Pervasive translation is a widespread phenomenon that plays a critical role in the emergence of novel microproteins, but the diversity of translation patterns contributing to their generation remains unclear. Based on 54 ribosome profiling (Ribo-Seq) datasets, we investigated the yeast Ribo-Seq landscape using a representation framework that allows the comprehensive inventory and classification of the entire diversity of Ribo-Seq signals, including non-canonical ones. We show that if coding regions occupy specific areas of the Ribo-Seq landscape, noncoding regions encompass a wide diversity of Ribo-Seq signals and, conversely, populate the entire landscape. Our results show that pervasive translation can, nevertheless, be associated with high specificity, with 1055 noncoding ORFs exhibiting canonical Ribo-Seq signals. Using mass spectrometry under standard conditions or proteasome inhibition with an in-house analysis protocol, we report 239 microproteins originating from noncoding ORFs that display canonical but also non-canonical Ribo-Seq signals. Each condition yields dozens of additional microprotein candidates with comparable translation properties, suggesting a larger population of volatile microproteins that are challenging to detect. Our findings suggest that non-canonical translation signals may harbor valuable information and underscore the significance of considering them in proteogenomic studies. Finally, we show that the translation outcome of a noncoding ORF is primarily determined by the initiating codon and the codon distribution in its two alternative frames, rather than features indicative of functionality. Our results enable us to propose a topology of a species’ Ribo-Seq landscape, opening the way to comparative analyses of this translation landscape under different conditions.

中文翻译：

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酵母的核糖体分析景观揭示了普遍翻译的高度多样性


普遍翻译是一种普遍存在的现象，在新型微蛋白的出现中起着关键作用，但导致其产生的翻译模式的多样性仍不清楚。基于 54 个核糖体分析 （Ribo-Seq） 数据集，我们使用表示框架研究了酵母 Ribo-Seq 景观，该框架允许对 Ribo-Seq 信号的整个多样性进行全面盘点和分类，包括非经典信号。我们表明，如果编码区占据 Ribo-Seq 景观的特定区域，那么非编码区则包含各种各样的 Ribo-Seq 信号，反之，则填充整个景观。我们的结果表明，普遍翻译仍然可以与高特异性相关，1055 个非编码 ORF 表现出经典的 Ribo-Seq 信号。使用标准条件下的质谱法或蛋白酶体抑制与内部分析方案，我们报告了 239 种源自非编码 ORF 的微蛋白，这些微蛋白显示经典和非经典 Ribo-Seq 信号。每种条件都会产生数十种具有相似翻译特性的额外候选微蛋白，这表明存在更大的挥发性微蛋白群体，难以检测。我们的研究结果表明，非经典翻译信号可能含有有价值的信息，并强调了在蛋白质基因组学研究中考虑它们的重要性。最后，我们表明非编码 ORF 的翻译结果主要取决于起始密码子和其两个替代框架中的密码子分布，而不是指示功能的特征。 我们的结果使我们能够提出一个物种的 Ribo-Seq 景观的拓扑结构，为在不同条件下对这种平移景观的比较分析开辟了道路。