Mosaic tile model for tRNA-enzyme recognition

Steinberg, Sergey V.; Kisselev, Lev L.

doi:10.1093/nar/21.8.1941

Cited by 9 publications

(2 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To test these and other hypotheses we need an automated, statistical and systematic approach to analyzing tRNA identity rules over many species. The first bioinformatic approaches to tRNA identity rules were implemented for Escherichia coli , Salmonella typhimurium ( 19 , 20 ) and yeast ( 21 ), but were not fully probabilistic and limited by the available data. More recently, Marck and Grosjean ( 22 ) comprehensively compared tDNA sequences from sequenced genomes.…”

Section: Introductionmentioning

confidence: 99%

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

Ardell

2006

Nucleic Acids Research

View full text Add to dashboard Cite

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 α-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 α-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 α-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.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Ardell

2006

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Bioinformatics studies of these sorts of molecules can be misleading if the genes are grouped in a manner that reveals variation that would otherwise be explained by a different grouping parameter. Several bioinformatics studies of tRNA have appeared (McClain and Nicholas 1987;Steinberg and Kisselev 1993;Marck and Grosjean 2002;Ardell and Andersson 2006). Most of these studies have focused on the determinants of tRNA amino acid identity.…”

Section: Introductionmentioning

confidence: 99%

Anticodon-dependent conservation of bacterial tRNA gene sequences

Saks

Conery²

2007

RNA

View full text Add to dashboard Cite

The residues in tRNA that account for its tertiary fold and for its specific aminoacylation are well understood. In contrast, relatively little is known about the residues in tRNA that dictate its ability to transit the different sites of the ribosome. Yet protein synthesis cannot occur unless tRNA properly engages with the ribosome. This study analyzes tRNA gene sequences from 145 fully sequenced bacterial genomes. Grouping the sequences according to the anticodon triplet reveals that many residues in tRNA, including some that are distal to the anticodon loop, are conserved in an anticodon-dependent manner. These residues evade detection when tRNA genes are grouped according to amino acid family. The conserved residues include those at positions 32, 38, and 37 of the anticodon loop, which are already known to influence tRNA translational performance. Therefore, it seems likely that the newly detected anticodon-associated residues also influence tRNA performance on the ribosome. Remarkably, tRNA genes that belong to the same amino acid family and therefore share identical residues at the second and third anticodon positions have diverged, during bacterial evolution, into highly conserved groups that are defined by the residue at the first (wobble) anticodon position. Current ideas about the properties of tRNA and the translation mechanism do not fully account for this phenomenon. The results of the present study provide a foundation for studying the adaptation of individual tRNAs to the translation machinery and for future studies of the translation mechanism.

show abstract