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The identification of ubiquitination sites of IBTK by shotgun proteomics

ABSTRACT: Previous study reported that eIF4A1 protein stability is subject to control by the ubiquitin-proteasome pathway, and deubiquitinase USP9X elevated eIF4A1 protein level by promoting eIF4A1 deubiquitination. However, the E3 ubiquitin ligases responsible for eIF4A1 proteolysis is not determined. Our research suggested that IBTK mediated non-degradative ubiquitination of eIF4A1, thus probable ubiquitination sites of eIF4A1 were identified by MS analysis.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Huiru Sun

LAB HEAD: Chenji Wang

PROVIDER: PXD039031 | Pride | 2024-05-10

REPOSITORIES: Pride

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			Action	DRS
	Orbi07669-HL-WCJ-SHR-ub-peptide.xlsx	Xlsx
	Orbi07669-HL-WCJ-SHR-ub-protein.xlsx	Xlsx
	Orbi07669-HL-WCJ-SHR-ub.raw	Raw
	Orbi07669-HL-WCJ-SHR-ub.xlsx	Xlsx

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Project description:Progression through neuronal loss of substantia nigra pars compacta with Parkinson’s disease depends on various protein post-translational modifications mainly comprising phosphorylation, ubiquitination, acetylation, and methylation. Phosphorylation and ubiquitination regulate major physiological changes and cellular signaling pathways during dopaminergic neuronal death. Phosphorylation and ubiquitination dyshomeostasis of substantia nigra pars compacta tissue occurs earlier than movement symptom appearance. Although many phosphorylation and ubiquitination sites have been identified through site-specific methods, systematic quantitative proteomic analysis of pre-symptomatic Parkinson’s disease remains unexplored. Using quantitative proteomics, we have globally profiled ubiquitination and phosphorylation in substantia nigra pars compacta tissue of a Parkinson’s disease transgenic mouse model (A30P*A53T α-synuclein, hm2α-SYN-39 mouse strain) at pre-symptomatic stage; Our datasets of 5,351 phosphorylation sites in 2,136 proteins and 3,971 ubiquitination sites in 1,595 proteins provide valuable insight into pre-symptomatic Parkinson’s disease. After in-depth analysis of the relationship between phosphorylation and ubiquitination sites, we concluded that correlation of the relationship increased with decreasing distance. Subsequent bioinformatic analyses, including gene ontology annotation, domain annotation, subcellular localization, KEGG pathway annotation, functional cluster analysis, and motif analysis were performed to annotate quantifiable targets of phosphorylation and ubiquitination sites. Individual simultaneous phosphorylation and ubiquitination proteins that were differentially quantified were screened. The endocytosis pathway is likely regulated by both phosphorylation and ubiquitination at the molecular protein Epn2 (S439 and K135) in early-stage Parkinson’s disease. Therefore, this elucidation of the dysregulation of phosphorylation and ubiquitination has implications for understanding the pathophysiological mechanism of dopaminergic neuron degeneration and for developing novel therapeutics for Parkinson’s disease.

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The identification of ubiquitination sites of IBTK by shotgun proteomics

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