Dataset Information

Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation

ABSTRACT: The Ubiquitin-like molecule NEDD8 controls several biological processes and is a promising target for therapeutic intervention. NEDDylation occurs through specific NEDD8 enzymes (canonical) or enzymes of the Ubiquitin system (atypical). Identification of NEDD8 sites on substrates is critical for delineating the processes controlled by NEDDylation. By combining the use of the NEDD8 R74K mutant with anti-diGly antibodies we identified 1101 unique NEDDylation sites in 620 proteins. Bioinformatics analysis reveals that canonical and atypical NEDDylation have distinct proteomes; the spliceosome/mRNA surveillance/DNA replication and ribosome/proteasome respectively. The data also reveal the formation of poly-NEDD8, hybrid NEDD8-Ubiquitin and NEDD8-SUMO-2 chains as potential molecular signals. In particular, NEDD8-SUMO-2 chains are induced upon proteotoxic stress (atypical) through NEDDylation of K11 in SUMO-2 and conjugates accumulate in previously described nucleolus-related inclusions. The study uncovers a diverse proteome for NEDDylation, and is consistent with the concept of extensive cross-talk between Ubiquitin and Ubls under proteotoxic stress conditions.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Colonic Epithelium, Colon

DISEASE(S): Colon Cancer

SUBMITTER: Petra Beli

LAB HEAD: Petra Beli

PROVIDER: PXD022812 | Pride | 2021-02-10

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20170210_QEP1_PBE_JH_Sofia_HCT116_NEDP1_KD_Nedd8_double_diGly_SCX_01.raw	Raw
	20170210_QEP1_PBE_JH_Sofia_HCT116_NEDP1_KD_Nedd8_double_diGly_SCX_02.raw	Raw
	20170210_QEP1_PBE_JH_Sofia_HCT116_NEDP1_KD_Nedd8_double_diGly_SCX_03.raw	Raw
	20170210_QEP1_PBE_JH_Sofia_HCT116_NEDP1_KD_Nedd8_double_diGly_SCX_04.raw	Raw
	20170210_QEP1_PBE_JH_Sofia_HCT116_NEDP1_KD_Nedd8_double_diGly_SCX_05.raw	Raw

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Publications

Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation.

Lobato-Gil Sofia S Heidelberger Jan B JB Maghames Chantal C Bailly Aymeric A Brunello Lorene L Rodriguez Manuel S MS Beli Petra P Xirodimas Dimitris P DP

Cell reports 20210101 3

The ubiquitin-like molecule NEDD8 controls several biological processes and is a promising target for therapeutic intervention. NEDDylation occurs through specific NEDD8 enzymes (canonical) or enzymes of the ubiquitin system (atypical). Identification of NEDD8 sites on substrates is critical for delineating the processes controlled by NEDDylation. By combining the use of the NEDD8 R74K mutant with anti-di-glycine (anti-diGly) antibodies, we identified 1,101 unique NEDDylation sites in 620 protei ...[more]

PMID: 33472076

Similar Datasets

Project description:The heart undergoes significant structural, metabolic, gene expression and functional alterations during the perinatal to postnatal transition. While recent studies have identified multiple epigenetic and transcriptional regulators of cardiac maturation, post-transcriptional mechanisms regulating this process remain poorly understood. Neddylation is a post-translational modification that conjugates a small ubiquitin-like protein, NEDD8, to protein substrates via an E1-E2-E3 enzymatic cascade. The goal of this study was to define the role of neddylation in perinatal cardiac development and cardiac maturation. Neddylation was inhibited in adult mouse hearts by cardiac-specific deletion of NAE1 gene, a regulatory subunit of NEDD8 E1 enzyme, or in neonatal cardiomyocytes (CMs) with a pharmacological neddylation inhibitor, MLN4924. The impact on cardiac transcriptome, metabolism, maturation and function was assessed. Mosaic deletion of NAE1 in ~40% neonatal CMs disrupted aspects of maturation, including transverse-tubule formation, cellular hypertrophy and fetal/adult isoform switching, whereas deletion of NAE1 in over 80% CMs led to rapid development of cardiomyopathy and heart failure. Transcriptome analysis demonstrated an association of metabolic derangement with immature cardiomyocyte signature. Biochemical, ultrastructural and metabolomics analyses confirmed downregulation of fatty acid and oxidative phosphorylation genes, deficits in fatty acid utilization, mitochondrial dysfunction, and significantly altered metabolic profiles in NAE1-deficient hearts or MLN4924-treated neonatal CMs. Mechanistically, we found that HIF1α, a transcription factor known to promote glycolysis and suppress oxidative metabolism, is a putative NEDD8 target. Inhibition of neddylation resulted in HIF1α accumulation and activation, which contributed to diminished fatty acid utilization. Taken together, we conclude that neddylation plays a crucial role in CM maturation and postnatal cardiac development through sustaining the glycolytic to oxidative metabolic switch in perinatal hearts.