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Coevolution between Stop Codon Usage and Release Factors in Bacterial Species.

Yulong Wei1, Juan Wang1, Xuhua Xia2

  • 1Department of Biology, University of Ottawa, Ottawa, ON, Canada.

Molecular Biology and Evolution
|June 15, 2016
PubMed
Summary

Bacterial stop codon usage, particularly UAA and UGA, is influenced by gene expression levels and the abundance of release factors (RF1 and RF2). UAG is not a minor stop codon, contrary to recent claims.

Keywords:
RF1RF2gene expression.prfAprfBrelease factorsstop codontranslation termination

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Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Bacteria utilize three stop codons (UAA, UAG, UGA) for translation termination.
  • The usage of these stop codons is influenced by termination efficiency, mutation bias, and the relative abundance of release factors (RF1 and RF2).

Purpose of the Study:

  • To investigate the relationship between bacterial stop codon usage, gene expression levels, and the abundance of release factors.
  • To re-evaluate the status of UAG as a minor stop codon in bacteria.

Main Methods:

  • Quantified RF1 and RF2 levels in 14 bacterial species.
  • Analyzed stop codon usage in highly expressed genes (HEGs) and lowly expressed genes (LEGs).
  • Correlated stop codon usage with the proportion of AT at third codon sites (PAT3) and the ratio of RF2 to total release factors (PRF2).

Main Results:

  • UAA is over-represented in HEGs, while UGA is under-represented, irrespective of RF2 abundance.
  • UGA usage increases with PRF2, but decreases significantly at high PAT3 values, explaining UGA reassignment in some lineages.
  • UAG usage remains consistently low across all PAT3 ranges, and it does not meet the criteria for a minor stop codon.

Conclusions:

  • Bacterial stop codon usage is a complex interplay between gene expression, release factor availability, and genomic AT content.
  • The findings challenge the notion of UAG as a minor stop codon in bacteria.
  • Provides a more accurate model for understanding stop codon usage patterns in bacteria.