Satapathy Siddhartha Sankar, Powdel Bhesh Raj, Buragohain Alak Kumar, Ray Suvendra Kumar
Department of Computer Science and Engineering, Tezpur University, Napaam, Tezpur 784028, Assam, India.
Department of Statistics, Darrang College, Tezpur 784001, Assam, India.
DNA Res. 2016 Oct 1;23(5):441-449. doi: 10.1093/dnares/dsw027.
The different triplets encoding the same amino acid, termed as synonymous codons, are not equally abundant in a genome. Factors such as G + C% and tRNA are known to influence their abundance in a genome. However, the order of the nucleotide in each codon per se might also be another factor impacting on its abundance values. Of the synonymous codons for specific amino acids, some are preferentially used in the high expression genes that are referred to as the 'optimal codons' (OCs). In this study, we compared OCs of the 18 amino acids in 221 species of bacteria. It is observed that there is amino acid specific influence for the selection of OCs. There is also influence of phylogeny in the choice of OCs for some amino acids such as Glu, Gln, Lys and Leu. The phenomenon of codon bias is also supported by the comparative studies of the abundance values of the synonymous codons with same G + C. It is likely that the order of the nucleotides in the triplet codon is also perhaps involved in the phenomenon of codon usage bias in organisms.
编码相同氨基酸的不同三联体被称为同义密码子，它们在基因组中的丰度并不相同。已知诸如G + C%和tRNA等因素会影响它们在基因组中的丰度。然而，每个密码子中核苷酸的顺序本身也可能是影响其丰度值的另一个因素。在特定氨基酸的同义密码子中，有些在高表达基因中被优先使用，这些被称为“最优密码子”（OCs）。在本研究中，我们比较了221种细菌中18种氨基酸的最优密码子。观察到在最优密码子的选择上存在氨基酸特异性影响。对于某些氨基酸如Glu、Gln、Lys和Leu，系统发育也会影响最优密码子的选择。对具有相同G + C的同义密码子丰度值的比较研究也支持了密码子偏好现象。三联体密码子中核苷酸的顺序很可能也参与了生物体中密码子使用偏好现象。
