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Cited by 108RNA and protein synthesis mechanismsRNA modifications and cancerGenomics and Phylogenetic Studies

tRNA properties help shape codon pair preferences in open reading frames

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Buchan, J. R.·2006·Nucleic Acids Research
DOI 10.1093/nar/gkj488PMC PMC1363775
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Abstract

Translation elongation is an accurate and rapid process, dependent upon efficient juxtaposition of tRNAs in the ribosomal A- and P-sites. Here, we sought evidence of A- and P-site tRNA interaction by examining bias in codon pair choice within open reading frames from a range of genomes. Three distinct and marked effects were revealed once codon and dipeptide biases had been subtracted. First, in the majority of genomes, codon pair preference is primarily determined by a tetranucleotide combination of the third nucleotide of the P-site codon, and all 3 nt of the A-site codon. Second, pairs of rare codons are generally under-used in eukaryotes, but over-used in prokaryotes. Third, the analysis revealed a highly significant effect of tRNA-mediated selection on codon pairing in unicellular eukaryotes, Bacillus subtilis, and the gamma proteobacteria. This was evident because in these organisms, synonymous codons decoded in the A-site by the same tRNA exhibit significantly similar P-site pairing preferences. Codon pair preference is thus influenced by the identity of A-site tRNAs, in combination with the P-site codon third nucleotide. Multivariate analysis identified conserved nucleotide positions within A-site tRNA sequences that modulate codon pair preferences. Structural features that regulate tRNA geometry within the ribosome may govern genomic codon pair patterns, driving enhanced translational fidelity and/or rate.

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  • The main selective effects on codon context are found in the nucleotides following the codon in the 3' direction.

    “The main selective effects on codon context are found in the nucleotides following the codon in the 3' direction [16,18,19,22].”

    From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [16]

    The Discussion reports significant interactions between a codon’s third nucleotide (cP3) and nucleotides in the following A-site codon. But it calls cP3 itself cardinal to pairing frequencies, so it does not locate the main effects solely in nucleotides following the codon. No page number is available in our copy. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • Specific preferred or avoided nucleotide patterns differ among species.

    “It has been found that the specific preferred or avoided nucleotide patterns differ among species [16,22].”

    From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [16]

  • Effects of codon context are influenced by physical interactions between tRNA isoacceptors in the ribosomal P- and A-sites.

    “Previous studies suggest that the effects of codon context are influenced by the physical interactions between tRNA isoacceptors in the ribosomal P- and A-sites [1,16,23].”

    From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [16]

  • In five gamma proteobacteria, Bacillus subtilis and two yeasts, A-site codons decoded by the same tRNA have similar patterns of P-site codon pairing preference.

    “It has been shown that in five gamma proteobacteria, Bacillus subtilis and two yeasts, the A-site codons decoded by the same tRNA have similar patterns of P-site codon pairing preference [16].”

    From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [16]

  • Codon context might be influenced by certain structural constraints imposed by two tRNAs occupying the ribosomal P- and A-sites.

    “In addition, it has been suggested that codon context might be influenced by certain structural constraints imposed by two tRNAs occupying the ribosomal P- and A-sites [1,16,23].”

    From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [16]

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Authors
Buchan, J. R.
Affiliations
University of Aberdeen (GB)
Corresponding author
Buchan, J. R.
ORCID
Buchan, J. R.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2006-02-06
Volume
34
Issue
3
Pages
1015-1027
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkj488
PMC
PMC1363775
OpenAlex
W2162592907
Cited by
108
References
51
Citations by year
2026: 1 · 2025: 3 · 2024: 4 · 2023: 6 · 2022: 4 · 2021: 7 · 2020: 8 · 2019: 7 · 2018: 2 · 2017: 12 · 2016: 4 · 2015: 9 · 2014: 9 · 2013: 5 · 2012: 6
FWCI
1.91
Type
journal article
Language
en
Open access
Licence
other-oa
Locations
  • Nucleic Acids Research (publishedVersion, other-oa)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Tenovus
  • Biotechnology and Biological Sciences Research Council
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
tRNA, ribosomal A site, ribosomal P site, translation elongation, rare codons, tRNA structure, translation fidelity, open reading frames, Bacillus subtilis, Gammaproteobacteria, eukaryotes, prokaryotes
MeSH terms
Bacillus subtilis, Bacteria, Codon, RNA, Transfer, Yeasts, Cluster Analysis, Open Reading Frames, Base Pairing, Gammaproteobacteria, Genomics

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