PXD048045-2

PXD048045 is an original dataset announced via ProteomeXchange.

Title	Loss of the E3 ubiquitin ligase Trim9 or Trim67 alters the post-synaptic density proteome
Description	During development, neurons undergo expansive growth and shape change to achieve their mature morphology and physiological function. As cellular remodeling occurs, proteins are synthesized, transported, degraded, and recycled. As such, protein levels and localization are tightly regulated. E3 ubiquitin ligases play a key role in proteostasis by altering protein localization, intracellular trafficking, and protein lifetime via the addition of ubiquitin modifiers. TRIM9 and TRIM67 are brain-enriched E3 ubiquitin ligases implicated in numerous stages of neuronal morphogenesis. We previously demonstrated both proteins are required for axon pathfinding and growth cone shape changes in developing neurons. In particular, TRIM9 and TRIM67 regulate filopodia number and stability in early stages of neuronal development. Our published in vivo studies suggest TRIM9 and TRIM67 may function at the synapse as well. We observed distinct deficits in spatial learning and memory of Trim9-/- and Trim67-/- mice in the Morris Water Maze test, compared to their littermate controls. Furthermore, adult-born neurons in the dentate gyrus in Trim9-/- mice also displayed a decreased number of dendritic spines. Here we demonstrate TRIM9 and TRIM67 localize to the post-synaptic density (PSD), a structure attached to the post-synaptic membrane in dendritic spines. We identified 148 proteins that were significantly changed (p < 0.05) in the Trim67-/- mice compared to their Trim67+/+ littermates. Gene Ontology analysis of these proteins demonstrated enrichment of several cellular pathways, including peptidyl-amino acid modification, microtubule dynamics, and Ras signal transduction. Likewise, we identified 109 proteins that were significantly changed (p < 0.05) in the Trim9-/- mice compared to their Trim9+/+ littermates. Following Gene Ontology analysis, we observed the prominent enrichment of one pathway in our significantly different proteins: the actin cytoskeleton. Changes in these actin cytoskeleton proteins were bidirectional, suggesting the presence of altered cytoskeletal architecture and organization in the Trim9-/- PSD.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:22:23.929.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Laura Herring
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-21 08:01:14	ID requested
1	2024-01-16 18:52:41	announced
⏵ 2	2024-10-22 06:22:24	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Synapse

Post-synaptic density

TRIM9

TRIM67

E3 ubiquitin ligase

Stephanie Gupton
contact affiliation	UNC-Chapel Hill
contact email	sgupton@email.unc.edu
lab head
Laura Herring
contact affiliation	UNC-Chapel Hill
contact email	laura_herring@med.unc.edu
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/2024/01/PXD048045

PRIDE project URI

• PRIDE
  1. PXD048045
     1. Label: PRIDE project
     2. Name: Loss of the E3 ubiquitin ligase Trim9 or Trim67 alters the post-synaptic density proteome