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

Abstract

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 C 1-metabolism in methanotrophic bacteria can represent an efficient tool for metabolic engineering or ecosystem modeling.

Authors:
 [1];  [2];  [2];  [3];  [3];  [4]; ORCiD logo [4];  [2]
  1. San Diego State Univ., San Diego, CA (United States); Institute of Cytology and Genetics and Novosibirsk State Univ., Novosibirsk (Russia)
  2. San Diego State Univ., San Diego, CA (United States)
  3. Metabolon, Inc., Durham, NC (United States)
  4. National Renewable Energy Lab. (NREL), Golden, CO (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)
OSTI Identifier:
1422031
Report Number(s):
NREL/JA-5100-70511
Journal ID: ISSN 2045-2322
Grant/Contract Number:  
AC36-08GO28308
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; metabolic engineering; methane utilization; methylomicrobium alcaliphilum

Citation Formats

Akberdin, Ilya R., Thompson, Merlin, Hamilton, Richard, Desai, Nalini, Alexander, Danny, Henard, Calvin A., Guarnieri, Michael T., and Kalyuzhnaya, Marina G. Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach. United States: N. p., 2018. Web. doi:10.1038/s41598-018-20574-z.
Akberdin, Ilya R., Thompson, Merlin, Hamilton, Richard, Desai, Nalini, Alexander, Danny, Henard, Calvin A., Guarnieri, Michael T., & Kalyuzhnaya, Marina G. Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach. United States. doi:10.1038/s41598-018-20574-z.
Akberdin, Ilya R., Thompson, Merlin, Hamilton, Richard, Desai, Nalini, Alexander, Danny, Henard, Calvin A., Guarnieri, Michael T., and Kalyuzhnaya, Marina G. Tue . "Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach". United States. doi:10.1038/s41598-018-20574-z. https://www.osti.gov/servlets/purl/1422031.
@article{osti_1422031,
title = {Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach},
author = {Akberdin, Ilya R. and Thompson, Merlin and Hamilton, Richard and Desai, Nalini and Alexander, Danny and Henard, Calvin A. and Guarnieri, Michael T. and Kalyuzhnaya, Marina G.},
abstractNote = {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 20ZR an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20ZR. 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.},
doi = {10.1038/s41598-018-20574-z},
journal = {Scientific Reports},
number = 1,
volume = 8,
place = {United States},
year = {2018},
month = {2}
}

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