Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.

<h4>Background</h4>In yeast coding sequences, once a particular codon has been used, subsequent occurrence of the same amino acid tends to use codons sharing the same tRNA. Such a phenomenon of co-tRNA codons pairing bias (CTCPB) is also found in some other eukaryotes but it is not known...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Zhu-Qing Shao, Yan-Mei Zhang, Xue-Ying Feng, Bin Wang, Jian-Qun Chen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/27f3608d1be7417fb7b57b1dc919dd4e
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:27f3608d1be7417fb7b57b1dc919dd4e
record_format	dspace
spelling	oai:doaj.org-article:27f3608d1be7417fb7b57b1dc919dd4e2021-11-18T07:25:08ZSynonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.1932-620310.1371/journal.pone.0033547https://doaj.org/article/27f3608d1be7417fb7b57b1dc919dd4e2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22432034/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>In yeast coding sequences, once a particular codon has been used, subsequent occurrence of the same amino acid tends to use codons sharing the same tRNA. Such a phenomenon of co-tRNA codons pairing bias (CTCPB) is also found in some other eukaryotes but it is not known whether it occurs in prokaryotes.<h4>Methodology/principal findings</h4>In this study, we focused on a total of 773 bacterial genomes to investigate their synonymous codon pairing preferences. After calculating the actual frequencies of synonymous codon pairs and comparing them with their expected values, we detected an obvious pairing bias towards identical codon pairs. This seems consistent with the previously reported CTCPB phenomenon, since identical codons are certainly read by the same tRNA. However, among co-tRNA but non-identical codon pairs, only 22 were often found overrepresented, suggesting that many co-tRNA codons actually do not preferentially pair together in prokaryotes. Therefore, the previously reported co-tRNA codons pairing rule needs to be more rigorously defined. The affinity differences between a tRNA anticodon and its readable codons should be taken into account. Moreover, both within-gene-shuffling tests and phylogenetic analyses support the idea that translational selection played an important role in shaping the observed synonymous codon pairing pattern in prokaryotes.<h4>Conclusions</h4>Overall, a high level of synonymous codon pairing bias was detected in 73% investigated bacterial species, suggesting the synonymous codon ordering strategy has been prevalently adopted by prokaryotes to improve their translational efficiencies. The findings in this study also provide important clues to better understand the complex dynamics of translational process.Zhu-Qing ShaoYan-Mei ZhangXue-Ying FengBin WangJian-Qun ChenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 3, p e33547 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zhu-Qing Shao Yan-Mei Zhang Xue-Ying Feng Bin Wang Jian-Qun Chen Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.
description	<h4>Background</h4>In yeast coding sequences, once a particular codon has been used, subsequent occurrence of the same amino acid tends to use codons sharing the same tRNA. Such a phenomenon of co-tRNA codons pairing bias (CTCPB) is also found in some other eukaryotes but it is not known whether it occurs in prokaryotes.<h4>Methodology/principal findings</h4>In this study, we focused on a total of 773 bacterial genomes to investigate their synonymous codon pairing preferences. After calculating the actual frequencies of synonymous codon pairs and comparing them with their expected values, we detected an obvious pairing bias towards identical codon pairs. This seems consistent with the previously reported CTCPB phenomenon, since identical codons are certainly read by the same tRNA. However, among co-tRNA but non-identical codon pairs, only 22 were often found overrepresented, suggesting that many co-tRNA codons actually do not preferentially pair together in prokaryotes. Therefore, the previously reported co-tRNA codons pairing rule needs to be more rigorously defined. The affinity differences between a tRNA anticodon and its readable codons should be taken into account. Moreover, both within-gene-shuffling tests and phylogenetic analyses support the idea that translational selection played an important role in shaping the observed synonymous codon pairing pattern in prokaryotes.<h4>Conclusions</h4>Overall, a high level of synonymous codon pairing bias was detected in 73% investigated bacterial species, suggesting the synonymous codon ordering strategy has been prevalently adopted by prokaryotes to improve their translational efficiencies. The findings in this study also provide important clues to better understand the complex dynamics of translational process.
format	article
author	Zhu-Qing Shao Yan-Mei Zhang Xue-Ying Feng Bin Wang Jian-Qun Chen
author_facet	Zhu-Qing Shao Yan-Mei Zhang Xue-Ying Feng Bin Wang Jian-Qun Chen
author_sort	Zhu-Qing Shao
title	Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.
title_short	Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.
title_full	Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.
title_fullStr	Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.
title_full_unstemmed	Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.
title_sort	synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/27f3608d1be7417fb7b57b1dc919dd4e
work_keys_str_mv	AT zhuqingshao synonymouscodonorderingasubtlebutprevalentstrategyofbacteriatoimprovetranslationalefficiency AT yanmeizhang synonymouscodonorderingasubtlebutprevalentstrategyofbacteriatoimprovetranslationalefficiency AT xueyingfeng synonymouscodonorderingasubtlebutprevalentstrategyofbacteriatoimprovetranslationalefficiency AT binwang synonymouscodonorderingasubtlebutprevalentstrategyofbacteriatoimprovetranslationalefficiency AT jianqunchen synonymouscodonorderingasubtlebutprevalentstrategyofbacteriatoimprovetranslationalefficiency
_version_	1718423463785398272

Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.

Ejemplares similares