PXD017888

PXD017888 is an original dataset announced via ProteomeXchange.

Title	RNF4 interactome in heatshocked HeLa cells
Description	Exposure of cells to heat or oxidative stress causes misfolding of proteins. To avoid toxic protein aggregation, cells have evolved nuclear and cytosolic protein quality control (PQC) systems. In response to proteotoxic stress cells also limit protein synthesis by triggering transient storage of mRNAs and RNA binding proteins (RBPs) in cytosolic stress granules (SGs). We demonstrate that the SUMO-targeted ubiquitin ligase (StUbL) pathway, which is part of the nuclear proteostasis network, regulates SG dynamics. We provide evidence that inactivation of SUMO deconjugases under proteotoxic stress initiates SUMO-primed, RNF4-dependent ubiquitylation of RBPs that typically condense into SGs. Impairment of SUMO-primed ubiquitylation drastically delays SG resolution upon stress release. Importantly, the StUbL system regulates compartmentalization of an amyotrophic lateral sclerosis (ALS)-associated mutant of FUS in SGs. We propose that the StUbL system functions as surveillance pathway for aggregation-prone RBPs in the nucleus thereby linking the nuclear and cytosolic axis of proteotoxic stress response. To better understand the role of RNF4 in the proteotoxic stress response we aimed to identify RNF4-associated protein complexes in cells exposed to heat stress. To allow immuno-affinity purification of endogenous RNF4 on anti-Flag agarose beads we used CRISPR/Cas9-mediated gene editing to integrate a C-terminal 3xFlag epitope tag into the genomic locus of RNF4 in HeLa cells. For the IP-MS experiment HeLa-RNF4-3xFlag cells or parental untagged control cells were exposed to heat stress for 1 h and RNF4-3xFlag together with associated proteins was captured on anti-Flag affinity beads. Tryptic peptides were analyzed by LC-MS/MS and data from three replicates were quantified by the Max Quant label-free quantification (LFQ) algorithm.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:51:31.736.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jan Keiten-Schmitz
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-04 23:55:11	ID requested
1	2023-06-30 01:57:22	announced
2	2023-11-14 06:58:29	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:51:32	announced	2024-10-22: Updated project metadata.

10.1016/J.MOLCEL.2020.05.017;

submitter keyword: HeLa RNF4 heatshock interactome

Stefan Müller
contact affiliation	Institute of Biochemistry II, Goethe University, Medical School, Frankfurt, Germany
contact email	ste.mueller@em.uni-frankfurt.de
lab head
Jan Keiten-Schmitz
contact affiliation	Goethe University, Frankfurt am Main, Germany
contact email	keiten-schmitz@em.uni-frankfurt.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/06/PXD017888

PRIDE project URI

• PRIDE
  1. PXD017888
     1. Label: PRIDE project
     2. Name: RNF4 interactome in heatshocked HeLa cells