The ribosome-associated protein quality control (RQC) system that resolves stalled translation events is activated when ribosomes collide and form disome, trisome, or higher-order complexes. However, it is unclear whether this system distinguishes collision complexes formed on defective mRNAs from those with functional roles on endogenous transcripts. Here, we performed disome and trisome footprint profiling in yeast and found collisions were enriched on diverse sequence motifs known to slow translation. When 60S recycling was inhibited, disomes accumulated at stop codons and could move into the 3′ UTR to reinitiate translation. The ubiquitin ligase and RQC factor Hel2/ZNF598 generally recognized collisions but did not induce degradation of endogenous transcripts. However, loss of Hel2 triggered the integrated stress response, via phosphorylation of eIF2α, thus linking these pathways. Our results suggest that Hel2 has a role in sensing ribosome collisions on endogenous mRNAs, and such events may be important for cellular homeostasis.

当核糖体碰撞并形成二体、三体或高阶复合体时，会激活解决停滞翻译事件的核糖体相关蛋白质量控制 (RQC) 系统。然而，尚不清楚该系统是否区分了在有缺陷的 mRNA 上形成的碰撞复合物与对内源性转录物具有功能作用的碰撞复合物。在这里，我们在酵母中进行了二体和三体足迹分析，发现碰撞在已知缓慢翻译的不同序列基序上得到了丰富。当 60S 循环被抑制时，二体在终止密码子处积累并可以移动到 3' UTR 以重新启动翻译。泛素连接酶和 RQC 因子 Hel2/ZNF598 通常可以识别碰撞，但不会诱导内源性转录物的降解。然而，Hel2 的缺失触发了综合应激反应，通过 eIF2α 的磷酸化，从而将这些途径联系起来。我们的结果表明，Hel2 在感知内源性 mRNA 上的核糖体碰撞中起作用，并且此类事件可能对细胞稳态很重要。