The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition

Ganji, Rakesh; Paulo, João A.; Xi, Yuecheng; Kline, Ian; Zhu, Jiang; Clemen, Christoph S.; Weihl, Conrad C.; Purdy, John; Gygi, Steven P.; Raman, Malavika

doi:10.1038/s41467-023-36298-2

Cited by 14 publications

(10 citation statements)

References 90 publications

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“…One possibility is that mtHSP70 knockdown leads to an alteration in membrane fluidity, compromising the dimerization of the UPR ER sensors. This is further corroborated by recent findings that the knockdown of ER-resident proteins alters the ER membrane lipid content, increasing mitochondria and ER contact through increasing membrane order 26 . Furthermore, alterations in lipid content within the ER membrane have been shown to induce UPR ER in the absence of aberrant proteostasis 27 , providing further evidence that membrane lipid content can directly influence the UPR ER signaling pathways.…”

Section: Resultssupporting

confidence: 81%

Unveiling the Intercompartmental Signaling Axis: Mitochondrial to ER Stress Response (MERSR) and its Impact on Proteostasis

Li,

Xin,

Yang

et al. 2023

Preprint

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Maintaining protein homeostasis is essential for cellular health. During times of protein stress, cells deploy unique defense mechanisms to achieve resolution. Our previous research uncovered a cross-compartmental Mitochondrial to Cytosolic Stress Response (MCSR), a unique stress response activated by the perturbation of mitochondrial proteostasis, which ultimately results in the improvement of proteostasis in the cytosol. Here, we found that this signaling axis also influences the unfolded protein response of the endoplasmic reticulum (UPRER), suggesting the presence of a Mitochondria to ER Stress Response (MERSR). During MERSR, the IRE1 branch of UPRER is inhibited, introducing a previously unknown regulatory component of MCSR. Moreover, proteostasis is enhanced through the upregulation of the PERK-eIF2a signaling pathway, increasing phosphorylation of eIF2a and improving the ER's capacity to manage greater proteostasis load. MERSR activation in both poly-glutamine (poly-Q) and amyloid-beta (Abeta) C. elegans disease models also leads to improvement in both aggregate burden and overall disease outcome. These findings shed light on the coordination between the mitochondria and the ER in maintaining cellular proteostasis and provide further evidence for the importance of intercompartmental signaling.

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Section: Resultssupporting

confidence: 81%

Unveiling the Intercompartmental Signaling Axis: Mitochondrial to ER Stress Response (MERSR) and its Impact on Proteostasis

Li,

Xin,

Yang

et al. 2023

Preprint

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“…4C–E ). After we had made this discovery (published on bioRxiv in May 2022), an independent study confirmed that FAF2 (UBXD8) localizes to the ER and mitochondria in human cells 47 and a subsequent study suggested that this protein is involved in regulating mitochondria-ER contact sites 48 . These complementary findings showcase the potential of CLASP as a discovery tool that can guide functional follow-up experiments.…”

Section: Resultsmentioning

confidence: 98%

Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies

Zhu,

Akkaya,

Ruta

et al. 2024

Nat Commun

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The functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome. Biochemical and imaging-based follow-up studies confirm that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. We also validate the CLASP concept in synaptic vesicles, demonstrating its applicability to different sub-cellular compartments. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, and establishes a method for concomitant profiling of sub-organelle and membrane proteomes.

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“…The TMT-based proteomics was performed exactly as previously described (Ganji et al, 2023 ). Briefly, 100 μg protein of each sample was obtained by cell lysis in lysis buffer (8 M Urea, 200 mM N-(2-Hydroxyethyl)piperazine-N′-(3-propanesulfonic acid) (EPPS) pH 8.5) followed by reduction using 5 mM tris(2-carboxyethyl)phosphine (TCEP), alkylation with 14 mM iodoacetamide and quenched using 5 mM dithiothreitol.…”

Section: Methodsmentioning

confidence: 99%

UBXN1 maintains ER proteostasis and represses UPR activation by modulating translation

Ahlstedt,

Ganji,

Mukkavalli

et al. 2024

EMBO Rep

Self Cite

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ER protein homeostasis (proteostasis) is essential for proper folding and maturation of proteins in the secretory pathway. Loss of ER proteostasis can lead to the accumulation of misfolded or aberrant proteins in the ER and triggers the unfolded protein response (UPR). In this study, we find that the p97 adaptor UBXN1 is an important negative regulator of the UPR. Loss of UBXN1 sensitizes cells to ER stress and activates the UPR. This leads to widespread upregulation of the ER stress transcriptional program. Using comparative, quantitative proteomics we show that deletion of UBXN1 results in a significant enrichment of proteins involved in ER-quality control processes including those involved in protein folding and import. Notably, we find that loss of UBXN1 does not perturb p97-dependent ER-associated degradation (ERAD). Our studies indicate that loss of UBXN1 increases translation in both resting and ER-stressed cells. Surprisingly, this process is independent of p97 function. Taken together, our studies have identified a new role for UBXN1 in repressing translation and maintaining ER proteostasis in a p97 independent manner.

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The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition

Cited by 14 publications

References 90 publications

Unveiling the Intercompartmental Signaling Axis: Mitochondrial to ER Stress Response (MERSR) and its Impact on Proteostasis

Unveiling the Intercompartmental Signaling Axis: Mitochondrial to ER Stress Response (MERSR) and its Impact on Proteostasis

Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies

UBXN1 maintains ER proteostasis and represses UPR activation by modulating translation

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