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An Insight into Codon Pattern Analysis of Autophagy Genes Associated with Virus Infection

Shailja Singhal1, Utsang Kumar1, Taha Alqahtani2

  • 1Department of Biochemistry and Genetics, Barkatullah University, Bhopal, 462026, India.

Current Pharmaceutical Design
|April 19, 2023
PubMed
Abstract

Insights

Genetic manipulation of autophagy genes can curb viral infections by altering codon usage. This study analyzed codon patterns in 41 autophagy genes, offering insights for developing antiviral strategies.

Area of Science:

  • Molecular Biology
  • Virology
  • Genetics

Background:

  • Autophagy and apoptosis are key cellular processes for homeostasis.
  • Autophagy is linked to various diseases, including viral infections.
  • Altering gene expression via genetic manipulation is a potential antiviral strategy.

Purpose of the Study:

  • To analyze codon usage patterns in autophagy genes relevant to viral infections.
  • To identify molecular patterns, codon preferences, and biases in these genes.
  • To inform genetic manipulation strategies for controlling viral infections.

Main Methods:

  • Bioinformatic analysis of codon patterns (synonymous codon usage, codon bias, codon pair bias).
  • Statistical analysis of codon usage in 41 autophagy genes.
  • Identification of preferred and rare codons and codon pairs.

Main Results:

  • Distinct codon preferences (A/T vs. G/C ending codons) were observed among genes.
  • AAA-GAA and CAG-CTG were the most frequent codon pairs.
  • CGA, TCG, CCG, and GCG were identified as rarely used codons.

Conclusions:

  • Codon usage analysis provides insights for genetic manipulation of autophagy genes.
  • Gene modification tools like CRISPR can be used to target these genes.
  • Codon deoptimization and optimization strategies can effectively modulate gene expression for antiviral purposes, as shown for the HO-1 gene.
Keywords:
Autophagy geneRSCUcodon usage biasevolutionary forcesgene expressionnucleotide compositionodds ratio

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