title: A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2 capture and conversion to methane.
abstract: Methane is a major energy source for heating and electricity. Its production by methanogenic bacteria is widely known in nature. M. maripaludis S2 is a fully sequenced hydrogenotrophic methanogen and an excellent laboratory strain with robust genetic tools. However, a quantitative systems biology model to complement these tools is absent in the literature. To understand and enhance its methanogenesis from CO2, this work presents the first constraint-based genome-scale metabolic model (iMM518). It comprises 570 reactions, 556 distinct metabolites, and 518 genes along with gene-protein-reaction (GPR) associations, and covers 30% of open reading frames (ORFs). The model was validated using biomass growth data and experimental phenotypic studies from the literature. Its comparison with the in silico models of Methanosarcina barkeri, Methanosarcina acetivorans, and Sulfolobus solfataricus P2 shows M. maripaludis S2 to be a better organism for producing methane. Using the model, genes essential for growth were identified, and the efficacies of alternative carbon, hydrogen and nitrogen sources were studied. The model can predict the effects of reengineering M. maripaludis S2 to guide or expedite experimental efforts.
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576. cheiak@nus.edu.sg.
authors.forename: Nishu
authors.initials: N
authors.lastname: Goyal
authors.forename: Hanifah
authors.initials: H
authors.lastname: Widiastuti
authors.forename: I A
authors.initials: IA
authors.lastname: Karimi
authors.forename: Zhi
authors.initials: Z
authors.lastname: Zhou
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D002244:Carbon / Q000378:metabolism; D057486:Carbon Cycle / Q000187:drug effects / Q000235:genetics; D002245:Carbon Dioxide / Q000378:metabolism*; D003198:Computer Simulation; D003470:Culture Media; D005561:Formates / Q000378:metabolism; D055786:Gene Knockout Techniques; D020745:Genome, Archaeal / Q000235:genetics*; D006859:Hydrogen / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000187:drug effects / Q000235:genetics; D008697:Methane / Q000378:metabolism*; D017017:Methanococcus / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D008954:Models, Biological; D009584:Nitrogen / Q000494:pharmacology; D016366:Open Reading Frames / Q000235:genetics; D015203:Reproducibility of Results; D013379:Substrate Specificity / Q000187:drug effects
chemical_list: D000596:Amino Acids; D003470:Culture Media; D005561:Formates; D002245:Carbon Dioxide; D002244:Carbon; D006859:Hydrogen; D009584:Nitrogen; D008697:Methane