翻译效率
密码子使用偏好性
生物
核糖体分析
翻译(生物学)
遗传学
基因
核糖体
信使核糖核酸
蛋白质生物合成
起始密码子
真核翻译
同义替换
计算生物学
基因组
核糖核酸
作者
Kenji Nakahigashi,Yuki Takai,Yuh Shiwa,Masahiko Wada,Masayuki Honma,Hirofumi Yoshikawa,Masaru Tomita,Akio Kanai,Hirotada Mori
出处
期刊:BMC Genomics
[Springer Nature]
日期:2014-01-01
卷期号:15 (1): 1115-1115
被引量:60
标识
DOI:10.1186/1471-2164-15-1115
摘要
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.
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