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Nucleic Acids Research 2006 34(3):893-904; doi:10.1093/nar/gkj449
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Published online 9 February 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase

David H. Ardell* and Siv G. E. Andersson

Department of Molecular Evolution, Evolutionary Biology Center Norbyvägen 18C Uppsala University SE-752 36 Uppsala Sweden

*To whom correspondence should be addressed at David Ardell, Linnaeus Center for Bioinformatics, Biomedical Center, Box 598, SE-751 24 Uppsala Sweden. Tel: +46 18 471 66 94; Fax: +46 18 471 66 98; Email: dave.ardell{at}lcb.uu.se

Received November 21, 2005. Revised December 23, 2005. Accepted January 3, 2006.

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 tRNAHis 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 tDNAHis 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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