfA expression is independent of other known regulators of srfA expression, namely, comQXP, rapC, and spx. Gel mobility shift and footprint assays revealed that PerR binds directly to two tandemly arranged noncanonical PerR boxes located in the upstream promoter region of srfA. A transcriptional srfA-lacZ fusion lacking both PerR boxes showed diminished and PerR-independent expression, indicating that the PerR boxes we identified function as positive cis elements for srfA transcription.

Bacillus subtilis↗

PubMed2004

Mutational analysis of the helix-turn-helix region of Bacillus subtilis response regulator DegU, and identification of cis-acting sequences for DegU in the aprE and comK promoters.

The DegS-DegU two-component system in Bacillus subtilis regulates exoprotease production and competence development. Phosphorylated and unphosphorylated forms of DegU are required for activation of aprE and comK, respectively. Alanine-scanning mutagenesis of the helix-turn-helix region of DegU and in vivo examination of 27 DegU variants revealed five common mutants that showed severe reduction of gene expression of both aprE and comK because of reduced DNA-binding activity. This observation suggested that the DegU-recognized cis-sequences might not be considerably changed for either promoter. We identified a DegU-recognized inverted repeat in the comK promoter using various mutant comK-lacZ fusions. Inspection of the aprE promoter sequence revealed a tandem repeat consisting of short AT-rich sequences containing a consensus one, 5'-TAAAT-3', which was found in the downstream half of the inverted repeat involved in comK activation. Oligonucleotide-directed replacement of the short AT-rich sequences located in the center of each motif decreased DegU-dependent aprE expression, implying that the repeat is required for the activation of aprE. Based on these results, it was concluded that DegU would function through the inverted repeat in the comK promoter and the tandem repeat in the aprE promoter.

Alanine↗

PubMed2004

Bacillus subtilis SalA (YbaL) negatively regulates expression of scoC, which encodes the repressor for the alkaline exoprotease gene, aprE.

During the course of screening for exoprotease-deficient mutants among Bacillus subtilis gene disruptants, a strain showing such a phenotype was identified. The locus responsible for this phenotype was the previously unknown gene ybaL, which we renamed salA. The predicted gene product encoded by salA belongs to the Mrp family, which is widely conserved among archaea, prokaryotes, and eukaryotes. Disruption of salA resulted in a decrease in the expression of a lacZ fusion of the aprE gene encoding the major extracellular alkaline protease. The decrease was recovered by the cloned salA gene on a plasmid, demonstrating that the gene is involved in aprE expression. Determination of the cis-acting region of SalA on the upstream region of aprE, together with epistatic analyses with scoC, abrB, and spo0A mutations that also affect aprE expression, suggested that salA deficiency affects aprE-lacZ expression through the negative regulator ScoC. Northern and reverse transcription-PCR analyses revealed enhanced levels of scoC transcripts in the salA mutant cells in the transition and early stationary phases. Concomitant with these observations, larger amounts of the ScoC protein were detected in the mutant cells by Western analysis. From these results we conclude that SalA negatively regulates scoC expression. It was also found that the expression of a salA-lacZ fusion was increased by salA deficiency, suggesting that salA is autoregulated.

Amino Acid Sequence↗

PubMed2003

Binding of response regulator DegU to the aprE promoter is inhibited by RapG, which is counteracted by extracellular PhrG in Bacillus subtilis.

We screened the putative rap-phr (response regulator aspartyl-phosphate phosphatase-phosphatase regulator) systems identified in the Bacillus subtilis genome for a rap gene that affects aprE (alkaline protease gene) expression by using a multicopy plasmid. We found that rapG was involved in the regulation of aprE, which belongs to the regulon of DegU, the response regulator of the DegS-DegU two-component system. Disruption of rapG and phrG resulted in enhancement and reduction of aprE-lacZ expression, respectively, suggesting that PhrG inhibits RapG activity. Addition of 1-30 nM of a synthetic pentapeptide (PhrG; NH2-EKMIG-COOH) to the phrG disruptant completely rescued aprE-lacZ expression, indicating that the PhrG peptide is indeed involved in aprE-lacZ expression. Surprisingly, either introduction of multicopy phrG or addition of the PhrG peptide at high concentrations (100-300 nM) to the phrG cells decreased aprE-lacZ expression. These results are reminiscent of the previous observation that at higher concentrations the PhrC peptide inhibits srfA-lacZ expression directed by ComA, the regulator of the ComP-ComA two-component system. Because the Rap proteins belong to a family of aspartyl protein phosphatases, we tried to investigate the possible influence of RapG on dephosphorylation of DegU-P (phosphorylated DegU) in vitro. RapG, however, did not affect dephosphorylation of DegU-P under the adopted experimental conditions. Therefore, we hypothesized that RapG might inhibit the binding activity of DegU to the target promoters. We analysed the interaction of DegU and RapG using the aprE promoter and another target, a comK promoter. Gel shift analysis revealed that RapG served as the inhibitor of DegU binding to the promoter regions of aprE and comK and that this inhibition was counteracted by the PhrG peptide.

Artificial Gene Fusion↗

PubMed2003

Involvement of ClpX protein in the post-transcriptional regulation of a competence specific transcription factor, ComK protein, of Bacillus subtilis.

ComK protein of Bacillus subtilis positively regulates the transcription of several late competence genes as well as comK itself. We constructed a clpX disrupted mutant of B. subtilis and studied its effect on the regulation of ComK activation. When Pspac, which controls the comK gene in a multicopy plasmid, was induced by the addition of IPTG, comK transcripts were detected in both the clpX mutant and the wild type. However, the ComK protein could not be detected in the clpX disrupted mutant. To obtain further information, we constructed several comK-lacZ translational fusions covering different lengths of the comK gene, whose transcription is controlled by an IPTG inducible Pspac promoter. We found that both the expression of comK-lacZ directed beta-galactosidase and the accumulation of ComK-LacZ fused protein, derived from the fusion containing the entire comK open reading frame, were extremely reduced in the clpX mutant compared with the wild type, while the accumulation of comK-lacZ transcripts in the clpX mutant after the addition of IPTG was about half that in the clpX+ background. On the other hand, transcription, translation and activity of comK-lacZ were detected in both the clpX mutant and the wild type when the comK-lacZ fusion lacking the 3' region of the comK gene was induced. These results indicate that ClpX plays an important role in the regulation of ComK at the post-transcriptional level.

ATPases Associated with Diverse Cellular Activitie↗

PubMed2003

Inhibition of Bacillus subtilis aprE expression by lincomycin at the posttranscriptional level through inhibition of ppGpp synthesis.

Expression of the Bacillus subtilis alkaline protease gene aprE is controlled by many positive and negative regulators at the transcriptional level. During the course of screening for organic compounds that affect the expression of a translational aprE'-'lacZ fusion, we found that lincomycin (Lm), erythromycin and chloramphenicol exhibited an inhibitory effect in concentrations that hardly affected cell growth. The antibiotics are known to inhibit protein synthesis by binding to ribosomes. We chose one of them, Lm, for further study. We have previously shown that aprE expression requires guanosine 3',5'-bisdiphosphate (ppGpp) synthesized on the ribosome by the stringent factor RelA. An examination of Lm-treated cells showed that the levels of ppGpp were greatly reduced in these cells, and the inhibitory effect of the antibiotic was not seen in relA-disruption mutants. Transcriptional levels of aprE, however, were not influenced by Lm treatment as shown by using a transcriptional aprE-lacZ fusion as well as quantitative RT-PCR. Furthermore, disruption of relA did not affect the expression of transcriptional aprE-lacZ. From these results, we conclude that aprE expression is controlled by the stringent control at the posttranscriptional level, and that Lm inhibits this process by inhibiting ppGpp synthesis on the ribosome.

Anti-Bacterial Agents↗

PubMed2002

Recent progress in Bacillus subtilis two-component regulation.

Two-component regulatory systems serve to control gene expression in response to environmental and physiological changes. They are widespread among a variety of organisms and most often found in prokaryotes. One of the gram-positive microorganisms Bacillus subtilis is a well-studied bacterium whose complete nucleotide sequence has been determined. Thus, it is now possible to study transcription of the whole genome with microarray analysis. In this review we summarize the recent progress in B. subtilis two-component regulatory systems by describing the known systems and those for which the function was recently assigned. Also included is an attempt to construct a partial transcriptional network involving several two-component systems. The studies described here are based on the data from traditional genetics and biochemistry, and from microarray analysis of 29 two-component systems.

Bacillus subtilis↗

PubMed2002

Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK.

The Bacillus subtilis competence transcription factor ComK is required for establishment of competence for genetic transformation. In an attempt to study the ComK factor further, we explored the genes regulated by ComK using the DNA microarray technique. In addition to the genes known to be dependent on ComK for expression, we found many genes or operons whose ComK dependence was not known previously. Among these genes, we confirmed the ComK dependence of 16 genes by using lacZ fusions, and three genes were partially dependent on ComK. Transformation efficiency was significantly reduced in an smf disruption mutant, although disruption of the other ComK-dependent genes did not result in significant decreases in transformation efficiency. Nucleotide sequences similar to that of the ComK box were found for most of the newly discovered genes regulated by ComK.

Bacillus subtilis↗

PubMed2002

Med, a cell-surface localized protein regulating a competence transcription factor gene, comK, in Bacillus subtilis.

Med was found as a positive regulator for comK, a master regulator for late competence genes. It was found by Western analysis that the ComK level was decreased in a med mutant. Experiments using an alkaline phosphatase fusion with Med and Western analysis of Med were done because a putative lipo-modification signal is found at the N-terminus of Med. The results obtained are consistent with the localization of Med at the cell surface. An implication of the cell-surface localization of Med is discussed in terms of comK regulation.

Amino Acid Sequence↗