PXD034247-1

PXD034247 is an original dataset announced via ProteomeXchange.

Title	Affinity purification of in vivo assembled whirlin-associated protein complexes from the zebrafish retina - GST
Description	Mutations in WHRN lead to Usher syndrome type 2d (USH2d) or to non-syndromic hearing impairment (DFNB31). The WHRN-encoded gene product whirlin directly interacts with the intracellular regions of the other two Usher syndrome type 2 (USH2)-associated proteins, usherin and ADGRV1. Together with PDZD7, these proteins form the transiently present ankle link complex necessary for maturation of the inner ear hair bundle. In photoreceptors, usherin and ADGRV1 are also scaffolded by whirlin and constitute similar fibrous links between the periciliary membrane and the connecting cilium. However, the molecular mechanism of retinal degeneration as a consequence of compromised USH2-associated protein complex formation and function remains elusive. To better understand the function of the USH2-associated proteins in the photoreceptors, we aimed to isolate and characterize whirlin-associated protein complexes from zebrafish photoreceptor cells. We generated transgenic zebrafish that express Strep/FLAG-tagged Whrna, a zebrafish ortholog of human whirlin, under the control of a photoreceptor-specific promoter. Affinity purification of Strep/FLAG-tagged Whrna and associated proteins from adult transgenic zebrafish retinas followed by mass spectrometry analysis identified 19 novel candidate interaction partners. Pull down experiments and dedicated yeast two-hybrid assays confirmed the association of Whrna with 7 of the co-purified proteins. Several of the co-purified proteins are part of the synaptic proteome, which suggest a role for whirlin in the photoreceptor synapse. Future studies will elucidate which of the identified protein-protein interactions contribute to the development of the retinal phenotype observed in USH2d patients.
HostingRepository	PRIDE
AnnounceDate	2023-12-28
AnnouncementXML	Submission_2023-12-28_11:05:15.708.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karsten Boldt
SpeciesList	scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955;
ModificationList	acetylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-01 05:02:28	ID requested
⏵ 1	2023-12-28 11:05:16	announced
2	2024-10-22 06:18:49	announced	2024-10-22: Updated project metadata.

10.1016/j.jprot.2022.104666;

Schellens RTW, Slijkerman RWN, Hetterschijt L, Peters TA, Broekman S, Clem, é, nt A, Westerfield M, Phillips JB, Boldt K, Kremer H, De Vrieze E, Van Wijk E, Affinity purification of in vivo assembled whirlin-associated protein complexes from the zebrafish retina. J Proteomics, 266():104666(2022) [pubmed]

submitter keyword: complexes, cilia, GST,zebrafish

Dr. Karsten Boldt
contact affiliation	Eberhard Karls University Tübingen, Institute for Ophthalmic Research
contact email	karsten.boldt@uni-tuebingen.de
lab head
Karsten Boldt
contact affiliation	Medical Bioanalytics
contact email	karsten.boldt@uni-tuebingen.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/2023/12/PXD034247

PRIDE project URI

• PRIDE
  1. PXD034247
     1. Label: PRIDE project
     2. Name: Affinity purification of in vivo assembled whirlin-associated protein complexes from the zebrafish retina - GST