DELE1 oligomerization promotes integrated stress response activation

Abstract

Mitochondria are dynamic organelles that must continually adapt and respond to cellular stress. Recent studies demonstrated that mitochondrial stress can be relayed from mitochondria to the cytosol by the release of a C-terminal proteolytic fragment of DELE1 that binds to the eIF2α kinase HRI to initiate integrate stress response (ISR) signaling. Here, we report the cryo-electron microscopy structure of the active, C-terminal cleavage product of human DELE1 at ~3.8 Å resolution. Our structure reveals that DELE1 assembles into a high-order oligomer that is observed both in vitro and in mammalian cells. Structurally, the oligomer consists of eight DELE1 monomers that assemble with D4 symmetry via two sets of distinct hydrophobic inter-subunit interactions. We identified the key residues involved in DELE1 oligomerization, and confirmed their role in stabilizing the octamer in vitro and in cells using mutagenesis. Further, we show that assembly impaired DELE1 mutants are compromised in their ability to induce ISR activation in cell culture models. Together, our findings provide molecular insights into the activity of DELE1 and how it signals to promote ISR activity following mitochondrial insult.

DELE1 promotes translation-associated homeostasis, growth, and survival in mitochondrial myopathy

“…1B). Additionally, the predicted truncated protein product (resulting from the predicted frameshift mutation p.Arg21GInfsTer19), if expressed, would lack part of the targeting sequence needed for mitochondrial localization and the tetratricopeptide repeat (TPR) domains required for HRI binding and downstream signaling (Yang et al , 2023).…”

Pharmacologic Activation of a Compensatory Integrated Stress Response Kinase Promotes Mitochondrial Remodeling in PERK-deficient Cells

“…Initially, we tested the ability of these compounds to activate a luciferase-based reporter of ATF4 translation (ATF4-FLuc) as an indicator of ISR activity in HEK293T cells ( Fig. S1A ) (Yang et al , 2022). We confirmed that thapsigargin (Tg), a SERCA inhibitor that activates the ER stress responsive PERK ISR kinase, robustly increases ATF4-FLuc activity ( Fig.…”

“…OMA1 -deficient HEK293T cells, DELE1 -deficient HEK293T cells, and HRI -deficient HEK293T cells were described previously (Guo et al ., 2020) and cultured at 37°C and 5% CO2 in DMEM (Corning-Cellgro) supplemented with 10% fetal bovine serum (FBS; Omega Scientific), 2 mM L-glutamine (GIBCO), 100 Units/mL penicillin, and 100 mg/mL streptomycin (GIBCO). HEK293T cells stably expressing ATF4-FLuc or ATF4-mAPPLE CRISPRi-depleted of HRI , GCN2 , PERK , or PKR were described previously (Guo et al ., 2020; Yang et al ., 2022) and cultured at 37°C and 5% CO2 in DMEM (Corning-Cellgro) supplemented with 10% fetal bovine serum (FBS; Omega Scientific), 2 mM L-glutamine (GIBCO), 100 Units/mL penicillin, and 100 mg/mL streptomycin (GIBCO). MEF mtGFP cells (kind gift from Peter Schultz, TSRI)(Wang et al , 2012) were cultured at 37°C and 5% CO2 in DMEM (Corning-Cellgro) supplemented with 10% fetal bovine serum (FBS; Omega Scientific), 2 mM L-glutamine (GIBCO), 100 Units/mL penicillin, and 100 mg/mL streptomycin (GIBCO).…”

“… A. Illustration showing the ATF4-FLuc and ATF4-mApple ISR reporters (Guo et al ., 2020; Yang et al ., 2022). B. Activation of ATF4-FLuc ISR reporter stably expressed in HEK293T cells treated for 3 h with thapsigargin (Tg; 500 nM).…”

Signaling plasticity in the integrated stress response

“…Whether HRI forms coalescences in cells remains to be investigated. Recent structural findings have revealed that DELE1 organizes into an octamer capable of modulating HRI activity, raising the possibility that DELE1 multimers may template HRI multimerization to facilitate autophosphorylation (Yang et al, 2023).…”