Codon usage in bacteria: correlation with gene expressivity

Codon usage in bacteria: correlation with gene expressivity

1982 | M.Gouy and C.Gautier
The study by M. Gouy and C. Gautier explores the relationship between codon usage in bacteria and gene expressivity, focusing on *Escherichia coli*. They analyze 83 sequenced genes from the *E. coli* genome, including chromosome, plasmids, and transposons, and compare codon usage with gene expressivity, tRNA availability, and iso-tRNA specificity. Two indexes are used to summarize codon composition: one based on the differential usage of iso-tRNA species during translation, and another based on the choice between cytosine and uracil in the third base of codons. The study confirms a strong correlation between codon composition and mRNA expressivity, even among genes transcribed in the same operon. It discusses the influence of codon use on peptide elongation rate and protein yield, and examines the evolutionary aspect of codon selection in mRNA sequences. The study also investigates the relationship between codon usage and tRNA availability, noting that highly expressed genes tend to use codons corresponding to abundant tRNAs, leading to faster and more efficient translation. The P1 index, which measures the average number of codon-tRNA interactions per elongation cycle, is used to quantify this effect. Genes with high tRNA availability have lower P1 values, indicating more efficient translation. Conversely, genes with low tRNA availability have higher P1 values, indicating slower translation. The study also examines the choice between pyrimidines (cytosine and uracil) in the third base of codons. It finds that the choice of pyrimidine in this position is influenced by the energy level of the codon-anticodon interaction and the gene's expressivity. The P2 index, which measures the frequency of "right choices" between pyrimidines in codons, is used to quantify this effect. Genes with high expressivity tend to have higher P2 values, indicating a preference for codons that enhance translation efficiency. The study also examines the relationship between gene expressivity and codon usage within the same operon. It finds that genes with high expressivity tend to have codon usage that is optimized for efficient translation. This suggests that codon usage may be involved in tuning gene expressivity according to cell needs. However, direct experimentation is needed to confirm this hypothesis. Finally, the study discusses the evolutionary aspect of codon usage, noting that codon usage optimization implies strong evolutionary pressures. It suggests that codon usage may be involved in the overall optimization of gene sequences, and that this process is consistent with Darwinian evolution as a process of cumulative small variations. The study also notes that the relationship between codon usage and gene expressivity in *E. coli* may be valid for eukaryotic organisms as well.The study by M. Gouy and C. Gautier explores the relationship between codon usage in bacteria and gene expressivity, focusing on *Escherichia coli*. They analyze 83 sequenced genes from the *E. coli* genome, including chromosome, plasmids, and transposons, and compare codon usage with gene expressivity, tRNA availability, and iso-tRNA specificity. Two indexes are used to summarize codon composition: one based on the differential usage of iso-tRNA species during translation, and another based on the choice between cytosine and uracil in the third base of codons. The study confirms a strong correlation between codon composition and mRNA expressivity, even among genes transcribed in the same operon. It discusses the influence of codon use on peptide elongation rate and protein yield, and examines the evolutionary aspect of codon selection in mRNA sequences. The study also investigates the relationship between codon usage and tRNA availability, noting that highly expressed genes tend to use codons corresponding to abundant tRNAs, leading to faster and more efficient translation. The P1 index, which measures the average number of codon-tRNA interactions per elongation cycle, is used to quantify this effect. Genes with high tRNA availability have lower P1 values, indicating more efficient translation. Conversely, genes with low tRNA availability have higher P1 values, indicating slower translation. The study also examines the choice between pyrimidines (cytosine and uracil) in the third base of codons. It finds that the choice of pyrimidine in this position is influenced by the energy level of the codon-anticodon interaction and the gene's expressivity. The P2 index, which measures the frequency of "right choices" between pyrimidines in codons, is used to quantify this effect. Genes with high expressivity tend to have higher P2 values, indicating a preference for codons that enhance translation efficiency. The study also examines the relationship between gene expressivity and codon usage within the same operon. It finds that genes with high expressivity tend to have codon usage that is optimized for efficient translation. This suggests that codon usage may be involved in tuning gene expressivity according to cell needs. However, direct experimentation is needed to confirm this hypothesis. Finally, the study discusses the evolutionary aspect of codon usage, noting that codon usage optimization implies strong evolutionary pressures. It suggests that codon usage may be involved in the overall optimization of gene sequences, and that this process is consistent with Darwinian evolution as a process of cumulative small variations. The study also notes that the relationship between codon usage and gene expressivity in *E. coli* may be valid for eukaryotic organisms as well.
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Understanding Codon usage in bacteria%3A correlation with gene expressivity.