Towards a computational model of a methane producing archaeum

Joseph R. Peterson, Piyush Labhsetwar, Jeremy R. Ellermeier, Petra R A Kohler, Ankur Jain, Taekjip Ha, William W. Metcalf, Zaida Luthey-Schulten

Research output: Contribution to journalArticle

Abstract

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 m and 2.3 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.

Original languageEnglish (US)
Article number898453
JournalArchaea
Volume2014
DOIs
StatePublished - 2014
Externally publishedYes

Fingerprint

Archaea
Methane
methane
Methanol
methane production
Acetates
methanol
Methanosarcina
Protein Methyltransferases
Interference Microscopy
RNA
methanogenesis
Gene Regulatory Networks
acetate
Ribosomes
Cell Size
acetates
kinetics
Cell Culture Techniques
Adenosine Triphosphate

ASJC Scopus subject areas

  • Microbiology
  • Physiology
  • Ecology, Evolution, Behavior and Systematics
  • Medicine(all)

Cite this

Peterson, J. R., Labhsetwar, P., Ellermeier, J. R., Kohler, P. R. A., Jain, A., Ha, T., ... Luthey-Schulten, Z. (2014). Towards a computational model of a methane producing archaeum. Archaea, 2014, [898453]. https://doi.org/10.1155/2014/898453

Towards a computational model of a methane producing archaeum. / Peterson, Joseph R.; Labhsetwar, Piyush; Ellermeier, Jeremy R.; Kohler, Petra R A; Jain, Ankur; Ha, Taekjip; Metcalf, William W.; Luthey-Schulten, Zaida.

In: Archaea, Vol. 2014, 898453, 2014.

Research output: Contribution to journalArticle

Peterson, JR, Labhsetwar, P, Ellermeier, JR, Kohler, PRA, Jain, A, Ha, T, Metcalf, WW & Luthey-Schulten, Z 2014, 'Towards a computational model of a methane producing archaeum', Archaea, vol. 2014, 898453. https://doi.org/10.1155/2014/898453
Peterson JR, Labhsetwar P, Ellermeier JR, Kohler PRA, Jain A, Ha T et al. Towards a computational model of a methane producing archaeum. Archaea. 2014;2014. 898453. https://doi.org/10.1155/2014/898453
Peterson, Joseph R. ; Labhsetwar, Piyush ; Ellermeier, Jeremy R. ; Kohler, Petra R A ; Jain, Ankur ; Ha, Taekjip ; Metcalf, William W. ; Luthey-Schulten, Zaida. / Towards a computational model of a methane producing archaeum. In: Archaea. 2014 ; Vol. 2014.
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