MapMaker and PathTracer for tracking carbon in genome-scale metabolic models

Biotechnology Journal
Christopher J Tervo, Jennifer L Reed

Abstract

Constraint-based reconstruction and analysis (COBRA) modeling results can be difficult to interpret given the large numbers of reactions in genome-scale models. While paths in metabolic networks can be found, existing methods are not easily combined with constraint-based approaches. To address this limitation, two tools (MapMaker and PathTracer) were developed to find paths (including cycles) between metabolites, where each step transfers carbon from reactant to product. MapMaker predicts carbon transfer maps (CTMs) between metabolites using only information on molecular formulae and reaction stoichiometry, effectively determining which reactants and products share carbon atoms. MapMaker correctly assigned CTMs for over 97% of the 2,251 reactions in an Escherichia coli metabolic model (iJO1366). Using CTMs as inputs, PathTracer finds paths between two metabolites. PathTracer was applied to iJO1366 to investigate the importance of using CTMs and COBRA constraints when enumerating paths, to find active and high flux paths in flux balance analysis (FBA) solutions, to identify paths for putrescine utilization, and to elucidate a potential CO2 fixation pathway in E. coli. These results illustrate how MapMaker and PathTracer can be u...Continue Reading

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Citations

Feb 7, 2016·Metabolic Engineering·Xiaolin ZhangJennifer L Reed
May 25, 2016·Genome Biology·Qi ZhaoDaniel Segrè
Jan 10, 2017·PloS One·Yiran HuangJianyi Wang
Nov 30, 2016·Biotechnology Journal·Noushin HadadiVassily Hatzimanikatis
Aug 12, 2017·BMC Bioinformatics·Lisa Katharina BlaßElmar Heinzle
Dec 15, 2020·Metabolic Engineering·Irene Otero-Muras, Pablo Carbonell
Feb 3, 2021·PLoS Computational Biology·Yiran HuangFengfeng Zhou
Jan 26, 2021·Metabolic Engineering Communications·Sean G Mack, Ganesh Sriram
Mar 20, 2018·Synthetic and Systems Biotechnology·Lin WangCostas D Maranas
May 19, 2021·Bioinformatics·Jasmin Hafner, Vassily Hatzimanikatis

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