Genome-scale metabolic reconstruction and analysis of Sphingopyxis granuli strain TFA

Abstract

[Backgrounds]: Sphingopyxis granuli strain TFA is a Gram-negative bacterium belonging to Sphingomonadaceae family whose most studied metabolic feature is its ability to use the aromatic organic solvent tetralin as the sole carbon and energy source. Regarding other metabolism aspects, this bacterium is able to accumulate poly-hydroxybutyrate (PHB) as carbon reservoir and, recently, it has been described as the first Sphyngopyxis representative able of growing anaerobically using nitrate as final electron acceptor. As several oligotrophic bacteria have been assigned to this genus, it is interesting to study other features of its metabolism that remain poorly or not characterized at all. [Objectives]: The main objective of this work is to know better and deeply the TFA metabolic capabilities through the construction of a metabolic model at a genome scale. [Methods]: Initially, two models of TFA were constructed based on Escherichia coli and Pseudomonas putida models, using the MrBac server. They were merged to obtain the first draft in which each reaction was manually reviewed. In order to complete the model, missing reactions were incorporated to fill the gaps in metabolic pathways thanks to the TFA genome annotation and metabolic/biochemical databases such as KEGG, BRENDA, MetaCyc and BiGG or by similarity search in Uniprot/SwissProt and the Pseudomonas Database. [Conclusions]: The constructed model of TFA metabolism, iIG738, consist of 738 genes, 1392 reactions and 1107 metabolites classified in 95 metabolic subsystems. The reconstruction has highlighted diverse new carbon sources that TFA can use, which have been validated in vivo. Overall, iIG738 constitutes a powefull computational tool to evaluate, at system level, the metabolic traits of the oligotrophic bacterium TFA under a large array of environmental conditions.