Abstract
| Original language | English |
|---|---|
| Pages (from-to) | 1015-1027 |
| Number of pages | 13 |
| Journal | Nucleic Acids Research |
| Volume | 34 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - 2006 |
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Keywords
- Bacillus subtilis
- Bacteria
- Base Pairing
- Cluster Analysis
- Codon
- Gammaproteobacteria
- Genomics
- Open Reading Frames
- RNA, Transfer
- Yeasts
Cite this
tRNA properties help shape codon pair preferences in open reading frames. / Buchan, J Ross; Aucott, Lorna Sharman; Stansfield, Ian (Corresponding Author).
In: Nucleic Acids Research, Vol. 34, No. 3, 2006, p. 1015-1027.Research output: Contribution to journal › Article
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TY - JOUR
T1 - tRNA properties help shape codon pair preferences in open reading frames
AU - Buchan, J Ross
AU - Aucott, Lorna Sharman
AU - Stansfield, Ian
PY - 2006
Y1 - 2006
N2 - 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.
AB - 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.
KW - Bacillus subtilis
KW - Bacteria
KW - Base Pairing
KW - Cluster Analysis
KW - Codon
KW - Gammaproteobacteria
KW - Genomics
KW - Open Reading Frames
KW - RNA, Transfer
KW - Yeasts
U2 - 10.1093/nar/gkj488
DO - 10.1093/nar/gkj488
M3 - Article
C2 - 16473853
VL - 34
SP - 1015
EP - 1027
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 3
ER -