Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The function of ER-phagy receptors is regulated through phosphorylation-dependent ubiquitination pathways.

ABSTRACT: Selective autophagy of the endoplasmic reticulum (ER), known as ER-phagy, is an important regulator of ER remodeling and is critical to maintaining cellular homeostasis during environmental changes. We recently showed that members of the FAM134 family play a role during stress-induced ER-phagy. However, the mechanisms on how they are activated remain largely unknown. In this study, we analyzed mTOR-mediated phosphorylation of FAM134 as a trigger of FAM134-driven ER-phagy. An unbiased screen of kinase inhibitors revealed that CK2 is essential for ER-phagy driven by FAM134B and FAM134C after inhibition of mTOR. Using superresolution microscopy, we showed that CK2 activity is essential for the formation of high-density groups of FAM134B and FAM134C. Continually, the FAM134B and FAM134C proteins that carry point mutations of selected serine residues within their reticulon homology domain are unable to form high-density clusters. Furthermore, we provide evidence that ubiquitination regulates ER-phagy receptors and that dense clustering of FAM134B and FAM134C requires events upstream of ubiquitination. Treatment with the CK2 inhibitor SGC-CK2-1 or mutation of phosphosites prevents Torin1-induced ER-phagy flux as well as ubiquitination of FAM134 proteins, and consistently treatment with E1 inhibitor suppresses Torin1-induced ER-phagy flux. Therefore, we propose that CK2 dependent phosphorylation of ER-phagy receptors precedes ubiquitin-dependent activation of ER-phagy flux.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell

DISEASE(S): Osteosarcoma

SUBMITTER: Pablo Sanz Martinez

LAB HEAD: Alexandra Stolz

PROVIDER: PXD043003 | Pride | 2023-11-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Function of ERphagy receptors is regulated via phosphorylation-dependent ubiquitination pathways

Project description:Selective autophagy of the ER (ERphagy) is an important regulator of ER remodeling and critical to maintain cellular homeostasis upon environmental changes. ERphagy receptors link the ER with autophagic membrane thus regulating ERphagy flux. We recently showed that members of the FAM134 family play overlapping and distinct roles during stress-induced ERphagy. Yet the mechanisms on how they are activated remain largely unknown. In this study we analyzed mTOR-mediated dynamic phosphorylation of FAM134 as a trigger of FAM134-driven ERphagy. An unbiased screen of kinase inhibitors revealed CK2 to be essential for FAM134B- and FAM134C-driven ERphagy upon mTOR inhibition. Identified dynamic phosphorylation sites on FAM134C in cells were fitting with predicted CK2 targeting sites, indicating a direct regulatory role of CK2 in FAM134-driven ERphagy. Using super-resolution microscopy, we showed that activity of CK2 is essential for the formation of high-density clusters of FAM134B and FAM134C. Consistently, FAM134B and FAM134C proteins carrying point mutations of selected Serin residues, within their reticulon homology domain, are unable to form high-density clusters. In addition, we provide evidence that the ubiquitination machinery is required for ERphagy and that FAM134B and FAM134C clustering is activated by phospho-dependent ubiquitination. Treatment with CK2 inhibitor SGC-CK2-1 prevents Torin1-induced ERphagy flux as well as ubiquitination of FAM134 proteins and consistently, treatment with E1 inhibitor suppresses Torin1-induced ERphagy flux. Therefore, we propose CK2 dependent phosphorylation of ERphagy receptors precedes ubiquitin-dependent ERphagy flux activation.

2022-08-17 | PXD036103 | Pride

An mTORC1-CK2 axis controls starvation induced ER-phagy via FAM134C

Project description:The degradation of endoplasmic reticulum (ER) via selective autophagy is driven by the ER-phagy receptors that facilitate the incorporation of ER-fragments into nascent autophagosomes. How these receptors are regulated, in response to ER-phagy-inducing stimuluses, is largely unknown. Here we propose that starvation, as well as mTOR inhibition, triggers ER-phagy primarily through the activation of the ER-phagy receptor FAM134C. In physiological, nutrient reach, conditions FAM134C is phosphorylated by the Casein kinase 2 (CK2) protein at specific residues negatively affecting FAM134C interaction with the LC3 proteins, thereby preventing ER-phagy. Pharmacological or starvation-induced mTORC1 inhibition limits phosphorylation of FAM134C by CK2, hence promoting FAM134C activation and ER-phagy. Moreover, inhibition of CK2 or the expression of a phospho-mutant FAM134C protein is sufficient to stimulate ER-phagy. Conversely, starvation induced ER-phagy is inhibited in cells and mice that lack FAM134C or expressing a phospho-mimetic FAM134C protein. Overall, these data describe a new mechanism regulating ER-phagy and provides an example of cargo selectivity mechanism during starvation induced autophagy.

2022-10-14 | PXD030451 | Pride

Critical functions of FAM134 family members in endoplasmic reticulum remodeling, ER-phagy and collagen quality control

Project description:Degradation of the endoplasmic reticulum (ER) by selective autophagy (ER-phagy) is vital for cellular homeostasis. Here, we introduce FAM134A/RETREG2 and FAM134C/RETREG3 as new ER-phagy receptors. FAM134A and FAM134C exist in a relatively inactive state under basal conditions and require an activation signal to induce significant ER fragmentation. Molecular modeling and simulations implicate a single compact fold of FAM134A’s reticulon homology domain (RHD). In contrast, the RHDs of FAM134B and FAM134C are able to adopt at least three discrete conformations. These differences result in slower vesicle formation for FAM134A compared to FAM134C and mostly FAM134B. Global proteomic analyses of knockout MEFs indicate both distinct and overlapping roles for the Fam134s, with Fam134a being most distant from Fam134b and Fam134c. Fam134c appears to enhance and facilitate Fam134b’s role in maintaining pro-collagen-I levels and is therefore insufficient to compensate for its loss. By contrast, Fam134a has a particular mode of action in maintaining pro-collagen-I levels and is able to fully compensate loss of Fam134b or Fam134c upon over-expression in its wild-type or LIR mutant form.

2021-06-23 | PXD025626 | Pride

E3 ligase regulates FAM134B ubiquitination

Project description:FAM134B is a reticulon-homology domain (RHD)-containing protein that participates in membrane-shaping of the endoplasmic reticulum (ER)8 13. It also functions as a mammalian ER-phagy receptor, mediating the fragmentation and selective degradation of ER sheets in multiple cell types8. However, little is known about the molecular and biophysical mechanisms that control and/or switch between these two FAM134B functions.

2023-06-19 | PXD032750 | Pride

FAM134B homodimer ubiquitination

2023-06-19 | PXD032740 | Pride

Ubiquitination promotes FAM134B-mediated ER-phagy

2023-06-19 | PXD032721 | Pride

FAM134B oligomer ubiquitination and ER-phagy

2023-06-19 | PXD032741 | Pride

Binding partners of FAM134B WT and 17KR oligomers

2023-06-19 | PXD032743 | Pride

Proteome of Fam134A/B/C knock-out MEFs

Project description:Selective degradation of endoplasmic reticulum (ER) via autophagy receptors is important to maintain cell homeostasis. In this study we identify FAM134A/RETREG2 and FAM134C/RETREG3 as bona fide ER-phagy receptors containing a classical and functional LIR motif. In contrast to the other family member FAM134B/RETREG1, over-expressed FAM134A and C are in a relatively inactive state, under basal conditions, and require an activation signal to fragment significant amounts of ER. Global proteomes analysis of knockout MEFs suggests distinct and overlapping functions of the three FAM134. Common functions are the maintenance of the ER shape and delivery of mis-folded pro-collagen I to lysosomes. Single knockout of Fam134a or Fam134c lead to swollen ER and massive intracellular accumulation of pro-collagen I. In this context, Fam134a but not Fam134c over-expression is able to recover collagen I levels, in Fam134b knockout MEFs, indicating distinct modes of action. Moreover, we provide evidence that Fam134a has a LIR-independent function in maintaining collagen I homeostasis in a co-receptor complex together with Fam134c. This pathway works in parallel to Fam134b, which in contrast is self-sufficient to drive ER-phagy.

2021-06-23 | PXD021690 | Pride

ARL6IP1 is an interacting partner of the ER-phagy receptor FAM134B

Project description:ER-resident membrane-shaping proteins with central reticulon homology domains (RHDs) have been associated with neurodegenerative disorders such as ARL6IP1 and FAM134B.Mutations in ARL6IP1 cause SPG61, a neurodegenerative disorder characterized by progressive leg spasticity (hereditary spastic paraplegia/HSP) in combination with loss of sensory and pain perception, thus reproducing typical symptoms of HSAN {Kurth, 2009 #8;Novarino, 2014 #28;Nizon, 2018 #162}.Our objetive was to analyse FAM134B-ARL6IP1 protein protein interactionS to underlying mechanisms, required for effective ER-remodelling and ER-phagy.

2023-06-19 | PXD032718 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data