Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection
Artikel i vetenskaplig tidskrift, 2021

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.

metabolic innovation

genome-scale metabolic models

systems biology

genome analysis

Författare

Hongzhong Lu

Chalmers, Biologi och bioteknik, Systembiologi

Feiran Li

Chalmers, Biologi och bioteknik, Systembiologi

Le Yuan

Chalmers, Biologi och bioteknik, Systembiologi

Iván Domenzain Del Castillo Cerecer

Chalmers, Biologi och bioteknik, Systembiologi

Rosemary Yu

Hao Wang

Chalmers, Biologi och bioteknik, Systembiologi, CSBI

Gang Li

Chalmers, Biologi och bioteknik, Systembiologi

Yu Chen

Chalmers, Biologi och bioteknik, Systembiologi

Boyang Ji

Chalmers, Biologi och bioteknik, Systembiologi

Danmarks Tekniske Universitet (DTU)

Eduard Kerkhoven

Chalmers, Biologi och bioteknik, Systembiologi

Jens B Nielsen

Danmarks Tekniske Universitet (DTU)

Chalmers, Biologi och bioteknik, Systembiologi

BioInnovation Institute

Molecular Systems Biology

1744-4292 (ISSN)

Vol. 17 10 e10427

Ämneskategorier

Evolutionsbiologi

Bioinformatik och systembiologi

Genetik

DOI

10.15252/msb.202110427

PubMed

34676984

Mer information

Senast uppdaterat

2021-11-09