NatB Protects Procaspase-8 from UBR4-Mediated Degradation and Is Required for Full Induction of the Extrinsic Apoptosis Pathway

Abstract

N-terminal acetyltransferase B (NatB) is a major contributor to the N-terminal acetylome and is implicated in several key cellular processes including apoptosis and proteostasis. However, the molecular mechanisms linking NatB-mediated N-terminal acetylation to apoptosis and its relationship with protein homeostasis remain elusive. In this study, we generated mouse embryonic fibroblasts (MEFs) with an inactivated catalytic subunit of NatB (Naa20^-/-) to investigate the impact of NatB deficiency on apoptosis regulation. Through quantitative N-terminomics, label-free quantification, and targeted proteomics, we demonstrated that NatB does not influence the proteostasis of all its substrates. Instead, our focus on putative NatB-dependent apoptotic factors revealed that NatB serves as a protective shield against UBR4 and UBR1 Arg/N-recognin-mediated degradation. Notably, Naa20^-/- MEFs exhibited reduced responsiveness to an extrinsic pro-apoptotic stimulus, a phenotype that was partially reversible upon UBR4 Arg/N-recognin silencing and consequent inhibition of procaspase-8 degradation. Collectively, our results shed light on how the interplay between NatB-mediated acetylation and the Arg/N-degron pathway appears to impact apoptosis regulation, providing new perspectives in the field including in therapeutic interventions.

Keywords:

• N-terminal acetylation
• proteostasis
• NatB
• N-acetyltransferases
• N-terminomics
• E3 ubiquitin ligases
• N-degrons
• N-recognins
• apoptosis
• caspases

Data Availability

Mass-spectrometry based proteomics data are deposited in ProteomeXchange Consortium (https://proteomecentral.protemeexhange.org) via the PRIDE repository (https://www.ebi.ac.uk/pride/) with the data set identifier PXD029641, username: [email protected], Password: O8uvsKWw.

Author Contributions

Conceptualization, R.A, C.G. and M.C.R.; methodology design, C.G., R.A., M.C.R., T.M., JB.B., J.P.G., J.E., and B.C.; formal analysis, C.G., R.A., M.C.R., T.M., JB.B., J.P.G., J.E., B.C., V.R. and L.S.; investigation, C.G., R.A., M.C.R., T.M., JB.B., J.P.G., J.E., B.C., V.R. and L.S.; writing original draft, R.A, C.G. M.C.R. and J.P.G.; writing-review and editing, C.G., R.A., M.C.R., J.P.G., T.M., and JB.B.; visualization, C.G., R.A., M.C.R., J.P.G., T.M., and JB.B.; supervision, R.A, C.G. and M.C.R; project administration, R.A, C.G. and M.C.R; funding acquisition, R.A, C.G., and T.M.

Disclosure Statement

No potential conflict of interest was reported by the authors.

Materials and Correspondence

Correspondence and material requests should be addressed to Manuela Côrte-Real, Carmela Giglione, and Rafael Aldabe.

Additional information

Funding

This work was supported by the KatNat (ERA-NET, ANR-17-CAPS-0001-01) and CanMore (France-Germany PRCI, ANR-20 CE92-0040) grants funded by the French National Research Agency (ANR) to C.G. to support JB.B, by Foundation ARC (ARCPJA32020060002137) grants to T.M., by ISCIII Consolidation Program Grant and Ministerio Español de Economía y Competitividad Torres Quevedo Program (PTQ-13-06466) to support RA, by Departamento de Desarrollo Económico del Gobierno de Navarra (0011-1383-2018-000011) grant to RA, from the facilities and expertise of the I2BC proteomic platform (Proteomic-Gif, SICaPS) supported by IBiSA, Ile de France Region, Plan Cancer, CNRS and Paris-Saclay University, and from ProteoCure COST (European Cooperation in Science and Technology) action CA20113. The proteomic experiments were partially supported by Agence Nationale de la Recherche under projects ProFI (Proteomics French Infrastructure, ANR-10-INBS-08) and GRAL, a program from the Chemistry Biology Health (CBH) Graduate School of University Grenoble Alpes (ANR-17-EURE-0003). Joana P. Guedes acknowledges the PhD fellowship SFRH/BD/132070/2017 funded by FCT.