Mapping Hidden Potential Identity Elements by Computing the Average Discriminating Power of Individual tRNA Positions

Szenes, Áron; Pál, Gábor

doi:10.1093/dnares/dss008

Cited by 5 publications

(4 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Further tRNA searches in the three domains of life were performed using the Leipzig database ( 164 ) and the archaeal split tRNA databases ( 375 ), and on sequences specific to some phylogenetic groups ( 383 ). First, and as expected, positions in anticodon loops and at the top of the acceptor stems are predicted in Bacteria and Eukarya , with the highest probability in Bacteria ( 388 ). More interesting, positions 30–40 and 31–39 in the anticodon branch are predicted in several tRNAs as determinants, e.g.…”

Section: Expanding the World Of Trna Identitysupporting

confidence: 73%

“…More interesting, positions 30–40 and 31–39 in the anticodon branch are predicted in several tRNAs as determinants, e.g. the pair U 31 –A 39 in E. coli tRNA Trp and S. cerevisiae tRNA Met and the pairs U 30 ·G 40 and G 30 ·U 40 in eukaryal tRNAs Ile and S. cerevisiae tRNA Asp , respectively ( 383 , 388 ). With the exception of pair 30–40 in S. cerevisiae tRNA Asp slightly shifted from the predicted 31–39 pair, these findings are consistent with previous studies using a Bayesian search ( 385 ).…”

Section: Expanding the World Of Trna Identitymentioning

confidence: 99%

See 1 more Smart Citation

The tRNA identity landscape for aminoacylation and beyond

Giegé

Eriani

2023

Nucleic Acids Research

View full text Add to dashboard Cite

tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.

show abstract

Section: Expanding the World Of Trna Identitysupporting

confidence: 73%

Section: Expanding the World Of Trna Identitymentioning

confidence: 99%

The tRNA identity landscape for aminoacylation and beyond

Giegé

Eriani

2023

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Other studies showed that the aminoacylation specificity of some tRNA types, among distant species, may be determined by the very same base pair in their acceptor stem. This was demonstrated by both in vivo and in vitro (Giegé et al 1998), as well as computational analysis (Shaul et al 2010;Szenes and Pál 2012). Altogether, these studies suggest that the operational RNA code is common across species in some cases and species-specific in others.…”

Section: Introductionmentioning

confidence: 61%

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

Galili

Gingold

Shaul

et al. 2016

RNA

View full text Add to dashboard Cite

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.

show abstract

“…Since AARS do not directly recognize anticodons borne by tRNAs and thus the code, they evolve to dictate the relationship between codons and their corresponding anticodons in rather complex and dynamic ways [17] . Most strikingly, the tRNA pool and the AARS set are rather dynamic and have gone through membership change and recruiting process across taxa [18–25] .…”

Section: Introductionmentioning

confidence: 99%

Does the Genetic Code Have A Eukaryotic Origin?

Zhang

2013

Genomics, Proteomics &Amp; Bioinformatics

View full text Add to dashboard Cite

In the RNA world, RNA is assumed to be the dominant macromolecule performing most, if not all, core “house-keeping” functions. The ribo-cell hypothesis suggests that the genetic code and the translation machinery may both be born of the RNA world, and the introduction of DNA to ribo-cells may take over the informational role of RNA gradually, such as a mature set of genetic code and mechanism enabling stable inheritance of sequence and its variation. In this context, we modeled the genetic code in two content variables—GC and purine contents—of protein-coding sequences and measured the purine content sensitivities for each codon when the sensitivity (% usage) is plotted as a function of GC content variation. The analysis leads to a new pattern—the symmetric pattern—where the sensitivity of purine content variation shows diagonally symmetry in the codon table more significantly in the two GC content invariable quarters in addition to the two existing patterns where the table is divided into either four GC content sensitivity quarters or two amino acid diversity halves. The most insensitive codon sets are GUN (valine) and CAN (CAR for asparagine and CAY for aspartic acid) and the most biased amino acid is valine (always over-estimated) followed by alanine (always under-estimated). The unique position of valine and its codons suggests its key roles in the final recruitment of the complete codon set of the canonical table. The distinct choice may only be attributable to sequence signatures or signals of splice sites for spliceosomal introns shared by all extant eukaryotes.

show abstract

Mapping Hidden Potential Identity Elements by Computing the Average Discriminating Power of Individual tRNA Positions

Cited by 5 publications

References 76 publications

The tRNA identity landscape for aminoacylation and beyond

The tRNA identity landscape for aminoacylation and beyond

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

Does the Genetic Code Have A Eukaryotic Origin?

Contact Info

Product

Resources

About