Abstract
A genome-scale metabolic network reconstruction of Salinibacter ruber DSM13855 is presented here. To our knowledge, this is the first metabolic model of an organism in the phylum Rhodothermaeota. This model, which will be called iMB631, was reconstructed based on genomic and biochemical data available on the strain Salinibacter ruber DSM13855. This network consists of 1459 reactions, 1363 metabolites and 631 genes. Model evaluation was performed based on existing biochemical data in the literature and also by performing laboratory experiments. For growth on different carbon sources, we show that iMB631 is able to correctly predict the growth in 91% of cases where growth has been observed experimentally and 83% of conditions in which S. ruber did not grow. The F-score was 93%, demonstrating a generally acceptable performance of the model. Based on the predicted flux distributions, we found that under certain autotrophic condition, a reductive tricarboxylic acid cycle (rTCA) has fluxes in all necessary reactions to support autotrophic growth. To include special metabolites of the bacterium, salinixanthin biosynthesis pathway was modeled based on the pathway proposed recently. For years, main glucose consumption pathway has been under debates in S. ruber. Using flux balance analysis, iMB631 predicts pentose phosphate pathway, rather than glycolysis, as the active glucose consumption method in the S. ruber.
Highlights
Special characteristics of Salinibacter ruber and its metabolism Salinibacter is the type genus of Salinibacteriaceae, a recently described family of halophilic bacteria, living under extreme conditions of hypersaline brines with a high concentration of salt, up to saturation [1, 2]
We describe the reconstruction of a detailed genome-scale metabolic model (GEM) for Salinibacter ruber, the first reconstructed GEM for members of the bacterial phylum Rhodothermaeota and the first extremely halophilic bacterial GEM reconstructed to date
Our aim is to shed light on the unusual metabolism and salt adaptation mechanism of S. ruber using the systemic approach of GEM
Summary
Special characteristics of Salinibacter ruber and its metabolism Salinibacter is the type genus of Salinibacteriaceae, a recently described family of halophilic bacteria, living under extreme conditions of hypersaline brines with a high concentration of salt, up to saturation [1, 2]. Salinibacter ruber was the first bacterium shown to be active at hypersaline brines [3,4,5]. Despites phylogenetic affiliation of S. ruber to bacteria, it has many features in common with members of archaeal family Halobactreiaceae [6]. The most interesting feature of S. ruber is its haloadaptation mechanism [7] which has been shown to be the archaeal type of haloadaptation (i.e., the “salt-in” strategy) which is the intracellular accumulation of mineral ions, mostly K+ and Cl-. The salt-in strategy affects the whole proteome structure and goes along with extensive genome wide adjustments to prepare the whole enzymatic system to be functional under hypersaline cytoplasmic conditions [8, 9]
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