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Bioinformatics Advance Access originally published online on September 5, 2008
Bioinformatics 2008 24(21):2554-2556; doi:10.1093/bioinformatics/btn471
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DESHARKY: automatic design of metabolic pathways for optimal cell growth

Guillermo Rodrigo 1, Javier Carrera 1,2, Kristala Jones Prather 3 and Alfonso Jaramillo 4,5,*

1Instituto de Biologia Molecular y Celular de Plantas, CSIC, 2Instituto de Aplicaciones en Tecnologias de la Informacion y las Comunicaciones Avanzadas (ITACA), Universidad Politecnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain, 3Department of Chemical Engineering, Massachusetts Institute of Technology, Massachusetts Avenue 77, Cambridge MA 02139, USA, 4Laboratoire de Biochimie, Ecole Polytechnique - CNRS, Route de Saclay, 91128 Palaiseau Cedex and 5Epigenomics Project, Genopole, 523 Terrasses de l'Agora, 91034 Evry Cedex, France

*To whom correspondence should be addressed.


  Abstract

Motivation: The biological solution for synthesis or remediation of organic compounds using living organisms, particularly bacteria and yeast, has been promoted because of the cost reduction with respect to the non-living chemical approach. In that way, computational frameworks can profit from the previous knowledge stored in large databases of compounds, enzymes and reactions. In addition, the cell behavior can be studied by modeling the cellular context.

Results: We have implemented a Monte Carlo algorithm (DESHARKY) that finds a metabolic pathway from a target compound by exploring a database of enzymatic reactions. DESHARKY outputs a biochemical route to the host metabolism together with its impact in the cellular context by using mathematical models of the cell resources and metabolism. Furthermore, we provide the sequence of amino acids for the enzymes involved in the route closest phylogenetically to the considered organism. We provide examples of designed metabolic pathways with their genetic load characterizations. Here, we have used Escherichia coli as host organism. In addition, our bioinformatic tool can be applied for biodegradation or biosynthesis and its performance scales with the database size.

Availability: Software, a tutorial and examples are freely available and open source at http://soft.synth-bio.org/desharky.html

Contact: alfonso.jaramillo{at}polytechnique.fr

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Trey Ideker

Received on May 28, 2008; revised on August 14, 2008; accepted on September 2, 2008

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