Reconstruction of biochemical networks in microorganisms

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Abstract
Our ability to reconstruct genome-scale metabolic networks in microbial cells from genomic and high-throughput data has grown substantially in recent years. There are currently more than 25 genome-scale metabolic reconstructions of microbial cells, and 6–10 more are being produced each year. An increasing number of research groups around the world are working on genome-scale reconstructions of metabolism in their target organism. There is no single source that practitioners can access to learn about and understand the reconstruction process. This Review details the data flows and work flows that underlie the reconstruction process and thus provides a basis for newcomers in the field. Biological network reconstructions continue to grow in scope and are expected to include transcriptional regulation and protein synthesis over the next few years. Expansion in scope will probably also include small RNAs and two-component signalling networks. Genome-scale reconstructions are a common denominator in systems biology of microorganisms and are reaching an advanced stage of development, which indicates that systems analysis of microbial functions and phenotypes will progress in the years to come.