Constraint‐based modelling captures the metabolic versatility of Desulfovibrio vulgaris

Abstract

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 H /CO -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.

Organohalide-respiringDesulfolunaspecies isolated from marine environments

“…Similar to D. alaskensis G20 and D. vulgaris strain Hildenborough [68, 69], the two Ldhs were encoded by an organic acid oxidation gene cluster (DBB_24870—24970) including genes encoding lactate permease (DBB_24890), the Ldhs and pyruvate oxidoreductase (Por, DBB_24940). Based on previous studies with D. vulgaris Hildenborough [70], the electron transport pathway in strain DBB with lactate and sulfate could take one of the following routes: the Ldh’s either reduce menaquinone directly [70], or transfer electrons via the HdrD-like subunit [71] and DsrC (DBB_370, a high redox potential electron carrier with disulfide/dithiol (RSS/R(SH)2)) to QmoA [72]. The pyruvate produced by lactate oxidation is further oxidized by Por (DBB_310/24940), and the released electrons are carried/transferred by a flavodoxin (DBB_37290).…”

COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions

“…To assess the performance of the approach, we applied COMMIT to a well-described two-species community of Desulfovibrio vulgaris and Methanococcus maripaludis [ 54 – 56 ]. We removed reactions randomly from both networks (1%, 2%, 5%, and 10%) to see how many of those COMMIT would recover with considering the community composition and without.…”

Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling

“…The metabolic models within the δ-proteobacteria group are underrepresented among this phylum and only a few of them have been constructed, for instance for Geobacter spp. and Desulfovibrio vulgaris [51][52][53][54]. Thus, the model of B. bacteriovorus HD100, iCH457, represents a new model within this group, which, as depicted in Table 1, provides a complete reconstruction of this important bacterial group in terms of the metabolites and reactions included (confidence score = 2.1).…”