Widespread PERK-dependent repression of ER targets in response to ER stress

Abstract

The UPR (Unfolded Protein Response) is a well-orchestrated response to ER protein folding and processing overload, integrating both transcriptional and translational outputs. Its three arms in mammalian cells, the PERK translational response arm, together with the ATF6 and IRE1-XBP1-mediated transcriptional arms, have been thoroughly investigated.Using ribosome footprint profiling, we performed a deep characterization of gene expression programs involved in the early and late ER stress responses, within WT or PERK -/-Mouse Embryonic Fibroblasts (MEFs). We found that both repression and activation gene expression programs, affecting hundreds of genes, are significantly hampered in the absence of PERK. Specifically, PERK -/-cells do not show global translational inhibition, nor do they specifically activate early gene expression programs upon short exposure to ER stress. Furthermore, while PERK -/-cells do activate/repress late ER-stress response genes, the response is substantially weaker. Importantly, we highlight a widespread PERK-dependent repression gene expression program, consisting of ER targeted proteins, including transmembrane proteins, glycoproteins, and proteins with disulfide bonds. This phenomenon occurs in various different cell types, and has a major translational regulatory component. Moreover, we revealed a novel interplay between PERK and the XBP1-ATF6 arms of the UPR, whereby PERK attenuates the expression of a specific subset of XBP1-ATF6 targets, further illuminating the complexity of the integrated ER stress response.

Cellular proteostasis decline in human senescence

“…S7A,B). Previously, we have shown that the PERK-mediated repression of ER targets as part of the UPR involved eIF2⍺ phosphorylation (Gonen, 2019). We confirmed that eIF2⍺ phosphorylation occurred in both young and senescent cells upon HS, to a similar extent ( Fig.…”

“…We therefore reasoned that the HS treatment in our experiment has induced the UPR. Indeed, examination of the set of mRNAs that were previously identified as the PERK-dependent translational repression UPR signature (Gonen, 2019), which was found to be highly enriched for ER targets, confirmed that this set of mRNAs was significantly repressed in both young and senescent cells in response to HS, however repression was substantially greater in senescent cells (Fig. S7A,B).…”

“…6B, Table S4); which represent the major classes of ER targets. Widespread repression of ER targets has been previously reported by us and others (Gonen, 2019;Guan et al, 2017;Reid et al, 2014) to be a hallmark of the UPR, representing a significant translational regulatory response mediated by PERK (Gonen, 2019). We therefore reasoned that the HS treatment in our experiment has induced the UPR.…”

“…XBP1 and ATF6 targets were defined by Shoulders et al (Shoulders et al, 2013) following specific direct activation of XBP1 or ATF6 (termed XBP1 and ATF6 targets). PERK-dependent UPR repression signature gene set was defined according to Gonen et al (Gonen, 2019). Groups of chaperones significantly altered (induced or repressed) in aged brains (in Postcentral Gyrus, Prefrontal Cortex and Superior Frontal Gyrus, Fig.…”