ArticlePLoS computational biology2020
Determining the interaction status and evolutionary fate of duplicated homomeric proteins.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Evolutionary causes and consequences of gene duplication.Nature reviews. Genetics · 2026Review
- The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking.Nature communications · 2026Article
- Evolutionary persistence and divergence of thebioRxiv : the preprint server for biology · 2025Article
- Simple genetic mechanisms toward more intricate molecular complexes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Symmetry facilitated the evolution of heterospecificity and high-order stoichiometry in vertebrate hemoglobin.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Symmetry facilitated the evolution of heterospecificity and high-order stoichiometry in vertebrate hemoglobin.bioRxiv : the preprint server for biology · 2024Article
- A single septin from a polyextremotolerant yeast recapitulates many canonical functions of septin hetero-oligomers.Molecular biology of the cell · 2024Article
- Altered assembly paths mitigate interference among paralogous complexes.Nature communications · 2024Article
- Mutational biases favor complexity increases in protein interaction networks after gene duplication.Molecular systems biology · 2024Article
- Compensatory mutations potentiate constructive neutral evolution by gene duplication.bioRxiv : the preprint server for biology · 2024Article
- Unusual Evolution of Cephalopod Tryptophan Indole-Lyases.Journal of molecular evolution · 2023Article
- A hierarchical assembly pathway directs the unique subunit arrangement of TRiC/CCT.Molecular cell · 2023Article
- A Simple Evolutionary Model of Genetic Robustness After Gene Duplication.Journal of molecular evolution · 2022Article
- How gene duplication diversifies the landscape of protein oligomeric state and function.Current opinion in genetics & development · 2022Review
- Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins.PLoS computational biology · 2022Article
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Authors and funding
2 authors.
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Abstract
Oligomeric proteins are central to life. Duplication and divergence of their genes is a key evolutionary driver, also because duplications can yield very different outcomes. Given a homomeric ancestor, duplication can yield two paralogs that form two distinct homomeric complexes, or a heteromeric complex comprising both paralogs. Alternatively, one paralog remains a homomer while the other acquires a new partner. However, so far, conflicting trends have been noted with respect to which fate dominates, primarily because different methods and criteria are being used to assign the interaction status of paralogs. Here, we systematically analyzed all Saccharomyces cerevisiae and Escherichia coli oligomeric complexes that include paralogous proteins. We found that the proportions of homo-hetero duplication fates strongly depend on a variety of factors, yet that nonetheless, rigorous filtering gives a consistent picture. In E. coli about 50%, of the paralogous pairs appear to have retained the ancestral homomeric interaction, whereas in S. cerevisiae only ~10% retained a homomeric state. This difference was also observed when unique complexes were counted instead of paralogous gene pairs. We further show that this difference is accounted for by multiple cases of heteromeric yeast complexes that share common ancestry with homomeric bacterial complexes. Our analysis settles contradicting trends and conflicting previous analyses, and provides a systematic and rigorous pipeline for delineating the fate of duplicated oligomers in any organism for which protein-protein interaction data are available.
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