A computational screen for alternative genetic codes in over 250,000 genomes

The genetic code has been proposed to be a ‘frozen accident,’ but the discovery of alternative genetic codes over the past four decades has shown that it can evolve to some degree. Since most examples were found anecdotally, it is difficult to draw general conclusions about the evolutionary trajecto...

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Autores principales:	Yekaterina Shulgina, Sean R Eddy
Formato:	article
Lenguaje:	EN
Publicado:	eLife Sciences Publications Ltd 2021
Materias:	genetic code codon reassignment tRNA codetta Medicine R Science Q Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/7ee984b127284ab394a1bc64f8d7cb99
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id	oai:doaj.org-article:7ee984b127284ab394a1bc64f8d7cb99
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spelling	oai:doaj.org-article:7ee984b127284ab394a1bc64f8d7cb992021-12-02T16:32:56ZA computational screen for alternative genetic codes in over 250,000 genomes10.7554/eLife.714022050-084Xe71402https://doaj.org/article/7ee984b127284ab394a1bc64f8d7cb992021-11-01T00:00:00Zhttps://elifesciences.org/articles/71402https://doaj.org/toc/2050-084XThe genetic code has been proposed to be a ‘frozen accident,’ but the discovery of alternative genetic codes over the past four decades has shown that it can evolve to some degree. Since most examples were found anecdotally, it is difficult to draw general conclusions about the evolutionary trajectories of codon reassignment and why some codons are affected more frequently. To fill in the diversity of genetic codes, we developed Codetta, a computational method to predict the amino acid decoding of each codon from nucleotide sequence data. We surveyed the genetic code usage of over 250,000 bacterial and archaeal genome sequences in GenBank and discovered five new reassignments of arginine codons (AGG, CGA, and CGG), representing the first sense codon changes in bacteria. In a clade of uncultivated Bacilli, the reassignment of AGG to become the dominant methionine codon likely evolved by a change in the amino acid charging of an arginine tRNA. The reassignments of CGA and/or CGG were found in genomes with low GC content, an evolutionary force that likely helped drive these codons to low frequency and enable their reassignment.Yekaterina ShulginaSean R EddyeLife Sciences Publications Ltdarticlegenetic codecodon reassignmenttRNAcodettaMedicineRScienceQBiology (General)QH301-705.5ENeLife, Vol 10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	genetic code codon reassignment tRNA codetta Medicine R Science Q Biology (General) QH301-705.5
spellingShingle	genetic code codon reassignment tRNA codetta Medicine R Science Q Biology (General) QH301-705.5 Yekaterina Shulgina Sean R Eddy A computational screen for alternative genetic codes in over 250,000 genomes
description	The genetic code has been proposed to be a ‘frozen accident,’ but the discovery of alternative genetic codes over the past four decades has shown that it can evolve to some degree. Since most examples were found anecdotally, it is difficult to draw general conclusions about the evolutionary trajectories of codon reassignment and why some codons are affected more frequently. To fill in the diversity of genetic codes, we developed Codetta, a computational method to predict the amino acid decoding of each codon from nucleotide sequence data. We surveyed the genetic code usage of over 250,000 bacterial and archaeal genome sequences in GenBank and discovered five new reassignments of arginine codons (AGG, CGA, and CGG), representing the first sense codon changes in bacteria. In a clade of uncultivated Bacilli, the reassignment of AGG to become the dominant methionine codon likely evolved by a change in the amino acid charging of an arginine tRNA. The reassignments of CGA and/or CGG were found in genomes with low GC content, an evolutionary force that likely helped drive these codons to low frequency and enable their reassignment.
format	article
author	Yekaterina Shulgina Sean R Eddy
author_facet	Yekaterina Shulgina Sean R Eddy
author_sort	Yekaterina Shulgina
title	A computational screen for alternative genetic codes in over 250,000 genomes
title_short	A computational screen for alternative genetic codes in over 250,000 genomes
title_full	A computational screen for alternative genetic codes in over 250,000 genomes
title_fullStr	A computational screen for alternative genetic codes in over 250,000 genomes
title_full_unstemmed	A computational screen for alternative genetic codes in over 250,000 genomes
title_sort	computational screen for alternative genetic codes in over 250,000 genomes
publisher	eLife Sciences Publications Ltd
publishDate	2021
url	https://doaj.org/article/7ee984b127284ab394a1bc64f8d7cb99
work_keys_str_mv	AT yekaterinashulgina acomputationalscreenforalternativegeneticcodesinover250000genomes AT seanreddy acomputationalscreenforalternativegeneticcodesinover250000genomes AT yekaterinashulgina computationalscreenforalternativegeneticcodesinover250000genomes AT seanreddy computationalscreenforalternativegeneticcodesinover250000genomes
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A computational screen for alternative genetic codes in over 250,000 genomes

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