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

Methane (CH 4) is a valuable fuel, constituting 70-95% of natural gas, and a potent greenhouse gas. Release of CH 4 into the atmosphere contributes to climate change. Biological CH 4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H 2 plus CO 2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO 2. 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 H 2 plus CO 2. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation andmore » 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 CH 4 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/).« less
Authors:
 [1] ;  [1] ;  [2] ;  [3] ;  [4] ;  [5]
  1. Virginia Polytechnic Institute and State University, Blacksburg, VA (United States). Department of Biochemistry
  2. European Molecular Biology Laboratory, Hinxton (United Kingdom). European Bioinformatics Institute (EMBL-EBI)
  3. Universidade de São Paulo (Brazil). Department of Biochemistry; Virginia Polytechnic Institute and State University, Blacksburg, VA (United States). Virginia Bioinformatics Institute
  4. 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
  5. Virginia Polytechnic Institute and State University, Blacksburg, VA (United States). Department of Biochemistry, Virginia Bioinformatics Institute and Department of Biological Sciences
Publication Date:
Grant/Contract Number:
SC0005011
Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 5; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Research Org:
Virginia Polytechnic Institute and State University, Blacksburg, VA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; Gene Ontology; biomass; biodegradation; methanogenesis; methanogen; bioenergy; carbon cycle; waste treatment
OSTI Identifier:
1457512

Purwantini, Endang, Torto-Alalibo, Trudy, Lomax, Jane, Setubal, Joao C., Tyler, Brett M., and Mukhopadhyay, Biswarup. Genetic resources for methane production from biomass described with the Gene Ontology. United States: N. p., Web. doi:10.3389/fmicb.2014.00634.
Purwantini, Endang, Torto-Alalibo, Trudy, Lomax, Jane, Setubal, Joao C., Tyler, Brett M., & Mukhopadhyay, Biswarup. Genetic resources for methane production from biomass described with the Gene Ontology. United States. doi:10.3389/fmicb.2014.00634.
Purwantini, Endang, Torto-Alalibo, Trudy, Lomax, Jane, Setubal, Joao C., Tyler, Brett M., and Mukhopadhyay, Biswarup. 2014. "Genetic resources for methane production from biomass described with the Gene Ontology". United States. doi:10.3389/fmicb.2014.00634. https://www.osti.gov/servlets/purl/1457512.
@article{osti_1457512,
title = {Genetic resources for methane production from biomass described with the Gene Ontology},
author = {Purwantini, Endang and Torto-Alalibo, Trudy and Lomax, Jane and Setubal, Joao C. and Tyler, Brett M. and Mukhopadhyay, Biswarup},
abstractNote = {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/).},
doi = {10.3389/fmicb.2014.00634},
journal = {Frontiers in Microbiology},
number = ,
volume = 5,
place = {United States},
year = {2014},
month = {12}
}

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