Convergence and minimal mutation criteria for evaluating early events in tRNA evolution.

Cedergren, Robert; Larue, Bernard; Sankoff, David; Lapalme, Guy; Grosjean, Henri

doi:10.1073/pnas.77.5.2791

Cited by 42 publications

(26 citation statements)

References 24 publications

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“…Early on, phylogenetic studies of E. coli and Haemophilus influenzae tRNA gene sequences hinted that the isoacceptors in some amino acid families may have diverged during the course of evolution (Squires and Carbon 1971;Cedergren et al 1980;Fitch and Upper 1987;Staves et al 1987Staves et al , 1988Saks et al 1998). However, the significance of these observations was unclear because a full complement of tRNA gene sequences was available for only a limited number of species.…”

Section: Discussionmentioning

confidence: 99%

Anticodon-dependent conservation of bacterial tRNA gene sequences

Saks

Conery²

2007

RNA

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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.

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Section: Discussionmentioning

confidence: 99%

Anticodon-dependent conservation of bacterial tRNA gene sequences

Saks

Conery²

2007

RNA

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“…The various sub-trees of metazoa, protozoa, mycophyta, plants, Gram-negative and Gram-positive bacteria were constructed stepwise and separately by using similar criteria as described for constructing tRNA trees (18), and considering biologically supported affinities, previous 5S tree data (13,14) and tree data derived from RNase T1 catalogues of bacterial 16S rRNAs (19).…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic tree derived from bacterial, cytosol and organelle 5S rRNA sequences

1981

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ABSTACTA phylogenetic tree was constructed by computer analysis of 47 completely determined 5S rRNA sequences. The wheat mitochondrial sequence is significantly more related to prokaryotic than to eukaryotic sequences, and its affinity to that of the thermophilic Gram-negative bacterium Thermus aquaticus is comparable to the affinity between Anacystis nidulans and chloroplastic sequences. This strongly supports the idea of an endosymbiotic origin of plant mitochondria.A comparison of the plant cytosol and chloroplast sub-trees suggests a similar rate of nucleotide substitution in nuclear genes and chloroplastic genes. Other features of the tree are a common precursor of protozoa and metazoa, which appears to be more related to the fungal than to the plant protosequence, and an early divergence of the archebacterial sequence (Halobacterium cutirubrum) from the prokaryotic branch.

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“…Despite interest in tRNA phylogeny as a source of information about the evolution of the genetic code (Eigen and Winkler-Oswatitsch 1981a,b;Fitch and Upper 1987;Eigen et al 1989;Di Giulio 1994, 1995, 1999, 2006, and, although tRNAs were among the first nucleic acid sequences to be used for phylogenetic reconstruction (Cedergren et al 1980;Sankoff et al 1982), the phylogenetic trees obtained from tRNAs are often radically different from the trees relating the species. tRNAs are now considered especially poor candidates for phylogenetic studies for several reasons.…”

Section: Introductionmentioning

confidence: 99%

Stable tRNA-based phylogenies using only 76 nucleotides

Widmann

Harris²,

Lozupone³

et al. 2010

RNA

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tRNAs are among the most ancient, highly conserved sequences on earth, but are often thought to be poor phylogenetic markers because they are short, often subject to horizontal gene transfer, and easily change specificity. Here we use an algorithm now commonly used in microbial ecology, UniFrac, to cluster 175 genomes spanning all three domains of life based on the phylogenetic relationships among their complete tRNA pools. We find that the overall pattern of similarities and differences in the tRNA pools recaptures universal phylogeny to a remarkable extent, and that the resulting tree is similar to the distribution of bootstrapped rRNA trees from the same genomes. In contrast, the trees derived from tRNAs of identical specificity or of individual isoacceptors generally produced trees of lower quality. However, some tRNA isoacceptors were very good predictors of the overall pattern of organismal evolution. These results show that UniFrac can extract meaningful biological patterns from even phylogenies with high level of statistical inaccuracy and horizontal gene transfer, and that, overall, the pattern of tRNA evolution tracks universal phylogeny and provides a background against which we can test hypotheses about the evolution of individual isoacceptors.

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Convergence and minimal mutation criteria for evaluating early events in tRNA evolution.

Cited by 42 publications

References 24 publications

Anticodon-dependent conservation of bacterial tRNA gene sequences

Anticodon-dependent conservation of bacterial tRNA gene sequences

Phylogenetic tree derived from bacterial, cytosol and organelle 5S rRNA sequences

Stable tRNA-based phylogenies using only 76 nucleotides

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