Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
Biophys J. 2022 Oct 18;121(20):3962-3974. doi: 10.1016/j.bpj.2022.08.025. Epub 2022 Aug 24.
Many cellular condensates are heterotypic mixtures of proteins and RNA formed in complex environments. Magnesium ions (Mg) and ATP can impact RNA folding, and local intracellular levels of these factors can vary significantly. However, the effect of ATP:Mg on the material properties of protein-RNA condensates is largely unknown. Here, we use an in vitro condensate model of nucleoli, made from nucleophosmin 1 (NPM1) proteins and ribosomal RNA (rRNA), to study the effect of ATP:Mg. While NPM1 dynamics remain unchanged at increasing Mg concentrations, the internal RNA dynamics dramatically slowed until a critical point, where gel-like states appeared, suggesting the RNA component alone forms a viscoelastic network that undergoes maturation driven by weak multivalent interactions. ATP reverses this arrest and liquefies the gel-like structures. ATP:Mg also influenced the NPM1-rRNA composition of condensates and enhanced the partitioning of two clients: an arginine-rich peptide and a small nuclear RNA. By contrast, larger ribosome partitioning shows dependence on ATP:Mg and can become reversibly trapped around NPM1-rRNA condensates. Lastly, we show that dissipative enzymatic reactions that deplete ATP can be used to control the shape, composition, and function of condensates. Our results illustrate how intracellular environments may regulate the state and client partitioning of RNA-containing condensates.
许多细胞凝聚物是蛋白质和 RNA 在复杂环境中形成的异质混合物。镁离子(Mg)和 ATP 可以影响 RNA 折叠,并且这些因素的局部细胞内水平可能会有很大差异。然而,ATP:Mg 对蛋白质-RNA 凝聚物的物质性质的影响在很大程度上是未知的。在这里,我们使用核仁的体外凝聚物模型,由核磷蛋白 1(NPM1)蛋白和核糖体 RNA(rRNA)制成,研究 ATP:Mg 的影响。虽然随着 Mg 浓度的增加,NPM1 动力学保持不变,但内部 RNA 动力学显著减慢,直到出现凝胶状状态,表明 RNA 成分本身形成粘弹性网络,由弱多价相互作用驱动成熟。ATP 逆转这种阻滞并使凝胶状结构液化。ATP:Mg 还影响凝聚物中 NPM1-rRNA 的组成,并增强了两个客户的分配:富含精氨酸的肽和小核 RNA。相比之下,更大的核糖体分配显示出对 ATP:Mg 的依赖性,并且可以可逆地被困在 NPM1-rRNA 凝聚物周围。最后,我们表明,消耗 ATP 的耗散酶反应可用于控制凝聚物的形状、组成和功能。我们的结果说明了细胞内环境如何调节含 RNA 的凝聚物的状态和客户分配。