PMC:4301621 / 6523-10821 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4301621","sourcedb":"PMC","sourceid":"4301621","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4301621","text":"Characterization of the M. alpina GSMM iCY1106\nThe genome-scale metabolic model iCY1106 reconstructed in this study included 1106 genes representing 9.51% of the 11631 protein-coding genes in the genome of M. alpina ATCC 32222. The model consisted of 1854 reactions and 1732 metabolites (Table 1). Compared with the previous model constructed by Vongsangnak [21], iCY1106 is more detailed and contains a higher degree of functional information that can be used in in silico simulations. During the construction of iCY1106, some missing gene were added from the Vongsangnak’s model such as MA-090-247, which encodes an asparaginase (EC: 3.5.1.1), and catalyzes the transformation of L-asparagine into L-aspartate. When compared with the existing model, many improvements in iCY1106 are apparent. (1) A total of 139 transport proteins were annotated based on TCDB and TransportDB. (2) A total of 216 exchange reactions were added into model iCY1106. (3) Biomass composition of M. alpina was calculated based on literature mining. (4) Additional chemical reactions were also included. (5) The reversibility of some reactions was redefined according to MetaCyc and BioPath databases. For example, in the published model, the reaction catalyzed by aldehyde dehydrogenase (EC: 1.2.1.3) was reversible, whereas this reaction is irreversible according to BioPath. The flux distribution of iCY1106 was normal following this change.\nTable 1 General features of model i CY1106\nFeatures i CY1106 Existed model a\nGenome feature\n Genome size (Mb) 38.38 38.38\n Total open reading frames (ORFs) 11631 11631\nMetabolic model\n Total reactions 1854 1183\n Biochemical reactions 1391 1183\n Transport reactions 247 none\n Exchange reactions 216 none\n Metabolites 1732 1660\n ORFs associated in model 1106 1042\n ORF coverageb (%) 9.51 8.95\naThe existed model was constructed by Vongsangnak et al. [21]; bThe number of ORFs incorporated in model iCY1106 divided by the total number of ORFs.\nIn model iCY1106, four compartments (extracellular, cytoplasmic, peroxisome and mitochondrial compartments) were linked by 141 trans-plasma membrane transport reactions, 98 cytoplasmic-mitochondrial transport reactions and eight cytoplasmic-peroxisome transport reactions (Additional file 1). The extracellular compartment contained 267 reactions, including 216 exchange reactions and 51 metabolic reactions. These metabolic reactions catalyzed by extracellular enzymes may enable M. alpina to adapt to different environmental conditions. For example, M. alpina grows on different carbohydrates such as glycerol [24], sucrose [24], d-mannose [25], and raffinose [25] using various extracellular galactosidases. The peroxisome compartment contained 34 reactions mostly related to glyoxylate metabolism.\nMetabolic reactions in the model iCY1106 were divided into ten metabolic subsystems (Figure 1). The largest subsystem was lipid metabolism (fatty acid biosynthesis, fatty acid elongation, steroid, glycerolipid, glycerophospholipid and sphingolipid metabolism) that accounted for 23.53% of the total reactions. Reactions involving the synthesis of PUFAs such as DGLA, ARA, and EPA are listed in model iCY1106. For most subsystems, most categories were more abundant in iCY1106 than in the Vongsangnak’s model, with the exception of Amino Acid Metabolism and Nucleotide Metabolism (Figure 1a). Since there were six compartments (cytosol, mitochondria, peroxisome, extracellular, plasma membrane and unclassified compartment) in Vongsangnak’s model, some reactions occur in multiple compartments at the same time. When ignoring compartments, not including transport reactions and exchange reactions, these two models shared 566 reactions (Additional file 2). Vongsangnak’s model and iCY1106 included 179 and 621 unique reactions, respectively (Figure 1b). Compared with model iYL619_PCP of the oleaginous yeast Y. lipolytica [20], lipid metabolism accounted for a higher proportion (16.7%, 191 of total 1142 reactions) of reactions in iCY1106. Amino acid and carbohydrate metabolism subsystems were 13.17% and 11.66%, respectively, in iCY1106.\nFigure 1 The comparison between Vongsangnak’s model and i CY1106. a: reaction distribution in subsystems between these two models; b: shared reactions and unique reactions between models.","divisions":[{"label":"title","span":{"begin":0,"end":46}},{"label":"p","span":{"begin":47,"end":1967}},{"label":"table-wrap","span":{"begin":1423,"end":1967}},{"label":"label","span":{"begin":1423,"end":1430}},{"label":"caption","span":{"begin":1431,"end":1466}},{"label":"p","span":{"begin":1431,"end":1466}},{"label":"table","span":{"begin":1467,"end":1816}},{"label":"tr","span":{"begin":1467,"end":1502}},{"label":"th","span":{"begin":1467,"end":1476}},{"label":"th","span":{"begin":1476,"end":1485}},{"label":"th","span":{"begin":1486,"end":1502}},{"label":"tr","span":{"begin":1503,"end":1517}},{"label":"td","span":{"begin":1503,"end":1517}},{"label":"tr","span":{"begin":1518,"end":1547}},{"label":"td","span":{"begin":1518,"end":1535}},{"label":"td","span":{"begin":1536,"end":1541}},{"label":"td","span":{"begin":1542,"end":1547}},{"label":"tr","span":{"begin":1548,"end":1593}},{"label":"td","span":{"begin":1548,"end":1581}},{"label":"td","span":{"begin":1582,"end":1587}},{"label":"td","span":{"begin":1588,"end":1593}},{"label":"tr","span":{"begin":1594,"end":1609}},{"label":"td","span":{"begin":1594,"end":1609}},{"label":"tr","span":{"begin":1610,"end":1636}},{"label":"td","span":{"begin":1610,"end":1626}},{"label":"td","span":{"begin":1627,"end":1631}},{"label":"td","span":{"begin":1632,"end":1636}},{"label":"tr","span":{"begin":1637,"end":1669}},{"label":"td","span":{"begin":1637,"end":1659}},{"label":"td","span":{"begin":1660,"end":1664}},{"label":"td","span":{"begin":1665,"end":1669}},{"label":"tr","span":{"begin":1670,"end":1699}},{"label":"td","span":{"begin":1670,"end":1690}},{"label":"td","span":{"begin":1691,"end":1694}},{"label":"td","span":{"begin":1695,"end":1699}},{"label":"tr","span":{"begin":1700,"end":1728}},{"label":"td","span":{"begin":1700,"end":1719}},{"label":"td","span":{"begin":1720,"end":1723}},{"label":"td","span":{"begin":1724,"end":1728}},{"label":"tr","span":{"begin":1729,"end":1751}},{"label":"td","span":{"begin":1729,"end":1741}},{"label":"td","span":{"begin":1742,"end":1746}},{"label":"td","span":{"begin":1747,"end":1751}},{"label":"tr","span":{"begin":1752,"end":1787}},{"label":"td","span":{"begin":1752,"end":1777}},{"label":"td","span":{"begin":1778,"end":1782}},{"label":"td","span":{"begin":1783,"end":1787}},{"label":"tr","span":{"begin":1788,"end":1816}},{"label":"td","span":{"begin":1788,"end":1806}},{"label":"td","span":{"begin":1807,"end":1811}},{"label":"td","span":{"begin":1812,"end":1816}},{"label":"table-wrap-foot","span":{"begin":1817,"end":1967}},{"label":"p","span":{"begin":1817,"end":1967}},{"label":"p","span":{"begin":1967,"end":2768}},{"label":"label","span":{"begin":4110,"end":4118}}],"tracks":[{"project":"2_test","denotations":[{"id":"25582171-23541380-14905478","span":{"begin":359,"end":361},"obj":"23541380"},{"id":"25582171-23541380-14905479","span":{"begin":1875,"end":1877},"obj":"23541380"},{"id":"25582171-21365447-14905480","span":{"begin":2580,"end":2582},"obj":"21365447"},{"id":"25582171-21365447-14905481","span":{"begin":2594,"end":2596},"obj":"21365447"},{"id":"25582171-23236514-14905482","span":{"begin":3892,"end":3894},"obj":"23236514"}],"attributes":[{"subj":"25582171-23541380-14905478","pred":"source","obj":"2_test"},{"subj":"25582171-23541380-14905479","pred":"source","obj":"2_test"},{"subj":"25582171-21365447-14905480","pred":"source","obj":"2_test"},{"subj":"25582171-21365447-14905481","pred":"source","obj":"2_test"},{"subj":"25582171-23236514-14905482","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93eca9","default":true}]}]}}