ArticlePloS one2013
Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 72 citations in OpenAlex.
- 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
- Traces of a Primitive RNA Ring in Current Genomes.Biology · 2025Article
- Tracing the birth and intrinsic disorder of loops and domains in protein evolution.Biophysical reviews · 2024Review
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction.Life (Basel, Switzerland) · 2024Review
- Tracing the birth of structural domains from loops during protein evolution.Scientific reports · 2023Article
- Screening for Primordial RNA-Peptide Interactions Using High-Density Peptide Arrays.Life (Basel, Switzerland) · 2023Article
- Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-Modular Coupling.International journal of molecular sciences · 2022Article
- Structural Computational Analysis of the Natural History of Class I aminoacyl-tRNA Synthetases Suggests their Role in Establishing the Genetic Code.Journal of molecular evolution · 2021Article
- The Combinatorial Fusion Cascade to Generate the Standard Genetic Code.Life (Basel, Switzerland) · 2021Article
- Evolution of networks of protein domain organization.Scientific reports · 2021Article
- Menzerath-Altmann's Law of Syntax in RNA Accretion History.Life (Basel, Switzerland) · 2021Article
- The Compressed Vocabulary of Microbial Life.Frontiers in microbiology · 2021Article
- The Ancient Operational Code is Embedded in the Amino Acid Substitution Matrix and aaRS Phylogenies.Journal of molecular evolution · 2020Article
- Review
- Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis.Evolutionary bioinformatics online · 2019Review
- Evolution of macromolecular structure: a 'double tale' of biological accretion and diversification.Science progress · 2018Review
- Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding.Molecular biology and evolution · 2018Article
- Rooted tRNAomes and evolution of the genetic code.Transcription · 2018Article
- Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes.Frontiers in microbiology · 2018Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.