The Ubiquitin-Specific Protease USP15 Promotes RIG-I–Mediated Antiviral Signaling by Deubiquitylating TRIM25

Abstract

Ubiquitylation is an important mechanism for regulating innate immune responses to viral infections. Attachment of lysine 63 (Lys63)–linked ubiquitin chains to the RNA sensor retinoic acid–inducible gene-I (RIG-I) by the ubiquitin E3 ligase tripartite motif protein 25 (TRIM25) leads to the activation of RIG-I and stimulates production of the antiviral cytokines interferon-α (IFN-α) and IFN-β. Conversely, Lys48-linked ubiquitylation of TRIM25 by the linear ubiquitin assembly complex (LUBAC) stimulates the proteasomal degradation of TRIM25, thereby inhibiting the RIG-I signaling pathway. Here, we report that ubiquitin-specific protease 15 (USP15) deubiquitylates TRIM25, preventing the LUBAC-dependent degradation of TRIM25. Through protein purification and mass spectrometry analysis, we identified USP15 as an interaction partner of TRIM25 in human cells. Knockdown of endogenous USP15 by specific small interfering RNA markedly enhanced the ubiquitylation of TRIM25. In contrast, expression of wild-type USP15, but not its catalytically inactive mutant, reduced the Lys48-linked ubiquitylation of TRIM25, leading to its stabilization. Furthermore, ectopic expression of USP15 enhanced the TRIM25- and RIG-I–dependent production of type I IFN and suppressed RNA virus replication. In contrast, depletion of USP15 resulted in decreased IFN production and markedly enhanced viral replication. Together, these data identify USP15 as a critical regulator of the TRIM25- and RIG-I–mediated antiviral immune response, thereby highlighting the intricate regulation of innate immune signaling.

Antagonism of type I interferon by flaviviruses

“…Specifically, TRIM25 has been shown to interact with the first CARD of RIG-I and to promote K63-linked ubiquitination of the RIG-I’s Lys172 residue, RIG-I tetramerization, and MAVS interaction [81–83]. In addition, TRIM25 activity itself is also regulated by PTMs mediated by the ubiquitin specific protease15 (USP15), and the linear ubiquitin assembly complex (LUBAC) [84]. …”

Ubiquitination in the antiviral immune response

“…Specifically, the NZF of HOIL-1L competes with TRIM25 for RIG-I binding, ultimately preventing TRIM25-mediated ubiquitination and activation of RIG-I [89]. USP15, identified as an interaction partner of TRIM25 by mass spectrometry, was recently shown to counteract the inhibitory effect of LUBAC [90]. Mechanistically, USP15 was found to bind to TRIM25 specifically during the later stages of viral infection, removing the LUBAC-induced K48-linked polyubiquitination of TRIM25 at its SPRY domain.…”

Changes in PUB22 Ubiquitination Modes Triggered by MITOGEN-ACTIVATED PROTEIN KINASE3 Dampen the Immune Response

“…Heterooligomerization may also account for the remnant degradation levels of the inactive Trp40Ala variant. A second possibility is that the phosphorylated variant is recognized by an additional stabilizing factor such as a ubiquitin-specific protease that contributes to its stabilization, as shown for TRIM25 and TRAF6 (Pauli et al, 2014;Lin et al, 2015a).…”