PXD022403

PXD022403 is an original dataset announced via ProteomeXchange.

Title	Discovery of arginine methylation, phosphorylation and their co-occurrence in condensate-associated proteins in Saccharomyces cerevisiae
Description	The formation of condensates in membraneless organelles is thought to be driven by protein phase separation. Arginine methylation and serine/threonine phosphorylation are important in the phase separation process, however these post-translational modifications are often present in intrinsically disordered regions that are difficult to analyse with standard proteomic techniques. Here we use a multi-protease and multi-MS/MS fragmentation approach, coupled with heavy methyl SILAC and phospho- or methyl-peptide enrichment, for the analysis of arginine methylation and serine/threonine phosphorylation, and to understand their co-occurrence in condensate-associated proteins. For Saccharomyces cerevisiae, we report a 50% increase in the known arginine methylproteome, involving 15 proteins that are almost all condensate-associated. Importantly, some of these proteins have arginine methylation on all predicted sites – providing evidence that this modification can be pervasive. We explored whether arginine methylated condensate-associated proteins are also phosphorylated, and found 12 such proteins to carry phosphoserine or phosphothreonine. In Npl3, Ded1 and Ssbp1, single peptides were found to carry both modifications, indicating a co-occurrence in close proximity and on the same protein molecule. We show that these co-modifications occur in regions of disorder and that arginine methylation is typically on basic regions of disorder. For phosphorylation, its association with charged regions of condensate-associated proteins was less consistent, although some regions with multisite phosphorylation sites were strongly acidic. We conclude that arginine-methylated proteins associated with condensates are typically co-modified with protein phosphorylation.
HostingRepository	PRIDE
AnnounceDate	2021-09-21
AnnouncementXML	Submission_2021-09-21_02:57:25.787.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joshua Hamey
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monomethylated residue; phosphorylated residue; methylated arginine; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-06 01:39:30	ID requested
1	2021-09-16 21:47:05	announced
⏵ 2	2021-09-21 02:57:26	announced	2021-09-21: Updated project metadata.

Hamey JJ, Nguyen A, Wilkins MR, . J Proteome Res, 20(5):2420-2434(2021) [pubmed]

10.1021/ACS.JPROTEOME.0C00927;

submitter keyword: yeast,methylation, phosphorylation, crosstalk

Marc Wilkins
contact affiliation	School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW, Australia
contact email	m.wilkins@unsw.edu.au
lab head
Joshua Hamey
contact affiliation	University of New South Wales
contact email	j.hamey@unsw.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD022403
     1. Label: PRIDE project
     2. Name: Discovery of arginine methylation, phosphorylation and their co-occurrence in condensate-associated proteins in Saccharomyces cerevisiae