title: Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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-protein-reaction 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.
  
  
  CONCLUSIONS
  This effort paves the way in informing the search for thermodynamically feasible ways of (co)utilizing novel carbon substrates in the domain Archaea.
authors.affiliation: Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA. hnbokaee@psu.edu.
authors.forename: Hadi
authors.initials: H
authors.lastname: Nazem-Bokaee
authors.affiliation: Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA. sxg375@psu.edu.
authors.forename: Saratram
authors.initials: S
authors.lastname: Gopalakrishnan
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. jgf3@psu.edu.
authors.forename: James G
authors.initials: JG
authors.lastname: Ferry
authors.affiliation: Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA. tuw14@psu.edu.|Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. tuw14@psu.edu.
authors.forename: Thomas K
authors.initials: TK
authors.lastname: Wood
authors.affiliation: Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA. costas@psu.edu.
authors.forename: Costas D
authors.initials: CD
authors.lastname: Maranas
mesh_terms: D056804:Biofuels; D002244:Carbon / Q000378:metabolism*; D017020:Methanosarcina / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D056804:Biofuels; D002244:Carbon