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Ma M, Welch RD, Garza AG. The σ 54 system directly regulates bacterial natural product genes. Sci Rep 2021; 11:4771. [PMID: 33637792 PMCID: PMC7910581 DOI: 10.1038/s41598-021-84057-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023] Open
Abstract
Bacterial-derived polyketide and non-ribosomal peptide natural products are crucial sources of therapeutics and yet little is known about the conditions that favor activation of natural product genes or the regulatory machinery controlling their transcription. Recent findings suggest that the σ54 system, which includes σ54-loaded RNA polymerase and transcriptional activators called enhancer binding proteins (EBPs), might be a common regulator of natural product genes. Here, we explored this idea by analyzing a selected group of putative σ54 promoters identified in Myxococcus xanthus natural product gene clusters. We show that mutations in putative σ54-RNA polymerase binding regions and in putative Nla28 EBP binding sites dramatically reduce in vivo promoter activities in growing and developing cells. We also show in vivo promoter activities are reduced in a nla28 mutant, that Nla28 binds to wild-type fragments of these promoters in vitro, and that in vitro binding is lost when the Nla28 binding sites are mutated. Together, our results indicate that M. xanthus uses σ54 promoters for transcription of at least some of its natural product genes. Interestingly, the vast majority of experimentally confirmed and putative σ54 promoters in M. xanthus natural product loci are located within genes and not in intergenic sequences.
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Affiliation(s)
- Muqing Ma
- grid.264484.80000 0001 2189 1568Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244 USA
| | - Roy D. Welch
- grid.264484.80000 0001 2189 1568Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244 USA
| | - Anthony G. Garza
- grid.264484.80000 0001 2189 1568Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244 USA
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2
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Tao CC, Yang Y, Li F, Qiao L, Wu Y, Sun XD, Zhang YY, Li CL. Cloning short DNA into plasmids by one-step PCR. Thorac Cancer 2020; 11:3409-3415. [PMID: 33015950 PMCID: PMC7605993 DOI: 10.1111/1759-7714.13660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/30/2020] [Accepted: 08/30/2020] [Indexed: 11/30/2022] Open
Abstract
Background Plasmid construction of small fragments of interest (such as insertion of small fragment marker genes, expression of shRNA, siRNA, etc) is the basis of many biomolecular experiments. Here, we describe a method to clone short DNA into vectors by polymerase chain reaction (PCR), named one‐step PCR cloning. Our method uses PCR to amplify the entire circular plasmid. The PCR was performed by the primers containing the gene of short DNA with overlapping sequences between 10–15 bp. The PCR products were then transformed into E. coli and cyclized by homologous recombination in vivo. Methods The pEGFP‐N1‐HA plasmid was constructed by one‐step PCR and transformation. Cells were transfected with pEGFP‐N1‐HA and pEGFP‐N1 plasmid using TurboFect transfection reagent. Protein expression was detected by western blotting and the HA‐GFP fusion protein was detected by confocal microscopy. Results The pEGFP‐N1‐HA plasmid was successfully constructed and HA expression in cells. Conclusions Free from the limitations of restriction enzyme sites and omitting the ligation process, our method offers a flexible and economical option of plasmid construction. Key points
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Affiliation(s)
- Cheng-Cheng Tao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ying Yang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Fang Li
- Department of Medical Oncology, Sichuan Cancer Hospital and Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ling Qiao
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yue Wu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiao-Dong Sun
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuan-Yuan Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.,School of Biological Sciences and Technology, Chengdu Medical College, Chengdu, China
| | - Chang-Long Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
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3
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A cascade of coregulating enhancer binding proteins initiates and propagates a multicellular developmental program. Proc Natl Acad Sci U S A 2011; 108:E431-9. [PMID: 21670274 DOI: 10.1073/pnas.1105876108] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The signal transduction networks that initiate multicellular development in bacteria remain largely undefined. Here, we report that Myxococcus xanthus regulates entry into its multicellular developmental program using a novel strategy: a cascade of transcriptional activators known as enhancer binding proteins (EBPs). The EBPs in the cascade function in sequential stages of early development, and several lines of evidence indicate that the cascade is propagated when EBPs that function at one stage of development directly regulate transcription of an EBP gene important for the next developmental stage. We also show that the regulatory cascade is designed in a novel way that extensively expands on the typical use of EBPs: Instead of using only one EBP to regulate a particular gene or group of genes, which is the norm in other bacterial systems, the cascade uses multiple EBPs to regulate EBP genes that are positioned at key transition points in early development. Based on the locations of the putative EBP promoter binding sites, several different mechanisms of EBP coregulation are possible, including the formation of coregulating EBP transcriptional complexes. We propose that M. xanthus uses an EBP coregulation strategy to make expression of EBP genes that modulate stage-stage transitions responsive to multiple signal transduction pathways, which provide information that is important for a coordinated decision to advance the developmental process.
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Functional Characterization of Vibrio alginolyticus Twin-Arginine Translocation System: Its Roles in Biofilm Formation, Extracellular Protease Activity, and Virulence Towards Fish. Curr Microbiol 2010; 62:1193-9. [DOI: 10.1007/s00284-010-9844-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Accepted: 11/24/2010] [Indexed: 10/18/2022]
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Wang Q, Liu Q, Ma Y, Rui H, Zhang Y. LuxO controls extracellular protease, haemolytic activities and siderophore production in fish pathogen Vibrio alginolyticus. J Appl Microbiol 2008; 103:1525-34. [PMID: 17953563 DOI: 10.1111/j.1365-2672.2007.03380.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIMS To characterize the luxO gene in fish pathogen Vibrio alginolyticus MVP01 and investigate its roles in regulation of extracellular products (ECP) and siderophore production. METHODS AND RESULTS The luxO gene was cloned from V. alginolyticus MVP01. Genetic analysis revealed that it encoded a protein with high similarity to other LuxO homologues. The luxO in-frame deletion mutant and rpoN null mutant were constructed with suicide plasmids. We demonstrated that sole deletion in LuxO increased the secretion of extracellular protease and haemolytic products, but decreased siderophore production for V. alginolyticus MVP01. Mutants with null rpoN displayed significantly enhanced protease level and siderophore production while notable reduction in haemolytic activities of ECP. CONCLUSIONS Vibrio alginolyticus harbours functional luxO gene that regulates the secretion of extracellular protease and haemolytic materials as well as siderophore production in either sigma(54) dependent or independent manners. SIGNIFICANCE AND IMPACT OF THE STUDY The current study demonstrated that V. alginolyticus MVP01 produces extracellular protease and haemolytic activity material as well as siderophore, which may be characteristics of the virulence of the strain. Revelations that secretion of these products is under the regulation of LuxO and sigma(54) as well as the potential quorum sensing systems in V. alginolyticus MVP01 will expedite the understanding of vibriosis pathogenesis.
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Affiliation(s)
- Q Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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6
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Mitra R, Das HK, Dixit A. Identification of a positive transcription regulatory element within the coding region of the nifLA operon in Azotobacter vinelandii. Appl Environ Microbiol 2005; 71:3716-24. [PMID: 16000781 PMCID: PMC1169038 DOI: 10.1128/aem.71.7.3716-3724.2005] [Citation(s) in RCA: 8] [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
Nitrogen fixation in Azotobacter vinelandii is regulated by the nifLA operon. NifA activates the transcription of nif genes, while NifL antagonizes the transcriptional activator NifA in response to fixed nitrogen and molecular oxygen levels. However, transcriptional regulation of the nifLA operon of A. vinelandii itself is not fully understood. Using the S1 nuclease assay, we mapped the transcription start site of the nifLA operon, showing it to be similar to the sigma54-dependent promoters. We also identified a positive cis-acting regulatory element (+134 to +790) of the nifLA operon within the coding region of the nifL gene of A. vinelandii. Deletion of this element results in complete loss of promoter activity. Several protein factors bind to this region, and the specific binding sites have been mapped by DNase I foot printing. Two of these sites, namely dR1 (+134 to +204) and dR2 (+745 to +765), are involved in regulating the nifLA promoter activity. The absence of NtrC-like binding sites in the upstream region of the nifLA operon in A. vinelandii makes the identification of these downstream elements a highly significant finding. The interaction of the promoter with the proteins binding to the dR2 region spanning +745 to +765 appears to be dependent on the face of the helix as introduction of 4 bases just before this region completely disrupts promoter activity. Thus, the positive regulatory element present within the BglII-BglII fragment may play, in part; an important role in nifLA regulation in A. vinelandii.
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Affiliation(s)
- Ranjana Mitra
- Gene Regulation Laboratory, Centre for Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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Abstract
A great deal of progress has been made in the studies of fruiting body development and social gliding in Myxocococcus xanthus in the past few years. This includes identification of the bone fide C-signal and a receptor for type IV pili, and development of a model for the mechanism of adventurous gliding motility. It is anticipated that the next few years will see even more progress as the complete genome sequence is available and genomic and proteomic tools are applied to the study of M. xanthus social behaviors.
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Affiliation(s)
- Heidi B Kaplan
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, 6431 Fannin, 1.765 JFB, Houston, TX 77030, USA.
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8
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Sun H, Shi W. Genetic studies of mrp, a locus essential for cellular aggregation and sporulation of Myxococcus xanthus. J Bacteriol 2001; 183:4786-95. [PMID: 11466282 PMCID: PMC99533 DOI: 10.1128/jb.183.16.4786-4795.2001] [Citation(s) in RCA: 81] [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
Under starvation conditions, Myxococcus xanthus undergoes a complex developmental process which includes cellular aggregation and sporulation. A transposon insertion mutant (the Tn5-Omega280 mutant) with defects in both aggregation and sporulation was analyzed in this study. The Tn5-Omega280 mutant was found to have a disrupted NtrC-like response regulator designated Myxococcus regulatory protein B (mrpB). Further sequencing analyses revealed a histidine kinase homolog (mrpA) immediately upstream of mrpB and a cyclic AMP receptor protein-like transcriptional regulator (mrpC) downstream of mrpB. In-frame deletion analyses revealed that both the mrpB and mrpC genes were required for cellular aggregation and sporulation but that only mrpA was required for sporulation only. Site-specific mutagenesis of the putative phosphorylation site of MrpB, D58, showed that a D58A mutation caused defects in both aggregation and sporulation but that a D58E mutation resulted in only a sporulation defect. Further genetic and molecular analyses with reporter genes and reverse transcription-PCR indicated that mrpA and mrpB are cotranscribed but that mrpC is transcribed independently and that all of these genes are developmentally regulated. In addition, MrpB is essential for transcription of mrpC and MrpC regulates its own transcription. These data indicate that Mrp proteins are important components required for M. xanthus development. The complicated interaction between Mrp proteins may play an important role in regulating developmental gene expression in M. xanthus.
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Affiliation(s)
- H Sun
- Molecular Biology Institute and School of Dentistry, University of California, Los Angeles, California 90095, USA
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Hager E, Tse H, Gill RE. Identification and characterization of spdR mutations that bypass the BsgA protease-dependent regulation of developmental gene expression in Myxococcus xanthus. Mol Microbiol 2001; 39:765-80. [PMID: 11169116 DOI: 10.1046/j.1365-2958.2001.02266.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The BsgA protease of Myxococcus xanthus is an intracellular protease closely related to the Lon protease of Escherichia coli. BsgA is required for normal levels of developmentally induced gene expression. In this report, we describe the identification of mutations that suppress the developmental defect of bsgA mutants. These mutations localized to the spdR gene (suppressor protease deficiency regulator) that appears to play a role in the regulation of early developmental gene expression. Mutations in spdR fully restored the ability of a bsgA mutant to form fruiting bodies and spores and, with one exception, restored the expression of several development-specific lacZ fusions. spdR mutants exhibited characteristic phenotypic properties including increased expression of the development-specific tps gene during vegetative growth, formation of fruiting bodies and spores on semi-rich nutrient medium and completion of starvation-induced development in a shorter time period than wild-type strains. The spdR locus was cloned and sequenced and found to encode a member of the NtrC family of two-component transcriptional regulators. One interpretation of these data is that SpdR acts, directly or otherwise, to regulate developmental gene expression negatively and that the BsgA protease is required to relieve this inhibitory effect at the onset of development. However, Western immunoblot analysis indicated that SpdR is present at a relatively constant level during growth and early development in both wild-type and BsgA protease-deficient cells. This finding suggests that BsgA does not function to degrade SpdR at the onset of development.
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Affiliation(s)
- E Hager
- Department of Microbiology, University of Colorado Health Sciences Center, 4200 East 9th Ave., Campus Box B-175, Denver, CO 80262, USA
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10
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Cho K, Treuner-Lange A, O'Connor KA, Zusman DR. Developmental aggregation of Myxococcus xanthus requires frgA, an frz-related gene. J Bacteriol 2000; 182:6614-21. [PMID: 11073903 PMCID: PMC111401 DOI: 10.1128/jb.182.23.6614-6621.2000] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Myxococcus xanthus is a gram-negative bacterium which has a complex life cycle that includes multicellular fruiting body formation. Frizzy mutants are characterized by the formation of tangled filaments instead of hemispherical fruiting bodies on fruiting agar. Mutations in the frz genes have been shown to cause defects in directed motility, which is essential for both vegetative swarming and fruiting body formation. In this paper, we report the discovery of a new gene, called frgA (for frz-related gene), which confers a subset of the frizzy phenotype when mutated. The frgA null mutant showed reduced swarming and the formation of frizzy aggregates on fruiting agar. However, this mutant still displayed directed motility in a spatial chemotaxis assay, whereas the majority of frz mutants fail to show directed movements in this assay. Furthermore, the frizzy phenotype of the frgA mutant could be complemented extracellularly by wild-type cells or strains carrying non-frz mutations. The phenotype of the frgA mutant is similar to that of the abcA mutant and suggests that both of these mutants could be defective in the production or export of extracellular signals required for fruiting body formation rather than in the sensing of such extracellular signals. The frgA gene encodes a large protein of 883 amino acids which lacks homologues in the databases. The frgA gene is part of an operon which includes two additional genes, frgB and frgC. The frgB gene encodes a putative histidine protein kinase, and the frgC gene encodes a putative response regulator. The frgB and frgC null mutants, however, formed wild-type fruiting bodies.
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Affiliation(s)
- K Cho
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3204, USA
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11
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Miyamoto CM, Lin YH, Meighen EA. Control of bioluminescence in Vibrio fischeri by the LuxO signal response regulator. Mol Microbiol 2000; 36:594-607. [PMID: 10844649 DOI: 10.1046/j.1365-2958.2000.01875.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bioluminescence in the marine bacterium Vibrio fischeri is controlled by the excretion of a N-acyl homoserine lactone (HSL) autoinducer which interacts with a regulator, LuxR, and activates transcription of the lux operon at high-cell density. This system has become the prototype for quorum sensing in many bacteria. Although light emission in Vibrio harveyi is also regulated by a N-acyl-HSL inducer, in sharp contrast, a completely different and more complex system is involved in quorum sensing which is mediated via LuxO, the response regulator of a phosphorelay signal transduction system. In the present work, luxO and the overlapping luxU gene, also involved in the phosphorelay system in V. harveyi, have been discovered in V. fischeri. By gene replacement technology, a V. fischeri luxO- mutant was generated whose phenotype was similar to that of V. harveyi luxO- showing that LuxO is involved in control of luminescence in V. fischeri. This mutant could be complemented with luxO from either V. fischeri or V. harveyi resulting in the restoration of the dependence of luminescence intensity on cell density. In contrast to V. harveyi luxO-, light emission of V. fischeri luxO- was stimulated by the N-acyl-HSL autoinducer indicating that luxO is part of a second signal transduction system controlling luminescence in this species. The presence of a luxO-based phosphorelay regulatory system as well as the luxR-based system in V. fischeri suggests that the former system, originally discovered in V. harveyi, may be a general regulatory mechanism in luminescent bacteria.
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Affiliation(s)
- C M Miyamoto
- Department of Biochemistry, Room 813, McIntyre Medical Sciences Building, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada, H3G 1Y6
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Gorski L, Gronewold T, Kaiser D. A sigma(54) activator protein necessary for spore differentiation within the fruiting body of Myxococcus xanthus. J Bacteriol 2000; 182:2438-44. [PMID: 10762243 PMCID: PMC111305 DOI: 10.1128/jb.182.9.2438-2444.2000] [Citation(s) in RCA: 28] [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] Open
Abstract
Insertion of an internal DNA fragment into the act1 gene, which encodes one of several sigma(54)-activator proteins in Myxococcus xanthus, produced a mutant defective in fruiting body development. While fruiting-body aggregation appears normal in the mutant, it fails to sporulate (<10(-6) the wild-type number of viable spores). The A and C intercellular signals, which are required for sporulation, are produced by the mutant. But, while it produces A-factor at levels as high as that of the wild type, the mutant produces much less C-signal than normal, as measured either by C-factor bioassay or by the total amount of C-factor protein detected with specific antibody. Expression of three C-factor-dependent reporters is altered in the mutant: the level of expression of Omega4414 is about 15% of normal, and Omega4459 and Omega4403 have alterations in their time course. Finally, the methylation of FrzCD protein is below normal in the mutant. It is proposed that Act1 protein responds to C-signal reception by increasing the expression of the csgA gene. This C-signal-dependent increase constitutes a positive feedback in the wild type. The act1 mutant, unable to raise the level of csgA expression, carries out only those developmental steps for which a low level of C-signaling is adequate.
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Affiliation(s)
- L Gorski
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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Abstract
The bioluminescent marine bacterium Vibrio harveyi controls light production (lux) by an elaborate quorum-sensing circuit. V. harveyi produces and responds to two different autoinducer signals (AI-1 and AI-2) to modulate the luciferase structural operon (luxCDABEGH) in response to changes in cell-population density. Unlike all other Gram-negative quorum-sensing organisms, V. harveyi regulates quorum sensing using a two-component phosphorylation-dephosphorylation cascade. Each autoinducer is recognized by a cognate hybrid sensor kinase (called LuxN and LuxQ). Both sensors transduce information to a shared phosphorelay protein called LuxU, which in turn conveys the signal to the response regulator protein LuxO. Phospho-LuxO is responsible for repression of luxCDABEGH expression at low cell density. In the present study, we demonstrate that LuxO functions as an activator protein via interaction with the alternative sigma factor, sigma54 (encoded by rpoN). Our results suggest that LuxO, together with sigma54, activates the expression of a negative regulator of luminescence. We also show that phenotypes other than lux are regulated by LuxO and sigma54, demonstrating that in Vibrio harveyi, quorum sensing controls multiple processes.
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Affiliation(s)
- B N Lilley
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544-1014, USA
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Rombel I, North A, Hwang I, Wyman C, Kustu S. The bacterial enhancer-binding protein NtrC as a molecular machine. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:157-66. [PMID: 10384279 DOI: 10.1101/sqb.1998.63.157] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- I Rombel
- Department of Plant and Microbial Biology, University of California, Berkeley 94720, USA
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Debarbouille M, Gardan R, Arnaud M, Rapoport G. Role of bkdR, a transcriptional activator of the sigL-dependent isoleucine and valine degradation pathway in Bacillus subtilis. J Bacteriol 1999; 181:2059-66. [PMID: 10094682 PMCID: PMC93617 DOI: 10.1128/jb.181.7.2059-2066.1999] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new gene, bkdR (formerly called yqiR), encoding a regulator with a central (catalytic) domain was found in Bacillus subtilis. This gene controls the utilization of isoleucine and valine as sole nitrogen sources. Seven genes, previously called yqiS, yqiT, yqiU, yqiV, bfmBAA, bfmBAB, and bfmBB and now referred to as ptb, bcd, buk, lpd, bkdA1, bkdA2, and bkdB, are located downstream from the bkdR gene in B. subtilis. The products of these genes are similar to phosphate butyryl coenzyme A transferase, leucine dehydrogenase, butyrate kinase, and four components of the branched-chain keto acid dehydrogenase complex: E3 (dihydrolipoamide dehydrogenase), E1alpha (dehydrogenase), E1beta (decarboxylase), and E2 (dihydrolipoamide acyltransferase). Isoleucine and valine utilization was abolished in bcd and bkdR null mutants of B. subtilis. The seven genes appear to be organized as an operon, bkd, transcribed from a -12, -24 promoter. The expression of the bkd operon was induced by the presence of isoleucine or valine in the growth medium and depended upon the presence of the sigma factor SigL, a member of the sigma 54 family. Transcription of this operon was abolished in strains containing a null mutation in the regulatory gene bkdR. Deletion analysis showed that upstream activating sequences are involved in the expression of the bkd operon and are probably the target of bkdR. Transcription of the bkd operon is also negatively controlled by CodY, a global regulator of gene expression in response to nutritional conditions.
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Affiliation(s)
- M Debarbouille
- Unité de Biochimie Microbienne, Institut Pasteur, URA 1300 du Centre National de la Recherche Scientifique, 75724 Paris Cedex 15, France.
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16
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Abstract
Nitrogen metabolism genes of Bacillus subtilis are regulated by the availability of rapidly metabolizable nitrogen sources, but not by any mechanism analogous to the two-component Ntr regulatory system found in enteric bacteria. Instead, at least three regulatory proteins independently control the expression of gene products involved in nitrogen metabolism in response to nutrient availability. Genes expressed at high levels during nitrogen-limited growth are controlled by two related proteins, GlnR and TnrA, which bind to similar DNA sequences under different nutritional conditions. The TnrA protein is active only during nitrogen limitation, whereas GlnR-dependent repression occurs in cells growing with excess nitrogen. Although the nitrogen signal regulating the activity of the GlnR and TnrA proteins is not known, the wild-type glutamine synthetase protein is required for the transduction of this signal to the GlnR and TnrA proteins. Examination of GlnR- and TnrA-regulated gene expression suggests that these proteins allow the cell to adapt to growth during nitrogen-limited conditions. A third regulatory protein, CodY, controls the expression of several genes involved in nitrogen metabolism, competence and acetate metabolism in response to growth rate. The highest levels of CodY-dependent repression occur in cells growing rapidly in a medium rich in amino acids, and this regulation is relieved during the transition to nutrient-limited growth. While the synthesis of amino acid degradative enzymes in B. subtilis is substrate inducible, their expression is generally not regulated in response to nitrogen availability by GlnR and TnrA. This pattern of regulation may reflect the fact that the catabolism of amino acids produced by proteolysis during sporulation and germination provides the cell with substrates for energy production and macromolecular synthesis. As a result, expression of amino acid degradative enzymes may be regulated to ensure that high levels of these enzymes are present in sporulating cells and in dormant spores.
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Affiliation(s)
- S H Fisher
- Department of Microbiology, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA.
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Abstract
In response to starvation, myxobacteria build multicellular fruiting bodies that contain many thousands of cells and that have particular species-specific shapes. To coordinate fruiting body development, the myxobacterial cells signal to each other. The timing of and cellular responses to these signals help to give form to the fruiting body. Following identification of several signal molecules, important transcriptional regulators and other signals have recently been identified. Steps on signal transduction pathways have also been defined.
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Affiliation(s)
- D Kaiser
- Department of Biochemistry, Beckman Center, B300, Stanford University School of Medicine, Stanford, CA 94305-5329, USA.
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Gorski L, Kaiser D. Targeted mutagenesis of sigma54 activator proteins in Myxococcus xanthus. J Bacteriol 1998; 180:5896-905. [PMID: 9811647 PMCID: PMC107663 DOI: 10.1128/jb.180.22.5896-5905.1998] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/1997] [Accepted: 09/09/1998] [Indexed: 11/20/2022] Open
Abstract
Myxococcus xanthus DNA segments related to the highly conserved central sequence of sigma54 activator proteins have been investigated. A genetic technique designed to inactivate a gene that encodes such an activator by inserting a plasmid-borne internal fragment of the putative gene has been tested. When the internal fragment inserted by homologous recombination into the corresponding chromosomal locus, the expected duplication of the gene was observed by Southern hybridization. The single restriction fragment characteristic of each segment was replaced in the insertion strains by two hybridizing fragments, and one of these fragments hybridized with the kanamycin resistance gene of the plasmid vector. The combined molecular weights of the two fragments from the insertion strains were equal to the molecular weight of the original fragment plus the expected molecular weight contributed by the vector. In the duplication, one copy is expected to have an N-terminal deletion and the other copy is expected to have a C-terminal deletion. In most cases, the net result should be loss of activator function. If an activator is essential for vegetative growth, then it should not be possible to obtain the insertion strain by plasmid integration. Indeed, integrants for three of the segments were not obtained in repeated trials; however, a plausible explanation for these results other than lethality can be offered. Of the seven insertions validated by Southern hybridization, four strains exhibited defects in the development of fruiting bodies. One of these failed to develop in submerged culture, though it developed normally on agar. The other three showed arrested development of fruiting bodies, each at a morphologically different stage of aggregation. One of the mutants may be defective in the reception pathway of A-signal.
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Affiliation(s)
- L Gorski
- Department of Biochemistry and Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305-5329, USA
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19
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Morel-Deville F, Fauvel F, Morel P. Two-component signal-transducing systems involved in stress responses and vancomycin susceptibility in Lactobacillus sakei. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 10):2873-2883. [PMID: 9802029 DOI: 10.1099/00221287-144-10-2873] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fragments of five rrp genes encoding response regulators (RRs) in Lactobacillus sakei were amplified by PCR using degenerate oligonucleotide primers. The five rrp genes were part of distinct loci that also comprised hpk genes encoding histidine protein kinases (HPKs). The putative RRs belonged to the OmpR-PhoB subclass of response regulators that consist of N-terminal receiver and C-terminal DNA-binding domains. The putative HPKs were members of the EnvZ-NarX family of orthodox histidine protein kinases which possess two transmembrane segments in a non-conserved N-terminal domain and a C-terminal cytoplasmic kinase domain. Insertional inactivation of the rrp genes indicated that the RRs are implicated in susceptibility to the glycopeptide antibiotic vancomycin, and to extreme pH, temperature and oxidative conditions.
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Affiliation(s)
| | - Franck Fauvel
- Laboratoire de Recherche sur la Viandel and La boratoire de Genetique Microbiennez
| | - Patrice Morel
- lnstitut National de la Recherche AgronomiqueDomaine de Vilvert, 78352 Jouy-en-Josas CedexFrance
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20
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Klose KE, Novik V, Mekalanos JJ. Identification of multiple sigma54-dependent transcriptional activators in Vibrio cholerae. J Bacteriol 1998; 180:5256-9. [PMID: 9748465 PMCID: PMC107568 DOI: 10.1128/jb.180.19.5256-5259.1998] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/1998] [Accepted: 07/29/1998] [Indexed: 11/20/2022] Open
Abstract
In the pathogenic bacterium Vibrio cholerae, the alternate sigma factor sigma54 is required for expression of multiple sets of genes, including an unidentified gene(s) necessary for enhanced colonization within the host. To identify sigma54-dependent transcriptional activators involved in colonization, PCR was performed with V. cholerae chromosomal DNA and degenerate primers, revealing six novel and distinct coding sequences with homology to sigma54-dependent activators. One sequence had high homology to the luxO gene of V. harveyi, which in that organism is involved in quorum sensing. Phenotypes of V. cholerae strains containing mutations in each of the six putative sigma54-dependent activator genes identified one as a probable ntrC homologue. None of the mutant strains exhibited a defect in the ability to colonize infant mice, suggesting the presence of additional sigma54-dependent activators not identified by this technique.
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Affiliation(s)
- K E Klose
- Department of Microbiology, University of Texas Health Science Center, San Antonio, Texas 78284-7758, USA
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Klose KE, Mekalanos JJ. Distinct roles of an alternative sigma factor during both free-swimming and colonizing phases of the Vibrio cholerae pathogenic cycle. Mol Microbiol 1998; 28:501-20. [PMID: 9632254 DOI: 10.1046/j.1365-2958.1998.00809.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Vibrio cholerae, the bacterium that causes cholera, has a pathogenic cycle consisting of a free-swimming phase outside its host, and a sessile virulent phase when colonizing the human small intestine. We have cloned the V. cholerae homologue of the rpoN gene (encoding sigma54) and determined its role in the cholera pathogenic cycle by constructing an rpoN null mutant. The V. cholerae rpoN mutant is non-motile; examination of this mutant by electron microscopy revealed that it lacks a flagellum. In addition to flagellar synthesis, sigma54 is involved in glutamine synthetase expression. Moreover, the rpoN mutant is defective for colonization in an infant mouse model of cholera. We present evidence that the colonization defect is distinct from the non-motile and Gln phenotypes of the rpoN mutant, implicating multiple and distinct roles of sigma54 during the V. cholerae pathogenic cycle. RNA polymerase containing sigma54 (sigma54-holoenzyme) has an absolute requirement for an activator protein to initiate transcription. We have identified three regulatory genes, flrABC (flagellar regulatory proteins ABC) that are additionally required for flagellar synthesis. The flrA and flrC gene products are sigma54-activators and form a flagellar transcription cascade. flrA and flrC mutants are also defective for colonization; this phenotype is probably independent of non-motility. An flrC constitutive mutation (M114-->I) was isolated that is independent of its cognate kinase FlrB. Expression of the constitutive FlrCM114-->I from the cholera toxin promoter resulted in a change in cell morphology, implicating involvement of FlrC in cell division. Thus, sigma54 holoenzyme, FlrA and FlrC transcribe genes for flagellar synthesis and possibly cell division during the free-swimming phase of the V. cholerae life cycle, and some as yet unidentified gene(s) that aid colonization within the host.
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Affiliation(s)
- K E Klose
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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Dworkin J, Ninfa AJ, Model P. A protein-induced DNA bend increases the specificity of a prokaryotic enhancer-binding protein. Genes Dev 1998; 12:894-900. [PMID: 9512522 PMCID: PMC316635 DOI: 10.1101/gad.12.6.894] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/1997] [Accepted: 01/27/1998] [Indexed: 02/06/2023]
Abstract
Control of transcription in prokaryotes often involves direct contact of regulatory proteins with RNA polymerase from binding sites located adjacent to the target promoter. Alternatively, in the case of genes transcribed by Escherichia coli RNA polymerase holoenzyme containing the alternate sigma factor sigma54, regulatory proteins bound at more distally located enhancer sites can activate transcription via DNA looping by taking advantage of the increasing flexibility of DNA over longer distances. While this second mechanism offers a greater possible flexibility in the location of these binding sites, it is not clear how the specificity offered by the proximity of the regulatory protein and the polymerase intrinsic to the first mechanism is maintained. Here we demonstrate that integration host factor (IHF), a protein that induces a sharp bend in DNA, acts both to inhibit DNA-looping-dependent transcriptional activation by an inappropriate enhancer-binding protein and to facilitate similar activation by an appropriate enhancer-binding protein. These opposite effects have the consequence of increasing the specificity of activation of a promoter that is susceptible to regulation by proteins bound to a distal site.
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Affiliation(s)
- J Dworkin
- Laboratory of Genetics, The Rockefeller University, New York, New York 10021, USA.
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Yang C, Kaplan HB. Myxococcus xanthus sasS encodes a sensor histidine kinase required for early developmental gene expression. J Bacteriol 1997; 179:7759-67. [PMID: 9401035 PMCID: PMC179739 DOI: 10.1128/jb.179.24.7759-7767.1997] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Initiation of Myxococcus xanthus multicellular development requires integration of information concerning the cells' nutrient status and density. A gain-of-function mutation, sasB7, that bypasses both the starvation and high cell density requirements for developmental expression of the 4521 reporter gene, maps to the sasS gene. The wild-type sasS gene was cloned and sequenced. This gene is predicted to encode a sensor histidine protein kinase that appears to be a key element in the transduction of starvation and cell density inputs. The sasS null mutants express 4521 at a basal level, form defective fruiting bodies, and exhibit reduced sporulation efficiencies. These data indicate that the wild-type sasS gene product functions as a positive regulator of 4521 expression and participates in M. xanthus development. The N terminus of SasS is predicted to contain two transmembrane domains that would locate the protein to the cytoplasmic membrane. The sasB7 mutation, an E139K missense mutation, maps to the predicted N-terminal periplasmic region. The C terminus of SasS contains all of the conserved residues typical of the sensor histidine protein kinases. SasS is predicted to be the sensor protein in a two-component system that integrates information required for M. xanthus developmental gene expression.
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Affiliation(s)
- C Yang
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 77030, USA
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24
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Abstract
Type IV pili are required for social gliding motility in Myxococcus xanthus. In this work, the expression of pilin (the pilA gene product) during vegetative growth and fruiting-body development was examined. A polyclonal antibody against the pilA gene product (prepilin) was prepared, along with a pilA-lacZ fusion, and was used to assay expression of pilA in M. xanthus in different mutant backgrounds. pilA expression required the response regulator pilR but was negatively regulated by the putative sensor kinase pilS. pilA expression did not require pilB, pilC, or pilT. pilA was also autoregulated; a mutation which altered an invariant glutamate five residues from the presumed prepilin processing site eliminated this autoregulation, as did a deletion of the pilA gene. Primer extension and S1 nuclease analysis identified a sigma54 promoter upstream of pilA, consistent with the homology of pilR to the NtrC family of response regulators. Expression of pilA was found to be developmentally regulated; however, the timing of this expression pattern was not entirely dependent on pilS or pilR. Finally, pilA expression was induced by high nutrient concentrations, an effect that was also not dependent on pilS or pilR.
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Affiliation(s)
- S S Wu
- Department of Biochemistry, Stanford University School of Medicine, California 94305, USA
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Morel-Deville F, Ehrlich SD, Morel P. Identification by PCR of genes encoding multiple response regulators. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 5):1513-1520. [PMID: 9168601 DOI: 10.1099/00221287-143-5-1513] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Environmental sensing in bacteria often involves the concerted action of sensor kinases and response regulators. Degenerate oligonucleotide primers were designed on the basis of amino acid similarity in the response regulators of these two-component systems. The primers were used in PCR to specifically amplify an internal DNA segment corresponding to the receiver module domain from genes encoding response regulators. Amplification products of the expected size were obtained from 12 different Gram-positive and Gram-negative bacteria. Sequence analysis revealed that 22 DNA fragments, which clearly originated from response regulator genes, were amplified from Escherichia coli, Agrobacterium tumefaciens, Bacillus subtilis and Lactobacillus bulgaricus. In each of these four species the receiver module of putative response regulator genes, which do not seem to be related to any of the already characterized genes, was identified. This simple and powerful method is therefore particularly useful for discovering new signal transduction systems which cannot be revealed by usual genetic studies.
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Affiliation(s)
- Francoise Morel-Deville
- Laboratoire de Recherche sur la Viand, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France
| | - S Dusko Ehrlich
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France
| | - Patrice Morel
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France
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Keseler IM, Kaiser D. sigma54, a vital protein for Myxococcus xanthus. Proc Natl Acad Sci U S A 1997; 94:1979-84. [PMID: 9050890 PMCID: PMC20028 DOI: 10.1073/pnas.94.5.1979] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/1996] [Indexed: 02/03/2023] Open
Abstract
The rpoN gene encoding the transcription factor sigma54 in Myxococcus xanthus has been cloned using a heterologous rpoN probe. The sequence of the cross-hybridizing DNA confirmed the existence of an ORF 1518 bp long that encodes a well conserved member of the sigma54 family of sigma factors. Low- as well as high-stringency hybridizations detected only a single rpoN gene in the M. xanthus chromosome. In other bacteria, sigma54 is an alternative sigma, and null mutants are viable. However, all attempts to construct a strain containing a null mutation in the M. xanthus rpoN have been unsuccessful. Partial diploids of rpoN+/rpoN null are viable. Recombination experiments with such partial diploids showed the impossibility of constructing, either by segregation or by transduction, a viable null haploid under any of a wide range of growth conditions. The product of the rpoN gene, sigma54, therefore appears to be essential for growth in M. xanthus.
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Affiliation(s)
- I M Keseler
- Department of Biochemistry, Stanford University School of Medicine, CA 94305-5307, USA
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