Comparative analysis of RNA families reveals distinct repertoires for each domain of life.

The RNA world hypothesis, that RNA genomes and catalysts preceded DNA genomes and genetically-encoded protein catalysts, has been central to models for the early evolution of life on Earth. A key part of such models is continuity between the earliest stages in the evolution of life and the RNA reper...

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Autores principales:	Marc P Hoeppner, Paul P Gardner, Anthony M Poole
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/be3405a2544548a6b596978dc09de2ac
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spelling	oai:doaj.org-article:be3405a2544548a6b596978dc09de2ac2021-11-18T05:52:44ZComparative analysis of RNA families reveals distinct repertoires for each domain of life.1553-734X1553-735810.1371/journal.pcbi.1002752https://doaj.org/article/be3405a2544548a6b596978dc09de2ac2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23133357/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The RNA world hypothesis, that RNA genomes and catalysts preceded DNA genomes and genetically-encoded protein catalysts, has been central to models for the early evolution of life on Earth. A key part of such models is continuity between the earliest stages in the evolution of life and the RNA repertoires of extant lineages. Some assessments seem consistent with a diverse RNA world, yet direct continuity between modern RNAs and an RNA world has not been demonstrated for the majority of RNA families, and, anecdotally, many RNA functions appear restricted in their distribution. Despite much discussion of the possible antiquity of RNA families, no systematic analyses of RNA family distribution have been performed. To chart the broad evolutionary history of known RNA families, we performed comparative genomic analysis of over 3 million RNA annotations spanning 1446 families from the Rfam 10 database. We report that 99% of known RNA families are restricted to a single domain of life, revealing discrete repertoires for each domain. For the 1% of RNA families/clans present in more than one domain, over half show evidence of horizontal gene transfer (HGT), and the rest show a vertical trace, indicating the presence of a complex protein synthesis machinery in the Last Universal Common Ancestor (LUCA) and consistent with the evolutionary history of the most ancient protein-coding genes. However, with limited interdomain transfer and few RNA families exhibiting demonstrable antiquity as predicted under RNA world continuity, our results indicate that the majority of modern cellular RNA repertoires have primarily evolved in a domain-specific manner.Marc P HoeppnerPaul P GardnerAnthony M PoolePublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 11, p e1002752 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Marc P Hoeppner Paul P Gardner Anthony M Poole Comparative analysis of RNA families reveals distinct repertoires for each domain of life.
description	The RNA world hypothesis, that RNA genomes and catalysts preceded DNA genomes and genetically-encoded protein catalysts, has been central to models for the early evolution of life on Earth. A key part of such models is continuity between the earliest stages in the evolution of life and the RNA repertoires of extant lineages. Some assessments seem consistent with a diverse RNA world, yet direct continuity between modern RNAs and an RNA world has not been demonstrated for the majority of RNA families, and, anecdotally, many RNA functions appear restricted in their distribution. Despite much discussion of the possible antiquity of RNA families, no systematic analyses of RNA family distribution have been performed. To chart the broad evolutionary history of known RNA families, we performed comparative genomic analysis of over 3 million RNA annotations spanning 1446 families from the Rfam 10 database. We report that 99% of known RNA families are restricted to a single domain of life, revealing discrete repertoires for each domain. For the 1% of RNA families/clans present in more than one domain, over half show evidence of horizontal gene transfer (HGT), and the rest show a vertical trace, indicating the presence of a complex protein synthesis machinery in the Last Universal Common Ancestor (LUCA) and consistent with the evolutionary history of the most ancient protein-coding genes. However, with limited interdomain transfer and few RNA families exhibiting demonstrable antiquity as predicted under RNA world continuity, our results indicate that the majority of modern cellular RNA repertoires have primarily evolved in a domain-specific manner.
format	article
author	Marc P Hoeppner Paul P Gardner Anthony M Poole
author_facet	Marc P Hoeppner Paul P Gardner Anthony M Poole
author_sort	Marc P Hoeppner
title	Comparative analysis of RNA families reveals distinct repertoires for each domain of life.
title_short	Comparative analysis of RNA families reveals distinct repertoires for each domain of life.
title_full	Comparative analysis of RNA families reveals distinct repertoires for each domain of life.
title_fullStr	Comparative analysis of RNA families reveals distinct repertoires for each domain of life.
title_full_unstemmed	Comparative analysis of RNA families reveals distinct repertoires for each domain of life.
title_sort	comparative analysis of rna families reveals distinct repertoires for each domain of life.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/be3405a2544548a6b596978dc09de2ac
work_keys_str_mv	AT marcphoeppner comparativeanalysisofrnafamiliesrevealsdistinctrepertoiresforeachdomainoflife AT paulpgardner comparativeanalysisofrnafamiliesrevealsdistinctrepertoiresforeachdomainoflife AT anthonympoole comparativeanalysisofrnafamiliesrevealsdistinctrepertoiresforeachdomainoflife
_version_	1718424752258809856

Comparative analysis of RNA families reveals distinct repertoires for each domain of life.

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