Phase separation of soluble proteins into insoluble deposits is associated with numerous diseases. However, protein deposits can also function as membrane-less compartments for many cellular processes. What are the fitness costs and benefits of forming such deposits in different conditions? Using a model protein that phase separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast. The environmental condition and the cellular demand for the protein function emerge as key determinants of fitness. Protein deposit formation can lead to cell-to-cell differences in free protein abundance between individuals. This results in variable manifestation of protein function and a continuous range of phenotypes in a cell population, favoring survival of some individuals in certain environments. Thus, protein deposit formation by phase separation might be a mechanism to sense protein concentration in cells and to generate phenotypic variability. The selectable phenotypic variability, previously described for prions, could be a general property of proteins that can form phase separated assemblies and may influence cell fitness.Stand-first textUsing a model protein that phase separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast.Bullet pointsThe presented approach identifies and quantifies different fitness effects associated with protein deposit formation due to phase separationThe environmental condition and the cellular demand for the protein function emerge as key determinants of fitness upon protein deposit formationVariability in protein deposit formation can lead to cell-to-cell differences in free protein abundance between individualsProtein phase separation can generate a continuous range of phenotypes in a cell population

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Condensation, or liquid-like phase separation, is a phenomenon indispensable for the spatiotemporal regulation of molecules within the cell. Recent studies indicate that the composition and molecular organization of phase-separated organelles such as Stress Granules (SGs) and Processing Bodies (PBs) are highly variable and dynamic. A dense contact network involving both RNAs and proteins controls the formation of SGs and PBs and an intricate molecular architecture, at present poorly understood, guarantees that these assemblies sense and adapt to different stresses and environmental changes. Here, we investigated the physico-chemical properties of SGs and PBs components and studied the architecture of their interaction networks. We observed that proteins and RNAs establishing the largest amount of contacts have distinct structural characteristics. More specifically, we found that structural disorder is enriched in all protein-RNA, protein-protein and RNA-RNA interactions. Intriguingly, enrichment in the disorder of proteins is linked to increased number of interactions with single-stranded regions in RNAs. Our findings support the hypothesis that SGs and PBs can quickly assemble and disassemble thanks to the activity of unfolded domains in proteins and single-stranded regions in RNAs, guaranteeing the formation of dynamic contacts.