Weak interactions drive selective proteome demixing and tune the differential response to environmental perturbations

The intracellular space is a crowded environment where macromolecules perform distinct tasks despite pervasive "non-specific" interactions. Whether these interactions are functionally relevant and how they influence cellular organization remains unclear. Here, we developed QuPID-MS, which measures the propensity of proteins to phase separate in native cell extracts proteome-wide. We find that weak interactions drive condensation of half of the proteome in a crowding- and temperature-dependent manner and we present evidence that this proteome demixing occurs in cells. Importantly, protein condensation properties are conserved and broadly change when cells adapt to new environments, demonstrating that weak interactions are regulated and linked to function. Indeed, condensation of the growth regulator TORC1 coincides with its rapid inactivation, while high solubility of the stress-activated Hog1 ensures its activity across conditions. We thus uncover a fundamental organizing principle that allows tuning of cell growth to environmental fluctuations while ensuring other processes function robustly despite perturbations. HighlightsO_LIQuantitative PEG induced demixing-MS (QuPID-MS) measures the tendency of proteins to condense in native cell extract. C_LIO_LI53% of the yeast proteome is condensation-prone and demixes in a crowding- and temperature-dependent manner. C_LIO_LIThe propensity to form condensates is globally modulated when cells adapt to new environmental conditions C_LIO_LIWeak interactions selectively organize the proteome in cells and differentially affect proteins involved in growth, signaling, and stress response. C_LIO_LIDynamic proteome demixing allows coupling of macromolecule synthesis to environmental fluctuations while ensuring other processes function robustly despite perturbations. C_LI Graphical AbstractProposed model for how selective proteome demixing tunes the differential cellular response to perturbations O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/739830v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@15481b4org.highwire.dtl.DTLVardef@10f67acorg.highwire.dtl.DTLVardef@5f50d3org.highwire.dtl.DTLVardef@1b34ee3_HPS_FORMAT_FIGEXP M_FIG C_FIG