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Towards a Computational Model of a Methane Producing Archaeum

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 μm and 2.3 μm, respectively, wh...

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Autores principales: Peterson, Joseph R., Labhsetwar, Piyush, Ellermeier, Jeremy R., Kohler, Petra R. A., Jain, Ankur, Ha, Taekjip, Metcalf, William W., Luthey-Schulten, Zaida
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960522/
https://www.ncbi.nlm.nih.gov/pubmed/24729742
http://dx.doi.org/10.1155/2014/898453
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author Peterson, Joseph R.
Labhsetwar, Piyush
Ellermeier, Jeremy R.
Kohler, Petra R. A.
Jain, Ankur
Ha, Taekjip
Metcalf, William W.
Luthey-Schulten, Zaida
author_facet Peterson, Joseph R.
Labhsetwar, Piyush
Ellermeier, Jeremy R.
Kohler, Petra R. A.
Jain, Ankur
Ha, Taekjip
Metcalf, William W.
Luthey-Schulten, Zaida
author_sort Peterson, Joseph R.
collection PubMed
description 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 μm and 2.3 μm, 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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spelling pubmed-39605222014-04-13 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 Archaea Research Article 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 μm and 2.3 μm, 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. Hindawi Publishing Corporation 2014-03-04 /pmc/articles/PMC3960522/ /pubmed/24729742 http://dx.doi.org/10.1155/2014/898453 Text en Copyright © 2014 Joseph R. Peterson et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
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
title Towards a Computational Model of a Methane Producing Archaeum
title_full Towards a Computational Model of a Methane Producing Archaeum
title_fullStr Towards a Computational Model of a Methane Producing Archaeum
title_full_unstemmed Towards a Computational Model of a Methane Producing Archaeum
title_short Towards a Computational Model of a Methane Producing Archaeum
title_sort towards a computational model of a methane producing archaeum
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960522/
https://www.ncbi.nlm.nih.gov/pubmed/24729742
http://dx.doi.org/10.1155/2014/898453
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