Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.

The genetic code shapes the genetic repository. Its origin has puzzled molecular scientists for over half a century and remains a long-standing mystery. Here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-tRNA synthetase enzymes and their interactions with...

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Main Authors:	Gustavo Caetano-Anollés, Minglei Wang, Derek Caetano-Anollés
Format:	article
Language:	EN
Published:	Public Library of Science (PLoS) 2013
Subjects:	Medicine R Science Q
Online Access:	https://doaj.org/article/b20d4aa6222746e194071a9541effddd
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spelling	oai:doaj.org-article:b20d4aa6222746e194071a9541effddd2021-11-18T08:58:34ZStructural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.1932-620310.1371/journal.pone.0072225https://doaj.org/article/b20d4aa6222746e194071a9541effddd2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23991065/?tool=EBIhttps://doaj.org/toc/1932-6203The genetic code shapes the genetic repository. Its origin has puzzled molecular scientists for over half a century and remains a long-standing mystery. Here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-tRNA synthetase enzymes and their interactions with tRNA. A timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the 'operational' RNA code and the late implementation of the standard genetic code. The emergence of codon specificities and amino acid charging involved tight coevolution of aminoacyl-tRNA synthetases and tRNA structures as well as episodes of structural recruitment. Remarkably, amino acid and dipeptide compositions of single-domain proteins appearing before the standard code suggest archaic synthetases with structures homologous to catalytic domains of tyrosyl-tRNA and seryl-tRNA synthetases were capable of peptide bond formation and aminoacylation. Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness were likely internalized into the emerging genetic system with the early rise of modern protein structure.Gustavo Caetano-AnollésMinglei WangDerek Caetano-AnollésPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 8, p e72225 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gustavo Caetano-Anollés Minglei Wang Derek Caetano-Anollés Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.
description	The genetic code shapes the genetic repository. Its origin has puzzled molecular scientists for over half a century and remains a long-standing mystery. Here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-tRNA synthetase enzymes and their interactions with tRNA. A timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the 'operational' RNA code and the late implementation of the standard genetic code. The emergence of codon specificities and amino acid charging involved tight coevolution of aminoacyl-tRNA synthetases and tRNA structures as well as episodes of structural recruitment. Remarkably, amino acid and dipeptide compositions of single-domain proteins appearing before the standard code suggest archaic synthetases with structures homologous to catalytic domains of tyrosyl-tRNA and seryl-tRNA synthetases were capable of peptide bond formation and aminoacylation. Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness were likely internalized into the emerging genetic system with the early rise of modern protein structure.
format	article
author	Gustavo Caetano-Anollés Minglei Wang Derek Caetano-Anollés
author_facet	Gustavo Caetano-Anollés Minglei Wang Derek Caetano-Anollés
author_sort	Gustavo Caetano-Anollés
title	Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.
title_short	Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.
title_full	Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.
title_fullStr	Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.
title_full_unstemmed	Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.
title_sort	structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/b20d4aa6222746e194071a9541effddd
work_keys_str_mv	AT gustavocaetanoanolles structuralphylogenomicsretrodictstheoriginofthegeneticcodeanduncoverstheevolutionaryimpactofproteinflexibility AT mingleiwang structuralphylogenomicsretrodictstheoriginofthegeneticcodeanduncoverstheevolutionaryimpactofproteinflexibility AT derekcaetanoanolles structuralphylogenomicsretrodictstheoriginofthegeneticcodeanduncoverstheevolutionaryimpactofproteinflexibility
_version_	1718421103979790336

Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.

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