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Factors affecting codon usage in Yersinia pestis.

Zhuo-Cheng Hou1, Ning Yang

  • 1College of Animal Science and Technology, China Agricultural University, Beijing 100094, China.

Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao Acta Biochimica Et Biophysica Sinica
|June 11, 2003
PubMed
Summary

Synonymous codon usage in Yersinia pestis, the plague bacterium, is influenced by gene expression levels and replication-transcriptional selection. These factors, along with gene length and composition, shape codon bias in the Y. pestis genome.

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Area of Science:

  • Genomics
  • Molecular Evolution
  • Microbial Genetics

Background:

  • The complete genome of Yersinia pestis, the bacterium responsible for plague, has been sequenced.
  • Understanding synonymous codon usage patterns is crucial for insights into evolutionary processes.

Purpose of the Study:

  • To analyze the factors influencing synonymous codon usage patterns in Yersinia pestis.
  • To investigate the role of gene expression, replication-transcriptional selection, gene length, and composition in shaping codon usage bias.

Main Methods:

  • Analysis of coding sequences (≥300 bp) from the Yersinia pestis genome.
  • Correspondence analysis (COA) to correlate gene expression with codon usage.
  • GC-skew analysis to assess selection pressures.

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  • Calculation of Codon Adaptation Index (CAI), GC3s, and effective number of codons (Nc).

    • Main Results:

    • Highly expressed genes in Y. pestis showed a preference for 'C' or 'G' at synonymous sites, while lowly expressed genes preferred 'A' or 'T'.
    • Gene expression level was significantly correlated with the primary axis of COA (R=0.63, P<0.0001), confirming its role in codon usage bias.
    • GC-skew analysis indicated that codon usage is affected by replication-transcriptional selection. Gene length and composition also showed variations in codon usage metrics.

    Conclusions:

    • Gene expressivity, replication-transcriptional selection, gene length, and gene composition are key determinants of codon usage variation in Yersinia pestis.
    • These findings provide a deeper understanding of the evolutionary forces shaping the genome of this important human pathogen.