An Operational RNA Code for Faithful Assignment of AUG Triplets to Methionine

Jones, Thomas; Brown, Cassidy L.; Geslain, Renaud; Alexander, Rebecca W.; Pouplana, Lluı́s Ribas de

doi:10.1016/j.molcel.2007.12.021

Cited by 8 publications

(11 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The most parsimonious way for maintaining the fidelity of the genetic code should have been through the direct recognition of tRNA anticodons by cognate synthetases. Yet, the anticodon is not always the principal determinant for aminoacylation (Shimada et al 2001;Weygand-Durasevic et al 2002;Jones et al 2008), and in some cases, no physical contact is made between the aaRS and the anticodon (Park and Schimmel 1988). A set of ''identity elements'' classified as ''determinants'' and ''antideterminants'' ), distributed over the stems and loops of the tRNA molecule, participate in its interaction with enzymes and the ribosome during maturation, modification, biological function, and degradation (Wolfson et al 2001).…”

Section: Introductionmentioning

confidence: 99%

Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications

Shaul¹,

Berel²,

Benjamini³

et al. 2009

RNA

View full text Add to dashboard Cite

It has been suggested that tRNA acceptor stems specify an operational RNA code for amino acids. In the last 20 years several attributes of the putative code have been elucidated for a small number of model organisms. To gain insight about the ensemble attributes of the code, we analyzed 4925 tRNA sequences from 102 bacterial and 21 archaeal species. Here, we used a classification and regression tree (CART) methodology, and we found that the degrees of degeneracy or specificity of the RNA codes in both Archaea and Bacteria differ from those of the genetic code. We found instances of taxon-specific alternative codes, i.e., identical acceptor stem determinants encrypting different amino acids in different species, as well as instances of ambiguity, i.e., identical acceptor stem determinants encrypting two or more amino acids in the same species. When partitioning the data by class of synthetase, the degree of code ambiguity was significantly reduced. In cryptographic terms, a plausible interpretation of this result is that the class distinction in synthetases is an essential part of the decryption rules for resolving the subset of RNA code ambiguities enciphered by identical acceptor stem determinants of tRNAs acylated by enzymes belonging to the two classes. In evolutionary terms, our findings lend support to the notion that in the pre-DNA world, interactions between tRNA acceptor stems and synthetases formed the basis for the distinction between the two classes; hence, ambiguities in the ancient RNA code were pivotal for the fixation of these enzymes in the genomes of ancestral prokaryotes.

show abstract

Section: Introductionmentioning

confidence: 99%

Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications

Shaul¹,

Berel²,

Benjamini³

et al. 2009

RNA

View full text Add to dashboard Cite

show abstract

“…pQE-70-MpMRS elution yielded two protein bands of 128 kDa (the full-length protein) and 63 kDa (corresponding to translation from an internal start site that represents the MRS portion of the polypeptide). The 63-kDa Mp⌬MRS was further purified by ion exchange chromatography as described previously (12). Monomeric E. coli MRS was expressed from a pET28a vector and purified by nickel affinity chromatography as reported (27).…”

Section: Methodsmentioning

confidence: 99%

“…The strength of this anticodon recognition element is illustrated by the determination that EcMRS can methionylate in vitro transcripts of the E. coli tRNA Ile major isoacceptor in which its GAU anticodon is changed to the methionine CAU (11) (12).…”

mentioning

confidence: 99%

“…E. coli and other gammaproteobacteria encode a tRNA CAU Ile with a C3-G70 base pair common also to its tRNA CAU Met and tRNA CAU fMet species (17). Thus the key 3-70 base pair used by MpMRS to reject tRNA CAU Ile is not used by EcMRS to differentiate its cognate from nearcognate tRNA CAU (12).…”

mentioning

confidence: 99%

“…The resulting plasmids pQE-70-SpMRS1, pQE-70-HpMRS, pQE-70-BfMRS, pQE-70-MsMRS, and pQE-70-BbMRS were verified by sequencing. Cloning of MpMRS and EcMRS was previously described (12,27).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Evidence for Late Resolution of the AUX Codon Box in Evolution

Jones

Pouplana

Alexander

2013

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Background: Protein biosynthesis requires accurate tRNA aminoacylation. Results: Bacterial methionyl-tRNA synthetases (MRSs) vary in their ability to reject near-cognate tRNA Ile transcripts containing the methionine-specifying CAU anticodon. Conclusion: Given the degree of near-cognate discrimination among bacterial MRSs, aspects of genetic code accuracy likely were fixed relatively late in evolution.Significance: This varied discrimination may reflect differing cellular needs for translational accuracy versus plasticity.

show abstract

Bacterial wobble modifications of NNA‐decoding tRNAs

Nilsson

Alexander

2019

IUBMB Life

Self Cite

View full text Add to dashboard Cite

Nucleotides of transfer RNAs (tRNAs) are highly modified, particularly at the anticodon. Bacterial tRNAs that read A‐ending codons are especially notable. The U34 nucleotide canonically present in these tRNAs is modified by a wide range of complex chemical constituents. An additional two A‐ending codons are not read by U34‐containing tRNAs but are accommodated by either inosine or lysidine at the wobble position (I34 or L34). The structural basis for many N34 modifications in both tRNA aminoacylation and ribosome decoding has been elucidated, and evolutionary conservation of modifying enzymes is also becoming clearer. Here we present a brief review of the structure, function, and conservation of wobble modifications in tRNAs that translate A‐ending codons. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1158–1166, 2019

show abstract

An Operational RNA Code for Faithful Assignment of AUG Triplets to Methionine

Cited by 8 publications

References 48 publications

Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications

Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications

Evidence for Late Resolution of the AUX Codon Box in Evolution

Bacterial wobble modifications of NNA‐decoding tRNAs

Contact Info

Product

Resources

About