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Synonymous codon usage in Lactococcus lactis: mutational bias versus translational selection.

S K Gupta1, T K Bhattacharyya, T C Ghosh

  • 1Bioinformatics Centre Bose Institute, P 1/12, CIT Scheme VII M, Kolkata 700 054, India.

Journal of Biomolecular Structure & Dynamics
|December 25, 2003
PubMed
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This study analyzed codon usage bias in Lactococcus lactis, finding that while AT-ending codons are common, translational selection also influences gene expression. Highly expressed genes show a preference for C and T ending codons, indicating complex evolutionary pressures.

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Lactococcus lactis is an AT-rich organism, suggesting a bias towards A/T at the third codon position.
  • Understanding codon usage bias is crucial for predicting gene expression and optimizing protein production.

Purpose of the Study:

  • To analyze the codon usage bias of all known genes in Lactococcus lactis.
  • To investigate the factors influencing codon usage variation, including compositional bias and translational selection.

Main Methods:

  • Multivariate statistical analyses (correspondence analysis) on codon counts and relative synonymous codon usage (RSCU).
  • Comparison of gene clusters based on expression levels, hydrophobicity, and codon usage patterns.

Main Results:

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  • AT-ending codons are predominant, but highly expressed genes show a significant preference for C and T ending codons.
  • Translational selection, in addition to compositional bias, appears to shape codon usage in highly expressed genes.
  • Amino acid composition influences codon usage, while gene length and replication strand position have minimal impact.

Conclusions:

  • Codon usage in Lactococcus lactis is shaped by both compositional biases and translational selection.
  • The study highlights the interplay of various factors in determining codon usage patterns in prokaryotes.
  • Further research into translational selection mechanisms in AT-rich organisms is warranted.