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Parini C, Guglielmetti S, Mora D, Ricci G. Complete sequence and structural organization of pFL5 and pFL7, two cryptic plasmids from Bacillus licheniformis. Plasmid 2004; 51:192-202. [PMID: 15109826 DOI: 10.1016/j.plasmid.2004.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 02/09/2004] [Indexed: 10/26/2022]
Abstract
The complete nucleotide sequences of two plasmids, pFL5 and pFL7, isolated from soil bacteria, Bacillus licheniformis FL5 and FL7, have been determined. The plasmids pFL5 and pFL7 were analyzed and found to be 9150 and 7853 bp in size with a G+C content of 41.0 and 43.6 mol%, respectively. Computer assisted analysis of sequence data revealed 11 possible ORFs in pFL5, four of which could be assigned no function from homology searches. Instead, eight putative ORFs were identified in pFL7, two of which appeared to have no biological function. All the ORFs were preceded by a ribosome binding site. The ORFs 9.5 and 6.7, each of 340 amino acids, were postulated to encode a replication protein similar to known replication proteins of rolling circle replicons, particularly those of the pC194 family. The structural organization of the two pFL plasmids is similar to the pTA plasmids family, with only a few putative coding regions that cannot be attributed to these plasmid backbone genes. In contrast to pTA plasmids, the majority of the genes have an orientation of transcription opposite to the direction of replication. The identified probable sso sequences seem to belong to a different group of those found in Bacillus plasmids; in fact, a significant level of homology was found with ssoA group sequences. These plasmids seem to be related to plasmids identified within the Bacillus subtilis group, confirming the low-level diversity among these replicons.
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Affiliation(s)
- C Parini
- Department of Food Science and Microbiology, University of Milan, Via Celoria 2, 20133, Italy.
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52
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Zhang S, Haldenwang WG. RelA is a component of the nutritional stress activation pathway of the Bacillus subtilis transcription factor sigma B. J Bacteriol 2003; 185:5714-21. [PMID: 13129942 PMCID: PMC193951 DOI: 10.1128/jb.185.19.5714-5721.2003] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The general stress regulon of Bacillus subtilis is induced by the activation of the sigma(B) transcription factor. Activation of sigma(B) occurs when one of two phosphatases (RsbU and RsbP), each responding to a unique type of stress, actuates a positive regulator of sigma(B) by dephosphorylation. Nutritional stress triggers the RsbP phosphatase. The mechanism by which RsbP becomes active is unknown; however, its activation coincides with culture conditions that are likely to reduce the cell's levels of high-energy nucleotides. We now present evidence that RelA, a (p)ppGpp synthetase and the key enzyme of the stringent response, plays a role in nutritional stress activation of sigma(B). An insertion mutation that disrupts relA blocks the activation of sigma(B) in response to PO(4) or glucose limitation and inhibits the drop in ATP/GTP levels that normally accompanies sigma(B) induction under these conditions. In contrast, the activation of sigma(B) by physical stress (e.g., ethanol treatment) is not affected by the loss of RelA. RelA's role in sigma(B) activation appears to be distinct from its participation in the stringent response. Amino acid analogs which induce the stringent response and RelA-dependent (p)ppGpp synthesis do not trigger sigma(B) activity. In addition, neither a missense mutation in relA (relA240GE) nor a null mutation in rplK (rplK54), either of which is sufficient to inhibit the stringent response and RelA-dependent (p)ppGpp synthesis, fails to block sigma(B) activation by PO(4) or glucose limitation.
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Affiliation(s)
- Shuyu Zhang
- Department of Microbiology and Immunology, University of Texas Health Science Center, San Antonio, Texas 78229-3900, USA
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53
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Core L, Perego M. TPR-mediated interaction of RapC with ComA inhibits response regulator-DNA binding for competence development in Bacillus subtilis. Mol Microbiol 2003; 49:1509-22. [PMID: 12950917 DOI: 10.1046/j.1365-2958.2003.03659.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Bacillus subtilis Rap family of proteins are characterized by protein-protein interaction modules containing the so-called tetratricopeptide repeats (TPRs). The six TPR motifs of RapC mediate its interaction with the pentapeptide inhibitor PhrC (ERGMT) or with its target protein ComA, a phosphorylation-dependent response regulator transcription factor for genetic competence. Our results show that RapC interaction with ComA inhibits the response regulator's ability to bind its target DNA promoter but does not affect its phosphorylation state. RapC binds equally well to ComA or to ComA approximately P. The PhrC pentapeptide binds to RapC and inhibits its interaction with ComA. The D195 residue in TPR3 and the P263 residue in TPR5 of RapC are critical for the interaction with PhrC as their mutation to asparagine or leucine, respectively, prevents peptide inhibitory activity. The RapC mechanism of regulating ComA activity is a new example of how TPR motifs and their structural organization have been adapted for different specific functions within the B. subtilis Rap family.
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Affiliation(s)
- Leighton Core
- Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM-116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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54
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Stephenson S, Mueller C, Jiang M, Perego M. Molecular analysis of Phr peptide processing in Bacillus subtilis. J Bacteriol 2003; 185:4861-71. [PMID: 12897006 PMCID: PMC166482 DOI: 10.1128/jb.185.16.4861-4871.2003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Bacillus subtilis, an export-import pathway regulates production of the Phr pentapeptide inhibitors of Rap proteins. Processing of the Phr precursor proteins into the active pentapeptide form is a key event in the initiation of sporulation and competence development. The PhrA (ARNQT) and PhrE (SRNVT) peptides inhibit the RapA and RapE phosphatases, respectively, whose activity is directed toward the Spo0F approximately P intermediate response regulator of the sporulation phosphorelay. The PhrC (ERGMT) peptide inhibits the RapC protein acting on the ComA response regulator for competence with regard to DNA transformation. The structural organization of PhrA, PhrE, and PhrC suggested a role for type I signal peptidases in the processing of the Phr preinhibitor, encoded by the phr genes, into the proinhibitor form. The proinhibitor was then postulated to be cleaved to the active pentapeptide inhibitor by an additional enzyme. In this report, we provide evidence that Phr preinhibitor proteins are subject to only one processing event at the peptide bond on the amino-terminal end of the pentapeptide. This processing event is most likely independent of type I signal peptidase activity. In vivo and in vitro analyses indicate that none of the five signal peptidases of B. subtilis (SipS, SipT, SipU, SipV, and SipW) are indispensable for Phr processing. However, we show that SipV and SipT have a previously undescribed role in sporulation, competence, and cell growth.
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Affiliation(s)
- Sophie Stephenson
- Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
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55
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Rosen R, Ron EZ. Proteome analysis in the study of the bacterial heat-shock response. MASS SPECTROMETRY REVIEWS 2002; 21:244-265. [PMID: 12533799 DOI: 10.1002/mas.10031] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In recent years, it has become clear that, in addition to the regulation of the expression of specific genes, there are global regulatory systems that control the simultaneous expression of a large number of genes in response to a variety of environmental stresses. The first of these global control systems, and of substantial importance, is the heat-shock response. The heat-shock response is characterized by the induction of a large set of proteins (heat-shock proteins-HSPs) upon shifts to higher temperature and upon exposure to conditions in which proteins are denatured (i.e., alcohols, heavy metals). The heat-shock response is universal and many of the heat-shock proteins are highly conserved among species. In bacteria, the heat-shock response has been studied extensively in several Gram-positive bacteria (Bacillus subtilis) and in the Gram-negative bacteria (i.e., Escherichia coli, Agrobacterium tumefaciens). The first recognition of the molecular abundance of the bacterial heat-shock proteins took place with the introduction of high-resolution two-dimensional polyacrylamide gels (2D gels) to analyze complex mixtures of cellular proteins. Two-dimensional gels, followed by mass spectrometry, were used to define the heat-shock stimulons in several bacteria, and to study the regulatory elements that control the heat-shock response. Here, we review the heat-shock response and its regulation in bacteria. The review will emphasize the use of proteome analysis in the study of this response, and will point out those open questions that can be investigated with proteomics, including mass spectrometry techniques.
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Affiliation(s)
- Ran Rosen
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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56
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Abstract
AIMS The pathogen Bacillus cereus, which is associated with a number of foods including dairy products, was studied for its response to acid stress during the exponential phase. METHODS AND RESULTS Bacillus cereus was found to adapt to acid stress (pH 4.6) when pre-exposed to a non-lethal, inducing pH of 6.3 or to inducing concentrations of heat, ethanol, salt or hydrogen peroxide. Cells were found to maintain their internal pH at a higher level than the external acid pH and adapted cells had a higher internal pH than unadapted cells. A constitutive acid-sensitive mutant that was also heat- and ethanol-sensitive was found to be capable of high levels of adaptation despite its lack of induction of proteins induced in the wild type by exposure to moderate pH (6.3) values. CONCLUSIONS A number of proteins were found to be underexpressed in the mutant compared with the wild type at pH 6.3, including some with homology to ribosomal proteins and to the sporulation regulator RapK, while one differentially expressed band contained two proteins, one of which was homologous to the competence regulator CodY. SIGNIFICANCE AND IMPACT OF THE STUDY The work has implications for the processing of B. cereus-associated foods by acidification. The linked developmental processes of stationary phase, sporulation and possibly competence appear to be involved in the response to acid stress.
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Affiliation(s)
- N Browne
- Department of Biology and Institute of Bioengineering and Agroecology, National University of Ireland, Maynooth, Co. Kildare, Ireland
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57
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Ishikawa S, Core L, Perego M. Biochemical characterization of aspartyl phosphate phosphatase interaction with a phosphorylated response regulator and its inhibition by a pentapeptide. J Biol Chem 2002; 277:20483-9. [PMID: 11923303 DOI: 10.1074/jbc.m201086200] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RapA and RapB proteins are aspartyl phosphate phosphatases that specifically dephosphorylate the Spo0F approximately P intermediate response regulator of the phosphorelay signal transduction system for sporulation initiation in Bacillus subtilis. The approximately 48-kDa His-tag derivative proteins were purified by metal affinity chromatography, and their molecular and biochemical characteristics were studied. RapA and RapB were found to be dimers in solution. Enzymatic activity was strongly dependent upon maintaining reducing conditions during purification and storage. RapA phosphatase activity on Spo0F approximately P is inhibited in vivo by a pentapeptide generated from the phrA gene. Native gel assays demonstrated that the RapA dimer forms a stable complex with two molecules of Spo0F approximately P or with its PhrA pentapeptide inhibitor. The pentapeptide was shown to displace Spo0F approximately P from a preformed complex with RapA. The structural organization of Rap phosphatases in tetratricopeptide repeats provides insights on the mechanisms of RapA interaction with its substrate and its inhibitor.
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Affiliation(s)
- Shu Ishikawa
- Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
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58
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Dixon LG, Spiegelman GB. Glucose-resistant sporulation in Bacillus subtilis crsA47 mutants does not depend on promoter switching at the spo0A gene. J Bacteriol 2002; 184:1458-61. [PMID: 11844779 PMCID: PMC134852 DOI: 10.1128/jb.184.5.1458-1461.2002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2001] [Accepted: 11/30/2001] [Indexed: 11/20/2022] Open
Abstract
We have found that sporulation in Bacillus subtilis crsA47 mutants does not require the sigma(H)-dependent promoter of the spo0A gene. This implies that the glucose-resistant sporulation phenotype of this strain is not related to the switch from the vegetative-stage sigma(A)-dependent promoter to the sigma(H)-dependent promoter at the spo0A gene.
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Affiliation(s)
- Laurie G Dixon
- Department of Microbiology and Immunology, University of British Columbia, 6174 University Blvd., Vancouver, British Columbia, Canada V6T 1Z3
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59
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Kanamaru K, Stephenson S, Perego M. Overexpression of the PepF oligopeptidase inhibits sporulation initiation in Bacillus subtilis. J Bacteriol 2002; 184:43-50. [PMID: 11741842 PMCID: PMC134765 DOI: 10.1128/jb.184.1.43-50.2002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The yjbG gene encoding the homologue of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis (Monnet et al., J. Biol. Chem. 269:32070-32076, 1994; Nardi et al., J. Bacteriol. 179:4164-4171, 1997) has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when present in the cells on a multicopy plasmid. Genetic analysis suggested that the inhibitory effect is due to hydrolysis of the PhrA peptide in a form as small as the pentapeptide (ARNQT). Inactivation of PhrA results in deregulation of the RapA phosphatase and thus dephosphorylation of the Spo0F approximately P response regulator component of the phosphorelay for sporulation initiation. When overexpressed, the B. subtilis PepF is most likely hydrolyzing additional peptides of the Phr family, as is the case for PhrC involved in control of competence development. Chromosomal inactivation of the yjbG/pepF gene did not give rise to any detectable phenotype. The function of PepF in B. subtilis remains unknown. Limited experiments with a yjbG paralogue called yusX indicated that a frameshift is present, making the corresponding gene product inactive.
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Affiliation(s)
- Kyoko Kanamaru
- Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
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60
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Kim HJ, Jourlin-Castelli C, Kim SI, Sonenshein AL. Regulation of the bacillus subtilis ccpC gene by ccpA and ccpC. Mol Microbiol 2002; 43:399-410. [PMID: 11985717 DOI: 10.1046/j.1365-2958.2002.02751.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacillus subtilis CcpC, a LysR-type transcriptional regulator, represses the transcription of genes for citrate synthase (citZ) and aconitase (citB) in response to citrate availability. Transcription of ccpC was shown to initiate at two promoters, P1, located just upstream of the ccpC gene, and P2, located within or upstream of the neighbouring ykuL gene. Expression from the ccpC-specific promoter (P1) was negatively regulated by CcpC but independent of the carbon source in the medium. Gel shift and DNase I footprinting experiments revealed that CcpC binds to an interrupted dyad sequence that surrounds the ccpC transcriptional start point. Transcription of ccpC from the upstream promoter (P2) was repressed by glucose in a CcpA-dependent manner. A putative CcpA binding site (cre) was identified upstream of the -35 region of the P1 promoter. Transcriptional fusion studies demonstrated that glucose repression of ccpC expression from the P2 promoter depends on this cre site. In addition, DNase I footprinting experiments showed that CcpA specifically binds to this cre site and that the introduction of mutations (cre*) into this site abolished the binding. These results suggest that CcpA may control CcpC synthesis by acting as a road-block to readthrough transcription from the P2 promoter.
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Affiliation(s)
- Hyun-Jin Kim
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
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61
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Abstract
One of the strongest and most noticeable responses of a Bacillus subtilis cell to a range of stress and starvation conditions is the dramatic induction of a large number of general stress proteins. The alternative sigma factor sigma B is responsible for the induction of the genes encoding these general stress proteins that occurs following heat, ethanol, salt or acid stress, or during energy depletion. sigma B was detected more than 20 years ago by Richard Losick and William Haldenwang as the first alternative sigma factor of bacteria, but interest in sigma B declined after it was realized that sigma B is not involved in sporulation. It later turned out that sigma B, whose activity itself is tightly controlled, is absolutely required for the induction of this regulon, not only in B. subtilis, but also in other Gram-positive bacteria. These findings may have been responsible for the recent revival of interest in sigma B. This chapter summarizes the current information on this sigma B response including the latest results on the signal transduction pathways, the structure of the regulon and its physiological role. More than 150 general stress proteins/genes belong to this sigma B regulon, which is believed to provide the non-growing cell with a non-specific, multiple and preventive stress resistance. sigma B-dependent stress proteins are involved in non-specific protection against oxidative stress and also protect cells against heat, acid, alkaline or osmotic stress. A cell in the transition from a growing to a non-growing state induced by energy depletion will be equipped with a comprehensive stress resistance machine to protect it against future stress. The protection against oxidative stress may be an essential part of this response. In addition, preloading of cells with sigma B-dependent stress proteins, induced by mild heat or salt stress, will protect cells against a severe, potentially lethal, future stress. Both the specific protection against an acute emerging stress, as well as the non-specific, prospective protection against future stress, are adaptive functions crucial for surviving stress and starvation in nature. We suggest that the sigma B response is one essential component of a survival strategy that ensures survival in a quiescent, vegetative state as an alternative to sporulation. The role of sigma B in related Gram-positive bacteria (including cyanobacteria) with special emphasis on pathogenic bacteria is discussed.
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Affiliation(s)
- M Hecker
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Mikrobiologie, Friedrich-Ludwig-Jahn-Strasse 15, D-17487 Greifswald, Germany
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62
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Core LJ, Ishikawa S, Perego M. A free terminal carboxylate group is required for PhrA pentapeptide inhibition of RapA phosphatase. Peptides 2001; 22:1549-53. [PMID: 11587784 DOI: 10.1016/s0196-9781(01)00491-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In the Bacillus subtilis phosphorelay signal transduction system for sporulation initiation, signals competing with the differentiation process are interpreted by aspartyl-phosphate phosphatases that specifically dephosphorylate the Spo0F or Spo0A response regulators. The RapA phosphatase is regulated by the PhrA pentapeptide that directly and specifically inhibits its activity. PhrA specificity for RapA inhibition is dependent upon the amino acid sequence of the peptide. Here we show that the pentapeptide affinity for the phosphatase requires a free carboxylate group at the C-terminal amino acid. A free C-terminal carboxylic acid PhrA pentapeptide inhibits RapA phosphatase activity at a 1:1 ratio and it is approximately 200 fold more active than a C-terminal amide peptide. Therefore, coordination of the terminal carboxylate group appears to be critical for peptide binding to RapA.
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Affiliation(s)
- L J Core
- Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM-116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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63
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Perego M. A new family of aspartyl phosphate phosphatases targeting the sporulation transcription factor Spo0A of Bacillus subtilis. Mol Microbiol 2001; 42:133-43. [PMID: 11679073 DOI: 10.1046/j.1365-2958.2001.02611.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The initiation of the sporulation developmental pathway in Bacillus subtilis is controlled by the phospho-relay, a multicomponent signal transduction system. Multiple positive and negative signals are integrated by the phosphorelay through the opposing activities of histidine protein kinases and aspartyl phosphate phosphatases. Three members of the Rap family of phosphatases (RapA, RapB and RapE) specifically dephosphorylate the Spo0F approximately P response regulator intermediate, while the Spo0A approximately P transcription factor is specifically dephosphorylated by the Spo0E phosphatase and, as shown here, the newly identified YnzD and YisI proteins. The products of the YnzD and YisI genes are highly homologous to Spo0E and define a new family of phosphatases with a distinct signature motif in their amino acid sequence. As negative regulators of the developmental pathway, YnzD and YisI inhibit spore formation if over-expressed, while a chromosomal deletion of their coding sequences results in increased sporulation frequency. Transcription of the ynzD, yisI and spo0E genes is differentially regulated and generally induced by growth conditions antithetical to sporulation. Negative signals interpreted by aspartyl phosphate phosphatases appear to be a common mechanism in Gram-positive spore-forming microorganisms.
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Affiliation(s)
- M Perego
- Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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64
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Abstract
Aspartyl-phosphate phosphatases are integral components of the phosphorelay signal transduction system for sporulation initiation in Bacillus subtilis. The Rap and Spo0E families of protein phosphatases specifically dephosphorylate the sporulation response regulators Spo0F and Spo0A, respectively. The phosphatases interpret regulatory signals antithetical to sporulation and the Rap phosphatases are subject to inactivation by specific pentapeptides generated from an inactive peptide precursor. Additional regulatory signals are brought about by the complex activation circuit that generates the Phr pentapeptide inhibitors of Rap phosphatases. Phr peptide's recognition of the Rap phosphatase targets is remarkably specific. Specificity is dictated by the amino acid sequence of the pentapeptide. The identification of tetratricopeptide repeats in the Rap proteins may explain the mechanism by which Phr peptides bind to and inhibit the activity of Rap phosphatases.
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Affiliation(s)
- M Perego
- Division of Cellular Biology, Department of Molecular and Experimental Medicine, MEM-116, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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65
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Jarmer H, Larsen TS, Krogh A, Saxild HH, Brunak S, Knudsen S. Sigma A recognition sites in the Bacillus subtilis genome. MICROBIOLOGY (READING, ENGLAND) 2001; 147:2417-2424. [PMID: 11535782 DOI: 10.1099/00221287-147-9-2417] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A hidden Markov model of sigma(A) RNA polymerase cofactor recognition sites in Bacillus subtilis, containing either the common or the extended -10 motifs, has been constructed based on experimentally verified sigma(A) recognition sites. This work suggests that more information exists at the initiation site of transcription in both types of promoters than previously thought. When tested on the entire B. subtilis genome, the model predicts that approximately half of the sigma(A) recognition sites are of the extended type. Some of the response-regulator aspartate phosphatases were among the predictions of promoters containing extended sites. The expression of rapA and rapB was confirmed by site-directed mutagenesis to depend on the extended -10 region.
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Affiliation(s)
- Hanne Jarmer
- Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Thomas S Larsen
- Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Anders Krogh
- Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Hans Henrik Saxild
- Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Steen Knudsen
- Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark
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66
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Belitsky BR, Brill J, Bremer E, Sonenshein AL. Multiple genes for the last step of proline biosynthesis in Bacillus subtilis. J Bacteriol 2001; 183:4389-92. [PMID: 11418582 PMCID: PMC95331 DOI: 10.1128/jb.183.14.4389-4392.2001] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2001] [Accepted: 04/25/2001] [Indexed: 11/20/2022] Open
Abstract
The complete Bacillus subtilis genome contains four genes (proG, proH, proI, and comER) with the potential to encode Delta(1)-pyrroline-5-carboxylate reductase, a proline biosynthetic enzyme. Simultaneous defects in three of these genes (proG, proH, and proI) were required to confer proline auxotrophy, indicating that the products of these genes are mostly interchangeable with respect to the last step in proline biosynthesis.
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Affiliation(s)
- B R Belitsky
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.
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67
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Ratnayake-Lecamwasam M, Serror P, Wong KW, Sonenshein AL. Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels. Genes Dev 2001; 15:1093-103. [PMID: 11331605 PMCID: PMC312684 DOI: 10.1101/gad.874201] [Citation(s) in RCA: 278] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
CodY, a highly conserved protein in the low G + C, gram-positive bacteria, regulates the expression of many Bacillus subtilis genes that are induced as cells make the transition from rapid exponential growth to stationary phase and sporulation. This transition has been associated with a transient drop in the intracellular pool of GTP. Many stationary-phase genes are also induced during exponential-growth phase by treatment of cells with decoyinine, a GMP synthetase inhibitor. The effect of decoyinine on an early-stationary-phase gene is shown here to be mediated through CodY and to reflect a reduction in guanine nucleotide accumulation. CodY proved to bind GTP in vitro. Moreover, CodY-mediated repression of target promoters was dependent on a high concentration of GTP, comparable to that found in rapidly growing exponential-phase cells. Because a codY-null mutant was able to sporulate under conditions of nutrient excess, CodY also appears to be a critical factor that normally prevents sporulation under such conditions. Thus, B. subtilis CodY is a novel GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional conditions and regulates the transcription of early-stationary-phase and sporulation genes, allowing the cell to adapt to nutrient limitation.
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Affiliation(s)
- M Ratnayake-Lecamwasam
- Tufts University School of Medicine, Department of Molecular Biology and Microbiology, Boston, Massachusetts 02111, USA
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68
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Reizer J, Reizer A, Perego M, Saier MH. Characterization of a family of bacterial response regulator aspartyl-phosphate (RAP) phosphatases. MICROBIAL & COMPARATIVE GENOMICS 2001; 2:103-11. [PMID: 9689219 DOI: 10.1089/omi.1.1997.2.103] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We have characterized a novel family of response regulator aspartyl-phosphate (RAP) phosphatases found exclusively in gram-positive bacteria. The family consists of 15 members, 12 of which are from Bacillus subtilis. The N-terminal domains proved to be more highly conserved than the C-terminal domains, and a signature sequence for the family was derived from the former domains. Phylogenetic analyses revealed clustering patterns showing that all Bacillus proteins are closely related. Most of the Bacillus RAP phosphatase genes are followed by and are translationally coupled to small nonhomologous phosphatase regulator (phr) genes that encode exported peptides with regulatory functions. Most of the paralogous RAP phosphatases of B. subtilis may serve related functions in signal transduction systems. They appear to have arisen by relatively recent gene duplication events that occurred after the divergence of major groups within the gram-positive bacterial kingdom. We suggest that the N-terminal domains of the RAP phosphatases function in catalysis, whereas the C-terminal domains function in regulation.
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Affiliation(s)
- J Reizer
- Department of Biology, University of California at San Diego, La Jolla, USA
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69
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Tran LS, Nagai T, Itoh Y. Divergent structure of the ComQXPA quorum-sensing components: molecular basis of strain-specific communication mechanism in Bacillus subtilis. Mol Microbiol 2000; 37:1159-71. [PMID: 10972833 DOI: 10.1046/j.1365-2958.2000.02069.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Bacillus subtilis, the ComQXPA quorum-sensing system controls cell density-dependent phenotypes such as the production of degradative enzymes and antibiotics and the development of genetic competence. Bacillus subtilis (natto) NAF12, a mutant defective in poly-gamma-glutamate (gamma-PGA) production, was derived from B. subtilis (natto) NAF4 by Tn917-LTV1 insertional mutagenesis. Determination of the mutant DNA sequences flanking the Tn917-LTV1 insert revealed that the insertion had inactivated comP in this mutant, indicating that gamma-PGA synthesis in B. subtilis (natto) is under the control of the ComP-ComA signal transduction system. A comparison of the amino acid sequences revealed striking variation in the primary structures of ComQ (44% identity), ComX (26%) and the sensor domain of ComP (36%) between B. subtilis (natto) NAF4 and B. subtilis 168. In contrast, the amino acid and nucleotide sequences of the kinase domains of ComP and of the ComA response regulator share 95% and 100% identity respectively. The comP genes of NAF4 and 168 restored the impaired competence of B. subtilis BD1658 (comP:cat) and gamma-PGA production of B. subtilis (natto) NAF12 (comP:Tn917-LTV1) to only 15% of the level achieved by the respective parent comP genes. However, when introduced together with the cognate comQ and comX genes, the comP genes restored the relevant defect of the heterologous comP mutants nearly to wild-type levels. Analogous to the comCDE system of Streptococcus strains and the agrBCDE system of Staphylococcus aureus, the concerted variation in the comQXP genes appears to establish specific intercellular communication between B. subtilis strains sharing the same pheromone system.
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Affiliation(s)
- L S Tran
- Division of Applied Microbiology, National Food Research Institute, Ministry of Agriculture, Forestry and Fisheries, Kannondai 2-1-2, Tsukuba 305-8642, Japan
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70
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Fouet A, Namy O, Lambert G. Characterization of the operon encoding the alternative sigma(B) factor from Bacillus anthracis and its role in virulence. J Bacteriol 2000; 182:5036-45. [PMID: 10960085 PMCID: PMC94649 DOI: 10.1128/jb.182.18.5036-5045.2000] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2000] [Accepted: 06/19/2000] [Indexed: 11/20/2022] Open
Abstract
The operon encoding the general stress transcription factor sigma(B) and two proteins of its regulatory network, RsbV and RsbW, was cloned from the gram-positive bacterium Bacillus anthracis by PCR amplification of chromosomal DNA with degenerate primers, by inverse PCR, and by direct cloning. The gene cluster was very similar to the Bacillus subtilis sigB operon both in the primary sequences of the gene products and in the order of its three genes. However, the deduced products of sequences upstream and downstream from this operon showed no similarity to other proteins encoded by the B. subtilis sigB operon. Therefore, the B. anthracis sigB operon contains three genes rather than eight as in B. subtilis. The B. anthracis operon is preceded by a sigma(B)-like promoter sequence, the expression of which depends on an intact sigma(B) transcription factor in B. subtilis. It is followed by another open reading frame that is also preceded by a promoter sequence similarly dependent on B. subtilis sigma(B). We found that in B. anthracis, both these promoters were induced during the stationary phase and induction required an intact sigB gene. The sigB operon was induced by heat shock. Mutants from which sigB was deleted were constructed in a toxinogenic and a plasmidless strain. These mutants differed from the parental strains in terms of morphology. The toxinogenic sigB mutant strain was also less virulent than the parental strain in the mouse model. B. anthracis sigma(B) may therefore be a minor virulence factor.
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Affiliation(s)
- A Fouet
- Toxines et Pathogénie Bactériennes (URA 1858, CNRS), Institut Pasteur, Paris, France.
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71
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Shin BS, Choi SK, Smith I, Park SH. Analysis of tnrA alleles which result in a glucose-resistant sporulation phenotype in Bacillus subtilis. J Bacteriol 2000; 182:5009-12. [PMID: 10940050 PMCID: PMC111386 DOI: 10.1128/jb.182.17.5009-5012.2000] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis cells cannot sporulate in the presence of catabolites such as glucose. During the analysis of Tn10-generated mutants, we found that deletion of the C-terminal region of the tnrA gene, which encodes a global regulator that positively regulates a number of genes in response to nitrogen limitation, results in a catabolite-resistant sporulation phenotype. Analyses of nrg-lacZ and nasB-lacZ, which are activated by TnrA under nitrogen limitation, showed that C-terminally truncated TnrA activates nitrogen-regulated genes constitutively. The relief of catabolite repression of sporulation may result from the uncontrolled expression of the TnrA-regulated genes.
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Affiliation(s)
- B S Shin
- Laboratory of Microbial and Bioprocess Engineering, Korea Research Institute of Bioscience and Biotechnology, Yusong, Taejon, Korea 305-600
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72
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Nagai T, Tran LS, Inatsu Y, Itoh Y. A new IS4 family insertion sequence, IS4Bsu1, responsible for genetic instability of poly-gamma-glutamic acid production in Bacillus subtilis. J Bacteriol 2000; 182:2387-92. [PMID: 10762236 PMCID: PMC111298 DOI: 10.1128/jb.182.9.2387-2392.2000] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Certain Bacillus subtilis strains, such as B. subtilis (natto) starter strains for the manufacture of natto (fermented soybeans), produce capsular poly-gamma-glutamate (gammaPGA). In B. subtilis (natto), gammaPGA synthesis is controlled by the ComP-ComA two-component regulatory system and thereby induced at the beginning of the stationary growth phase. We have found a new insertion sequence (IS), designated IS4Bsu1, in the comP gene of a spontaneous gammaPGA-negative mutant of B. subtilis (natto) NAF4. IS4Bsu1 (1,406 bp), the first IS discovered in B. subtilis, encodes a putative transposase (Tpase) with a predicted M(r) of 34,895 (374 residues) which displays similarity to the Tpases of IS4 family members. Southern blot analyses have identified 6 to 11 copies of IS4Bsu1, among which 6 copies were at the same loci, in the chromosomes of B. subtilis (natto) strains, including NAF4, three commercial starters, and another three gammaPGA-producing B. subtilis (natto) strains. All of the eight spontaneous gammaPGA(-) mutants, which were derived from five independent NAF4 cultures, had a new additional IS4Bsu1 copy in comP at six different positions within 600 bp of the 5'-terminal region. The target sites of IS4Bsu1 were determined to be AT-rich 9-bp sequences by sequencing the flanking regions of IS4Bsu1 in mutant comP genes. These results indicate that IS4Bsu1 transposes by the replicative mechanism, in contrast to other IS4 members that use the conservative mechanism, and that most, if not all, of spontaneous gammaPGA(-) mutants appear to have resulted from the insertion of IS4Bsu1 exclusively into comP. The presence of insertion hot spots in comP, which is essential for gammaPGA synthesis, as well as high transposition activity, would account for the high frequency of spontaneous gammaPGA(-) mutation by IS4Bsu1 in B. subtilis (natto).
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Affiliation(s)
- T Nagai
- National Food Research Institute, Ministry of Agriculture, Forestry and Fisheries, Tsukuba 305-8642, Japan
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73
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Jourlin-Castelli C, Mani N, Nakano MM, Sonenshein AL. CcpC, a novel regulator of the LysR family required for glucose repression of the citB gene in Bacillus subtilis. J Mol Biol 2000; 295:865-78. [PMID: 10656796 DOI: 10.1006/jmbi.1999.3420] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Synergistic carbon catabolite repression of the Bacillus subtilis aconitase (citB) gene by glucose and a source of 2-ketoglutarate is dependent on DNA sequences located upstream of the gene. Mutations in a dyad symmetry element centered at position -66 and in a repeat of the downstream arm of the dyad symmetry at position -27 cause derepressed citB expression. In this work, a protein able to bind to a DNA fragment containing these elements was purified and identified. This protein, named CcpC (Catabolite control protein C), shares sequence similarity with members of the LysR family of transcriptional regulators. In addition to binding to the citB promoter, CcpC bound to the promoter of the citZ gene, which encodes the cell's major citrate synthase and is subject to carbon catabolite repression. In a ccpC null mutant, expression of both citB and citZ was derepressed in glucose-glutamine minimal medium, indicating that CcpC is a negative regulator of citB and citZ gene expression. DNase I footprinting experiments showed that CcpC binds to two sites within the citB promoter region, corresponding to the dyad symmetry and -27 elements. In the presence of citrate, a putative inducer, only the dyad symmetry element was fully protected by CcpC. When the dyad symmetry element was mutated, CcpC was no longer able to bind to either the dyad symmetry or -27 elements. Repression of citB and citZ gene expression during anaerobiosis also proved to be mediated by CcpC.
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Affiliation(s)
- C Jourlin-Castelli
- Department of Molecular Biology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA
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74
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Jiang M, Grau R, Perego M. Differential processing of propeptide inhibitors of Rap phosphatases in Bacillus subtilis. J Bacteriol 2000; 182:303-10. [PMID: 10629174 PMCID: PMC94277 DOI: 10.1128/jb.182.2.303-310.2000] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the phosphorelay signal transduction system for sporulation initiation in Bacillus subtilis, the opposing activities of histidine kinases and aspartyl phosphate phosphatases determine the cell's decision whether to continue with vegetative growth or to initiate the differentiation process. Regulated dephosphorylation of the Spo0A and Spo0F response regulators allows a variety of negative signals from physiological processes that are antithetical to sporulation to impact on the activation level of the phosphorelay. Spo0F approximately P is the known target of two related phosphatases, RapA and RapB. In addition to RapA and RapB, a third member of the Rap family of phosphatases, RapE, specifically dephosphorylated the Spo0F approximately P intermediate in response to competence development. RapE phosphatase activity was found to be controlled by a pentapeptide (SRNVT) generated from within the carboxy-terminal domain of the phrE gene product. A synthetic PhrE pentapeptide could (i) complement the sporulation deficiency caused by deregulated RapE activity of a phrE mutant and (ii) inhibit RapE-dependent dephosphorylation of Spo0F approximately P in in vitro experiments. The PhrE pentapeptide did not inhibit the phosphatase activity of RapA and RapB. These results confirm previous conclusions that the specificity for recognition of the target phosphatase is contained within the amino acid sequence of the pentapeptide inhibitor.
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Affiliation(s)
- M Jiang
- The Scripps Research Institute, Department of Molecular Medicine, Division of Cellular Biology, La Jolla, California 92037, USA
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75
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Lazazzera BA, Kurtser IG, McQuade RS, Grossman AD. An autoregulatory circuit affecting peptide signaling in Bacillus subtilis. J Bacteriol 1999; 181:5193-200. [PMID: 10464187 PMCID: PMC94022 DOI: 10.1128/jb.181.17.5193-5200.1999] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The competence and sporulation factor (CSF) of Bacillus subtilis is an extracellular pentapeptide produced from the product of phrC. CSF has at least three activities: (i) at low concentrations, it stimulates expression of genes activated by the transcription factor ComA; at higher concentrations, it (ii) inhibits expression of those same genes and (iii) stimulates sporulation. Because the activities of CSF are concentration dependent, we measured the amount of extracellular CSF produced by cells. We found that by mid-exponential phase, CSF accumulated to concentrations (1 to 5 nM) that stimulate ComA-dependent gene expression. Upon entry into stationary phase, CSF reached 50 to 100 nM, concentrations that stimulate sporulation and inhibit ComA-dependent gene expression. Transcription of phrC was found to be controlled by two promoters: P1, which precedes rapC, the gene upstream of phrC; and P2, which directs transcription of phrC only. Both RapC and CSF were found to be part of autoregulatory loops that affect transcription from P1, which we show is activated by ComA approximately P. RapC negatively regulates its own expression, presumably due to its ability to inhibit accumulation of ComA approximately P. CSF positively regulates its own expression, presumably due to its ability to inhibit RapC activity. Transcription from P2, which is controlled by the alternate sigma factor sigma(H), increased as cells entered stationary phase, contributing to the increase in extracellular CSF at this time. In addition to controlling transcription of phrC, sigmaH appears to control expression of at least one other gene required for production of CSF.
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Affiliation(s)
- B A Lazazzera
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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76
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Piazza F, Tortosa P, Dubnau D. Mutational analysis and membrane topology of ComP, a quorum-sensing histidine kinase of Bacillus subtilis controlling competence development. J Bacteriol 1999; 181:4540-8. [PMID: 10419951 PMCID: PMC103584 DOI: 10.1128/jb.181.15.4540-4548.1999] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
ComP is a sensor histidine kinase of Bacillus subtilis required for the signal transduction pathway that initiates the development of competence for genetic transformation. It is believed that ComP senses the presence of ComX, a modified extracellular peptide pheromone, and donates a phosphate to ComA, thereby activating this transcription factor for binding to the srfA promoter. In the present study, fusions to the Escherichia coli proteins PhoA and LacZ and analysis of its susceptibility to the protease kallikrein were used to probe the membrane topology of ComP. These data suggest that ComP contains six or eight membrane-spanning segments and two large extracytoplasmic loops in its N-terminal membrane-associated domain. Deletions were introduced involving the large extracellular loops to explore the role of the N-terminal domain of ComP in signal transduction. The absence of the second loop conferred a phenotype in which ComP was active in the absence of ComX. The implications of these data are discussed.
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Affiliation(s)
- F Piazza
- Public Health Research Institute, New York, New York 10016, USA
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77
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Liao CT, Wen YD, Wang WH, Chang BY. Identification and characterization of a stress-responsive promoter in the macromolecular synthesis operon of Bacillus subtilis. Mol Microbiol 1999; 33:377-88. [PMID: 10411753 DOI: 10.1046/j.1365-2958.1999.01480.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacillus subtilis DB1005 is a temperature-sensitive (Ts) sigA mutant. Induction of sigmaA has been observed exclusively in this mutant harbouring extra copies of the plasmid-borne Ts sigA gene transcriptionally controlled by the P1P2 promoters of the B. subtilis macromolecular synthesis (MMS; rpoD or sigA) operon. Investigation of the mechanisms leading to the induction has allowed us to identify a sigmaB-type promoter, P7, in the MMS operon for the first time. Therefore, at least seven promoters in total are responsible for the regulation of the B. subtilis MMS operon, including the four known sigmaA- and sigmaH-type promoters, as well as two incompletely defined promoters. The P7 promoter was activated in B. subtilis after the imposition of heat, ethanol and salt stresses, indicating that the MMS operon of B. subtilis is subjected to the control of general stress. The significant heat induction of P7 in B. subtilis DB1005 harbouring a plasmid-borne Ts sigA gene can be explained by a model of competition between sigmaA and sigmaB for core binding; very probably, the sigmaB factor binds more efficiently to core RNA polymerase under heat shock. This mechanism may provide a means for the expression of the B. subtilis MMS operon when sigmaA becomes defective in core binding.
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Affiliation(s)
- C T Liao
- Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan, Republic of China
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78
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Abstract
Deletion of the citC gene, coding for isocitrate dehydrogenase, arrests sporulation of Bacillus subtilis at stage I after bipolar localization of the cell division protein FtsZ but before formation of the asymmetric septum. A spontaneous extragenic suppressor mutation that overcame the stage I block was found to map within the spoVG gene. The suppressing mutation and other spoVG loss-of-function mutations enabled citC mutant cells to form asymmetric septa and to activate the forespore-specific sigma factor sigmaF. However, little induction of mother cell-specific, sigmaE-dependent sporulation genes was observed in a citC spoVG double mutant, indicating that there is an additional defect(s) in compartmentalized gene expression in the citC mutant. These other defects could be partially overcome by reducing the synthesis of citrate, by buffering the medium, or by adding excess MnCl2. Overexpression of the spoVG gene in wild-type cells significantly delayed sigmaF activation. Increased expression and stability of SpoVG in citC mutant cells may contribute to the citC mutant phenotype. Inactivation of the spoVG gene caused a population of otherwise wild-type cells to produce a small number of minicells during growth and caused sporulating cells to complete asymmetric septation more rapidly than normal. Unlike the case for inactivation of the cell division inhibitor gene minD, many of these minicells contained DNA and appeared only when the primary sporulation signal transduction pathway, the Spo0A phosphorelay, was active. These results suggest that SpoVG interferes with or is a negative regulator of the pathway leading to asymmetric septation.
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Affiliation(s)
- K Matsuno
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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79
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Msadek T. When the going gets tough: survival strategies and environmental signaling networks in Bacillus subtilis. Trends Microbiol 1999; 7:201-7. [PMID: 10354595 DOI: 10.1016/s0966-842x(99)01479-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Regulatory pathways involving two-component histidine kinase/response regulator proteins of Bacillus subtilis are highly interconnected and form a signal transduction network controlling stationary-phase adaptive responses. These include chemotaxis and motility, degradative enzyme synthesis, antibiotic production, natural competence for DNA uptake, and sporulation. Many of these responses are mutually exclusive, with different control levels involving protein-environment, protein-protein and protein-DNA interactions, allowing the bacteria to adapt rapidly to environmental changes.
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Affiliation(s)
- T Msadek
- Unité de Biochimie Microbienne, URA 1300 du Centre National de la Recherche Scientifique, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France.
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80
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Belitsky BR, Sonenshein AL. Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol 1998; 180:6298-305. [PMID: 9829940 PMCID: PMC107716 DOI: 10.1128/jb.180.23.6298-6305.1998] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/1998] [Accepted: 09/28/1998] [Indexed: 11/20/2022] Open
Abstract
The complete Bacillus subtilis genome contains two genes with the potential to encode glutamate dehydrogenase (GlutDH) enzymes. Mutations in these genes were constructed and characterized. The rocG gene proved to encode a major GlutDH whose synthesis was induced in media containing arginine or ornithine or, to a lesser degree, proline and was repressed by glucose. A rocG null mutant was impaired in utilization of arginine, ornithine, and proline as nitrogen or carbon sources. The gudB gene was expressed under all growth conditions tested but codes for a GlutDH that seemed to be intrinsically inactive. Spontaneous mutations in gudB that removed a 9-bp direct repeat within the wild-type gudB sequence activated the GudB protein and allowed more-efficient utilization of amino acids of the glutamate family.
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Affiliation(s)
- B R Belitsky
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.
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81
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Hecker M, Völker U. Non-specific, general and multiple stress resistance of growth-restricted Bacillus subtilis cells by the expression of the sigmaB regulon. Mol Microbiol 1998; 29:1129-36. [PMID: 9767581 DOI: 10.1046/j.1365-2958.1998.00977.x] [Citation(s) in RCA: 169] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Bacillus subtilis cells respond almost immediately to different stress conditions by increasing the production of general stress proteins (GSPs). The genes encoding the majority of the GSPs that are induced by heat, ethanol, salt stress or by starvation for glucose, oxygen or phosphate belong to the sigmaB-dependent general stress regulon. Despite a good understanding of the complex regulation of the activity of sigmaB and knowledge of a very large number of general stress genes controlled by sigmaB, first insights into the physiological role of this nonspecific stress response have been obtained only very recently. To explore the physiological role of this reguIon, we and others identified sigmaB-dependent general stress genes and compared the stress tolerance of wild-type cells with mutants lacking sigmaB or general stress proteins. The proteins encoded by sigmaB-dependent general stress genes can be divided into at least five functional groups that most probably provide growth-restricted B. subtilis cells with a multiple stress resistance in anticipation of future stress. In particular, sigB mutants are impaired in non-specific resistance to oxidative stress, which requires the sigmaB-dependent dps gene encoding a DNA-protecting protein. Protection against oxidative damage of membranes, proteins or DNA could be the most essential component of sigmaB mediated general stress resistance in growth-arrested aerobic gram-positive bacteria. Other general stress genes have both a sigmaB-dependent induction pathway and a second sigmaB-independent mechanism of stress induction, thereby partially compensating for a sigmaB deficiency in a sigB mutant. In contrast to sigB mutants, null mutations in genes encoding those proteins, such as cIpP or cIpC, cause extreme sensitivity to salt or heat.
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Affiliation(s)
- M Hecker
- Ernst-Moritz-Arndt-Universität Greifwald, Institut für Mikrobiologie und Molekularbiologie, Greifswald, Germany.
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82
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Abstract
The major regulator of sporulation initiation in Bacillus subtilis is the phosphorelay, a multicomponent signal transduction system. A myriad of signals, both positive and negative, from the environment, cell cycle and metabolism is received and interpreted by the phosphorelay and integrated through the opposing activity of protein kinases and protein aspartate phosphatases to create an extremely sophisticated regulatory network.
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Affiliation(s)
- M Perego
- Dept of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
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83
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Sato T, Kobayashi Y. The ars operon in the skin element of Bacillus subtilis confers resistance to arsenate and arsenite. J Bacteriol 1998; 180:1655-61. [PMID: 9537360 PMCID: PMC107075 DOI: 10.1128/jb.180.7.1655-1661.1998] [Citation(s) in RCA: 157] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Bacillus subtilis skin element confers resistance to arsenate and arsenite. The ars operon in the skin element contains four genes in the order arsR, ORF2, arsB, and arsC. Three of these genes are homologous to the arsR, arsB, and arsC genes from the staphylococcal plasmid pI258, while no homologs of ORF2 have been found. Inactivation of arsR, arsB, or arsC results in either constitutive expression of ars, an arsenite- and arsenate-sensitive phenotype, or an arsenate-sensitive phenotype, respectively. These results suggest that ArsR, ArsB, and ArsC function as a negative regulator, a membrane-associated protein need for extrusion of arsenite, and arsenate reductase, respectively. Expression of the ars operon was induced by arsenate, arsenite, and antimonite. Northern hybridization and primer extension analysis showed that synthesis of a full-length ars transcript of about 2.4 kb was induced by arsenate and that the ars promoter contains sequences that resemble the -10 and -35 regions of promoters that are recognized by E sigmaA.
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Affiliation(s)
- T Sato
- Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan.
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84
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Lee K, Ebbole DJ. Tissue-specific repression of starvation and stress responses of the Neurospora crassa con-10 gene is mediated by RCO1. Fungal Genet Biol 1998; 23:269-78. [PMID: 9680957 DOI: 10.1006/fgbi.1998.1044] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Neurospora crassa con-10 gene is weakly expressed in mycelia but is induced approximately 1000-fold during macroconidiation. Studies of the promoter elements and trans-acting factors that regulate con-10 expression are needed to gain a detailed understanding of developmental regulation. The rco-1 mutant displays a 10-fold elevated basal level of expression of con-10. In contrast to the wild type, con-10 expression in mycelia of the rco-1 mutant was rapidly induced to high levels by starvation for carbon or nitrogen and by heat shock. Although con-10 is developmentally induced late in conidiation, con-10 was inducible by heat shock shortly after exposure of the wild-type mycelium to air. These findings support the view that RCO1 is a cell type-specific repressor of con-10. We propose that inactivation of RCO1 allows developing conidiophores to adjust the timing of con-10 induction in response to stress.
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Affiliation(s)
- K Lee
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station 77843-2132, USA
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85
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Rivolta C, Soldo B, Lazarevic V, Joris B, Mauël C, Karamat D. A 35.7 kb DNA fragment from the Bacillus subtilis chromosome containing a putative 12.3 kb operon involved in hexuronate catabolism and a perfectly symmetrical hypothetical catabolite-responsive element. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 4):877-884. [PMID: 9579062 DOI: 10.1099/00221287-144-4-877] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Bacillus subtilis strain 168 chromosomal region extending from 109 degrees to 112 degrees has been sequenced. Among the 35 ORFs identified, cotT and rapA were the only genes that had been previously mapped and sequenced. Out of ten ORFs belonging to a single putative transcription unit, seven are probably involved in hexuronate catabolism. Their sequences are homologous to Escherichia coli genes exuT, uidB, uxaA, uxaB, uxaC, uxuA and uxuB, which are all required for the uptake of free D-glucuronate, D-galacturonate and beta-glucuronide, and their transformation into glyceraldehyde 3-phosphate and pyruvate via 2-keto-3-deoxygluconate. The remaining three ORFs encode two dehydrogenases and a transcriptional regulator. The operon is preceded by a putative catabolite-responsive element (CRE), located between a hypothetical promoter and the RBS of the first gene. This element, the longest and the only so far described that is fully symmetrical, consists of a 26 bp palindrome matching the theoretical B. subtilis CRE sequence. The remaining predicted amino acid sequences that share homologies with other proteins comprise: a cytochrome P-450, a glycosyltransferase, an ATP-binding cassette transporter, a protein similar to the formate dehydrogenase alpha-subunit (FdhA), protein similar to NADH dehydrogenases, and three homologues of polypeptides that have undefined functions.
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Affiliation(s)
- Carlo Rivolta
- Institut de Génétique et de Biologie Microbiennes, Université de Lausanne, Rue César-Roux 19, CH-1005 Lausanne, Switzerland
| | - Blazenka Soldo
- Institut de Génétique et de Biologie Microbiennes, Université de Lausanne, Rue César-Roux 19, CH-1005 Lausanne, Switzerland
| | - Vladimir Lazarevic
- Institut de Génétique et de Biologie Microbiennes, Université de Lausanne, Rue César-Roux 19, CH-1005 Lausanne, Switzerland
| | - Bernard Joris
- Centre d'lngénierie des Protéines, Université de Liêge, Institut de Chimie, B6, Sart Tilman, B-4000 Liêge, Belgium
| | - Catherine Mauël
- Institut de Génétique et de Biologie Microbiennes, Université de Lausanne, Rue César-Roux 19, CH-1005 Lausanne, Switzerland
| | - Dimitri Karamat
- Institut de Génétique et de Biologie Microbiennes, Université de Lausanne, Rue César-Roux 19, CH-1005 Lausanne, Switzerland
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86
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Meijer WJ, Wisman GB, Terpstra P, Thorsted PB, Thomas CM, Holsappel S, Venema G, Bron S. Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from gram-positive bacteria. FEMS Microbiol Rev 1998; 21:337-68. [PMID: 9532747 DOI: 10.1111/j.1574-6976.1998.tb00357.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Most small plasmids of Gram-positive bacteria use the rolling-circle mechanism of replication and several of these have been studied in considerable detail at the DNA level and for the function of their genes. Although most of the common laboratory Bacillus subtilis 168 strains do not contain plasmids, several industrial strains and natural soil isolates do contain rolling-circle replicating (RCR) plasmids. So far, knowledge about these plasmids was mainly limited to: (i) a classification into seven groups, based on size and restriction patterns; and (ii) DNA sequences of the replication region of a limited number of them. To increase the knowledge, also with respect to other functions specified by these plasmids, we have determined the complete DNA sequence of four plasmids, representing different groups, and performed computer-assisted and experimental analyses on the possible function of their genes. The plasmids analyzed are pTA1015 (5.8 kbp), pTA1040 (7.8 kbp), pTA1050 (8.4 kbp), and pTA1060 (8.7 kbp). These plasmids have a structural organization similar to most other known RCR plasmids. They contain highly related replication functions, both for leading and lagging strand synthesis. pTA1015 and pTA1060 contain a mobilization gene enabling their conjugative transfer. Strikingly, in addition to the conserved replication modules, these plasmids contain unique module(s) with genes which are not present on known RCR plasmids of other Gram-positive bacteria. Examples are genes encoding a type I signal peptidase and genes encoding proteins belonging to the family of response regulator aspartate phosphatases. The latter are likely to be involved in the regulation of post-exponential phase processes. The presence of these modules on plasmids may reflect an adaptation to the special conditions to which the host cells were exposed.
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Affiliation(s)
- W J Meijer
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Haren, The Netherlands
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87
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Craig JE, Ford MJ, Blaydon DC, Sonenshein AL. A null mutation in the Bacillus subtilis aconitase gene causes a block in Spo0A-phosphate-dependent gene expression. J Bacteriol 1997; 179:7351-9. [PMID: 9393699 PMCID: PMC179685 DOI: 10.1128/jb.179.23.7351-7359.1997] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The citB gene of Bacillus subtilis encodes aconitase, the enzyme of the Krebs citric acid cycle, which is responsible for the interconversion of citrate and isocitrate. A B. subtilis strain with an insertion mutation in the citB gene was devoid of aconitase activity and aconitase protein, required glutamate for growth in minimal medium, and was unable to sporulate efficiently in nutrient broth sporulation medium. Mutant cells failed to form the asymmetric septum characteristic of sporulating cells and were defective in transcription of the earliest-expressed spo genes, that is, the genes dependent on the Spo0A phosphorelay. However, this early block in sporulation was partially overcome when cells of the citB mutant were induced to sporulate by resuspension in a poor medium. Accumulation of citrate in the mutant cells or in their culture fluid may be responsible for the early block, possibly because citrate can chelate divalent cations needed for the activity of the phosphorelay.
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Affiliation(s)
- J E Craig
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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88
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Belitsky BR, Gustafsson MC, Sonenshein AL, Von Wachenfeldt C. An lrp-like gene of Bacillus subtilis involved in branched-chain amino acid transport. J Bacteriol 1997; 179:5448-57. [PMID: 9287000 PMCID: PMC179416 DOI: 10.1128/jb.179.17.5448-5457.1997] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The azlB locus of Bacillus subtilis was defined previously by a mutation conferring resistance to a leucine analog, 4-azaleucine (J. B. Ward, Jr., and S. A. Zahler, J. Bacteriol. 116:727-735, 1973). In this report, azlB is shown to be the first gene of an operon apparently involved in branched-chain amino acid transport. The product of the azlB gene is an Lrp-like protein that negatively regulates expression of the azlBCDEF operon. Resistance to 4-azaleucine in azlB mutants is due to overproduction of AzlC and AzlD, two novel hydrophobic proteins.
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Affiliation(s)
- B R Belitsky
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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89
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Perego M. A peptide export-import control circuit modulating bacterial development regulates protein phosphatases of the phosphorelay. Proc Natl Acad Sci U S A 1997; 94:8612-7. [PMID: 9238025 PMCID: PMC23044 DOI: 10.1073/pnas.94.16.8612] [Citation(s) in RCA: 155] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/1997] [Accepted: 06/13/1997] [Indexed: 02/04/2023] Open
Abstract
The phosphorelay signal transduction system activates developmental transcription in sporulation of Bacillus subtilis by phosphorylation of aspartyl residues of the Spo0F and Spo0A response regulators. The phosphorylation level of these response regulators is determined by the opposing activities of protein kinases and protein aspartate phosphatases that interpret positive and negative signals for development in a signal integration circuit. The RapA protein aspartate phosphatase of the phosphorelay is regulated by a peptide that directly inhibits its activity. This peptide is proteolytically processed from an inactive pre-inhibitor protein encoded in the phrA gene. The pre-inhibitor is cleaved by the protein export apparatus to a putative pro-inhibitor that is further processed to the active inhibitor peptide and internalized by the oligopeptide permease. This export-import circuit is postulated to be a mechanism for timing phosphatase activity where the processing enzymes regulate the rate of formation of the active inhibitor. The processing events may, in turn, be controlled by a regulatory hierarchy. Chromosome sequencing has revealed several other phosphatase-prepeptide gene pairs in B. subtilis, suggesting that the use of this mechanism may be widespread in signal transduction.
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Affiliation(s)
- M Perego
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037,
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90
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Jin S, Levin PA, Matsuno K, Grossman AD, Sonenshein AL. Deletion of the Bacillus subtilis isocitrate dehydrogenase gene causes a block at stage I of sporulation. J Bacteriol 1997; 179:4725-32. [PMID: 9244258 PMCID: PMC179317 DOI: 10.1128/jb.179.15.4725-4732.1997] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A Bacillus subtilis mutant with a deletion of citC, the gene encoding isocitrate dehydrogenase, the third enzyme of the tricarboxylic acid branch of the Krebs cycle, had a greatly reduced ability to sporulate. Analysis of expression of lacZ fusions to various sporulation gene promoters revealed that in the citC mutant development is probably blocked between stage 0 and stage II. That is, genes expressed very early in sporulation, under the direct control of the Spo0A transcription factor, were induced normally in the citC mutant. However, genes expressed after asymmetric septation (stage II) in wild-type cells were not induced in the citC mutant. Analysis of cell morphology by thin-section electron microscopy and immunofluorescence microscopy showed that the mutant formed axial chromosomal filaments and accumulated rings of FtsZ protein at potential polar division sites but failed to form asymmetric division septa, indicating that sporulation is blocked at stage I. The growth and sporulation defects of the B. subtilis citC mutant were fully overcome by introduction and expression of the Escherichia coli icd gene, encoding an isocitrate dehydrogenase similar to the enzyme from B. subtilis.
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Affiliation(s)
- S Jin
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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91
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Kumano M, Tamakoshi A, Yamane K. A 32 kb nucleotide sequence from the region of the lincomycin-resistance gene (22 degrees-25 degrees) of the Bacillus subtilis chromosome and identification of the site of the lin-2 mutation. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 8):2775-2782. [PMID: 9274031 DOI: 10.1099/00221287-143-8-2775] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A 32 kb nucleotide sequence in the region of the lincomycin-resistance gene, located from 22 degrees to 25 degrees on the Bacillus subtilis chromosome, was determined. Among 32 putative ORFs identified, four [lipA for lipase, natA, natB and yzaE (renamed yccK)] have already been reported, although the functions of NatA, NatB and YccK remain to be characterized. Six putative products were found to exhibit significant similarity to known proteins in the databases, namely L-asparaginase precursor, protein aspartate phosphatase, alpha-glucosidase, two tellurite-resistance proteins and a hypothetical protein from B. subtilis. The region of the tellurite-resistance gene, consisting of seven ORFs, seems to correspond to an operon. The products of 14 ORFs exhibited considerable or limited similarity to known proteins. The sequenced region seems to be rich in membrane proteins, since at least 16 gene products appeared to contain membrane-spanning domains. The site of the lin-2 mutation (two nucleotide replacements) was mapped and identified by sequencing. This site is located between a putative promoter and the SD sequence of ImrA (yccB) [a putative repressor of the lmr operon, which consists of lmrA and lmrB (yccA)]. LmrB is a homologue of proteins involved in drug-export systems and seems likely to be the protein responsible for resistance to lincomycin.
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Affiliation(s)
- Miyuki Kumano
- Institute of Biological Sciences, University of Tsukuba, Tsukuba-shi, Ibaraki 305, Japan
| | - Atsuo Tamakoshi
- Institute of Biological Sciences, University of Tsukuba, Tsukuba-shi, Ibaraki 305, Japan
| | - Kunio Yamane
- Institute of Biological Sciences, University of Tsukuba, Tsukuba-shi, Ibaraki 305, Japan
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92
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Lazazzera BA, Solomon JM, Grossman AD. An exported peptide functions intracellularly to contribute to cell density signaling in B. subtilis. Cell 1997; 89:917-25. [PMID: 9200610 DOI: 10.1016/s0092-8674(00)80277-9] [Citation(s) in RCA: 196] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Competence development and sporulation in B. subtilis are partly controlled by peptides that accumulate in culture medium as cells grow to high density. We constructed two genes that encode mature forms of two different signaling molecules, the PhrA peptide that stimulates sporulation, and CSF, the competence- and sporulation-stimulating factor. Both pentapeptides are normally produced by secretion and processing of precursor molecules. The mature pentapeptides were functional when expressed inside the cell, indicating that they normally need to be imported to function. Furthermore, at physiological concentrations (10 nM), CSF was transported into the cell by the oligopeptide permease encoded by spo0K (opp). CSF was shown to have at least three different targets corresponding to its three activities: stimulating competence gene expression at low concentrations, and inhibiting competence gene expression and stimulating sporulation at high concentrations.
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Affiliation(s)
- B A Lazazzera
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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93
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Bernhardt JR, V Lker U, V Lker A, Antelmann H, Schmid R, Mach H, Hecker M. Specific and general stress proteins in Bacillus subtilis--a two-deimensional protein electrophoresis study. MICROBIOLOGY (READING, ENGLAND) 1997; 143:999-1017. [PMID: 9296790 DOI: 10.1099/00221287-143-3-999] [Citation(s) in RCA: 149] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A computer-aided analysis of high resolution two-dimensional polyacrylamide gels was used to investigate the changes in the protein synthesis profile in B. subtilis wild-type strains and sigB mutants in response to heat shock, salt and ethanol stress, and glucose of phosphate starvation. The data provided evidence that the induction of a least 42 general stress proteins absolutely required the alternative sigma factor sigmaB. However, at least seven stress proteins, among them ClpC, ClpP, Sod, AhpC and AhpF, remained stress-inducible in a sigB mutant. Such a detailed analysis also premitted the description of subgroups of general stress proteins which are subject to additional regulatory circuits, indicating a very thorough fine-tuning of this complex response. The relative synthesis rate of the general stress proteins constituted up to 40% of the total protein synthesis of stressed cells and thereby emphasizes the importance of the stress regulon. Besides the induction of these general or rather unspecific stress proteins, the induction of stress-specific proteins is shown and discussed.
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Affiliation(s)
- J Rg Bernhardt
- Institut f�r Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universit�t Greifswald, 17487 Greifswald, Friedrich-Ludwig-Jahn-StraBe 15, Germany
| | - Uwe V Lker
- Institut f�r Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universit�t Greifswald, 17487 Greifswald, Friedrich-Ludwig-Jahn-StraBe 15, Germany
| | - Andrea V Lker
- Institut f�r Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universit�t Greifswald, 17487 Greifswald, Friedrich-Ludwig-Jahn-StraBe 15, Germany
| | - Haike Antelmann
- Institut f�r Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universit�t Greifswald, 17487 Greifswald, Friedrich-Ludwig-Jahn-StraBe 15, Germany
| | - Roland Schmid
- Universit�t Osnabr�ck, Abteilung f�r Mikrobiologie, 49076 Osnabr�ck, Germany
| | - Hiltraut Mach
- Institut f�r Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universit�t Greifswald, 17487 Greifswald, Friedrich-Ludwig-Jahn-StraBe 15, Germany
| | - Michael Hecker
- Institut f�r Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universit�t Greifswald, 17487 Greifswald, Friedrich-Ludwig-Jahn-StraBe 15, Germany
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94
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Belitsky BR, Sonenshein AL. Altered transcription activation specificity of a mutant form of Bacillus subtilis GltR, a LysR family member. J Bacteriol 1997; 179:1035-43. [PMID: 9023181 PMCID: PMC178795 DOI: 10.1128/jb.179.4.1035-1043.1997] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A mutation (gltR24) that allows Bacillus subtilis glutamate synthase (gltAB) gene expression in the absence of its positive regulator, GltC, was identified. Cloning and sequencing of the gltR gene revealed that the putative gltR product belongs to the LysR family of transcriptional regulators and is thus related to GltC. A null mutation in gltR had no effect on gltAB expression under any environmental condition tested, suggesting that gltR24 is a gain-of-function mutation. GltR24-dependent transcription of gltAB, initiated at the same base pair as GltC-dependent transcription, was responsive to the nitrogen source in the medium and required the integrity of sequences upstream of the gltAB promoter that are also necessary for GltC-dependent expression. Expression of the gltC gene, transcribed divergently from gltA from an overlapping promoter, was not affected by GltR. Both wild-type GltR and GltR24 negatively regulated their own expression. The gltR gene was mapped to 233 degrees on the B. subtilis chromosome, very close to the azlB locus.
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Affiliation(s)
- B R Belitsky
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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95
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96
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Serror P, Sonenshein AL. CodY is required for nutritional repression of Bacillus subtilis genetic competence. J Bacteriol 1996; 178:5910-5. [PMID: 8830686 PMCID: PMC178446 DOI: 10.1128/jb.178.20.5910-5915.1996] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The acquisition of genetic competence by Bacillus subtilis is repressed when the growth medium contains Casamino Acids. This repression was shown to be exerted at the level of expression from the promoters of the competence-regulatory genes srfA and comK and was relieved in strains carrying a null mutation in the codY gene. DNase I footprinting experiments showed that purified CodY binds directly to the srfA and comK promoter regions.
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Affiliation(s)
- P Serror
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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97
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Abstract
Cell-cell and starvation signals are funneled through the phosphorelay to initiate sporulation by activating the transcription regulator SpoOA. Activation of SpoOA leads to synthesis of the transcription factors sigmaF and sigmaE. Substantial advances have been made in our understanding of the signal circuitry of the phosphorelay and of the cell-type-specific activation of the sigma factors.
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Affiliation(s)
- P J Piggot
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia. Pennsylvania 19140, USA.
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98
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Solomon JM, Lazazzera BA, Grossman AD. Purification and characterization of an extracellular peptide factor that affects two different developmental pathways in Bacillus subtilis. Genes Dev 1996; 10:2014-24. [PMID: 8769645 DOI: 10.1101/gad.10.16.2014] [Citation(s) in RCA: 215] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have purified and characterized an extracellular peptide factor that serves as a cell density signal for both competence development and sporulation in Bacillus subtilis. This competence and sporulation stimulating factor (CSF) was purified from conditioned medium (culture supernatant) based on its ability to stimulate expression of srfA (comS) in cells at low cell density. CSF is a 5-amino-acid peptide, glu-arg-gly-met-thr (ERGMT), that is, the carboxy-terminal 5 amino acids of the 40-amino-acid peptide encoded by phrC. No detectable CSF was produced in a phrC null mutant. The activity of chemically synthesized CSF (ERGMT) was virtually indistinguishable from that of CSF that was purified from culture supernatants. At relatively low concentrations (1-10 nM), CSF stimulated expression of srfA, whereas high concentrations of CSF stimulated the ability of cells at low cell density to sporulate. Stimulation of srfA expression by CSF requires the oligopeptide permease encoded by spo0K, a member of the ATP-binding-cassette family of transporters, and the putative phosphatase encoded by rapC, the gene immediately upstream of phrC. RapC was found to be a negative regulator of srfA expression, suggesting that the target of RapC is the transcription factor encoded by comA. We propose that CSF is transported into the cell by the Spo0K oligopeptide permease and stimulates competence gene expression by inhibiting (either directly or indirectly) the RapC phosphatase.
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Affiliation(s)
- J M Solomon
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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99
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Serror P, Sonenshein AL. Interaction of CodY, a novel Bacillus subtilis DNA-binding protein, with the dpp promoter region. Mol Microbiol 1996; 20:843-52. [PMID: 8793880 DOI: 10.1111/j.1365-2958.1996.tb02522.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The product of the codY gene is required for nutritional repression of the Bacillus subtillis dipeptide permease operon (dpp), an operon expressed at early stationary phase in nutrient-rich medium. Though unrelated to any known DNA-binding protein, CodY was shown to bind specifically to the dpp promoter region. DNase I footprinting experiments revealed that the CodY-protected region encompasses the dpp transcription start site and overlaps with the region protected by another regulatory protein, AbrB. CodY and AbrB were found to compete, in vitro, for binding to the dpp promoter region. Binding of CodY was altered in mutants defective in nutritional regulation.
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Affiliation(s)
- P Serror
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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100
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Zhang L, Higgins ML, Piggot PJ, Karow ML. Analysis of the role of prespore gene expression in the compartmentalization of mother cell-specific gene expression during sporulation of Bacillus subtilis. J Bacteriol 1996; 178:2813-7. [PMID: 8631668 PMCID: PMC178015 DOI: 10.1128/jb.178.10.2813-2817.1996] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A hallmark of sporulation of Bacillus subtilis is the formation of two distinct cells by an asymmetric division. The development programs in these two cells involve the compartmentalized activities of sigma E in the larger mother cell and of sigma F in the smaller prespore. Activation of sigma E requires expression of the sigma F-directed gene spoIIR. By immunofluorescence microscopy of a strain containing a spoIIR-lacZ fusion, we have shown that spoIIR is transcribed exclusively in the prespore. By placing spoIIR under the control of PspoIIE, it was possible to express spoIIR before the spore septum was formed. Strains containing the PspoIIE-spoIIR construct activated sigma E only in the mother cell in organisms that underwent the asymmetric sporulation division. Thus, compartmentalization of sigma E activity did not require the compartmentalization of spoIIR expression. Nor did the compartmentalization of sigma E require SpoIIAA, SpoIIAB, sigma F, or sigma F-dependent transcription, all of which are required for prespore-specific gene expression. It is inferred that although sigma F and sigma E direct compartmentalized gene expression, neither of these sigma factors, nor the genes under their control, directs the process of compartmentalization.
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Affiliation(s)
- L Zhang
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia 19140, USA
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