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TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA sythetase
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
2006 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 34, no 3, 893-904 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2006. Vol. 34, no 3, 893-904 p.
Keyword [en]
Alphaproteobacteria/classification/enzymology/*genetics, DNA; Bacterial/classification, Databases; Nucleic Acid, Evolution; Molecular, Gene Transfer; Horizontal, Genome; Bacterial, Genomics, Histidine-tRNA Ligase/classification/*genetics, Models; Statistical, Phylogeny, RNA; Transfer/classification/genetics, RNA; Transfer; His/chemistry/classification/*genetics, RNA; Transfer; Met/classification, Research Support; Non-U.S. Gov't, Research Support; U.S. Gov't; Non-P.H.S., Variation (Genetics)
National Category
Biological Sciences Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:uu:diva-77112DOI: 10.1093/nar/gkj449PubMedID: 16473847OAI: oai:DiVA.org:uu-77112DiVA: diva2:105024
Available from: 2006-04-04 Created: 2006-04-04 Last updated: 2017-12-14Bibliographically approved

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