PXD027992

PXD027992 is an original dataset announced via ProteomeXchange.

Title	Nanodiscs-based proteomics to identify lipid-interacting proteins in yeast
Description	Many soluble proteins interact with membranes to perform important biological functions, including signal transduction, regulation, transport, trafficking and biogenesis. Despite their importance, these protein-membrane interactions are difficult to characterize due to their often-transient nature as well as phospholipids’ poor solubility in aqueous solution. Here, we employ nanodiscs – small, water-soluble patches of lipid bilayer encircled with amphipathic scaffold proteins – along with quantitative proteomics to identify lipid-binding proteins in S. cerevisiae. Using nanodiscs reconstituted with yeast total lipid extracts or only phosphatidylethanolamine (PE-nanodiscs), we capture several known membrane-interacting proteins, including the Rab GTPases Sec4 and Ypt1, which play key roles in vesicle trafficking. Utilizing PE-nanodiscs enriched with phosphatidic acid (PEPA-nanodiscs), we specifically capture a member of the Hsp40/J-protein family, Caj1, whose function has recently been linked to membrane protein quality control. We show that Caj1 interaction with liposomes containing PA is modulated by pH and PE lipids, and depends on two patches of positively charged residues near the C-terminus of the protein. The protein Caj1 is the first example of an Hsp40/J-domain protein with affinity for membranes and phosphatidic acid lipid specificity. These findings highlight the utility of the nanodisc system to identify and characterize protein-lipid interactions that may not be evident using other methods.
HostingRepository	PRIDE
AnnounceDate	2021-12-30
AnnouncementXML	Submission_2021-12-30_14:08:52.265.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	John Young
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-17 23:07:12	ID requested
⏵ 1	2021-12-30 14:08:52	announced

Zhang XX, Young JW, Foster LJ, Duong F, Nanodisc-Based Proteomics Identify Caj1 as an Hsp40 with Affinity for Phosphatidic Acid Lipids. J Proteome Res, 20(10):4831-4839(2021) [pubmed]

submitter keyword: Nanodiscs, SILAC labeling, Hsp40, Caj1, Rab GTPase

Franck Duong
contact affiliation	Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC, Canada
contact email	fduong@mail.ubc.ca
lab head
John Young
contact affiliation	University of Oxford
contact email	john.young@chem.ox.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD027992
     1. Label: PRIDE project
     2. Name: Nanodiscs-based proteomics to identify lipid-interacting proteins in yeast