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 availab...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2019-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0216336 |
| _version_ | 1818590358622175232 |
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| author | Maryam Bagheri Sayed-Amir Marashi Mohammad Ali Amoozegar |
| author_facet | Maryam Bagheri Sayed-Amir Marashi Mohammad Ali Amoozegar |
| author_sort | Maryam Bagheri |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-16T09:55:17Z |
| format | Article |
| id | doaj.art-92462b03293a42989d62ed6e48d4da55 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-16T09:55:17Z |
| publishDate | 2019-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-92462b03293a42989d62ed6e48d4da552022-12-21T22:35:57ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-01145e021633610.1371/journal.pone.0216336A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber.Maryam BagheriSayed-Amir MarashiMohammad Ali AmoozegarA 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.https://doi.org/10.1371/journal.pone.0216336 |
| spellingShingle | Maryam Bagheri Sayed-Amir Marashi Mohammad Ali Amoozegar A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber. PLoS ONE |
| title | A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber. |
| title_full | A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber. |
| title_fullStr | A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber. |
| title_full_unstemmed | A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber. |
| title_short | A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber. |
| title_sort | genome scale metabolic network reconstruction of extremely halophilic bacterium salinibacter ruber |
| url | https://doi.org/10.1371/journal.pone.0216336 |
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