Compartmentalization is an essential feature of eukaryotic life and is achieved both via membrane-bound organelles, such as mitochondria, and membrane-less biomolecular condensates, such as the nucleolus. Known biomolecular condensates typically exhibit liquid-like properties and are visualized by microscopy on the scale of ~1 µm (refs. ^1,2). They have been studied mostly by microscopy, examining select individual proteins. So far, several dozen biomolecular condensates are known, serving a multitude of functions, for example, in the regulation of transcription³, RNA processing⁴ or signalling^5,6, and their malfunction can cause diseases^7,8. However, it remains unclear to what extent biomolecular condensates are utilized in cellular organization and at what length scale they typically form. Here we examine native cytoplasm from Xenopus egg extract on a global scale with quantitative proteomics, filtration, size exclusion and dilution experiments. These assays reveal that at least 18% of the proteome is organized into mesoscale biomolecular condensates at the scale of ~100 nm and appear to be stabilized by RNA or gelation. We confirmed mesoscale sizes via imaging below the diffraction limit by investigating protein permeation into porous substrates with defined pore sizes. Our results show that eukaryotic cytoplasm organizes extensively via biomolecular condensates, but at surprisingly short length scales.

区室化是真核生命的一个基本特征，是通过膜结合的细胞器（例如线粒体）和无膜生物分子凝聚体（例如核仁）来实现的。已知的生物分子缩合物通常表现出类似液体的特性，并且可以通过显微镜以约 1 µm 的尺度观察（参考文献^1,2）。它们主要通过显微镜进行研究，检查选定的单个蛋白质。迄今为止，已知有几十种生物分子缩合物，它们具有多种功能，例如，在转录调节³、RNA 加工⁴或信号传导^5,6中，它们的功能障碍可能导致疾病^7,8。然而，目前尚不清楚生物分子凝聚物在细胞组织中的利用程度以及它们通常形成的长度规模。在这里，我们通过定量蛋白质组学、过滤、尺寸排除和稀释实验在全球范围内检查爪蟾卵提取物的天然细胞质。这些测定表明，至少 18% 的蛋白质组被组织成约 100 nm 尺度的中尺度生物分子凝聚物，并且似乎通过 RNA 或凝胶化而稳定。我们通过研究蛋白质渗透到具有确定孔径的多孔基质中，通过低于衍射极限的成像来确认介观尺寸。我们的结果表明，真核细胞质通过生物分子凝聚体广泛组织，但长度尺度却惊人地短。