Biomolecular condensates, such as the nucleolus, stress granules/processing bodies and germ granules, are multiphase assemblages whose formation mechanisms and significance remain poorly understood. Here we identify protein constituents of the spatiotemporally ordered P, Z and M multiphase condensates in Caenorhabditis elegans germ granules using optimized TurboID-mediated proximity biotin labelling. These include 462, 41 and 86 proteins localizing to P, Z and M condensates, respectively, of which 522 were previously unknown protein constituents. Each condensate’s proteins are enriched for distinct classes of structured and intrinsically disordered domains, suggesting divergent functions and assembly mechanisms. Through a functional screen, we identify a germ granule protein, HERD-1, which prevents the mixing of P, Z and M condensates. Mixing in herd-1 mutants correlates with disorganization of germline small RNA pathways and prolonged epigenetic inheritance of RNA interference-induced gene silencing. Forced mixing of these condensate components using a nanobody with specific binding activity against green fluorescent protein also extends epigenetic inheritance. We propose that active maintenance of germ granule immiscibility helps to organize and regulate small RNA-driven transgenerational epigenetic inheritance in C. elegans.

生物分子凝聚物，如核仁、应激颗粒/加工体和胚芽颗粒，是多相组合，其形成机制和意义仍然知之甚少。在这里，我们使用优化的 TurboID 介导的邻近生物素标记鉴定秀丽隐杆线虫胚芽颗粒中时空有序的 P、Z 和 M 多相缩合物的蛋白质成分。这些蛋白质包括 462 个、 41 个和 86 个蛋白质，分别定位于 P、 Z 和 M 凝聚物，其中 522 个是以前未知的蛋白质成分。每种凝聚物的蛋白质都富集于不同类别的结构化和内在无序结构域，表明不同的功能和组装机制。通过功能筛选，我们鉴定了一种胚芽颗粒蛋白 HERD-1，它可以防止 P、Z 和 M 缩合物的混合。herd-1 突变体中的混合与种系小 RNA 通路的紊乱和 RNA 干扰诱导的基因沉默的表观遗传遗传延长相关。使用对绿色荧光蛋白具有特异性结合活性的纳米抗体强制混合这些凝聚物组分也延长了表观遗传学。我们提出，积极维持胚芽颗粒的不混溶性有助于组织和调节秀丽隐杆线虫中小 RNA 驱动的跨代表观遗传遗传。