Journal
ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL
Volume 2014, Issue -, Pages -Publisher
HINDAWI LTD
DOI: 10.1155/2014/898453
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Funding
- Office of Science (BER), U.S. Department of Energy [DE-FG02-10ER6510]
- NASA Astrobiology Institute [NNA13AA91A, DE-FG02-02ER15296]
- National Institutes of Health (NIH) [U19 AI083025, GM065367]
- National Science Foundation (NSF) Physics Frontier Center Grant [PHY-0822613]
- National Science Foundation (NSF) Molecular Biophysics Training Grant [PHS 5 T32 GM008276]
- NASA [NNA13AA91A, 475572] Funding Source: Federal RePORTER
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Progress towards a complete model of the methanogenic archaeum Methanosarcina acetivorans is reported. We characterized size distribution of the cells using differential interference contrast microscopy, finding them to be ellipsoidal with mean length and width of 2.9 mu m and 2.3 mu m, respectively, when grown on methanol and 30% smaller when grown on acetate. We used the single molecule pull down (SiMPull) technique to measure average copy number of the Mcr complex and ribosomes. A kinetic model for the methanogenesis pathways based on biochemical studies and recent metabolic reconstructions for several related methanogens is presented. In this model, 26 reactions in the methanogenesis pathways are coupled to a cell mass production reaction that updates enzyme concentrations. RNA expression data (RNA-seq) measured for cell cultures grown on acetate and methanol is used to estimate relative protein production per mole of ATP consumed. The model captures the experimentally observed methane production rates for cells growing on methanol and is most sensitive to the number of methyl-coenzyme-M reductase (Mcr) and methyl-tetrahydromethanopterin: coenzyme-M methyltransferase (Mtr) proteins. A draft transcriptional regulation network based on known interactions is proposed which we intend to integrate with the kinetic model to allow dynamic regulation.
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