Codon usage divergence of important functional genes in Mycobacterium tuberculosis

Area of Science:

• Genomics
• Molecular Biology
• Microbiology

Background:

• Sequence characteristics of Mycobacterium tuberculosis are crucial for understanding host adaptation, metabolism, genetic diversity, drug resistance, and infectivity.
• Analyzing codon usage patterns in Mycobacterium tuberculosis provides significant insights into its genetic makeup and evolutionary strategies.

Purpose of the Study:

• To explore the codon usage patterns of coding sequences in 200 complete genomes of Mycobacterium tuberculosis.
• To evaluate the divergence degree of 21 specific functional genes based on their codon usage parameters.

Main Methods:

• Downloaded 200 random complete Mycobacterium tuberculosis genomes from NCBI.
• Calculated codon bias index, effective number of codons, relative synonymous codon usage, and base composition for 21 functional genes.
• Assessed gene divergence by analyzing differences in relative synonymous codon usage and standard deviations of codon usage parameters.

Main Results:

• All analyzed genes exhibited high GC content and significant codon usage bias for amino acids.
• Genes with a high effective number of codons, such as those in the Myco-bacterial membrane protein large family, showed higher divergence.
• Genes with lower divergence, including ag85A and sigH, were highly conserved and identified as potential drug targets.

Conclusions:

• Codon usage patterns in Mycobacterium tuberculosis reflect gene divergence and conservation.
• Understanding these patterns aids in comprehending Mycobacterium tuberculosis evolution and developing gene-based tuberculosis control strategies.