Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach

Akberdin, Ilya R.; Thompson, Merlin; Hamilton, Richard; Desai, Nalini; Alexander, Danny; Henard, Calvin A.; Guarnieri, Michael T.; Kalyuzhnaya, Marina G.

doi:10.1038/s41598-018-20574-z

Title: Methane utilization in Methylomicrobium alcaliphilum 20Z^R: a systems approach

Journal Article · Tue Feb 06 00:00:00 EST 2018 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-018-20574-z· OSTI ID:1422031

Akberdin, Ilya R. ^[1]; Thompson, Merlin ^[2]; Hamilton, Richard ^[2]; Desai, Nalini ^[3]; Alexander, Danny ^[3]; Henard, Calvin A. ^[4];

^[4]; Kalyuzhnaya, Marina G. ^[2]

San Diego State Univ., San Diego, CA (United States); Institute of Cytology and Genetics and Novosibirsk State Univ., Novosibirsk (Russia)
San Diego State Univ., San Diego, CA (United States)
Metabolon, Inc., Durham, NC (United States)
National Renewable Energy Lab. (NREL), Golden, CO (United States)

Biological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated is limited. Attractive growth and methane-conversion rates, a complete and expert-annotated genome sequence, as well as large enzymatic, ¹³C-labeling, and transcriptomic datasets make Methylomicrobium alcaliphilum 20Z^R an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20Z^R. A set of novel metabolic reactions governing carbon distribution across central pathways in methanotrophic bacteria was predicted by in-silico simulations and confirmed by global non-targeted metabolomics and enzymatic evidences. Our data highlight the importance of substitution of ATP-linked steps with PPi-dependent reactions and support the presence of a carbon shunt from acetyl-CoA to the pentose-phosphate pathway and highly branched TCA cycle. The diverged TCA reactions promote balance between anabolic reactions and redox demands. As a result, the computational framework of C₁-metabolism in methanotrophic bacteria can represent an efficient tool for metabolic engineering or ecosystem modeling.

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Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office

Grant/Contract Number:: AC36-08GO28308

OSTI ID:: 1422031

Report Number(s):: NREL/JA-5100-70511

Journal Information:: Scientific Reports, Vol. 8, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 62 works

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Title: Methane utilization in Methylomicrobium alcaliphilum 20Z^R: a systems approach