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Title: Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans

Abstract

Methanosarcina acetivorans is a model archaeon with renewed interest due to its unique reversible methane production pathways. However, the mechanism and relevant pathways implicated in (co)utilizing novel carbon substrates in this organism are still not fully understood. This paper provides a comprehensive inventory of thermodynamically feasible routes for anaerobic methane oxidation, co-reactant utilization, and maximum carbon yields of major biofuel candidates by M. acetivorans. Here, an updated genome-scale metabolic model of M. acetivorans is introduced (iMAC868 containing 868 genes, 845 reactions, and 718 metabolites) by integrating information from two previously reconstructed metabolic models (i.e., iVS941 and iMB745), modifying 17 reactions, adding 24 new reactions, and revising 64 gene-proteinreaction associations based on newly available information. The new model establishes improved predictions of growth yields on native substrates and is capable of correctly predicting the knockout outcomes for 27 out of 28 gene deletion mutants. By tracing a bifurcated electron flow mechanism, the iMAC868 model predicts thermodynamically feasible (co)utilization pathway of methane and bicarbonate using various terminal electron acceptors through the reversal of the aceticlastic pathway. In conclusion, this effort paves the way in informing the search for thermodynamically feasible ways of (co)utilizing novel carbon substrates in the domain Archaea.

Authors:
; ; ; ;
Publication Date:
Research Org.:
Pennsylvania State Univ., University Park, PA (United States)
Sponsoring Org.:
USDOE Advanced Research Projects Agency - Energy (ARPA-E)
OSTI Identifier:
1618800
Alternate Identifier(s):
OSTI ID: 1238778
Grant/Contract Number:  
ARPA-E DE-AR0000431; AR0000431
Resource Type:
Published Article
Journal Name:
Microbial Cell Factories
Additional Journal Information:
Journal Name: Microbial Cell Factories Journal Volume: 15 Journal Issue: 1; Journal ID: ISSN 1475-2859
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Methanosarcina acetivorans; genome-scale metabolic model; methane utilization

Citation Formats

Nazem-Bokaee, Hadi, Gopalakrishnan, Saratram, Ferry, James G., Wood, Thomas K., and Maranas, Costas D. Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans. United Kingdom: N. p., 2016. Web. doi:10.1186/s12934-015-0404-4.
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Nazem-Bokaee, Hadi, Gopalakrishnan, Saratram, Ferry, James G., Wood, Thomas K., & Maranas, Costas D. Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans. United Kingdom. https://doi.org/10.1186/s12934-015-0404-4
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Nazem-Bokaee, Hadi, Gopalakrishnan, Saratram, Ferry, James G., Wood, Thomas K., and Maranas, Costas D. Sun . "Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans". United Kingdom. https://doi.org/10.1186/s12934-015-0404-4.
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@article{osti_1618800,
title = {Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans},
author = {Nazem-Bokaee, Hadi and Gopalakrishnan, Saratram and Ferry, James G. and Wood, Thomas K. and Maranas, Costas D.},
abstractNote = {Methanosarcina acetivorans is a model archaeon with renewed interest due to its unique reversible methane production pathways. However, the mechanism and relevant pathways implicated in (co)utilizing novel carbon substrates in this organism are still not fully understood. This paper provides a comprehensive inventory of thermodynamically feasible routes for anaerobic methane oxidation, co-reactant utilization, and maximum carbon yields of major biofuel candidates by M. acetivorans. Here, an updated genome-scale metabolic model of M. acetivorans is introduced (iMAC868 containing 868 genes, 845 reactions, and 718 metabolites) by integrating information from two previously reconstructed metabolic models (i.e., iVS941 and iMB745), modifying 17 reactions, adding 24 new reactions, and revising 64 gene-proteinreaction associations based on newly available information. The new model establishes improved predictions of growth yields on native substrates and is capable of correctly predicting the knockout outcomes for 27 out of 28 gene deletion mutants. By tracing a bifurcated electron flow mechanism, the iMAC868 model predicts thermodynamically feasible (co)utilization pathway of methane and bicarbonate using various terminal electron acceptors through the reversal of the aceticlastic pathway. In conclusion, this effort paves the way in informing the search for thermodynamically feasible ways of (co)utilizing novel carbon substrates in the domain Archaea.},
doi = {10.1186/s12934-015-0404-4},
journal = {Microbial Cell Factories},
number = 1,
volume = 15,
place = {United Kingdom},
year = {Sun Jan 17 00:00:00 EST 2016},
month = {Sun Jan 17 00:00:00 EST 2016}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1186/s12934-015-0404-4
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Cited by: 28 works
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Figures / Tables:

Table 1 Table 1: Growth yield predictions of iMAC868 model of M. acetivorans compared with predictions of previous models iVS941 and iMB745
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