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

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https://ir.library.oregonstate.edu/concern/articles/pr76f4854

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Abstract
  • 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/).
  • This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Frontiers Research Foundation. The published article can be found at: http://www.frontiersin.org/Microbiology.
  • Keywords: Carbon cycle, Gene Ontology, Bioenergy, Methanogen, Biodegradation, Waste treatment, Biomass, Methanogenesis
  • Keywords: Carbon cycle, Gene Ontology, Bioenergy, Methanogen, Biodegradation, Waste treatment, Biomass, Methanogenesis
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  • Purwantini, E., Torto-Alalibo, T., Lomax, J., Setubal, J. C., Tyler, B. M., & Mukhopadhyay, B. (2014). Genetic resources for methane production from biomass described with the Gene Ontology. Frontiers in Microbiology, 5, 634. doi:10.3389/fmicb.2014.00634
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  • 5
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  • This work was supported by grant DE-SC0005011 from the US Department of Energy. João C. Setubal was funded by CNPq and FAPESP, and Jane Lomax was supported by EMBL-EBI corefunds.
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file details TylerBrettGRBGeneticResourcesMethane.pdf 07/25/2017 公开
file details TylerBrettGRBGeneticResourcesMethane_TableS1.xlsx 07/25/2017 公开