PMC:4301621 / 15086-17871
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4301621","sourcedb":"PMC","sourceid":"4301621","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4301621","text":"Simulation and verification of model iCY1106\nFBA with constraints was used to investigate the metabolic properties of model iCY1106. YE medium was used to simulate the growth rate and ARA production, the maximum uptake rate of all 20 amino acids were set at 0.01 mmol gDW−1 h-1 [26], and the glucose consumption rate was set at 0.8 mmol gDW−1 h-1 [8], and 2.0 mmol gDW−1 h-1 [1] respectively, and the in silico growth rate were closed to experimental values (differences were only 0.8% and 9.48%; Table 3). To investigate ARA production in silico, the growth rate was fixed at 0.03 h-1 [8], and the ARA exchange reaction was set as the objective function. Under these conditions, the ARA rate was 0.128 mmol gDW−1 h−1 by FBA. This in silico value was lower than the experimentally determined value of 0.149 mmol gDW−1 h−1 (14.09%) [8], and this may due to the use of two different M. alpina strains (ATCC 32222 and ME-1) for modeling and experimental components, with ME-1 being the higher ARA producing strain [27]. Furthermore, the difficulties associated with accurately modeling the yeast extract may have resulted in a nutritional deficiency in the model.\nTable 3 Comparison of in silico and in vivo growth rates of M . alpina\nMedia condition (mmol gDW −1 h −1 ) Growth rate (h −1 ) Ref.\nin vivo in silico\nGlc (v = 0.8) 0.0696 0.0690 [8]\nGlc (v = 2.0) 0.1708 0.1546 [1]\nin vivo: experimental results; in silico: simulation results.\nThe capability of utilizing 14 different carbon sources for cell growth was qualitatively predicted by the model iCY1106 using FBA (Additional file 4). Each substance was the sole carbon source and the rate of uptake was 1.0 mmol gDW−1 h−1. Initially, there were four types of carbon source (ethanol, xylose, maltose, and rhamnose), and the model could not achieve growth with any individual carbon source. For ethanol, the reaction catalyzed by alcohol dehydrogenase (EC: 1.1.1.1) was irreversible, but should be reversible according to the MetaCyc database. For rhamnose, the lack of L-rhamnulose-1-phosphate lactaldehyde-lyase (EC: 4.1.2.19) meant that rhamnose could not generate glycerone phosphate, which could otherwise be used by the glycolysis pathway. After elimination of initial discrepancies using the continuous gap filling process, a 100% match was acquired. This indicated that model iCY1106 could predict catabolic pathways of various carbon sources including common sugars and alcohols. A similar FBA simulation of nitrogen sources (ammonium, nitrate, urea, and amino acids) also generated results that were consistent with experimental fermentation data. Both glutamate and glycine supported M. alpina growth, confirming that the model performed well for predicting the utilization of different carbon and nitrogen sources.","divisions":[{"label":"title","span":{"begin":0,"end":44}},{"label":"p","span":{"begin":45,"end":1443}},{"label":"table-wrap","span":{"begin":1161,"end":1443}},{"label":"label","span":{"begin":1161,"end":1168}},{"label":"caption","span":{"begin":1169,"end":1233}},{"label":"p","span":{"begin":1169,"end":1233}},{"label":"table","span":{"begin":1234,"end":1380}},{"label":"tr","span":{"begin":1234,"end":1297}},{"label":"th","span":{"begin":1234,"end":1271}},{"label":"th","span":{"begin":1271,"end":1291}},{"label":"th","span":{"begin":1292,"end":1297}},{"label":"tr","span":{"begin":1298,"end":1316}},{"label":"th","span":{"begin":1298,"end":1306}},{"label":"th","span":{"begin":1306,"end":1316}},{"label":"tr","span":{"begin":1317,"end":1348}},{"label":"td","span":{"begin":1317,"end":1330}},{"label":"td","span":{"begin":1331,"end":1337}},{"label":"td","span":{"begin":1338,"end":1344}},{"label":"td","span":{"begin":1345,"end":1348}},{"label":"tr","span":{"begin":1349,"end":1380}},{"label":"td","span":{"begin":1349,"end":1362}},{"label":"td","span":{"begin":1363,"end":1369}},{"label":"td","span":{"begin":1370,"end":1376}},{"label":"td","span":{"begin":1377,"end":1380}},{"label":"table-wrap-foot","span":{"begin":1381,"end":1443}},{"label":"p","span":{"begin":1381,"end":1443}}],"tracks":[{"project":"2_test","denotations":[{"id":"25582171-22124721-14905484","span":{"begin":279,"end":281},"obj":"22124721"},{"id":"25582171-17439233-14905485","span":{"begin":376,"end":377},"obj":"17439233"},{"id":"25582171-17439233-14905486","span":{"begin":1378,"end":1379},"obj":"17439233"}],"attributes":[{"subj":"25582171-22124721-14905484","pred":"source","obj":"2_test"},{"subj":"25582171-17439233-14905485","pred":"source","obj":"2_test"},{"subj":"25582171-17439233-14905486","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ecd693","default":true}]}]}}