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Evolution of Viral Proteins Originated De Novo by Overprinting
New protein-coding genes can originate either through modification of existing genes or de novo. Recently, the importance of de novo origination has been recognized in eukaryotes, although eukaryotic genes originated de novo are relatively rare and difficult to identify. In contrast, viruses contain...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494269/ https://www.ncbi.nlm.nih.gov/pubmed/22821011 http://dx.doi.org/10.1093/molbev/mss179 |
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author | Sabath, Niv Wagner, Andreas Karlin, David |
author_facet | Sabath, Niv Wagner, Andreas Karlin, David |
author_sort | Sabath, Niv |
collection | PubMed |
description | New protein-coding genes can originate either through modification of existing genes or de novo. Recently, the importance of de novo origination has been recognized in eukaryotes, although eukaryotic genes originated de novo are relatively rare and difficult to identify. In contrast, viruses contain many de novo genes, namely those in which an existing gene has been “overprinted” by a new open reading frame, a process that generates a new protein-coding gene overlapping the ancestral gene. We analyzed the evolution of 12 experimentally validated viral genes that originated de novo and estimated their relative ages. We found that young de novo genes have a different codon usage from the rest of the genome. They evolve rapidly and are under positive or weak purifying selection. Thus, young de novo genes might have strain-specific functions, or no function, and would be difficult to detect using current genome annotation methods that rely on the sequence signature of purifying selection. In contrast to young de novo genes, older de novo genes have a codon usage that is similar to the rest of the genome. They evolve slowly and are under stronger purifying selection. Some of the oldest de novo genes evolve under stronger selection pressure than the ancestral gene they overlap, suggesting an evolutionary tug of war between the ancestral and the de novo gene. |
format | Online Article Text |
id | pubmed-3494269 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-34942692012-11-09 Evolution of Viral Proteins Originated De Novo by Overprinting Sabath, Niv Wagner, Andreas Karlin, David Mol Biol Evol Research Articles New protein-coding genes can originate either through modification of existing genes or de novo. Recently, the importance of de novo origination has been recognized in eukaryotes, although eukaryotic genes originated de novo are relatively rare and difficult to identify. In contrast, viruses contain many de novo genes, namely those in which an existing gene has been “overprinted” by a new open reading frame, a process that generates a new protein-coding gene overlapping the ancestral gene. We analyzed the evolution of 12 experimentally validated viral genes that originated de novo and estimated their relative ages. We found that young de novo genes have a different codon usage from the rest of the genome. They evolve rapidly and are under positive or weak purifying selection. Thus, young de novo genes might have strain-specific functions, or no function, and would be difficult to detect using current genome annotation methods that rely on the sequence signature of purifying selection. In contrast to young de novo genes, older de novo genes have a codon usage that is similar to the rest of the genome. They evolve slowly and are under stronger purifying selection. Some of the oldest de novo genes evolve under stronger selection pressure than the ancestral gene they overlap, suggesting an evolutionary tug of war between the ancestral and the de novo gene. Oxford University Press 2012-12 2012-07-19 /pmc/articles/PMC3494269/ /pubmed/22821011 http://dx.doi.org/10.1093/molbev/mss179 Text en © The Author 2012. Published by Oxford University Press on behalf of the society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Sabath, Niv Wagner, Andreas Karlin, David Evolution of Viral Proteins Originated De Novo by Overprinting |
title | Evolution of Viral Proteins Originated De Novo by Overprinting |
title_full | Evolution of Viral Proteins Originated De Novo by Overprinting |
title_fullStr | Evolution of Viral Proteins Originated De Novo by Overprinting |
title_full_unstemmed | Evolution of Viral Proteins Originated De Novo by Overprinting |
title_short | Evolution of Viral Proteins Originated De Novo by Overprinting |
title_sort | evolution of viral proteins originated de novo by overprinting |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494269/ https://www.ncbi.nlm.nih.gov/pubmed/22821011 http://dx.doi.org/10.1093/molbev/mss179 |
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