PXD021770

PXD021770 is an original dataset announced via ProteomeXchange.

Title	Identification of proximal SUMO-dependent interactors using SUMO-ID
Description	Proximity-dependent labelling (PL) methods are based on promiscuous labeling enzymes that produce reactive molecules that covalently bind neighbor proteins. Labeled proteins can be then purified and identified using affinity-purification coupled to mass spectrometry methods39. Proximity-dependent biotin identification (BioID)40 uses a promiscuously active Escherichia coli biotin ligase (BirA*) generated by a point mutation (R118G) to biotinylate lysines in nearby proteins within an estimated range of 10 nm41. By fusing BirA* to specific proteins, BioID efficiently identifies interactors at physiological levels in living cells42, 43. It has been extensively used in the Ub field, for instance, to identify substrates of E3 ligases44-46. Recently, a more efficient version of BioID, termed TurboID, has been developed47. TurboID can proximally biotinylate in 10 minutes to the same levels as BioID does in 18 hours, thus making it more suitable for transient protein-protein interaction (PPI) detection. Several studies have developed split-versions and applied “protein fragment complementation” (PCA) to BioID and TurboID, where proximal biotinylation is dependent on the proximity of the fusion partners, opening new opportunities for spatial and temporal identification of complex-dependent interactomes48-50. To study how SUMOylation and SUMO-SIM interactions can lead to other roles and fates for particular substrates poses particular challenges. SUMOylation occurs transiently and often in a small percentage of a given substrate. Modified proteins can be readily deSUMOylated and SUMO can be recycled and passed to other substrates. SUMO-SIM interactions are also difficult to analyze due to their weak affinity (Kd ranging from 1-100 µM). To overcome those technical issues, we developed SUMO-ID, a new strategy based on Split-TurboID to identify SUMO- interactors of specific substrates dependent on SUMO conjugation or interaction. Using PML as a model, we demonstrate that SUMO-ID can enrich for factors that depend on PML-SUMO interaction. Importantly, those are represented among proximal interactors of PML identified using full-length TurboID. We also applied SUMO-ID to a less-characterized SUMO substrate, Spalt like transcription factor 1 (SALL1), and identified both known and novel interactors that depend on intact SUMOylation sites in SALL1. SUMO-ID is thus a powerful tool to study transient and dynamic SUMO-dependent interaction events.
HostingRepository	PRIDE
AnnounceDate	2023-04-11
AnnouncementXML	Submission_2023-04-11_06:02:36.354.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	MikelAzkargorta
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	sumoylated lysine
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-01 00:05:00	ID requested
1	2021-09-20 05:28:23	announced
⏵ 2	2023-04-11 06:02:37	announced	2023-04-11: Updated project metadata.

Barroso-Gomila O, Trulsson F, Muratore V, Canosa I, Merino-Cacho L, Cortazar AR, P, é, rez C, Azkargorta M, Iloro I, Carracedo A, Aransay AM, Elortza F, Mayor U, Vertegaal ACO, Barrio R, Sutherland JD, Identification of proximal SUMO-dependent interactors using SUMO-ID. Nat Commun, 12(1):6671(2021) [pubmed]

submitter keyword: PML,SUMO, TurboID, protein-protein interaction, BioID

FelixElortza
contact affiliation	Proteomics Service CIC bioGUNE Bizkaia Tech. Park Build. 800 Derio 48160 Spain
contact email	felortza@cicbiogune.es
lab head
MikelAzkargorta
contact affiliation	Proteomics Platform CIC bioGUNE
contact email	mazkargorta@cicbiogune.es
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/2021/09/PXD021770

PRIDE project URI

• PRIDE
  1. PXD021770
     1. Label: PRIDE project
     2. Name: Identification of proximal SUMO-dependent interactors using SUMO-ID