Kahali Bratati, Basak Surajit, Ghosh Tapash Chandra
Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India.
J Biomol Struct Dyn. 2008 Jun;25(6):655-61. doi: 10.1080/07391102.2008.10507212.
Biased usage of synonymous codons has been elucidated under the perspective of cellular tRNA abundance and more recently by the mRNA secondary structure folding stability of the corresponding genes. Taking advantage of publicly available gene expression data for Escherichia coli, a comprehensive investigation of the three classes of genes having different codon usage biases was performed from the standpoint of tRNA abundance, mRNA secondary structure folding stability, and translational error minimization procedure. We detected the different evolutionary forces for translational and/or transcriptional regulation of highly expressed genes depending upon their codon bias. Additionally, the possible role of mRNA folding stability in maintaining the overall high expressivity of the set of lowly biased genes has been articulated. These novel findings certainly strengthen the understanding of the codon usage bias in the Escherichia coli genome.
同义密码子的偏向性使用已从细胞tRNA丰度的角度得到阐释，最近又通过相应基因的mRNA二级结构折叠稳定性得以阐明。利用公开可得的大肠杆菌基因表达数据，从tRNA丰度、mRNA二级结构折叠稳定性以及翻译错误最小化程序的角度，对具有不同密码子使用偏向性的三类基因进行了全面研究。我们检测到，根据密码子偏向性的不同，高表达基因在翻译和/或转录调控方面存在不同的进化驱动力。此外，还阐明了mRNA折叠稳定性在维持低偏向性基因集整体高表达水平方面可能发挥的作用。这些新发现无疑加深了我们对大肠杆菌基因组中密码子使用偏向性的理解。
