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

BMC Bioinformatics
Sunisa ChatsurachaiHiroshi Shimizu

Abstract

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,...Continue Reading

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Citations

Nov 22, 2013·Bioinformatics·Satoshi OhnoChikara Furusawa
May 18, 2013·Biotechnology Advances·Yoshihiro Toya, Hiroshi Shimizu
Jan 3, 2013·Biotechnology Advances·Jae Ho ShinSang Yup Lee
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May 15, 2013·Journal of Bioscience and Bioengineering·Sunisa ChatsurachaiHiroshi Shimizu
Jan 1, 2012·Computational and Structural Biotechnology Journal·Paula Jouhten
Apr 8, 2014·Journal of Biotechnology·Alfred Fernández-CastanéJean-Loup Faulon

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Software Mentioned

PathPred
PostgreSQL
OptStrain
BRENDA
Python IDLE
OptKnock
ENZYME
GLPK
PathMiner
MATLAB

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