Compositional features and codon usage pattern of TP63 gene

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• The TP63 gene encodes tumor protein p63, a homolog of p53, involved in stress, signal transduction, and cell cycle control.
• Codon usage bias (CUB) reflects evolutionary forces like natural selection and mutational pressure influencing gene expression.
• No prior bioinformatic analysis existed for TP63 transcript variants' base distribution and CUB.

Purpose of the Study:

• To investigate the base distribution and codon usage bias (CUB) of TP63 gene transcript variants (isoforms) using bioinformatic approaches.
• To understand the evolutionary forces shaping the CUB of the TP63 gene.

Main Methods:

• Bioinformatic analysis of TP63 gene isoforms.
• Assessment of base composition, including GC content.
• Calculation of the effective number of codons (ENC) to measure CUB.
• Analysis of relative synonymous codon usage (RSCU) for specific codons.
• Correlation analysis between nucleotide composition, CUB, and protein aromaticity.

Main Results:

• TP63 isoforms showed GC content above 50%, indicating GC richness.
• The mean effective number of codons (ENC) was 51.83, signifying low overall CUB for the TP63 gene.
• Natural selection acted against the CTA codon in 8 out of 13 isoforms.
• Five codons (CTG, CAG, ATC, AAC, GCC) were over-represented (RSCU > 1.6).
• Both mutational pressure and natural selection were identified as key factors molding TP63's CUB.
• CUB variation correlated with the aromaticity of the p63 protein.

Conclusions:

• The TP63 gene exhibits low codon usage bias, influenced by both mutational pressure and natural selection.
• Specific codon preferences and avoidance patterns were observed across TP63 isoforms.
• The codon usage bias in TP63 is linked to the protein's aromaticity, suggesting functional implications.