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Astorch-Cardona A, Odin GP, Chavagnac V, Dolla A, Gaussier H, Rommevaux C. Linking Zetaproteobacterial diversity and substratum type in iron-rich microbial mats from the Lucky Strike hydrothermal field (EMSO-Azores observatory). Appl Environ Microbiol 2024; 90:e0204123. [PMID: 38193671 PMCID: PMC10880625 DOI: 10.1128/aem.02041-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Zetaproteobacteria have been reported in different marine and terrestrial environments all over the globe. They play an essential role in marine iron-rich microbial mats, as one of their autotrophic primary producers, oxidizing Fe(II) and producing Fe-oxyhydroxides with different morphologies. Here, we study and compare the Zetaproteobacterial communities of iron-rich microbial mats from six different sites of the Lucky Strike Hydrothermal Field through the use of the Zetaproteobacterial operational taxonomic unit (ZetaOTU) classification. We report for the first time the Zetaproteobacterial core microbiome of these iron-rich microbial mats, which is composed of four ZetaOTUs that are cosmopolitan and essential for the development of the mats. The study of the presence and abundance of different ZetaOTUs among sites reveals two clusters, which are related to the lithology and permeability of the substratum on which they develop. The Zetaproteobacterial communities of cluster 1 are characteristic of poorly permeable substrata, with little evidence of diffuse venting, while those of cluster 2 develop on hydrothermal slabs or deposits that allow the percolation and outflow of diffuse hydrothermal fluids. In addition, two NewZetaOTUs 1 and 2 were identified, which could be characteristic of anthropic iron and unsedimented basalt, respectively. We also report significant correlations between the abundance of certain ZetaOTUs and that of iron oxide morphologies, indicating that their formation could be taxonomically and/or environmentally driven. We identified a new morphology of Fe(III)-oxyhydroxides that we named "corals." Overall, our work contributes to the knowledge of the biogeography of this bacterial class by providing additional data from the Atlantic Ocean, a lesser-studied ocean in terms of Zetaproteobacterial diversity.IMPORTANCEUp until now, Zetaproteobacterial diversity studies have revealed possible links between Zetaproteobacteria taxa, habitats, and niches. Here, we report for the first time the Zetaproteobacterial core microbiome of iron-rich mats from the Lucky Strike Hydrothermal Field (LSHF), as well as two new Zetaproteobacterial operational taxonomic units (NewZetaOTUs) that could be substratum specific. We highlight that the substratum on which iron-rich microbial mats develop, especially because of its permeability to diffuse hydrothermal venting, has an influence on their Zetaproteobacterial communities. Moreover, our work adds to the knowledge of the biogeography of this bacterial class by providing additional data from the hydrothermal vent sites along the Mid-Atlantic Ridge. In addition to the already described iron oxide morphologies, we identify in our iron-rich mats a new morphology that we named corals. Finally, we argue for significant correlations between the relative abundance of certain ZetaOTUs and that of iron oxide morphologies, contributing to the understanding of the drivers of iron oxide production in iron-oxidizing bacteria.
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Affiliation(s)
- Aina Astorch-Cardona
- Aix-Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Giliane P. Odin
- Laboratoire Géomatériaux et Environnement, Université Gustave Eiffel, Marne-la-Vallée, France
| | - Valérie Chavagnac
- Géosciences Environnement Toulouse, CNRS UMR 5563 (CNRS/UPS/IRD/CNES), Université de Toulouse, Observatoire Midi-Pyrénées, Toulouse, France
| | - Alain Dolla
- Aix-Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Hélène Gaussier
- Aix-Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Céline Rommevaux
- Aix-Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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Fenouil R, Pradel N, Belahbib H, Roumagnac M, Bartoli M, Ben Hania W, Denis Y, Garel M, Tamburini C, Ollivier B, Summers Z, Armougom F, Dolla A. Adaptation Strategies to High Hydrostatic Pressures in Pseudothermotoga species Revealed by Transcriptional Analyses. Microorganisms 2023; 11:microorganisms11030773. [PMID: 36985346 PMCID: PMC10057702 DOI: 10.3390/microorganisms11030773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Pseudothermotoga elfii strain DSM9442 and P. elfii subsp. lettingae strain DSM14385 are hyperthermophilic bacteria. P. elfii DSM9442 is a piezophile and was isolated from a depth of over 1600 m in an oil-producing well in Africa. P. elfii subsp. lettingae is piezotolerant and was isolated from a thermophilic bioreactor fed with methanol as the sole carbon and energy source. In this study, we analyzed both strains at the genomic and transcriptomic levels, paying particular attention to changes in response to pressure increases. Transcriptomic analyses revealed common traits of adaptation to increasing hydrostatic pressure in both strains, namely, variations in transport membrane or carbohydrate metabolism, as well as species-specific adaptations such as variations in amino acid metabolism and transport for the deep P. elfii DSM9442 strain. Notably, this work highlights the central role played by the amino acid aspartate as a key intermediate of the pressure adaptation mechanisms in the deep strain P. elfii DSM9442. Our comparative genomic and transcriptomic analysis revealed a gene cluster involved in lipid metabolism that is specific to the deep strain and that was differentially expressed at high hydrostatic pressures and might, thus, be a good candidate for a piezophilic gene marker in Pseudothermotogales.
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Affiliation(s)
- Romain Fenouil
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Nathalie Pradel
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
- Correspondence: (N.P.); (A.D.)
| | - Hassiba Belahbib
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Marie Roumagnac
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Manon Bartoli
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Wajdi Ben Hania
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Yann Denis
- Institut de Microbiologie de la Méditerranée, CNRS—Aix Marseille Université, Marseille, France
| | - Marc Garel
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Christian Tamburini
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Zarath Summers
- LanzaTech, Illinois Science and Technology Park, Skokie, IL 60077, USA
| | - Fabrice Armougom
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Alain Dolla
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
- Correspondence: (N.P.); (A.D.)
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Pardoux R, Dolla A, Aubert C. Metal-containing PAS/GAF domains in bacterial sensors. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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Fiévet A, Merrouch M, Brasseur G, Eve D, Biondi EG, Valette O, Pauleta SR, Dolla A, Dermoun Z, Burlat B, Aubert C. OrpR is a σ 54 -dependent activator using an iron-sulfur cluster for redox sensing in Desulfovibrio vulgaris Hildenborough. Mol Microbiol 2021; 116:231-244. [PMID: 33595838 PMCID: PMC8359166 DOI: 10.1111/mmi.14705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 01/15/2023]
Abstract
Enhancer binding proteins (EBPs) are key players of σ54 -regulation that control transcription in response to environmental signals. In the anaerobic microorganism Desulfovibrio vulgaris Hildenborough (DvH), orp operons have been previously shown to be coregulated by σ54 -RNA polymerase, the integration host factor IHF and a cognate EBP, OrpR. In this study, ChIP-seq experiments indicated that the OrpR regulon consists of only the two divergent orp operons. In vivo data revealed that (i) OrpR is absolutely required for orp operons transcription, (ii) under anaerobic conditions, OrpR binds on the two dedicated DNA binding sites and leads to high expression levels of the orp operons, (iii) increasing the redox potential of the medium leads to a drastic down-regulation of the orp operons expression. Moreover, combining functional and biophysical studies on the anaerobically purified OrpR leads us to propose that OrpR senses redox potential variations via a redox-sensitive [4Fe-4S]2+ cluster in the sensory PAS domain. Overall, the study herein presents the first characterization of a new Fe-S redox regulator belonging to the σ54 -dependent transcriptional regulator family probably advantageously selected by cells adapted to the anaerobic lifestyle to monitor redox stress conditions.
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Affiliation(s)
| | | | | | - Danaé Eve
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | | | | | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Dept. Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Alain Dolla
- Aix Marseille Univ, Toulon Univ, CNRS, IRD, MIO, Marseille, France
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Roumagnac M, Pradel N, Bartoli M, Garel M, Jones AA, Armougom F, Fenouil R, Tamburini C, Ollivier B, Summers ZM, Dolla A. Responses to the Hydrostatic Pressure of Surface and Subsurface Strains of Pseudothermotoga elfii Revealing the Piezophilic Nature of the Strain Originating From an Oil-Producing Well. Front Microbiol 2020; 11:588771. [PMID: 33343528 PMCID: PMC7746679 DOI: 10.3389/fmicb.2020.588771] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
Microorganisms living in deep-oil reservoirs face extreme conditions of elevated temperature and hydrostatic pressure. Within these microbial communities, members of the order Thermotogales are predominant. Among them, the genus Pseudothermotoga is widespread in oilfield-produced waters. The growth and cell phenotypes under hydrostatic pressures ranging from 0.1 to 50 MPa of two strains from the same species originating from subsurface, Pseudothermotoga elfii DSM9442 isolated from a deep African oil-producing well, and surface, P. elfii subsp. lettingae isolated from a thermophilic sulfate-reducing bioreactor, environments are reported for the first time. The data support evidence for the piezophilic nature of P. elfii DSM9442, with an optimal hydrostatic pressure for growth of 20 MPa and an upper limit of 40 MPa, and the piezotolerance of P. elfii subsp. lettingae with growth occurring up to 20 MPa only. Under the experimental conditions, both strains produce mostly acetate and propionate as volatile fatty acids with slight variations with respect to the hydrostatic pressure for P. elfii DSM9442. The data show that the metabolism of P. elfii DSM9442 is optimized when grown at 20 MPa, in agreement with its piezophilic nature. Both Pseudothermotoga strains form chained cells when the hydrostatic pressure increases, especially P. elfii DSM9442 for which 44% of cells is chained when grown at 40 MPa. The viability of the chained cells increases with the increase in the hydrostatic pressure, indicating that chain formation is a protective mechanism for P. elfii DSM9442.
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Affiliation(s)
- Marie Roumagnac
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Nathalie Pradel
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Manon Bartoli
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Marc Garel
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Aaron A Jones
- ExxonMobil Research and Engineering Company, Annandale, NJ, United States
| | - Fabrice Armougom
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Romain Fenouil
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Christian Tamburini
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Zarath M Summers
- ExxonMobil Research and Engineering Company, Annandale, NJ, United States
| | - Alain Dolla
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
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Summers ZM, Belahbib H, Pradel N, Bartoli M, Mishra P, Tamburini C, Dolla A, Ollivier B, Armougom F. A novel Thermotoga strain TFO isolated from a Californian petroleum reservoir phylogenetically related to Thermotoga petrophila and T. naphthophila, two thermophilic anaerobic isolates from a Japanese reservoir: Taxonomic and genomic considerations. Syst Appl Microbiol 2020; 43:126132. [DOI: 10.1016/j.syapm.2020.126132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
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7
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Pardoux R, Fiévet A, Carreira C, Brochier-Armanet C, Valette O, Dermoun Z, Py B, Dolla A, Pauleta SR, Aubert C. The bacterial Mrp ORP is a novel Mrp/NBP35 protein involved in iron-sulfur biogenesis. Sci Rep 2019; 9:712. [PMID: 30679587 PMCID: PMC6345978 DOI: 10.1038/s41598-018-37021-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/29/2018] [Indexed: 12/20/2022] Open
Abstract
Despite recent advances in understanding the biogenesis of iron-sulfur (Fe-S) proteins, most studies focused on aerobic bacteria as model organisms. Accordingly, multiple players have been proposed to participate in the Fe-S delivery step to apo-target proteins, but critical gaps exist in the knowledge of Fe-S proteins biogenesis in anaerobic organisms. Mrp/NBP35 ATP-binding proteins are a subclass of the soluble P-loop containing nucleoside triphosphate hydrolase superfamily (P-loop NTPase) known to bind and transfer Fe-S clusters in vitro. Here, we report investigations of a novel atypical two-domain Mrp/NBP35 ATP-binding protein named MrpORP associating a P-loop NTPase domain with a dinitrogenase iron-molybdenum cofactor biosynthesis domain (Di-Nase). Characterization of full length MrpORP, as well as of its two domains, showed that both domains bind Fe-S clusters. We provide in vitro evidence that the P-loop NTPase domain of the MrpORP can efficiently transfer its Fe-S cluster to apo-target proteins of the ORange Protein (ORP) complex, suggesting that this novel protein is involved in the maturation of these Fe-S proteins. Last, we showed for the first time, by fluorescence microscopy imaging a polar localization of a Mrp/NBP35 protein.
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Affiliation(s)
| | | | - Cíntia Carreira
- Microbial Stress Lab. UCIBIO, REQUIMTE, Department Química, Faculdade de Ciências e Tecnologica, Universidade NOVA de Lisboa, Campus da Caparica, Caparica, 2829-516, Portugal
| | - Céline Brochier-Armanet
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
| | | | | | - Béatrice Py
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Alain Dolla
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Sofia R Pauleta
- Microbial Stress Lab. UCIBIO, REQUIMTE, Department Química, Faculdade de Ciências e Tecnologica, Universidade NOVA de Lisboa, Campus da Caparica, Caparica, 2829-516, Portugal
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8
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Schoeffler M, Gaudin AL, Ramel F, Valette O, Denis Y, Hania WB, Hirschler-Réa A, Dolla A. Growth of an anaerobic sulfate-reducing bacterium sustained by oxygen respiratory energy conservation after O 2 -driven experimental evolution. Environ Microbiol 2018; 21:360-373. [PMID: 30394641 DOI: 10.1111/1462-2920.14466] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 11/30/2022]
Abstract
Desulfovibrio species are representatives of microorganisms at the boundary between anaerobic and aerobic lifestyles, since they contain the enzymatic systems required for both sulfate and oxygen reduction. However, the latter has been shown to be solely a protective mechanism. By implementing the oxygen-driven experimental evolution of Desulfovibrio vulgaris Hildenborough, we have obtained strains that have evolved to grow with energy derived from oxidative phosphorylation linked to oxygen reduction. We show that a few mutations are sufficient for the emergence of this phenotype and reveal two routes of evolution primarily involving either inactivation or overexpression of the gene encoding heterodisulfide reductase. We propose that the oxygen respiration for energy conservation that sustains the growth of the O2 -evolved strains is associated with a rearrangement of metabolite fluxes, especially NAD+ /NADH, leading to an optimized O2 reduction. These evolved strains are the first sulfate-reducing bacteria that exhibit a demonstrated oxygen respiratory process that enables growth.
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Affiliation(s)
- Marine Schoeffler
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Anne-Laure Gaudin
- Aix Marseille Université, CNRS, LCB, Marseille, France.,GERME SA, Technopôle de Château Gombert, Marseille, France
| | - Fanny Ramel
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Odile Valette
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Yann Denis
- Aix Marseille Université, CNRS, IMM, Marseille, France
| | - Wagdi Ben Hania
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Agnès Hirschler-Réa
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Alain Dolla
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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9
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Belahbib H, Summers ZM, Fardeau ML, Joseph M, Tamburini C, Dolla A, Ollivier B, Armougom F. Towards a congruent reclassification and nomenclature of the thermophilic species of the genus Pseudothermotoga within the order Thermotogales. Syst Appl Microbiol 2018; 41:555-563. [PMID: 29801938 DOI: 10.1016/j.syapm.2018.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/20/2018] [Accepted: 04/27/2018] [Indexed: 11/24/2022]
Abstract
The phylum Thermotogae gathers thermophilic, hyperthermophic, mesophilic, and thermo-acidophilic anaerobic bacteria that are mostly originated from geothermally heated environments. The metabolic and phenotypic properties harbored by the Thermotogae species questions the evolutionary events driving the emergence of this early branch of the universal tree of life. Recent reshaping of the Thermotogae taxonomy has led to the description of a new genus, Pseudothermotoga, a sister group of the genus Thermotoga within the order Thermotogales. Comparative genomics of both Pseudothermotoga and Thermotoga spp., including 16S-rRNA-based phylogenetic, pan-genomic analysis as well as signature indel conservation, provided evidence that Thermotoga caldifontis and Thermotoga profunda species should be reclassified within the genus Pseudothermotoga and renamed as Pseudothermotoga caldifontis comb. nov. (type strain=AZM44c09T) and Pseudothermotoga profunda comb. nov. (type strain=AZM34c06T), respectively. In addition, based upon whole-genome relatedness indices and DNA-DNA Hybridization results, the reclassification of Pseudothermotoga lettingae and Pseudothermotoga subterranea as latter heterotypic synonyms of Pseudothermotoga elfii is proposed. Finally, potential genetic elements resulting from the distinct evolutionary story of the Thermotoga and Pseudothermotoga clades are discussed.
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Affiliation(s)
- Hassiba Belahbib
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Zarath M Summers
- ExxonMobil Research and Engineering Company, 1545 Route 22 East, Annandale, NJ 08801, United States
| | | | - Manon Joseph
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Alain Dolla
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Fabrice Armougom
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France.
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Fadhlaoui K, Ben Hania W, Armougom F, Bartoli M, Fardeau ML, Erauso G, Brasseur G, Aubert C, Hamdi M, Brochier-Armanet C, Dolla A, Ollivier B. Obligate sugar oxidation inMesotogaspp., phylumThermotogae, in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor. Environ Microbiol 2017; 20:281-292. [DOI: 10.1111/1462-2920.13995] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 11/02/2017] [Accepted: 11/06/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Khaled Fadhlaoui
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
- Laboratoire d'Ecologie et de Technologie Microbienne; Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Centre Urbain Nord; Tunis BP 676, 1080 Tunisia
| | - Wagdi Ben Hania
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
| | - Fabrice Armougom
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
| | - Manon Bartoli
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
| | | | - Gaël Erauso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
| | | | | | - Moktar Hamdi
- Laboratoire d'Ecologie et de Technologie Microbienne; Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Centre Urbain Nord; Tunis BP 676, 1080 Tunisia
| | - Céline Brochier-Armanet
- Université de Lyon; Université Lyon 1; CNRS; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918; Villeurbanne F-69622 France
| | - Alain Dolla
- Aix Marseille Univ, CNRS, LCB; Marseille France
| | - Bernard Ollivier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO; Marseille France
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Cadby IT, Faulkner M, Cheneby J, Long J, van Helden J, Dolla A, Cole JA. Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide. Sci Rep 2017; 7:16228. [PMID: 29176637 PMCID: PMC5701242 DOI: 10.1038/s41598-017-16403-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/08/2017] [Indexed: 01/06/2023] Open
Abstract
The sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative electron acceptors to sulfate to support growth. Like other sulphate reducing bacteria, it can also protect itself against nitrosative stress caused by NO generated when nitrite accumulates. By combining in vitro experiments with bioinformatic and RNA-seq data, metabolic responses to nitrate or NO and how nitrate and nitrite reduction are coordinated with the response to nitrosative stress were revealed. Although nitrate and nitrite reduction are tightly regulated in response to substrate availability, the global responses to nitrate or NO were largely regulated independently. Multiple NADH dehydrogenases, transcription factors of unknown function and genes for iron uptake were differentially expressed in response to electron acceptor availability or nitrosative stress. Amongst many fascinating problems for future research, the data revealed a YtfE orthologue, Ddes_1165, that is implicated in the repair of nitrosative damage. The combined data suggest that three transcription factors coordinate this regulation in which NrfS-NrfR coordinates nitrate and nitrite reduction to minimize toxicity due to nitrite accumulation, HcpR1 serves a global role in regulating the response to nitrate, and HcpR2 regulates the response to nitrosative stress.
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Affiliation(s)
- Ian T Cadby
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Matthew Faulkner
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- The Institute of Integrative Biology, Bioscience building, University of Liverpool, Liverpool, Merseyside, L69 7ZB, UK
| | - Jeanne Cheneby
- Aix Marseille Univ, INSERM, TAGC, UMR_S 1090, 163, Avenue de Luminy, 13288, Marseille, France
| | - Justine Long
- Aix Marseille Univ, INSERM, TAGC, UMR_S 1090, 163, Avenue de Luminy, 13288, Marseille, France
| | - Jacques van Helden
- Aix Marseille Univ, INSERM, TAGC, UMR_S 1090, 163, Avenue de Luminy, 13288, Marseille, France
| | - Alain Dolla
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Jeffrey A Cole
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
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Valette O, Tran TTT, Cavazza C, Caudeville E, Brasseur G, Dolla A, Talla E, Pieulle L. Biochemical Function, Molecular Structure and Evolution of an Atypical Thioredoxin Reductase from Desulfovibrio vulgaris. Front Microbiol 2017; 8:1855. [PMID: 29033913 PMCID: PMC5627308 DOI: 10.3389/fmicb.2017.01855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/11/2017] [Indexed: 11/19/2022] Open
Abstract
Thioredoxin reductase (TR) regulates the intracellular redox environment by reducing thioredoxin (Trx). In anaerobes, recent findings indicate that the Trx redox network is implicated in the global redox regulation of metabolism but also actively participates in protecting cells against O2. In the anaerobe Desulfovibrio vulgaris Hildenborough (DvH), there is an intriguing redundancy of the Trx system which includes a classical system using NADPH as electron source, a non-canonical system using NADH and an isolated TR (DvTRi). The functionality of DvTRi was questioned due to its lack of reactivity with DvTrxs. Structural analysis shows that DvTRi is a NAD(P)H-independent TR but its reducer needs still to be identified. Moreover, DvTRi reduced by an artificial electron source is able to reduce in turn DvTrx1 and complexation experiments demonstrate a direct interaction between DvTRi and DvTrx1. The deletion mutant tri exhibits a higher sensitivity to disulfide stress and the gene tri is upregulated by O2 exposure. Having DvTRi in addition to DvTR1 as electron source for reducing DvTrx1 must be an asset to combat oxidative stress. Large-scale phylogenomics analyses show that TRi homologs are confined within the anaerobes. All TRi proteins displayed a conserved TQ/NGK motif instead of the HRRD motif, which is selective for the binding of the 2′-phosphate group of NADPH. The evolutionary history of TRs indicates that tr1 is the common gene ancestor in prokaryotes, affected by both gene duplications and horizontal gene events, therefore leading to the appearance of TRi through subfunctionalization over the evolutionary time.
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Affiliation(s)
| | - Tam T T Tran
- Aix-Marseille Univ, CNRS, LCB, Marseille, France
| | - Christine Cavazza
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, Grenoble, France.,UMR 5249, Laboratoire de Chimie et Biologie des Métaux, Centre National de la Recherche Scientifique, Grenoble, France.,DRF/BIG/CBM, CEA-Grenoble, Grenoble, France
| | | | | | - Alain Dolla
- Aix-Marseille Univ, CNRS, LCB, Marseille, France
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13
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Amrani A, van Helden J, Bergon A, Aouane A, Ben Hania W, Tamburini C, Loriod B, Imbert J, Ollivier B, Pradel N, Dolla A. Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses. Environ Microbiol Rep 2016; 8:520-526. [PMID: 27264199 DOI: 10.1111/1758-2229.12427] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/10/2016] [Accepted: 05/20/2016] [Indexed: 06/05/2023]
Abstract
Desulfovibrio piezophilus strain C1TLV30(T) is a mesophilic piezophilic sulfate-reducer isolated from Wood Falls at 1700 m depth in the Mediterranean Sea. In this study, we analysed the effect of the hydrostatic pressure on this deep-sea living bacterium at the physiologic and transcriptomic levels. Our results showed that lactate oxidation and energy metabolism were affected by the hydrostatic pressure. Especially, acetyl-CoA oxidation pathway and energy conservation through hydrogen and formate recycling would be more important when the hydrostatic pressure is above (26 MPa) than below (0.1 MPa) the optimal one (10 MPa). This work underlines also the role of the amino acid glutamate as a piezolyte for the Desulfovibrio genus. The transcriptomic analysis revealed 146 differentially expressed genes emphasizing energy production and conversion, amino acid transport and metabolism and cell motility and signal transduction mechanisms as hydrostatic pressure responding processes. This dataset allowed us to identify a sequence motif upstream of a subset of differentially expressed genes as putative pressure-dependent regulatory element.
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Affiliation(s)
- Amira Amrani
- Aix-Marseille Université, Université du Sud Toulon-Var, IRD, CNRS/INSU, MIO, UM110, Marseille, Cedex 09, 13288, France
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Jacques van Helden
- Inserm, U1090; TGML/TAGC, Marseille, F-13009, France
- Aix-Marseille Université, UMR_S 1090; TGML/TAGC, Marseille, F-13007, France
| | - Aurélie Bergon
- Inserm, U1090; TGML/TAGC, Marseille, F-13009, France
- Aix-Marseille Université, UMR_S 1090; TGML/TAGC, Marseille, F-13007, France
| | - Aicha Aouane
- Service de Microscopie Electronique, IBDML, Marseille, Cedex 09, 13288, France
| | - Wajdi Ben Hania
- Aix-Marseille Université, Université du Sud Toulon-Var, IRD, CNRS/INSU, MIO, UM110, Marseille, Cedex 09, 13288, France
| | - Christian Tamburini
- Aix-Marseille Université, Université du Sud Toulon-Var, IRD, CNRS/INSU, MIO, UM110, Marseille, Cedex 09, 13288, France
| | - Béatrice Loriod
- Inserm, U1090; TGML/TAGC, Marseille, F-13009, France
- Aix-Marseille Université, UMR_S 1090; TGML/TAGC, Marseille, F-13007, France
| | - Jean Imbert
- Inserm, U1090; TGML/TAGC, Marseille, F-13009, France
- Aix-Marseille Université, UMR_S 1090; TGML/TAGC, Marseille, F-13007, France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, IRD, CNRS/INSU, MIO, UM110, Marseille, Cedex 09, 13288, France
| | - Nathalie Pradel
- Aix-Marseille Université, Université du Sud Toulon-Var, IRD, CNRS/INSU, MIO, UM110, Marseille, Cedex 09, 13288, France
| | - Alain Dolla
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
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14
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Ben Hania W, Fadhlaoui K, Brochier-Armanet C, Persillon C, Postec A, Hamdi M, Dolla A, Ollivier B, Fardeau ML, Le Mer J, Erauso G. Draft genome sequence of Mesotoga strain PhosAC3, a mesophilic member of the bacterial order Thermotogales, isolated from a digestor treating phosphogypsum in Tunisia. Stand Genomic Sci 2015; 10:12. [PMID: 26464750 PMCID: PMC4603820 DOI: 10.1186/1944-3277-10-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 11/30/2014] [Indexed: 11/10/2022] Open
Abstract
Mesotoga strain PhosAc3 was the first mesophilic cultivated member of the order Thermotogales. This genus currently contain two described species, M. prima and M. infera. Strain PhosAc3, isolated from a Tunisian digestor treating phosphogypsum, is phylogenetically closely related to M. prima strain MesG1.Ag.4.2(T). Strain PhosAc3 has a genome of 3.1 Mb with a G+C content of 45.2%. It contains 3,051 protein-coding genes of which 74.6% have their best reciprocal BLAST hit in the genome of the type species, strain MesG1.Ag.4.2(T). For this reason we propose to assign strain PhosAc3 as a novel ecotype of the Mesotoga prima species. However, in contrast with the M. prima type strain, (i) it does not ferment sugars but uses them only in the presence of elemental sulfur as terminal electron acceptor, (ii) it produces only acetate and CO2 from sugars, whereas strain MesG1.Ag.4.2(T) produces acetate, butyrate, isobutyrate, isovalerate, 2-methyl-butyrate and (iii) sulfides are also end products of the elemental sulfur reduction in theses growth conditions.
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Affiliation(s)
- Wajdi Ben Hania
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, F-13288 Marseille, cedex 09, France ; Laboratoire d'Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Faculté des Sciences de Carthage, Centre Urbain Nord, BP 676, Tunis, 1080 Tunisia
| | - Khaled Fadhlaoui
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, F-13288 Marseille, cedex 09, France ; Laboratoire d'Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Faculté des Sciences de Carthage, Centre Urbain Nord, BP 676, Tunis, 1080 Tunisia
| | - Céline Brochier-Armanet
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, 43 boulevard du 11 novembre 1918, Villeurbanne, F-69622 France
| | | | - Anne Postec
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, F-13288 Marseille, cedex 09, France
| | - Moktar Hamdi
- Laboratoire d'Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Faculté des Sciences de Carthage, Centre Urbain Nord, BP 676, Tunis, 1080 Tunisia
| | - Alain Dolla
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, F-13009 France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, F-13288 Marseille, cedex 09, France
| | - Marie-Laure Fardeau
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, F-13288 Marseille, cedex 09, France
| | - Jean Le Mer
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, F-13288 Marseille, cedex 09, France
| | - Gaël Erauso
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, F-13288 Marseille, cedex 09, France
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15
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Vita N, Valette O, Brasseur G, Lignon S, Denis Y, Ansaldi M, Dolla A, Pieulle L. The primary pathway for lactate oxidation in Desulfovibrio vulgaris. Front Microbiol 2015; 6:606. [PMID: 26167158 PMCID: PMC4481167 DOI: 10.3389/fmicb.2015.00606] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/02/2015] [Indexed: 12/16/2022] Open
Abstract
The ability to respire sulfate linked to lactate oxidation is a key metabolic signature of the Desulfovibrio genus. Lactate oxidation by these incomplete oxidizers generates reductants through lactate dehydrogenase (LDH) and pyruvate-ferredoxin oxidoreductase (PFOR), with the latter catalyzing pyruvate conversion into acetyl-CoA. Acetyl-CoA is the source of substrate-level phosphorylation through the production of ATP. Here, we show that these crucial steps are performed by enzymes encoded by a nonacistronic transcriptional unit named now as operon luo (for lactate utilization operon). Using a combination of genetic and biochemical techniques, we assigned a physiological role to the operon genes DVU3027-28 and DVU3032-33. The growth of mutant Δ26-28 was highly disrupted on D-lactate, whereas the growth of mutant Δ32-33 was slower on L-lactate, which could be related to a decrease in the activity of D-lactate or L-lactate oxidase in the corresponding mutants. The DVU3027-28 and DVU3032-33 genes thus encode functional D-LDH and L-LDH enzymes, respectively. Scanning of the genome for lactate utilization revealed several lactate permease and dehydrogenase homologs. However, transcriptional compensation was not observed in any of the mutants except for lactate permease. Although there is a high degree of redundancy for lactate oxidase, it is not functionally efficient in LDH mutants. This result could be related to the identification of several operon enzymes, including LDHs, in the PFOR activity bands, suggesting the occurrence of a lactate-oxidizing supermolecular structure that can optimize the performance of lactate utilization in Desulfovibrio species.
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Affiliation(s)
- Nicolas Vita
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Odile Valette
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Gaël Brasseur
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Sabrina Lignon
- CNRS, IMM-FR3479, Plate-forme Protéomique-IBISA Marseille-Protéomique Marseille, France
| | - Yann Denis
- IMM-FR3479, Plate-forme Transcriptomique Marseille, France
| | | | - Alain Dolla
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Laetitia Pieulle
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France ; Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
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16
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Ramel F, Brasseur G, Pieulle L, Valette O, Hirschler-Réa A, Fardeau ML, Dolla A. Growth of the obligate anaerobe Desulfovibrio vulgaris Hildenborough under continuous low oxygen concentration sparging: impact of the membrane-bound oxygen reductases. PLoS One 2015; 10:e0123455. [PMID: 25837676 PMCID: PMC4383621 DOI: 10.1371/journal.pone.0123455] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/04/2015] [Indexed: 11/18/2022] Open
Abstract
Although obligate anaerobe, the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) exhibits high aerotolerance that involves several enzymatic systems, including two membrane-bound oxygen reductases, a bd-quinol oxidase and a cc(b/o)o3 cytochrome oxidase. Effect of constant low oxygen concentration on growth and morphology of the wild-type, single (Δbd, Δcox) and double deletion (Δcoxbd) mutant strains of the genes encoding these oxygen reductases was studied. When both wild-type and deletion mutant strains were cultured in lactate/sulfate medium under constant 0.02% O2 sparging, they were able to grow but the final biomasses and the growth yield were lower than that obtained under anaerobic conditions. At the end of the growth, lactate was not completely consumed and when conditions were then switched to anaerobic, growth resumed. Time-lapse microscopy revealed that a large majority of the cells were then able to divide (over 97%) but the time to recover a complete division event was longer for single deletion mutant Δbd than for the three other strains. Determination of the molar growth yields on lactate suggested that a part of the energy gained from lactate oxidation was derived toward cells protection/repairing against oxidative conditions rather than biosynthesis, and that this part was higher in the single deletion mutant Δbd and, to a lesser extent, Δcox strains. Our data show that when DvH encounters oxidative conditions, it is able to stop growing and to rapidly resume growing when conditions are switched to anaerobic, suggesting that it enters active dormancy sate under oxidative conditions. We propose that the pyruvate-ferredoxin oxidoreductase (PFOR) plays a central role in this phenomenon by reversibly switching from an oxidative-sensitive fully active state to an oxidative-insensitive inactive state. The oxygen reductases, and especially the bd-quinol oxidase, would have a crucial function by maintaining reducing conditions that permit PFOR to stay in its active state.
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Affiliation(s)
- Fanny Ramel
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Gael Brasseur
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | | | - Odile Valette
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Agnès Hirschler-Réa
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO, UM110, 13288 Marseille, Cedex 09, France
| | - Marie Laure Fardeau
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO, UM110, 13288 Marseille, Cedex 09, France
| | - Alain Dolla
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
- * E-mail:
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17
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Khelifi N, Amin Ali O, Roche P, Grossi V, Brochier-Armanet C, Valette O, Ollivier B, Dolla A, Hirschler-Réa A. Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus. ISME J 2014; 8:2153-66. [PMID: 24763368 PMCID: PMC4992073 DOI: 10.1038/ismej.2014.58] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 03/11/2014] [Accepted: 03/16/2014] [Indexed: 11/08/2022]
Abstract
The thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus strain VC-16 (DSM 4304), which is known to oxidize fatty acids and n-alkenes, was shown to oxidize saturated hydrocarbons (n-alkanes in the range C10-C21) with thiosulfate or sulfate as a terminal electron acceptor. The amount of n-hexadecane degradation observed was in stoichiometric agreement with the theoretically expected amount of thiosulfate reduction. One of the pathways used by anaerobic microorganisms to activate alkanes is addition to fumarate that involves alkylsuccinate synthase as a key enzyme. A search for genes encoding homologous enzymes in A. fulgidus identified the pflD gene (locus-tag AF1449) that was previously annotated as a pyruvate formate lyase. A phylogenetic analysis revealed that this gene is of bacterial origin and was likely acquired by A. fulgidus from a bacterial donor through a horizontal gene transfer. Based on three-dimensional modeling of the corresponding protein and molecular dynamic simulations, we hypothesize an alkylsuccinate synthase activity for this gene product. The pflD gene expression was upregulated during the growth of A. fulgidus on an n-alkane (C16) compared with growth on a fatty acid. Our results suggest that anaerobic alkane degradation in A. fulgidus may involve the gene pflD in alkane activation through addition to fumarate. These findings highlight the possible importance of hydrocarbon oxidation at high temperatures by A. fulgidus in hydrothermal vents and the deep biosphere.
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Affiliation(s)
- Nadia Khelifi
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, Marseille, France
| | - Oulfat Amin Ali
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, Marseille, France
| | - Philippe Roche
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Vincent Grossi
- Université de Lyon, Université Lyon 1, CNRS, UMR 5276, Laboratoire de Géologie de Lyon, Villeurbanne, France
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Odile Valette
- Aix Marseille Université, CNRS, LCB UMR 7283, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, Marseille, France
| | - Alain Dolla
- Aix Marseille Université, CNRS, LCB UMR 7283, Marseille, France
| | - Agnès Hirschler-Réa
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, Marseille, France
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18
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Amrani A, Bergon A, Holota H, Tamburini C, Garel M, Ollivier B, Imbert J, Dolla A, Pradel N. Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure. PLoS One 2014; 9:e106831. [PMID: 25215865 PMCID: PMC4162548 DOI: 10.1371/journal.pone.0106831] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/01/2014] [Indexed: 11/24/2022] Open
Abstract
RNA-seq was used to study the response of Desulfovibrio hydrothermalis, isolated from a deep-sea hydrothermal chimney on the East-Pacific Rise at a depth of 2,600 m, to various hydrostatic pressure growth conditions. The transcriptomic datasets obtained after growth at 26, 10 and 0.1 MPa identified only 65 differentially expressed genes that were distributed among four main categories: aromatic amino acid and glutamate metabolisms, energy metabolism, signal transduction, and unknown function. The gene expression patterns suggest that D. hydrothermalis uses at least three different adaptation mechanisms, according to a hydrostatic pressure threshold (HPt) that was estimated to be above 10 MPa. Both glutamate and energy metabolism were found to play crucial roles in these mechanisms. Quantitation of the glutamate levels in cells revealed its accumulation at high hydrostatic pressure, suggesting its role as a piezolyte. ATP measurements showed that the energy metabolism of this bacterium is optimized for deep-sea life conditions. This study provides new insights into the molecular mechanisms linked to hydrostatic pressure adaptation in sulfate-reducing bacteria.
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Affiliation(s)
- Amira Amrani
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Aurélie Bergon
- Inserm, U1090, TGML/TAGC, Marseille, France
- Aix Marseille Université, UMR_S 1090, TGML/TAGC, Marseille, France
| | - Hélène Holota
- Inserm, U1090, TGML/TAGC, Marseille, France
- Aix Marseille Université, UMR_S 1090, TGML/TAGC, Marseille, France
| | - Christian Tamburini
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
| | - Marc Garel
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
| | - Jean Imbert
- Inserm, U1090, TGML/TAGC, Marseille, France
- Aix Marseille Université, UMR_S 1090, TGML/TAGC, Marseille, France
| | - Alain Dolla
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
- * E-mail: (AD); (NP)
| | - Nathalie Pradel
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
- * E-mail: (AD); (NP)
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Fiévet A, Cascales E, Valette O, Dolla A, Aubert C. IHF is required for the transcriptional regulation of the Desulfovibrio vulgaris Hildenborough orp operons. PLoS One 2014; 9:e86507. [PMID: 24466126 PMCID: PMC3897727 DOI: 10.1371/journal.pone.0086507] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/10/2013] [Indexed: 01/08/2023] Open
Abstract
Transcriptional activation of σ(54)-dependent promoters is usually tightly regulated in response to environmental cues. The high abundance of potential σ(54)-dependent promoters in the anaerobe bacteria, Desulfovibrio vulgaris Hildenborough, reflects the high versatility of this bacteria suggesting that σ(54) factor is the nexus of a large regulatory network. Understanding the key players of σ(54)-regulation in this organism is therefore essential to gain insights into the adaptation to anaerobiosis. Recently, the D. vulgaris orp genes, specifically found in anaerobe bacteria, have been shown to be transcribed by the RNA polymerase coupled to the σ(54) alternative sigma factor. In this study, using in vitro binding experiments and in vivo reporter fusion assays in the Escherichia coli heterologous host, we showed that the expression of the divergent orp promoters is strongly dependent on the integration host factor IHF. Bioinformatic and mutational analysis coupled to reporter fusion activities and mobility shift assays identified two functional IHF binding site sequences located between the orp1 and orp2 promoters. We further determined that the D. vulgaris DVU0396 (IHFα) and DVU1864 (IHFβ) subunits are required to control the expression of the orp operons suggesting that they form a functionally active IHF heterodimer. Interestingly results obtained from the in vivo inactivation of DVU0396, which is required for orp operons transcription, suggest that several functionally IHF active homodimer or heterodimer are present in D. vulgaris.
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Affiliation(s)
- Anouchka Fiévet
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS, Marseille, France
| | - Eric Cascales
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, CNRS, Marseille, France
| | - Odile Valette
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS, Marseille, France
| | - Alain Dolla
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS, Marseille, France
| | - Corinne Aubert
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS, Marseille, France
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Ramel F, Amrani A, Pieulle L, Lamrabet O, Voordouw G, Seddiki N, Brèthes D, Company M, Dolla A, Brasseur G. Membrane-bound oxygen reductases of the anaerobic sulfate-reducing Desulfovibrio vulgaris Hildenborough: roles in oxygen defence and electron link with periplasmic hydrogen oxidation. Microbiology (Reading) 2013; 159:2663-2673. [PMID: 24085836 DOI: 10.1099/mic.0.071282-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cytoplasmic membranes of the strictly anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough contain two terminal oxygen reductases, a bd quinol oxidase and a cc(b/o)o3 cytochrome oxidase (Cox). Viability assays pointed out that single Δbd, Δcox and double ΔbdΔcox deletion mutant strains were more sensitive to oxygen exposure than the WT strain, showing the involvement of these oxygen reductases in the detoxification of oxygen. The Δcox strain was slightly more sensitive than the Δbd strain, pointing to the importance of the cc(b/o)o3 cytochrome oxidase in oxygen protection. Decreased O2 reduction rates were measured in mutant cells and membranes using lactate, NADH, ubiquinol and menadiol as substrates. The affinity for oxygen measured with the bd quinol oxidase (Km, 300 nM) was higher than that of the cc(b/o)o3 cytochrome oxidase (Km, 620 nM). The total membrane activity of the bd quinol oxidase was higher than that of the cytochrome oxidase activity in line with the higher expression of the bd oxidase genes. In addition, analysis of the ΔbdΔcox mutant strain indicated the presence of at least one O2-scavenging membrane-bound system able to reduce O2 with menaquinol as electron donor with an O2 affinity that was two orders of magnitude lower than that of the bd quinol oxidase. The lower O2 reductase activity in mutant cells with hydrogen as electron donor and the use of specific inhibitors indicated an electron transfer link between periplasmic H2 oxidation and membrane-bound oxygen reduction via the menaquinol pool. This linkage is crucial in defence of the strictly anaerobic bacterium Desulfovibrio against oxygen stress.
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Affiliation(s)
- F Ramel
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - A Amrani
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - L Pieulle
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - O Lamrabet
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - G Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary T2N 1N4, AB, Canada
| | - N Seddiki
- Laboratoire de Métabolisme Énergétique Cellulaire, IBGC-CNRS, et Université Bordeaux Segalen, 1 Rue Camille Saint-Saëns, 33077 Bordeaux CEDEX, France
| | - D Brèthes
- Laboratoire de Métabolisme Énergétique Cellulaire, IBGC-CNRS, et Université Bordeaux Segalen, 1 Rue Camille Saint-Saëns, 33077 Bordeaux CEDEX, France
| | - M Company
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - A Dolla
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - G Brasseur
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
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Pradel N, Ji B, Gimenez G, Talla E, Lenoble P, Garel M, Tamburini C, Fourquet P, Lebrun R, Bertin P, Denis Y, Pophillat M, Barbe V, Ollivier B, Dolla A. The first genomic and proteomic characterization of a deep-sea sulfate reducer: insights into the piezophilic lifestyle of Desulfovibrio piezophilus. PLoS One 2013; 8:e55130. [PMID: 23383081 PMCID: PMC3559428 DOI: 10.1371/journal.pone.0055130] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 12/18/2012] [Indexed: 01/19/2023] Open
Abstract
Desulfovibrio piezophilus strain C1TLV30(T) is a piezophilic anaerobe that was isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents a unique model for studying the adaptation of sulfate-reducing bacteria to hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this piezophilic bacterium. An analysis of the genome revealed the presence of seven genomic islands as well as gene clusters that are most likely linked to life at a high hydrostatic pressure. Comparative genomics and differential proteomics identified the transport of solutes and amino acids as well as amino acid metabolism as major cellular processes for the adaptation of this bacterium to hydrostatic pressure. In addition, the proteome profiles showed that the abundance of key enzymes that are involved in sulfate reduction was dependent on hydrostatic pressure. A comparative analysis of orthologs from the non-piezophilic marine bacterium D. salexigens and D. piezophilus identified aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the amino acids preferentially replaced by arginine, histidine, alanine and threonine in the piezophilic strain. This work reveals the adaptation strategies developed by a sulfate reducer to a deep-sea lifestyle.
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Affiliation(s)
- Nathalie Pradel
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
- * E-mail: (NP); (AD)
| | - Boyang Ji
- Aix-Marseille Université, CNRS, LCB, UMR 7283, Marseille, France
| | | | - Emmanuel Talla
- Aix-Marseille Université, CNRS, LCB, UMR 7283, Marseille, France
| | - Patricia Lenoble
- Laboratoire de Finition C.E.A., Institut de Génomique – Genoscope, Evry, France
| | - Marc Garel
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
| | - Christian Tamburini
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
| | | | - Régine Lebrun
- Plate-formes Protéomique et Transcriptomique FR3479, IBiSA Marseille-Protéomique. IMM - CNRS, Marseille, France
| | - Philippe Bertin
- UMR 7156, CNRS, Université Louis Pasteur, Strasbourg, France
| | - Yann Denis
- Plate-formes Protéomique et Transcriptomique FR3479, IBiSA Marseille-Protéomique. IMM - CNRS, Marseille, France
| | | | - Valérie Barbe
- Laboratoire de Finition C.E.A., Institut de Génomique – Genoscope, Evry, France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France
| | - Alain Dolla
- Aix-Marseille Université, CNRS, LCB, UMR 7283, Marseille, France
- * E-mail: (NP); (AD)
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Le Fourn C, Brasseur G, Brochier-Armanet C, Pieulle L, Brioukhanov A, Ollivier B, Dolla A. An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales. Environ Microbiol 2011; 13:2132-45. [PMID: 21366819 DOI: 10.1111/j.1462-2920.2011.02439.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hyperthermophile Thermotoga maritima, although strictly anaerobic, is able to grow in the presence of low amounts of O(2). Here, we show that this bacterium consumes O(2) via a three-partner chain involving an NADH oxidoreductase (NRO), a rubredoxin (Rd) and a flavo-diiron protein (FprA) (locus tags: TM_0754, TM_0659 and TM_0755, respectively). In vitro experiments showed that the NADH-dependent O(2) consumption rate was 881.9 (± 106.7) mol O(2) consumed min(-1) per mol of FprA at 37°C and that water was the main end-product of the reaction. We propose that this O(2) reduction chain plays a central role in the O(2) tolerance of T. maritima. Phylogenetic analyses suggest that the genes coding for these three components were acquired by an ancestor of Thermotogales from an ancestor of Thermococcales via a single gene transfer. This event likely also involved two ROS scavenging enzymes (neelaredoxin and rubrerythrin) that are encoded by genes clustered with those coding for FprA, NRO and Rd in the ancestor of Thermococcales. Such genomic organization would have provided the ancestor of Thermotogales with a complete set of enzymes dedicated to O(2)-toxicity defence. Beside Thermotogales and Thermococcales, horizontal gene transfers have played a major role in disseminating these enzymes within the hyperthermophilic anaerobic prokaryotic communities, allowing them to cope with fluctuating oxidative conditions that exist in situ.
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Affiliation(s)
- Céline Le Fourn
- Laboratoire Interactions et Modulateurs de Réponses - CNRS UPR3243 - IFR88, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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Lesgards JF, Gauthier C, Iovanna J, Vidal N, Dolla A, Stocker P. Effect of reactive oxygen and carbonyl species on crucial cellular antioxidant enzymes. Chem Biol Interact 2011; 190:28-34. [PMID: 21216240 DOI: 10.1016/j.cbi.2010.12.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 10/18/2022]
Abstract
Numerous reactive oxygen species (ROS) and reactive carbonyl species (RCS) issuing from lipid and sugar oxidation are known to damage a large number of proteins leading to enzyme inhibition and alteration of cellular functions. Whereas studies in literature only focus on the reactivity of one or two of these compounds, we aimed at comparing in the same conditions of incubations (4 and 24h at 37°C) the effects of both various RCS (4-hydroxynonenal, 4-hydroxyhexenal, acrolein, methylglyoxal, glyoxal, malondialdehyde) and ROS (H₂O₂, AAPH) on the activity of key enzymes involved in cellular oxidative stress: superoxide dismutase (Cu,Zn-SOD), glutathione peroxidase (GPx), glutathione S-transferase (GST) and glucose-6-phosphate dehydrogenase (G6PDH). This was realized both in vitro on purified proteins and MIAPaCa-2 cells. Incubation of these enzymes with RCS resulted in a significant time- and concentration-dependent inhibition for both pure enzymes and in cell lysates. Among all RCS and ROS, hydroxynonenal (HNE) was observed as the most toxic for all studied enzymes except for SOD and is followed by hydrogen peroxide. At 100μM, HNE resulted in a 50% reduction of GPx, 56% of GST, 65% of G6PDH, and only 10% of Cu,Zn-SOD. Meanwhile it seems that concentrations used in our study are closer to biological conditions for ROS than for RCS. H₂O₂ and AAPH-induced peroxyl radicals may be probably more toxic towards the studied enzymes in vivo.
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Affiliation(s)
- Jean-François Lesgards
- Biosciences (Institut des sciences moléculaire de Marseille), université Paul Cézanne - UMR 6263, 13397 Marseille, France
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Pieulle L, Stocker P, Vinay M, Nouailler M, Vita N, Brasseur G, Garcin E, Sebban-Kreuzer C, Dolla A. Study of the thiol/disulfide redox systems of the anaerobe Desulfovibrio vulgaris points out pyruvate:ferredoxin oxidoreductase as a new target for thioredoxin 1. J Biol Chem 2011; 286:7812-7821. [PMID: 21199874 DOI: 10.1074/jbc.m110.197988] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Sulfate reducers have developed a multifaceted adaptative strategy to survive against oxidative stresses. Along with this oxidative stress response, we recently characterized an elegant reversible disulfide bond-dependent protective mechanism in the pyruvate:ferredoxin oxidoreductase (PFOR) of various Desulfovibrio species. Here, we searched for thiol redox systems involved in this mechanism. Using thiol fluorescent labeling, we show that glutathione is not the major thiol/disulfide balance-controlling compound in four different Desulfovibrio species and that no other plentiful low molecular weight thiol can be detected. Enzymatic analyses of two thioredoxins (Trxs) and three thioredoxin reductases allow us to propose the existence of two independent Trx systems in Desulfovibrio vulgaris Hildenborough (DvH). The TR1/Trx1 system corresponds to the typical bacterial Trx system. We measured a TR1 apparent K(m) value for Trx1 of 8.9 μM. Moreover, our results showed that activity of TR1 was NADPH-dependent. The second system named TR3/Trx3 corresponds to an unconventional Trx system as TR3 used preferentially NADH (K(m) for NADPH, 743 μM; K(m) for NADH, 5.6 μM), and Trx3 was unable to reduce insulin. The K(m) value of TR3 for Trx3 was 1.12 μM. In vitro experiments demonstrated that the TR1/Trx1 system was the only one able to reactivate the oxygen-protected form of Desulfovibrio africanus PFOR. Moreover, ex vivo pulldown assays using the mutant Trx1(C33S) as bait allowed us to capture PFOR from the DvH extract. Altogether, these data demonstrate that PFOR is a new target for Trx1, which is probably involved in the protective switch mechanism of the enzyme.
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Affiliation(s)
- Laetitia Pieulle
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and.
| | - Pierre Stocker
- the Equipe Biosciences iSm2, UMR6263, Case 342, FST Université Paul Cézanne, St. Jérome, 13397 Marseille Cedex 20, France
| | - Manon Vinay
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Matthieu Nouailler
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Nicolas Vita
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Gaël Brasseur
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Edwige Garcin
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Corinne Sebban-Kreuzer
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
| | - Alain Dolla
- From the Laboratoire Interactions et Modulateurs de Réponses, CNRS-UPR3243-IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 and
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Brioukhanov AL, Durand MC, Dolla A, Aubert C. Response of Desulfovibrio vulgaris Hildenborough to hydrogen peroxide: enzymatic and transcriptional analyses. FEMS Microbiol Lett 2010; 310:175-81. [PMID: 20695895 DOI: 10.1111/j.1574-6968.2010.02061.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We studied the effect of hydrogen peroxide (H(2)O(2)) stress on the anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. In a lactate/sulfate medium, growth was affected from 0.1 mM H(2)O(2) and totally inhibited at 0.7 mM. Surprisingly, transcript analyses revealed that the PerR regulon exhibited opposite regulation in the presence of 0.1 and 0.3 mM H(2)O(2). The variations in peroxidase- and superoxide dismutase-specific activities in the cell-free extracts of H(2)O(2)-stressed cultures were related to changes in the corresponding transcript abundance. Our data suggest that sod, sor, ngr and tpx genes, in addition to the PerR regulon, belong to the H(2)O(2) stimulon.
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Affiliation(s)
- Andrei L Brioukhanov
- Laboratoire Interactions et Modulateurs de Réponses, IFR88, CNRS, Marseille, France
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Dermoun Z, Foulon A, Miller MD, Harrington DJ, Deacon AM, Sebban-Kreuzer C, Roche P, Lafitte D, Bornet O, Wilson IA, Dolla A. TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions. J Mol Biol 2010; 400:463-76. [PMID: 20471400 DOI: 10.1016/j.jmb.2010.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 04/28/2010] [Accepted: 05/07/2010] [Indexed: 11/28/2022]
Abstract
The COG database was used for a comparative genome analysis with genomes from anaerobic and aerobic microorganisms with the aim of identifying proteins specific to the anaerobic way of life. A total of 33 COGs were identified, five of which correspond to proteins of unknown function. We focused our study on TM0486 from Thermotoga maritima, which belongs to one of these COGs of unknown function, namely COG0011. The crystal structure of the protein was determined at 2 A resolution. The structure adopts a beta alpha beta beta alpha beta ferredoxin-like fold and assembles as a homotetramer. The structure also revealed the presence of a pocket in each monomer that bound an unidentified ligand. NMR and calorimetry revealed that TM0486 specifically bound thiamin with a K(d) of 1.58 microM, but not hydroxymethyl pyrimidine (HMP), which has been implicated as a potential ligand. We demonstrated that the TM0486 gene belongs to the same multicistronic unit as TM0483, TM0484 and TM0485. Although these three genes have been assigned to the transport of HMP, with TM0484 being the periplasmic thiamin/HMP-binding protein and TM0485 and TM0483 the transmembrane and the ATPase components, respectively, our results led us to conclude that this operon encodes an ABC transporter dedicated to thiamin, with TM0486 transporting charged thiamin in the cytoplasm. Given that this transcriptional unit was up-regulated when T. maritima was exposed to oxidative conditions, we propose that, by chelating cytoplasmic thiamin, TM0486 and, by extension, proteins belonging to COG0011 are involved in the response mechanism to stress that could arise during aerobic conditions.
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Affiliation(s)
- Zorah Dermoun
- IMR-CNRS, IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
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Rivas MG, Carepo MSP, Mota CS, Korbas M, Durand MC, Lopes AT, Brondino CD, Pereira AS, George GN, Dolla A, Moura JJG, Moura I. Molybdenum Induces the Expression of a Protein Containing a New Heterometallic Mo-Fe Cluster in Desulfovibrio alaskensis. Biochemistry 2009; 48:873-82. [DOI: 10.1021/bi801773t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Maria G. Rivas
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Marta S. P. Carepo
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Cristiano S. Mota
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Malgorzata Korbas
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Marie-Claire Durand
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Ana T. Lopes
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Carlos D. Brondino
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Alice S. Pereira
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Graham N. George
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Alain Dolla
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Isabel Moura
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, S7N 5E5, Canada, Unité Interactions et Modulateurs de Réponses, IBSM−CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France, and Physics Department, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
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Herpoël-Gimbert I, Margeot A, Dolla A, Jan G, Mollé D, Lignon S, Mathis H, Sigoillot JC, Monot F, Asther M. Comparative secretome analyses of two Trichoderma reesei RUT-C30 and CL847 hypersecretory strains. Biotechnol Biofuels 2008; 1:18. [PMID: 19105830 PMCID: PMC2631499 DOI: 10.1186/1754-6834-1-18] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 12/23/2008] [Indexed: 05/05/2023]
Abstract
BACKGROUND Due to its capacity to produce large amounts of cellulases, Trichoderma reesei is increasingly been researched in various fields of white biotechnology, especially in biofuel production from lignocellulosic biomass. The commercial enzyme mixtures produced at industrial scales are not well characterized, and their proteinaceous components are poorly identified and quantified. The development of proteomic methods has made it possible to comprehensively overview the enzymes involved in lignocellulosic biomass degradation which are secreted under various environmental conditions. RESULTS The protein composition of the secretome produced by industrial T. reesei (strain CL847) grown on a medium promoting the production of both cellulases and hemicellulases was explored using two-dimensional electrophoresis and MALDI-TOF or LC-MS/MS protein identification. A total of 22 protein species were identified. As expected, most of them are potentially involved in biomass degradation. The 2D map obtained was then used to compare the secretomes produced by CL847 and another efficient cellulolytic T. reesei strain, Rut-C30, the reference cellulase-overproducing strain using lactose as carbon source and inducer of cellulases. CONCLUSION This study provides the most complete mapping of the proteins secreted by T. reesei to date. We report on the first use of proteomics to compare secretome composition between two cellulase-overproducing strains Rut-C30 and CL847 grown under similar conditions. Comparison of protein patterns in both strains highlighted many unexpected differences between cellulase cocktails. The results demonstrate that 2D electrophoresis is a promising tool for studying cellulase production profiles, whether for industrial characterization of an entire secretome or for a more fundamental study on cellulase expression at genome-wide scale.
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Affiliation(s)
- Isabelle Herpoël-Gimbert
- INRA, UMR1163, Biotechnologie des Champignons Filamenteux, F-13000 Marseille, France
- Universités Aix-Marseille I & II, UMR1163, BCF, F-13000 Marseille, France
| | - Antoine Margeot
- IFP, Biotechnology Department, Avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
| | - Alain Dolla
- IMR, FRE3083 – CNRS, Institut de Biologie Structurale et Microbiologie, Chemin Joseph-Aiguier, 13402 Marseille cedex 20, France
| | - Gwénaël Jan
- INRA, UMR1253, Science et Technologie du Lait et de l'Oeuf, F-35000 Rennes, France
- Agrocampus Rennes, UMR1253, STLO, F-35000 Rennes, France
| | - Daniel Mollé
- INRA, UMR1253, Science et Technologie du Lait et de l'Oeuf, F-35000 Rennes, France
- Agrocampus Rennes, UMR1253, STLO, F-35000 Rennes, France
| | - Sabrina Lignon
- Plate-forme protéomique, Institut de Biologie structurale et Microbiologie, Chemin Joseph-Aiguier, 13402 Marseille cedex 20, France
| | - Hughes Mathis
- IFP, Biotechnology Department, Avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
| | - Jean-Claude Sigoillot
- INRA, UMR1163, Biotechnologie des Champignons Filamenteux, F-13000 Marseille, France
- Universités Aix-Marseille I & II, UMR1163, BCF, F-13000 Marseille, France
| | - Frédéric Monot
- IFP, Biotechnology Department, Avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
| | - Marcel Asther
- INRA, UMR1163, Biotechnologie des Champignons Filamenteux, F-13000 Marseille, France
- Universités Aix-Marseille I & II, UMR1163, BCF, F-13000 Marseille, France
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Le Fourn C, Fardeau ML, Ollivier B, Lojou E, Dolla A. The hyperthermophilic anaerobe Thermotoga Maritima is able to cope with limited amount of oxygen: insights into its defence strategies. Environ Microbiol 2008; 10:1877-87. [DOI: 10.1111/j.1462-2920.2008.01610.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Vita N, Hatchikian EC, Nouailler M, Dolla A, Pieulle L. Disulfide Bond-Dependent Mechanism of Protection against Oxidative Stress in Pyruvate-Ferredoxin Oxidoreductase of Anaerobic Desulfovibrio Bacteria. Biochemistry 2007; 47:957-64. [DOI: 10.1021/bi7014713] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolas Vita
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Unité Propre de Recherche (UPR) 9036, Centre National de la Recherche Scientifique (CNRS) 31, Chemin Joseph Aiguier, 13402 Marseille, cedex 20, France
| | - E. Claude Hatchikian
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Unité Propre de Recherche (UPR) 9036, Centre National de la Recherche Scientifique (CNRS) 31, Chemin Joseph Aiguier, 13402 Marseille, cedex 20, France
| | - Matthieu Nouailler
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Unité Propre de Recherche (UPR) 9036, Centre National de la Recherche Scientifique (CNRS) 31, Chemin Joseph Aiguier, 13402 Marseille, cedex 20, France
| | - Alain Dolla
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Unité Propre de Recherche (UPR) 9036, Centre National de la Recherche Scientifique (CNRS) 31, Chemin Joseph Aiguier, 13402 Marseille, cedex 20, France
| | - Laetitia Pieulle
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Unité Propre de Recherche (UPR) 9036, Centre National de la Recherche Scientifique (CNRS) 31, Chemin Joseph Aiguier, 13402 Marseille, cedex 20, France
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Santos-Silva T, Dias JM, Dolla A, Durand MC, Gonçalves LL, Lampreia J, Moura I, Romão MJ. Crystal structure of the 16 heme cytochrome from Desulfovibrio gigas: a glycosylated protein in a sulphate-reducing bacterium. J Mol Biol 2007; 370:659-73. [PMID: 17531266 DOI: 10.1016/j.jmb.2007.04.055] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 04/16/2007] [Accepted: 04/19/2007] [Indexed: 11/20/2022]
Abstract
Sulphate-reducing bacteria have a wide variety of periplasmic cytochromes involved in electron transfer from the periplasm to the cytoplasm. HmcA is a high molecular mass cytochrome of 550 amino acid residues that harbours 16 c-type heme groups. We report the crystal structure of HmcA isolated from the periplasm of Desulfovibrio gigas. Crystals were grown using polyethylene glycol 8K and zinc acetate, and diffracted beyond 2.1 A resolution. A multiple-wavelength anomalous dispersion experiment at the iron absorption edge enabled us to obtain good-quality phases for structure solution and model building. DgHmcA has a V-shape architecture, already observed in HmcA isolated from Desulfovibrio vulgaris Hildenborough. The presence of an oligosaccharide molecule covalently bound to an Asn residue was observed in the electron density maps of DgHmcA and confirmed by mass spectrometry. Three modified monosaccharides appear at the highly hydrophobic vertex, possibly acting as an anchor of the protein to the cytoplasmic membrane.
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Affiliation(s)
- Teresa Santos-Silva
- REQUIMTE, CQFB, Departamento de Química, FCT-UNL, 2829-516 Caparica, Portugal
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Renesto P, Azza S, Dolla A, Fourquet P, Vestris G, Gorvel JP, Raoult D. Rickettsia conorii and R. prowazekii proteome analysis by 2DE-MS: a step toward functional analysis of rickettsial genomes. Ann N Y Acad Sci 2006; 1063:90-3. [PMID: 16481497 DOI: 10.1196/annals.1355.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In this work, we present a comparative two-dimensional (2D) PAGE analysis of Rickettsia conorii and Rickettsia prowazekii. This analysis reveals protein spots that were either unique to or common to both strains, some of them being identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry.
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Abstract
Sulfate-reducing bacteria (SRB) are strict anaerobes that are often found in biotopes where oxic conditions can temporarily exist. The bacteria have developed several defense strategies in order to survive exposure to oxygen. These strategies includes peculiar behaviors in the presence of oxygen, like aggregation or aerotaxis, and enzymatic systems dedicated to the reduction and the elimination of oxygen and its reactive species. Sulfate-reducing bacteria, and specially Desulfovibrio species, possess a variety of enzymes acting together to achieve an efficient defense against oxidative stress. The function and occurrence of these enzymatic systems are described.
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Affiliation(s)
- Alain Dolla
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS - 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France.
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Fournier M, Aubert C, Dermoun Z, Durand MC, Moinier D, Dolla A. Response of the anaerobe Desulfovibrio vulgaris Hildenborough to oxidative conditions: proteome and transcript analysis. Biochimie 2006; 88:85-94. [PMID: 16040186 DOI: 10.1016/j.biochi.2005.06.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Accepted: 06/20/2005] [Indexed: 10/25/2022]
Abstract
The method of two-dimensional protein gel electrophoresis was used to evaluate the changes at the proteins level following oxygen exposure of the anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Fifty-seven proteins showed significant differential expression. The cellular concentration of 35 proteins decreased while that of nineteen increased as a specific consequence of oxidative conditions. The proteins that were less abundant belonged to various functional categories such as nucleic acid and protein biosynthesis, detoxification mechanisms, or cell division. Interestingly, quantitative real-time PCR revealed that the genes encoding detoxification enzymes (rubrerythrins, superoxide reductase) are down regulated. The loss of viability of D. vulgaris Hildenborough under these oxidative conditions (Fournier et al., J. Biol. Chem. 279 (2004) 1785) can be directly related to the decrease in the cellular concentrations of these proteins, thereby specifying the toxicity of oxygen for the cells. Among the proteins that were more abundant under oxygen exposure, several thiol-specific peroxidases (thiol-peroxidase, BCP-like protein, and putative glutaredoxin) were identified. Using RT-PCR, the up-regulation of the genes encoding the thiol-peroxidase and the BCP was demonstrated. That is the first time that these proteins have been shown to be involved in the defense of D. vulgaris toward an oxidative stress. Several hypothetical proteins were also shown to be differentially expressed. A function in the defense mechanism against an oxidative stress is proposed for these uncharacterized proteins.
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Affiliation(s)
- Marjorie Fournier
- Laboratoire de bioénergétique et ingénierie des protéines, IBSM-CNRS, BIP, 31, chemin Joseph-Aiguier, 13402 Marseille cedex 20, France
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ElAntak L, Dolla A, Durand MC, Bianco P, Guerlesquin F. Role of the Tetrahemic Subunit in Desulfovibrio vulgaris Hildenborough Formate Dehydrogenase. Biochemistry 2005; 44:14828-34. [PMID: 16274230 DOI: 10.1021/bi0515366] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH), the genome sequencing revealed the presence of three operons encoding formate dehydrogenases. fdh1 encodes an alphabetagamma trimeric enzyme containing 11 heme binding sites; fdh2 corresponds to an alphabetagamma trimeric enzyme with a tetrahemic subunit; fdh3 encodes an alphabeta dimeric enzyme. In the present work, spectroscopic measurements demonstrated that the reduction of cytochrome c(553) was obtained in the presence of the trimeric FDH2 and not with the dimeric FDH3, suggesting that the tetrahemic subunit (FDH2C) is essential for the interaction with this physiological electron transfer partner. To further study the role of the tetrahemic subunit, the fdh2C gene was cloned and expressed in Desulfovibrio desulfuricans G201. The recombinant FDH2C was purified and characterized by optical and NMR spectroscopies. The heme redox potentials measured by electrochemistry were found to be identical in the whole enzyme and in the recombinant subunit, indicating a correct folding of the recombinant protein. The mapping of the interacting site by 2D heteronuclear NMR demonstrated a similar interaction of cytochrome c(553) with the native enzyme and the recombinant subunit. The presence of hemes c in the gamma subunit of formate dehydrogenases is specific of these anaerobic sulfate-reducing bacteria and replaces heme b subunit generally found in the enzymes involved in anaerobic metabolisms.
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Affiliation(s)
- Latifa ElAntak
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Renesto P, Azza S, Dolla A, Fourquet P, Vestris G, Gorvel JP, Raoult D. Proteome analysis of Rickettsia conorii by two-dimensional gel electrophoresis coupled with mass spectrometry. FEMS Microbiol Lett 2005; 245:231-8. [PMID: 15837377 DOI: 10.1016/j.femsle.2005.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Revised: 03/04/2005] [Accepted: 03/04/2005] [Indexed: 10/25/2022] Open
Abstract
The availability of genome sequence offers the opportunity to further expand our knowledge about proteins expressed by Rickettsia conorii, strictly intracellular bacterium responsible for Mediterranean spotted fever. Using two-dimensional polyacrylamide gel electrophoresis combined with MALDI-TOF mass spectrometry, we established the first reference map of R. conorii proteome. This approach also allowed identification of GroEL as the major antigen recognized by rabbit serum and sera of infected patients. Altogether, this work opens the way to characterize the proteome of R. conorii, to compare protein profiles of different isolates or of bacteria maintained under different experimental conditions and to identify immunogenic proteins as potential vaccine targets.
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Affiliation(s)
- Patricia Renesto
- Unité des Rickettsies, CNRS UMR 6020, IFR-48, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille, France.
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Fournier M, Dermoun Z, Durand MC, Dolla A. A New Function of the Desulfovibrio vulgaris Hildenborough [Fe] Hydrogenase in the Protection against Oxidative Stress. J Biol Chem 2004; 279:1787-93. [PMID: 14594815 DOI: 10.1074/jbc.m307965200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sulfate-reducing bacteria, like Desulfovibrio vulgaris Hildenborough, have developed a set of reactions allowing them to survive in oxic environments and even to reduce molecular oxygen to water. D. vulgaris contains a cytoplasmic superoxide reductase (SOR) and a periplasmic superoxide dismutase (SOD) involved in the elimination of superoxide anions. To assign the function of SOD, the periplasmic [Fe] hydrogenase activity was followed in both wild-type and sod deletant strains. This activity was lower in the strain lacking the SOD than in the wild-type when the cells were exposed to oxygen for a short time. The periplasmic SOD is thus involved in the protection of sensitive iron-sulfur-containing enzyme against superoxide-induced damages. Surprisingly, production of the periplasmic [Fe] hydrogenase was higher in the cells exposed to oxygen than in those kept in anaerobic conditions. A similar increase in the amount of [Fe] hydrogenase was observed when an increase in the redox potential was induced by addition of chromate. Viability of the strain lacking the gene encoding [Fe] hydrogenase after exposure to oxygen for 1 h was lower than that of the wild-type. These data reveal for the first time that production of the periplasmic [Fe] hydrogenase is up-regulated in response to an oxidative stress. A new function of the periplasmic [Fe] hydrogenase in the protective mechanisms of D. vulgaris Hildenborough toward an oxidative stress is proposed.
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Affiliation(s)
- Marjorie Fournier
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS 31, Chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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Schütz M, Schoepp-Cothenet B, Lojou E, Woodstra M, Lexa D, Tron P, Dolla A, Durand MC, Stetter KO, Baymann F. The naphthoquinol oxidizing cytochrome bc1 complex of the hyperthermophilic knallgasbacterium Aquifex aeolicus: properties and phylogenetic relationships. Biochemistry 2003; 42:10800-8. [PMID: 12962505 DOI: 10.1021/bi034452a] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phylogenetic analysis of constituent proteins of Rieske/cytochrome b complexes [Schütz et al. (2000) J. Mol. Biol. 300, 663-675] indicated that the respective enzyme from the hyperthermophile Aquifex (A.) aeolicus is closely related to proteobacterial counterparts, in disagreement with positioning of its parent species on small subunit rRNA trees. An assessment of the details and possible reasons for this discrepancy necessitates a thorough understanding of the biochemical and biophysical properties of the enzyme in addition to the bioinformatic data. The cytochrome bc(1) complex from A. aeolicus, which is part of the "Knallgasreaction" pathway, was therefore studied in membranes and in detergent-solubilized, isolated complex. Hemes b(L) (E(m,7) = -190 mV; g(z)= 3.7), b(H) (E(m,7) = -60 mV; g(z )= 3.45), and c(1) (E(m,7) = +160 mV; g(z )= 3.55) were identified by EPR and optical spectroscopy in combination with electrochemical methods. Two electrochemically distinct (E(m,7) = +95 mV; E(m,7) = +210 mV) Rieske centers were detected in membranes, and the +210 mV species was shown to correspond to the Rieske center of the cyt bc(1) complex. The gene coding for this latter Rieske protein was heterologously expressed in Escherichia coli, and the resulting protein was characterized in detail. The pool quinone of A. aeolicus was determined to be naphthoquinone. The redox poises of the individual electron-transfer steps are compared to those of other Rieske/cyt b complexes. The Aquifex enzyme was found to represent the only extant naphthoquinol oxidizing true cyt bc(1) complex described so far. An improved scenario for the phylogenetic positioning of the Aquifex cyt bc(1) complex is proposed.
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Affiliation(s)
- Michael Schütz
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UPR9036), CNRS, 31, chemin Joseph-Aiguier, F-13402 Marseille Cedex 20, France
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ElAntak L, Morelli X, Bornet O, Hatchikian C, Czjzek M, Dolla A, Guerlesquin F. The cytochrome c3-[Fe]-hydrogenase electron-transfer complex: structural model by NMR restrained docking. FEBS Lett 2003; 548:1-4. [PMID: 12885397 DOI: 10.1016/s0014-5793(03)00718-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cytochrome c(3) (M(r) 13000) is a low redox potential cytochrome specific of the anaerobic metabolism in sulfate-reducing bacteria. This tetrahemic cytochrome is an intermediate between the [Fe]-hydrogenase and the cytochrome Hmc in Desulfovibrio vulgaris Hildenborough strain. The present work describes the structural model of the cytochrome c(3)-[Fe]-hydrogenase complex obtained by nuclear magnetic resonance restrained docking. This model connects the distal cluster of the [Fe]-hydrogenase to heme 4 of the cytochrome, the same heme found in the interaction with cytochrome Hmc. This result gives evidence that cytochrome c(3) is an electron shuttle between the periplasmic hydrogenase and the Hmc membrane-bound complex.
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Affiliation(s)
- Latifa ElAntak
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Cedex 20, Marseille, France.
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Fournier M, Zhang Y, Wildschut JD, Dolla A, Voordouw JK, Schriemer DC, Voordouw G. Function of oxygen resistance proteins in the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris hildenborough. J Bacteriol 2003; 185:71-9. [PMID: 12486042 PMCID: PMC141827 DOI: 10.1128/jb.185.1.71-79.2003] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two mutant strains of Desulfovibrio vulgaris Hildenborough lacking either the sod gene for periplasmic superoxide dismutase or the rbr gene for rubrerythrin, a cytoplasmic hydrogen peroxide (H(2)O(2)) reductase, were constructed. Their resistance to oxidative stress was compared to that of the wild-type and of a sor mutant lacking the gene for the cytoplasmic superoxide reductase. The sor mutant was more sensitive to exposure to air or to internally or externally generated superoxide than was the sod mutant, which was in turn more sensitive than the wild-type strain. No obvious oxidative stress phenotype was found for the rbr mutant, indicating that H(2)O(2) resistance may also be conferred by two other rbr genes in the D. vulgaris genome. Inhibition of Sod activity by azide and H(2)O(2), but not by cyanide, indicated it to be an iron-containing Sod. The positions of Fe-Sod and Sor were mapped by two-dimensional gel electrophoresis (2DE). A strong decrease of Sor in continuously aerated cells, indicated by 2DE, may be a critical factor in causing cell death of D. vulgaris. Thus, Sor plays a key role in oxygen defense of D. vulgaris under fully aerobic conditions, when superoxide is generated mostly in the cytoplasm. Fe-Sod may be more important under microaerophilic conditions, when the periplasm contains oxygen-sensitive, superoxide-producing targets.
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Affiliation(s)
- Marjorie Fournier
- Department of Biological Sciences. Department of Biochemistry and Molecular Biology, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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Czjzek M, ElAntak L, Zamboni V, Morelli X, Dolla A, Guerlesquin F, Bruschi M. The crystal structure of the hexadeca-heme cytochrome Hmc and a structural model of its complex with cytochrome c(3). Structure 2002; 10:1677-86. [PMID: 12467575 DOI: 10.1016/s0969-2126(02)00909-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sulfate-reducing bacteria contain a variety of multi-heme c-type cytochromes. The cytochrome of highest molecular weight (Hmc) contains 16 heme groups and is part of a transmembrane complex involved in the sulfate respiration pathway. We present the 2.42 A resolution crystal structure of the Desulfovibrio vulgaris Hildenborough cytochrome Hmc and a structural model of the complex with its physiological electron transfer partner, cytochrome c(3), obtained by NMR restrained soft-docking calculations. The Hmc is composed of three domains, which exist independently in different sulfate-reducing species, namely cytochrome c(3), cytochrome c(7), and Hcc. The complex involves the last heme at the C-terminal region of the V-shaped Hmc and heme 4 of cytochrome c(3), and represents an example for specific cytochrome-cytochrome interaction.
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Affiliation(s)
- Mirjam Czjzek
- Architecture et Fonction des Macromolécules Biologiques, IBSM-CNRS et Université Aix-Marseille I et II, 31 Chemin Joseph-Aiguier, 13402 Marseille cedex 20, France.
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Chardin B, Dolla A, Chaspoul F, Fardeau ML, Gallice P, Bruschi M. Bioremediation of chromate: thermodynamic analysis of the effects of Cr(VI) on sulfate-reducing bacteria. Appl Microbiol Biotechnol 2002; 60:352-60. [PMID: 12436319 DOI: 10.1007/s00253-002-1091-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2002] [Revised: 07/01/2002] [Accepted: 07/07/2002] [Indexed: 10/27/2022]
Abstract
Developing new bioremediation processes for soils and effluents polluted by Cr(VI) requires the selection of the most efficient and the most heavy-metal-resistant bacteria. The effects of Cr(VI) on bioenergetic metabolism in two sulfate-reducing bacteria (SRB), Desulfovibrio vulgaris Hildenborough and Desulfomicrobium norvegicum, were monitored using isothermal microcalorimetry. The complete reduction of Cr(VI) to Cr(III) was studied by spectrophotometry and by speciation using a combination of high-performance liquid chromatography and inductively coupled plasma-mass spectrometry. Results revealed that Cr(VI) induces an inhibition of growth with concomitant production of energy, which can be compared to the reaction of the bacteria to a stress such as oxidative stress. Moreover, the sensitivity of bacteria towards this metal is as a characteristic of the strain, which leads to differences in the kinetics of Cr(VI) reduction. The study by microcalorimetry of heavy metal effects on SRB bioenergetic metabolism thus appears an appropriate tool to identify better strains to be used for industrial bioremediation process development.
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Affiliation(s)
- B Chardin
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Biologie Structurale et Microbiologie - CNRS, 31 ch. Joseph Aiguier, 13009 Marseille, France
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Lojou E, Durand M, Dolla A, Bianco P. Hydrogenase Activity Control at Desulfovibrio vulgaris Cell-Coated Carbon Electrodes: Biochemical and Chemical Factors Influencing the Mediated Bioelectrocatalysis. ELECTROANAL 2002. [DOI: 10.1002/1521-4109(200207)14:13<913::aid-elan913>3.0.co;2-n] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Elantak L, Bornet O, Morelli X, Dolla A, Guerlesquin F. Sequential NMR assignment of the ferri-cytochrome c3 from Desulfovibrio vulgaris Hildenborough. J Biomol NMR 2002; 23:69-70. [PMID: 12061720 DOI: 10.1023/a:1015365012019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Pohorelic BKJ, Voordouw JK, Lojou E, Dolla A, Harder J, Voordouw G. Effects of deletion of genes encoding Fe-only hydrogenase of Desulfovibrio vulgaris Hildenborough on hydrogen and lactate metabolism. J Bacteriol 2002; 184:679-86. [PMID: 11790737 PMCID: PMC139517 DOI: 10.1128/jb.184.3.679-686.2002] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The physiological properties of a hyd mutant of Desulfovibrio vulgaris Hildenborough, lacking periplasmic Fe-only hydrogenase, have been compared with those of the wild-type strain. Fe-only hydrogenase is the main hydrogenase of D. vulgaris Hildenborough, which also has periplasmic NiFe- and NiFeSe-hydrogenases. The hyd mutant grew less well than the wild-type strain in media with sulfate as the electron acceptor and H(2) as the sole electron donor, especially at a high sulfate concentration. Although the hyd mutation had little effect on growth with lactate as the electron donor for sulfate reduction when H(2) was also present, growth in lactate- and sulfate-containing media lacking H(2) was less efficient. The hyd mutant produced, transiently, significant amounts of H(2) under these conditions, which were eventually all used for sulfate reduction. The results do not confirm the essential role proposed elsewhere for Fe-only hydrogenase as a hydrogen-producing enzyme in lactate metabolism (W. A. M. van den Berg, W. M. A. M. van Dongen, and C. Veeger, J. Bacteriol. 173:3688-3694, 1991). This role is more likely played by a membrane-bound, cytoplasmic Ech-hydrogenase homolog, which is indicated by the D. vulgaris genome sequence. The physiological role of periplasmic Fe-only hydrogenase is hydrogen uptake, both when hydrogen is and when lactate is the electron donor for sulfate reduction.
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Affiliation(s)
- Brant K J Pohorelic
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
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Assfalg M, Bertini I, Turano P, Bruschi M, Durand MC, Giudici-Orticoni MT, Dolla A. A quick solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans and mechanistic implications. J Biomol NMR 2002; 22:107-122. [PMID: 11883773 DOI: 10.1023/a:1014202405862] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Lysines 9 and 10 in Desulfuromonas acetoxidans cytochrome c7, which could be involved in the interaction mechanism with the redox partners, have been replaced by alanine residues using site-directed mutagenesis. The solution structure of the fully oxidized form of K9-10A cytochrome c7, which is paramagnetic with three paramagnetic centers, has been determined via 1H NMR. The assignment of the spectra has been performed through an automatic program whose algorithm and strategy are here described. The assignment of the NOESY spectra has been further extended by back calculating the NOESY maps. The final number of meaningful NOE-based upper distance limits was 1186. In the Restrained Energy Minimization calculations, 147 pseudocontact shift constraints were also included, which showed consistency with NOE-based constraints and therefore further contribute to validate the structure quality. A final family of 35 conformers was calculated with RMSD values with respect to the mean structure of 0.69 +/- 0.17 A and 1.05 +/- 0.14 A for the backbone and heavy atoms, respectively. The overall fold of the molecule is maintained with respect to the native protein. The loop present between heme III and heme IV results to be highly disordered also in the present structure although its overall shape mainly resembles that of the oxidized native protein, and the two strands which give rise to the short beta-sheet present at the N-terminus and connected by a turn containing the mutated residues, are less clearly defined. If this loop is neglected, the RMSD values are 0.52 +/- 0.07 A and 0.92 +/- 0.06 A for the backbone and heavy atoms, respectively, which represent a reasonable resolution. The relative distances and orientations of the three hemes are maintained, as well as the orientation of the imidazole rings of the axial histidine ligands, with the only exception of heme IV. Such difference probably reflects minor conformational changes due to the substitution of the vicinal Lys 10 with an Ala. The replacement of the two lysines does not affect the reduction potentials of the three hemes, consistently with the expectations on the basis of the structure and electrostatic calculations. However, the replacement of the two lysines affects the reactivity of the mutant cytochrome c7 with [Fe] hydrogenase, inducing a change in Km. This finding is in agreement with the identification of the protein area around heme IV as the interacting site.
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Affiliation(s)
- Michael Assfalg
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
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Dolla A, Pohorelic BK, Voordouw JK, Voordouw G. Deletion of the hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough hampers hydrogen metabolism and low-redox-potential niche establishment. Arch Microbiol 2000; 174:143-51. [PMID: 11041344 DOI: 10.1007/s002030000183] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough encodes a transmembrane redox protein complex (the Hmc complex) that has been proposed to catalyze electron transport linking periplasmic hydrogen oxidation to cytoplasmic sulfate reduction. We have replaced a 5-kb DNA fragment containing most of the hmc operon by the cat gene. The resulting chloramphenicol-resistant mutant D. vulgaris H801 grows normally when lactate or pyruvate serve as electron donors for sulfate reduction. Growth with hydrogen as electron donor for sulfate reduction (acetate and CO2 as the carbon source) is impaired. These results confirm the importance of the Hmc complex in electron transport from hydrogen to sulfate. Mutant H801 is also deficient in low-redox-potential niche establishment. On plates, colony development takes 14 days longer than colony development of the wild-type strain, when the cells use hydrogen as the electron donor. This result suggests that, in addition to transmembrane electron transport from hydrogen to sulfate, the redox reactions catalyzed by the Hmc complex are crucial in establishment of the required low-redox-potential niche that allows single cells to grow into colonies.
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Affiliation(s)
- A Dolla
- Department of Biological Sciences, The University of Calgary, Alberta, Canada
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Herbaud ML, Aubert C, Durand MC, Guerlesquin F, Thöny-Meyer L, Dolla A. Escherichia coli is able to produce heterologous tetraheme cytochrome c(3) when the ccm genes are co-expressed. Biochim Biophys Acta 2000; 1481:18-24. [PMID: 11004576 DOI: 10.1016/s0167-4838(00)00117-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The production of Desulfovibrio vulgaris Hildenborough cytochrome c(3) (M(r) 13000), which is a tetraheme cytochrome, in Escherichia coli was examined. This cytochrome was successfully produced in an E. coli strain co-expressing the ccmABCDEFGH genes involved in the cytochrome c maturation process. The apocytochrome c(3) was matured in either anaerobic or aerobic conditions, but aerobic growth in the presence of delta-aminolevulinic acid was found to be best for cytochrome c(3) production. Site-directed mutagenesis was performed to investigate the effect of the presence of four amino acids in between the two cysteines of the heme binding sites 2 and 4 on the maturation of holocytochrome c(3) in E. coli.
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Affiliation(s)
- M L Herbaud
- Unite de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, Marseilles, France
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Morelli X, Dolla A, Czjzek M, Palma PN, Blasco F, Krippahl L, Moura JJ, Guerlesquin F. Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex. Biochemistry 2000; 39:2530-7. [PMID: 10704202 DOI: 10.1021/bi992306s] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The combination of docking algorithms with NMR data has been developed extensively for the studies of protein-ligand interactions. However, to extend this development for the studies of protein-protein interactions, the intermolecular NOE constraints, which are needed, are more difficult to access. In the present work, we describe a new approach that combines an ab initio docking calculation and the mapping of an interaction site using chemical shift variation analysis. The cytochrome c553-ferredoxin complex is used as a model of numerous electron-transfer complexes. The 15N-labeling of both molecules has been obtained, and the mapping of the interacting site on each partner, respectively, has been done using HSQC experiments. 1H and 15N chemical shift analysis defines the area of both molecules involved in the recognition interface. Models of the complex were generated by an ab initio docking software, the BiGGER program (bimolecular complex generation with global evaluation and ranking). This program generates a population of protein-protein docked geometries ranked by a scoring function, combining relevant stabilization parameters such as geometric complementarity surfaces, electrostatic interactions, desolvation energy, and pairwise affinities of amino acid side chains. We have implemented a new module that includes experimental input (here, NMR mapping of the interacting site) as a filter to select the accurate models. Final structures were energy minimized using the X-PLOR software and then analyzed. The best solution has an interface area (1037.4 A2) falling close to the range of generally observed recognition interfaces, with a distance of 10.0 A between the redox centers.
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Affiliation(s)
- X Morelli
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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Abstract
To explore the physiological role of tetraheme cytochrome c(3) in the sulfate-reducing bacterium Desulfovibrio desulfuricans G20, the gene encoding the preapoprotein was cloned, sequenced, and mutated by plasmid insertion. The physical analysis of the DNA from the strain carrying the integrated plasmid showed that the insertion was successful. The growth rate of the mutant on lactate with sulfate was comparable to that of the wild type; however, mutant cultures did not achieve the same cell densities. Pyruvate, the oxidation product of lactate, served as a poor electron source for the mutant. Unexpectedly, the mutant was able to grow on hydrogen-sulfate medium. These data support a role for tetraheme cytochrome c(3) in the electron transport pathway from pyruvate to sulfate or sulfite in D. desulfuricans G20.
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Affiliation(s)
- B J Rapp-Giles
- Biochemistry Department, University of Missouri-Columbia, Columbia, Missouri 65211, USA
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