PCBP2 maintains antiviral signaling homeostasis by regulating cGAS enzymatic activity via antagonizing its condensation

doi:10.21203/rs.3.rs-133300/v1

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PCBP2 maintains antiviral signaling homeostasis by regulating cGAS enzymatic activity via antagonizing its condensation

https://doi.org/10.21203/rs.3.rs-133300/v1

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published 23 Mar, 2022

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Cyclic GMP-AMP synthase (cGAS) plays a major role in detecting pathogenic DNA. It produces cyclic dinucleotide cGAMP, which subsequently binds to the adaptor protein STING and further triggers antiviral innate immune responses. However, the molecular mechanisms regulating cGAS enzyme activity remain largely unknown. Here, we characterize the cGAS-interacting protein Poly(rC)-binding protein 2 (PCBP2), which plays an important role in controlling cGAS enzyme activity, thereby mediating appropriate cGAS-STING signaling transduction. We found that PCBP2 overexpression reduced cGAS-STING antiviral signaling, whereas loss of PCBP2 significantly increased cGAS activity. Mechanistically, we showed that PCBP2 negatively regulated anti-DNA viral signaling by specifically interacting with cGAS but not other components. Moreover, PCBP2 inhibited cGAS enzyme activity by antagonizing cGAS condensation, thus ensuring the normal production of cGAMP and balancing cGAS-STING signal transduction. Collectively, our findings provide novel insight into mechanisms regulating cGAS-mediated antiviral innate immune signaling.

Immunology

Allergy & Immune Disorders

antiviral signaling

homeostasis

cGAS enzymatic activity

PCBP2

The innate immune system serves as the first line of host defense against viral infection using a number of sensors known as pattern recognition receptors (PRRs). PRRs specifically recognize conserved microbial components termed pathogen-associated molecular patterns (PAMPs). Nucleic acids derived from viruses function as PAMPs and are detected by PRRs, consequently initiating the innate immune response and resulting in the production of type I interferons (IFNs) and proinflammatory cytokines^{1, 2, 3}.

Cyclic GMP-AMP synthase (cGAS) functions as a cytosolic DNA sensor and plays a critical role in the innate immune response against DNA virus infection. cGAS catalyzes the conversion of ATP and GTP to cGAMP. cGAMP functions as an endogenous second messenger by binding to the endoplasmic reticulum membrane protein STING and activating the transcription factors IRF3 and NF-κB through the kinases TBK1/IKKi and IKK complex, respectively, subsequently inducing the production of IFNs and proinflammatory cytokines^{4, 5}. cGAS remains in an inactive state in resting cells and is activated upon binding to DNA⁶. Because cGAS can detect both self and non-self DNA, its activity must be strictly regulated to maintain the balance in innate immune responses, subsequently preventing the development of autoimmune diseases⁷. cGAS activity is regulated by multiple factors, including protein post-translational modifications, such as phosphorylation^{8, 9}, glutamylation¹⁰, sumoylation^{11, 12}, acetylation^{13, 14}, and ubiquitination^{15, 16}. In addition to these post-translational modifications, cGAS function has been found to be negatively regulated by several other factors. For example, previous studies demonstrated that Caspase1/3 cleaves cGAS to inhibit cGAS-STING signaling^{17, 18}, and Gasdermin D suppresses cGAS activity by disrupting K+ efflux¹⁹. The autophagy protein Beclin-1 was found to inhibit cGAS enzymatic activity²⁰, and p62 is involved in the autophagic degradation of cGAS^{15, 21}. Although previous studies have made significant progress in understanding the mechanisms regulating cGAS activity, how cGAS activity is tightly controlled to maintain immune homeostasis remains unclear.

Previous studies have indicated that cGAS can form dimers, undergo oligomerization after sensing cytosolic DNA^{6, 22, 23}, and form liquid droplets in vitro and in vivo ²⁴. DNA-induced liquid phase condensation of cGAS promotes its enzymatic activity to increase cGAMP production and plays an important role in antiviral signaling²⁴. However, the mechanisms that dynamically regulate cGAS condensation to initiate an appropriate immune response to pathogens and prevent overreaction are poorly understood.

PCBP2 belongs to a class of proteins that bind to poly(C) stretches of both RNA and DNA^{25, 26, 27}, and it plays important roles in regulating mRNA stability^{28, 29}, protein translation^{30, 31}, and protein-protein interactions^{32, 33}. A previous study demonstrated that PCBP2 is a negative modulator of innate immune responses against RNA virus infection by regulating MAVS stability via the HECT ubiquitin ligase AIP4³². However, whether PCBP2 is involved in cGAS-STING signaling is still unclear.

To further explore the mechanism underlying the regulation of cGAS in the context of viral infection, we performed co-immunoprecipitation (Co-IP) experiments in combination with mass spectrometry assays and identified PCBP2 as a cGAS-interacting protein. We showed that PCBP2 overexpression significantly impaired cGAS-STING signaling, whereas PCBP2 deficiency remarkably enhanced the innate immune response induced by DNA stimulation or DNA virus infection in various cell lines. In addition, PCBP2 reduction in mouse embryonic fibroblasts (MEFs) apparently reduced HSV-1 virus replication. Mechanistically, we found that PCBP2 could interact with cGAS and negatively affect its enzymatic activity. Furthermore, we determined that PCBP2 evidently attenuated cGAS oligomerization and cGAS-DNA phase separation. Collectively, we revealed that PCBP2 negatively regulates cGAS-mediated innate immune responses against DNA virus infection by attenuating the enzyme activity of cGAS. Thus, our findings provide new insight into the mechanisms of innate immune responses against DNA virus infection that function to maintain immune homeostasis.

Identification of PCBP2 as a cGAS-interacting factor

To better understand the molecular basis underlying the regulation of cGAS upon DNA virus infection, we aimed to identify proteins associated with cGAS. We infected human HEK293A cells with lentivirus expressing SFB-tagged cGAS or an empty vector for 48 h and then performed Co-IP experiments, followed by mass spectrometry analysis. Using this approach, we identified a number of proteins that were potentially associated with cGAS. Among these candidates, PCBP2 was of particular interest because it has been shown to regulate the MAVS-mediated antiviral response against RNA virus infection^{32, 33}. To verify the association of PCBP2 with cGAS, we co-expressed PCBP2 and cGAS in HEK293T cells and performed additional Co-IP experiments. The results showed that PCBP2 was associated with cGAS (Fig. 1a). To determine whether the interaction between PCBP2 and cGAS is direct, we generated recombinant cGAS-His and GST-PCBP2 purified from Escherichia coli (E. Coli) and performed in vitro pull-down experiments. As shown in Fig. 1b and c, cGAS-His efficiently pulled down GST-PCBP2 but not the GST-GFP control, and GST-PCBP2 but not the GST-GFP control pulled down cGAS-His, suggesting that PCBP2 directly binds to cGAS. Next, to determine whether PCBP2 forms a complex with cGAS under physiological conditions, we used an anti-cGAS antibody to perform Co-IP assays in THP-1 cells and found that PCBP2 was detected in the cGAS immuno-precipitants under normal physiological conditions. Interestingly, we also observed that HSV-1 infection enhanced cGAS-PCBP2 interaction (Fig. 1d), suggesting that endogenous cGAS and PCBP2 form a complex and that this interaction is regulated by viral infection in THP-1 cells. In addition, immunostaining assay results showed that PCBP2 was co-localized with cGAS following their co-transfection in HeLa cells (Fig. 1e). These data suggested that PCBP2 forms a complex with cGAS.

PCBP2 contains three heterogeneous nuclear ribonucleoprotein K-homology (KH) domains and a linker region³². To map which domain is required for PCBP2 to associate with cGAS, we generated a series of deleted forms of PCBP2, in which the KH1, KH2, linker, or KH3 domain was deleted. As shown by the results of Co-IP assays, KH3 but not KH1, KH2, or the linker was important for PCBP2-cGAS interactions (Fig. 1f). Next, we aimed to identify the domain in cGAS that is required for its interaction with PCBP2. Because cGAS contains a less-conserved N-terminal disordered region and highly conserved C-terminal catalytic domains harboring NTase and Mab21 domains⁴, we generated two deleted forms of cGAS for subsequent Co-IP experiments. As shown in Fig. 1g, C-terminal domain but not the N-terminal domain, were essential for the association between cGAS and PCBP2. These data suggested that the interaction between PCBP2 and cGAS is dependent on specific domains.

PCBP2 inhibits cGAS-STING antiviral signaling

Given that PCBP2 associates with cGAS and that this association is regulated by viral infection, we reasoned that PCBP2 might regulate cGAS-STING-mediated antiviral signaling by targeting cGAS. We first generated a cell-based luciferase reporter system to test the role of PCBP2 in the type-I IFN signaling induced by cGAS. In the control experiments, the co-expression of cGAS and STING activated the IFNβ promoter in HEK293T cells. In contrast, we found that PCBP2 overexpression significantly downregulated the activity of IFNβ induced by the co-expression of cGAS and STING, suggesting a role of PCBP2 in balancing cGAS-STING signaling activity (Fig. 2a). Of note, the stimulation of IFN-β requires the coordinated activation of both IRF3 and NF-κB transcription factors. To understand how PCBP2 regulates cGAS-STING signaling, we used an IFN-stimulated response element (ISRE) luciferase reporter that can be activated by IRF3 and an NF-κB luciferase reporter to perform cell-based luciferase assays. As shown in Fig. 2b and c, PCBP2 overexpression significantly reduced the activation of the ISRE reporter that was stimulated by the co-expression of cGAS and STING but had no effect on the NF-κB reporter. These results suggest that PCBP2 attenuated the cGAS-medicated induction of IFNβ activation by regulating IRF3 activation.

To verify our observation from reporter assays, we then performed quantitative reverse transcription PCR (qRT-PCR) analysis to measure the transcriptional levels of antiviral genes, such as IFNB1, IFIT1, and CXCL10, in human macrophage THP-1 cells with or without PCBP2 overexpression following the infection of herpes simplex virus type 1 (HSV-1), a double-stranded DNA virus.. As shown in Fig. 2d–f, PCBP2 overexpression significantly reduced the mRNA levels of IFNB1, IFIT1, and CXCL10 induced by HSV-1 infection. Given that the phosphorylation of TBK1 and IRF3 is a hallmark of activated antiviral signaling, we then tested whether PCBP2 overexpression affects the phosphorylation of these factors. As shown in Fig. 2g, we observed that PCBP2 overexpression in THP-1 cells significantly reduced the levels of phosphorylated TBK1 and IRF3 induced by Herring testis DNA (HT-DNA), which mimics viral DNA ligands that bind to cGAS. In addition, we tested whether PCBP2 regulates cGAS signaling in a mouse cell line and found that overexpressed PCBP2 significantly reduced HT-DNA-induced production of Ifnb1 and Ifit1 but not Il-6 in mouse fibroblast L929 cells (Supplementary Fig. 1a–c). Collectively, these findings suggest that PCBP2 overexpression antagonizes cGAS-mediated antiviral signaling.

The experiments described above indicated that the KH3 domain of PCBP2 is critical for its association with cGAS. We then examined whether the deletion of this domain affects the ability of PCBP2 to regulate cGAS signaling. As shown in Fig. 1h, luciferase reporter assays revealed that deletion of the KH3 domain of PCBP2 resulted in the loss of its ability to inhibit cGAS-STING activation, whereas other deletion mutants exhibited a similar inhibitory ability as full-length PCBP2. These results suggested that the KH3-mediated PCBP2-cGAS interaction is important for PCBP2 to antagonize cGAS-mediated antiviral signaling.

Depletion of PCBP2 enhances cGAS-STING signaling

Next, we tested whether the knockdown of endogenous PCBP2 affects cGAS-mediated antiviral signaling. For this purpose, we generated two lentiviral constructs expressing short hairpin RNAs (shRNAs) against different regions of human PCBP2 (shPCBP2-1 and shPCBP2-2). We infected THP-1 cells with a lentivirus carrying shPCBP2-1 or shPCBP2-2 and then performed western blotting. The results showed that shPCBP2-2 displayed a higher PCBP2 knockdown efficiency (Supplementary Fig. 2a), and thus it was selected for further experiments. As shown in Fig. 3a–c, PCBP2 knockdown significantly enhanced the mRNA level of IFNB1 and IFIT1 induced by HSV-1 infection, whereas the mRNA expression of IL6, a downstream target of NF-κB, was not significantly affected by PCBP2 knockdown compared with control cells (Fig. 3d). Consistently, the knockdown of PCBP2 in THP-1 cells further elevated the levels of phosphorylated TBK1 and IRF3, but not p65, stimulated by HT-DNA (Fig. 3e). To obtain more evidence supporting our conclusion, we studied the function of PCBP2 in mouse cells. We infected mouse macrophage Raw 264.7 cells with two shRNAs specifically targeting the coding region of mouse Pcbp2. As shown by qRT-PCR analysis, shPcbp2-2 exhibited a higher knockdown efficiency, and shPcbp2-2-mediated Pcbp2 knockdown significantly increased the production of Ifnb1, Ifnα4, and cxcl10 mRNA following HSV-1 virus infection compared with control cells (Supplementary Fig. 2b–e). We also observed similarly enhanced antiviral responses at different time points after HSV-1 infection (Fig. 3f–h). Collectively, these findings further support the notion that PCBP2 acts as a negative regulator to balance cGAS signaling.

Enhanced cGAS-STING signaling in Pcbp2-deficient cells

To further substantiate the biological role of PCBP2 in cGAS-STING signal transduction, we used the CRISPR-Cas9 method to generate a Pcbp2-knockout L929 cell line and examined whether deletion of Pcbp2 affects cGAS-mediated antiviral signaling. Wild-type and Pcbp2-deficient cells from two different clones were transfected with HT-DNA, and the results of qRT-PCR assays showed that the transcriptional levels of Ifnb1 and Ifit1 stimulated by HT-DNA were remarkably increased in Pcbp2^–/– cells compared with wild-type control cells (Fig. 4a, Supplementary Fig. 3a). Moreover, the levels of TBK1 and IRF3 phosphorylation induced by HT-DNA transfection were also enhanced in Pcbp2^–/– cells compared with Pcbp2^+/+ cells under the same experimental conditions (Fig. 4b). We also found that loss of Pcbp2 significantly increased the mRNA expression of Ifnb1 following HSV-1 infection in a time-independent manner (Fig. 4c). Moreover, rescue experiments revealed that the restored expression of Pcbp2 could reverse the enhanced Ifnb1 expression induced by HT-DNA transfection in Pcbp2-deficient cells (Fig. 4d). Consistently, we found that PCBP2 knockout in human THP-1 cells also enhanced the mRNA levels of IFNB1 and IFIT1 induced by HSV-1 infection (Fig. 4e and f) and increased levels of TBK1 and IRF3 phosphorylation induced by HT-DNA (Fig. 4g). These data further support the notion that PCBP2 functions as a negative regulator in cGAS-mediated antiviral signaling pathway.

To study the physiological function of PCBP2 in vivo, we next tried to generate Pcbp2-knockout mice using the CRISPR-Cas9 method. However, we failed to obtain Pcbp2^-/- mice after the intercrossing of heterozygotes, which was consistent with the previous study³⁴. Next, we aimed to isolate Pcbp2^-/-MEFs from 13.5-day-old embryos. We noted that the majority of Pcbp2^-/- embryos had died at day 13.5, but fortunately, two surviving Pcbp2^-/- embryos were obtained and dissected to isolate Pcbp2^-/- MEFs for further functional assays (Supplementary Fig.3b). As shown in Supplementary Fig. 3c–e, the level of Ifnb1 mRNA was significantly enhanced in Pcbp2^-/-MEFs compared with wild-type cells following stimulation with HSV-1, HT-DNA, or VACV70, which derives from the vaccinia virus DNA. Intriguingly, we found that the abundance of Ifnb1, Ifit1, and Cxcl10 mRNA in Pcbp2^+/- cells was also markedly higher than that in Pcbp2^+/+ cells following HSV-1 infection (Fig. 4h–j). Consistently, the levels of TBK1 and IRF3 phosphorylation induced by HSV-1 were enhanced in Pcbp2^+/– cells compared with their Pcbp2^+/+ counterparts (Fig. 4k). Furthermore, we tested whether PCBP2 was involved in controlling DNA virus amplification. As shown in Fig. 4l, the HSV-1 genomic DNA copy number was substantially lower in Pcbp2^+/-cells than that in wild-type cells. Collectively, our findings emphasize that PCBP2 negatively regulates cGAS-STING antiviral signaling.

PCBP2 modulates cGAS-STING signaling by specifically targeting cGAS

We next aimed to better understand the molecular mechanism by which PCBP2 antagonizes the cGAS-mediated antiviral response. To determine whether cGAS is a specific target of PCBP2, we performed Co-IP experiments to examine if PCBP2 can interact with other known components in the cGAS-STING pathway, such as STING, TBK1, and IRF3. First, we co-transfected HEK293T cells with PCBP2 and cGAS, STING, TBK1, or IRF3 and found that PCBP2 only pulled down cGAS but not the other components (Supplementary Fig. 4a). Second, we used an anti-PCBP2 antibody and performed endogenous Co-IP experiments in THP-1 cells in the presence or absence of HT-DNA stimulation. Only cGAS, but not the other components, was found to associate with PCBP2 (Fig. 5a). In addition, we observed that HT-DNA transfection increased the association between cGAS and PCBP2 (Fig. 5a). Thus, these findings suggest that PCBP2 likely specifically targets cGAS, thereby antagonizing cGAS-STING signaling activity.

Our results described thus far support an intriguing model that PCBP2 negatively regulates the cGAS-STING signaling pathway likely by specifically targeting cGAS. To test our model, we next investigated whether PCBP2 overexpression affected the activation of components downstream from cGAS, including STING, TBK1, and IRF3. In contrast to its role in antagonizing the activation of cGAS, PCBP2 failed to influence the activation of STING, TBK1, or IRF3-5D (a constitutively active form of IRF3) (Fig. 5b–e). In particular, we found that overexpression of PCBP2 did not affect the levels of IRF3 and TBK1 phosphorylation induced by the ectopic expression of STING (Supplementary Fig. 4b). Collectively, these data suggest that PCBP2 functions upstream of STING to regulate cGAS-STING signaling.

Given that cGAS catalyzes the synthesis of cGAMP, which functions as a second messenger by binding to and activating STING, and PCBP2 functions upstream of STING, we next examined whether PCBP2 was involved in regulating cGAMP-STING signaling. The results of reporter assays demonstrated that cGAMP treatment remarkably increased IFNb promotor activation in HEK293T cells stably expressing STING. However, PCBP2 overexpression had no effect on the activation of the IFNb promotor induced by cGAMP treatment (Supplementary Fig. 4c), suggesting that cGAMP activates STING through a PCBP2-independent mechanism. To confirm our observation, we measured the levels of phosphorylated TBK1 and IRF3 induced by cGAMP in THP-1 wild-type and PCBP2-deficient cells and found that loss of PCBP2 had no effect on the increased levels of phosphorylated TBK1 and IRF3 induced by cGAMP treatment compared with control cells (Fig. 5f). These results indicated that PCBP2 functions upstream of cGAMP-STING to negatively regulate cGAS-cGAMP-STING signaling.

PCBP2 attenuates the enzymatic activity of cGAS to balance cGAS signaling

Because cGAS is a synthase involved in the production of cGAMP, we reasoned that PCBP2 targets cGAS likely by negatively regulating its enzymatic activity, thus inhibiting cGAMP production. To test this hypothesis, we first used a 2'-3'-cGAMP ELISA kit to measure the levels of cGAMP in THP-1 wild-type and PCBP2-overexpressing cells induced by HSV-1 infection. cGAMP levels were significantly reduced in PCBP2-overexpressing cells compared with control cells, suggesting that PCBP2 inhibits cGAS-mediated cGAMP production in these cells (Fig. 5g). Consistently, PCBP2 deficiency significantly increased the amount of cGAMP induced by HT-DNA transfection in THP-1 cells (Fig. 5h). In addition, we measured the levels of cGAMP in wild-type and Pcbp2 knockdown Raw 264.7 cells and found that knockdown of Pcbp2 also augmented the level of cGAMP induced by HT-DNA (Supplementary Fig. 4d). We also observed that the abundance of cGAMP induced by HT-DNA was enhanced in Pcbp2^+/-MEFs compared with that in control cells (Fig. 5i). Moreover, we purified PCBP2 wild-type, PCBP2-ΔKH3, and cGAS from E. Coli and performed in vitro cGAMP synthesis assays. We found that PCBP2 inhibited cGAS enzymatic activity, whereas the PCBP2-ΔKH3 mutant did not exhibit this inhibitory ability (Fig. 5j). Collectively, these data suggest that PCBP2 acts upstream of cGAMPs and modulates cGAS signaling by regulating its enzymatic activity.

PCBP2 inhibits cGAS enzymatic activity by antagonizing its condensation

Next, we investigated how PCBP2 regulates the enzymatic activity of cGAS. Previous studies have shown that DNA binding induces cGAS conformational changes and that cGAS can form dimers and undergo oligomerization, which plays an important role in regulating its enzymatic activity^{6, 22}. Our experiments described above demonstrated that PCBP2 interacted with cGAS and inhibited its enzymatic activity. Thus, we hypothesized that PCBP2 likely modulated cGAS enzyme activity by regulating cGAS oligomerization. To test this hypothesis, we conducted the following experiments. First, HA-cGAS and Flag-cGAS were co-transfected with PCBP2 or an empty vector into HEK293T cells, and then Co-IP assays were conducted to examine whether PCBP2 affected the self-association of cGAS. As shown in Fig. 6a, the self-association of cGAS was affected by PCBP2 overexpression. Second, we performed semi-denaturing detergent agarose gel electrophoresis (SDD-AGE) assays to detect protein oligomerization. As shown in Fig. 6b, we found that overexpressed cGAS could form high molecular weight (HMW) polymers, whereas PCBP2 co-expression significantly reduced the levels of cGAS oligomerization in HEK293T cells. Conversely, PCBP2 knockout enhanced cGAS oligomerization induced by HT-DNA treatment in L929 cells (Fig. 6c). Similar results were obtained in PCBP2 knockout THP1 cells following HSV-1 infection (Supplementary Fig. 5a). In addition, we conducted an in vitro cGAS oligomerization assay and found that PCBP2 significantly attenuated cGAS oligomerization regardless of the presence or absence of HT-DNA treatments (Fig. 6d). Third, we conducted immunostaining experiments and found that PCBP2 overexpression significantly reduced the formation of cGAS granules in HEK293A cells (Fig. 6e). Conversely, cGAS formed substantially larger granules in L929 Pcbp2^-/- cells than in control cells after stimulation of ISD, a 45 bp double-stranded interferon stimulatory DNA (Fig. 6f). Furthermore, larger cGAS granules were also observed in THP-1 PCBP2^-/- cells compared with those in wild-type cells following ISD treatment (Supplementary Fig. 5b). Taken together, these data demonstrated that PCBP2 modulated cGAS oligomerization.

A previous study showed that cGAS could form liquid-like droplets after binding to DNA, which plays an important role in regulating cGAS activity²⁴. To test whether PCBP2 affects cGAS-DNA phase separation, we purified GFP-cGAS and GST-PCBP2 proteins and conducted in vitro protein phase separation analysis²⁴. As shown in Fig. 6g, GFP-cGAS formed larger droplets in the solution within 5 minutes after adding ISD. However, the addition of PCBP2 remarkably reduced the increased size of cGAS droplets induced by ISD treatment. We observed similar results when VACV70 (Fig. 6h) or HSV120 (120 bp dsDNA representing the genome of HSV-1) (Fig. 6i) was added. Collectively, these data demonstrate that PCBP2 modulates cGAS condensation.

cGAS functions as a cytosolic sensor to detect the pathogenic DNA of viruses³⁵, bacteria³⁶, or damaged self-DNA³⁷. After binding to DNA, cGAS becomes activated and catalyzes the synthesis of cGAMP, which binds to STING to active downstream signaling, subsequently inducing the production of IFNs and inflammatory cytokines^{4, 38}. cGAS-cGAMP-STING-mediated signaling is tightly regulated to maintain innate immune system homeostasis and prevent the overproduction of IFNs, which can be detrimental to the host and even lead to the development of autoimmune diseases⁷. Previous studies have reported several negative regulators of cGAS, such as AKT kinase⁸, p62²¹, Beclin1²⁰, Caspase 1/3^{17, 18}, Gasdermin D¹⁹, and TTLL6/4¹⁰. However, the processes that balance the activity of cGAS to avoid harmful overreaction remain largely unknown. In this study, we found that PCBP2 maintained proper cGAS signaling by targeting cGAS. Mechanistically, we found that PCBP2 attenuated the enzyme activity of cGAS to reduce cGAMP production by antagonizing cGAS condensation.

A previous study showed that PCBP2 mRNA and protein levels were induced by SeV infection. PCBP2 was mainly localized in the nuclei of untreated cells but could translocate to the cytosol, co-localize with MAVS in mitochondria upon SeV infection, and recruit the E3 ligase AIP4 to catalyze MAVS ubiquitination, thereby targeting it for degradation³². We tested whether PCBP2 exhibited a similar function upon HSV-1 infection. We observed no apparent enhancement of PCBP2 mRNA, whereas cGAS and IFNB1 mRNA were significantly increased following HSV-1 infection in THP-1 cells (Supplementary Fig. 6a–c). However, immunostaining assays revealed that PCBP2 could translocate to the perinuclear region, where it showed a punctate distribution in HeLa cells after transfection with HT-DNA (Supplementary Fig. 6d). Similarly, we observed that PCBP2 translocated to the cytosol when cells were infected with HSV-1 virus or transfected with cGAS (Supplementary Fig. 6d and e). These results suggested that PCBP2 can translocate to the cytoplasm and target cGAS to inhibit antiviral signaling upon DNA virus infection. How PCBP2 translocates to the cytosol following virus infection is an interesting question that requires further study.

Oligomerization is important for cGAS to exert its enzyme activity. Upon binding to DNA, cGAS can undergo oligomerization^{6, 22} and form liquid droplets in vitro and in vivo²⁴. Both DNA binding and self protein-protein association of cGAS are important for the formation of the cGAS oligomeric complex⁶; however, the mechanisms that dynamically regulate this complex to maintain an appropriate innate immune response are still unclear. In this study, we obtained extensive evidence supporting that PCBP2 inhibits cGAS oligomerization. First, we conducted Co-IP experiments and found that PCBP2 regulated cGAS self-association. Second, we conducted SDD-AGE assays and observed that PCBP2 overexpression reduced cGAS oligomerization in HEK293T cells, whereas PCBP2 deficiency enhanced cGAS oligomerization induced by HSV-1 infection and HT-DNA stimulation. We also demonstrated that PCBP2 significantly attenuated cGAS oligomerization in vitro. Third, we conducted immunostaining assays and found that PCBP2 overexpression reduced the size of cGAS granules. Conversely, cGAS formed substantially larger granules in PCBP2 knockout L929 and THP-1 cells compared with those in wild-type cells following ISD treatment. Forth, we performed in vitro phase separation and found that PCBP2 remarkably inhibited the DNA-induced liquid phase condensation of cGAS. Taken together, these data suggest that PCBP2 negatively regulates cGAS enzyme activity by modulating cGAS oligomerization to maintain the innate immune response. Importantly, our findings provide a novel understanding of the mechanism underlying the dynamic regulation of the cGAS oligomeric complex.

Ethics statements

All animal studies were carried out in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the Ministry of Science and Technology of the People’s Republic of China. The protocols for animal studies were approved by the Committee on the Ethics of Animal Experiments of the Institute of Zoology, Chinese Academy of Sciences (Beijing, China) (approval number: IOZ15001).

Cell culture

HEK293T, HeLa, L929, and RAW264.7 cells were obtained from the Shanghai Cell Bank of the Chinese Academy of Sciences (Shanghai, China). Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 1% penicillin, and 1% streptomycin. MEFs from wild-type and mutant mice were generated from 13.5-day-old embryos and cultured in complete DMEM containing 1 mM sodium pyruvate, 10 mM L-glutamine, 10 mM β-mercaptoethanol, and 1% nonessential amino acids. THP-1 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin, 1% streptomycin, 10 μM β- mercaptoethanol, and 5 mM HEPES.

Plasmids

Mammalian expression plasmids encoding Flag-tagged PCBP2, cGAS, STING, TBK1, IRF3, and IRF3-5D; hemagglutinin (HA)-tagged cGAS, STING, and PCBP2; SFB-cGAS, GFP-tagged cGAS and mCherry-tagged PCBP2; bacterial expression plasmids encoding histidine (His)-tagged cGAS and GFP-cGAS; and glutathione S-transferase (GST)-tagged PCBP2 were constructed using standard molecular biology methods. PCBP2 and cGAS mutants were generated by PCR using Pfu DNA polymerase. IFN-β-, NF-κB-, and ISRE-luciferase (Luc) reporter plasmids have been described previously³⁹.

Antibodies

Rabbit anti-phospho-IRF3, rabbit anti-IRF3, rabbit anti-phospho-TBK1 and rabbit anti-cGAS antibodies were from Cell Signaling Technology. Rabbit anti-TBK1 was from Abcam. Rabbit anti-PCBP2 was from Abcam and Proteintech. Mouse anti-PCBP2 was from Santa Cruz Biotechnology. Mouse anti-glyceraldehyde-3-phosphate dehydrogenase (GAPDH), mouse anti-α-Tublin and mouse anti-HA antibodies were from Sungene Biotechnology. Rabbit anti-Flag antibody was from Sigma. Mouse anti-Flag, rabbit anti-HA, rabbit anti-Myc, mouse anti-Myc antibodies were from MBL. Mouse/Rabbit anti-cGAS antibody was prepared in our laboratory, the cGAS antibody was generated by immunizing mice or rabbits with purified human cGAS full-length from E. coli.

DNA oligonucleotides.

All DNA oligonucleotides were synthesized by Tsingke Biological Technology Company. For Cy3- or biotin-labeled ISD, VACV70 or HSV120, the sense strand was modified at the 5' end; the antisense strand was not modified. The sequences of oligonucleotides used in this study were as follows:

ISD45:

5’-TACAGATCTACTAGTGATCTATGACTGATCTGTACATGATCTACA-3'.

VACV70: 5’-CCATCAGAAAGAGGTTTAATATTTTTGTGAGACCATGGAAGAGAGAAAGAGATAAAACTTTTTTACGACT-3’

HSV120: 5’-AGACGGTATATTTTTGCGTTATCACTGTCCCGGATTGGACACGGTCTTGTGGGATAGGCATGCCCAGAAGGCATATTGGGTTAACCCCTTTTTATTTGTGGCGGGTTTTTTGGAGGACTT-3’,

Luciferase reporter analysis and transfection

HEK293T cells were transfected using the standard calcium phosphate transfection method or polyethylenimine. A Renilla reporter plasmid and firefly luciferase reporter plasmids encoding IFNβ-Luc, NF-κB-Luc, or ISRE-Luc were co-transfected with the indicated expression plasmids. An empty control plasmid was used in the same experiment to ensure that the same amount of total DNA was transfected. Cells were lysed to measure luciferase activity. Firefly luciferase activity was normalized to Renilla activity. All reporter assays were repeated at least three times.

Co-IP and immunoblotting analysis
Cells were lysed in lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.5% Triton X-100, 10% glycerol, 1 mM EDTA) supplemented with a complete protease inhibitor cocktail (Roche). Clarified cell lysates were incubated with anti-Flag M2 agarose beads (Sigma Aldrich) for 4 h at 4ºC. The immunoprecipitated complexes were washed with lysis buffer containing 300 mM NaCl three times and subjected to immunoblotting with the indicated antibodies. For endogenous IP, cell lysates were incubated with a cGAS or PCBP2 antibody overnight at 4ºC, followed by further incubation with protein A/G beads (Pierce) for 2 h. Immunoblotting was carried out using standard procedures.

Identification of cGAS-interacting proteins by mass spectrometry

HEK293A cells were infected with lentivirus expressing SFB-tagged cGAS or an empty vector for 48 h and then lysed with lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% NP-40, 0.5% DOC, 0.1% SDS, 10% glycerol, 1 mM EDTA, 1 mM EGTA) containing a complete protease inhibitor cocktail, followed by centrifugation at 20,000 g for 10 min at 4°C. The supernatants were subjected to immunoprecipitation using S-protein agarose (Millipore). Immunoprecipitates were separated by SDS-PAGE, and the gel was stained with Coomassie brilliant blue. The entire lane was cut into 2-mm gel slices, digested with Trypsin, and subjected to LC-MS/MS assays using an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific). The mass spectrometry data were analyzed using Thermo Proteome Discovery (version 2.3), and tandem mass spectra were searched against the UniProt-Homo sapiens database. Ranking of the identified proteins was based on the peptide abundance ratio of sample/control and reproducibility among the MS analyses of different samples.

Expression and purification of recombinant proteins in E. coli

Constructs encoding human cGAS and GFP-tagged cGAS were cloned into the pET-28a vector carrying a C-terminal 6*His tag. GST-tagged full-length human PCBP2 and its mutant were inserted into a pGEX-4T-1 vector containing an N-terminal GST-tag. The plasmids were transformed into the BL21 E. Coli strain. The fusion proteins were purified from the cell lysates using Ni-Sepharose beads (GE Healthcare) or Glutathione-Sepharose beads (GE Healthcare) in accordance with the manufacturer’s protocols.

Immunofluorescence staining

HeLa, HEK293A, L929, or THP-1 cells were seeded on gelatin-coated glass coverslips and then transfected or infected as indicated. The cells were fixed with 4% paraformaldehyde for 15 min, permeabilized, and blocked with PBS containing 0.2% Triton-X-100 and 5% BSA for 25 min at room temperature. The cells were incubated with the primary antibody, followed by the secondary antibody. The cells were washed with PBST (PBS with 0.2% Tween 20) between each step. Images were acquired using a Zeiss LSM 710 META laser scanning confocal system.

Quantitative reverse-transcription polymerase chain reaction (qRT-PCR)

Total RNA was isolated using TRIZOL reagent (Invitrogen). cDNA was generated using the SuperScript II First-Strand cDNA Synthesis kit (TianGen Biotech). qRT-PCR was conducted in duplicate using a SYBR Green Master Mix (CoWin Biosciences) on a Light Cycler 480® (Roche). Relative mRNA levels were normalized to GAPDH or actin mRNA levels in each sample. Relative expression changes were calculated by the 2^-ΔΔCt method. Data are shown as the mRNA abundance relative to control groups. The primers used were listed in Supplemental table1.

Lentivirus-mediated PCBP2 overexpression and shRNA knockdown

Full-length cDNA encoding human PCBP2 was amplified and inserted into a pCDH-CMV-Puro vector. The lentivirus particles for PCBP2 overexpression were produced by co-transfecting a pCDH-CMV-Puro-PCBP2 construct into HEK293T cells with the packaging plasmids pMD2.G and pAS-MAX. To generate PCBP2-knockdown cells, we used pLKO.1-puro-based lentiviruses expressing specific short hairpin RNAs (shRNAs) against PCBP2. RAW264.7 cells or THP-1 cells were infected with lentiviruses expressing shRNAs against PCBP2 (shPCBP2) or control vector (pLKO), and the cells were selected with puromycin (2 μg/ml) to generate stable PCBP2 knockdown or control pLKO cells. The knockdown efficiency was determined by qRT-PCR or western blotting analysis. The shRNA sequences against human PCBP2 or mouse Pcbp2 are as follows:

Human PCBP2 shRNA-1#：

5’-ACCGGGCATTCCACAATCCATCATTGCTCGAGCAATGATGGATTGTGGAATGCTTTTT-3’

Human PCBP2 shRNA-2#:

5’-ACCGGCCATGATCCATCTGTGTAGTTCTCGAGAACTACACAGATGGATCATGGTTTTT-3’

Mouse Pcbp2 shRNA-1#:

5’-ACCGGCCCATCCATAATCCTGCTGTTCTCGAGAACAGCAGGATTATGGATGGGTTTTT-3’

Mouse Pcbp2 shRNA-2#:

5’-ACCGGTCCTGAGAGAATTATCACTTTCTCGAGAAAGTGATAATTCTCTCAGGATTTTT-3’

CRISPR/Cas9-mediated PCBP2-knockout cell lines

To generate PCBP2 knockout (PCBP2^-/-) cells, lenti-CRISPRv2-sgPCBP2-Puro vectors were constructed in accordance with the method described by Sanjana et al⁴⁰ and co-transfected with packaging plasmids into HEK293T cells. Two days after transfection, the viruses were harvested and used to infect THP-1 or L929 cells. The infected cells were selected with puromycin (2μg/ml) for at least 5 days. PCBP2-knockout cells were verified by immunoblotting. PCBP2 guide RNA sequences were as follows:

hPCBP2 sg-s: 5’-CACCG CAGGGTGACCGGGGGTCTAC-3’

hPCBP2 sg-as: 5’-AAAC GTAGACCCCCGGTCACCCGT C-3’

mPcbp2 sg-s: 5’-CACCG ATCTGTTAAGAAGATGCGCG-3’

mPcbp2 sg-as: 5’-AAAC CGCGCATCTTCTTAACAGAT C-3’

CRISPR/Cas9-mediated PCBP2-knockout mice

To generate Pcbp2 knockout mice, the CRISPR/Cas9-mediated gene deletion system was used. Cas9 mRNA and single-guide RNA targeting Pcbp2 sequences were co-injected into zygotes to obtain heterozygous mutants. Homozygous and heterozygous MEF cells were obtained from 13.5-day-old embryos by breeding heterozygote mutants. The sequences targeting Pcbp2 were (5’-3’): ATCTGTTAAGAAGATGCGCG. The mutant was obtained with 8 bp deletion in the forth exon of Pcbp2, which prematurely terminate protein translation. Pcbp2 homozygous or heterozygous MEF cells were verified by immunoblotting analysis.

cGAS enzyme activity assays and cGAMP quantification

cGAS activity was analyzed as described previously ^{4, 5}. An in vitro cGAS reaction assay was conducted by mixing recombinant human cGAS protein with GST-PCBP2 or GST control in the presence or absence of HT-DNA (50 ng/µl) in a low-salt buffer (20 mM HEPES, pH 7.5, 5 mM MgCl₂, 2 mM ATP, 2 mM GTP) and incubating the mixture at 37°C for 2 h. The reaction was terminated by heating at 95°C for 5 min to denature proteins, followed by centrifugation to remove the denatured proteins. The supernatant was incubated with L929-ISRE cells that were permeabilized with digitonin solution (50 mM HEPES pH 7.0, 100 mM KCl, 3 mM MgCl₂, 85 mM sucrose, 0.1 mM DTT, 0.2% BSA, 1 mM ATP, 0.1 mM GTP, and 10 μg/ml digitonin) at 37°C for 30 min. The cells were cultured at 37°C for 12 h and then lysed for luciferase assays. Serial dilutions of cGAMP were used to generate the standard curve for quantifying cGAMP concentrations in the reactions.

A 2'-3'-cGAMP ELISA kit (Cayman Chemical) was used to measure cGAMP levels in HT-DNA transfected cells. Briefly, cells were transfected with HT-DNA using Lipofectamine 2000. Four hours after transfection, the cells were harvested and lysed in 100 µl of hypotonic buffer (10 mM Tris-HCl, pH7.5, 5 mM KCl, and 3 mM MgCl2). Cell lysates were heated at 95°C for 5 min, followed by centrifugation to remove the denatured proteins. The heat-resistant supernatants were used to measure cGAMP abundance. The 2'-3'-cGAMP ELISA kit was used in accordance with the protocol of the manufacturers.

Measurement of HSV-1 genomic DNA copy numbers

Pcbp2^+/+ and Pcbp2^+/– MEFs were infected with HSV-1 (MOI=0.1) and incubated at 37°C in serum-free DMEM for 1 h. The cells were washed with warm PBS, cultured in complete DMEM for 18 h, and their genomic DNA was extracted. The HSV-1 genomic DNA copy numbers were determined by qRT-PCR using HSV-1-specific primers with the following sequence: 5’-TGGGACACATGCCTTCTTGG-3’; 5’-ACCCTTAGTCAGACTCTGTTACTTACCC-3’.

SDD-AGE assay

The cells were transfected as indicated and lysed in lysis buffer (0.5% Triton X-100, 50 mM Tris-HCl, 150 mM NaCl, 10% glycerol). The supernatants were separated by 1.5% SDD-AGE as previously described³⁹.

In vitro phase separation assay

Recombinant GFP-cGAS protein was mixed with GST or GST-PCBP2 and the indicated DNA in a glass-bottom cell culture dish. The mixtures were incubated in the buffer containing 20 mM Tris-HCl, pH 7.5, 150 mM NaCl, and 1 mg/ml BSA at room temperature, and images were captured at the indicated times. Phase-separated droplets were imaged using an ANDOR CR-DFLY-505 confocal microscope equipped with a sCMOS Zyla 4.2 plus camera, and images were analyzed using Imaris software.

Statistical analysis

Results of all statistical analyses are shown as mean ± SD. Significant differences between samples under different experimental conditions were performed using two-tailed Student’s t-test. For all tests, P values < 0.05 were considered statistically significant.

Author contributions

H.G., D.C., and Q.S. designed the experiments; H.G., J.Y, J.Z., P.Z., and L.L performed experiments; H.G., J.Y, J.Z., D.C., and Q.S. analyzed data; H.G., D.C., and Q.S. wrote the paper. All authors provided intellectual input, vetted and approved the final manuscript.

Acknowledgements

This work is supported by Natural Science Foundation of China (Grants 31970895) and the Open Research Program of State Key Laboratory of Membrane Biology.

Competing interests

The authors declare no competing interests.

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PCBP2 maintains antiviral signaling homeostasis by regulating cGAS enzymatic activity via antagonizing its condensation

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