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Emergence of novel domains in proteins
BACKGROUND: Proteins are composed of a combination of discrete, well-defined, sequence domains, associated with specific functions that have arisen at different times during evolutionary history. The emergence of novel domains is related to protein functional diversification and adaptation. But curr...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3599535/ https://www.ncbi.nlm.nih.gov/pubmed/23425224 http://dx.doi.org/10.1186/1471-2148-13-47 |
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author | Toll-Riera, Macarena Albà, M Mar |
author_facet | Toll-Riera, Macarena Albà, M Mar |
author_sort | Toll-Riera, Macarena |
collection | PubMed |
description | BACKGROUND: Proteins are composed of a combination of discrete, well-defined, sequence domains, associated with specific functions that have arisen at different times during evolutionary history. The emergence of novel domains is related to protein functional diversification and adaptation. But currently little is known about how novel domains arise and how they subsequently evolve. RESULTS: To gain insights into the impact of recently emerged domains in protein evolution we have identified all human young protein domains that have emerged in approximately the past 550 million years. We have classified them into vertebrate-specific and mammalian-specific groups, and compared them to older domains. We have found 426 different annotated young domains, totalling 995 domain occurrences, which represent about 12.3% of all human domains. We have observed that 61.3% of them arose in newly formed genes, while the remaining 38.7% are found combined with older domains, and have very likely emerged in the context of a previously existing protein. Young domains are preferentially located at the N-terminus of the protein, indicating that, at least in vertebrates, novel functional sequences often emerge there. Furthermore, young domains show significantly higher non-synonymous to synonymous substitution rates than older domains using human and mouse orthologous sequence comparisons. This is also true when we compare young and old domains located in the same protein, suggesting that recently arisen domains tend to evolve in a less constrained manner than older domains. CONCLUSIONS: We conclude that proteins tend to gain domains over time, becoming progressively longer. We show that many proteins are made of domains of different age, and that the fastest evolving parts correspond to the domains that have been acquired more recently. |
format | Online Article Text |
id | pubmed-3599535 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35995352013-03-17 Emergence of novel domains in proteins Toll-Riera, Macarena Albà, M Mar BMC Evol Biol Research Article BACKGROUND: Proteins are composed of a combination of discrete, well-defined, sequence domains, associated with specific functions that have arisen at different times during evolutionary history. The emergence of novel domains is related to protein functional diversification and adaptation. But currently little is known about how novel domains arise and how they subsequently evolve. RESULTS: To gain insights into the impact of recently emerged domains in protein evolution we have identified all human young protein domains that have emerged in approximately the past 550 million years. We have classified them into vertebrate-specific and mammalian-specific groups, and compared them to older domains. We have found 426 different annotated young domains, totalling 995 domain occurrences, which represent about 12.3% of all human domains. We have observed that 61.3% of them arose in newly formed genes, while the remaining 38.7% are found combined with older domains, and have very likely emerged in the context of a previously existing protein. Young domains are preferentially located at the N-terminus of the protein, indicating that, at least in vertebrates, novel functional sequences often emerge there. Furthermore, young domains show significantly higher non-synonymous to synonymous substitution rates than older domains using human and mouse orthologous sequence comparisons. This is also true when we compare young and old domains located in the same protein, suggesting that recently arisen domains tend to evolve in a less constrained manner than older domains. CONCLUSIONS: We conclude that proteins tend to gain domains over time, becoming progressively longer. We show that many proteins are made of domains of different age, and that the fastest evolving parts correspond to the domains that have been acquired more recently. BioMed Central 2013-02-20 /pmc/articles/PMC3599535/ /pubmed/23425224 http://dx.doi.org/10.1186/1471-2148-13-47 Text en Copyright ©2013 Toll-Riera and Alba; 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 Toll-Riera, Macarena Albà, M Mar Emergence of novel domains in proteins |
title | Emergence of novel domains in proteins |
title_full | Emergence of novel domains in proteins |
title_fullStr | Emergence of novel domains in proteins |
title_full_unstemmed | Emergence of novel domains in proteins |
title_short | Emergence of novel domains in proteins |
title_sort | emergence of novel domains in proteins |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3599535/ https://www.ncbi.nlm.nih.gov/pubmed/23425224 http://dx.doi.org/10.1186/1471-2148-13-47 |
work_keys_str_mv | AT tollrieramacarena emergenceofnoveldomainsinproteins AT albammar emergenceofnoveldomainsinproteins |