Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates

Variation in translation-elongation kinetics along a transcript’s coding sequence plays an important role in the maintenance of cellular protein homeostasis by regulating co-translational protein folding, localization, and maturation. Translation-elongation speed is influenced by molecular factors within mRNA and protein sequences. For example, when proline is present in the ribosome’s P- or A-site translation slows down, but the effect of other pairs of amino acids, in the context of all 400 possible pairs, has not been characterized. Here, we study Saccharomyces cerevisiae using a combination of mutational experiments, bioinformatics, and evolutionary analyses, and show that many different pairs of amino acids and their associated tRNA molecules predictably and causally encode translation rate information when these pairs are present in the A- and P-sites of the ribosome independent of other factors known to influence translation speed, including mRNA structure, wobble base pairing, tripeptide motifs, positively charged upstream nascent chain residues, and cognate tRNA concentration. The fast-translating pairs of amino acids that we identify are enriched seven-fold relative to the slow-translating pairs across Saccharomyces cerevisiae’s proteome, while the slow-translating pairs are enriched downstream of domain boundaries. Thus, the chemical identity of amino acid pairs contributes to variability in translation rates, elongation kinetics are causally encoded in the primary structure of proteins, and signatures of evolutionary selection indicate their potential role in co-translational processes.转录本编码区的翻译延伸动力学变异，通过调控共翻译蛋白质折叠、定位与成熟，在维持细胞蛋白质稳态中发挥重要作用。翻译延伸速度受mRNA与蛋白质序列中的分子因素影响。例如，当脯氨酸位于核糖体P位或A位时，翻译过程会减慢，但其余400种可能的氨基酸对组合的效应尚未被系统表征。本研究结合突变实验、生物信息学与进化分析，对酿酒酵母(Saccharomyces cerevisiae)展开研究，结果表明：当氨基酸对位于核糖体A位与P位时，多种不同的氨基酸对及其对应的转运RNA(tRNA)可稳定且因果性地编码翻译速率信息，且该效应独立于其他已知影响翻译速度的因素，包括mRNA结构、摆动碱基配对、三肽基序、上游带正电的新生链残基以及同源tRNA浓度。我们鉴定出的快速翻译氨基酸对，在酿酒酵母蛋白质组中的富集程度是慢速翻译氨基酸对的7倍；而慢速翻译氨基酸对则在结构域边界下游显著富集。综上，氨基酸对的化学属性可导致翻译速率产生变异，延伸动力学由蛋白质一级结构因果性编码，且进化选择的特征提示其在共翻译过程中具有潜在功能意义。