Kahali Bratati, Basak Surajit, Ghosh Tapash Chandra
Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India.
Biochem Biophys Res Commun. 2007 Mar 16;354(3):693-9. doi: 10.1016/j.bbrc.2007.01.038. Epub 2007 Jan 17.
Biased usage of synonymous codons has been elucidated under the perspective of cellular tRNA abundance for quite a long time now. Taking advantage of publicly available gene expression data for Saccharomyces cerevisiae, a systematic analysis of the codon and amino acid usages in two different coding regions corresponding to the regular (helix and strand) as well as the irregular (coil) protein secondary structures, have been performed. Our analyses suggest that apart from tRNA abundance, mRNA folding stability is another major evolutionary force in shaping the codon and amino acid usage differences between the highly and lowly expressed genes in S. cerevisiae genome and surprisingly it depends on the coding regions corresponding to the secondary structures of the encoded proteins. This is obviously a new paradigm in understanding the codon usage in S. cerevisiae. Differential amino acid usage between highly and lowly expressed genes in the regions coding for the irregular protein secondary structure in S. cerevisiae is expounded by the stability of the mRNA folded structure. Irrespective of the protein secondary structural type, the highly expressed genes always tend to encode cheaper amino acids in order to reduce the overall biosynthetic cost of production of the corresponding protein. This study supports the hypothesis that the tRNA abundance is a consequence of and not a reason for the biased usage of amino acid between highly and lowly expressed genes.
很长一段时间以来，从细胞tRNA丰度的角度对同义密码子的偏向性使用进行了阐释。利用公开可得的酿酒酵母基因表达数据，对与规则（螺旋和链）以及不规则（卷曲）蛋白质二级结构相对应的两个不同编码区域中的密码子和氨基酸使用情况进行了系统分析。我们的分析表明，除了tRNA丰度外，mRNA折叠稳定性是塑造酿酒酵母基因组中高表达和低表达基因之间密码子和氨基酸使用差异的另一个主要进化力量，令人惊讶的是，它取决于与编码蛋白质二级结构相对应的编码区域。这显然是理解酿酒酵母密码子使用的一个新范式。酿酒酵母中不规则蛋白质二级结构编码区域内高表达和低表达基因之间的氨基酸使用差异，是由mRNA折叠结构的稳定性来解释的。无论蛋白质二级结构类型如何，高表达基因总是倾向于编码成本较低的氨基酸，以降低相应蛋白质生产的总体生物合成成本。这项研究支持了这样一种假说，即tRNA丰度是高表达和低表达基因之间氨基酸偏向性使用的结果而非原因。
