mRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs in the tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and nonAUG TISs in 5′ untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational enhancer found across dicots and monocots, and humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, whereby cis-regulatory RNA signatures affect start site selection. The TIS prediction model provides global estimates of TISs to discover neglected protein-coding genes across plant genomes. The prevalence of cis-regulatory signatures across plant species, humans, and viruses suggests their broad and critical roles in reprogramming the translational landscape.

中文翻译：

---

对植物中替代翻译起始位点进行建模揭示了真核生物中进化保守的顺式调控密码

mRNA 翻译依赖于识别 mRNA 中的翻译起始位点 (TIS)。替代 TIS 在植物转录组中普遍存在，但其识别机制尚不清楚。利用核糖体分析和机器学习，我们开发了预测番茄（Solanum lycopersicum）中替代 TIS 的模型。不同的特征集可以预测 5' 非翻译区和编码序列中的 AUG 和非 AUG TIS，包括促进植物 TIS 活性的新型富含 CU 的序列，这是在双子叶植物和单子叶植物以及人类和病毒中发现的翻译增强子。我们的结果阐明了 TIS 识别的机制和进化基础，即顺式调节 RNA 特征影响起始位点选择。 TIS 预测模型提供 TIS 的全局估计，以发现植物基因组中被忽视的蛋白质编码基因。顺式调控特征在植物物种、人类和病毒中的普遍存在表明它们在重编程翻译景观中发挥着广泛而关键的作用。