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Codon Usage Analysis of Pro-Apoptotic Bim Gene Isoforms.

Rekha Khandia1, Azmat Ali Khan2, Athanasios Alexiou3

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

Journal of Alzheimer'S Disease : JAD
|March 7, 2022
PubMed
Summary

Bim gene expression is influenced by codon usage and molecular signatures. High usage of CpC dinucleotides in Bim isoforms suggests selection forces fine-tuning gene expression for proper cellular function.

Keywords:
Bim geneCAICpC dinucleotidecodon usagepro-apoptotic gene

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Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Bim is a pro-apoptotic protein crucial in physiological and pathological states.
  • Aberrant Bim expression is linked to various diseases.
  • Multiple Bim isoforms exist with differing apoptotic capacities.

Purpose of the Study:

  • To investigate the relationship between molecular signatures and codon selection in Bim isoforms.
  • To understand how codon usage influences Bim gene expression and protein function.

Main Methods:

  • Analysis of molecular signatures including nucleotide composition, codon usage, skews, and mRNA free energy.
  • Determination of codon adaptation index, relative synonymous codon usage, and dinucleotide odds ratio for Bim isoforms.
  • Correlation of these signatures with observed codon choices in the Bim gene.

Main Results:

  • Skew analysis revealed a preference for C over G, A, and T nucleotides, and G over T and A.
  • Increased C content at the first and third codon positions enhanced gene expression, while at the second, it decreased it.
  • An exceptionally high frequency of CpC dinucleotides was observed across all 31 Bim isoforms, suggesting selection for fine-tuning gene expression.
  • Mutational pressure was identified as a significant factor shaping codon usage bias in Bim isoforms.

Conclusions:

  • The high usage of CpC dinucleotides in Bim isoforms indicates strong selective pressure for precise regulation of Bim gene expression.
  • Understanding these molecular signatures provides insights into the control mechanisms of apoptosis and Bim-related diseases.