Dataset Information

Ubiquitinated proteome of E15.5 murine cortical neurons

ABSTRACT: TRIM9 and TRIM67 are neuronally-enriched E3 ubiquitin ligases essential for neuronal morphogenesis and responses to the axon guidance cue netrin-1. Deletion of either gene in the mouse results in subtle neuroanatomical anomalies yet overt deficits in spatial learning and memory. The identify of few TRIM9 or TRIM67 substrates are known. Here we performed ubiquitin remnant profiling approach (Xu et al., 2010)in cultured cortical neurons from murine wildtype, Trim9-/-, Trim67-/-, and Trim9-/-:Trim67-/- embryos cultured with or without netrin-1 supplementation to attempt to identify proteins with altered ubiquitination. Although batch variability hindered our ability to identify differential protein ubiquitination, the results delineate the neuronal ubiquitionome during neurite outgrowth, axon specification, and axon branching.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain, Neuron, Primary Cell

SUBMITTER: Stephanie Gupton

LAB HEAD: Stephanie L. Gupton

PROVIDER: PXD021818 | Pride | 2021-01-04

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	GU039_WT_digly_Shalini_9ul.raw	Raw
	GU040_WT_netrin_digly_Shalini_9ul.raw	Raw
	GU041_TRIM9_digly_Shalini_9ul.raw	Raw
	GU042_TRIM9_netrin_digly_Shalini_9ul.raw	Raw
	GU043_TRIM67_digly_Shalini_9ul.raw	Raw

Items per page:

1 - 5 of 37

Publications

The ubiquitylome of developing cortical neurons.

Menon Shalini S Goldfarb Dennis D Cousins Emily M EM Major M Ben MB Gupton Stephanie L SL

microPublication biology 20201128

PMID: 33274322

Similar Datasets

Project description:Huntington’s disease is caused by a polyglutamine repeat expansion at the N-terminus of the huntingtin protein which affects the function and folding of the protein, and results in intracellular protein aggregates. Here, we examined whether this mutation leads to altered ubiquitination of huntingtin and other proteins in both soluble and insoluble fractions of brain lysates of the Q175 knock-in Huntington disease mouse model and the Q20 wild-type mouse model. Ubiquitination sites are detected by identification of Gly-Gly (diGly) remnant motifs that remain on modified lysine residues after digestion. We identified K6, K9, K132, K804 and K837 as endogenous ubiquitination sites of soluble huntingtin, with wild-type huntingtin being mainly ubiquitinated at K132, K804 and K837. Mutant huntingtin protein levels were strongly reduced in the soluble fraction while K6 and K9 were mainly ubiquitinated. In the insoluble fraction increased levels of huntingtin K6 and K9 diGly sites were observed for mutant huntingtin as compared to wild type. Besides huntingtin, proteins with various roles, including membrane organization, transport, mRNA processing, gene transcription, translation, catabolic processes and oxidative phosphorylation, were differently expressed or ubiquitinated in wild-type and mutant huntingtin brain tissues. Correlating protein and diGly site fold-changes in the soluble fraction revealed that diGly site abundances of the majority of the proteins were not related to protein fold-changes, indicating that these proteins were differentially ubiquitinated in the Q175 mice. In contrast, both the fold-change of the protein level and diGly site level were increased for several proteins in the insoluble fraction, including ubiquitin, ubiquilin-2, sequestosome-1/p62 and myo5a. Our data sheds light on putative novel proteins involved in different cellular processes as well as their ubiquitination status in Huntington’s disease, which forms the basis for further mechanistic studies to understand the role of differential ubiquitination of huntingtin as well as ubiquitin-regulated processes in Huntington’s disease.