A nucleation distance sets the cell size-dependent P-body assembly

Cells rely on diverse intracellular structures, including phase-separated granules, to regulate biological processes. Processing body (P-body) is a type of membraneless condensate in the eukaryotic cytoplasm that mediates mRNA degradation and storage. While their molecular composition is well studied, the relationship between their spatial organization and cell geometry, particularly cell size and organelle distribution, remains unclear. Here, we develop a conceptual framework that models phase-separation nucleation and validates the nucleation distance of P-bodies in living yeast cells. Using microfluidic cell sorting and quantitative fluorescence microscopy, we find that small cells contain fewer but larger P- bodies, whereas large cells form more but smaller granules. Monte Carlo simulations of P- body nucleation accurately recapitulate these cell size-dependent patterns and reveal a nucleation distance of 2.2 µm. Furthermore, we demonstrate that increasing vacuolar volume reduces the effective cytoplasmic space and correspondingly raises P-body number, although cell size remains the dominant determinant. Our findings establish nucleation distance as a key parameter that links cell geometry to the biophysical regulation of condensate formation.