Proteomic Characterization of Ubiquitin Carboxyl-Terminal Hydrolase 19 Deficient Cells Reveals a Role for USP19 in the Secretion of Lysosomal Proteins

• DOI: 10.1016/j.mcpro.2024.100854
• Publication Date: 2024-10-09T19:44:32Z
• Authors: Simone Bonelli; Margot Lo Pinto; Yihong Ye; Stephan A. Müller; Stefan F. Lichten...; Simone Dario Scil...
• Keywords: Proteome; legumain; secretory autophagy; metabolism [Endopeptidases]; ubiquitin carboxyl-terminal hydrolase 19; genetics [Endopeptidases]; metabolism [Lysosomes]; proteomics; unconventional secretion; genetics [Cysteine Endopeptidases]; metabolism [Sequestosome-1 Protein]; Endopeptidases; Sequestosome-1 Protein; Autophagy; Humans; ddc:610; lysosomal proteins; Research; Proteins; metabolism [Proteins]; metabolism [Proteome]; lysosomal exocytosis; genetics [Proteins]; asparaginylendopeptidase; USP19 protein, human; Cysteine Endopeptidases; HEK293 Cells; metabolism [Cysteine Endopeptidases]; genetics [Sequestosome-1 Protein]; methods [Proteomics]; HeLa Cells

Ubiquitin carboxyl-terminal hydrolase 19 (USP19) is a unique deubiquitinase (DUB), characterized by multiple variants generated by alternative splicing. Several variants bear a C-terminal transmembrane domain that anchors them to the endoplasmic reticulum (ER). Other than regulating protein stability by preventing proteasome degradation, USP19 has been reported to rescue substrates from ER-associated protein degradation (ERAD) in a catalytic-independent manner, promote autophagy and address proteins to lysosomal degradation via endosomal microautophagy. USP19 has recently emerged as the protein responsible for the unconventional secretion of misfolded proteins including Parkinson's disease-associated protein α-synuclein. Despite mounting evidence that USP19 plays crucial roles in several biological processes, the underlying mechanisms are unclear due to lack of information on the physiological substrates of USP19. Herein, we used high-resolution quantitative proteomics to analyze changes in the secretome and cell proteome induced by loss of USP19 to identify proteins whose secretion or turnover is regulated by USP19. We found that ablation of USP19 induced significant proteomic alterations both in and out of the cell. Loss of USP19 impaired the release of several lysosomal proteins, including legumain (LGMN) and several cathepsins. In order to understand the underlaying mechanism, we dissected the USP19-regulated secretion of LGMN in several cell types. We found that LGMN was not a DUB substrate of USP19 and that its USP19-dependent release did not require their direct interaction. LGMN secretion occurred by a mechanism that involved the Golgi apparatus, autophagosome formation and lysosome function. This mechanism resembled the recently described "lysosomal exocytosis", by which lysosomal hydrolases are secreted, when ubiquitination of p62 is increased in cells lacking deubiquitinases such as USP15 and USP17. In conclusion, our proteomic characterization of USP19 has identified a collection of proteins in the secretome and within the cell that are regulated by USP19, which link USP19 to secretion of lysosomal proteins, including LGMN.