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Low-usage codons in Escherichia coli, yeast, fruit fly and primates.
S P Zhang1, G Zubay, E Goldman
1Fairchild Center for Biological Sciences, Columbia University, New York, NY 10027.
Gene
|August 30, 1991
Summary
This study analyzes low-usage codons across bacteria, yeast, fruit flies, and primates, finding that all species avoid specific codons, especially those with CG dinucleotides, in abundant proteins.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Codon usage bias influences protein expression and evolution.
- Understanding low-usage codons provides insights into translational regulation and genome evolution.
Purpose of the Study:
- To characterize low-usage codons in diverse species: Escherichia coli (ECO), Saccharomyces cerevisiae (YSC), Drosophila melanogaster (DRO), and primates (PRI).
- To identify patterns and commonalities in codon usage, particularly concerning the CG dinucleotide.
Main Methods:
- Comparative analysis of codon usage across four distinct species groups.
- Utilized three methods to identify low-usage codons: frequency summation, gene distribution scoring, and codon combination analysis.
- Analyzed 968 sequences (ECO), 484 (YSC), 244 (DRO), and 1518 (PRI).
Main Results:
- Each species exhibits a unique set of eight least-used codons, with all including arginine codons CGA and CGG.
- Yeast and primates share six low-usage codons, all containing the CG dinucleotide.
- Low-usage codons are avoided in genes encoding abundant proteins across all studied species.
Conclusions:
- The CG dinucleotide significantly influences low codon usage, especially in primates.
- High percentages of low-usage codons in proteins may indicate a detrimental effect of overproduction.
- Codon usage is largely independent of base composition but can be affected by dinucleotide frequencies.