Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates

Salazar, Juan Carlos; Ahel, Ivan; Orellana, Omar; Hansen, Debra T.; Krieger, Robert; Daniels, Lacy; Söll, Dieter

doi:10.1073/pnas.1936123100

Cited by 87 publications

(138 citation statements)

References 32 publications

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“…In contrast, GlnRS, generally held to be the most recently evolved aaRS, seems to have no obvious residual relationship to amino acid metabolism. Instead the simultaneous existence of both D-GluRS and ND-GluRS, as still observed in a few bacteria, would seem to facilitate the replacement of the indirect route of Gln-tRNA Gln synthesis by GlnRS (Salazar et al 2003;Skouloubris et al 2003), either by bacterial GluRS evolution or horizontal gene transfer from eukarya (Lamour et al 1994).…”

Section: Translating Glutamine and Asparaginementioning

confidence: 99%

Aminoacyl-tRNAs: setting the limits of the genetic code

Ibba¹,

Söll²

2004

Genes Dev.

Self Cite

151

117

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Aminoacyl-tRNAs (aa-tRNAs) are simple molecules with a single purpose-to serve as substrates for translation. They consist of mature tRNAs to which an amino acid has been esterified at the 3Ј-end. The 20 different types of aa-tRNA are made by the 20 different aminoacyl-tRNA synthetases (aaRSs, of which there are two classes), one for each amino acid of the genetic code . This would be fine if it were not for the fact that such a straightforward textbook scenario is not true in a single known living organism. aa-tRNAs lie at the heart of gene expression; they interpret the genetic code by providing the interface between nucleic acid triplets in mRNA and the corresponding amino acids in proteins. The synthesis of aa-tRNAs impacts the accuracy of translation, the expansion of the genetic code, and even provides tangible links to primary metabolism. These central roles vest immense power in aa-tRNAs, and recent studies show just how complex and diverse their synthesis is.

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Section: Translating Glutamine and Asparaginementioning

confidence: 99%

Aminoacyl-tRNAs: setting the limits of the genetic code

Ibba¹,

Söll²

2004

Genes Dev.

Self Cite

151

117

View full text Add to dashboard Cite

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“…Such an evolutionary speciation process is expected to be reflected in the co-evolution of the corresponding aminoacyl tRNA synthetases' genes in the same species. Indeed, some experimental work shows the coevolution of tRNAs with their corresponding aminoacyl tRNA synthetases' genes (Salazar et al 2003), and there is room for more such research. In the context of previous works showing the limitation in amino acid ligation when using tRNAs from species of different domains (Ripmaster et al 1995;Kobayashi et al 2003;Namgoong et al 2007;Shaul et al 2010), our results may suggest the existence of informative tRNA positions and code which are species-specific, across all the three domains of life.…”

Section: Discussionmentioning

confidence: 99%

Identifying the ligated amino acid of archaeal tRNAs based on positions outside the anticodon

Galili

Gingold

Shaul

et al. 2016

RNA

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Proper recognition of tRNAs by their aminoacyl-tRNA synthetase is essential for translation accuracy. Following evidence that the enzymes can recognize the correct tRNA even when anticodon information is masked, we search for additional nucleotide positions within the tRNA molecule that potentially contain information for amino acid identification. Analyzing 3936 sequences of tRNA genes from 86 archaeal species, we show that the tRNAs' cognate amino acids can be identified by the information embedded in the tRNAs' nucleotide positions without relying on the anticodon information. We present a small set of six to 10 informative positions along the tRNA, which allow for amino acid identification accuracy of 90.6% to 97.4%, respectively. We inspected tRNAs for each of the 20 amino acid types for such informative positions and found that tRNA genes for some amino acids are distinguishable from others by as few as one or two positions. The informative nucleotide positions are in agreement with nucleotide positions that were experimentally shown to affect the loaded amino acid identity. Interestingly, the knowledge gained from the tRNA genes of one archaeal phylum does not extrapolate well to another phylum. Furthermore, each species has a unique ensemble of nucleotides in the informative tRNA positions, and the similarity between the sets of positions of two distinct species reflects their evolutionary distance. Hence, we term this set of informative positions a "tRNA cipher." It is tempting to suggest that the diverging code identified here might also serve the aminoacyl tRNA synthetase in the task of tRNA recognition.

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“…Pseudomonas aeruginosa, Neisseria meningitidis, Thermus thermophilus, and Deinococcus radiodurans), GatCAB serves only as an Asp-AdT (64,65,(71)(72)(73)(74)(75)(76). In bacteria carrying both non-discriminating aaRSs (ND-GluRS and NDAspRS) such as Chlamydia trachomatis (66) and H. pylori (77)(78)(79), GatCAB serves as a Glu/Asp-AdT (66,68,69). The P. falciparum genome (11) encodes two putative D-AspRS enzymes, one of which (PF3D7_0514300) possesses a predicted N-terminal apicoplast-targeting sequence, suggesting that it is imported into the apicoplast (56,62).…”

Section: Discussionmentioning

confidence: 99%