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In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership

Aminoacyl tRNA synthetases (aaRS) are grouped into Class I and II based on primary and tertiary structure and enzyme properties suggesting two independent phylogenetic lineages. Analogously, tRNA molecules can also form two respective classes, based on the class membership of their corresponding aaR...

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Detalles Bibliográficos
Autores principales: Jakó, Éena, Ittzés, Péter, Szenes, Áron, Kun, Ádám, Szathmáry, Eörs, Pál, Gábor
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2018626/
https://www.ncbi.nlm.nih.gov/pubmed/17704131
http://dx.doi.org/10.1093/nar/gkm598
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author Jakó, Éena
Ittzés, Péter
Szenes, Áron
Kun, Ádám
Szathmáry, Eörs
Pál, Gábor
author_facet Jakó, Éena
Ittzés, Péter
Szenes, Áron
Kun, Ádám
Szathmáry, Eörs
Pál, Gábor
author_sort Jakó, Éena
collection PubMed
description Aminoacyl tRNA synthetases (aaRS) are grouped into Class I and II based on primary and tertiary structure and enzyme properties suggesting two independent phylogenetic lineages. Analogously, tRNA molecules can also form two respective classes, based on the class membership of their corresponding aaRS. Although some aaRS–tRNA interactions are not extremely specific and require editing mechanisms to avoid misaminoacylation, most aaRS–tRNA interactions are rather stereospecific. Thus, class-specific aaRS features could be mirrored by class-specific tRNA features. However, previous investigations failed to detect conserved class-specific nucleotides. Here we introduce a discrete mathematical approach that evaluates not only class-specific ‘strictly present’, but also ‘strictly absent’ nucleotides. The disjoint subsets of these elements compose a unique partition, named extended consensus partition (ECP). By analyzing the ECP for both Class I and II tDNA sets from 50 (13 archaeal, 30 bacterial and 7 eukaryotic) species, we could demonstrate that class-specific tRNA sequence features do exist, although not in terms of strictly conserved nucleotides as it had previously been anticipated. This finding demonstrates that important information was hidden in tRNA sequences inaccessible for traditional statistical methods. The ECP analysis might contribute to the understanding of tRNA evolution and could enrich the sequence analysis tool repertoire.
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spelling pubmed-20186262007-10-23 In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership Jakó, Éena Ittzés, Péter Szenes, Áron Kun, Ádám Szathmáry, Eörs Pál, Gábor Nucleic Acids Res RNA Aminoacyl tRNA synthetases (aaRS) are grouped into Class I and II based on primary and tertiary structure and enzyme properties suggesting two independent phylogenetic lineages. Analogously, tRNA molecules can also form two respective classes, based on the class membership of their corresponding aaRS. Although some aaRS–tRNA interactions are not extremely specific and require editing mechanisms to avoid misaminoacylation, most aaRS–tRNA interactions are rather stereospecific. Thus, class-specific aaRS features could be mirrored by class-specific tRNA features. However, previous investigations failed to detect conserved class-specific nucleotides. Here we introduce a discrete mathematical approach that evaluates not only class-specific ‘strictly present’, but also ‘strictly absent’ nucleotides. The disjoint subsets of these elements compose a unique partition, named extended consensus partition (ECP). By analyzing the ECP for both Class I and II tDNA sets from 50 (13 archaeal, 30 bacterial and 7 eukaryotic) species, we could demonstrate that class-specific tRNA sequence features do exist, although not in terms of strictly conserved nucleotides as it had previously been anticipated. This finding demonstrates that important information was hidden in tRNA sequences inaccessible for traditional statistical methods. The ECP analysis might contribute to the understanding of tRNA evolution and could enrich the sequence analysis tool repertoire. Oxford University Press 2007-08 2007-08-17 /pmc/articles/PMC2018626/ /pubmed/17704131 http://dx.doi.org/10.1093/nar/gkm598 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
Jakó, Éena
Ittzés, Péter
Szenes, Áron
Kun, Ádám
Szathmáry, Eörs
Pál, Gábor
In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership
title In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership
title_full In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership
title_fullStr In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership
title_full_unstemmed In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership
title_short In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership
title_sort in silico detection of trna sequence features characteristic to aminoacyl-trna synthetase class membership
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2018626/
https://www.ncbi.nlm.nih.gov/pubmed/17704131
http://dx.doi.org/10.1093/nar/gkm598
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