Table 1.
Comparison of general characteristics of iMB631 with previously reconstructed networks of halophiles, iOA584 and iOG490 representatives of bacterial and archaeal halophilic models respectively.
Table 2.
Comparison of experimental and predicted behavior of S. ruber DSM13855.
Table 3.
Comparison of previously published phenotypes of S. ruber DSM13855and predicted behavior of iMB631.
Fig 1.
Pentose phosphate pathway in iMB631.
For simplification, cofactors and byproducts are not shown. Each reaction’s flux is shown for glucose uptake rates of 0.5, 1, 2, 4 and 5 mmol/gDW/h. The cycle works in all 5 uptake rates. Though glycolysis pathway is presented in the model, no glucose uptake rate was found where all reactions have acceptable fluxes.
Fig 2.
Phosphorylation oxidative genes in S. ruber.
(A). gene direction and related position of their related position to each other. (B). distribution of gene clusters in the genome. Totally 42 genes were related to oxidative phosphorylation reactions which are localized at 14 segments of the main chromosome.
Fig 3.
Schematic representation of rTCA modified from KEGG map; map00720.
Reactions are coded by numbers in circles and described in Table 4. Critical reactions of the pathway i. e. those which are conducted by key enzymes are shown with numbers in white circles wherease others are circled in black. Comparison of the nessesary reactions of the pathway with those present in Salinibacter ruber DSM13855, suggests that this pathway can be present in Salinibacter’s metabolism. When these reactions where included in the reconstructed model, FBA analysis showed that it can carry out fluxes under low nutrition conditions.
Table 4.
Description of reactions of rTCA and their related genes and enzymes in S. ruber DSM13855.
Fig 4.
Comparison of reaction distribution in subsystems in three halophilic modes; iMB631, iOA584, iOG490.
Amino acid metabolism has the largest number of reactions in both extremophilic models but in moderate halophilic iOA584, transport reaction category is the major one, mostly used to import osmo-protectants and related compounds whereas peptidoglycan or S-layer biosynthesis has the smallest set in all three models.
Fig 5.
Enzyme classes in iMB631, iOA584 and iOG490.
Transferases (EC 2) are the main category of enzymes in all three models whereas isomerases (EC 5) comprise the smallest set. Category of hydrolase (EC 3) enzymes depleted considerably in the archaeal model in comparison to bacterial types.