10.1371/journal.pcbi.1006492
Oliver Hädicke
Oliver
Hädicke
Axel von Kamp
Axel
von Kamp
Timur Aydogan
Timur
Aydogan
Steffen Klamt
Steffen
Klamt
OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO<sub>2</sub> fixation potential of <i>Escherichia coli</i>
Public Library of Science
2018
CO 2 fixation
949 cytosolic carbon metabolites
CO 2 assimilation
OptMDFpathway
approach
tricarboxylic acid cycle
CO 2
MDF
Escherichia coli Constraint-based modeling techniques
CO 2 incorporation
genome-scale model i JO 1366
pathway
2018-09-24 17:26:01
Dataset
https://plos.figshare.com/articles/dataset/OptMDFpathway_Identification_of_metabolic_pathways_with_maximal_thermodynamic_driving_force_and_its_application_for_analyzing_the_endogenous_CO_sub_2_sub_fixation_potential_of_Escherichia_coli/7123451
<div><p>Constraint-based modeling techniques have become a standard tool for the <i>in silico</i> analysis of metabolic networks. To further improve their accuracy, recent methodological developments focused on integration of thermodynamic information in metabolic models to assess the feasibility of flux distributions by thermodynamic driving forces. Here we present <i>OptMDFpathway</i>, a method that extends the recently proposed framework of Max-min Driving Force (MDF) for thermodynamic pathway analysis. Given a metabolic network model, <i>OptMDFpathway</i> identifies both the optimal MDF for a desired phenotypic behavior as well as the respective pathway itself that supports the optimal driving force. <i>OptMDFpathway</i> is formulated as a mixed-integer linear program and is applicable to genome-scale metabolic networks. As an important theoretical result, we also show that there exists always at least one elementary mode in the network that reaches the maximal MDF. We employed our new approach to systematically identify all substrate-product combinations in <i>Escherichia coli</i> where product synthesis allows for concomitant net CO<sub>2</sub> assimilation via thermodynamically feasible pathways. Although biomass synthesis cannot be coupled to net CO<sub>2</sub> fixation in <i>E</i>. <i>coli</i> we found that as many as 145 of the 949 cytosolic carbon metabolites contained in the genome-scale model <i>i</i>JO1366 enable net CO<sub>2</sub> incorporation along thermodynamically feasible pathways with glycerol as substrate and 34 with glucose. The most promising products in terms of carbon assimilation yield and thermodynamic driving forces are orotate, aspartate and the C4-metabolites of the tricarboxylic acid cycle. We also identified thermodynamic bottlenecks frequently limiting the maximal driving force of the CO<sub>2</sub>-fixing pathways. Our results indicate that heterotrophic organisms like <i>E</i>. <i>coli</i> hold a possibly underestimated potential for CO<sub>2</sub> assimilation which may complement existing biotechnological approaches for capturing CO<sub>2</sub>. Furthermore, we envision that the developed <i>OptMDFpathway</i> approach can be used for many other applications within the framework of constrained-based modeling and for rational design of metabolic networks.</p></div>