ArticleJournal of molecular evolution2007
Signature of a primitive genetic code in ancient protein lineages.
Article in Journal of molecular evolution, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- The Role of Mutations, Addition of Amino Acids, and Exchange of Genetic Information in the Coevolution of Primitive Coding Systems.International journal of molecular sciences · 2025Article
- Order of amino acid recruitment into the genetic code resolved by last universal common ancestor's protein domains.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor's protein domains.bioRxiv : the preprint server for biology · 2024Article
- On the Nature of the Last Common Ancestor: A Story from its Translation Machinery.Journal of molecular evolution · 2024Review
- Clues to tRNA Evolution from the Distribution of Class II tRNAs and Serine Codons in the Genetic Code.Life (Basel, Switzerland) · 2016Article
- Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code.Journal of molecular evolution · 2015Article
- Genetic code evolution started with the incorporation of glycine, followed by other small hydrophilic amino acids.Journal of molecular evolution · 2014Article
- Experimental evolution of a green fluorescent protein composed of 19 unique amino acids without tryptophan.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2014Article
- The molecular signal for the adaptation to cold temperature during early life on Earth.Biology letters · 2013Article
- Inferring the ancient history of the translation machinery and genetic code via recapitulation of ribosomal subunit assembly orders.PloS one · 2010Article
- Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code.PloS one · 2008Article
- Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses.PLoS computational biology · 2008Article
- Transfer RNA and the origins of diversified life.Science progress · 2008Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genetic code is the syntactic foundation underlying the structure and function of every protein in the history of the biological world. Its highly ordered degenerate complexity suggests an incremental evolution, the result of a combination of selective, mechanistic, and random processes. These evolutionary processes are still poorly understood and remain an open question in the study of early life on Earth. We perform a compositional analysis of ribosomal proteins and ATPase subunits in bacterial and archaeal lineages, using conserved positions that came and remained under purifying selection before and up to the most recent common ancestor. An observable shift in amino acid usage at these conserved positions likely provides an untapped window into the history of protein sequence space, allowing events of genetic code expansion to be identified. We identify Cys, Glu, Phe, Ile, Lys, Val, Trp, and Tyr as recent additions to the genetic code, with Asn, Gln, Gly, and Leu among the more ancient. Our observations are consistent with a scenario in which genetic code expansion primarily favored amino acids that promoted an increase in polypeptide size and functionality. We propose that this expansion would have been critical in the takeover of many RNA-mediated processes, as well as the addition of novel biological functions inaccessible to an RNA-based physiology, such as crossing lipid membranes. Thus, expansion of the genetic code likely set the stage for the transition from RNA-based to protein-based life.
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