Suthers2009 - Genome-scale metabolic network of Mycoplasma genitalium (iPS189)

Suthers2009 - Genome-scale metabolic network
of Mycoplasma genitalium (iPS189)

This model is described in the article:

A genome-scale metabolic
reconstruction of Mycoplasma genitalium, iPS189.

Suthers PF, Dasika MS, Kumar VS,
Denisov G, Glass JI, Maranas CD.
PLoS Comput. Biol. 2009 Feb; 5(2):
e1000285
Abstract:

With a genome size of approximately 580 kb and approximately
480 protein coding regions, Mycoplasma genitalium is one of the
smallest known self-replicating organisms and, additionally,
has extremely fastidious nutrient requirements. The reduced
genomic content of M. genitalium has led researchers to suggest
that the molecular assembly contained in this organism may be a
close approximation to the minimal set of genes required for
bacterial growth. Here, we introduce a systematic approach for
the construction and curation of a genome-scale in silico
metabolic model for M. genitalium. Key challenges included
estimation of biomass composition, handling of enzymes with
broad specificities, and the lack of a defined medium.
Computational tools were subsequently employed to identify and
resolve connectivity gaps in the model as well as growth
prediction inconsistencies with gene essentiality experimental
data. The curated model, M. genitalium iPS189 (262 reactions,
274 metabolites), is 87% accurate in recapitulating in vivo
gene essentiality results for M. genitalium. Approaches and
tools described herein provide a roadmap for the automated
construction of in silico metabolic models of other
organisms.

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