Inhibition of cGAS DNA Sensing by a Herpesvirus Virion Protein

Abstract

Invading viral DNA can be recognized by the host cytosolic DNA sensor, cyclic GMP-AMP (cGAMP) synthase (cGAS), resulting in production of the second messenger cGAMP, which directs the adaptor protein STING to stimulate production of type I interferons (IFNs). Although several DNA viruses are sensed by cGAS, viral strategies targeting cGAS are virtually unknown. We report here that Kaposi's sarcoma-associated herpesvirus (KSHV) ORF52, an abundant gammaherpesvirus-specific tegument protein, subverts cytosolic DNA sensing by directly inhibiting cGAS enzymatic activity through a mechanism involving both cGAS binding and DNA binding. Moreover, ORF52 homologs in other gammaherpesviruses also inhibit cGAS activity and similarly bind cGAS and DNA, suggesting conserved inhibitory mechanisms. Furthermore, KSHV infection evokes cGAS-dependent responses that can limit the infection, and an ORF52 null mutant exhibits increased cGAS signaling. Our findings reveal a mechanism through which gammaherpesviruses antagonize host cGAS DNA sensing.

Figure 1. Inhibition of cGAS DNA-sensing signaling by KSHV ORF52

(A) KSHV ORF52 inhibits cGAS-induced IFNβ promoter activity. HEK293T–STING cells were transfected with IFNβ luciferase reporter and expression plasmids as indicated, and luciferase activity was assayed 24 h after transfection. The relative luciferase activity was expressed as arbitrary units by normalizing firefly luciferase activity to Renilla luciferase activity. (B) KSHV ORF52 inhibits cGAS-induced IRF3 dimerization and phosphorylation. HEK293T-STING cells were transfected with expression plasmids as indicated. Twenty-four h after transfection, cell lysates were analyzed for IRF3 dimerization by native gel electrophoresis. IRF3 phosphorylation and expression levels of the transfected genes were monitored by immunoblotting with antibodies. (C) KSHV ORF52 inhibits cGAS-induced antiviral response. HEK293T-STING cells transfected with specified plasmids were infected with vesicular stomatitis virus (VSV-GFP). The percentage of GFP-positive cells, as analyzed by FACS, is shown for each condition. (D–F) ORF52 inhibits cGAS DNA sensing signaling in THP-1 cells. THP1 Lucia™ ISG cells harboring pEasiLV-ORF52 or pEasiLV-empty were untreated or induced with 2 µg/ml doxycycline for 60 h then transfected with ISD45 or Poly(I:C) (2µg/ml) (D–E), or infected with VACV or SEV (F). The activity of secreted Lucia luciferase was determined, or cell lysates were harvested then analyzed for IRF3 dimerization and phosphorylation (E). (G–I) TAT-ORF52 protein inhibits cGAS DNA-sensing signaling in THP-1 cells. THP1 Lucia™ ISG cells were incubated with 1.25 µM or 2.5 µM TAT-ORF52 protein for 3 h, then transfected with ISD45 or Poly(I: C) (2µg/ml) (G and H) or infected with VACV or SEV (I). Analyses of luciferase activity or IRF3 dimerization were performed as in (D–F). **p<0.01 and ***p<0.001; Student’s t-test. See also Figures S1 and S2.

Figure 2. ORF52 inhibits cGAS enzymatic activity

(A–B) ORF52 affects the cGAS-DNA-sensing signaling pathway upstream of cGAMP. THP1 Lucia™ ISG cells harboring pEasiLV-ORF52 or pEasiLV-empty were induced with 2 µg/ml doxycycline for 60 h, then transfected with ISD45 or cGAMP (2µg/ml). IRF3 dimerization was analyzed (A) or the secreted Lucia activity was determined (B) as in Figure. 1. (C) Coomassie blue staining of purified hcGAS and ORF52 proteins. (D–E) ORF52 inhibits hcGAS enzymatic activity. Purified hcGAS protein (1 µM) was incubated with ISD45 (1 µM), [α-³²P]-ATP, ATP and GTP in reaction buffer containing different amount of ORF52 protein (0, 1, 2, or 4 µM). The reactions were stopped at the indicated time by boiling for 5 minutes. Synthesis of cGAMP was analyzed by thin-layer chromatography (TLC) (D), and the efficiency of cGAMP production was plotted against time (E). (F) ORF52 inhibits mouse cGAS activity. Mouse cGAS (mcGAS; 1 µM) was used for the enzyme assay and TLC as described in (D). ***p<0.001; Student’s t-test.

Figure 3. ORF52 binding to DNA is required for its inhibition of cGAS activity

(A) ORF52 affects the kinetics of cGAS-dependent cGAMP production. In vitro enzyme assay was performed as in Figure 2D with 2-fold serial dilutions of ISD45 (starting from 30 µM, from right to left) in presence or absence of ORF52 (4 µM) for 2 h. cGAMP production was detected by TLC and the initial reaction velocity was plotted against substrate concentration together with least-square fit to the Michaelis-Menten equation. (B) Fluorescence polarization analysis of hcGAS or ORF52 binding to DNA. FAM-labeled ISD45 was incubated with different amounts of ORF52 or hcGAS protein, and the K_d values were obtained from least-square fit to a hyperbolic binding isotherm. (C) Mutagenesis of ORF52 reveals that K68/69 are critical for its binding to DNA. GST-ORF52 protein was pulled down by dsDNA cellulose beads, and then eluted with the indicated salt concentration (upper panel). The GST-ORF52 charge-deficient mutants were pulled down by dsDNA cellulose beads, eluted with 300 mM NaCl, separated by SDS-PAGE, and visualized by Coomassie staining. (D) ORF52 mutants deficient in cGAS/DNA-binding display reduced inhibition of cGAS activity. In vitro enzyme assay was performed in the presence or absence of the indicated amount of ORF52 wild-type or mutant proteins, and the percentage of cGAMP production was plotted for each protein concentration (right panel). See also Figure S3.

Figure 4. Interaction between ORF52 and cGAS underlies the specific inhibition of cGAS-mediated signaling

(A) ORF52 binds to cGAS but not AIM2. Purified GST-ORF52 or GST proteins were used to pull down lysates of HEK293T cells transiently expressing Flag-hcGAS or Flag-hAIM2. The interaction was detected by western blot analysis using anti-FLAG antibody. (B) The interaction between ORF52 and hcGAS is not dependent on DNA. HEK293T cell lysate expressing Flag-hcGAS was untreated, or treated with Benzonase® (0.1 U/µl or 1 U/µl) or EB, for 2 h on ice, followed by pull-down assay with GST-ORF52 or GST protein. The interacted protein was detected with anti-FLAG antibody (left panel). The lysate DNA was separated by agarose gel electrophoresis and stained with EB (right panel). (C) ORF52 interacts with cGAS in vivo. Cells were transfected as indicated and lysates were immunoprecipitated with anti-ORF52 antibody, followed by western blot analysis with anti-FLAG and anti-ORF52 antibodies. Arrows indicate heavy chains of IgG. (D) Mapping the region of ORF52 required for its interaction with hcGAS. Serial 10-aa deletion mutants of GST-ORF52 were used to pull down lysates of HEK293T cells transiently expressing Flag-hcGAS. Interaction was detected by western blot analysis with anti-FLAG antibody, and comparable protein level was confirmed by Ponceau S. (E) THP1 Lucia™ ISG cells harboring ORF52-pEasiLV (WT or mutants) were mock treated or induced with doxycycline for 60 h, followed by mock transfection or transfection with ISD45. IRF3 dimerization was analyzed by native gel electrophoresis. (F) HEK293T/STING cells were transfected with expression plasmids of cGAS and ORF52 WT/mutants as indicated. Twenty-four h after transfection, cell lysates were analyzed for IRF3 dimerization by native gel electrophoresis. IRF3 phosphorylation and expression levels of the transfected genes were analyzed by western blot. See also Figures S3 and S4.

Figure 5. Homologues of ORF52 in other gammaherpesviruses also inhibit cGAS activity

(A) ORF52 homologs but not AIM2 DNA binding domain (AIM2ΔPYD) can inhibit hcGAS activity. The enzyme assay and TLC were performed as in Figure 2D, but with ORF52 homologs or AIM2ΔPYD. (B–C) ORF52 homologs inhibit the cGAS-induced IFN response. Experiments were performed as described in Figure 1A and 1B, but with ORF52 homologs. (D) ORF52 homologs bind to dsDNA. dsDNA cellulose beads were used to pull down His-tagged ORF52 protein and glutaredoxin 1 (GRX1) proteins, then the beads were boiled in 2 × Laemmli loading buffer and the eluted proteins were analyzed by SDS-PAGE and Coomassie staining. (E) ORF52 homologs all bind to hcGAS. His-ORF52 proteins were used to pull down lysates of HEK293T cells expressing Flag-hcGAS, and the input/eluates were probed with anti-FLAG or anti-His antibody. See also Figure S5.

Figure 6. KSHV ORF52 antagonizes cGAS-dependent induction of the innate immune response to primary infection

(A) HEK293T/cGAS-STING cells were infected by KSHV. At the indicated time after infection, cell lysates were analyzed by western blotting with the indicated antibodies. (B) KSHV primary infection and analysis of the indicated cell lines was performed as in (A). (C) HEK293T/cGAS-STING cells were infected by KSHV BAC16-wt or BAC16-Stop52 mutant. At the indicated time after infection, cell lysates were analyzed by western blotting with the indicated antibodies. (D) Flag-cGAS/293T cells were infected with KSHV at 50 genome copies/cell for 30 min, then cell lysates were prepared and immunoprecipitated with anti-ORF52 4H4 antibody. The immunocomplexes were analyzed by western blot with indicated antibodies. (E) cGAS was knocked out by CRISPR/Cas9-mediated genome editing in THP1 Lucia™ ISG cells. The knockout cell line and control were infected by KSHV, and the activity of secreted Lucia luciferase was assessed at 24 hpi. (F) THP-1 Lucia™ ISG cells were infected by KSHV BAC16-wt or BAC16-Stop52 mutant. Luciferase activity was measured as in (E). (G) LECs were mock treated or infected by KSHV at 25, 50, or 100 genome copies/cell. RNAs were isolated from cells and reverse transcribed. The levels of IFNβ and ISG54 mRNA were measured by qRT-PCR at 6 hpi. (H) LECs were infected by KSHV BAC16-wt or BAC16-Stop52 at 50 copies/cell. The levels of IFNβ and ISG54 mRNA were measured as in (G). (I) HUVECs or LECs were transduced with lentiviruses as indicated. At 24 h after transduction, they were infected with BAC16-wt, followed by fixation and FACS analyses of the GFP-positive cells the next day. *p<0.05 and **p<0.01; Student’s t-test. See also Figure S6.