The E3 ligase TRIM56 is a host restriction factor of Zika virus and depends on its RNA-binding activity but not miRNA regulation, for antiviral function

Abstract

Infection by Zika virus (ZIKV) is linked to microcephaly and other neurological disorders, posing a significant health threat. Innate immunity is the first line of defense against invading pathogens, but relatively little is understood regarding host intrinsic mechanisms that guard against ZIKV. Here, we show that host tripartite motif-containing protein 56 (TRIM56) poses a barrier to ZIKV infection in cells of neural, epithelial and fibroblast origins. Overexpression of TRIM56, but not an E3 ligase-dead mutant or one lacking a short C-terminal portion, inhibited ZIKV RNA replication. Conversely, depletion of TRIM56 increased viral RNA levels. Although the C-terminal region of TRIM56 bears sequence homology to NHL repeat of TRIM-NHL proteins that regulate miRNA activity, knockout of Dicer, which abolishes production of miRNAs, had no demonstrable effect on ZIKV restriction imposed by TRIM56. Rather, we found that TRIM56 is an RNA-binding protein that associates with ZIKV RNA in infected cells. Moreover, a recombinant TRIM56 fragment comprising the C-terminal 392 residues captured ZIKV RNA in cell-free reactions, indicative of direct interaction. Remarkably, deletion of a short C-terminal tail portion abrogated the TRIM56-ZIKV RNA interaction, concomitant with a loss in antiviral activity. Altogether, our study reveals TRIM56 is an RNA binding protein that acts as a ZIKV restriction factor and provides new insights into the antiviral mechanism by which this E3 ligase tackles flavivirus infections.

To TRIM or not to TRIM: the balance of host–virus interactions mediated by the ubiquitin system

“…In the case of Zika virus (ZIKV) infection, TRIM56 can indeed identify and capture vRNA [45]. Restriction of ZIKV by TRIM56 depended on an intact C-terminal region as well as its E3 ligase activity signifying, in contrast to what was observed with IAV, that TRIM56 may recognize vRNA and utilize its E3 ligase activity to prevent ZIKV replication through an as yet unresolved mechanism [45]. Viral restriction that is independent of a TRIM's E3 ubiquitin ligase function was recently described for TRIM25 [46].…”

“…Although the exact mechanism of restriction is unclear, this hypothesis is plausible as the C terminus of TRIM56 was found to have high sequence homology to the positively charged surfaces in NHL repeats, which would afford a means to interact with the negatively charged sugar phosphate backbone of vRNA () [44]. In the case of Zika virus (ZIKV) infection, TRIM56 can indeed identify and capture vRNA [45]. Restriction of ZIKV by TRIM56 depended on an intact C-terminal region as well as its E3 ligase activity signifying, in contrast to what was observed with IAV, that TRIM56 may recognize vRNA and utilize its E3 ligase activity to prevent ZIKV replication through an as yet unresolved mechanism [45].…”

The Roles of TRIMs in Antiviral Innate Immune Signaling

“…Consistent with previous researches, recent studies have shown that carboxy-terminal domains of TRIM56 inhibit IAV and Influenza B virus (IBV) replication by blocking viral RNA synthesis ( Liu et al, 2016a ). Similarly, TRIM56 could also be a host restriction factor of the Zika virus, depending on its RNA-binding activity ( Yang et al, 2019 ). TRIM22 can restrict retrovirus by interfering with viral Gag protein transport by regulating transcription factor specificity protein 1 (Sp1) (Sp1) ( Kajaste-Rudnitski et al, 2011 ; Turrini et al, 2015 ).…”

TRIM26 is a critical host factor for HCV replication and contributes to host tropism

“…TRIM22 and TRIM41 inhibit influenza A virus infection by targeting nucleoprotein for degradation (7,8). TRIM56 suppresses Zika virus (ZIKV) replication through sequestration of its genomic RNA (9).…”