An updated genome scale metabolic reconstruction of methanosarcina barkeri
Gonnerman, Matthew C.
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https://hdl.handle.net/2142/24426
Description
Title
An updated genome scale metabolic reconstruction of methanosarcina barkeri
Author(s)
Gonnerman, Matthew C.
Issue Date
2011-05-25T14:38:20Z
Director of Research (if dissertation) or Advisor (if thesis)
Price, Nathan D.
Department of Study
Chemical & Biomolecular Engr
Discipline
Chemical Engineering
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
M.S.
Degree Level
Thesis
Keyword(s)
Methanosarcina
barkeri
Methanogen
Metabolic
Reconstruction
Abstract
Methanosarcina barkeri is a methanogen, meaning that methane is the reduced product for energy generation. M. barkeri can grow on several substrates including methanol, acetate, methyl amines and a combination of hydrogen and carbon dioxide. The Methanosarcina barkeri genome was published in 2006 after the metabolic reconstruction of M. barkeri, iAF692, was published. The iAF692 reconstruction preformed the first large scale simulations of an Archaea.
Since the publication of iAF692, a deeper understanding of Archaea biology has shed light on previously unclear metabolic pathways. For methanogenesis, proton pumping has been updated to reflect an improved knowledge of the pathway. Cofactor biosynthesis has been updated to reflect a better understanding of methanogen anabolism. Metabolic networks such as pentose phosphate pathway, amino acid biosynthesis, and cell wall composition have also been updated to reflect Archaea specific biosynthesis pathways. This improved insight has led to an increase in predictive accuracy for knockouts and growth yield predictions for the updated M. barkeri reconstruction, iMG750. As with other metabolic reconstructions, iMG750 will be a useful tool in guiding experimental studies and predicting cellular behavior on a genome scale.
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