Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Lu, Hongzhong,1987Chalmers tekniska högskola,Chalmers University of Technology (författare)

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.

Li, Feiran,1993Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)feiranl (författare)
Yuan, Le,1994Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)leyu (författare)
Domenzain Del Castillo Cerecer, Iván,1991Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)ivand (författare)
Brown, Rosemary,1990Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)brown (författare)
Wang, Hao,1975Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)haowa (författare)
Li, Gang,1991Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)gangl (författare)
Chen, Yu,1990Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)cheyu (författare)
Ji, Boyang,1983Chalmers tekniska högskola,Chalmers University of Technology,Danmarks Tekniske Universitet,Technical University of Denmark(Swepub:cth)bojand (författare)
Kerkhoven, Eduard,1985Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)eduardk (författare)
Nielsen, Jens B,1962BioInnovation Institute (BII),Danmarks Tekniske Universitet,Technical University of Denmark,Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)nielsenj (författare)
Chalmers tekniska högskolaDanmarks Tekniske Universitet (creator_code:org_t)

Av författaren/redakt...: Lu, Hongzhong, 1 ...; Li, Feiran, 1993; Yuan, Le, 1994; Domenzain Del Ca ...; Brown, Rosemary, ...; Wang, Hao, 1975; visa fler...; Li, Gang, 1991; Chen, Yu, 1990; Ji, Boyang, 1983; Kerkhoven, Eduar ...; Nielsen, Jens B, ...; visa färre...

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