Kumar2011 - Genome-scale metabolic network of Methanosarcina acetivorans (iVS941)

Kumar2011 - Genome-scale metabolic network of Methanosarcina acetivorans (iVS941)

This model is described in the article:

Metabolic reconstruction of
the archaeon methanogen Methanosarcina Acetivorans.

Satish Kumar V, Ferry JG, Maranas
CD.
BMC Syst Biol 2011; 5: 28
Abstract:

BACKGROUND: Methanogens are ancient organisms that are key
players in the carbon cycle accounting for about one billion
tones of biological methane produced annually. Methanosarcina
acetivorans, with a genome size of ~5.7 mb, is the largest
sequenced archaeon methanogen and unique amongst the
methanogens in its biochemical characteristics. By following a
systematic workflow we reconstruct a genome-scale metabolic
model for M. acetivorans. This process relies on previously
developed computational tools developed in our group to correct
growth prediction inconsistencies with in vivo data sets and
rectify topological inconsistencies in the model. RESULTS: The
generated model iVS941 accounts for 941 genes, 705 reactions
and 708 metabolites. The model achieves 93.3% prediction
agreement with in vivo growth data across different substrates
and multiple gene deletions. The model also correctly
recapitulates metabolic pathway usage patterns of M.
acetivorans such as the indispensability of flux through
methanogenesis for growth on acetate and methanol and the
unique biochemical characteristics under growth on carbon
monoxide. CONCLUSIONS: Based on the size of the genome-scale
metabolic reconstruction and extent of validated predictions
this model represents the most comprehensive up-to-date effort
to catalogue methanogenic metabolism. The reconstructed model
is available in spreadsheet and SBML formats to enable
dissemination.

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