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Compositional variation in bacterial genes and proteins with potential expression level.

Sabyasachi Das1, Subhagata Ghosh, Archana Pan

  • 1Bioinformatics Center, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India.

FEBS Letters
|September 17, 2005
PubMed
Summary

Bacterial gene expression varies with guanine and cytosine content at specific codon sites, influencing protein characteristics. This study explores these codon usage patterns and their relation to gene expressivity in bacteria.

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Bioinformatics

Background:

  • Codon usage bias significantly impacts gene expression levels in prokaryotes.
  • The composition of guanine (G) and cytosine (C) at the third codon position (synonymous sites) is a key factor in this bias.

Purpose of the Study:

  • To investigate the distinct usage patterns of guanine and cytosine at the three codon positions in eubacterial genes.
  • To correlate these usage patterns with potential gene expressivity, as predicted by the Codon Adaptation Index (CAI).

Main Methods:

  • Analysis of guanine and cytosine frequencies at the third codon position (G(3) and C(3)) across diverse eubacterial genomes.
  • Correlation analysis between codon usage parameters (G(3), C(3), G-starting vs. C-starting codons) and the Codon Adaptation Index (CAI).

Related Experiment Videos

  • Evaluation of gene product characteristics (size, complexity, aromaticity, alcoholicity) in relation to CAI.

    • Main Results:

    • In bacteria with moderate/high GC-content, G(3) exhibits a biphasic relationship with CAI, while C(3) increases with CAI.
    • In AT-rich bacteria, CAI shows a negative correlation with G(3) and a non-specific correlation with C(3).
    • Gene products encoded by G-starting codons correlate positively with CAI, while those from C-starting codons show negative or random correlations. Protein size, complexity, and aromaticity decrease with increasing CAI, supporting a cost-minimization principle. Alcoholicity also decreases with expressivity.

    Conclusions:

    • Codon usage at the third position is distinctly related to gene expressivity and varies based on bacterial GC-content.
    • The observed trends support a cost-minimization strategy in gene expression for free-living eubacteria, influencing protein composition.
    • These findings provide insights into the evolutionary pressures shaping bacterial genomes and gene expression machinery.