Evolutionary principles of modular gene regulation in yeasts
Open accessAbstract
Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years [corrected]. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism. Paralogs have significantly contributed to regulatory divergence, typically within a very short window from their duplication. Paralogs from a whole genome duplication (WGD) event have a uniquely substantial contribution that extends over a longer span. Similar patterns occur when considering the evolution of the heat shock regulatory program measured in eight of the species, suggesting that these are general evolutionary principles. DOI:http://dx.doi.org/10.7554/eLife.00603.001.
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Paralogous duplication of genes encoding regulatory proteins is usually rapidly followed by functional reassignment.
“Paralogous duplication of genes encoding regulatory proteins is usually rapidly followed by functional reassignment (Thompson et al. 2013).”
From Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts (2026) · cites this paper as Thompson et al. 2013
The Results section, “Enhanced regulatory divergence during a short window post-duplication” (page unavailable), reports that most paralogs that are reassigned do so shortly after duplication. But the analysis concerns reassignment of genes to regulatory-expression modules, not specifically functional reassignment of proteins that regulate other genes. Its 53% figure also applies only to sporadically duplicated pairs in which at least one member was subsequently reassigned. (LLM, conf=0.88)
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- Authors
- Thompson, D. A., Roy, S., Chan, M., Styczynsky, M. P., Pfiffner, J., French, C., Socha, A., Thielke, A., Napolitano, S., Muller, P., Kellis, M., Konieczka, J. H., Wapinski, I., & Regev, A.
- Affiliations
- Broad Institute (US)
- Broad Institute of MIT and Harvard, Cambridge, United States
- MIT Computer Science and Artificial Intelligence Laboratory (US)
- Corresponding author
- Thompson, Dawn A
- Regev, Aviv
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2013-06-18
- Volume
- 2
- Pages
- e00603-e00603
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC3687341
- OpenAlex
- W2140090852
- Cited by
- 78
- References
- 73
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 5 · 2023: 2 · 2022: 5 · 2021: 7 · 2020: 5 · 2019: 5 · 2018: 4 · 2017: 7 · 2016: 12 · 2015: 16 · 2014: 6 · 2013: 1
- FWCI
- 5.22
- Type
- journal article
- Language
- en
- Update notices
- correction (2013-07-02)
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (2R01CA119176-01)
- Broad Institute
- Burroughs Wellcome Fund
- Computing Innovation Fellow
- Damon Runyon Cancer Research Foundation
- Alfred P. Sloan Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- yeast evolution, Ascomycota, phylogenetic divergence, gene regulatory modules, paralogs, whole-genome duplication, gene duplication, carbon metabolism, ploidy, heat shock response, glucose growth
- MeSH terms
- Ascomycota, Genes, Fungal, Phylogeny, Transcription, Genetic, Gene Expression Regulation, Fungal, Evolution, Molecular, Gene Duplication, Gene Expression Profiling
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