PXD005509-1

PXD005509 is an original dataset announced via ProteomeXchange.

Title	Phase separation of C9orf72 dipeptide repeats perturbs stress granule metabolism
Description	Liquid-liquid phase separation (LLPS) of RNA binding proteins underlies the formation of multiple membraneless organelles involved in RNA metabolism, including stress granules. Defects in stress granule homeostasis constitute a corner stone of ALS/FTLD pathogenesis. Phase separation of ALS-linked stress granule proteins has been shown to rely on hydrophobic interactions. Here we identify an active role for arginine-rich domains in these phase separations. Moreover, arginine-rich dipeptide repeats (DPRs) derived from C9orf72 hexanucleotide repeat expansions similarly undergo LLPS, and induce phase separation of a large set of proteins involved in RNA and stress granule metabolism. In the present proteomics experiment, we wondered which cellular proteins could interact with synthetic PR30 peptide. We took soluble HeLa cell lysate, to which we added increasing concentrations of PR30. The PR30 peptide spontaneously demixed, and could be separated from the solution by gentle centrifugation. Unexpectedly, the resulting pellet was largely resistant to washing steps, suggesting that PR induced the precipitation of different cellular proteins to the insoluble fraction. To see whether weak interactions could still be involved in the process, we also performed mild crosslinking with paraformaldehyde. Mass-spectroscopy (MS) analysis on both crosslinked and uncrosslinked samples identified 874 proteins that were detected and quantified in both conditions.
HostingRepository	PRIDE
AnnounceDate	2017-04-26
AnnouncementXML	Submission_2017-04-26_04:22:36.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Impens Francis
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2016-12-06 06:53:19	ID requested
⏵ 1	2017-04-26 04:22:37	announced

Boeynaems S, Bogaert E, Kovacs D, Konijnenberg A, Timmerman E, Volkov A, Guharoy M, De Decker M, Jaspers T, Ryan VH, Janke AM, Baatsen P, Vercruysse T, Kolaitis RM, Daelemans D, Taylor JP, Kedersha N, Anderson P, Impens F, Sobott F, Schymkowitz J, Rousseau F, Fawzi NL, Robberecht W, Van Damme P, Tompa P, Van Den Bosch L, Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics. Mol Cell, 65(6):1044-1055.e5(2017) [pubmed]

curator keyword: Biological

submitter keyword: Liquid-liquid phase separation, stress granules, arginine-rich dipeptide repeats, labelfree shotgun proteomics

Ludo Van Den Bosch
contact affiliation	KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium VIB, Vesalius Research Center, Laboratory of Neurobiology, 3000 Leuven, Belgium
contact email	ludo.vandenbosch@vib-kuleuven.be
lab head
Impens Francis
contact affiliation	VIB Proteomics Expertise Center
contact email	francis.impens@vib-ugent.be
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005509
     1. Label: PRIDE project
     2. Name: Phase separation of C9orf72 dipeptide repeats perturbs stress granule metabolism