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Determining the interaction status and evolutionary fate of duplicated homomeric proteins

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 co...

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Detalles Bibliográficos
Autores principales: Mallik, Saurav, Tawfik, Dan S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480870/
https://www.ncbi.nlm.nih.gov/pubmed/32853212
http://dx.doi.org/10.1371/journal.pcbi.1008145
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author Mallik, Saurav
Tawfik, Dan S.
author_facet Mallik, Saurav
Tawfik, Dan S.
author_sort Mallik, Saurav
collection PubMed
description 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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spelling pubmed-74808702020-09-18 Determining the interaction status and evolutionary fate of duplicated homomeric proteins Mallik, Saurav Tawfik, Dan S. PLoS Comput Biol Research Article 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. Public Library of Science 2020-08-27 /pmc/articles/PMC7480870/ /pubmed/32853212 http://dx.doi.org/10.1371/journal.pcbi.1008145 Text en © 2020 Mallik, Tawfik http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Mallik, Saurav
Tawfik, Dan S.
Determining the interaction status and evolutionary fate of duplicated homomeric proteins
title Determining the interaction status and evolutionary fate of duplicated homomeric proteins
title_full Determining the interaction status and evolutionary fate of duplicated homomeric proteins
title_fullStr Determining the interaction status and evolutionary fate of duplicated homomeric proteins
title_full_unstemmed Determining the interaction status and evolutionary fate of duplicated homomeric proteins
title_short Determining the interaction status and evolutionary fate of duplicated homomeric proteins
title_sort determining the interaction status and evolutionary fate of duplicated homomeric proteins
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480870/
https://www.ncbi.nlm.nih.gov/pubmed/32853212
http://dx.doi.org/10.1371/journal.pcbi.1008145
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