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Distribution of ADAT-Dependent Codons in the Human Transcriptome

Nucleotide modifications in the anticodons of transfer RNAs (tRNA) play a central role in translation efficiency, fidelity, and regulation of translation, but, for most of these modifications, the details of their function remain unknown. The heterodimeric adenosine deaminases acting on tRNAs (ADAT2...

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Autores principales: Rafels-Ybern, Àlbert, Attolini, Camille Stephan-Otto, Ribas de Pouplana, Lluís
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581194/
https://www.ncbi.nlm.nih.gov/pubmed/26230688
http://dx.doi.org/10.3390/ijms160817303
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author Rafels-Ybern, Àlbert
Attolini, Camille Stephan-Otto
Ribas de Pouplana, Lluís
author_facet Rafels-Ybern, Àlbert
Attolini, Camille Stephan-Otto
Ribas de Pouplana, Lluís
author_sort Rafels-Ybern, Àlbert
collection PubMed
description Nucleotide modifications in the anticodons of transfer RNAs (tRNA) play a central role in translation efficiency, fidelity, and regulation of translation, but, for most of these modifications, the details of their function remain unknown. The heterodimeric adenosine deaminases acting on tRNAs (ADAT2-ADAT3, or ADAT) are enzymes present in eukaryotes that convert adenine (A) to inosine (I) in the first anticodon base (position 34) by hydrolytic deamination. To explore the influence of ADAT activity on mammalian translation, we have characterized the human transcriptome and proteome in terms of frequency and distribution of ADAT-related codons. Eight different tRNAs can be modified by ADAT and, once modified, these tRNAs will recognize NNC, NNU and NNA codons, but not NNG codons. We find that transcripts coding for proteins highly enriched in these eight amino acids (ADAT-aa) are specifically enriched in NNC, NNU and NNA codons. We also show that the proteins most enriched in ADAT-aa are composed preferentially of threonine, alanine, proline, and serine (TAPS). We propose that the enrichment in ADAT-codons in these proteins is due to the similarities in the codons that correspond to TAPS.
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spelling pubmed-45811942015-09-28 Distribution of ADAT-Dependent Codons in the Human Transcriptome Rafels-Ybern, Àlbert Attolini, Camille Stephan-Otto Ribas de Pouplana, Lluís Int J Mol Sci Article Nucleotide modifications in the anticodons of transfer RNAs (tRNA) play a central role in translation efficiency, fidelity, and regulation of translation, but, for most of these modifications, the details of their function remain unknown. The heterodimeric adenosine deaminases acting on tRNAs (ADAT2-ADAT3, or ADAT) are enzymes present in eukaryotes that convert adenine (A) to inosine (I) in the first anticodon base (position 34) by hydrolytic deamination. To explore the influence of ADAT activity on mammalian translation, we have characterized the human transcriptome and proteome in terms of frequency and distribution of ADAT-related codons. Eight different tRNAs can be modified by ADAT and, once modified, these tRNAs will recognize NNC, NNU and NNA codons, but not NNG codons. We find that transcripts coding for proteins highly enriched in these eight amino acids (ADAT-aa) are specifically enriched in NNC, NNU and NNA codons. We also show that the proteins most enriched in ADAT-aa are composed preferentially of threonine, alanine, proline, and serine (TAPS). We propose that the enrichment in ADAT-codons in these proteins is due to the similarities in the codons that correspond to TAPS. MDPI 2015-07-29 /pmc/articles/PMC4581194/ /pubmed/26230688 http://dx.doi.org/10.3390/ijms160817303 Text en © 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Rafels-Ybern, Àlbert
Attolini, Camille Stephan-Otto
Ribas de Pouplana, Lluís
Distribution of ADAT-Dependent Codons in the Human Transcriptome
title Distribution of ADAT-Dependent Codons in the Human Transcriptome
title_full Distribution of ADAT-Dependent Codons in the Human Transcriptome
title_fullStr Distribution of ADAT-Dependent Codons in the Human Transcriptome
title_full_unstemmed Distribution of ADAT-Dependent Codons in the Human Transcriptome
title_short Distribution of ADAT-Dependent Codons in the Human Transcriptome
title_sort distribution of adat-dependent codons in the human transcriptome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581194/
https://www.ncbi.nlm.nih.gov/pubmed/26230688
http://dx.doi.org/10.3390/ijms160817303
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