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PLoS Comput Biol. 2009 Feb;5(2):e1000285. doi: 10.1371/journal.pcbi.1000285. Epub 2009 Feb 13.

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

Author information

1
Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America.

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.

PMID:
19214212
PMCID:
PMC2633051
DOI:
10.1371/journal.pcbi.1000285
[Indexed for MEDLINE]
Free PMC Article

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