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

Sofia Lobato-Gil (1) , Jan B Heidelberger (2) , Chantal Maghames (1) , Aymeric Bailly (1) , Lorene Brunello (1) , Manuel Rodriguez (3, 4) , Petra Beli (2) , Dimitris P Xirodimas (1)

1 CRBM - Centre de recherche en Biologie cellulaire de Montpellier
2 IMB - Institute of Molecular Biology [Mainz, Germany]
3 LCC - Laboratoire de chimie de coordination
4 IPBS - Institut de pharmacologie et de biologie structurale

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 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.

Mots clés: NEDD8; Atypical; Canonical; Proteotoxic stress; NEDP1; diGly signatures; Nucleolus-related inclusions; Hybrid chains; NEDD8-SUMO polymers

Domaines: Chimie de coordination

Sofia Lobato-Gil, Jan B Heidelberger, Chantal Maghames, Aymeric Bailly, Lorene Brunello, et al.. Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation. Cell Reports, 2021, 34 (3), pp.108635. ⟨10.1016/j.celrep.2020.108635⟩. ⟨hal-03176206⟩