Genetic resources for methane production from biomass described with the Gene Ontology

Purwantini, Endang; Torto-Alalibo, Trudy; Lomax, Jane; Setubal, Joao C.; Tyler, Brett M.; Mukhopadhyay, Biswarup

doi:10.3389/fmicb.2014.00634

Title: Genetic resources for methane production from biomass described with the Gene Ontology

Journal Article · Wed Dec 03 00:00:00 EST 2014 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2014.00634· OSTI ID:1457512

Purwantini, Endang ^[1]; Torto-Alalibo, Trudy ^[1]; Lomax, Jane ^[2]; Setubal, Joao C. ^[3]; Tyler, Brett M. ^[4]; Mukhopadhyay, Biswarup ^[5]

Virginia Polytechnic Institute and State University, Blacksburg, VA (United States). Department of Biochemistry
European Molecular Biology Laboratory, Hinxton (United Kingdom). European Bioinformatics Institute (EMBL-EBI)
Universidade de São Paulo (Brazil). Department of Biochemistry; Virginia Polytechnic Institute and State University, Blacksburg, VA (United States). Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University, Blacksburg, VA (United States). Virginia Bioinformatics Institute; Oregon State Univ., Corvallis, OR (United States). Center for Genome Research and Biocomputing
Virginia Polytechnic Institute and State University, Blacksburg, VA (United States). Department of Biochemistry, Virginia Bioinformatics Institute and Department of Biological Sciences

Methane (CH₄) is a valuable fuel, constituting 70-95% of natural gas, and a potent greenhouse gas. Release of CH₄ into the atmosphere contributes to climate change. Biological CH₄ production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H₂ plus CO₂, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO₂. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H₂ plus CO₂. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH₄ production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing "gold standards" for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/).

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Research Organization:: Virginia Polytechnic Institute and State University, Blacksburg, VA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0005011

OSTI ID:: 1457512

Journal Information:: Frontiers in Microbiology, Vol. 5; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 13 works

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