The Skp2 oncoprotein belongs to the family of F-box proteins that function as substrate recognition factors for SCF (Skp1, cullin, F-box protein) E3 ubiquitin-ligase complexes. Binding of the substrate to the SCF Skp2 complex catalyzes the conjugation of ubiquitin molecules to the bound substrate, resulting in multi-ubiquitination and rapid degradation by the 26 S proteasome. Using Skp2 as bait in a yeast two-hybrid screen, we have identified UBP43 as a novel substrate for Skp2. UBP43 belongs to the family of ubiquitin isopeptidases and specifically cleaves ISG15, a ubiquitin-like molecule that is induced by cellular stresses, such as type 1 interferons (IFN), nephrotoxic damage, and bacterial infection. UBP43 was originally identified as an up-regulated gene in knock-in mice expressing an acute myelogenous leukemia fusion protein, AML1-ETO, as well as in melanoma cell lines treated with IFN-␤. The phenotype of UBP43 knockout mice includes shortened life span, hypersensitivity to IFN, and neuronal damage, suggesting that tight regulation of ISG15 conjugation is critical for normal cellular function. In this study, we demonstrate that UBP43 is ubiquitinated in vivo and accumulates in cells treated with proteasome inhibitors. We also show that Skp2 promotes UBP43 ubiquitination and degradation, resulting in higher levels of ISG15 conjugates. In Skp2؊/؊ mouse cells, levels of UBP43 are consistently up-regulated, whereas levels of ISG15 conjugates are reduced. Our results demonstrate that the SCF Skp2 is involved in controlling UBP43 protein levels and may therefore play an important role in modulating type 1 IFN signaling.Modification of proteins by ubiquitin and ubiquitin-like (Ubl) 1 molecules, including SUMO, Nedd8, and ISG15, has emerged as a critical regulatory process in eukaryotes, controlling pathways such as the cell cycle, cellular stress response, intracellular signaling, development, and the immune response (1-5). Deregulation of ubiquitin or Ubl modification can cause autoimmune and neurodegenerative diseases, developmental abnormalities, and cancer.Conjugation of ubiquitin and Ubls involves a three-step mechanism initially demonstrated for ubiquitin as follows. A single E1 ubiquitin-activating enzyme activates the Ubl molecule via formation of a thioester bond. Activated Ubl is then transferred to one of a large family of E2 ubiquitin-conjugating enzymes. In most cases, E2 enzymes are targeted to appropriate substrates by a class of substrate receptor complexes termed E3 ubiquitin ligases. Together, the E2 and E3 enzymes catalyze the formation of isopeptide bonds between ubiquitin and lysine residues on the target proteins. In the case of multiubiquitination, additional ubiquitin molecules are added to form ubiquitin chains. The multiubiquitinated proteins are then recognized and rapidly degraded into short peptides by the 26 S proteasome (3, 6). Modification by ubiquitin and Ubl molecules is a reversible process mediated by a large family of isopeptidases that exist to remove these molecules from the...