Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes
- 1 January 1986
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 14 (13), 5125-5143
- https://doi.org/10.1093/nar/14.13.5125
Abstract
Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon usage revealed two distinct groups of genes. One group corresponds to highly expressed genes, and has much more extreme synonymous codon preference. The pattern of codon usage observed is consistent with that expected if a need to match abundant tRNAs, and intermediacy of tRNA-mRNA interaction energies are important selective constraints. Thus codon usage in the highly expressed group shows a higher correlation with tRNA abundance, a greater degree of third base pyrimidine bias, and a lesser tendency to the A+T richness which is characteristic of the yeast genome. The cluster analysis can be used to predict the likely level of gene expression of any gene, and identifies the pattern of codon usage likely to yield optimal gene expression in yeast.Keywords
This publication has 88 references indexed in Scilit:
- Synthetic oligonucleotide probes deduced from amino acid sequence data: Theoretical and practical considerationsJournal of Molecular Biology, 1985
- Mismatch-specific post-meiotic segregation frequency in yeast suggests a heteroduplex recombination intermediateNature, 1985
- Selection pressures on codon usage in the complete genome of bacteriophage T7Journal of Molecular Evolution, 1985
- Translation is a non-uniform process: Effect of tRNA availability on the rate of elongation of nascent polypeptide chainsJournal of Molecular Biology, 1984
- Yeast regulatory gene PPR1: I. Nucleotide sequence, restriction map and codon usageJournal of Molecular Biology, 1984
- The biosynthesis of the ubiquinol‐cytochrome c reductase complex in yeastJBIC Journal of Biological Inorganic Chemistry, 1984
- DNA sequences of yeast H3 and H4 histone genes from two non-allelic gene sets encode identical H3 and H4 proteinsJournal of Molecular Biology, 1983
- Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes: Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAsJournal of Molecular Biology, 1982
- Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational systemJournal of Molecular Biology, 1981
- Sequence of the gene for iso-l-cytochrome c in saccharomyces cerevisiaeCell, 1979