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PreprintCC BY-NDbioRxiv

Tracking cellular biomolecular condensate dynamics under proteostatic stress with middle-down phosphoproteomics

  • B. Pandi
  • D. C. M. Ng
  • P. Schaal
  • L. Alamillo
  • S. Binti
  • E. Lau
  • M. P. Y. Lam1
  1. 1University of Colorado School of Medicine
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Abstract

Coordination of biological function requires the partition of cellular components including into biomolecular condensates, but an overall landscape of how protein compartmentalize into higher-order assemblies under stress is still emerging. We apply proteome-wide solubility profiling to compare the compositions of NP-40-insoluble proteins and their phosphorylation status, using a new mass spectrometry-based hybrid bottom-up and chemical middle-down proteomics approach to analyze the solubility behavior of 8,740 proteins and 31,647 phosphopeptides under normal and ER stress conditions. Cell stress induces a pervasive differential partition of proteins in and out of detergent-insoluble cellular compartments. This differential partition is partially orthogonal to stress-induced abundance changes and comprises both phosphorylation-dependent and phosphorylation-independent mechanisms. Whereas phosphorylation-independent partition changes involve largely secretory pathway proteins and implicate higher-order assemblies of chaperones and clients, phosphorylation-based partitions suggest a dynamic rearrangement of biomolecular condensate compositions across cytoplasmic and nuclear ribonucleoprotein assemblies. The accumulation of serine/arginine rich (SR) proteins and other annotated nuclear speckle members in the condensate-rich proteome fractions emerges as a central feature of stress-induced remodeling. Our results establish global solubility dynamics as an integral component of proteome stress response and implicates broad involvements of splice factor spatial reorganization as a prominent facet of ER stress response.

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Cite

BibTeXRIS
BibTeX
@misc{pandi2026tracking,
  title = {{Tracking cellular biomolecular condensate dynamics under proteostatic stress with middle-down phosphoproteomics}},
  author = {B. Pandi and D. C. M. Ng and P. Schaal and L. Alamillo and S. Binti and E. Lau and M. P. Y. Lam},
  howpublished = {bioRxiv},
  year = {2026},
  month = sep,
  doi = {10.64898/2026.09.22.753649},
  url = {https://www.biorxiv.org/content/10.64898/2026.09.22.753649v1},
  note = {CC BY-ND},
}
RIS
TY  - UNPB
TI  - Tracking cellular biomolecular condensate dynamics under proteostatic stress with middle-down phosphoproteomics
AU  - B. Pandi
AU  - D. C. M. Ng
AU  - P. Schaal
AU  - L. Alamillo
AU  - S. Binti
AU  - E. Lau
AU  - M. P. Y. Lam
PY  - 2026
DA  - 2026/09/22
PB  - bioRxiv
DO  - 10.64898/2026.09.22.753649
UR  - https://www.biorxiv.org/content/10.64898/2026.09.22.753649v1
AB  - Coordination of biological function requires the partition of cellular components including into biomolecular condensates, but an overall landscape of how protein compartmentalize into higher-order assemblies under stress is still emerging. We apply proteome-wide solubility profiling to compare the compositions of NP-40-insoluble proteins and their phosphorylation status, using a new mass spectrometry-based hybrid bottom-up and chemical middle-down proteomics approach to analyze the solubility behavior of 8,740 proteins and 31,647 phosphopeptides under normal and ER stress conditions. Cell stress induces a pervasive differential partition of proteins in and out of detergent-insoluble cellular compartments. This differential partition is partially orthogonal to stress-induced abundance changes and comprises both phosphorylation-dependent and phosphorylation-independent mechanisms. Whereas phosphorylation-independent partition changes involve largely secretory pathway proteins and implicate higher-order assemblies of chaperones and clients, phosphorylation-based partitions suggest a dynamic rearrangement of biomolecular condensate compositions across cytoplasmic and nuclear ribonucleoprotein assemblies. The accumulation of serine/arginine rich (SR) proteins and other annotated nuclear speckle members in the condensate-rich proteome fractions emerges as a central feature of stress-induced remodeling. Our results establish global solubility dynamics as an integral component of proteome stress response and implicates broad involvements of splice factor spatial reorganization as a prominent facet of ER stress response.
ER  -