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

Cells rely on diverse intracellular structures, including phase-separated granules, to regulate biological processes. Processing bodies (P-bodies) are membraneless cytoplasmic condensates that mediate mRNA degradation and storage. Although their molecular composition is well studied, how their spatial organization relates to cell geometry, especially 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. Increasing vacuolar volume interferes with effective nucleation and increases P-body number, although cell size remains the dominant determinant. Monte Carlo simulations recapitulate these size-dependent patterns and reveal a nucleation distance of 2.4 μm. Together, our results establish nucleation distance as a key parameter linking cell geometry to the biophysical regulation of condensate formation.