A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons

Ambiguity in genetic codes exists in cases where certain stop codons are alternatively used to encode non-canonical amino acids. In selenoprotein transcripts, the UGA codon may either represent a translation termination signal or a selenocysteine (Sec) codon. Translating UGA to Sec requires selenium and specialized Sec incorporation machinery such as the interaction between the SECIS element and SBP2 protein, but how these factors quantitatively affect alternative assignments of UGA has not been fully investigated. We developed a model simulating the UGA decoding process. Our model is based on the following assumptions: (1) charged Sec-specific tRNAs (Sec-tRNASec) and release factors compete for a UGA site, (2) Sec-tRNASec abundance is limited by the concentrations of selenium and Sec-specific tRNA (tRNASec) precursors, and (3) all synthesis reactions follow first-order kinetics. We demonstrated that this model captured two prominent characteristics observed from experimental data. First, UGA to Sec decoding increases with elevated selenium availability, but saturates under high selenium supply. Second, the efficiency of Sec incorporation is reduced with increasing selenoprotein synthesis. We measured the expressions of four selenoprotein constructs and estimated their model parameters. Their inferred Sec incorporation efficiencies did not correlate well with their SECIS-SBP2 binding affinities, suggesting the existence of additional factors determining the hierarchy of selenoprotein synthesis under selenium deficiency. This model provides a framework to systematically study the interplay of factors affecting the dual definitions of a genetic codon.

遗传密码的歧义性存在于部分终止密码子被交替用于编码非标准氨基酸的场景中。在硒蛋白转录本内，UGA密码子既可充当翻译终止信号，也可作为硒半胱氨酸（selenocysteine, Sec）的编码密码子。将UGA翻译为Sec需要硒以及特异性的Sec掺入机制，例如SECIS元件（SECIS element）与SBP2蛋白（SBP2 protein）之间的相互作用，但目前尚未充分阐明这些因素如何定量影响UGA的双重分配功能。我们开发了一款模拟UGA解码过程的计算模型。该模型基于三项核心假设：（1）负载硒半胱氨酸的特异性转运RNA（Sec-tRNASec）与翻译释放因子竞争UGA结合位点；（2）Sec-tRNASec的丰度受硒与Sec特异性转运RNA（tRNASec）前体的浓度限制；（3）所有合成反应均遵循一级动力学规律。研究表明，该模型成功复现了实验数据中观察到的两项显著特征：其一，UGA向Sec的解码效率随硒可用性的提升而升高，但在高硒供应条件下会趋于饱和；其二，Sec掺入效率随硒蛋白合成水平的升高而降低。我们测定了四种硒蛋白构建体的表达水平，并估算了对应模型的参数。推导得到的Sec掺入效率与其SECIS-SBP2结合亲和力并未呈现显著相关性，这提示在硒缺乏条件下，存在额外因素决定硒蛋白合成的层级秩序。该模型为系统性研究影响遗传密码子双重定义的各类因素间的相互作用提供了研究框架。