Quantitative Studies of Composition and Formation of Yeast P Bodies




Xing, Wenmin

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Eukaryote cells organize their internal spaces into distinct compartments to achieve precise spatiotemporal regulation of biochemical reactions. One level of organization is achieved through membrane borders that form classical organelles such as nuclei and mitochondria. However, another widespread type of structures concentrates distinct molecular components without being enclosed by membranes--these are termed biomolecular condensates. Quantitative studies are lacking to mechanistically understand condensates within the complicated cellular environment. Toward this aim, I developed live cell imaging methods to quantitatively measure protein partitioning into condensates. Using P bodies, an archetypal biomolecular condensate that concentrate proteins and RNA, I first generated a quantitative inventory of the major proteins in yeast P bodies. I found that only 7 proteins are highly concentrated in P bodies while the 24 others examined are appreciably lower. P body concentration correlates inversely with cytoplasmic exchange rate. Based on the results, I proposed that the compositions of natural condensates can be classified into scaffold-like and client-like components based on their distinct partitioning and interaction network. To understand compositional specificity, I showed that sequence elements driving Dcp2 enrichment into P bodies are distributed across the protein, and that these elements act cooperatively. Multiple distributed enrichment elements provide a thermodynamic framework for regulating compositional specificity of P bodies. I further illustrated that changing the molecular interactions could shift phase boundaries, suggesting that behaviors of biomolecular condensates are dictated by molecular interactions. Taken together, my work provides a quantitative view of compositions and formation of natural biomolecular condensates.

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