ArticleNucleic acids research2018
Hierarchical groove discrimination by Class I and II aminoacyl-tRNA synthetases reveals a palimpsest of the operational RNA code in the tRNA acceptor-stem bases.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed.
- Structural Enzymology, Phylogenetics, Differentiation, and Symbolic Reflexivity at the Dawn of Biology.Genome biology and evolution · 2025Article
- The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery.Nucleic acids research · 2025Article
- A genomic database furnishes minimal functional glycyl-tRNA synthetases homologous to other, designed class II urzymes.Nucleic acids research · 2024Article
- Primordial aminoacyl-tRNA synthetases preferred minihelices to full-length tRNA.Nucleic acids research · 2024Article
- Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction.Life (Basel, Switzerland) · 2024Review
- Enzymic recognition of amino acids drove the evolution of primordial genetic codes.Nucleic acids research · 2024Article
- Genomic database furnishes a spontaneous example of a functional Class II glycyl-tRNA synthetase urzyme.bioRxiv : the preprint server for biology · 2024Article
- Origins of Genetic Coding: Self-Guided Molecular Self-Organisation.Entropy (Basel, Switzerland) · 2023Article
- Domain acquisition by class I aminoacyl-tRNA synthetase urzymes coordinated the catalytic functions of HVGH and KMSKS motifs.Nucleic acids research · 2023Article
- Biophysical Interactions Underpin the Emergence of Information in the Genetic Code.Life (Basel, Switzerland) · 2023Article
- Screening for Primordial RNA-Peptide Interactions Using High-Density Peptide Arrays.Life (Basel, Switzerland) · 2023Article
- The binding mode of orphan glycyl-tRNA synthetase with tRNA supports the synthetase classification and reveals large domain movements.Science advances · 2023Article
- A Leucyl-tRNA Synthetase Urzyme: Authenticity of tRNA Synthetase Catalytic Activities and Promiscuous Phosphorylation of Leucyl-5'AMP.International journal of molecular sciences · 2022Article
- X-shaped structure of bacterial heterotetrameric tRNA synthetase suggests cryptic prokaryote functions and a rationale for synthetase classifications.Nucleic acids research · 2021Article
- The Combinatorial Fusion Cascade to Generate the Standard Genetic Code.Life (Basel, Switzerland) · 2021Article
- Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis.Biomolecules · 2021Review
- Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.RNA (New York, N.Y.) · 2020Article
- Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding.International journal of molecular sciences · 2020Article
- Breaking a single hydrogen bond in the mitochondrial tRNAThe FEBS journal · 2020Article
- G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases.Journal of molecular evolution · 2020Article
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Abstract
Class I and II aaRS recognition of opposite grooves was likely among the earliest determinants fixed in the tRNA acceptor stem bases. A new regression model identifies those determinants in bacterial tRNAs. Integral coefficients relate digital dependent to independent variables with perfect agreement between observed and calculated grooves for all twenty isoaccepting tRNAs. Recognition is mediated by the Discriminator base 73, the first base pair, and base 2 of the acceptor stem. Subsets of these coefficients also identically compute grooves recognized by smaller numbers of aaRS. Thus, the model is hierarchical, suggesting that new rules were added to pre-existing ones as new amino acids joined the coding alphabet. A thermodynamic rationale for the simplest model implies that Class-dependent aaRS secondary structures exploited differential tendencies of the acceptor stem to form the hairpin observed in Class I aaRS•tRNA complexes, enabling the earliest groove discrimination. Curiously, groove recognition also depends explicitly on the identity of base 2 in a manner consistent with the middle bases of the codon table, confirming a hidden ancestry of codon-anticodon pairing in the acceptor stem. That, and the lack of correlation with anticodon bases support prior productive coding interaction of tRNA minihelices with proto-mRNA.
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