Article,
A Genome-Scale Metabolic Reconstruction of <italic>Mycoplasma genitalium</italic>, <italic>i</italic>PS189
PLoS Comput Biol, 5 (2): e1000285+ (February 2009)
DOI: 10.1371/journal.pcbi.1000285
Abstract
<title>Author Summary</title> <p>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 <italic>Mycoplasma genitalium</italic> 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 <italic>M. genitalium</italic> 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.</p>
