Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.

<h4>Background</h4>Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA) for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick base pairing between two nucleotides in RNA molecu...

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Autores principales:	Miguel M Fonseca, Sara Rocha, David Posada
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0f8aed815bea4e7ea2ce2cb81c2675b0
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spelling	oai:doaj.org-article:0f8aed815bea4e7ea2ce2cb81c2675b02021-11-18T07:19:16ZBase-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.1932-620310.1371/journal.pone.0036605https://doaj.org/article/0f8aed815bea4e7ea2ce2cb81c2675b02012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22590575/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA) for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick base pairing between two nucleotides in RNA molecules) to recognize one or more synonymous codons. Different hypotheses have been proposed to explain the factors that determine the nucleotide composition of wobble sites in vertebrate mitochondrial tRNA anticodons. Until now, the two major postulates--the "codon-anticodon adaptation hypothesis" and the "wobble versatility hypothesis"--have not been formally tested in vertebrate mitochondria because both make the same predictions regarding the composition of anticodon wobble sites. The same is true for the more recent "wobble cost hypothesis".<h4>Principal findings</h4>In this study we have analyzed the occurrence of synonymous codons and tRNA anticodon wobble sites in 1553 complete vertebrate mitochondrial genomes, focusing on three fish species with mtDNA codon usage bias reversal (L-strand is GT-rich). These mitogenomes constitute an excellent opportunity to study the evolution of the wobble nucleotide composition of tRNA anticodons because due to the reversal the predictions for the anticodon wobble sites differ between the existing hypotheses. We observed that none of the wobble sites of tRNA anticodons in these unusual mitochondrial genomes coevolved to match the new overall codon usage bias, suggesting that nucleotides at the wobble sites of tRNA anticodons in vertebrate mitochondrial genomes are determined by wobble versatility.<h4>Conclusions/significance</h4>Our results suggest that, at wobble sites of tRNA anticodons in vertebrate mitogenomes, selection favors the most versatile nucleotide in terms of wobble base-pairing stability and that wobble site composition is not influenced by codon usage. These results are in agreement with the "wobble versatility hypothesis".Miguel M FonsecaSara RochaDavid PosadaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 5, p e36605 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Miguel M Fonseca Sara Rocha David Posada Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.
description	<h4>Background</h4>Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA) for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick base pairing between two nucleotides in RNA molecules) to recognize one or more synonymous codons. Different hypotheses have been proposed to explain the factors that determine the nucleotide composition of wobble sites in vertebrate mitochondrial tRNA anticodons. Until now, the two major postulates--the "codon-anticodon adaptation hypothesis" and the "wobble versatility hypothesis"--have not been formally tested in vertebrate mitochondria because both make the same predictions regarding the composition of anticodon wobble sites. The same is true for the more recent "wobble cost hypothesis".<h4>Principal findings</h4>In this study we have analyzed the occurrence of synonymous codons and tRNA anticodon wobble sites in 1553 complete vertebrate mitochondrial genomes, focusing on three fish species with mtDNA codon usage bias reversal (L-strand is GT-rich). These mitogenomes constitute an excellent opportunity to study the evolution of the wobble nucleotide composition of tRNA anticodons because due to the reversal the predictions for the anticodon wobble sites differ between the existing hypotheses. We observed that none of the wobble sites of tRNA anticodons in these unusual mitochondrial genomes coevolved to match the new overall codon usage bias, suggesting that nucleotides at the wobble sites of tRNA anticodons in vertebrate mitochondrial genomes are determined by wobble versatility.<h4>Conclusions/significance</h4>Our results suggest that, at wobble sites of tRNA anticodons in vertebrate mitogenomes, selection favors the most versatile nucleotide in terms of wobble base-pairing stability and that wobble site composition is not influenced by codon usage. These results are in agreement with the "wobble versatility hypothesis".
format	article
author	Miguel M Fonseca Sara Rocha David Posada
author_facet	Miguel M Fonseca Sara Rocha David Posada
author_sort	Miguel M Fonseca
title	Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.
title_short	Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.
title_full	Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.
title_fullStr	Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.
title_full_unstemmed	Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.
title_sort	base-pairing versatility determines wobble sites in trna anticodons of vertebrate mitogenomes.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/0f8aed815bea4e7ea2ce2cb81c2675b0
work_keys_str_mv	AT miguelmfonseca basepairingversatilitydetermineswobblesitesintrnaanticodonsofvertebratemitogenomes AT sararocha basepairingversatilitydetermineswobblesitesintrnaanticodonsofvertebratemitogenomes AT davidposada basepairingversatilitydetermineswobblesitesintrnaanticodonsofvertebratemitogenomes
_version_	1718423579637317632

Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.

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