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03102nam a2200577Ia 4500 |
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10.15252-msb.202110427 |
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220427s2021 CNT 000 0 und d |
| 020 |
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|a 17444292 (ISSN)
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| 245 |
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|a Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection
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| 260 |
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|b John Wiley and Sons Inc
|c 2021
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| 856 |
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|z View Fulltext in Publisher
|u https://doi.org/10.15252/msb.202110427
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|a Yeasts are known to have versatile metabolic traits, while how these metabolic traits have evolved has not been elucidated systematically. We performed integrative evolution analysis to investigate how genomic evolution determines trait generation by reconstructing genome-scale metabolic models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize trait diversity and predict enzyme functionality, thereby signifying that sequence-level evolution has shaped reaction networks towards new metabolic functions. Strikingly, using GEMs, we can mechanistically map different evolutionary events, e.g. horizontal gene transfer and gene duplication, onto relevant subpathways to explain metabolic plasticity. This demonstrates that gene family expansion and enzyme promiscuity are prominent mechanisms for metabolic trait gains, while GEM simulations reveal that additional factors, such as gene loss from distant pathways, contribute to trait losses. Furthermore, our analysis could pinpoint to specific genes and pathways that have been under positive selection and relevant for the formulation of complex metabolic traits, i.e. thermotolerance and the Crabtree effect. Our findings illustrate how multidimensional evolution in both metabolic network structure and individual enzymes drives phenotypic variations. © 2021 The Authors. Published under the terms of the CC BY 4.0 license
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|a article
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|a Crabtree effect
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4 |
|a Evolution, Molecular
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| 650 |
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4 |
|a gene duplication
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| 650 |
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4 |
|a Gene Duplication
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| 650 |
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|a Gene Transfer, Horizontal
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| 650 |
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4 |
|a genetics
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| 650 |
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|a genome
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| 650 |
0 |
4 |
|a Genome
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| 650 |
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4 |
|a genome analysis
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| 650 |
0 |
4 |
|a genome analysis
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| 650 |
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4 |
|a genome-scale metabolic models
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| 650 |
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4 |
|a heat tolerance
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| 650 |
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4 |
|a horizontal gene transfer
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| 650 |
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4 |
|a metabolic innovation
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| 650 |
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4 |
|a Metabolic Networks and Pathways
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| 650 |
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4 |
|a metabolism
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| 650 |
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4 |
|a molecular evolution
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| 650 |
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4 |
|a multigene family
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| 650 |
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4 |
|a nonhuman
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| 650 |
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4 |
|a phenotypic variation
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| 650 |
0 |
4 |
|a Saccharomyces cerevisiae
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| 650 |
0 |
4 |
|a Saccharomyces cerevisiae
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| 650 |
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4 |
|a simulation
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| 650 |
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4 |
|a systems biology
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| 650 |
0 |
4 |
|a systems biology
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| 650 |
0 |
4 |
|a yeast
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| 700 |
1 |
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|a Chen, Y.
|e author
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| 700 |
1 |
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|a Domenzain, I.
|e author
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| 700 |
1 |
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|a Ji, B.
|e author
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| 700 |
1 |
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|a Kerkhoven, E.J.
|e author
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| 700 |
1 |
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|a Li, F.
|e author
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| 700 |
1 |
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|a Li, G.
|e author
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| 700 |
1 |
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|a Lu, H.
|e author
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| 700 |
1 |
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|a Nielsen, J.
|e author
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| 700 |
1 |
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|a Wang, H.
|e author
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| 700 |
1 |
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|a Yu, R.
|e author
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| 700 |
1 |
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|a Yuan, L.
|e author
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| 773 |
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|t Molecular Systems Biology
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