A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber

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.本研究报道了红嗜盐杆菌（Salinibacter ruber）DSM13855的基因组规模代谢网络重建模型。据我们所知，这是首个针对红嗜热菌门（Rhodothermaeota）生物的代谢模型。该模型命名为iMB631，基于红嗜盐杆菌DSM13855的已公开基因组数据与生化数据重建得到。该代谢网络包含1459个反应、1363个代谢物以及631个基因。模型评估基于文献中已有的生化数据，并结合实验室实验开展。针对不同碳源下的生长情况，研究结果表明iMB631能够准确预测91%的实验观测到生长的条件，以及83%的S. ruber未发生生长的条件。其F值（F-score）达93%，证明该模型整体性能可接受。基于预测得到的通量分布，我们发现在特定自养条件下，还原性三羧酸循环（reductive tricarboxylic acid cycle, rTCA）的所有必要反应均具备通量，可支撑自养生长。为纳入该细菌的特殊代谢物，研究人员基于近期提出的生物合成途径，对盐黄素（salinixanthin）的合成通路进行了建模。长期以来，S. ruber的主要葡萄糖消耗途径一直存在争议。借助通量平衡分析（flux balance analysis, FBA），iMB631预测出戊糖磷酸途径而非糖酵解是S. ruber中活跃的葡萄糖消耗方式。