Readthrough Events in Plants Reveal Unprecedented Plasticity of Stop Codons

Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcripts. Mass spectrometry evidence shows that stop codons involved in SCR events can be recoded as 20 standard amino acids, some of which are also supported by suppressor transfer RNA analysis. We also observe multiple functional signals in 34 maize extended proteins and characterize the structural and subcellular localization changes in the extended protein of BASIC TRANSCRIPTION FACTOR 3. Furthermore, the SCR events exhibit non-conserved signature and the extensions likely undergo protein-coding selection. Overall, our study not only characterizes that SCR events are commonly present in plants but also identifies the unprecedented recoding plasticity of stop codons, which provides important insights into the flexibility of genetic decoding.

终止密码子通读（Stop codon readthrough, SCR）具有重要的生物学意义，但目前该现象仍未得到充分解析。本研究借助蛋白质基因组学（proteogenomic）策略，在植物中共鉴定出1009个SCR事件。相较于非SCR转录本，植物SCR候选事件对应的转录本普遍长度更短，外显子数量及可变剪接变体数目也更少。质谱证据表明，参与SCR事件的终止密码子可被重编码为20种标准氨基酸，其中部分重编码结果还得到了抑制性转运RNA（suppressor transfer RNA）分析的验证。本研究还在34个玉米延伸蛋白中检测到多种功能信号，并对基础转录因子3（BASIC TRANSCRIPTION FACTOR 3）的延伸蛋白的结构与亚细胞定位变化进行了系统表征。此外，SCR事件呈现出非保守的序列特征，其延伸序列大概率处于蛋白质编码选择压力之下。综上，本研究不仅证实了SCR事件在植物中广泛存在，还揭示了终止密码子前所未有的重编码可塑性，这为理解遗传解码的灵活性提供了关键见解。