Anticodon-dependent conservation of bacterial tRNA gene sequences

Saks, Margaret E.; Conery, John S.

doi:10.1261/rna.345907

Cited by 24 publications

(33 citation statements)

References 52 publications

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“…Indeed, the thermodynamic effects of T-stem tRNA mutations determined here using E. coli EF-Tu are virtually identical to those previously determined for T. thermophilus (10,15,16). However, as discussed elsewhere, the sequences of individual tRNA species vary considerably among bacteria because multiple T-stem sequences can have a similar EF-Tu affinity (16,39,40).…”

Section: Discussionsupporting

confidence: 80%

Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding

Schrader

Chapman

Uhlenbeck

2011

Proc. Natl. Acad. Sci. U.S.A.

123

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To better understand why aminoacyl-tRNAs (aa-tRNAs) have evolved to bind bacterial elongation factor Tu (EF-Tu) with uniform affinities, mutant tRNAs with differing affinities for EF-Tu were assayed for decoding on Escherichia coli ribosomes. At saturating EF-Tu concentrations, weaker-binding aa-tRNAs decode their cognate codons similarly to wild-type tRNAs. However, tighter-binding aa-tRNAs show reduced rates of peptide bond formation due to slow release from EF-Tu•GDP. Thus, the affinities of aa-tRNAs for EF-Tu are constrained to be uniform by their need to bind tightly enough to form the ternary complex but weakly enough to release from EF-Tu during decoding. Consistent with available crystal structures, the identity of the esterified amino acid and three base pairs in the T stem of tRNA combine to define the affinity of each aa-tRNA for EF-Tu, both off and on the ribosome.T he ternary complex of bacterial elongation factor Tu (EF-Tu), GTP and aminoacyl-tRNA (aa-tRNA) binds to the ribosome and participates in a multistep decoding pathway in which GTP is hydrolyzed, EF-Tu•GDP is released, and the aa-tRNA enters the ribosomal A site (1-6). Although all elongator aa-tRNAs bind EF-Tu•GTP with similar affinities (7-9), studies with misacylated tRNAs reveal that the protein shows substantial specificity for both the esterified amino acid and the tRNA body (10-12). The nearly uniform EF-Tu binding affinity observed for tRNAs acylated with their correct (cognate) amino acid occurs because the sequence of each tRNA has evolved to compensate for the variable thermodynamic contribution of the esterified amino acid. Thus, weak-binding esterified amino acids such as glycine and alanine have corresponding tRNAs that bind the protein tightly, while tight-binding amino acids such as tyrosine or glutamine have corresponding tRNAs that bind poorly. The crystal structure of Thermus aquaticus EF-Tu•GTP bound to Saccharomyces cerevisiae Phe-tRNA Phe (13) reveals that the protein primarily forms extensive interactions with the helical phosphodiester backbone of the acceptor and T stems of tRNA Phe . Recent protein (14) and tRNA (15, 16) mutagenesis experiments indicate that much of the specificity is the result of interactions made between three amino acids of EF-Tu and three adjacent base pairs in the T stem (16). Additional mutagenesis experiments indicate that the thermodynamic contribution of each of the three base pairs is independent of the others, making it possible to adjust the affinity of aa-tRNAs to EF-Tu in a predictable manner.Although a detailed structural and thermodynamic understanding of how EF-Tu achieves uniform binding with different aa-tRNAs is beginning to emerge, the underlying selective pressures that lead to uniform binding are less clear. While aa-tRNAs must bind EF-Tu tightly enough to participate in translation, the high intracellular concentration of EF-Tu (17) ensures that they do not significantly compete with one another for the protein.It therefore seems unlikely that a minimum threshold binding af...

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Section: Discussionsupporting

confidence: 80%

Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding

Schrader

Chapman

Uhlenbeck

2011

Proc. Natl. Acad. Sci. U.S.A.

123

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“…Sec-UCA, Ser-UCA, Pro-AGG, Glu-CUC, Val-UAC, and Ala-CGC all had r > 0.80 (note that A at the first position of the anticodon is typically modified to I in tRNAs). In contrast, Ser-GCU, Val-AAC, Ile-AAU, Thr-UGU, and Ala-UGC all had r < 0.70; similar variability in tRNA conservation was recently observed by Saks and Conery (2007). It is unclear why the evolutionary rate of certain isoacceptors is higher then the others.…”

Section: à6mentioning

confidence: 65%

“…It is unclear why the evolutionary rate of certain isoacceptors is higher then the others. It is unlikely that the observed variation in the evolutionary rate of the different tRNA sequences is correlated with the evolution of the corresponding aminoacyltRNA synthetases, because their recognition patterns are the same among all the isoacceptor members of tRNA family and seem to be generally well conserved, at least in bacteria (Saks and Conery 2007).…”

Section: à6mentioning

confidence: 99%

“…First, the sequences are short (the canonical tRNA sequence is 76 nucleotides [nt]), including invariant regions such as the terminal CCA and regions under strong selective pressure such as the anticodon loop and nucleotides involved in tertiary interactions. Additional pressures conserving tRNA structure may be imposed by the sequence requirements of other components of the translation machinery that interact with tRNAs: For example, conserved nucleotide patterns in bacterial tRNAs that correlate with the anticodon sequences were recently identified (Saks and Conery 2007). Second, tRNAs are often involved in horizontal gene transfer, in part because mobile elements such as prophages carrying their own tRNAs are better able to express their genes after transfer (Canchaya et al 2004), and partly because many mobile elements preferentially integrate into or near tRNA genes (Williams 2002).…”

Section: Introductionmentioning

confidence: 99%

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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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“…Bacterial tRNAs possessing the same anticodon have a characteristic set of sequence restrictions distributed throughout the molecule that distinguish them from tRNAs with different anticodons (Saks and Conery 2007;Targanski and Cherkasova 2008). These multivalent tRNA consensus sequences reflect evolutionary adaptations that permit each tRNA to function with its particular combination of amino acid and anticodon without compromising translational rate and accuracy.…”

Section: Introductionmentioning

confidence: 99%

tRNA residues evolved to promote translational accuracy

Shepotinovskaya

Uhlenbeck

2013

RNA

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The decoding properties of 22 structurally conservative base-pair and base-triple mutations in the anticodon hairpin and tertiary core of Escherichia coli tRNA Ala GGC were determined under single turnover conditions using E. coli ribosomes. While all of the mutations were able to efficiently decode the cognate GCC codon, many showed substantial misreading of near-cognate GUC or ACC codons. Although all the misreading mutations were present in the sequences of other E. coli tRNAs, they were never found among bacterial tRNA Ala GGC sequences. This suggests that the sequences of bacterial tRNA Ala GGC have evolved to avoid reading incorrect codons.

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Anticodon-dependent conservation of bacterial tRNA gene sequences

Cited by 24 publications

References 52 publications

Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding

Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding

Stable tRNA-based phylogenies using only 76 nucleotides

tRNA residues evolved to promote translational accuracy

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