Choudhury M N, Uddin A, Chakraborty S
Department of Biotechnology, Assam University, Silchar, Assam, India.
Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, India.
Andrologia. 2018 Feb;50(1). doi: 10.1111/and.12787. Epub 2017 Jan 26.
The SRY gene is present within the sex-determining region of the Y chromosome which is responsible for maleness in mammals. The nonuniform usage of synonymous codons in the mRNA transcript for encoding a particular amino acid is the codon usage bias (CUB). Analysis of codon usage pattern is important to understand the genetic and molecular organisation of a gene. It also helps in heterologous gene expression, design of primer and synthetic gene. However, the analysis of codon usage bias of SRY gene was not yet studied. We have used bioinformatic tools to analyse codon usage bias of SRY gene across mammals. Codon bias index (CBI) indicated that the overall extent of codon usage bias was weak. The relative synonymous codon usage (RSCU) analysis suggested that most frequently used codons had an A or C at the third codon position. Compositional constraint played an important role in codon usage pattern as evident from correspondence analysis (CA). Significant correlation among nucleotides constraints indicated that both mutation pressure and natural selection affect the codon usage pattern. Neutrality plot suggested that natural selection might play a major role, while mutation pressure might play a minor role in codon usage pattern in SRY gene in different species of mammals.
SRY基因存在于Y染色体的性别决定区域内，该区域决定哺乳动物的雄性特征。在编码特定氨基酸的mRNA转录本中同义密码子的非均匀使用就是密码子使用偏好（CUB）。分析密码子使用模式对于理解基因的遗传和分子组织很重要。它也有助于异源基因表达、引物设计和合成基因。然而，SRY基因的密码子使用偏好分析尚未开展。我们利用生物信息学工具分析了哺乳动物中SRY基因的密码子使用偏好。密码子偏好指数（CBI）表明密码子使用偏好的总体程度较弱。相对同义密码子使用（RSCU）分析表明，最常用的密码子在第三个密码子位置有一个A或C。从对应分析（CA）可以明显看出，组成性限制在密码子使用模式中起重要作用。核苷酸限制之间的显著相关性表明，突变压力和自然选择都影响密码子使用模式。中性绘图表明，在不同种类的哺乳动物中，自然选择可能在SRY基因的密码子使用模式中起主要作用，而突变压力可能起次要作用。
