Human cytomegalovirus tegument protein pUL83 inhibits IFI16-mediated DNA sensing for immune evasion

Abstract

Nuclear sensing of viral DNA has emerged as an essential step in innate immune responses against herpesviruses. Here, we provide mechanistic insight into host recognition of human cytomegalovirus (HCMV) and subsequent immune evasion by this prominent DNA virus. We establish that the interferon-inducible protein IFI16 acts as a nuclear DNA sensor following HCMV infection, binding viral DNA and triggering expression of antiviral cytokines via the STING-TBK1-IRF3 signaling pathway. The HCMV tegument protein pUL83 inhibits this response by interacting with the IFI16 pyrin domain, blocking its oligomerization upon DNA sensing and subsequent immune signals. pUL83 disrupts IFI16 by concerted action of its N- and C-terminal domains, in which an evolutionarily conserved N-terminal pyrin association domain (PAD) binds IFI16. Additionally, phosphorylation of the N-terminal domain modulates pUL83-mediated inhibition of pyrin aggregation. Collectively, our data elucidate the interplay between host DNA sensing and HCMV immune evasion, providing targets for restoring antiviral immunity.

Figure 1. pUL83 antagonizes IFI16-mediated antiviral response

(A) mRNA levels of cytokines in HFFs infected with WT or ΔUL83 HCMV or mock-infected, at 3 or 6 hpi (moi = 5). Data shown as mean +/− SEM, n = 3. (B) Protein levels of IRF-1, IRF-3, NF-κB p65, and other markers were measured by Western blot in total cell lysates and nuclear fractions of HFFs infected as in (A). (C) mRNA levels of cytokines in HFFs infected with UV-treated WT or ΔUL83 HCMV, at 6 hpi (moi = 5). Western blots show IE-1, pUL83 and loading control (actin) protein levels. (D) HFFs stably expressing pUL83-Flag or control were infected with mock or ΔUL83 strain. Western blots show protein levels for pUL83 and IFI16. IF images show nuclear localization of pUL83-Flag. mRNA levels of cytokines measured by qPCR as in (A). (E) Endogenous IFI16, STING, TBK-1, IRF-3 and MAVS were stably knocked down in HFFs by shRNA. mRNA levels of cytokines in response to mock or ΔUL83 strain were measured as in (A). (F) Protein levels for IRF-1, NF-κB p65, and other markers in nuclear fraction or total lysates were measured by Western blot. See also Figure S1.

Figure 2. pUL83 blocks nuclear pyrin aggregation

(A) ChIP assays test the association of endogenous IFI16 with HCMV DNA and host DNA in infected HFFs. (B) Constructs of pUL83, IFI16 and other PYHIN proteins. (C) Co-IP assays of pUL83-Flag interaction with IFI16 constructs. (D) Co-IP assays of pUL83 interaction with pyrin domains of PYHIN proteins. (E) 293T cells were transfected with plasmids (1:5) of Pyrin-GFP and mCherry or pUL83-mCherry. Direct fluorescent images illustrate PY-GFPs. (F) As in (E), cells from random microscopy fields were analyzed for PY-GFP distributions. Bars: percentages of diffuse (yellow) or aggregation (blue) patterns as mean +/− SEM. (G) As in (E), bars show IFI16-PY-GFP distributions as a function of the pUL83-mCherry/mCherry ratio. (H) HEK293T cells transiently transfected with GFP alone or GFP fusions with full-length (FL), PY or HIN domains of IFI16, in the presence or absence of exogenous pUL83. Cell lysates were cross-linked and the oligomerization status was assessed by Western blotting with an anti-GFP antibody. (I) Western blot shows migration of endogenous IFI16 in infected HFFs cross-linked with glutaraldehyde. Protein levels in total lysates prior to crosslinking are shown. See also Figure S2, Movie S1.

Figure 3. Interference of pyrin aggregation requires both the Pyrin Association Domain (PAD) and the C-terminal domain of pUL83

(A) Schematic of pUL83 shows its bipartite structure, conservation scores, predicted disorder degrees, and phosphorylation sites. (B) Schematics of pUL83 constructs; those lacking NLS (red) were supplemented with SV40-NLS (orange) to ensure nuclear localization. (C) Interactions of pUL83-Flag constructs in (B) (preys) with IFI16-PY-GFP (bait) were tested by co-IP. (D) PAD-mCherry and pUL83-mCherry were tested for PY-interference as in Figure 2F; diffuse (yellow) or aggregation (blue) patterns shown as mean +/− SEM. (E) IF shows the ability of pUL83 constructs in (B) to interfere with IFI16-PY-GFP aggregation. (F) Two models for the role of the pUL83 linker in PY interference. (G) Mutants of PAD phosphosites were tested for pyrin-interference as in (D). Statistics: ns, not significant; *, p< 0.05; **, p< 0.01. Western blots show levels of pUL83 constructs. (H) Predicted structure models for pUL83 (rainbow) and IFI16 Pyrin (green). Docking shows arbitrary size fitting. (I) SDS-PAGE of recombinant complex of GST-PAD and sumo-IFI16-Pyrin. See also Figure S3

Figure 4. Working model for IFI16-mediated nuclear DNA sensing and pUL83-mediated immune evasion

IFI16 detects nuclear HCMV DNA via HIN domains, oligomerizes via the pyrin domain, and activates STING-mediated cytokine expression. pUL83 blocks IFI16 pyrin aggregation and hijacks IFI16 to help activate HCMV MIEP. pUL83 is partly inhibited by phosphorylation at S364. The balance between the DNA sensing and immune evasion determines the immunological outcome of HCMV infections.