Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
Comput Biol Chem. 2019 Dec;83:107119. doi: 10.1016/j.compbiolchem.2019.107119. Epub 2019 Aug 28.
The tumor protein p63encoded by the gene TP63 acts as a homologue of p53 protein. TP63 gene is the transformation factor with two initiation sites for transcriptional process and is related with stress, signal transduction and cell cycle control. The biasness in the preference of a few codons more frequently over other synonymous codons is the codon usage bias (CUB). Natural selection and mutational pressure are the two prime evolutionary forces acting on CUB. Here, the bioinformatic based analysis was performed to investigate the base distribution and CUB of TP63transcript variants (isoforms) as no work was performed earlier. Analysis of compositional features revealed variation in base content across TP63 gene isoforms and the GC content was more than 50%, indicating GC richness of its isoforms. The mean effective number of codons (ENC), a measure of CUB, was 51.83, i.e. overall CUB of TP63 gene was low. Among 13 isoforms of TP63 gene, nature selected against the CTA codon in 8 isoforms and favored five over-represented (RSCU > 1.6) codons namely CTG, CAG, ATC, AAC and GCC during evolution. Correlation between overall nucleotide composition and its 3rd codon position revealed that both mutational pressure and natural selection moulded its CUB. Further, the correlation between ENC and aromaticity depicted that variation of CUB was related to the degree of aromaticity of p63 protein.
基因 TP63 编码的肿瘤蛋白 p63 作为 p53 蛋白的同源物发挥作用。TP63 基因是转录过程有两个起始位点的转化因子，与应激、信号转导和细胞周期控制有关。少数密码子比其他同义密码子更频繁地偏好使用的偏差称为密码子使用偏性（CUB）。自然选择和突变压力是作用于 CUB 的两个主要进化力量。在这里，我们对 TP63 转录变体（异构体）的碱基分布和 CUB 进行了基于生物信息学的分析，因为之前没有进行过这项工作。组成特征的分析揭示了 TP63 基因异构体中碱基含量的变化，GC 含量超过 50%，表明其异构体的 GC 丰富度。有效密码子平均数（ENC）是衡量 CUB 的指标，其值为 51.83，即 TP63 基因的整体 CUB 较低。在 TP63 基因的 13 个异构体中，自然选择在 8 个异构体中对 CTA 密码子不利，在进化过程中，偏爱 5 个过表达（RSCU > 1.6）的密码子，即 CTG、CAG、ATC、AAC 和 GCC。总体核苷酸组成与其第三个密码子位置之间的相关性表明，突变压力和自然选择共同塑造了它的 CUB。此外，ENC 与芳香性之间的相关性表明，CUB 的变化与 p63 蛋白的芳香性程度有关。
