Abstract
Despite the increase in recent years in the portfolio of added-value chemicals that can be microbially produced, the design process still remains a complex system, costly and rather slow. To overcome such limitations, the development of Computer-Aided-Design (CAD) tools is necessary to design production pathways that systematically screen metabolic databases to select best genes to import into chassis organisms. Here, we showcase the XTMS CAD tool for pathway design, which exploits the ability for pathway ranking in our RetroPath retrosynthetic algorithm within an extended metabolic space that considers putative routes through enzyme promiscuity. The validity of the ranking function for the production of malonyl-CoA, an important precursor for added-value compounds, is shown.
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References
Cho, A., Yun, H., Park, J.H., Lee, S.Y., Park, S.: Prediction of novel synthetic pathways for the production of desired chemicals. BMC Systems Biology (2010)
McClymont, K., Orkun, S.: Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways. Nucl. Acids Res. (2013)
Campodonico, M.A., Andrews, B.A., Asenjo, J.A., Palsson, B.O., Feist, A.M.: Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metabolic Engineering (2014)
Carbonell, P., Parutto, P., Herisson, J., Pandit, S.B., Faulon, J.L.: XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res. (2014)
Carbonell, P., Planson, A.G., Fichera, D., Faulon, J.L.: A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Syst. Biol. (2011)
Feher, T., Planson, A.G., Carbonell, P., Fernandez-Castane, A., Grigoras, I., Dariy, E., Perret, A., Faulon, J.L.: Validation of RetroPath, a computer aided design tool for metabolic pathway engineering. Biotech. J. (2014)
Liu, D., Xiao, Y., Evans, B., Zhang, F.: Negative feedback regulation of fatty acid production based on a Malonyl-CoA Sensor Actuator. ACS Synth. Biol. (2013)
Faulon, J.L., Visco, D., Pophale, R.: The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR Studies. Journal of Chemical Information and Computer Sciences (2003)
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Delépine, B., Carbonell, P., Faulon, JL. (2014). XTMS in Action: Retrosynthetic Design in the Extended Metabolic Space of Heterologous Pathways for High-Value Compounds. In: Mendes, P., Dada, J.O., Smallbone, K. (eds) Computational Methods in Systems Biology. CMSB 2014. Lecture Notes in Computer Science(), vol 8859. Springer, Cham. https://doi.org/10.1007/978-3-319-12982-2_21
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DOI: https://doi.org/10.1007/978-3-319-12982-2_21
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-12981-5
Online ISBN: 978-3-319-12982-2
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