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Selection conflicts, gene expression, and codon usage trends in yeast.

Richard M Kliman1, Naheelah Irving, Maria Santiago

  • 1Department of Biological Sciences, Kean University, 1000 Morris Avenue, Union, NJ 08830, USA. rmkliman@cedarcrest.edu

Journal of Molecular Evolution
|September 10, 2003
PubMed
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Natural selection shapes synonymous codon usage in yeast, influencing gene expression and regional bias. Factors like recombination and gene length limit selection effectiveness, potentially due to linked selection.

Area of Science:

  • Genetics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Synonymous codon usage in yeast is influenced by natural selection on gene expression and regional compositional bias.
  • Codon usage is a valuable model for studying factors limiting selection effectiveness due to numerous targets and small selection coefficients.

Purpose of the Study:

  • To identify major trends in codon usage in Saccharomyces cerevisiae.
  • To investigate factors limiting the effectiveness of natural selection on codon usage.

Main Methods:

  • Factor analysis was applied to analyze codon usage patterns in 5836 yeast genes.
  • Correlation analysis was used to link codon usage trends with gene expression and genomic features.

Main Results:

Related Experiment Videos

  • The primary factor influencing codon usage strongly correlated with gene expression, supporting efficient translation models.
  • A secondary factor correlated with third codon position GC content, indicating regional compositional bias.
  • Preferred codon usage decreased with reduced recombination rates, increased gene length, and reduced intergenic spacing.

Conclusions:

  • Findings are consistent with the Hill-Robertson effect, where selection is less effective on linked targets.
  • Reduced gene expression in closely spaced genes may suggest selection conflicts arising from antagonistic pleiotropy.