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Exploring metazoan evolution through dynamic and holistic changes in protein families and domains
BACKGROUND: Proteins convey the majority of biochemical and cellular activities in organisms. Over the course of evolution, proteins undergo normal sequence mutations as well as large scale mutations involving domain duplication and/or domain shuffling. These events result in the generation of new p...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483195/ https://www.ncbi.nlm.nih.gov/pubmed/22862991 http://dx.doi.org/10.1186/1471-2148-12-138 |
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author | Wang, Zhengyuan Zarlenga, Dante Martin, John Abubucker, Sahar Mitreva, Makedonka |
author_facet | Wang, Zhengyuan Zarlenga, Dante Martin, John Abubucker, Sahar Mitreva, Makedonka |
author_sort | Wang, Zhengyuan |
collection | PubMed |
description | BACKGROUND: Proteins convey the majority of biochemical and cellular activities in organisms. Over the course of evolution, proteins undergo normal sequence mutations as well as large scale mutations involving domain duplication and/or domain shuffling. These events result in the generation of new proteins and protein families. Processes that affect proteome evolution drive species diversity and adaptation. Herein, change over the course of metazoan evolution, as defined by birth/death and duplication/deletion events within protein families and domains, was examined using the proteomes of 9 metazoan and two outgroup species. RESULTS: In studying members of the three major metazoan groups, the vertebrates, arthropods, and nematodes, we found that the number of protein families increased at the majority of lineages over the course of metazoan evolution where the magnitude of these increases was greatest at the lineages leading to mammals. In contrast, the number of protein domains decreased at most lineages and at all terminal lineages. This resulted in a weak correlation between protein family birth and domain birth; however, the correlation between domain birth and domain member duplication was quite strong. These data suggest that domain birth and protein family birth occur via different mechanisms, and that domain shuffling plays a role in the formation of protein families. The ratio of protein family birth to protein domain birth (domain shuffling index) suggests that shuffling had a more demonstrable effect on protein families in nematodes and arthropods than in vertebrates. Through the contrast of high and low domain shuffling indices at the lineages of Trichinella spiralis and Gallus gallus, we propose a link between protein redundancy and evolutionary changes controlled by domain shuffling; however, the speed of adaptation among the different lineages was relatively invariant. Evaluating the functions of protein families that appeared or disappeared at the last common ancestors (LCAs) of the three metazoan clades supports a correlation with organism adaptation. Furthermore, bursts of new protein families and domains in the LCAs of metazoans and vertebrates are consistent with whole genome duplications. CONCLUSION: Metazoan speciation and adaptation were explored by birth/death and duplication/deletion events among protein families and domains. Our results provide insights into protein evolution and its bearing on metazoan evolution. |
format | Online Article Text |
id | pubmed-3483195 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-34831952012-11-05 Exploring metazoan evolution through dynamic and holistic changes in protein families and domains Wang, Zhengyuan Zarlenga, Dante Martin, John Abubucker, Sahar Mitreva, Makedonka BMC Evol Biol Research Article BACKGROUND: Proteins convey the majority of biochemical and cellular activities in organisms. Over the course of evolution, proteins undergo normal sequence mutations as well as large scale mutations involving domain duplication and/or domain shuffling. These events result in the generation of new proteins and protein families. Processes that affect proteome evolution drive species diversity and adaptation. Herein, change over the course of metazoan evolution, as defined by birth/death and duplication/deletion events within protein families and domains, was examined using the proteomes of 9 metazoan and two outgroup species. RESULTS: In studying members of the three major metazoan groups, the vertebrates, arthropods, and nematodes, we found that the number of protein families increased at the majority of lineages over the course of metazoan evolution where the magnitude of these increases was greatest at the lineages leading to mammals. In contrast, the number of protein domains decreased at most lineages and at all terminal lineages. This resulted in a weak correlation between protein family birth and domain birth; however, the correlation between domain birth and domain member duplication was quite strong. These data suggest that domain birth and protein family birth occur via different mechanisms, and that domain shuffling plays a role in the formation of protein families. The ratio of protein family birth to protein domain birth (domain shuffling index) suggests that shuffling had a more demonstrable effect on protein families in nematodes and arthropods than in vertebrates. Through the contrast of high and low domain shuffling indices at the lineages of Trichinella spiralis and Gallus gallus, we propose a link between protein redundancy and evolutionary changes controlled by domain shuffling; however, the speed of adaptation among the different lineages was relatively invariant. Evaluating the functions of protein families that appeared or disappeared at the last common ancestors (LCAs) of the three metazoan clades supports a correlation with organism adaptation. Furthermore, bursts of new protein families and domains in the LCAs of metazoans and vertebrates are consistent with whole genome duplications. CONCLUSION: Metazoan speciation and adaptation were explored by birth/death and duplication/deletion events among protein families and domains. Our results provide insights into protein evolution and its bearing on metazoan evolution. BioMed Central 2012-08-03 /pmc/articles/PMC3483195/ /pubmed/22862991 http://dx.doi.org/10.1186/1471-2148-12-138 Text en Copyright ©2012 Wang et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Wang, Zhengyuan Zarlenga, Dante Martin, John Abubucker, Sahar Mitreva, Makedonka Exploring metazoan evolution through dynamic and holistic changes in protein families and domains |
title | Exploring metazoan evolution through dynamic and holistic changes in protein families and domains |
title_full | Exploring metazoan evolution through dynamic and holistic changes in protein families and domains |
title_fullStr | Exploring metazoan evolution through dynamic and holistic changes in protein families and domains |
title_full_unstemmed | Exploring metazoan evolution through dynamic and holistic changes in protein families and domains |
title_short | Exploring metazoan evolution through dynamic and holistic changes in protein families and domains |
title_sort | exploring metazoan evolution through dynamic and holistic changes in protein families and domains |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483195/ https://www.ncbi.nlm.nih.gov/pubmed/22862991 http://dx.doi.org/10.1186/1471-2148-12-138 |
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