1
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Edwards AN, McBride SM. The RgaS-RgaR two-component system promotes Clostridioides difficile sporulation through a small RNA and the Agr1 system. PLoS Genet 2023; 19:e1010841. [PMID: 37844084 PMCID: PMC10602386 DOI: 10.1371/journal.pgen.1010841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/26/2023] [Accepted: 10/02/2023] [Indexed: 10/18/2023] Open
Abstract
The ability to form a dormant spore is essential for the survival of the anaerobic pathogen, Clostridioides difficile, outside of the mammalian gastrointestinal tract. The initiation of sporulation is governed by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple sporulation factors control Spo0A phosphorylation; however, this regulatory pathway is not well defined in C. difficile. We discovered that RgaS and RgaR, a conserved orphan histidine kinase and orphan response regulator, function together as a cognate two-component regulatory system to directly activate transcription of several genes. One of these targets, agrB1D1, encodes gene products that synthesize and export a small quorum-sensing peptide, AgrD1, which positively influences expression of early sporulation genes. Another target, a small regulatory RNA now known as SpoZ, impacts later stages of sporulation through a small hypothetical protein and an additional, unknown regulatory mechanism(s). Unlike Agr systems in many organisms, AgrD1 does not activate the RgaS-RgaR two-component system, and thus, is not responsible for autoregulating its own production. Altogether, we demonstrate that C. difficile utilizes a conserved two-component system that is uncoupled from quorum-sensing to promote sporulation through two distinct regulatory pathways.
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Affiliation(s)
- Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
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2
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Alenezi T, Fu Y, Alrubaye B, Alanazi T, Almansour A, Wang H, Sun X. Potent Bile Acid Microbial Metabolites Modulate Clostridium perfringens Virulence. Pathogens 2023; 12:1202. [PMID: 37887718 PMCID: PMC10610205 DOI: 10.3390/pathogens12101202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Clostridium perfringens is a versatile pathogen, inducing diseases in the skin, intestine (such as chicken necrotic enteritis (NE)), and other organs. The classical sign of NE is the foul smell gas in the ballooned small intestine. We hypothesized that deoxycholic acid (DCA) reduced NE by inhibiting C. perfringens virulence signaling pathways. To evaluate the hypothesis, C. perfringens strains CP1 and wild-type (WT) HN13 and its mutants were cultured with different bile acids, including DCA and isoallolithocholic acid (isoalloLCA). Growth, hydrogen sulfide (H2S) production, and virulence gene expression were measured. Notably, isoalloLCA was more potent in reducing growth, H2S production, and virulence gene expression in CP1 and WT HN13 compared to DCA, while other bile acids were less potent compared to DCA. Interestingly, there was a slightly different impact between DCA and isoalloLCA on the growth, H2S production, and virulence gene expression in the three HN13 mutants, suggesting possibly different signaling pathways modulated by the two bile acids. In conclusion, DCA and isoalloLCA reduced C. perfringens virulence by transcriptionally modulating the pathogen signaling pathways. The findings could be used to design new strategies to prevent and treat C. perfringens-induced diseases.
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Affiliation(s)
- Tahrir Alenezi
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (T.A.); (Y.F.); (B.A.); (T.A.); (A.A.); (H.W.)
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA
- College of Medical Applied Sciences, The Northern Border University, Arar 91431, Saudi Arabia
| | - Ying Fu
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (T.A.); (Y.F.); (B.A.); (T.A.); (A.A.); (H.W.)
| | - Bilal Alrubaye
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (T.A.); (Y.F.); (B.A.); (T.A.); (A.A.); (H.W.)
| | - Thamer Alanazi
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (T.A.); (Y.F.); (B.A.); (T.A.); (A.A.); (H.W.)
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ayidh Almansour
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (T.A.); (Y.F.); (B.A.); (T.A.); (A.A.); (H.W.)
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA
| | - Hong Wang
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (T.A.); (Y.F.); (B.A.); (T.A.); (A.A.); (H.W.)
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA
| | - Xiaolun Sun
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (T.A.); (Y.F.); (B.A.); (T.A.); (A.A.); (H.W.)
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA
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3
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Edwards AN, McBride SM. The RgaS-RgaR two-component system promotes Clostridioides difficile sporulation through a small RNA and the Agr1 system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546640. [PMID: 37425791 PMCID: PMC10327067 DOI: 10.1101/2023.06.26.546640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The ability to form a dormant spore is essential for the survival of the anaerobic, gastrointestinal pathogen Clostridioides difficile outside of the mammalian gastrointestinal tract. The initiation of sporulation is governed by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple sporulation factors control Spo0A phosphorylation; however, this regulatory pathway is not well defined in C. difficile. We discovered that RgaS and RgaR, a conserved orphan histidine kinase and orphan response regulator, function together as a cognate two-component regulatory system to directly activate transcription of several genes. One of these targets, agrB1D1, encodes gene products that synthesize and export a small quorum-sensing peptide, AgrD1, which positively influences expression of early sporulation genes. Another target, a small regulatory RNA now known as SrsR, impacts later stages of sporulation through an unknown regulatory mechanism(s). Unlike Agr systems in many organisms, AgrD1 does not activate the RgaS-RgaR two-component system, and thus, is not responsible for autoregulating its own production. Altogether, we demonstrate that C. difficile utilizes a conserved two-component system that is uncoupled from quorum-sensing to promote sporulation through two distinct regulatory pathways.
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Affiliation(s)
- Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
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4
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Neuwirth T, Letzel AC, Tank C, Ishida K, Cyrulies M, Schmölz L, Lorkowski S, Hertweck C. Induced Production, Synthesis, and Immunomodulatory Action of Clostrisulfone, a Diarylsulfone from Clostridium acetobutylicum. Chemistry 2020; 26:15855-15858. [PMID: 32996646 PMCID: PMC7756337 DOI: 10.1002/chem.202003500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/29/2020] [Indexed: 01/25/2023]
Abstract
The anaerobe Clostridium acetobutylicum belongs to the most important industrially used bacteria. Whereas genome mining points to a high potential for secondary metabolism in C. acetobutylicum, the functions of most biosynthetic gene clusters are cryptic. We report that the addition of supra‐physiological concentrations of cysteine triggered the formation of a novel natural product, clostrisulfone (1). Its structure was fully elucidated by NMR, MS and the chemical synthesis of a reference compound. Clostrisulfone is the first reported natural product with a diphenylsulfone scaffold. A biomimetic synthesis suggests that pentamethylchromanol‐derived radicals capture sulfur dioxide to form 1. In a cell‐based assay using murine macrophages a biphasic and dose‐dependent regulation of the LPS‐induced release of nitric oxide was observed in the presence of 1.
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Affiliation(s)
- Toni Neuwirth
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Anne-Catrin Letzel
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Cedric Tank
- BioPilotPlant, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Michael Cyrulies
- BioPilotPlant, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Lisa Schmölz
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Straße 25, 07743, Jena, Germany
| | - Stefan Lorkowski
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Straße 25, 07743, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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5
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Transcriptional Profiling of the Probiotic Escherichia coli Nissle 1917 Strain under Simulated Microgravity. Int J Mol Sci 2020; 21:ijms21082666. [PMID: 32290466 PMCID: PMC7215827 DOI: 10.3390/ijms21082666] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/05/2020] [Accepted: 04/09/2020] [Indexed: 12/16/2022] Open
Abstract
Long-term space missions affect the gut microbiome of astronauts, especially the viability of some pathogens. Probiotics may be an effective solution for the management of gut microbiomes, but there is a lack of studies regarding the physiology of probiotics in microgravity. Here, we investigated the effects of microgravity on the probiotic Escherichia coli Nissle 1917 (EcN) by comparing transcriptomic data during exponential and stationary growth phases under simulated microgravity and normal gravity. Microgravity conditions affected several physiological features of EcN, including its growth profile, biofilm formation, stress responses, metal ion transport/utilization, and response to carbon starvation. We found that some changes, such as decreased adhesion ability and acid resistance, may be disadvantageous to EcN relative to gut pathogens under microgravity, indicating the need to develop probiotics optimized for space flight.
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6
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Lensmire JM, Hammer ND. Nutrient sulfur acquisition strategies employed by bacterial pathogens. Curr Opin Microbiol 2019; 47:52-58. [DOI: 10.1016/j.mib.2018.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/04/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
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7
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Wüthrich D, Wenzel C, Bavan T, Bruggmann R, Berthoud H, Irmler S. Transcriptional Regulation of Cysteine and Methionine Metabolism in Lactobacillus paracasei FAM18149. Front Microbiol 2018; 9:1261. [PMID: 29942297 PMCID: PMC6004538 DOI: 10.3389/fmicb.2018.01261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/24/2018] [Indexed: 11/13/2022] Open
Abstract
Lactobacillus paracasei is common in the non-starter lactic acid bacteria (LAB) community of raw milk cheeses. This species can significantly contribute to flavor formation through amino acid metabolism. In this study, the DNA and RNA of L. paracasei FAM18149 were sequenced using next-generation sequencing technologies to reconstruct the metabolism of the sulfur-containing amino acids cysteine and methionine. Twenty-three genes were found to be involved in cysteine biosynthesis, the conversion of cysteine to methionine and vice versa, the S-adenosylmethionine recycling pathway, and the transport of sulfur-containing amino acids. Additionally, six methionine-specific T-boxes and one cysteine-specific T-box were found. Five of these were located upstream of genes encoding transporter functions. RNA-seq analysis and reverse-transcription quantitative polymerase reaction assays showed that expression of genes located downstream of these T-boxes was affected by the absence of either cysteine or methionine. Remarkably, the cysK2-ctl1-cysE2 operon, which is associated with te methionine-to-cysteine conversion and is upregulated in the absence of cysteine, showed high read coverage in the 5′-untranslated region and an antisense-RNA in the 3′-untranslated region. This indicates that this operon is regulated by the combination of cis- and antisense-mediated regulation mechanisms. The results of this study may help in the selection of L. paracasei strains to control sulfuric flavor formation in cheese.
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Affiliation(s)
- Daniel Wüthrich
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
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8
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Zouch H, Karray F, Armougom F, Chifflet S, Hirschler-Réa A, Kharrat H, Kamoun L, Ben Hania W, Ollivier B, Sayadi S, Quéméneur M. Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia). Front Microbiol 2017; 8:1583. [PMID: 28871244 PMCID: PMC5566975 DOI: 10.3389/fmicb.2017.01583] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 08/04/2017] [Indexed: 11/13/2022] Open
Abstract
Anaerobic biotechnology using sulfate-reducing bacteria (SRB) is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG), an acidic (pH ~3) by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of anaerobic marine microorganisms to convert sulfate from PG into sulfide, in order to look for marine SRB of biotechnological interest. A series of sulfate-reducing enrichment cultures were performed using different electron donors (i.e., acetate, formate, or lactate) and sulfate sources (i.e., sodium sulfate or PG) as electron acceptors. Significant sulfide production was observed from enrichment cultures inoculated with marine sediments, collected near the effluent discharge point of a Tunisian fertilizer industry (Sfax, Tunisia). Sulfate sources impacted sulfide production rates from marine sediments as well as the diversity of SRB species belonging to Deltaproteobacteria. When PG was used as sulfate source, Desulfovibrio species dominated microbial communities of marine sediments, while Desulfobacter species were mainly detected using sodium sulfate. Sulfide production was also affected depending on the electron donor used, with the highest production obtained using formate. In contrast, low sulfide production (acetate-containing cultures) was associated with an increase in the population of Firmicutes. These results suggested that marine Desulfovibrio species, to be further isolated, are potential candidates for bioremediation of PG by immobilizing metals and metalloids thanks to sulfide production by these SRB.
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Affiliation(s)
- Hana Zouch
- Laboratory of Environmental Bioprocesses, LMI COSYS-Med, Biotechnology Center of SfaxSfax, Tunisia
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, LMI COSYS-Med, Biotechnology Center of SfaxSfax, Tunisia
| | - Fabrice Armougom
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Sandrine Chifflet
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Agnès Hirschler-Réa
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Hanen Kharrat
- Laboratory of Environmental Bioprocesses, LMI COSYS-Med, Biotechnology Center of SfaxSfax, Tunisia
| | - Lotfi Kamoun
- Department of Research, Tunisian Chemical GroupSfax, Tunisia
| | - Wajdi Ben Hania
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Bernard Ollivier
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
| | - Sami Sayadi
- Laboratory of Environmental Bioprocesses, LMI COSYS-Med, Biotechnology Center of SfaxSfax, Tunisia
| | - Marianne Quéméneur
- Laboratory of Environmental Bioprocesses, LMI COSYS-Med, Biotechnology Center of SfaxSfax, Tunisia
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110Marseille, France
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9
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Control of Clostridium difficile Physiopathology in Response to Cysteine Availability. Infect Immun 2016; 84:2389-405. [PMID: 27297391 DOI: 10.1128/iai.00121-16] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/31/2016] [Indexed: 11/20/2022] Open
Abstract
The pathogenicity of Clostridium difficile is linked to its ability to produce two toxins: TcdA and TcdB. The level of toxin synthesis is influenced by environmental signals, such as phosphotransferase system (PTS) sugars, biotin, and amino acids, especially cysteine. To understand the molecular mechanisms of cysteine-dependent repression of toxin production, we reconstructed the sulfur metabolism pathways of C. difficile strain 630 in silico and validated some of them by testing C. difficile growth in the presence of various sulfur sources. High levels of sulfide and pyruvate were produced in the presence of 10 mM cysteine, indicating that cysteine is actively catabolized by cysteine desulfhydrases. Using a transcriptomic approach, we analyzed cysteine-dependent control of gene expression and showed that cysteine modulates the expression of genes involved in cysteine metabolism, amino acid biosynthesis, fermentation, energy metabolism, iron acquisition, and the stress response. Additionally, a sigma factor (SigL) and global regulators (CcpA, CodY, and Fur) were tested to elucidate their roles in the cysteine-dependent regulation of toxin production. Among these regulators, only sigL inactivation resulted in the derepression of toxin gene expression in the presence of cysteine. Interestingly, the sigL mutant produced less pyruvate and H2S than the wild-type strain. Unlike cysteine, the addition of 10 mM pyruvate to the medium for a short time during the growth of the wild-type and sigL mutant strains reduced expression of the toxin genes, indicating that cysteine-dependent repression of toxin production is mainly due to the accumulation of cysteine by-products during growth. Finally, we showed that the effect of pyruvate on toxin gene expression is mediated at least in part by the two-component system CD2602-CD2601.
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Martin-Verstraete I, Peltier J, Dupuy B. The Regulatory Networks That Control Clostridium difficile Toxin Synthesis. Toxins (Basel) 2016; 8:E153. [PMID: 27187475 PMCID: PMC4885068 DOI: 10.3390/toxins8050153] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 05/03/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022] Open
Abstract
The pathogenic clostridia cause many human and animal diseases, which typically arise as a consequence of the production of potent exotoxins. Among the enterotoxic clostridia, Clostridium difficile is the main causative agent of nosocomial intestinal infections in adults with a compromised gut microbiota caused by antibiotic treatment. The symptoms of C. difficile infection are essentially caused by the production of two exotoxins: TcdA and TcdB. Moreover, for severe forms of disease, the spectrum of diseases caused by C. difficile has also been correlated to the levels of toxins that are produced during host infection. This observation strengthened the idea that the regulation of toxin synthesis is an important part of C. difficile pathogenesis. This review summarizes our current knowledge about the regulators and sigma factors that have been reported to control toxin gene expression in response to several environmental signals and stresses, including the availability of certain carbon sources and amino acids, or to signaling molecules, such as the autoinducing peptides of quorum sensing systems. The overlapping regulation of key metabolic pathways and toxin synthesis strongly suggests that toxin production is a complex response that is triggered by bacteria in response to particular states of nutrient availability during infection.
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Affiliation(s)
- Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bactéries Anaérobes, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux Paris, Paris 75015, France.
- UFR Sciences du vivant, University Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris 75015, France.
| | - Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobes, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux Paris, Paris 75015, France.
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobes, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux Paris, Paris 75015, France.
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11
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André G, Haudecoeur E, Courtois E, Monot M, Dupuy B, Rodionov DA, Martin-Verstraete I. Cpe1786/IscR of Clostridium perfringens represses expression of genes involved in Fe-S cluster biogenesis. Res Microbiol 2016; 168:345-355. [PMID: 27020244 DOI: 10.1016/j.resmic.2016.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/14/2016] [Accepted: 03/16/2016] [Indexed: 12/27/2022]
Abstract
Cpe1786 of Clostridium perfringens is an Rrf2-type regulator containing the three-cysteine residues coordinating a Fe-S in IscR, the repressor controlling Fe-S homeostasis in enterobacteria. The cpe1786 gene formed an operon with iscSU involved in Fe-S biogenesis and tmrU. This operon was transcribed from a σA-dependent promoter. We showed that in the heterologous host Bacillus subtilis, Cpe1786, renamed IscRCp, negatively controlled its own transcription. We constructed an iscR mutant in C. perfringens. We then compared the expression profile of strain 13 and of the iscR mutant. IscRCp controlled expression of genes involved in Fe-S biogenesis, in amino acid or sugar metabolisms, in fermentation pathways and in host compound utilization. We then demonstrated, using a ChIP-PCR experiment, that IscRCp interacted with its promoter region in vivo in C. perfringens and with the promoter of cpe2093 encoding an amino acid ABC transporter. We utilized a comparative genomic approach to infer a candidate IscR binding motif and reconstruct IscR regulons in clostridia. We showed that point mutations in the conserved motif of 29 bp identified upstream of iscR decreased the cysteine-dependent repression of iscR mediated by IscRCp.
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Affiliation(s)
- Gaelle André
- Institut Pasteur, Laboratoire de Pathogénèse des Bactéries anaérobies, 28 rue du Docteur Roux, 75015 Paris, France; Université Paris 7-Denis Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Elise Haudecoeur
- Institut Pasteur, Laboratoire de Pathogénèse des Bactéries anaérobies, 28 rue du Docteur Roux, 75015 Paris, France; Université Paris 7-Denis Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Emmanuelle Courtois
- Institut Pasteur, Laboratoire de Pathogénèse des Bactéries anaérobies, 28 rue du Docteur Roux, 75015 Paris, France; Université Paris 7-Denis Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Marc Monot
- Institut Pasteur, Laboratoire de Pathogénèse des Bactéries anaérobies, 28 rue du Docteur Roux, 75015 Paris, France; Université Paris 7-Denis Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Bruno Dupuy
- Institut Pasteur, Laboratoire de Pathogénèse des Bactéries anaérobies, 28 rue du Docteur Roux, 75015 Paris, France; Université Paris 7-Denis Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Dmitry A Rodionov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Laboratoire de Pathogénèse des Bactéries anaérobies, 28 rue du Docteur Roux, 75015 Paris, France; Université Paris 7-Denis Diderot, Sorbonne Paris Cité, 75205 Paris, France.
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12
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Ferrario C, Duranti S, Milani C, Mancabelli L, Lugli GA, Turroni F, Mangifesta M, Viappiani A, Ossiprandi MC, van Sinderen D, Ventura M. Exploring Amino Acid Auxotrophy in Bifidobacterium bifidum PRL2010. Front Microbiol 2015; 6:1331. [PMID: 26635786 PMCID: PMC4656816 DOI: 10.3389/fmicb.2015.01331] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/12/2015] [Indexed: 01/01/2023] Open
Abstract
The acquisition and assimilation strategies followed by members of the infant gut microbiota to retrieve nitrogen from the gut lumen are still largely unknown. In particular, no information on these metabolic processes is available regarding bifidobacteria, which are among the first microbial colonizers of the human intestine. Here, evaluation of amino acid auxotrophy and prototrophy of Bifidobacterium bifidum, with particular emphasis on B. bifidum strain PRL2010 (LMG S-28692), revealed a putative auxotrophy for cysteine. In addition, we hypothesized that cysteine plays a role in the oxidative stress response in B. bifidum. The use of glutathione as an alternative reduced sulfur compound did not alleviate cysteine auxotrophy of this strain, though it was shown to stimulate expression of the genes involved in cysteine biosynthesis, reminiscent of oxidative stress response. When PRL2010 was grown on a medium containing complex substrates, such as whey proteins or casein hydrolysate, we noticed a distinct growth-promoting effect of these compounds. Transcriptional analysis involving B. bifidum PRL2010 cultivated on whey proteins or casein hydrolysate revealed that the biosynthetic pathways for cysteine and methionine are modulated by the presence of casein hydrolysate. Such findings support the notion that certain complex substrates may act as potential prebiotics for bifidobacteria in their ecological niche.
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Affiliation(s)
- Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | | | | | - Maria C Ossiprandi
- Department of Medical-Veterinary Science, University of Parma Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, University College Cork, National University of Ireland Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
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What a difference a cluster makes: The multifaceted roles of IscR in gene regulation and DNA recognition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1101-12. [PMID: 25641558 DOI: 10.1016/j.bbapap.2015.01.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 01/21/2015] [Indexed: 11/22/2022]
Abstract
Iron-sulfur clusters are essential cofactors in a myriad of metabolic pathways. Therefore, their biogenesis is tightly regulated across a variety of organisms and environmental conditions. In Gram-negative bacteria, two pathways - ISC and SUF - concur for maintaining intracellular iron-sulfur cluster balance. Recently, the mechanism of iron-sulfur cluster biosynthesis regulation by IscR, an iron-sulfur cluster-containing regulator encoded by the isc operon, was found to be conserved in some Gram-positive bacteria. Belonging to the Rrf2 family of transcriptional regulators, IscR displays a single helix-turn-helix DNA-binding domain but is able to recognize two distinct DNA sequence motifs, switching its specificity upon cluster ligation. This review provides an overview of gene regulation by iron-sulfur cluster-containing sensors, in the light of the recent structural characterization of cluster-less free and DNA-bound IscR, which provided insights into the molecular mechanism of nucleotide sequence recognition and discrimination of this unique transcription factor. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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The unique regulation of iron-sulfur cluster biogenesis in a Gram-positive bacterium. Proc Natl Acad Sci U S A 2014; 111:E2251-60. [PMID: 24847070 DOI: 10.1073/pnas.1322728111] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Iron-sulfur clusters function as cofactors of a wide range of proteins, with diverse molecular roles in both prokaryotic and eukaryotic cells. Dedicated machineries assemble the clusters and deliver them to the final acceptor molecules in a tightly regulated process. In the prototypical Gram-negative bacterium Escherichia coli, the two existing iron-sulfur cluster assembly systems, iron-sulfur cluster (ISC) and sulfur assimilation (SUF) pathways, are closely interconnected. The ISC pathway regulator, IscR, is a transcription factor of the helix-turn-helix type that can coordinate a [2Fe-2S] cluster. Redox conditions and iron or sulfur availability modulate the ligation status of the labile IscR cluster, which in turn determines a switch in DNA sequence specificity of the regulator: cluster-containing IscR can bind to a family of gene promoters (type-1) whereas the clusterless form recognizes only a second group of sequences (type-2). However, iron-sulfur cluster biogenesis in Gram-positive bacteria is not so well characterized, and most organisms of this group display only one of the iron-sulfur cluster assembly systems. A notable exception is the unique Gram-positive dissimilatory metal reducing bacterium Thermincola potens, where genes from both systems could be identified, albeit with a diverging organization from that of Gram-negative bacteria. We demonstrated that one of these genes encodes a functional IscR homolog and is likely involved in the regulation of iron-sulfur cluster biogenesis in T. potens. Structural and biochemical characterization of T. potens and E. coli IscR revealed a strikingly similar architecture and unveiled an unforeseen conservation of the unique mechanism of sequence discrimination characteristic of this distinctive group of transcription regulators.
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El Meouche I, Peltier J, Monot M, Soutourina O, Pestel-Caron M, Dupuy B, Pons JL. Characterization of the SigD regulon of C. difficile and its positive control of toxin production through the regulation of tcdR. PLoS One 2013; 8:e83748. [PMID: 24358307 PMCID: PMC3865298 DOI: 10.1371/journal.pone.0083748] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 11/07/2013] [Indexed: 02/04/2023] Open
Abstract
Clostridium difficile intestinal disease is mediated largely by the actions of toxins A (TcdA) and B (TcdB), whose production occurs after the initial steps of colonization involving different surface or flagellar proteins. In B. subtilis, the sigma factor SigD controls flagellar synthesis, motility, and vegetative autolysins. A homolog of SigD encoding gene is present in the C.difficile 630 genome. We constructed a sigD mutant in C. difficile 630 ∆erm to analyze the regulon of SigD using a global transcriptomic approach. A total of 103 genes were differentially expressed between the wild-type and the sigD mutant, including genes involved in motility, metabolism and regulation. In addition, the sigD mutant displayed decreased expression of genes involved in flagellar biosynthesis, and also of genes encoding TcdA and TcdB as well as TcdR, the positive regulator of the toxins. Genomic analysis and RACE-PCR experiments allowed us to characterize promoter sequences of direct target genes of SigD including tcdR and to identify the SigD consensus. We then established that SigD positively regulates toxin expression via direct control of tcdR transcription. Interestingly, the overexpression of FlgM, a putative anti-SigD factor, inhibited the positive regulation of motility and toxin synthesis by SigD. Thus, SigD appears to be the first positive regulator of the toxin synthesis in C. difficile.
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Affiliation(s)
- Imane El Meouche
- Laboratoire G.R.A.M. (EA 2656 IFR 23 IHURBM), Université de Rouen, Rouen, France
| | - Johann Peltier
- Laboratoire G.R.A.M. (EA 2656 IFR 23 IHURBM), Université de Rouen, Rouen, France
- * E-mail:
| | - Marc Monot
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Olga Soutourina
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Martine Pestel-Caron
- Laboratoire G.R.A.M. (EA 2656 IFR 23 IHURBM), Université de Rouen, Rouen, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Jean-Louis Pons
- Laboratoire G.R.A.M. (EA 2656 IFR 23 IHURBM), Université de Rouen, Rouen, France
- Laboratoire Ecosystème intestinal, Probiotiques, Antibiotiques (EA 4065, IFR IMTCE), Université Paris Descartes, Paris, France
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16
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Structural requirement in Clostridium perfringens collagenase mRNA 5' leader sequence for translational induction through small RNA-mRNA base pairing. J Bacteriol 2013; 195:2937-46. [PMID: 23585542 DOI: 10.1128/jb.00148-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Gram-positive anaerobic bacterium Clostridium perfringens is pathogenic to humans and animals, and the production of its toxins is strictly regulated during the exponential phase. We recently found that the 5' leader sequence of the colA transcript encoding collagenase, which is a major toxin of this organism, is processed and stabilized in the presence of the small RNA VR-RNA. The primary colA 5'-untranslated region (5'UTR) forms a long stem-loop structure containing an internal bulge and masks its own ribosomal binding site. Here we found that VR-RNA directly regulates colA expression through base pairing with colA mRNA in vivo. However, when the internal bulge structure was closed by point mutations in colA mRNA, translation ceased despite the presence of VR-RNA. In addition, a mutation disrupting the colA stem-loop structure induced mRNA processing and ColA-FLAG translational activation in the absence of VR-RNA, indicating that the stem-loop and internal bulge structure of the colA 5' leader sequence is important for regulation by VR-RNA. On the other hand, processing was required for maximal ColA expression but was not essential for VR-RNA-dependent colA regulation. Finally, colA processing and translational activation were induced at a high temperature without VR-RNA. These results suggest that inhibition of the colA 5' leader structure through base pairing is the primary role of VR-RNA in colA regulation and that the colA 5' leader structure is a possible thermosensor.
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Schmidt MC, Rocha AM, Padmanabhan K, Shpanskaya Y, Banfield J, Scott K, Mihelcic JR, Samatova NF. NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems. PLoS Comput Biol 2012; 8:e1002490. [PMID: 22589706 PMCID: PMC3349732 DOI: 10.1371/journal.pcbi.1002490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 03/08/2012] [Indexed: 02/07/2023] Open
Abstract
Understanding of genotype-phenotype associations is important not only for furthering our knowledge on internal cellular processes, but also essential for providing the foundation necessary for genetic engineering of microorganisms for industrial use (e.g., production of bioenergy or biofuels). However, genotype-phenotype associations alone do not provide enough information to alter an organism's genome to either suppress or exhibit a phenotype. It is important to look at the phenotype-related genes in the context of the genome-scale network to understand how the genes interact with other genes in the organism. Identification of metabolic subsystems involved in the expression of the phenotype is one way of placing the phenotype-related genes in the context of the entire network. A metabolic system refers to a metabolic network subgraph; nodes are compounds and edges labels are the enzymes that catalyze the reaction. The metabolic subsystem could be part of a single metabolic pathway or span parts of multiple pathways. Arguably, comparative genome-scale metabolic network analysis is a promising strategy to identify these phenotype-related metabolic subsystems. Network Instance-Based Biased Subgraph Search (NIBBS) is a graph-theoretic method for genome-scale metabolic network comparative analysis that can identify metabolic systems that are statistically biased toward phenotype-expressing organismal networks. We set up experiments with target phenotypes like hydrogen production, TCA expression, and acid-tolerance. We show via extensive literature search that some of the resulting metabolic subsystems are indeed phenotype-related and formulate hypotheses for other systems in terms of their role in phenotype expression. NIBBS is also orders of magnitude faster than MULE, one of the most efficient maximal frequent subgraph mining algorithms that could be adjusted for this problem. Also, the set of phenotype-biased metabolic systems output by NIBBS comes very close to the set of phenotype-biased subgraphs output by an exact maximally-biased subgraph enumeration algorithm ( MBS-Enum ). The code (NIBBS and the module to visualize the identified subsystems) is available at http://freescience.org/cs/NIBBS.
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Affiliation(s)
- Matthew C. Schmidt
- Department of Computer Science, North Carolina State University, Raleigh, North Carolina, United States of America
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Andrea M. Rocha
- Department of Civil and Environmental Engineering, University of South Florida, Tampa, Florida, United States of America
| | - Kanchana Padmanabhan
- Department of Computer Science, North Carolina State University, Raleigh, North Carolina, United States of America
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Yekaterina Shpanskaya
- Neuroscience Department, Duke University, Durham, North Carolina, United States of America
| | - Jill Banfield
- Departments of Earth and Planetary Science, University of California, Berkeley, California, United States of America
- Environmental Science, Policy, & Management, University of California, Berkeley, California, United States of America
- Geochemistry Department, Lawrence Berkeley National Laboratory Earth Sciences Division, Berkeley, California, United States of America
| | - Kathleen Scott
- Department of Integrative Biology, University of South Florida, Tampa, Florida, United States of America
| | - James R. Mihelcic
- Department of Civil and Environmental Engineering, University of South Florida, Tampa, Florida, United States of America
| | - Nagiza F. Samatova
- Department of Computer Science, North Carolina State University, Raleigh, North Carolina, United States of America
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
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18
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Complex transcriptional regulation of citrate metabolism in Clostridium perfringens. Anaerobe 2011; 18:48-54. [PMID: 21945821 DOI: 10.1016/j.anaerobe.2011.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/26/2011] [Accepted: 09/12/2011] [Indexed: 11/23/2022]
Abstract
A Gram-positive, spore-forming bacterium, Clostridium perfringens, possesses genes for citrate metabolism, which might play an important role in the utilization of citrate as a sole carbon source. In this study, we identified a chromosomal citCDEFX-mae-citS operon in C. perfringens strain 13, which is transcribed on three mRNAs of different sizes. Expression of the cit operon was significantly induced when 5 mM extracellular citrate was added to the growth medium. Most interestingly, three regulatory systems were found to be involved in the regulation of the expression of cit genes: 1) the two upstream divergent genes citG and citI; 2) two different two-component regulatory systems, CitA/CitB (TCS6 consisted of CPE0531/CPE0532) and TCS5 (CPE0518/CPE0519); and 3) the global two-component VirR/VirS-VR-RNA regulatory system known to regulate various genes for toxins and degradative enzymes. Our results suggest that in C. perfringens the citrate metabolism might be strictly controlled by a complex regulatory system.
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The key sigma factor of transition phase, SigH, controls sporulation, metabolism, and virulence factor expression in Clostridium difficile. J Bacteriol 2011; 193:3186-96. [PMID: 21572003 DOI: 10.1128/jb.00272-11] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Toxin synthesis in Clostridium difficile increases as cells enter into stationary phase. We first compared the expression profiles of strain 630E during exponential growth and at the onset of stationary phase and showed that genes involved in sporulation, cellular division, and motility, as well as carbon and amino acid metabolism, were differentially expressed under these conditions. We inactivated the sigH gene, which encodes an alternative sigma factor involved in the transition to post-exponential phase in Bacillus subtilis. Then, we compared the expression profiles of strain 630E and the sigH mutant after 10 h of growth. About 60% of the genes that were differentially expressed between exponential and stationary phases, including genes involved in motility, sporulation, and metabolism, were regulated by SigH, which thus appears to be a key regulator of the transition phase in C. difficile. SigH positively controls several genes required for sporulation. Accordingly, sigH inactivation results in an asporogeneous phenotype. The spo0A and CD2492 genes, encoding the master regulator of sporulation and one of its associated kinases, and the spoIIA operon were transcribed from a SigH-dependent promoter. The expression of tcdA and tcdB, encoding the toxins, and of tcdR, encoding the sigma factor required for toxin production, increased in a sigH mutant. Finally, SigH regulates the expression of genes encoding surface-associated proteins, such as the Cwp66 adhesin, the S-layer precursor, and the flagellum components. Among the 286 genes positively regulated by SigH, about 40 transcriptional units presenting a SigH consensus in their promoter regions are good candidates for direct SigH targets.
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