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Abstract
Methanogenic archaea are the only organisms that produce CH4 as part of their energy-generating metabolism. They are ubiquitous in oxidant-depleted, anoxic environments such as aquatic sediments, anaerobic digesters, inundated agricultural fields, the rumen of cattle, and the hindgut of termites, where they catalyze the terminal reactions in the degradation of organic matter. Methanogenesis is the only metabolism that is restricted to members of the domain Archaea. Here, we discuss the importance of model organisms in the history of methanogen research, including their role in the discovery of the archaea and in the biochemical and genetic characterization of methanogenesis. We also discuss outstanding questions in the field and newly emerging model systems that will expand our understanding of this uniquely archaeal metabolism.
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Affiliation(s)
- Kyle C. Costa
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
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Li J, Akinyemi TS, Shao N, Chen C, Dong X, Liu Y, Whitman WB. Genetic and Metabolic Engineering of Methanococcus spp. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Bender KS, Madigan MT, Williamson KL, Mayer MH, Parenteau MN, Jahnke LL, Welander PV, Sanguedolce SA, Brown AC, Sattley WM. Genomic Features of the Bundle-Forming Heliobacterium Heliophilum fasciatum. Microorganisms 2022; 10:microorganisms10050869. [PMID: 35630314 PMCID: PMC9147875 DOI: 10.3390/microorganisms10050869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023] Open
Abstract
Eight species of heliobacteria have had their genomes sequenced. However, only two of these genomes have been analyzed in detail, those from the thermophilic Heliomicrobium (Hmi.) modesticaldum and the alkaliphilic Heliorestis (Hrs.) convoluta. Here we present analyses of the draft genome sequence of a species of heliobacterium that grows optimally at a moderate temperature and neutral pH. The organism, Heliophilum (Hph.) fasciatum, is phylogenetically unique among cultured heliobacteria and was isolated from rice soil, a common habitat for heliobacteria. The Hph. fasciatum genome contains 3.14 Mbp—similar to that of other reported heliobacteria—but has a G+C base ratio that lies between that of Hmi. modesticaldum and Hrs. convoluta. Many of the genomic features of Hmi. modesticaldum and Hrs. convoluta, such as the absence of genes encoding autotrophic pathways, the presence of a superoperonal cluster of photosynthesis-related genes, and genes encoding endospore-specific proteins, are also characteristic of the Hph. fasciatum genome. However, despite the fact that Hph. fasciatum is diazotrophic, classical nif genes encoding the alpha and beta subunits of dinitrogenase (nifDK) present in other heliobacteria could not be identified. Instead, genes encoding several highly divergent NifDK homologs were present, at least one of which likely encodes a functional dinitrogenase and another a methylthio-alkane reductase (MarDK) for sulfur assimilation. A classical NifH (dinitrogenase reductase) homolog was also absent in Hph. fasciatum, but a related protein was identified that likely carries out this function as well as electron delivery to MarDK. The N2-fixing system of Hph. fasciatum is therefore distinct from that of other heliobacteria and may have unusual properties.
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Affiliation(s)
- Kelly S. Bender
- Microbiology Program, School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (K.S.B.); (M.T.M.); (K.L.W.)
| | - Michael T. Madigan
- Microbiology Program, School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (K.S.B.); (M.T.M.); (K.L.W.)
| | - Kyleigh L. Williamson
- Microbiology Program, School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (K.S.B.); (M.T.M.); (K.L.W.)
| | - Marisa H. Mayer
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA; (M.H.M.); (M.N.P.); (L.L.J.)
| | - Mary N. Parenteau
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA; (M.H.M.); (M.N.P.); (L.L.J.)
| | - Linda L. Jahnke
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA; (M.H.M.); (M.N.P.); (L.L.J.)
| | - Paula V. Welander
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA;
| | - Sophia A. Sanguedolce
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (S.A.S.); (A.C.B.)
| | - Abigail C. Brown
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (S.A.S.); (A.C.B.)
| | - W. Matthew Sattley
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA; (S.A.S.); (A.C.B.)
- Correspondence: ; Tel.: +1-765-677-2128
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