Codon usage in bacteria: correlation with gene expressivity
Nucleic Acids Research · 1982 · 1.3K citations · 32 references
GeneticsBacteriologyMolecular BiologyMolecular GeneticsGenomicsGene TranscriptionProtein SynthesisCodon UsageGene TranslationSequence AnalysisDna ReplicationMolecular MicrobiologyGene ExpressionFunctional GenomicsMrna ExpressivityGene ExpressivityProtein BiosynthesisBiologyNatural SciencesMicrobiologyMedicine
The sequence database now contains more than 600 protein‑coding genes, including 107 from prokaryotes. The study analyzes codon usage in 83 E. coli genes, examining its relationship to gene expressivity, regulation, tRNA specificity, and evolutionary selection. Codon frequencies were calculated for each gene and summarized with two indices: one reflecting iso‑tRNA usage differences and another based on cytosine versus uracil at the third codon position.
The nucleic acid sequence bank now contains over 600 protein coding genes of which 107 are from prokaryotic organisms. Codon frequencies in each new prokaryotic gene are given. Analysis of genetic code usage in the 83 sequenced genes of the Escherichia coli genome (chromosome, transposons and plasmids) is presented, taking into account new data on gene expressivity and regulation as well as iso-tRNA specificity and cellular concentration. The codon composition of each gene is summarized using two indexes: one is based on the differential usage of iso-tRNA species during gene translation, the other on choice between Cytosine and Uracil for third base. A strong relationship between codon composition and mRNA expressivity is confirmed, even for genes transcribed in the same operon. The influence of codon use of peptide elongation rate and protein yield is discussed. Finally, the evolutionary aspect of codon selection in mRNA sequences is studied.
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Jeffrey L. Bennetzen, B. D. Hall · Journal of Biological Chemistry · 1982
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