A reconstrução metabólica do Mycoplasma genitalium

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

Patrick F. Suthers1, Madhukar S. Dasika1, Vinay Satish Kumar2, Gennady Denisov3, John I. Glass3, Costas D. Maranas1*

1 Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America, 2 Department of Industrial Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America, 3 J. Craig Venter Institute, Rockville, Maryland, United States of America

Abstract

With a genome size of ~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.

Author Summary

There is growing interest in elucidating the minimal number of genes needed for life. This challenge is important not just for fundamental but also practical considerations arising from the need to design microorganisms exquisitely tuned for particular applications. The genome of the pathogen Mycoplasma genitalium is believed to be a close approximation to the minimal set of genes required for bacterial growth. In this paper, we constructed a genome-scale metabolic model of M. genitalium that mathematically describes a unified characterization of its biochemical capabilities. The model accounts for 189 of the 482 genes listed in the latest genome annotation. We used computational tools during the process to bridge network gaps in the model and restore consistency with experimental data that determined which gene deletions led to cell death (i.e., are essential). We achieved 87% correct model predictions for essential genes and 89% for non-essential genes. We subsequently used the metabolic model to determine components that must be part of the growth medium. The approaches and tools described here provide a roadmap for the automated metabolic reconstruction of other organisms. This task is becoming increasingly critical as genome sequencing for new organisms is proceeding at an ever-accelerating pace.

Citation: Suthers PF, Dasika MS, Kumar VS, Denisov G, Glass JI, et al. (2009) A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189. PLoS Comput Biol 5(2): e1000285. doi:10.1371/journal.pcbi.1000285

Editor: Herbert M. Sauro, University of Washington, United States of America

Received: May 28, 2008; Accepted: January 2, 2009; Published: February 13, 2009

Copyright: © 2009 Suthers et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: This work was supported by the Department of Energy grant DE-FG02-05ER25684.

Competing interests: The authors have declared that no competing interests exist.

* E-mail: costas@psu.edu

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