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Related Experiment Videos

[Codon usage bias of Catharanthus roseus].

Ying Li1, Xue-Jun Kuang1, Xiao-Xuan Zhu1

  • 1Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.

Zhongguo Zhong Yao Za Zhi = Zhongguo Zhongyao Zazhi = China Journal of Chinese Materia Medica
|September 22, 2017
PubMed
Summary

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Catharanthus roseus prefers codons ending in A or T, differing significantly from E. coli. Saccharomyces cerevisiae may be a better host for expressing C. roseus genes due to fewer rare codons.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Understanding codon usage bias is crucial for gene expression and species evolution.
  • Catharanthus roseus (C. roseus) has complex gene expression patterns.
  • Terpenoid indole alkaloids (TIAs) are important secondary metabolites in C. roseus.

Purpose of the Study:

  • To analyze codon usage bias in C. roseus.
  • To provide guidance for heterologous gene expression and species evolution studies.
  • To compare codon usage patterns between C. roseus, E. coli, and S. cerevisiae.

Main Methods:

  • Analysis of codon composition and usage bias in 30,437 C. roseus coding sequences.
  • Calculation of rare codon proportions for E. coli and S. cerevisiae in 25 TIA biosynthesis genes.
Keywords:
Catharanthus roseusbiosynthetic pathwayscodon biasgenometerpenoid indole alkaloids

Related Experiment Videos

  • Assessment of relative synonymous codon usage (RSCU).

    • Main Results:

    • Average GC content of C. roseus genes was 42.47%, with 35.89% at the third codon position.
    • 28 codons had an RSCU > 1, with 26 ending in A or T.
    • TIA biosynthesis genes in C. roseus contained significantly more E. coli rare codons than S. cerevisiae rare codons.

    Conclusions:

    • C. roseus preferentially uses codons ending in A or T.
    • C. roseus codon usage rules differ more from E. coli than S. cerevisiae.
    • S. cerevisiae is a potentially more suitable host for heterologous expression of C. roseus genes.