Volume 10, Issue 2 p. 190-201
Brief Report

Constraint-based modelling captures the metabolic versatility of Desulfovibrio vulgaris

Jason J. Flowers

Jason J. Flowers

Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA

Search for more papers by this author
Matthew A. Richards

Matthew A. Richards

Institute for Systems Biology, Seattle, WA, USA

Search for more papers by this author
Nitin Baliga

Nitin Baliga

Institute for Systems Biology, Seattle, WA, USA

Search for more papers by this author
Birte Meyer

Birte Meyer

Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA

Search for more papers by this author
David A. Stahl

Corresponding Author

David A. Stahl

Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA

For correspondence. Email: [email protected]; Tel. (206) 685-8502; Fax (206) 685-9185.Search for more papers by this author
First published: 26 January 2018
Citations: 8

Summary

A refined Desulfovibrio vulgaris Hildenborough flux balance analysis (FBA) model (iJF744) was developed, incorporating 1016 reactions that include 744 genes and 951 metabolites. A draft model was first developed through automatic model reconstruction using the ModelSeed Server and then curated based on existing literature. The curated model was further refined by incorporating three recently proposed redox reactions involving the Hdr-Flx and Qmo complexes and a lactate dehydrogenase (LdhAB, DVU 3027-3028) indicated by mutation and transcript analyses to serve electron transfer reactions central to syntrophic and respiratory growth. Eight different variations of this model were evaluated by comparing model predictions to experimental data determined for four different growth conditions - three for sulfate respiration (with lactate, pyruvate or H2/CO2-acetate) and one for fermentation in syntrophic coculture. The final general model supports (i) a role for Hdr-Flx in the oxidation of DsrC and ferredoxin, and reduction of NAD+ in a flavin-based electron confurcating reaction sequence, (ii) a function of the Qmo complex in receiving electrons from the menaquinone pool and potentially from ferredoxin to reduce APS and (iii) a reduction of the soluble DsrC by LdhAB and a function of DsrC in electron transfer reactions other than sulfite reduction.