title: Deletion of immunoproteasome subunits imprints on the transcriptome and has a broad impact on peptides presented by major histocompatibility complex I molecules.
abstract: Proteasome-mediated proteolysis plays a crucial role in many basic cellular processes. In addition to constitutive proteasomes (CPs), which are found in all eukaryotes, jawed vertebrates also express immunoproteasomes (IPs). Evidence suggests that the key role of IPs may hinge on their impact on the repertoire of peptides associated to major histocompatibility complex (MHC) I molecules. Using a label-free quantitative proteomics approach, we identified 417 peptides presented by MHC I molecules on primary mouse dendritic cells (DCs). By comparing MHC I-associated peptides (MIPs) eluted from primary DCs and thymocytes, we found that the MIP repertoire concealed a cell type-specific signature correlating with cell function. Notably, mass spectrometry analyses of DCs expressing or not IP subunits MECL1 and LMP7 showed that IPs substantially increase the abundance and diversity of MIPs. Bioinformatic analyses provided evidence that proteasomes harboring LMP7 and MECL1 have specific cleavage preferences and recognize unstructured protein regions. Moreover, while differences in MIP repertoire cannot be attributed to potential effects of IPs on gene transcription, IP subunits deficiency altered mRNA levels of a set of genes controlling DC function. Regulated genes segregated in clusters that were enriched in chromosomes 4 and 8. Our peptidomic studies performed on untransfected primary cells provide a detailed account of the MHC I-associated immune self. This work uncovers the dramatic impact of IP subunits MECL1 and LMP7 on the MIP repertoire and their non-redundant influence on expression of immune-related genes.
authors.affiliation: Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada.
authors.forename: Danielle
authors.initials: D
authors.lastname: de Verteuil
authors.forename: Tara L
authors.initials: TL
authors.lastname: Muratore-Schroeder
authors.forename: Diana P
authors.initials: DP
authors.lastname: Granados
authors.forename: Marie-Hélène
authors.initials: MH
authors.lastname: Fortier
authors.forename: Marie-Pierre
authors.initials: MP
authors.lastname: Hardy
authors.forename: Alexandre
authors.initials: A
authors.lastname: Bramoullé
authors.forename: Etienne
authors.initials: E
authors.lastname: Caron
authors.forename: Krystel
authors.initials: K
authors.lastname: Vincent
authors.forename: Sylvie
authors.initials: S
authors.lastname: Mader
authors.forename: Sébastien
authors.initials: S
authors.lastname: Lemieux
authors.forename: Pierre
authors.initials: P
authors.lastname: Thibault
authors.forename: Claude
authors.initials: C
authors.lastname: Perreault
mesh_terms: D000818:Animals; D015153:Blotting, Western; D002853:Chromatography, Liquid; D005434:Flow Cytometry; D020869:Gene Expression Profiling; D015395:Histocompatibility Antigens Class I / Q000737:chemistry*; D051379:Mice; D008810:Mice, Inbred C57BL; D020411:Oligonucleotide Array Sequence Analysis; D010455:Peptides / Q000737:chemistry*; D046988:Proteasome Endopeptidase Complex / Q000276:immunology*; D053719:Tandem Mass Spectrometry
chemical_list: D015395:Histocompatibility Antigens Class I; D010455:Peptides; D046988:Proteasome Endopeptidase Complex