Mazumder Gulshana A, Uddin Arif, Chakraborty Supriyo
Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150, Assam, India.
Mol Biochem Parasitol. 2018 Oct;225:15-26. doi: 10.1016/j.molbiopara.2018.08.007. Epub 2018 Aug 24.
Unequal usage of synonymous codons in the gene transcript for an amino acid is known as codon usage bias (CUB). It is a unique property of gene as well as genome. Mutation and natural selection are known to be the major factors that influence CUB. Other factors encompass gene expression level, GC content, codon position, recombination rate, RNA stability and gene length. CUB analysis helps in in-depth understanding of the molecular biology, genetics and genome evolution in a species. We used bioinformatic methods to explore the pattern of CUB in MT-ATP6 gene in different classes of platyhelminthes. The analysis is based on genetic code of translational table 14 of National Center of Biotechnology Information (NCBI) where the codon AAA codes for asparagine and TAA for tyrosine amino acid. The synonymous codon usage order (SCUO), an index of CUB, values in different classes namely cestoda, monogenea, rabditophora, trematoda and turbellaria of platyhelminths were found to be 0.43, 0.32, 0.49, 0.40 and 0.36, respectively which suggest that the codon usage bias of ATP6 gene was low (SCUO < 0.50). Highly significant correlation (p < 0.001) was found between SCUO and various GC contents indicating that GC composition had an influence on CUB. From the relative synonymous codon usage (RSCU) analysis on codons, we found most of the over-represented codons in all the classes were A/T ending types, which suggested that the preferred codons were influenced by compositional constraints. The PR2 plot revealed asymmetric usage of AT and GC bases among the four fold degenerate codon families with greater usage of G and T over A and C. Highly significant correlation (p < 0.001) was found between overall nucleotide composition and its 3rd codon position suggesting that both natural selection and mutation pressure might have influenced the CUB among different classes. Neutrality analysis revealed that natural selection might play a major role. Mutational responsive index (MRI) and translational selection (P2) values elucidated that selection for translational efficiency moderately affected the codon usage bias in MT-ATP6 gene.
氨基酸基因转录本中同义密码子的不均衡使用被称为密码子使用偏好（CUB）。它是基因以及基因组的一种独特属性。已知突变和自然选择是影响CUB的主要因素。其他因素包括基因表达水平、GC含量、密码子位置、重组率、RNA稳定性和基因长度。CUB分析有助于深入了解一个物种的分子生物学、遗传学和基因组进化。我们使用生物信息学方法来探究不同类扁形动物中MT - ATP6基因的CUB模式。该分析基于美国国立生物技术信息中心（NCBI）翻译表14的遗传密码，其中密码子AAA编码天冬酰胺，TAA编码酪氨酸氨基酸。同义密码子使用顺序（SCUO）作为CUB的一个指标，在扁形动物的不同类别即绦虫纲、单殖纲、蛭纲、吸虫纲和涡虫纲中的值分别为0.43、0.32、0.49、0.40和0.36，这表明ATP6基因的密码子使用偏好较低（SCUO < 0.50）。在SCUO和各种GC含量之间发现了高度显著的相关性（p < 0.001），表明GC组成对CUB有影响。从对密码子的相对同义密码子使用（RSCU）分析中，我们发现所有类别中大多数过度代表的密码子都是以A/T结尾的类型，这表明偏好密码子受到组成限制的影响。PR2图揭示了在四倍简并密码子家族中AT和GC碱基的不对称使用，其中G和T的使用多于A和C。在总体核苷酸组成与其第三个密码子位置之间发现了高度显著的相关性（p < 0.001），这表明自然选择和突变压力可能都对不同类别之间的CUB产生了影响。中性分析表明自然选择可能起主要作用。突变响应指数（MRI）和平移选择（P2）值阐明，对翻译效率的选择适度影响了MT - ATP6基因中的密码子使用偏好。
