Nakahigashi Kenji, Takai Yuki, Shiwa Yuh, Wada Mei, Honma Masayuki, Yoshikawa Hirofumi, Tomita Masaru, Kanai Akio, Mori Hirotada
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
BMC Genomics. 2014 Dec 16;15(1):1115. doi: 10.1186/1471-2164-15-1115.
There is a significant difference between synonymous codon usage in many organisms, and it is known that codons used more frequently generally showed efficient decoding rate. At the gene level, however, there are conflicting reports on the existence of a correlation between codon adaptation and translation efficiency, even in the same organism.
To resolve this issue, we cultured Escherichia coli under conditions designed to maintain constant levels of mRNA and protein and subjected the cells to ribosome profiling (RP) and mRNA-seq analyses. We showed that the RP results correlated more closely with protein levels generated under similar culture conditions than with the mRNA abundance from the mRNA-seq. Our result indicated that RP/mRNA ratio could be used as a measure of translation efficiency at gene level. On the other hand, the RP data showed that codon-specific ribosome density at the decoding site negatively correlated with codon usage, consistent with the hypothesis that preferred codons display lower ribosome densities due to their faster decoding rate. However, highly codon-adapted genes showed higher ribosome densities at the gene level, indicating that the efficiency of translation initiation, rather than higher elongation efficiency of preferred codons, exerted a greater effect on ribosome density and thus translation efficiency.
These findings indicate that evolutionary pressure on highly expressed genes influenced both codon bias and translation initiation efficiency and therefore explains contradictory findings that codon usage bias correlates with translation efficiency of native genes, but not with the artificially created gene pool, which was not subjected to evolution pressure.
许多生物体中同义密码子的使用存在显著差异，且已知使用频率较高的密码子通常具有较高的解码效率。然而，在基因水平上，即使在同一生物体中，关于密码子适应性与翻译效率之间是否存在相关性也存在相互矛盾的报道。
为了解决这个问题，我们在旨在维持mRNA和蛋白质水平恒定的条件下培养大肠杆菌，并对细胞进行核糖体图谱分析（RP）和mRNA测序分析。我们发现，RP结果与相似培养条件下产生的蛋白质水平的相关性比与mRNA测序得到的mRNA丰度的相关性更紧密。我们的结果表明，RP/mRNA比值可作为基因水平翻译效率的一个衡量指标。另一方面，RP数据显示，解码位点的密码子特异性核糖体密度与密码子使用呈负相关，这与以下假设一致：由于其更快的解码速率，偏好密码子显示出较低的核糖体密度。然而，高度密码子适应的基因在基因水平上显示出更高的核糖体密度，这表明翻译起始效率而非偏好密码子更高的延伸效率对核糖体密度进而对翻译效率产生了更大的影响。
这些发现表明，对高表达基因的进化压力影响了密码子偏好和翻译起始效率，因此解释了相互矛盾的发现：密码子使用偏好与天然基因的翻译效率相关，但与未经历进化压力的人工创建的基因库的翻译效率无关。
