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Codon usage and evolutionary rates of proteins

I Barrai1, C Scapoli, C Nesti

  • 1Department of Evolutionary Biology, University of Ferrara, Italy.

Journal of Theoretical Biology
|February 7, 1994
PubMed
Summary

Protein evolutionary rates correlate with specific codon usage. Some codons speed up evolution, while others, like those in signal sequences, slow it down, impacting gene evolution.

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Genetics

Background:

  • Codon usage bias is a known phenomenon in gene sequences.
  • The relationship between codon usage and protein evolutionary rates is not fully understood.

Purpose of the Study:

  • To investigate the correlation between codon usage patterns and protein evolutionary rates in higher vertebrates.
  • To identify specific codons that are associated with accelerated or decelerated protein evolution.

Main Methods:

  • Analysis of 61 codons and three terminators in protein-coding sequences from 31 higher vertebrate protein families.
  • Calculation of Observed/Expected (O/E) frequency ratios for each codon within protein families.
  • Statistical correlation analysis between O/E ratios and protein evolutionary rates.

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Main Results:

  • A significant positive correlation was found between the O/E ratios of eight specific codons (AAC, TAT, ATA, GAA, ACA, AAT, ATG, CGA) and protein evolutionary rates.
  • A significant negative correlation was observed for codons AAG and GAG.
  • Terminator O/E ratios showed a negative correlation with evolutionary rates, significant for TAA and TGA.

Conclusions:

  • Functional constraints on proteins, especially in signal sequences, likely influence codon usage and evolutionary rates.
  • Specific codons are associated with varying rates of protein evolution in vertebrates.
  • Vertebrate terminator codons TAA and TGA may be evolutionarily older than TAG.