Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts

Stress-induced condensation of mRNA and proteins into stress granules is conserved across eukaryotes, yet the function, formation mechanisms, and relation to well-studied conserved transcriptional responses remain largely unresolved. Stress-induced exposure of ribosome-free mRNA following translational shutoff is thought to cause condensation by allowing new multivalent RNA-dependent interactions, with RNA length and associated interaction capacity driving increased condensation. Here we show that, in striking contrast, virtually all mRNA species condense in response to multiple unrelated stresses in budding yeast, length plays a minor role, and instead, stress-induced transcripts are preferentially excluded from condensates, enabling their selective translation. Using both endogenous genes and reporter constructs, we show that translation initiation blockade, rather than resulting ribosome-free RNA, causes condensation. These translation initiation-inhibited condensates (TIICs) are biochemically detectable even when stress granules, defined as microscopically visible foci, are absent or blocked. TIICs occur in unstressed yeast cells, and, during stress, grow before the appearance of visible stress granules. Stress-induced transcripts are excluded from TIICs primarily due to the timing of their expression, rather than their sequence features. Together, our results reveal a simple system by which cells redirect translational activity to newly synthesized transcripts during stress, with broad implications for cellular regulation in changing conditions.应激诱导的信使RNA（mRNA）与蛋白质凝聚形成应激颗粒（stress granules）的过程在真核生物中高度保守，但其具体功能、形成机制，以及与已被充分研究的保守转录应答之间的关联仍未得到充分阐释。以往研究认为，翻译关闭后无核糖体信使RNA的应激暴露，会通过允许新的多价RNA依赖相互作用引发凝聚，其中RNA长度及其相关相互作用能力会推动凝聚程度提升。但本研究得出了截然不同的结论：在酿酒酵母中，几乎所有mRNA物种都会响应多种不相关的应激而发生凝聚，而RNA长度仅发挥次要作用；相反，应激诱导的转录本会优先被排除在凝聚物之外，从而实现其选择性翻译。我们通过内源基因与报告基因构建体（reporter constructs）的实验证实，引发凝聚的并非翻译关闭后释放的无核糖体RNA，而是翻译起始阻断过程本身。这类翻译起始抑制凝聚物（translation initiation-inhibited condensates, TIICs）即便在定义为显微镜下可见灶点的应激颗粒缺失或被阻断时，仍可通过生化手段检测到。TIICs可在未受应激的酵母细胞中存在，且在应激过程中会早于可见应激颗粒形成并长大。应激诱导的转录本之所以被排除在TIICs之外，主要是因其表达时序特征，而非序列特性。综上，本研究揭示了一套简洁的细胞机制：细胞可在应激过程中将翻译活性重定向至新合成的转录本，这一发现对于理解多变环境下的细胞调控具有广泛意义。