Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, Assam, India.
Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
Mitochondrion. 2017 Nov;37:17-26. doi: 10.1016/j.mito.2017.06.004. Epub 2017 Jun 28.
Animal mitochondrial genome harbours 13 protein coding genes which regulate the process of respiration. The mitochondrial NADH dehydrogenase 1 (MT-ND1) gene, one of the 13 protein-coding genes, encodes the NADH dehydrogenase 1 enzyme of the respiratory chain. Analysis of codon usage bias (CUB) acquires importance for better understanding of the molecular biology, new gene discovery, design of transgenes and gene evolution. The MT-ND1 gene seems to be a good candidate for analyzing codon usage pattern, since no work has yet been reported. Moreover, it is still not clear which factors significantly influence the codon usage pattern. In the present study, comparative analysis of codon usage pattern, expression level and influencing factors for MT-ND1 gene from 100 different species each of pisces, aves and mammals were used for CUB analysis. Our result suggests that the gene is AT rich in pisces, aves and mammals and most of the nucleotides significantly differ among them as revealed from t-test. CUB was not remarkable as reflected by high value of effective number of codons and it also significantly differs among pisces, aves and mammals. Although we found that CUB is mainly influenced by natural selection and mutation pressure for MT-ND1 gene as suggested by correlation and correspondence analysis but neutrality plot further revealed that natural selection played a major role and mutation pressure played a minor role in codon usage pattern. Additionally, t-test analysis showed that the MT-ND1 gene has a wide significant discrepancy in codon choices in pisces, aves and mammals. This study has contributed to boost our understanding about the mechanism of distribution of the codons and the factors that may influence the evolution of the MT-ND1 gene.
动物的线粒体基因组包含 13 个编码蛋白质的基因，这些基因调控着呼吸过程。线粒体 NADH 脱氢酶 1（MT-ND1）基因是这 13 个编码蛋白质的基因之一，它编码呼吸链中的 NADH 脱氢酶 1 酶。分析密码子使用偏性（CUB）对于更好地理解分子生物学、新基因的发现、转基因的设计和基因进化具有重要意义。MT-ND1 基因似乎是分析密码子使用模式的一个很好的候选基因，因为迄今为止还没有报道过相关工作。此外，哪些因素显著影响密码子使用模式仍不清楚。在本研究中，我们使用来自 100 种不同鱼类、鸟类和哺乳动物的每个物种的 MT-ND1 基因进行了密码子使用模式、表达水平和影响因素的比较分析，以进行 CUB 分析。我们的结果表明，该基因在鱼类、鸟类和哺乳动物中富含 AT，并且大多数核苷酸在它们之间存在显著差异，如 t 检验所示。由于有效密码子数的值较高，因此 CUB 不显著，并且在鱼类、鸟类和哺乳动物之间也存在显著差异。尽管我们发现 CUB 主要受到自然选择和突变压力的影响，但相关和对应分析表明，对于 MT-ND1 基因，但中性作图进一步表明，自然选择在密码子使用模式中起主要作用，而突变压力起次要作用。此外，t 检验分析表明，MT-ND1 基因在鱼类、鸟类和哺乳动物中在密码子选择上存在广泛的显著差异。这项研究有助于我们更好地理解密码子分布的机制以及可能影响 MT-ND1 基因进化的因素。
