ArticlePLoS computational biology2014
Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 56 citations in OpenAlex.
- Evolutionary causes and consequences of gene duplication.Nature reviews. Genetics · 2026Review
- Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multifunctionality.Journal of molecular evolution · 2024Review
- Computational Study of Network and Type-I Functional Divergence in Alcohol Dehydrogenase Enzymes Across Species Using Molecular Dynamics Simulation.Biomolecules · 2024Article
- Characterization and organization of telomeric-linked helicase (tlh) gene families in Fusarium oxysporum.Current genetics · 2024Article
- The fitness cost of spurious phosphorylation.The EMBO journal · 2024Article
- The fitness cost of spurious phosphorylation.bioRxiv : the preprint server for biology · 2023Article
- Evolutionary conservation of sequence motifs at sites of protein modification.The Journal of biological chemistry · 2023Article
- Paralog-based synthetic lethality: rationales and applications.Frontiers in oncology · 2023Review
- Divergent Dimethylarginine Dimethylaminohydrolase Isoenzyme Expression in the Central Nervous System.Cellular and molecular neurobiology · 2022Article
- Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning.PLoS computational biology · 2022Article
- Article
- Recurrent sequence evolution after independent gene duplication.BMC evolutionary biology · 2020Article
- Diversity and evolution of cytochrome P450s of Jacobaea vulgaris and Jacobaea aquatica.BMC plant biology · 2020Article
- Exploring whole-genome duplicate gene retention with complex genetic interaction analysis.Science (New York, N.Y.) · 2020Article
- Article
- Proteome-wide signatures of function in highly diverged intrinsically disordered regions.eLife · 2019Article
- Evidence for Stabilizing Selection Driving Mutational Turnover of Short Motifs in the Eukaryotic Complementary Sex Determiner (Csd) Protein.G3 (Bethesda, Md.) · 2018Article
- Deciphering the emergence, genetic diversity and evolution of classical swine fever virus.Scientific reports · 2017Article
- Evolution of intrinsic disorder in eukaryotic proteins.Cellular and molecular life sciences : CMLS · 2017Review
- Convergence of Domain Architecture, Structure, and Ligand Affinity in Animal and Plant RNA-Binding Proteins.Molecular biology and evolution · 2017Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared null distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to SWI5 after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.