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Gasteazoro F, Catucci G, Barbieri L, De Angelis M, Dalla Costa A, Sadeghi SJ, Gilardi G, Valetti F. Cascade reactions with two non-physiological partners for NAD(P)H regeneration via renewable hydrogen. Biotechnol J 2024; 19:e2300567. [PMID: 38581100 DOI: 10.1002/biot.202300567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024]
Abstract
An attractive application of hydrogenases, combined with the availability of cheap and renewable hydrogen (i.e., from solar and wind powered electrolysis or from recycled wastes), is the production of high-value electron-rich intermediates such as reduced nicotinamide adenine dinucleotides. Here, the capability of a very robust and oxygen-resilient [FeFe]-hydrogenase (CbA5H) from Clostridium beijerinckii SM10, previously identified in our group, combined with a reductase (BMR) from Bacillus megaterium (now reclassified as Priestia megaterium) was tested. The system shows a good stability and it was demonstrated to reach up to 28 ± 2 nmol NADPH regenerated s-1 mg of hydrogenase-1 (i.e., 1.68 ± 0.12 U mg-1, TOF: 126 ± 9 min-1) and 0.46 ± 0.04 nmol NADH regenerated s-1 mg of hydrogenase-1 (i.e., 0.028 ± 0.002 U mg-1, TOF: 2.1 ± 0.2 min-1), meaning up to 74 mg of NADPH and 1.23 mg of NADH produced per hour by a system involving 1 mg of CbA5H. The TOF is comparable with similar systems based on hydrogen as regenerating molecule for NADPH, but the system is first of its kind as for the [FeFe]-hydrogenase and the non-physiological partners used. As a proof of concept a cascade reaction involving CbA5H, BMR and a mutant BVMO from Acinetobacter radioresistens able to oxidize indole is presented. The data show how the cascade can be exploited for indigo production and multiple reaction cycles can be sustained using the regenerated NADPH.
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Affiliation(s)
- Francisco Gasteazoro
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
- CICATA Unidad Morelos, Instituto Politécnico Nacional, Mexico D. F., Mexico
| | - Gianluca Catucci
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Lisa Barbieri
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
- University School for Advanced Studies IUSS Pavia, Pavia, Italy
| | - Melissa De Angelis
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | | | - Sheila J Sadeghi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
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Hassa J, Tubbesing TJ, Maus I, Heyer R, Benndorf D, Effenberger M, Henke C, Osterholz B, Beckstette M, Pühler A, Sczyrba A, Schlüter A. Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics. Microorganisms 2023; 11:2412. [PMID: 37894070 PMCID: PMC10608942 DOI: 10.3390/microorganisms11102412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.
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Affiliation(s)
- Julia Hassa
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Tom Jonas Tubbesing
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Irena Maus
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Robert Heyer
- Multidimensional Omics Data Analyses Group, Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, Dortmund 44139, Germany
- Multidimensional Omics Data Analyses Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Dirk Benndorf
- Biosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Straße 55, Postfach 1458, 06366 Köthen, Germany
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Mathias Effenberger
- Bavarian State Research Center for Agriculture, Institute for Agricultural Engineering and Animal Husbandry, Vöttinger Straße 36, 85354 Freising, Germany
| | - Christian Henke
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Benedikt Osterholz
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Michael Beckstette
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Alexander Sczyrba
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Andreas Schlüter
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
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Hisatomi A, Kastawa NWEPG, Song I, Ohkuma M, Fukiya S, Sakamoto M. Claveliimonas bilis gen. nov., sp. nov., deoxycholic acid-producing bacteria isolated from human faeces, and reclassification of Sellimonas monacensis Zenner et al. 2021 as Claveliimonas monacensis comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37737068 DOI: 10.1099/ijsem.0.006030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
Obligately anaerobic, Gram-stain-positive, bacilli, strains 12BBH14T, 9CFEGH4 and 10CPCBH12, were isolated from faecal samples of healthy Japanese people. Strain 12BBH14T showed the highest 16S rRNA gene sequence similarity to Sellimonas monacensis Cla-CZ-80T (97.5 %) and 'Lachnoclostridium phocaeense' Marseille-P3177T (97.2 %). Strain 12BBH14T was also closely related to Eubacterium sp. c-25 with 99.7 % 16S rRNA gene sequence similarity. The 16S rRNA gene sequence analysis showed that strains 12BBH14T, 9CFEGH4 and 10CPCBH12 formed a monophyletic cluster with Eubacterium sp. c-25. Near this monophyletic cluster, S. monacensis Cla-CZ-80T and 'L. phocaeense' Marseille-P3177T formed a cluster and did not form a cluster with other Sellimonas species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 12BBH14T, 9CFEGH4, 10CPCBH12 and Eubacterium sp. c-25 were higher than the cut-off values of species demarcation (>88 % dDDH and >98 % ANI), indicating that these four strains are the same species. On the other hand, the dDDH and ANI values of these strains were lower than the cut-off values of species demarcation against other strains (<29 % dDDH and <76 % ANI). Moreover, the average amino acid identity values among these strains were higher than the genus boundary. These results indicate that the isolates should be considered to belong to a new genus of the family Lachnospiraceae. Based on the collected data, strains 12BBH14T, 9CFEGH4 and 10CPCBH12 represent a novel species of a novel genus, for which the name Claveliimonas bilis gen. nov., sp. nov. is proposed. The type strain of C. bilis is 12BBH14T (=JCM 35899T=DSM 115701T). Eubacterium sp. c-25 belongs to C. bilis. In addition, S. monacensis is transferred to the genus Claveliimonas as Claveliimonas monacensis comb. nov.
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Affiliation(s)
- Atsushi Hisatomi
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | | | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Satoru Fukiya
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Kim S, Li H, Jin Y, Armad J, Gu H, Mani S, Cui JY. Maternal PBDE exposure disrupts gut microbiome and promotes hepatic proinflammatory signaling in humanized PXR-transgenic mouse offspring over time. Toxicol Sci 2023; 194:209-225. [PMID: 37267213 PMCID: PMC10375318 DOI: 10.1093/toxsci/kfad056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
Developmental exposure to the persistent environmental pollutant, polybrominated diphenyl ethers (PBDEs), is associated with increased diabetes prevalence. The microbial tryptophan metabolite, indole-3-propionic acid (IPA), is associated with reduced risk of type 2 diabetes and lower-grade inflammation and is a pregnane X receptor (PXR) activator. To explore the role of IPA in modifying the PBDE developmental toxicity, we orally exposed humanized PXR-transgenic (hPXR-TG) mouse dams to vehicle, 0.1 mg/kg/day DE-71 (an industrial PBDE mixture), DE-71+IPA (20 mg/kg/day), or IPA, from 4 weeks preconception to the end of lactation. Pups were weaned at 21 days of age and IPA supplementation continued in the corresponding treatment groups. Tissues were collected at various ages until 6 months of age (n = 5 per group). In general, the effect of maternal DE-71 exposure on the gut microbiome of pups was amplified over time. The regulation of hepatic cytokines and prototypical xenobiotic-sensing transcription factor target genes by DE-71 and IPA was age- and sex-dependent, where DE-71-mediated mRNA increased selected cytokines (Il10, Il12p40, Il1β [both sexes], and [males]). The hepatic mRNA of the aryl hydrocarbon receptor (AhR) target gene Cyp1a2 was increased by maternal DE-71 and DE-71+IPA exposure at postnatal day 21 but intestinal Cyp1a1 was not altered by any of the exposures and ages. Maternal DE-71 exposure persistently increased serum indole, a known AhR ligand, in age- and sex-dependent manner. In conclusion, maternal DE-71 exposure produced a proinflammatory signature along the gut-liver axis, including gut dysbiosis, dysregulated tryptophan microbial metabolism, attenuated PXR signaling, and elevated AhR signaling in postweaned hPXR-TG pups over time, which was partially corrected by IPA supplementation.
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Affiliation(s)
- Sarah Kim
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Hao Li
- Departments of Medicine, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, Florida 34987-2352, USA
| | - Jasmine Armad
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Haiwei Gu
- Center for Translational Science, Florida International University, Port St. Lucie, Florida 34987-2352, USA
| | - Sridhar Mani
- Departments of Medicine, Molecular Pharmacology, and Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Julia Y Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, USA
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Chen X, Molenda O, Brown CT, Toth CRA, Guo S, Luo F, Howe J, Nesbø CL, He C, Montabana EA, Cate JHD, Banfield JF, Edwards EA. " Candidatus Nealsonbacteria" Are Likely Biomass Recycling Ectosymbionts of Methanogenic Archaea in a Stable Benzene-Degrading Enrichment Culture. Appl Environ Microbiol 2023; 89:e0002523. [PMID: 37098974 PMCID: PMC10231131 DOI: 10.1128/aem.00025-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/20/2023] [Indexed: 04/27/2023] Open
Abstract
The Candidate Phyla Radiation (CPR), also referred to as superphylum Patescibacteria, is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum Parcubacteria, previously referred to as OD1, is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within the clade "Candidatus Nealsonbacteria." Because of its persistence over many years, we hypothesized that "Ca. Nealsonbacteria" DGGOD1a must play an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, and phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10-fold) increase in the absolute abundance of "Ca. Nealsonbacteria" DGGOD1a only when the consortium was amended with crude cell lysate. These results implicate "Ca. Nealsonbacteria" in biomass recycling. Fluorescence in situ hybridization and cryogenic transmission electron microscope images revealed that "Ca. Nealsonbacteria" DGGOD1a cells were attached to larger archaeal Methanothrix cells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of other "Ca. Nealsonbacteria" found in anoxic environments. IMPORTANCE An anaerobic microbial enrichment culture was used to study members of candidate phyla that are difficult to grow in the lab. We were able to visualize tiny "Candidatus Nealsonbacteria" cells attached to a large Methanothrix cell, revealing a novel episymbiosis.
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Affiliation(s)
- Xu Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Christopher T. Brown
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
| | - Courtney R. A. Toth
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Shen Guo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jane Howe
- Department of Materials Science and Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Camilla L. Nesbø
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Christine He
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Elizabeth A. Montabana
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Jillian F. Banfield
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Earth and Planetary Science, University of California, Berkeley, California, USA
- Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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Payne N, Kpebe A, Guendon C, Baffert C, Maillot M, Haurogné T, Tranchida F, Brugna M, Shintu L. NMR-based metabolomic analysis of the physiological role of the electron-bifurcating FeFe-hydrogenase Hnd in Solidesulfovibrio fructosivorans under pyruvate fermentation. Microbiol Res 2023; 268:127279. [PMID: 36592576 DOI: 10.1016/j.micres.2022.127279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Solidesulfovibrio fructosivorans (formely Desulfovibrio fructosovorans), an anaerobic sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases catalyzing the reversible oxidation of hydrogen gas (H2) into protons and electrons. One of these, named Hnd, was demonstrated to be an electron-bifurcating hydrogenase Hnd (Kpebe et al., 2018). It couples the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin with electrons derived from H2 and whose function has been recently shown to be involved in ethanol production under pyruvate fermentation (Payne 2022). To understand further the physiological role of Hnd in S. fructosivorans, we compared the mutant deleted of part of the hnd gene with the wild-type strain grown on pyruvate without sulfate using NMR-based metabolomics. Our results confirm that Hnd is profoundly involved in ethanol metabolism, but also indirectly intervenes in global carbon metabolism and additional metabolic processes such as the biosynthesis of branched-chain amino acids. We also highlight the metabolic reprogramming induced by the deletion of hndD that leads to the upregulation of several NADP-dependent pathways.
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Affiliation(s)
- Natalie Payne
- Aix Marseille Univ, CNRS, BIP, Marseille, France; Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France
| | | | | | | | | | | | - Fabrice Tranchida
- Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France
| | | | - Laetitia Shintu
- Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France.
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Feng G, Zeng Y, Wang HZ, Chen YT, Tang YQ. Proteiniphilum and Methanothrix harundinacea became dominant acetate utilizers in a methanogenic reactor operated under strong ammonia stress. Front Microbiol 2023; 13:1098814. [PMID: 36687577 PMCID: PMC9853277 DOI: 10.3389/fmicb.2022.1098814] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/15/2022] [Indexed: 01/09/2023] Open
Abstract
Microorganisms in anaerobic digestion (AD) are easily affected by ammonia, especially acetoclastic methanogens. Thus, in ammonia-suppressed AD systems, acetate degradation is reported to be carried out mainly by the cooperation of syntrophic acetate oxidizers and hydrogenotrophic methanogens. Previous studies have revealed ammonia inhibition on microbial flora by AD performance, but the effect mechanism of ammonia on microbial metabolism remains poorly understood. In this study, we constructed a mesophilic chemostat fed with acetate as the sole carbon source, gradually increased the total ammonia nitrogen (TAN) concentration from 1 g L-1 to 6 g L-1, and employed the 16S rRNA gene, metagenomics, and metatranscriptomics analysis to characterize the microbial community structure and metabolic behavior. The results showed that even at the TAN of 6 g L-1 (pH 7.5), the methanogenesis kept normal, the biogas production was approximately 92% of that at TAN of 1 g L-1 and the acetate degradation ratio reached 99%, suggesting the strong TAN tolerance of the microbial community enriched. 16S rRNA gene analysis suggested that the microbial community structure changed along with the TAN concentration. Methanothrix predominated in methanogens all the time, in which the dominant species was gradually replaced from M. soehngenii to M. harundinacea with the increased TAN. Dominant bacterial species also changed and Proteiniphilum showed a significant positive correlation with increased TAN. Meta-omics analysis showed that the absolute dominant microorganisms at TAN of 6 g L-1 were M. harundinacea and Proteiniphilum, both of which highly expressed genes for anti-oxidative stress. M. harundinacea and the second dominant methanogen Methanosarcina highly expressed both acetate cleavage and CO2 reduction pathways, suggesting the possibility that these two pathways contributed to methanogenesis together. Proteiniphilum and some other species in Firmicutes and Synergistetes were likely acetate oxidizers in the community as they highly expressed genes for syntrophic acetate oxidization, H2 generation, and electron transfer. These results suggested that Proteiniphilum as well as M. harundinacea have strong ammonia tolerance and played critical roles in acetate degradation under ammonia-suppressed conditions. The achievements of the study would contribute to the regulation and management of the AD process.
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Affiliation(s)
- Gao Feng
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Yan Zeng
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, Sichuan, China
| | - Hui-Zhong Wang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Ya-Ting Chen
- Institute for Disaster Management and Reconstruction, Sichuan University, Chengdu, Sichuan, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China,Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, Sichuan, China,Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, Chengdu, Sichuan, China,*Correspondence: Yue-Qin Tang,
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8
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Unique H 2-utilizing lithotrophy in serpentinite-hosted systems. THE ISME JOURNAL 2023; 17:95-104. [PMID: 36207493 PMCID: PMC9751293 DOI: 10.1038/s41396-022-01197-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 01/08/2022] [Accepted: 01/17/2022] [Indexed: 11/08/2022]
Abstract
Serpentinization of ultramafic rocks provides molecular hydrogen (H2) that can support lithotrophic metabolism of microorganisms, but also poses extremely challenging conditions, including hyperalkalinity and limited electron acceptor availability. Investigation of two serpentinization-active systems reveals that conventional H2-/CO2-dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, "Ca. Lithacetigenota", that exclusively inhabits serpentinite-hosted systems and harbors genes encoding alternative modes of H2-utilizing lithotrophy. Rather than CO2, these putative metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein-the glycine reductase. A survey of microbiomes shows that glycine reductases are diverse and nearly ubiquitous in serpentinite-hosted environments. "Ca. Lithacetigenota" glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation by Terrabacteria for gaining energy from geogenic H2 even under hyperalkaline, CO2-poor conditions. Unique non-CO2-reducing metabolisms presented here shed light on potential strategies that extremophiles may employ for overcoming a crucial obstacle in serpentinization-associated environments, features potentially relevant to primordial lithotrophy in early Earth.
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Sheridan PO, Louis P, Tsompanidou E, Shaw S, Harmsen HJ, Duncan SH, Flint HJ, Walker AW. Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria. Microb Genom 2022; 8. [PMID: 35077342 PMCID: PMC8914356 DOI: 10.1099/mgen.0.000739] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lactate accumulation in the human gut is linked to a range of deleterious health impacts. However, lactate is consumed and converted to the beneficial short-chain fatty acids butyrate and propionate by indigenous lactate-utilizing bacteria. To better understand the underlying genetic basis for lactate utilization, transcriptomic analyses were performed for two prominent lactate-utilizing species from the human gut, Anaerobutyricum soehngenii and Coprococcus catus, during growth on lactate, hexose sugar or hexose plus lactate. In A. soehngenii L2-7 six genes of the lactate utilization (lct) cluster, including NAD-independent d-lactate dehydrogenase (d-iLDH), were co-ordinately upregulated during growth on equimolar d- and l-lactate (dl-lactate). Upregulated genes included an acyl-CoA dehydrogenase related to butyryl-CoA dehydrogenase, which may play a role in transferring reducing equivalents between reduction of crotonyl-CoA and oxidation of lactate. Genes upregulated in C. catus GD/7 included a six-gene cluster (lap) encoding propionyl CoA-transferase, a putative lactoyl-CoA epimerase, lactoyl-CoA dehydratase and lactate permease, and two unlinked acyl-CoA dehydrogenase genes that are candidates for acryloyl-CoA reductase. A d-iLDH homologue in C. catus is encoded by a separate, partial lct, gene cluster, but not upregulated on lactate. While C. catus converts three mols of dl-lactate via the acrylate pathway to two mols propionate and one mol acetate, some of the acetate can be re-used with additional lactate to produce butyrate. A key regulatory difference is that while glucose partially repressed lct cluster expression in A. soehngenii, there was no repression of lactate-utilization genes by fructose in the non-glucose utilizer C. catus. This suggests that these species could occupy different ecological niches for lactate utilization in the gut, which may be important factors to consider when developing lactate-utilizing bacteria as novel candidate probiotics.
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Affiliation(s)
- Paul O Sheridan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Petra Louis
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Eleni Tsompanidou
- Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Sophie Shaw
- Centre for Genome-Enabled Biology and Medicine, 23 St. Machar Drive, AB24 3RY Aberdeen, UK
| | - Hermie J Harmsen
- Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Sylvia H Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Harry J Flint
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Alan W Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
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10
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Payne N, Kpebe A, Guendon C, Baffert C, Ros J, Lebrun R, Denis Y, Shintu L, Brugna M. The electron-bifurcating FeFe-hydrogenase Hnd is involved in ethanol metabolism in Desulfovibrio fructosovorans grown on pyruvate. Mol Microbiol 2022; 117:907-920. [PMID: 35066935 DOI: 10.1111/mmi.14881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 11/28/2022]
Abstract
Desulfovibrio fructosovorans, a sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases catalyzing the reversible oxidation of H2 into protons and electrons. Among them, Hnd is an electron-bifurcating hydrogenase, coupling the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin with electrons derived from H2 . It was previously hypothesized that its biological function involves the production of NADPH necessary for biosynthetic purposes. However, it was subsequently demonstrated that Hnd is instead a NAD+ -reducing enzyme, thus its specific function has yet to be established. To understand the physiological role of Hnd in D. fructosovorans, we compared the hnd deletion mutant with the wild-type strain grown on pyruvate. Growth, metabolites production and comsumption, and gene expression were compared under three different growth conditions. Our results indicate that hnd is strongly regulated at the transcriptional level and that its deletion has a drastic effect on the expression of genes for two enzymes, an aldehyde ferredoxin oxidoreductase and an alcohol dehydrogenase. We demonstrated here that Hnd is involved in ethanol metabolism when bacteria grow fermentatively and proposed that Hnd might oxidize part of the H2 produced during fermentation generating both NADH and reduced ferredoxin for ethanol production via its electron bifurcation mechanism.
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Affiliation(s)
| | | | | | | | - Julien Ros
- CNRS, Aix Marseille Univ, BIP, Marseille, France
| | - Régine Lebrun
- CNRS, Aix Marseille Univ, Plate-forme Protéomique de l'IMM, FR 3479, Marseille Protéomique (MaP), Marseille, France
| | - Yann Denis
- CNRS, Aix Marseille Univ, Plate-forme Transcriptomique, Marseille, France
| | - Laetitia Shintu
- CNRS, Aix Marseille Univ, Centrale Marseille, ISM2, Marseille, France
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11
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Zheng S, Li M, Liu Y, Liu F. Desulfovibrio feeding Methanobacterium with electrons in conductive methanogenic aggregates from coastal zones. WATER RESEARCH 2021; 202:117490. [PMID: 34364064 DOI: 10.1016/j.watres.2021.117490] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/23/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Geobacter, as a typical electroactive microorganism, is the "engine" of interspecies electron transfer (IET) between microorganisms. However, it does not have a dominant position in all natural environments. It is not known what performs a similar function as Geobacter in coastal zones. Metagenomic and metatranscriptomic analysis revealed that Desulfovibrio and Methanobacterium species were the most abundant in electrochemically active aggregates. Metatranscriptomic analysis showed that Desulfovibrio species highly expressed genes for ethanol metabolism and extracellular electron transfer involving cytochromes, pili and flagella. Methanobacterium species in the aggregates also expressed genes for enzymes involved in reducing carbon dioxide to methane. Pure cultures demonstrated that the isolated Desulfovibrio sp. strain JY contributed to aggregate conductivity and directly transferred electrons to Methanothrix harundinacea, which is unable to use H2 or formate. Most importantly, further coculture studies indicated that Methanobacterium strain YSL might directly accept electrons from the Desulfovibrio strain JY for the reduction of carbon dioxide to methane in the aggregate. This finding suggested that the possibility of DIET by Desulfovibrio similar to Geobacter species in conductive methanogenic aggregates can not be excluded.
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Affiliation(s)
- Shiling Zheng
- Key Laboratory of Coastal Biology and Biological Resources Utilization, CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, PR China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, PR China
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Biological Resources Utilization, CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China.
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12
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Baffert C, Kpebe A, Avilan L, Brugna M. Hydrogenases and H 2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus. Adv Microb Physiol 2019; 74:143-189. [PMID: 31126530 DOI: 10.1016/bs.ampbs.2019.03.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H2 metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H2 metabolism.
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Affiliation(s)
- Carole Baffert
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Arlette Kpebe
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Luisana Avilan
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Myriam Brugna
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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13
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Kpebe A, Benvenuti M, Guendon C, Rebai A, Fernandez V, Le Laz S, Etienne E, Guigliarelli B, García-Molina G, de Lacey AL, Baffert C, Brugna M. A new mechanistic model for an O 2-protected electron-bifurcating hydrogenase, Hnd from Desulfovibrio fructosovorans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1302-1312. [PMID: 30463674 DOI: 10.1016/j.bbabio.2018.09.364] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/22/2018] [Accepted: 09/16/2018] [Indexed: 10/28/2022]
Abstract
The genome of the sulfate-reducing and anaerobic bacterium Desulfovibrio fructosovorans encodes different hydrogenases. Among them is Hnd, a tetrameric cytoplasmic [FeFe] hydrogenase that has previously been described as an NADP-specific enzyme (Malki et al., 1995). In this study, we purified and characterized a recombinant Strep-tagged form of Hnd and demonstrated that it is an electron-bifurcating enzyme. Flavin-based electron-bifurcation is a mechanism that couples an exergonic redox reaction to an endergonic one allowing energy conservation in anaerobic microorganisms. One of the three ferredoxins of the bacterium, that was named FdxB, was also purified and characterized. It contains a low-potential (Em = -450 mV) [4Fe4S] cluster. We found that Hnd was not able to reduce NADP+, and that it catalyzes the simultaneous reduction of FdxB and NAD+. Moreover, Hnd is the first electron-bifurcating hydrogenase that retains activity when purified aerobically due to formation of an inactive state of its catalytic site protecting against O2 damage (Hinact). Hnd is highly active with the artificial redox partner (methyl viologen) and can perform the electron-bifurcation reaction to oxidize H2 with a specific activity of 10 μmol of NADH/min/mg of enzyme. Surprisingly, the ratio between NADH and reduced FdxB varies over the reaction with a decreasing amount of FdxB reduced per NADH produced, indicating a more complex mechanism than previously described. We proposed a new mechanistic model in which the ferredoxin is recycled at the hydrogenase catalytic subunit.
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Affiliation(s)
- Arlette Kpebe
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | - Martino Benvenuti
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | - Chloé Guendon
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | - Amani Rebai
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France
| | - Victoria Fernandez
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France
| | - Sébastien Le Laz
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | | | - Antonio L de Lacey
- Instituto de Catálisis y Petroleoquímica, CSIC, c/ Marie Curie 2, Madrid, Spain.
| | - Carole Baffert
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
| | - Myriam Brugna
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 09, France.
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14
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part II. {[Fe2S2](SγCys)4} proteins. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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15
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Practical applications of hydrogenase I from Pyrococcus furiosus for NADPH generation and regeneration. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1381-1177(03)00071-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Dermoun Z, De Luca G, Asso M, Bertrand P, Guerlesquin F, Guigliarelli B. The NADP-reducing hydrogenase from Desulfovibrio fructosovorans: functional interaction between the C-terminal region of HndA and the N-terminal region of HndD subunits. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1556:217-25. [PMID: 12460679 DOI: 10.1016/s0005-2728(02)00364-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The hndABCD operon from Desulfovibrio fructosovorans encodes an uncommon heterotetrameric NADP-reducing iron hydrogenase. The presence of a [2Fe-2S] cluster likely located in the C-terminal region of the HndA subunit has already been revealed. We have cloned and expressed the truncated hndA gene in Escherichia coli to isolate the structural [2Fe-2S] module. Optical and EPR spectra are found identical to that of the native HndA subunit and the midpoint redox potential (-385 mV) is similar to that of the native protein (-395 mV). These results clearly demonstrate that the C-terminal region of HndA is a structurally independent [2Fe2S] ferredoxin-like domain. In the same way, the N-terminal domain of the HndD subunit was overproduced in E. coli and characterized. The presence of a [2Fe-2S] cluster was evidenced by optical spectroscopy. The midpoint redox potential (-380 mV) of this domain was found very close to that of the truncated HndA subunit but the EPR properties were significantly different. The various EPR properties allowed us to observe an electron exchange between the two [2Fe-2S] ferredoxin-like domains of the HndA and HndD subunits. Moreover, domain-domain interactions, observed by far-western experiments, indicate that these subunits are direct partners in the native complex.
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Affiliation(s)
- Zorah Dermoun
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Centre National de la Recherche Scientifique, IBSM, 31 Chemin Joseph Aiguier, 13402 cedex 20, Marseille, France.
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17
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Casalot L, De Luca G, Dermoun Z, Rousset M, de Philip P. Evidence for a fourth hydrogenase in Desulfovibrio fructosovorans. J Bacteriol 2002; 184:853-6. [PMID: 11790758 PMCID: PMC139505 DOI: 10.1128/jb.184.3.853-856.2002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A strain devoid of the three hydrogenases characterized for Desulfovibrio fructosovorans was constructed using marker exchange mutagenesis. As expected, the H(2)-dependent methyl viologen reduction activity of the strain was null, but physiological studies showed no striking differences between the mutated and wild-type strains. The H(+)-D(2) exchange activity measured in the mutated strain indicates the presence of a fourth hydrogenase in D. fructosovorans.
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Affiliation(s)
- Laurence Casalot
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
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18
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De Luca G, de Philip P, Dermoun Z, Rousset M, Verméglio A. Reduction of technetium(VII) by Desulfovibrio fructosovorans is mediated by the nickel-iron hydrogenase. Appl Environ Microbiol 2001; 67:4583-7. [PMID: 11571159 PMCID: PMC93206 DOI: 10.1128/aem.67.10.4583-4587.2001] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Resting cells of the sulfate-reducing bacterium Desulfovibrio fructosovorans grown in the absence of sulfate had a very high Tc(VII)-reducing activity, which led to the formation of an insoluble black precipitate. The involvement of a periplasmic hydrogenase in Tc(VII) reduction was indicated (i) by the requirement for hydrogen as an electron donor, (ii) by the tolerance of this activity to oxygen, and (iii) by the inhibition of this activity by Cu(II). Moreover, a mutant carrying a deletion in the nickel-iron hydrogenase operon showed a dramatic decrease in the rate of Tc(VII) reduction. The restoration of Tc(VII) reduction by complementation of this mutation with nickel-iron hydrogenase genes demonstrated the specific involvement of the periplasmic nickel-iron hydrogenase in the mechanism in vivo. The Tc(VII)-reducing activity was also observed with cell extracts in the presence of hydrogen. Under these conditions, Tc(VII) was reduced enzymatically to soluble Tc(V) or precipitated to an insoluble black precipitate, depending on the chemical nature of the buffer used. The purified nickel-iron hydrogenase performed Tc(VII) reduction and precipitation at high rates. These series of genetic and biochemical approaches demonstrated that the periplasmic nickel-iron hydrogenase of sulfate-reducing bacteria functions as a Tc(VII) reductase. The role of cytochrome c(3) in the mechanism is also discussed.
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Affiliation(s)
- G De Luca
- CEA Cadarache, DSV/DEVM/Laboratoire de Bioénergétique Cellulaire, 13108 Saint Paul-Lez-Durance, France
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