Steinberg S V, Kisselev L L
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow.
Biochimie. 1992 Apr;74(4):337-51. doi: 10.1016/0300-9084(92)90111-q.
A number of experimental approaches have been developed for identification of recognition (identity) sites in tRNAs. Along with them a theoretical methodology has been proposed by McClain et al that is based on concomitant analysis of all tRNA sequences from a given species. This approach allows an evaluation of nucleotide combinations present in isoacceptor tRNAs specific for the given amino acid, and not present in equivalent positions in cloverleaf structure in other tRNAs of the same organism. These elements predicted from computer analysis of the databank could be tested experimentally for their participation in forming recognition sites. The correlation between theoretical predictions and experimental data appeared promising. The aim of the present work consisted of introducing further improvements into McClain's procedure by: i), introducing into analysis a variable region in tRNAs which had not been previously considered; to accomplish this, 'normalization' of variable nucleotides was suggested, based on primary and tertiary structures of tRNAs; ii), developing a new procedure for comparison of patterns for synonymous and non-synonymous tRNAs from different organisms; iii), analysis of 3- and 4-positional contacts between tRNAs and enzymes in addition to a formerly used 2-positional model. A systematic application of McClain's procedure to mammalian, yeast and E coli tRNAs led to the following results: i), imitancy patterns for non-synonymous tRNAs of any amino acid specificity and from any organisms analysed so far overlap by no more than 30%, providing a structural basis for discrimination with high fidelity between cognate and non-cognate tRNAs; ii), the predicted identity sites are non-randomly distributed within tRNA molecules; the dominant role is ascribed to only two regions--anticodon and amino acid stem which are located far apart from one another at extremes of all tRNA molecules; iii), the imitancy patterns for synonymous tRNAs in lower (yeast) and higher (mammalian) eukaryotes are similar but not identical; iv), distribution of predicted identity sites in the cloverleaf structure in prokaryotes and eukaryotes is essentially different: in eubacterial tRNAs the major role in recognition plays anticodon and/or amino acid acceptor stem, whereas in eukaryotic (both unicellular and multicellular) tRNAs the remaining part of the molecules is also involved in recognition; v), the imitancy patterns of synonymous tRNAs from prokaryotes and eukaryotes are dissimilar, this observation leads to the prediction that the tRNA identity sites for the same amino acid in prokaryotes and eukaryotes may differ.
已经开发出多种实验方法来鉴定tRNA中的识别（身份）位点。与此同时，麦克莱恩等人提出了一种理论方法，该方法基于对给定物种的所有tRNA序列的同步分析。这种方法可以评估特定氨基酸的同工受体tRNA中存在的核苷酸组合，而在同一生物体的其他tRNA的三叶草结构的等效位置中不存在。通过对数据库的计算机分析预测的这些元件可以通过实验测试它们是否参与形成识别位点。理论预测与实验数据之间的相关性似乎很有前景。本研究的目的是通过以下方式对麦克莱恩的程序进行进一步改进：i），在分析中引入以前未考虑的tRNA可变区；为了实现这一点，基于tRNA的一级和三级结构，提出了可变核苷酸的“标准化”；ii），开发一种新的程序，用于比较来自不同生物体的同义tRNA和非同义tRNA的模式；iii），除了以前使用的二位模型之外，分析tRNA与酶之间在3位和4位的接触。将麦克莱恩的程序系统地应用于哺乳动物、酵母和大肠杆菌的tRNA，得到了以下结果：i），到目前为止，所分析的任何氨基酸特异性和任何生物体的非同义tRNA的模仿模式重叠不超过30%，为高保真地区分同源和非同源tRNA提供了结构基础；ii），预测的识别位点在tRNA分子内非随机分布；主要作用仅归因于两个区域——反密码子和氨基酸茎，它们在所有tRNA分子的两端彼此相距很远；iii），低等（酵母）和高等（哺乳动物）真核生物中同义tRNA的模仿模式相似但不相同；iv），原核生物和真核生物三叶草结构中预测的识别位点分布基本不同：在真细菌tRNA中，识别的主要作用由反密码子和/或氨基酸接受茎发挥，而在真核生物（单细胞和多细胞）tRNA中，分子的其余部分也参与识别；v），原核生物和真核生物同义tRNA的模仿模式不同，这一观察结果导致预测原核生物和真核生物中相同氨基酸的tRNA识别位点可能不同。
