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Related Experiment Videos

Relationship between codon biased genes, microarray expression values and physiological characteristics of

Antonio J Martín-Galiano1, Jerry M Wells2, Adela G de la Campa1

  • 1Unidad de Genética Bacteriana (CSIC), Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.

Microbiology (Reading, England)
|July 17, 2004
PubMed
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This study predicts gene expression in Streptococcus pneumoniae using codon profiles, identifying highly expressed genes involved in metabolism and infection. Some genes with distinct codon usage may have been acquired via horizontal gene transfer.

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Gene expression levels are crucial for bacterial function and adaptation.
  • Codon usage bias can reflect gene expression levels and evolutionary history.
  • Streptococcus pneumoniae is a significant human pathogen requiring understanding of its gene regulation.

Purpose of the Study:

  • To predict gene expression levels in Streptococcus pneumoniae using a codon-profile strategy.
  • To investigate the relationship between codon usage, gene function, and horizontal gene transfer.
  • To correlate predicted translation rates with measured mRNA abundance.

Main Methods:

  • Utilized a codon-profile strategy to predict gene expression.
  • Applied correspondence analysis to identify ORFs with distinctive codon profiles.

Related Experiment Videos

  • Compared codon adaptation index (CAI) values with microarray fluorescence intensity data.

    • Main Results:

    • Predicted highly expressed (PHE) genes included metabolic enzymes, sugar transporters, and some virulence factors.
    • Identified a subset of ORFs with lower G+C content and distinct codon profiles, suggesting horizontal gene acquisition.
    • Found significant correlation between predicted expression and mRNA levels for PHE genes and high CAI genes, but also identified non-PHE genes with high mRNA abundance.

    Conclusions:

    • Codon usage is a useful predictor of gene expression in S. pneumoniae, distinguishing between highly and lowly expressed genes.
    • A distinct group of genes, potentially acquired through horizontal transfer, includes virulence factors and DNA acquisition functions.
    • Gene expression regulation in S. pneumoniae involves both codon bias and transcriptional/post-transcriptional mechanisms affecting mRNA levels.