Stress-Independent Activation of XBP1s and/or ATF6 Reveals Three Functionally Diverse ER Proteostasis Environments

TLDR

The unfolded protein response maintains ER proteostasis through transcription factors XBP1s and ATF6, yet their specific functional consequences remain poorly understood. The study aims to develop a stress‑independent, small‑molecule method to selectively activate XBP1s and/or ATF6 within the same cell. Using this approach, transcriptomic and quantitative proteomic analyses were performed to assess how the distinct transcriptional programs remodel the ER proteostasis network. The results show that activating XBP1s and/or ATF6 creates three distinct ER proteostasis environments that differentially affect folding, trafficking, and degradation of destabilized client proteins without perturbing the global proteome, highlighting a strategy for selective restoration of aberrant ER proteostasis.

Abstract

The unfolded protein response (UPR) maintains endoplasmic reticulum (ER) proteostasis through the activation of transcription factors such as XBP1s and ATF6. The functional consequences of these transcription factors for ER proteostasis remain poorly defined. Here, we describe methodology that enables orthogonal, small-molecule-mediated activation of the UPR-associated transcription factors XBP1s and/or ATF6 in the same cell independent of stress. We employ transcriptomics and quantitative proteomics to evaluate ER proteostasis network remodeling owing to the XBP1s and/or ATF6 transcriptional programs. Furthermore, we demonstrate that the three ER proteostasis environments accessible by activating XBP1s and/or ATF6 differentially influence the folding, trafficking, and degradation of destabilized ER client proteins without globally affecting the endogenous proteome. Our data reveal how the ER proteostasis network is remodeled by the XBP1s and/or ATF6 transcriptional programs at the molecular level and demonstrate the potential for selective restoration of aberrant ER proteostasis of pathologic, destabilized proteins through arm-selective UPR activation.