Rates of aminoacyl-tRNA selection at 29 sense codons in vivo

Curran, James F.; Yarus, Michael

doi:10.1016/0022-2836(89)90170-8

Cited by 217 publications

(252 citation statements)

References 42 publications

Supporting

Mentioning

235

Contrasting

Order By: Relevance

“…The mRNAs of highly expressed genes, supposed to have higher rates of translation so that the encoded proteins are synthesized abundantly, preferentially use a subset of codons that maximizes the rate of translation (Ikemura & Ozeki, 1983;Ikemura, 1985;Sharp & Li, 1987;Anderson & Kurland, 1990;Lobry & Gautier, 1994). It is well documented that some codons are translated more slowly than others and abundant codons are mostly translated at a higher rate (Carter et al, 1986;Harms & Umbarger, 1987;Bonekamp et al, 1989;Curran & Yarus, 1989;Sorensen et al, 1989;Sorensen & Pedersen, 1991). It has been further suggested that there is some optimization in the choice of amino acid types used in abundant proteins (Lobry & Gautier, 1994).…”

Section: Rationalementioning

confidence: 99%

“…Rare codons (as defined in Materials and methods and indicated by * in Table 6) are 12 in number. Bonekamp et al (1989) and Curran and Yarus (1989) observed that, whereas different codons are translated at different rates and abundant codons are mostly translated at a higher rate, certain rare codons are also translated at an unexpectedly higher rate. It is noteworthy that at least four of the eight avoided codons in both highly expressed genes and in slow regions belong to this latter category of rare codons.…”

Section: Synonymous Codon Usage In the Slow Mrna Regionsmentioning

confidence: 99%

“…Codon usage in slow regions can also be compared with observed translation rates (given in the final column of Table 6) where known (Curran & Yarus, 1989). It is noteworthy that in six (Phe, Tyr, Gln, Pro, Ser, Arg) of nine amino acid types for which the translation speed is known for the synonymous co- in slow regions.…”

Section: Codon Usage and Translation Ratesmentioning

confidence: 99%

“…8 Translation speed of the codon as reported in Curran and Yarus (1989). Values are given only for those codons for which the translation rates have been measured in the cited paper.…”

Section: Codon Usage and Translation Ratesmentioning

confidence: 99%

“…Values are given only for those codons for which the translation rates have been measured in the cited paper. These values, denoted as RtRNA/Rshlf, in Curran and Yarus (1989), were measured by placing aminoacyl-tRNA selection at individual codons in competition with a frameshift assumed to have a uniform rate and they indicate the relative rates of association between the codon and the cognate aminoacyl-tRNA. set of mRNAs from highly expressed genes.…”

Section: Codon Usage and Translation Ratesmentioning

confidence: 99%

See 4 more Smart Citations

Ribosome‐mediated translational pause and protein domain organization

1996

View full text Add to dashboard Cite

Because regions on the messenger ribonucleic acid differ in the rate at which they are translated by the ribosome and because proteins can fold cotranslationally on the ribosome, a question arises as to whether the kinetics of translation influence the folding events in the growing nascent polypeptide chain. Translationally slow regions were identified on mRNAs for a set of 37 multidomain proteins from Escherichia coli with known three-dimensional structures. The frequencies of individual codons in mRNAs of highly expressed genes from E. coli were taken as a measure of codon translation speed. Analysis of codon usage in slow regions showed a consistency with the experimentally determined translation rates of codons; abundant codons that are translated with faster speeds compared with their synonymous codons were found to be avoided; rare codons that are translated at an unexpectedly higher rate were also found to be avoided in slow regions. The statistical significance of the occurrence of such slow regions on mRNA spans corresponding to the oligopeptide domain termini and linking regions on the encoded proteins was assessed. The amino acid type and the solvent accessibility of the residues coded by such slow regions were also examined. The results indicated that protein domain boundaries that mark higher-order structural organization are largely coded by translationally slow regions on the RNA and are composed of such amino acids that are stickier to the ribosome channel through which the synthesized polypeptide chain emerges into the cytoplasm. The translationally slow nucleotide regions on mRNA possess the potential to form hairpin secondary structures and such structures could further slow the movement of ribosome. The results point to an intriguing correlation between protein synthesis machinery and in vivo protein folding. Examination of available mutagenic data indicated that the effects of some of the reported mutations were consistent with our hypothesis.Keywords: codon usage; domain linkers; peptide channel; protein folding; ribosome; translation The rate of protein translation is nonuniform along the mRNA (Varenne et al., 1984). Ribosomes seem to pause as well as stack at specific regions on mRNA (Chaney & Morris, 1979;Wolin &Walter, 1988;Kim et al., 1991;Kim & Hollingsworth, 1992). Two of the mRNA features that slow the ribosome during translation are the presence of slow codons (Varenne et al., 1984;Bonekamp et al., 1985;Wolin & Walter, 1988) and the formation of higher order nucleotide structures (Chaney & Morris, 1979;Tu et al., 1992). The resultant translational pause may temporally separate the adjacent regions on the growing nascent polypeptide. Given that proteins can fold cotranslationally with the possible involvement of the ribosome (Phillips, 1966;Baldwin, 1975;Yonath, 1992;Kudlicki et al., 1994;Wiedmann et al., 1994;Brimacombe, 1995), the temporal separation might exert a phenotypic effect on the structural organization of the encoded protein. We show that as much as 70% of the do...

show abstract

Section: Rationalementioning

confidence: 99%

Section: Synonymous Codon Usage In the Slow Mrna Regionsmentioning

confidence: 99%

Section: Codon Usage and Translation Ratesmentioning

confidence: 99%

“…8 Translation speed of the codon as reported in Curran and Yarus (1989). Values are given only for those codons for which the translation rates have been measured in the cited paper.…”

Section: Codon Usage and Translation Ratesmentioning

confidence: 99%

Section: Codon Usage and Translation Ratesmentioning

confidence: 99%

See 3 more Smart Citations

Ribosome‐mediated translational pause and protein domain organization

1996

View full text Add to dashboard Cite

show abstract

The Mechanism of Recoding in Pro‐ and Eukaryotes

Poole¹,

Major²,

Cridge³

et al. 2004

Protein Synthesis and Ribosome Structure

View full text Add to dashboard Cite

The Mechanism of Recording in Pro‐ and Eukaryotes

Poole

Major

Cridge

et al. 2008

Protein Science Encyclopedia

View full text Add to dashboard Cite

Originally published in: Protein Synthesis and Ribosome Structure. Edited by Knud H. Nierhaus and Daniel N. Wilson. Copyright © 2004 Wiley‐VCH Verlag GmbH & Co. KGaA Weinheim. Print ISBN: 3‐527‐30638‐1 The sections in this article are Introduction Maintaining Decoding Accuracy and the Reading Frame The Use of a Stop Signal for both Elongation and Termination of Protein Synthesis The Mechanism for Sec Incorporation at UGA Sites in Bacterial mRNAs The Gene Products The Mechanism of Sec Incorporation The Competition between Sec Incorporation and Canonical Decoding of UGA by RF2 Mechanism for Sec Incorporation at UGA Sites in Eukaryotic and Archaeal mRNAs The Gene Products The Mechanism of Sec Incorporation at Specific UGA Stop Codons Why does Recoding Occur at Stop Signals? The Stop Signal of Prokaryotic Genomes — Engineered for High Efficiency Decoding? The Stop Signal of Eukaryotic Genomes – Diversity Contributes to Recoding Readthrough of a Stop Signal: Decoding Stop as Sense Bypassing of a Stop Codon: ‘Free‐wheeling’ on the mRNA Frameshifting Around Stop or Sense Codons Forward Frameshifting: the +1 Event Programed −1 Frameshifting: A Common Mechanism used by Many Viruses During Gene Expression Conclusion

show abstract

Rates of aminoacyl-tRNA selection at 29 sense codons in vivo

Cited by 217 publications

References 42 publications

Ribosome‐mediated translational pause and protein domain organization

Ribosome‐mediated translational pause and protein domain organization

The Mechanism of Recoding in Pro‐ and Eukaryotes

The Mechanism of Recording in Pro‐ and Eukaryotes

Contact Info

Product

Resources

About