Subcellular spatiotemporal proteomics delineates distinct phases of ER stress proteostatic response

Abstract

Endoplasmic reticulum (ER) stress is associated with many human diseases, but current understanding of how ER stress responses reshape the stressed proteome over time is still emerging. Specifically, how organellar protein quality control and clearance pathways coordinate to maintain proteostasis in early and prolonged ER stress is unclear. Here we describe a spatiotemporal proteomic strategy termed simultaneous proteome localization and turnover analysis with time resolution (SPLAT-TR) to interrogate the synthesis, degradation, and localization changes of over 4,000 proteins in early (1-4 hours) and prolonged (16-24 hours) ER stress. As ER stress progresses, each time point is distinguished by distinct protein translocation and clearance regulations, coupled to differential organellar proteostasis and usage of protein degradation pathways. Mitochondria show a bimodal response, with a shift from early activation of respiratory protein towards protein quality control pathways in prolonged stress, coinciding with energetics decline. In the Golgi, the increased clearance of collagen proteins is paradoxically coupled to an increased synthesis of secretory pathway components, suggesting removal by secretion. In the ER, the proteome remodels under prolonged stress via increased synthesis of UFMylation and ER-phagy-related proteins coupled to the selective degradation of ER membrane and microdomain proteins. Inhibition of UFMylation alters ER-phagy receptor usage and synergistically induces stress-induced cell death. These results present a systematic delineation of cell compartment proteostasis under unfolded protein response and highlight the utility of SPLAT-TR to investigate time-dependent cellular events.

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BibTeX RIS

BibTeX

@misc{alamillo2026subcellular,
  title = {{Subcellular spatiotemporal proteomics delineates distinct phases of ER stress proteostatic response}},
  author = {L. Alamillo and T. Paiz and A. Black and M. C. Juber and E. M. Arends and J. G. Cox and D. C. M. Ng and T. A. McKinsey and M. P. Y. Lam and E. Lau},
  howpublished = {bioRxiv},
  year = {2026},
  month = sep,
  doi = {10.64898/2026.09.25.754245},
  url = {https://www.biorxiv.org/content/10.64898/2026.09.25.754245v1},
  note = {CC BY-NC-ND},
}

RIS

TY  - UNPB
TI  - Subcellular spatiotemporal proteomics delineates distinct phases of ER stress proteostatic response
AU  - L. Alamillo
AU  - T. Paiz
AU  - A. Black
AU  - M. C. Juber
AU  - E. M. Arends
AU  - J. G. Cox
AU  - D. C. M. Ng
AU  - T. A. McKinsey
AU  - M. P. Y. Lam
AU  - E. Lau
PY  - 2026
DA  - 2026/09/25
PB  - bioRxiv
DO  - 10.64898/2026.09.25.754245
UR  - https://www.biorxiv.org/content/10.64898/2026.09.25.754245v1
AB  - Endoplasmic reticulum (ER) stress is associated with many human diseases, but current understanding of how ER stress responses reshape the stressed proteome over time is still emerging. Specifically, how organellar protein quality control and clearance pathways coordinate to maintain proteostasis in early and prolonged ER stress is unclear. Here we describe a spatiotemporal proteomic strategy termed simultaneous proteome localization and turnover analysis with time resolution (SPLAT-TR) to interrogate the synthesis, degradation, and localization changes of over 4,000 proteins in early (1-4 hours) and prolonged (16-24 hours) ER stress. As ER stress progresses, each time point is distinguished by distinct protein translocation and clearance regulations, coupled to differential organellar proteostasis and usage of protein degradation pathways. Mitochondria show a bimodal response, with a shift from early activation of respiratory protein towards protein quality control pathways in prolonged stress, coinciding with energetics decline. In the Golgi, the increased clearance of collagen proteins is paradoxically coupled to an increased synthesis of secretory pathway components, suggesting removal by secretion. In the ER, the proteome remodels under prolonged stress via increased synthesis of UFMylation and ER-phagy-related proteins coupled to the selective degradation of ER membrane and microdomain proteins. Inhibition of UFMylation alters ER-phagy receptor usage and synergistically induces stress-induced cell death. These results present a systematic delineation of cell compartment proteostasis under unfolded protein response and highlight the utility of SPLAT-TR to investigate time-dependent cellular events.
ER  -

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