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An in silico platform for the design of heterologous pathways in nonnative metabolite production

Sunisa Chatsurachai1, Chikara Furusawa23* and Hiroshi Shimizu3*

Author affiliations

1 Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan

2 Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan

3 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan

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Citation and License

BMC Bioinformatics 2012, 13:93  doi:10.1186/1471-2105-13-93

Published: 11 May 2012



Microorganisms are used as cell factories to produce valuable compounds in pharmaceuticals, biofuels, and other industrial processes. Incorporating heterologous metabolic pathways into well-characterized hosts is a major strategy for obtaining these target metabolites and improving productivity. However, selecting appropriate heterologous metabolic pathways for a host microorganism remains difficult owing to the complexity of metabolic networks. Hence, metabolic network design could benefit greatly from the availability of an in silico platform for heterologous pathway searching.


We developed an algorithm for finding feasible heterologous pathways by which nonnative target metabolites are produced by host microorganisms, using Escherichia coli, Corynebacterium glutamicum, and Saccharomyces cerevisiae as templates. Using this algorithm, we screened heterologous pathways for the production of all possible nonnative target metabolites contained within databases. We then assessed the feasibility of the target productions using flux balance analysis, by which we could identify target metabolites associated with maximum cellular growth rate.


This in silico platform, designed for targeted searching of heterologous metabolic reactions, provides essential information for cell factory improvement.