TRIMmunity: the roles of the TRIM E3-ubiquitin ligase family in innate antiviral immunity

Abstract

Tripartite motif (TRIM) proteins have been implicated in multiple cellular functions, including antiviral activity. Research efforts so far indicate that the antiviral activity of TRIMs relies, for the most part, on their function as E3-ubiquitin ligases. A substantial number of the TRIM family members have been demonstrated to mediate innate immune cell signal transduction and subsequent cytokine induction. In addition, a subset of TRIMs has been shown to restrict viral replication by directly targeting viral proteins. Although the body of work on the cellular roles of TRIM E3-ubiquitin ligases has rapidly grown over the last years, many aspects of their molecular workings and multi-functionality remain unclear. The antiviral function of many TRIMs seems to be conferred by specific isoforms, by sub-cellular localization and in cell-type-specific contexts. Here we review recent findings on TRIM antiviral functions, current limitations and an outlook for future research.

Keywords: E3-ubiquitin ligase; antiviral response; innate immunity; restriction factors; tripartite motif.

Figure 1. Model of TRIM E3-ubiquitin ligase function

Ubiquitin conjugation requires an E1 activating enzyme in the presence of ATP and mono-ubiquitin. The E2-conjugating enzyme then forms an intermediate thioester with ubiquitin. TRIMs act as E3-ligases and confer specificity to the reaction. TRIMs recognizing the E2 through the RING domain and interact with the substrate, in general, through the C-terminal region. Deubiquitinases (DUB) hydrolyze poly-ubiquitin chains which are then recycled.

Figure 2. TRIM subgroup classification

TRIM members are classified based on their C-terminal domain composition as defined by Ozato et al . Adapted from Versteeg et al.

Figure 3. TRIMs located on human chromosome 11

Schematic representation of a cluster of TRIMs closely related to TRIM5 that map to human chromosome 11. The TRIMs with known antiviral activity are indicated.

Figure 4. Direct antiviral activity of TRIMs

Stages of retroviral replication cycle targeted by different TRIMs. TRIM5α blocks HIV-1 replication by targeting the capsid and preventing uncoating of the virus. At the same time, TRIM5α has been proposed to stimulate innate immune signaling upon capsid recognition. By catalyzing the synthesis of unanchored K63-linked poly-ubiquitin chains that bind and activate TAK1-dependent NF-κB. TRIM1/8/11/31 inhibit entry, between uncoating and viral gene integration. TRIM24/28/33 inhibit endogenous retrovirus (ERV) gene transcription. TRIM11/22/28/32 have been reported to inhibit retrovirus gene transcription. TRIM11/14//19/21/26/32 inhibit release and TRIM15/22 inhibit assembly. TRIM21 recognizes and targets antibody-opsonized viruses for proteasomal degradation.

Figure 5. The role of TRIM19/PML in antiviral defense, signal transduction and induction by IFNs

Mechanisms of TRIM19 up-regulation upon viral infection via IFN production. TRIM19 is an important effector of the IFN-mediated antiviral response. TRIM19 exerts its functions by interacting with other proteins including SP100 and DAXX to form nuclear bodies (NB). These protein complexes in NB are important in regulation of transcription, storage of proteins, sumoylation and antiviral functions. TRIM19 can regulate chromatin remodeling of the MHC-1 locus, and inhibit replication of viruses like influenza virus, Thogoto virus, herpes simplex virus-1 (HSV-1), Ebola virus, lymphocytic choriomeningitis virus (LCMV), Lassa virus, vesicular stomatitis virus (VSV), rabies virus, HIV-1, human foamy virus (HFV). TRIM19 also negatively regulates IFNγ signaling by inhibiting STAT1 transcriptional activity. The cytoplasmic isoform of TRIM19 (cPML) binds to the TGFβ receptor and serves as an adaptor molecule to recruit SARA and SMAD2/3 for TGFβ signaling.

Figure 6. TRIM19/PML isoforms

TRIM19 isoforms, depicted here as PML I – PML VII are shown according to the nomenclature described by Jensen et al . All TRIM19/PML isoforms retain the first 3 exons which encode for the RBCC motif: RING (R), B-box (B1 and B2), and the coiled-coil domain (CC). The isoforms I to VII PMLI to PMLVII differ by alternative splicing of exons 7 to 9. The cytoplasmic form of TRIM19 (cPML) is the result of alternative splicing of exons 4–6. Adapted from Nisole et al. .

Figure 7. TRIMs in innate immune signaling

Upon microbial infection, pattern recognition receptors (TLRs and RLRs) recognize pathogen products to trigger downstream signaling pathways to induce IFN-I and pro-inflammatory cytokines. TLR3 recognizes double stranded RNA (dsRNA), TLR4 recognizes bacterial lipopolysaccharide (LPS), RIG-I recognizes single stranded RNA (ssRNA), MDA5 recognizes dsRNA and DDX41 recognizes double stranded DNA (dsDNA). In the RIG-I/MDA5 pathway, TRIM25 ubiquitinates RIGI for binding to MAVS. TRIM44 stabilizes MAVS. TRIM21 can act as both a positive and negative regulator of IFNβ. TRIM27 inhibits NF-κB and IFN activation mediated by IKKα/β/ε. TRIM30 degrades TAB2-TAB3 to inhibit production of IL-6 and TNFα. TRIM23 enhances NEMO function by promoting K63-linked ubiquitination. TRIM21 is involved in the inhibition of IKKβ and IRF7 and positive or negative regulation of IRF3 and IRF8. TRIM32 and TRIM56 ubiquitinate STING to promote dsDNA signaling. TRIM56 also positively regulates TRIF-mediated signaling whereas TRIM38 inhibits it. TRIM21 negatively regulates IFN production upon dsDNA signaling by ubiquitinating and targeting DDX41 for degradation. TRIM21 and TRIM28 inhibit IRF7 activation. TRIM5α catalyzes the synthesis of unanchored K63-linked poly-ubiquitin chains that bind and activate TAK1 kinase. TRIM21 acts as an antibody receptor bound to viruses to activate TAK1. TRIMs in green and red represent positive and negative regulatory functions, respectively.