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Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses
Transfer RNAs (tRNAs) are ancient molecules that are central to translation. Since they probably carry evolutionary signatures that were left behind when the living world diversified, we reconstructed phylogenies directly from the sequence and structure of tRNA using well-established phylogenetic me...
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265525/ https://www.ncbi.nlm.nih.gov/pubmed/18369418 http://dx.doi.org/10.1371/journal.pcbi.1000018 |
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author | Sun, Feng-Jie Caetano-Anollés, Gustavo |
author_facet | Sun, Feng-Jie Caetano-Anollés, Gustavo |
author_sort | Sun, Feng-Jie |
collection | PubMed |
description | Transfer RNAs (tRNAs) are ancient molecules that are central to translation. Since they probably carry evolutionary signatures that were left behind when the living world diversified, we reconstructed phylogenies directly from the sequence and structure of tRNA using well-established phylogenetic methods. The trees placed tRNAs with long variable arms charging Sec, Tyr, Ser, and Leu consistently at the base of the rooted phylogenies, but failed to reveal groupings that would indicate clear evolutionary links to organismal origin or molecular functions. In order to uncover evolutionary patterns in the trees, we forced tRNAs into monophyletic groups using constraint analyses to generate timelines of organismal diversification and test competing evolutionary hypotheses. Remarkably, organismal timelines showed Archaea was the most ancestral superkingdom, followed by viruses, then superkingdoms Eukarya and Bacteria, in that order, supporting conclusions from recent phylogenomic studies of protein architecture. Strikingly, constraint analyses showed that the origin of viruses was not only ancient, but was linked to Archaea. Our findings have important implications. They support the notion that the archaeal lineage was very ancient, resulted in the first organismal divide, and predated diversification of tRNA function and specificity. Results are also consistent with the concept that viruses contributed to the development of the DNA replication machinery during the early diversification of the living world. |
format | Text |
id | pubmed-2265525 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-22655252008-03-08 Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses Sun, Feng-Jie Caetano-Anollés, Gustavo PLoS Comput Biol Research Article Transfer RNAs (tRNAs) are ancient molecules that are central to translation. Since they probably carry evolutionary signatures that were left behind when the living world diversified, we reconstructed phylogenies directly from the sequence and structure of tRNA using well-established phylogenetic methods. The trees placed tRNAs with long variable arms charging Sec, Tyr, Ser, and Leu consistently at the base of the rooted phylogenies, but failed to reveal groupings that would indicate clear evolutionary links to organismal origin or molecular functions. In order to uncover evolutionary patterns in the trees, we forced tRNAs into monophyletic groups using constraint analyses to generate timelines of organismal diversification and test competing evolutionary hypotheses. Remarkably, organismal timelines showed Archaea was the most ancestral superkingdom, followed by viruses, then superkingdoms Eukarya and Bacteria, in that order, supporting conclusions from recent phylogenomic studies of protein architecture. Strikingly, constraint analyses showed that the origin of viruses was not only ancient, but was linked to Archaea. Our findings have important implications. They support the notion that the archaeal lineage was very ancient, resulted in the first organismal divide, and predated diversification of tRNA function and specificity. Results are also consistent with the concept that viruses contributed to the development of the DNA replication machinery during the early diversification of the living world. Public Library of Science 2008-03-07 /pmc/articles/PMC2265525/ /pubmed/18369418 http://dx.doi.org/10.1371/journal.pcbi.1000018 Text en Sun, Caetano-Anollés. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Sun, Feng-Jie Caetano-Anollés, Gustavo Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses |
title | Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses |
title_full | Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses |
title_fullStr | Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses |
title_full_unstemmed | Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses |
title_short | Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses |
title_sort | evolutionary patterns in the sequence and structure of transfer rna: early origins of archaea and viruses |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265525/ https://www.ncbi.nlm.nih.gov/pubmed/18369418 http://dx.doi.org/10.1371/journal.pcbi.1000018 |
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