A pathway for every product? Tools to discover and design plant metabolism

Jeffryes, James G.; Seaver, Samuel M. D.; Faria, José P.; Henry, Christopher S.

doi:10.1016/j.plantsci.2018.03.025

A pathway for every product? Tools to discover and design plant metabolism

Journal Article · Fri Mar 30 00:00:00 EDT 2018 · Plant Science

DOI:https://doi.org/10.1016/j.plantsci.2018.03.025· OSTI ID:1474405

Jeffryes, James G. ^[1]; Seaver, Samuel M. D. ^[1]; Faria, José P. ^[1]; Henry, Christopher S. ^[1]

Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division

The vast diversity of plant natural products is a powerful indication of the biosynthetic capacity of plant metabolism. Synthetic biology seeks to capitalize on this ability by understanding and reconfiguring the biosynthetic pathways that generate this diversity to produce novel products with improved efficiency. In this work, we review the algorithms and databases that presently support the design and manipulation of metabolic pathways in plants, starting from metabolic models of native biosynthetic pathways, progressing to novel combinations of known reactions, and finally proposing new reactions that may be carried out by existing enzymes. We show how these tools are useful for proposing new pathways as well as identifying side reactions that may affect engineering goals.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL)

Sponsoring Organization:: National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1474405

Journal Information:: Plant Science, Journal Name: Plant Science Journal Issue: C Vol. 273; ISSN 0168-9452

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks Jankowski, Matthew D.; Henry, Christopher S.; Broadbelt, Linda J. Biophysical Journal, Vol. 95, Issue 3 https://doi.org/10.1529/biophysj.107.124784	journal	August 2008
Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis Kotera, Masaaki; Goto, Susumu Biophysics and Physicobiology, Vol. 13, Issue 0 https://doi.org/10.2142/biophysico.13.0_195	journal	January 2016
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm Seaver, Samuel M. D.; Bradbury, Louis M. T.; Frelin, Océane Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.00142	journal	March 2015
Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software Peach, Megan L.; Zakharov, Alexey V.; Liu, Ruifeng Future Medicinal Chemistry, Vol. 4, Issue 15 https://doi.org/10.4155/fmc.12.150	journal	October 2012

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