Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts
Journal article, 2020
The Saccharomycotina subphylum (budding yeasts) spans 400 million years of evolution and includes species that thrive in diverse environments. To study niche-adaptation, we identify changes in gene expression in three divergent yeasts grown in the presence of various stressors. Duplicated and non-conserved genes are significantly more likely to respond to stress than genes that are conserved as single-copy orthologs. Next, we develop a sorting method that considers evolutionary origin and duplication timing to assign an evolutionary age to each gene. Subsequent analysis reveals that genes that emerged in recent evolutionary time are enriched amongst stress-responsive genes for each species. This gene expression pattern suggests that budding yeasts share a stress adaptation mechanism, whereby selective pressure leads to functionalization of young genes to improve growth in adverse conditions. Further characterization of young genes from species that thrive in harsh environments can inform the design of more robust strains for biotechnology.
Systems analysis
Industrial microbiology
Applied microbiology
Author
Tyler Doughty
Novo Nordisk Foundation
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Iván Domenzain Del Castillo Cerecer
Novo Nordisk Foundation
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Aaron Millan-Oropeza
University Paris-Saclay
Noemi Montini
APC Microbiome Ireland
Philip A. de Groot
Delft University of Technology
Rui Pereira
Novo Nordisk Foundation
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Jens B Nielsen
Novo Nordisk Foundation
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Céline Henry
University Paris-Saclay
J. M. Daran
Delft University of Technology
Verena Siewers
Novo Nordisk Foundation
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
John P. Morrissey
APC Microbiome Ireland
Nature Communications
2041-1723 (ISSN) 20411723 (eISSN)
Vol. 11 1 2144Subject Categories
Evolutionary Biology
Bioinformatics and Systems Biology
Genetics
DOI
10.1038/s41467-020-16073-3