Deciphering the reading of the genetic code by near-cognate tRNA

Some codons of the genetic code can be read not only by cognate, but also by near-cognate tRNAs. This flexibility is thought to be conferred mainly by a mismatch between the third base of the codon and the first of the anticodon (the so-called wobble position). However, this simplistic explanation underestimates the importance of nucleotide modifications in the decoding process. Using a system in which only near-cognate tRNAs can decode a specific codon, we investigated the role of six modifications of the anticodon, or adjacent nucleotides, of the tRNAs specific for Tyr, Gln, Lys, Trp, Cys and Arg in Saccharomyces cerevisiae. Modifications almost systematically rendered these tRNAs able to act as near-cognate tRNAs at stop codons, even though they involve non-canonical base-pairs, without markedly affecting their ability to decode cognate or near-cognate sense codons. These findings reveal an important effect of modifications to tRNA decoding with implications for understanding the flexibility of the genetic code.遗传密码的部分密码子，不仅可被同源tRNA（cognate tRNA）识别，亦可被近同源tRNA（near-cognate tRNA）识别。学界普遍认为，这种灵活性主要由密码子第三位碱基与反密码子第一位碱基（即所谓的摆动位（wobble position））之间的错配所赋予。然而，这一过于简化的解释低估了核苷酸修饰在解码过程中的重要性。我们借助仅允许近同源tRNA识别特定密码子的实验体系，对酿酒酵母（Saccharomyces cerevisiae）中针对酪氨酸（Tyr）、谷氨酰胺（Gln）、赖氨酸（Lys）、色氨酸（Trp）、半胱氨酸（Cys）及精氨酸（Arg）的特异性tRNA的反密码子或邻近核苷酸的六种修饰的作用展开了研究。这些修饰几乎无一例外地使这些tRNA能够在终止密码子（stop codons）处充当近同源tRNA——即便这些修饰涉及非经典碱基配对（non-canonical base-pairs）——且未对其识别同源或近同源有义密码子（sense codons）的能力造成显著影响。这些发现揭示了tRNA解码相关修饰的重要作用，为理解遗传密码的灵活性提供了关键启示。