A cell-free assay implicates a role of sphingomyelin and cholesterol in STING phosphorylation

Stimulator of interferon genes (STING) is essential for the type I interferon response induced by microbial DNA from virus or self-DNA from mitochondria/nuclei. In response to emergence of such DNAs in the cytosol, STING translocates from the endoplasmic reticulum to the Golgi, and activates TANK-binding kinase 1 (TBK1) at the trans-Golgi network (TGN). Activated TBK1 then phosphorylates STING at Ser365, generating an interferon regulatory factor 3-docking site on STING. How this reaction proceeds specifically at the TGN remains poorly understood. Here we report a cell-free reaction in which endogenous STING is phosphorylated by TBK1. The reaction utilizes microsomal membrane fraction prepared from TBK1-knockout cells and recombinant TBK1. We observed agonist-, TBK1-, “ER-to-Golgi” traffic-, and palmitoylation-dependent phosphorylation of STING at Ser365, mirroring the nature of STING phosphorylation in vivo. Treating the microsomal membrane fraction with sphingomyelinase or methyl-β-cyclodextrin, an agent to extract cholesterol from membranes, suppressed the phosphorylation of STING by TBK1. Given the enrichment of sphingomyelin and cholesterol in the TGN, these results may provide the molecular basis underlying the specific phosphorylation reaction of STING at the TGN.

www.nature.com/scientificreports/ STING activation, besides STING palmitoylation. However, because of the technical difficulty to deplete these lipids in cells, their involvement in the activation of STING signalling pathway has not been addressed.
In this work, we report a cell-free reaction in which endogenous STING is phosphorylated at Ser365 by recombinant TBK1. With this reaction, we demonstrate that sphingomyelin and cholesterol in the Golgi membrane are critical for STING activation.

Results
A cell-free reaction in which endogenous STING is phosphorylated by recombinant TBK1. To directly assess the roles of Golgi lipids in STING activation, we sought to develop a cell-free assay in which endogenous STING is phosphorylated by TBK1. To eliminate any contribution of cytosolic/endogenous TBK1 to STING phosphorylation, we decided to use microsomal membrane fraction prepared from TBK1-deficient cells as a membrane source containing endogenous STING.
TBK1-knockout (KO) mouse embryonic fibroblasts (MEFs) were generated using the CRISPR-Cas9 technology ( Fig. 1a and Supplementary Fig. S1). We then validated the phosphorylation and membrane traffic of STING in these cells. TBK1-KO MEFs were stimulated with DMXAA, a membrane-permeable mouse-specific STING agonist. We chose 60 min for DMXAA treatment, because STING localized exclusively to the Golgi and activated TBK1 at this time point 22 (Fig. 1b). As expected, 60 min after DMXAA stimulation, we observed the phosphorylation of STING at Ser365 in parental wild-type (WT) MEFs (Fig. 1a). In contrast, the phosphorylation was mostly suppressed in TBK1-KO MEFs.
DMXAA-stimulated TBK1-KO MEFs were harvested in isotonic buffer and homogenized. The homogenates were then centrifuged at 3000 × g for 5 min and the resulting post-nuclear supernatants were further centrifuged at 100,000 × g for 60 min. The membrane fraction that floated just above 2 M sucrose cushion was collected and used as microsomal membrane fraction for the following in vitro reactions.
The microsomal membrane fraction was incubated with ATP and 100 ng of recombinant TBK1 at 37 °C for the indicated time periods (Fig. 2a,b). In the conditions where microsomal membrane fraction prepared from DMXAA-stimulated MEFs was used, the amount of phosphorylated STING at Ser365 increased gradually up to 60 min of incubation (Fig. 2b). The amount of STING was decreased after 120 min of incubation, suggesting the proteolytic degradation of STING ( Supplementary Fig. S2). When microsomal membrane fraction of unstimulated cells was used for the reaction, the phosphorylated STING disappeared (Fig. 2b). These results suggested that STING phosphorylation by TBK1 stringently requires the agonist (DMXAA) stimulation.
Titration of the amount of TBK1 in the reaction showed that 100 ng of recombinant TBK1 was sufficient to detect the phosphorylated STING (Fig. 2c). Thus, we routinely used 100 ng of recombinant TBK1 at the following experiments. The phosphorylation reaction of STING by TBK1 was temperature-sensitive ( Fig. 2d) and required ATP (Fig. 2e). In sum, a cell-free assay to phosphorylate endogenous STING at Ser365 was developed with the use of recombinant TBK1.
"ER-to-Golgi" traffic-and palmitoylation-dependent phosphorylation. The exocytic membrane traffic from the ER to the Golgi is required for the activation of the STING signalling pathway 15,22,23,30 . The treatment of cells with BFA (a fungal macrocyclic lactone that blocks "ER-to-Golgi" traffic 31 ) suppressed the translocation of STING to the Golgi 22 ( Supplementary Fig. S3), the emergence of p-TBK1/p-STING/p-IRF3 15 , and abolished the STING signalling 22 . Thus, we examined if the phosphorylation of STING in the cell-free assay also required the translocation of STING to the Golgi. Microsomal membrane fraction was prepared from cells treated with BFA and DMXAA. When the microsomal membrane fraction was subjected to the in vitro reaction, we found no phosphorylated STING (Fig. 3a). Addition of STING agonist i.e., DMXAA or 2′3′-cGAMP, to the in vitro reaction with the microsomal membrane fraction prepared from unstimulated cells did not promote the phosphorylation of STING ( Fig. 3b and Supplementary Fig. S4). These results suggested that (1) the binding of STING with its agonist alone was not sufficient to make STING the substrate for TBK1 and (2) STING translocation from the ER to the Golgi, which subsequently occurred after the binding of STING with its agonist, was required for the phosphorylation of STING.
STING undergoes palmitoylation at the Golgi and the inhibition of palmitoylation with 2-bromopalmitate (2-BP) suppressed the STING-dependent downstream signalling 22 . Microsomal membrane fraction was prepared from cells treated with 2-BP and DMXAA. When the microsomal membrane fraction was subjected to the in vitro reaction, we found no phosphorylated STING (Fig. 3c), consistently with the in vivo observation 22 . A role of cholesterol and sphingomyelin in STING activation. We previously suggested the role of sphingomyelin in STING activation by the experiment with D-ceramide-C6 22 , an agent to disrupt lipid domain containing sphingomyelin 32 . We sought to address directly the role of lipids constituting the lipid domain in STING activation with the cell-free reaction. Microsomal membrane fraction prepared from DMXAA-stimulated cells was digested with recombinant bacterial sphingomyelinase (bSMase), and then subjected to the in vitro reaction. As shown in Fig. 4a, we found no phosphorylated STING with bSMase-digested membranes. Pre-treatment of the microsomal membrane fraction with methyl-β-cyclodextrin, an agent to extract cholesterol from membranes, also suppressed the phosphorylation of STING by TBK1 in dose-dependent fashion (Fig. 4b).
These results suggested the role of sphingomyelin and cholesterol in STING activation.

Discussion
In the present study, we developed a cell-free assay in which endogenous STING is phosphorylated by recombinant TBK1. The assay showed the dependency of STING phosphorylation on the STING agonist, TBK1, "ER-to-Golgi" traffic, and palmitoylation, which mirrored the nature of STING phosphorylation in vivo. With Scientific Reports | (2021) 11:11996 | https://doi.org/10.1038/s41598-021-91562-z www.nature.com/scientificreports/ the assay, we provided an in vitro evidence that sphingomyelin and cholesterol in the Golgi membranes were involved in the STING activation. The assay should provide a useful biochemical complement to cell biological studies presently used to understand the molecular mechanism underlying the STING activation. Protein palmitoylation has been implicated in the clustering of a number of proteins into a specific lipid microdomain "raft" enriched in cholesterol and sphingomyelin 33 . Cholesterol is suggested to be enriched at the TGN, and cholesterol together with sphingomyelin generated by sphingomyelin synthase 1 are thought to form lipid rafts at the TGN 32 . Together with the present findings by the cell-free experiments, we hypothesize that palmitoylated STING becomes clustered at the TGN with the aid of the raft, which facilitates the recruitment of TBK1 10,11 for phosphorylation of STING 13 . www.nature.com/scientificreports/ Sphingomyelin at the TGN is demonstrated to be essential for transport carrier formation 32 . Cholesterol at the Golgi, the levels of which is regulated by oxysterol-binding protein, is essential for the Golgi localization of intra-Golgi v-SNAREs by ensuring proper COP-I vesicle transport 34 . Caveolin-1, a protein to form caveolae at the plasma membrane, accumulates in the Golgi when the cholesterol level in the Golgi is low 35 . The present study demonstrates another role of sphingomyelin and cholesterol at the Golgi/TGN in cellular signalling. The
Cell culture. MEFs 22 were cultured in DMEM supplemented with 10% fetal bovine serum and penicillin/ streptomycin/glutamine in a 5% CO 2 incubator.

Generation of TBK1-KO cells by CRISPR-Cas9.
MEFs that stably expressed Cas9 were established using lentivirus. HEK293T cells were co-transfected with lentiCas9-blast, psPAX2, and pMD2.G. The medium that contains the lentivirus was collected and filtered through 0.45 µm PVDF filter. WT MEFs were incubated with the medium for 6 h and then selected with blasticidin (5 µg/mL) for several days. Single-guide RNAs (sgRNA) were designed to target mouse TBK1 genomic loci. The sgRNA (sense: 5′-cac-cgCAT AAG CTT CCT TCG CCC AG-3′, antisense: 5′-aaacCTG GGC GAA GGA AGC TTA TGc-3′) was cloned into a lentiGuide-Puro vector. The lentiviral plasmids, psPAX2, and pMD2.G were then co-transfected into HEK293T cells and the lentivirus-containing medium was collected. Cas9-expressing MEFs were incubated with the medium for 6 h and selected with puromycin (2 µg/mL) for several days. Single colonies were then isolated and the expression of TBK1 in each clone was analyzed by western blot. The genomic sequences of the clones were confirmed by Sanger sequencing. Briefly, genomic DNA was first isolated, and PCR was performed to amplify the targeted regions using the following primers: 5′-TGCC GGA TCC CTG AGA GGG TAC AGG TTG CC-3′ (sense primer, BamHI site is underlined) and 5′-CACC GAA TTC CTA GCC TGA AAG GCC TGG TG-3′ (antisense primer, EcoRI site is underlined). The PCR products were subsequently cloned into a pMX vector for sequencing analysis. For comparison, the same regions in the parental line were also sequenced. The sequencing data for the control and the knockout cells were then analyzed using Benchling.
Immunocytochemistry. Cells were fixed with 4% paraformaldehyde in PBS at room temperature for 15 min and permeabilized with digitonin (50 µg/mL) in 3% BSA-PBS at room temperature for 5 min. Cells were then incubated with primary antibodies, then with secondary antibodies conjugated with Alexa fluorophore. In vitro assay of recombinant TBK1-dependent phosphorylation of STING. Cells were collected in an ice-cold buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1 mM EGTA, 2 mM DTT, 200 mM sucrose) containing protease inhibitors (25955-11, nacalai tesque), and phosphatase inhibitors (8 mM NaF, 12 mM β-glycerophosphate, 1 mM Na 3 VO 4 , 1.2 mM Na 2 MoO 4 , 5 µM cantharidin, and 2 mM imidazole), homogenized with 2 passages through a 27-gauge needle after 6 passages through a 23-gauge needle, and centrifuged at 3,000 × g for 5 min at 4 °C. The post-nuclear supernatant was overlaid on 10 µL of 2 M sucrose and centrifuged at 100,000 × g for 1 h at 4 °C. The membrane fractions were resuspended in a buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1 mM EGTA, 2 mM DTT, 200 mM sucrose, 20 mM MgCl 2 , protease inhibitors, and phosphatase inhibitors), and incubated with ATP (1 mM) and recombinant TBK1 (100 ng) at 37 °C for 30 min. The samples were then subjected to SDS-PAGE and phosphorylation of STING was detected by western blot.
Western blot. Proteins were separated in polyacrylamide gel and then transferred to polyvinylidene difluoride membranes (Millipore). These membranes were incubated with primary antibodies, followed by secondary antibodies conjugated to horseradish peroxidase. The proteins were visualized by enhanced chemiluminescence using a Fusion SOLO.7S.EDGE (Vilber-Lourmat).