ArticleNucleic acids research2006
TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 67 citations in OpenAlex.
- Rewiring of Aminoacyl-tRNA Synthetase Localization and Interactions in Plants With Extensive Mitochondrial tRNA Gene Loss.Molecular biology and evolution · 2023Article
- The tRNA identity landscape for aminoacylation and beyond.Nucleic acids research · 2023Review
- Microevolution of CG23-I Hypervirulent Klebsiella pneumoniae during Recurrent Infections in a Single Patient.Microbiology spectrum · 2022Article
- tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes.Nucleic acids research · 2021Article
- Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure-Function Map.Journal of molecular evolution · 2021Article
- Rational Design of Aptamer-Tagged tRNAs.International journal of molecular sciences · 2020Article
- tRNA functional signatures classify plastids as late-branching cyanobacteria.BMC evolutionary biology · 2019Article
- Chemical footprinting and kinetic assays reveal dual functions for highly conserved eukaryotic tRNAThe Journal of biological chemistry · 2019Article
- Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes.Molecular biology and evolution · 2019Article
- Protein-only RNase P function in Escherichia coli: viability, processing defects and differences between PRORP isoenzymes.Nucleic acids research · 2017Article
- Evolutionary gain of highly divergent tRNA specificities by two isoforms of human histidyl-tRNA synthetase.Cellular and molecular life sciences : CMLS · 2017Article
- Transfer RNAs with novel cloverleaf structures.Nucleic acids research · 2017Article
- Bioinformatic Analysis Reveals Archaeal tRNALife (Basel, Switzerland) · 2017Article
- Coding of Class I and II Aminoacyl-tRNA Synthetases.Advances in experimental medicine and biology · 2017Review
- Article
- Repairing tRNA termini: News from the 3' end.RNA biology · 2016Article
- tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes.Nucleic acids research · 2016Article
- Aminoacyl-tRNA Synthetases in the Bacterial World.EcoSal Plus · 2016Review
- tRNA acceptor stem and anticodon bases form independent codes related to protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Life without post-transcriptional addition of G-1: two alternatives for tRNAHis identity in Eukarya.RNA (New York, N.Y.) · 2015Article
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present TFAM, an automated, statistical method to classify the identity of tRNAs. TFAM, currently optimized for bacteria, classifies initiator tRNAs and predicts the charging identity of both typical and atypical tRNAs such as suppressors with high confidence. We show statistical evidence for extensive variation in tRNA identity determinants among bacterial genomes due to variation in overall tDNA base content. With TFAM we have detected the first case of eukaryotic-like tRNA identity rules in bacteria. An alpha-proteobacterial clade encompassing Rhizobiales, Caulobacter crescentus and Silicibacter pomeroyi, unlike a sister clade containing the Rickettsiales, Zymomonas mobilis and Gluconobacter oxydans, uses the eukaryotic identity element A73 instead of the highly conserved prokaryotic element C73. We confirm divergence of bacterial histidylation rules by demonstrating perfect covariation of alpha-proteobacterial tRNA(His) acceptor stems and residues in the motif IIb tRNA-binding pocket of their histidyl-tRNA synthetases (HisRS). Phylogenomic analysis supports lateral transfer of a eukaryotic-like HisRS into the alpha-proteobacteria followed by in situ adaptation of the bacterial tDNA(His) and identity rule divergence. Our results demonstrate that TFAM is an effective tool for the bioinformatics, comparative genomics and evolutionary study of tRNA identity.
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