CODON PAIRS, CODON CONTEXT AND TRANSLATIONAL EFFICIENCY

大肠杆菌、酵母菌、小鼠、大鼠对密码子的利用模式 而人类(大概还有所有的有机体)都有很强的偏见， 超越了先前注意到的蛋白质编码序列中的偏向。这个密码子 配对偏向与密码子的使用、氨基酸配对偏向或邻近无关 二核苷酸偏向。密码子对偏向仅限于最近的邻居和 这是方向性的。密码子对的偏向可能是 相邻tRNA相互作用的生物学后果 在翻译核糖体表面的分子，以及 相邻同源tRNA的亲和性影响翻译 每对密码子的步长。确实是对文献的一种调查 揭示了许多支持这些类型的tRNA-tRNA相互作用的报告， 这里提出的证据表明，在大肠杆菌中， 密码子对的翻译速度比未被充分表达的密码子慢得多 成对的。提出了物种特定密码子对的利用 模式已经演变，因此翻译的动力学可以 不受氨基酸序列限制的控制，并且 翻译步长是相关的，也许是以一种可预测的方式， 密码子对利用的物种特定模式。如果这是 这种情况下，那么了解这种关系将是非常有意义的 具有重要的功能意义和现实意义。的目标是 这里提出的研究是为了进一步检验两者之间的相关性 密码子对偏差和翻译效率，并检验假设 这种密码子对的偏向是由 翻译表面tRNA分子间的相互作用 核糖体。

Codon pair utilization patterns in Escherichia coli, yeast, mouse, rat and human (and presumably all organisms) are highly biased, above and beyond previously noted biases in protein coding sequences. This codon pair bias is independent of codon usage, amino acid pair bias or adjacent dinucleotide bias. Codon pair bias is limited to nearest neighbors and it is directional. It is possible that codon pair bias is the result of the biological consequences of interactions between adjacent tRNA molecules on the surface of a translating ribosome, and that the compatibilities of adjacent cognate tRNA influence the translational step-times across each codon pair. Indeed a survey of the literature reveals many reports that support these types of tRNA-tRNA interactions, and evidence is presented here that, in E coli, highly over-represented codon pairs are translated much more slowly than under-represented codon pairs. It is proposed that species-specific codon pair utilization patterns have evolved so that the kinetics of translation can be controlled without constraints on amino acid sequences, and that translational step-times are related, perhaps in a predictable manner, to the species-specific patterns of codon pair utilization. If this is the case, then an understanding of this relationship would be of great functional significance and practical importance. The goal of the research proposed here is to further examine the correlation between codon pair bias and translational efficiency, and to test the hypothesis that codon pair bias is the result of the biological consequences of interactions between tRNA molecules on the surface of a translating ribosome.