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首页> 外文期刊>Yeast >Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
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Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae

机译：酿酒酵母密码子偏倚与mRNA浓度和蛋白质长度的关系

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In 1982, Ikemura reported a strikingly unequal usage of different synonymous codons, in five Saccharomyces cerevisiae nuclear genes having high protein levels. To study this trend in detail, we examined data from three independent studies that used oligonncleotide arrays or SAGE to estimate mRNA concentrations for nearly all genes in the genome. Correlation coefficients were calculated for the relationship of mRNA concentration to four commonly used measures of synonymous codon usage bias: the codon adaptation index (CAI), the codon bias index (CBI), the frequency of optimal codons (Fop), and the effective number Of codons (N_c). mRNA concentration was best approximated as an exponential function of each of these four measures. Of the four, the CAI was the most strongly correlated with mRNA concentration (r_s=0.62+-0.01, n=2525, p<10~(-17)). When we controlled for CAI, mRNA concentration and protein length were negatively correlated (partial r_s =-0.23 +- 0.01, n = 4765, p < 10~(-17)). This may result from selection to reduce the size of abundant proteins to minimize transcriptional and translational costs. When we controlled for mRNA concentration, protein length and CAI were positively correlated (partial r_s = 0.16 +- 0.01, n =4765, p < 10~(-17)). This may reflect more effective selection in longer genes against missense errors during translation. The correlation coefficients between the mRNA levels of individual genes, as measured by different investigators and methods, were low, in the range r_s = 0.39-0.68.
机译：1982年，Ikemura报告了在五个具有高蛋白水平的酿酒酵母核基因中，不同同义密码子的使用方式显着不同。为了详细研究这种趋势，我们检查了来自三项独立研究的数据，这些研究使用寡核苷酸阵列或SAGE估计了基因组中几乎所有基因的mRNA浓度。计算mRNA浓度与四种常用的同义密码子使用偏倚度量之间的关系的相关系数：密码子适应指数（CAI），密码子偏倚指数（CBI），最佳密码子频率（Fop）和有效数密码子（N_c）。最好将mRNA浓度近似地作为这四个指标中每个指标的指数函数。在这四个中，CAI与mRNA浓度之间的相关性最强（r_s = 0.62 + -0.01，n = 2525，p <10〜（-17））。当我们控制CAI时，mRNA浓度和蛋白质长度呈负相关（部分r_s = -0.23 +-0.01，n = 4765，p <10〜（-17））。这可能是由于选择以减少丰富蛋白质的大小以最小化转录和翻译成本而导致的。当我们控制mRNA浓度时，蛋白质长度和CAI正相关（部分r_s = 0.16 +-0.01，n = 4765，p <10〜（-17））。这可能反映了在更长的基因中针对翻译过程中错义错误进行了更有效的选择。通过不同的研究人员和方法测量，单个基因的mRNA水平之间的相关系数很低，范围为r_s = 0.39-0.68。

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