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Imaura Y, Okamoto S, Hino T, Ogami Y, Katayama YA, Tanimura A, Inoue M, Kamikawa R, Yoshida T, Sako Y. Isolation, Genomic Sequence and Physiological Characterization of Parageobacillus sp. G301, an Isolate Capable of Both Hydrogenogenic and Aerobic Carbon Monoxide Oxidation. Appl Environ Microbiol 2023; 89:e0018523. [PMID: 37219438 PMCID: PMC10304674 DOI: 10.1128/aem.00185-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/06/2023] [Indexed: 05/24/2023] Open
Abstract
Prokaryotes that can oxidize carbon monoxide (CO oxidizers) can use this gas as a source of carbon or energy. They oxidize carbon monoxide with carbon monoxide dehydrogenases (CODHs): these are divided into nickel-containing CODH (Ni-CODH), which are sensitive to O2, and molybdenum-containing CODH (Mo-CODH), which can function aerobically. The oxygen conditions required for CO oxidizers to oxidize CO may be limited, as those which have been isolated and characterized so far contain either Ni- or Mo-CODH. Here, we report a novel CO oxidizer, Parageobacillus sp. G301, which is capable of CO oxidation using both types of CODH based on genomic and physiological characterization. This thermophilic, facultatively anaerobic Bacillota bacterium was isolated from the sediments of a freshwater lake. Genomic analyses revealed that strain G301 possessed both Ni-CODH and Mo-CODH. Genome-based reconstruction of its respiratory machinery and physiological investigations indicated that CO oxidation by Ni-CODH was coupled with H2 production (proton reduction), whereas CO oxidation by Mo-CODH was coupled with O2 reduction under aerobic conditions and nitrate reduction under anaerobic conditions. G301 would thus be able to thrive via CO oxidation under a wide range of conditions, from aerobic environments to anaerobic environments, even with no terminal electron acceptors other than protons. Comparative genome analyses revealed no significant differences in genome structures and encoded cellular functions, except for CO oxidation between CO oxidizers and non-CO oxidizers in the genus Parageobacillus; CO oxidation genes are retained exclusively for CO metabolism and related respiration. IMPORTANCE Microbial CO oxidation has received much attention because it contributes to global carbon cycling in addition to functioning as a remover of CO, which is toxic to many organisms. Some microbial CO oxidizers, including both bacteria and archaea, exhibit sister relationships with non-CO oxidizers even in genus-level monophyletic groups. In this study, we demonstrated that a new isolate, Parageobacillus sp. G301, is capable of both anaerobic (hydrogenogenic) and aerobic CO oxidation, which has not been previously reported. The discovery of this new isolate, which is versatile in CO metabolism, will accelerate research on CO oxidizers with diverse CO metabolisms, expanding our understanding of microbial diversity. Through comparative genomic analyses, we propose that CO oxidation genes are not essential genetic elements in the genus Parageobacillus, providing insights into the factors which shape the punctate distribution of CO oxidizers in the prokaryote tree, even in genus-level monophyletic groups.
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Affiliation(s)
| | | | - Taiki Hino
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yusuke Ogami
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Ayumi Tanimura
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masao Inoue
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- R-GIRO, Ritsumeikan University, Kusatsu, Shiga, Japan
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiko Sako
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Chaignaud P, Gruffaz C, Borreca A, Fouteau S, Kuhn L, Masbou J, Rouy Z, Hammann P, Imfeld G, Roche D, Vuilleumier S. A Methylotrophic Bacterium Growing with the Antidiabetic Drug Metformin as Its Sole Carbon, Nitrogen and Energy Source. Microorganisms 2022; 10:2302. [PMID: 36422372 PMCID: PMC9699525 DOI: 10.3390/microorganisms10112302] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 08/31/2023] Open
Abstract
Metformin is one of the most prescribed antidiabetic agents worldwide and is also considered for other therapeutic applications including cancer and endocrine disorders. It is largely unmetabolized by human enzymes and its presence in the environment has raised concern, with reported toxic effects on aquatic life and potentially also on humans. We report on the isolation and characterisation of strain MD1, an aerobic methylotrophic bacterium growing with metformin as its sole carbon, nitrogen and energy source. Strain MD1 degrades metformin into dimethylamine used for growth, and guanylurea as a side-product. Sequence analysis of its fully assembled genome showed its affiliation to Aminobacter niigataensis. Differential proteomics and transcriptomics, as well as mini-transposon mutagenesis of the strain, point to genes and proteins essential for growth with metformin and potentially associated with hydrolytic C-N cleavage of metformin or with cellular transport of metformin and guanylurea. The obtained results suggest the recent evolution of the growth-supporting capacity of strain MD1 to degrade metformin. Our results identify candidate proteins of the enzymatic system for metformin transformation in strain MD1 and will inform future research on the fate of metformin and its degradation products in the environment and in humans.
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Affiliation(s)
- Pauline Chaignaud
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Christelle Gruffaz
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Adrien Borreca
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, 67000 Strasbourg, France
- Institut Terre et Environnement de Strasbourg, UMR 7063 CNRS, ENGEES, Université de Strasbourg, 67000 Strasbourg, France
| | - Stéphanie Fouteau
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université d’Evry, Université Paris-Saclay, CEDEX, 91057 Evry, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, FR 1589 CNRS, CEDEX, 67084 Strasbourg, France
| | - Jérémy Masbou
- Institut Terre et Environnement de Strasbourg, UMR 7063 CNRS, ENGEES, Université de Strasbourg, 67000 Strasbourg, France
| | - Zoé Rouy
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université d’Evry, Université Paris-Saclay, CEDEX, 91057 Evry, France
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, FR 1589 CNRS, CEDEX, 67084 Strasbourg, France
| | - Gwenaël Imfeld
- Institut Terre et Environnement de Strasbourg, UMR 7063 CNRS, ENGEES, Université de Strasbourg, 67000 Strasbourg, France
| | - David Roche
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université d’Evry, Université Paris-Saclay, CEDEX, 91057 Evry, France
| | - Stéphane Vuilleumier
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, 67000 Strasbourg, France
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Oren A, Garrity G. Notification of changes in taxonomic opinion previously published outside the IJSEM. List of changes in taxonomic opinion no. 35. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Exploiting Aerobic Carboxydotrophic Bacteria for Industrial Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 180:1-32. [PMID: 34894287 DOI: 10.1007/10_2021_178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Aerobic carboxydotrophic bacteria are a group of microorganisms which possess the unique trait to oxidize carbon monoxide (CO) as sole energy source with molecular oxygen (O2) to produce carbon dioxide (CO2) which subsequently is used for biomass formation via the Calvin-Benson-Bassham cycle. Moreover, most carboxydotrophs are also able to oxidize hydrogen (H2) with hydrogenases to drive the reduction of carbon dioxide in the absence of CO. As several abundant industrial off-gases contain significant amounts of CO, CO2, H2 as well as O2, these bacteria come into focus for industrial application to produce chemicals and fuels from such gases in gas fermentation approaches. Since the group of carboxydotrophic bacteria is rather unknown and not very well investigated, we will provide an overview about their lifestyle and the underlying metabolic characteristics, introduce promising members for industrial application, and give an overview of available genetic engineering tools. We will point to limitations and discuss challenges, which have to be overcome to apply metabolic engineering approaches and to utilize aerobic carboxydotrophs in the industrial environment.
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Artuso I, Turrini P, Pirolo M, Lugli GA, Ventura M, Visca P. Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter. Microorganisms 2021; 9:microorganisms9061332. [PMID: 34205374 PMCID: PMC8235418 DOI: 10.3390/microorganisms9061332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/01/2022] Open
Abstract
Bacteria belonging to the genus Aminobacter are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of A. anthyllidis LMG 26462T and the presence of unclassified Aminobacter strains. Here, we determined the genome sequence of A. anthyllidis LMG 26462T and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus Aminobacter. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified Aminobacter strains belong to valid Aminobacter species or are putative new species. Since some members of the genus Aminobacter can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all Aminobacter species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all Aminobacter species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only A. anthyllidis LMG 26462T contains a symbiosis island implicated in nodulation and nitrogen fixation.
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Affiliation(s)
- Irene Artuso
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy; (I.A.); (P.T.)
| | - Paolo Turrini
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy; (I.A.); (P.T.)
| | - Mattia Pirolo
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark;
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy; (G.A.L.); (M.V.)
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy; (G.A.L.); (M.V.)
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, 43124 Parma, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy; (I.A.); (P.T.)
- Correspondence: ; Tel.: +39-0657336347
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