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Methodology for Accurate Detection of Mitochondrial DNA Methylation
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Codon usage bias analysis of mitochondrial protein-coding genes in 12 species of Candida

Fen Wang1, Nan Zhang, Chunling Zhao

  • 1School of Basic Medical Science, Southwest Medical University, Luzhou 646000, People's Republic of China.songzhangyong83529@126.com.

Journal of Genetics
|July 19, 2023
PubMed

Insights

Fungal infections are rising, driving research into new antifungal strategies. This study analyzes codon usage bias in Candida mitochondrial genes, revealing mutation pressure as a key factor influencing gene evolution and potential drug resistance.

Area of Science:

  • Microbiology and Molecular Biology
  • Genetics and Genomics
  • Antifungal Drug Discovery

Background:

  • Increasing incidence of fungal infections and challenges in current antifungal treatments, including drug resistance and adverse effects.
  • Fungal mitochondria are implicated in pathogenicity and drug resistance, making them a target for novel therapies.
  • Understanding gene expression patterns, such as codon usage bias, is crucial for developing effective antifungal strategies.

Purpose of the Study:

  • To investigate codon usage bias patterns in mitochondrial genes across 12 species of *Candida*.
  • To identify factors influencing codon usage bias in *Candida* mitochondrial genes.
  • To provide insights into fungal mitochondrial gene evolution and potential targets for antifungal drug development.

Main Methods:

  • Analysis of nucleotide composition and codon usage bias in *Candida* mitochondrial genes.
  • Calculation of Relative Synonymous Codon Usage (RSCU) and Codon Adaptation Index (CAI).
  • Correlation analysis between codon bias, nucleotide composition (GC content), and other evolutionary pressures.

Main Results:

  • *Candida* mitochondrial genes predominantly use A/T bases over G/C bases.
  • Specific codons (UUA, AGU, CCU, GCU, UGA, AGA, GGU) were identified as preferentially used.
  • CAI values varied, with *ATP9* in *C. parapsilosis* showing the highest and *ND6* in *C. auris* the lowest; CAI correlated with codon bias and GC content.
  • Mutation pressure was identified as the dominant factor influencing codon bias, followed by nucleotide composition and selection pressure.

Conclusions:

  • Codon usage bias in *Candida* mitochondrial genes is shaped by multiple factors, with GC content and mutation pressure being critical.
  • These findings offer novel insights into the evolutionary dynamics of fungal mitochondrial genes.
  • Understanding codon usage bias can guide the development of new antifungal therapies targeting mitochondrial functions.

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