A New Look at Codon Usage and Protein Expression.
A New Look at Codon Usage and Protein Expression.
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DOI：
10.29007/d4tz
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发表时间：
2019
期刊：
影响因子：
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通讯作者：
Emrich S
中科院分区：
文献类型：
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作者：
Wright G;Rodriguez A;Clark PL;Emrich S
%MinMax是一个基因内翻译延伸率模型，它依赖于密码子的使用频率。从历史上看，%MinMax使用表格来测量生物体中所有基因的密码子使用偏差，例如在hiv - cut中发现的那些。在本文中，我们提供的证据表明，基于所有基因的密码子使用偏差不足以准确测量绝对翻译率。我们表明，由另一个模型（ROC-SEMPPR）生成的替代“高φ”密码子使用表是一个有前途的替代方案。通过创建一个混合模型，未来的密码子使用分析及其应用（例如密码子协调）可能更准确地测量翻译延伸的“速度”。我们还建议采用高φ替代密码子适应指数（CAI），这是基于高表达基因的密码子使用偏差的经典度量。值得注意的是，我们的新替代方案与传统CAI一样与经验数据具有良好的相关性，而无需使用实验确定的表达计数作为输入。
%MinMax, a model of intra-gene translational elongation rate, relies on codon usage frequencies. Historically, %MinMax has used tables that measure codon usage bias for all genes in an organism, such as those found at HIVE-CUT. In this paper, we provide evidence that codon usage bias based on all genes is insufficient to accurately measure absolute translation rate. We show that alternative “High-ϕ” codon usage tables, generated by another model (ROC-SEMPPR), are a promising alternative. By creating a hybrid model, future codon usage analyses and their applications (e.g., codon harmonization) are likely to more accurately measure the “tempo” of translation elongation. We also suggest a High-ϕ alternative to the Codon Adaptation Index (CAI), a classic metric of codon usage bias based on highly expressed genes. Significantly, our new alternative is equally well correlated with empirical data as traditional CAI without using experimentally determined expression counts as input.