Molecular Biology and Evolution, Vol 16, 1752-1762, Copyright © 1999 by Society for Molecular Biology and Evolution
R Percudani and S Ottonello
The transfer RNA gene complement of Saccharomyces cerevisiae was utilized
for a whole-genome analysis of the deviation from a neutral usage of
pyrimidine-ending cognate codons, that is, codons read by a single tRNA
species having either inosine or guanosine as the first anticodon base.
Mutational pressure at the wobble position was estimated from the base
composition of the noncoding portion of the yeast genome. The selective
pressure for translational efficiency was inferred from the degree of codon
adaptation to tRNA gene redundancy and from mRNA abundance data derived
from yeast transcriptome analysis. Amino acid conservation in orthologous
comparisons with wholly sequenced microbial genomes was used to estimate
translational accuracy requirements. A close correspondence was observed
between the usage of wobble position pyrimidines and the frequency
predicted by mutational bias. However, in the case of four cognate pairs
(Gly: ggu/ggc; Asn: aau/aac; Phe: uuu/uuc; Tyr: uau/ uac) all read by
guanosine-starting anticodons, we found evidence for a strong selective
pressure driven by translational efficiency. Only for the glycine pair,
wobble pyrimidine choice also appears to fulfill a translational accuracy
requirement. Wobble pyrimidine selection is strictly related to the number
of hydrogen bonds formed by alternative cognate codons: whenever a
different number of hydrogen bonds can be formed at the wobble position,
there is selection against six- or nine-hydrogen-bonded codon- anticodon
pairs. Our results indicate that an intrinsic codon preference, critically
dependent on the stability of codon-anticodon interaction and mainly
reflecting selection for the optimization of translational efficiency, is
built into the translational apparatus.
ORIGINAL ARTICLE
Selection at the wobble position of codons read by the same tRNA in Saccharomyces cerevisiae
Institute of Biochemical Sciences, University of Parma, Italy.
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