Sense codons are found in specific contexts.
Sense codons are found in specific contexts.
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DOI：
10.1016/0022-2836(85)90239-6
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发表时间：
1985-04
影响因子：
5.6
通讯作者：
M. Yarus;L. Folley
中科院分区：
文献类型：
--
作者：
M. Yarus;L. Folley
利用计算机方法对结构基因中密码子的序列环境进行了统计研究。将一组基因产物丰富的大肠杆菌与一组基因产物水平较低的大肠杆菌进行比较，以检测与表达相关的潜在差异。结果显示在密码子附近的核苷酸具有显著的非随机性。出乎意料的是，这些影响在具有稀有产物的基因中更大、更均匀。弱表达基因的影响强度表明，这种非随机序列环境会降低表达。在弱表达的一组基因中，密码子的5 ‘邻位和3 ’邻位的所有位置都是偏置的。在高表达基因中，下一个密码子的第一个核苷酸是唯一受影响的位点。弱表达基因的非随机性分布表明，序列偏差主要是由于直接作用于密码子/反密码子的二级或三级结构的约束。在高表达基因中，观察到的偏倚表明密码子/反密码子与密码子/反密码子外的一个位点之间存在相互作用。在弱表达基因中，非随机近邻序列的大部分倾向可以归因于附近核苷酸与密码子的摆动核苷酸之间的相关性，尽管选择这种相关性会改变氨基酸序列。在低水平表达的基因中，受欢迎的模式是R YYR或Y RRY。R表示嘌呤，Y表示嘧啶；空间是密码子之间的边界。这种对邻近序列的偏好似乎可能是遗传环境效应的物理基础。在这种假设下，这种序列偏差会影响表达。在此基础上，我们预测了减少表达的上下文突变的新位点，并提出了具有最佳翻译活性的信息设计策略。
The sequence environment of codons in structural genes has been investigated statistically, using computer methods. A set ofEscherichia coligenes with abundant products was compared with a set having low gene product levels, in order to detect potential differences associated with expression.The results show striking non-randomness in the nucleotides occurring near codons. These effects are, unexpectedly, very much larger and more homogeneous among the genes with rare products. The intensity of effects in weakly expressed genes suggests that such non-random sequence environments decrease expression.In the weakly expressed set of genes, the 5′ neighbor of a codon, and all positions of the 3′ neighbor codon are biased. In the highly expressed genes, the first nucleotide of the next codon is a uniquely affected site.The distribution of non-randomness in weakly expressed genes suggests that sequence bias is primarily due to a constraint acting directly on the secondary or tertiary structure of the codon/anticodon. In highly expressed genes, the observed bias suggests an interaction between the codon/anticodon and a site outside the codon/anticodon.Much of the tendency to non-random near-neighbor sequences in weakly expressed genes can be ascribed to a correlation between nearby nucleotides and the wobble nucleotide of the codon, despite the fact that selection of such correlations will alter the amino acid sequence. The favored pattern, in genes expressed at low level, is R YYR or Y RRY. R indicates purine, Y indicates pyrimidine; the space is the boundary between codons.It seems likely that this preference for nearby sequences is the physical basis of the genetic context effect. Under this assumption such sequence biases will affect expression. On this basis, we predict new sites for contextual mutations which decrease expression, and suggest strategy for the design of messages having optimal translational activity.