Proteome-wide profiling reveals compartment-specific RNA buffering of protein aggregation during stress
- 1Institute of Biochemistry, Justus Liebig University Giessen, Giessen, Germany
Abstract
Cellular adaptation to stress requires extensive remodeling of RNA metabolism. The rewiring of the RNA-protein interaction landscape and the assembly of biomolecular condensates are central to this response, yet the global stress-induced reorganization of macromolecular RNA-protein assemblies remains incompletely characterized. Here, we apply R-DeeP, a density gradient approach coupled to quantitative mass spectrometry, to profile the RNA-dependent sedimentation behaviour of the Saccha-romyces cerevisiae proteome during heat and salt stress. We demonstrate that stress triggers a profound, stress-specific reorganization of the RNA interactome. Many proteins undergo pronounced, selective shifts into high-molecular weight fractions, indicative of aggregation. RNase treatment markedly exacerbates this aggregation, consistent with the model that RNA acts as a general chaperone that keeps proteins with intrinsically disordered regions soluble. Strikingly, our data demonstrate that this protection is compartmentalised. Nuclear proteins are partially shielded from stress-induced aggregation. This protection coincides with the nuclear accumulation of RNA caused by a block of RNA export during stress, and RNase treatment abolishes this protection. Nuclear RNA retention may therefore act as a buffer that actively increases the local chaperoning capacity of the nucleus. In contrast, cytoplasmic proteins, including translation factors and ribonucleoprotein granule components, exhibit increased aggregation under stress. Fluorescence microscopy confirmed that increased biochemical aggregation in density gradients reflects changes in assembly state in vivo. For many stress-induced aggregators, these changes are visible as spatial reorganisation in stressed cells, such as the formation of foci. Our findings suggest that cells use subcellular RNA distribution to tune the condensation and/or aggregation threshold of proteins in a compartment-specific manner.
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BibTeX
@misc{seidler2026proteomewide,
title = {{Proteome-wide profiling reveals compartment-specific RNA buffering of protein aggregation during stress}},
author = {J. F. Seidler and F. Thelen and N. B. Wäber and J. Weber and L. Lohle and T. Timm and G. Lochnit and J. Blom and A. Goesmann and K. Strässer and C. Kilchert},
howpublished = {bioRxiv},
year = {2026},
month = nov,
doi = {10.64898/2026.11.04.764228},
url = {https://www.biorxiv.org/content/10.64898/2026.11.04.764228v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Proteome-wide profiling reveals compartment-specific RNA buffering of protein aggregation during stress
AU - J. F. Seidler
AU - F. Thelen
AU - N. B. Wäber
AU - J. Weber
AU - L. Lohle
AU - T. Timm
AU - G. Lochnit
AU - J. Blom
AU - A. Goesmann
AU - K. Strässer
AU - C. Kilchert
PY - 2026
DA - 2026/11/04
PB - bioRxiv
DO - 10.64898/2026.11.04.764228
UR - https://www.biorxiv.org/content/10.64898/2026.11.04.764228v1
AB - Cellular adaptation to stress requires extensive remodeling of RNA metabolism. The rewiring of the RNA-protein interaction landscape and the assembly of biomolecular condensates are central to this response, yet the global stress-induced reorganization of macromolecular RNA-protein assemblies remains incompletely characterized. Here, we apply R-DeeP, a density gradient approach coupled to quantitative mass spectrometry, to profile the RNA-dependent sedimentation behaviour of the Saccha-romyces cerevisiae proteome during heat and salt stress. We demonstrate that stress triggers a profound, stress-specific reorganization of the RNA interactome. Many proteins undergo pronounced, selective shifts into high-molecular weight fractions, indicative of aggregation. RNase treatment markedly exacerbates this aggregation, consistent with the model that RNA acts as a general chaperone that keeps proteins with intrinsically disordered regions soluble. Strikingly, our data demonstrate that this protection is compartmentalised. Nuclear proteins are partially shielded from stress-induced aggregation. This protection coincides with the nuclear accumulation of RNA caused by a block of RNA export during stress, and RNase treatment abolishes this protection. Nuclear RNA retention may therefore act as a buffer that actively increases the local chaperoning capacity of the nucleus. In contrast, cytoplasmic proteins, including translation factors and ribonucleoprotein granule components, exhibit increased aggregation under stress. Fluorescence microscopy confirmed that increased biochemical aggregation in density gradients reflects changes in assembly state in vivo. For many stress-induced aggregators, these changes are visible as spatial reorganisation in stressed cells, such as the formation of foci. Our findings suggest that cells use subcellular RNA distribution to tune the condensation and/or aggregation threshold of proteins in a compartment-specific manner.
ER -