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Infection-specific phosphorylation of glutamyl-prolyl tRNA synthetase induces antiviral immunity

Abstract

The mammalian cytoplasmic multi-tRNA synthetase complex (MSC) is a depot system that regulates non-translational cellular functions. Here we found that the MSC component glutamyl-prolyl-tRNA synthetase (EPRS) switched its function following viral infection and exhibited potent antiviral activity. Infection-specific phosphorylation of EPRS at Ser990 induced its dissociation from the MSC, after which it was guided to the antiviral signaling pathway, where it interacted with PCBP2, a negative regulator of mitochondrial antiviral signaling protein (MAVS) that is critical for antiviral immunity. This interaction blocked PCBP2-mediated ubiquitination of MAVS and ultimately suppressed viral replication. EPRS-haploid (Eprs+/−) mice showed enhanced viremia and inflammation and delayed viral clearance. This stimulus-inducible activation of MAVS by EPRS suggests an unexpected role for the MSC as a regulator of immune responses to viral infection.

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Figure 1: EPRS induces antiviral immune responses to RNA viruses.
Figure 2: EPRS is critical for antiviral defense against RNA viruses in mouse BMDMs.
Figure 3: EPRS is essential for antiviral immunity in mice.
Figure 4: Virus-induced phosphorylation of EPRS induces its release from the MSC.
Figure 5: EPRS interacts with PCBP2, a negative regulator of MAVS.
Figure 6: Domain mapping required for the interaction between EPRS and PCBP2.
Figure 7: EPRS blocks PCBP2-mediated ubiquitination and degradation of MAVS.
Figure 8: An EPRS-derived L1 peptide has antiviral activity.

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Acknowledgements

Supported by the KRIBB Initiative Program (KGM4541622 to M.H.K.), the National Research Foundation of Korea, funded by the Ministry of Science, ICT & Future Planning of Korea (NRF-2010-0029767 and 2014R1A2A1A01005971 to M.H.K.; NRF-M3A6A4-2010-0029785 to S.K.; and 2015020957 to J.-S.L.), the Korea Institute of Oriental Medicine (K12050 to J.-S.L.), the Ministry for Food, Agriculture, Forestry and Fisheries (315044031SB010 to J.-S.L.) and the Korea Health Industry Development Institute (HI14C3484 to C.L.).

Author information

Authors and Affiliations

Authors

Contributions

E.-Y.L. and H.-C.L. performed most of the experiments with help from H.-K.K., S.Y.J., J.H., J.-H.K. and T.-H.K. S.-J.P. and C.L. performed mass spectrometry. Y.-H.K. and C.-H.L. performed immunohistochemical analysis. J.H.K., S.-Y.K. and Y.-K.C. performed RNA-seq analysis. A.A., J.U.J., P.L.F. and S.K. contributed to the discussion and provided critical reagents. E.-Y.L., J.-S.L. and M.H.K. designed the study and wrote the manuscript. All of the authors helped with data analysis.

Corresponding authors

Correspondence to Jong-Soo Lee or Myung Hee Kim.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 EPRS expression in multiple cell lines upon viral infection.

(a,b) EPRS is slightly induced upon viral induction. qPCR of Eprs mRNA (a) and immunoblot analysis of corresponding endogenous EPRS expression (b) in multiple cell lines, including C57/B6 mouse-derived BMDM, U937, RAW264.7, A549, and 293T cells infected with PR8-GFP or VSV-GFP. (c) qPCR analysis of representative Isg mRNA expression under the same conditions as in (a). (d) qPCR analysis of Eprs mRNA in U937 and RAW264.7 cells treated with IFN-β (1000 units/ml). Isg15 mRNA was analyzed as a control. (e) qPCR analysis of Eprs mRNA in RIG-I-sufficient (Ddx58+/+) or RIG-I-deficient (Ddx58-/-) MEF cells infected with VSV-GFP. Data are representative of two (a-e) independent biological replicates with similar results (mean and s.d. of triplicate in a,c-e).

Supplementary Figure 2 Antiviral effects of EPRS in EPRS-deficient or EPRS-overexpressing immune cells.

(a) Immunoblot analysis of EPRS expression. (b) Viral titer after infection with HSV-GFP (MOI = 1). RAW264.7 cells were transfected with non-targeting control siRNA (siCtrl) or siEPRS (a,b). (c) Fluorescence microscopy images, (d) virus replication, and (e) secreted IFN-β or IL-6 levels in 293T cells transfected with siCtrl or siEPRS for 36 h, followed by infection with VSV-GFP (MOI = 0.0001). (f) Immunoblot analysis of EPRS expression. (g) Fluorescence microscopy images, (h) PR8 titer, and (i) secreted IFN-β or IL-6 level in cells infected with PR8-GFP (MOI = 1). (j) Fluorescence microscopy images, (k) VSV titer, and (l) secreted IFN-β or IL-6 level in stable EPRS-deficient cells infected with VSV-GFP (MOI = 0.5). RAW264.7 cells were transduced with non-targeting control shRNA (shCtrl) or EPRS shRNA (shEPRS), followed by selection with puromycin (f–l). (m) Immunoblot analysis of EPRS expression. (n) Fluorescence microscopy images, (o) VSV titers, and (p) secreted IFN-β or IL-6 level in EPRS-overexpressing cells infected with VSV-GFP (MOI = 0.5). RAW264.7 cells were transfected with a FLAG-tagged empty vector (Ctrl) or with EPRS-FLAG (EPRS) plasmids, followed by selection with puromycin (m–p). Scale bars, 100 μm (c,g,j,n). *P < 0.05, **P < 0.01, and ***P < 0.001 (Student’s t-test; d,e,h,i,k,l,o,p). Data are representative of three (a-p) independent biological replicates with similar results (mean and s.d. of triplicate in b,d,e,h,i,k,l,o,p).

Supplementary Figure 3 EPRS deficiency in mouse BMDMs reduces antiviral innate immune responses.

(a) Immunoblot analysis of EPRS expression in BMDMs. BMDMs were transfected with non-targeting control siRNA (siCtrl) or siEPRS for 36 h. (b) Plaque assay to determine virus titers and (c) ELISA to measure IFN-β and IL-6 levels at 12 and 24 h post-infection. BMDMs were infected with PR8-GFP (MOI = 3) or VSV-GFP (MOI = 5) (b,c). (d) IFN-β and IL-6 levels measured in the culture supernatants from BMDMs treated with 40 μg of Poly(I:C). (e) Induction of Ifnb mRNA or IFN-related antiviral genes in virus-infected cells. RAW264.7 cells were transfected with siCtrl or siEPRS for 36 h, followed by infection with PR8-GFP (MOI = 1) for 12 h. The graphs show the -fold induction of the indicated genes after normalization against Gapdh. (f) Viral titer (determined by plaque assay) and (g) secreted IFN-β or IL-6 levels in cell culture supernatants after infection with HSV-GFP. BMDMs from Eprs+/+ and Eprs+/ – mice were infected with HSV-GFP (MOI = 2) (f,g). *P < 0.05, **P < 0.01, and ***P < 0.001 (Student’s t-test; b–d). Data are representative of three (b-d) or two (e-g) independent biological replicates with similar results (mean and s.d. of triplicate in b-g).

Supplementary Figure 4 Dissociation of EPRS from the MSC upon viral infection.

(a,b) Viral infection induces dissociation of EPRS from the MSC component proteins. Lysates of RAW264.7 cells infected with PR8-GFP (MOI = 1) were subjected to immunoprecipitation with an anti-EPRS (a) or with an anti-KRS (b), followed by immunoblot analysis with anti-KRS, anti-MRS, anti-AIMP3, and anti-GAPDH (a), or with anti-EPRS and anti-AIMP3 (b), respectively. (c) Confocal microscopy of endogenous EPRS (red) and KRS (green) in HeLa cells infected with PR8 (MOI = 5) for 6 or 12 h. IFN-γ (1000 units/ml) treatment for 12 h was used for comparison. Cells were permeabilized with a lower dose of digitonin (20 μg/ml, 5 min) than used in Fig. 4b (25 μg/ml, 10 min). Scale bar, 10 μm (2 μm in magnified images). (d) Confocal microscopy of endogenous EPRS (red) and NSAP1 (green) in HeLa cells infected with PR8 (MOI = 5) for 6 or 12 h, or in cells treated with IFN-γ (1000 units/ml) for 12 h. Scale bar, 10 μm. Data are representative of three independent biological replicates with similar results (a-d).

Supplementary Figure 5 Identification of the viral-infection-specific phosphorylation site in EPRS.

(a) Silver-stained Strep-EPRS (indicated by an asterisk) purified by Strep precipitation assay of 293T cells infected or uninfected (–) with PR8-GFP (MOI = 5). EV, Strep-empty vector. (b) MS/MS spectra for a doubly charged EPRS peptide EYIPGQPPLSQSSDSpS*PTR (MH+ = 2125.93, z = 2+) obtained under uninfected (upper) and PR8-infected (lower panel) conditions. The peptides contain the S886 phosphorylation site (marked by an asterisk). (c–e) Extracted ion chromatogram (XIC) of the tryptic digests under uninfected (upper) and infected (lower panel) conditions, corresponding to doubly charged EYIPGQPPLSQSSDSSPTR (MH+ = 2044.96, z = 2+) (c), doubly charged NQGGGLSSSGAGEGQGPK (MH+ = 1586.72, z = 2+) (d), and triply charged KDPSKNQGGGLSSSGAGEGQGPK (MH+ = 2142.02, z = 3+) (e) peptides from non-phosphorylated (left) and phosphorylated (right, marked by an asterisk) EPRS. ND, not detected. (f) Immunoblot analysis of phosphomimetic (S990D) and phosphorylation-resistant (S990A) EPRS against with anti-phospho-EPRS(Ser990) in 293T cells. (g–j) Immunoblot analysis of EPRS Ser990 phosphorylation in RAW264.7 cells infected with PR8-GFP (MOI =1) (g), 293T cells infected with PR8-GFP (MOI = 5) (h) or VSV-GFP (MOI = 0.001) (i), or cells transfected with 2 μg of Poly(I:C) (j). (k,l) Secreted IFN-γ levels from U937 (k) or RAW264.7 (l) cells infected with PR8-GFP or VSV-GFP. Cells treated with IFN-γ (1000 units/ml) were used as a positive control. (m) Immunoblot analysis of Cp expression in PR8-GFP-infected RAW264.7 cells. Data are representative of three (g-m) independent biological replicates with similar results (mean and s.d. of triplicate in k,l).

Supplementary Figure 6 Non-translational role of EPRS in regulating antiviral immune responses.

(a,b) Purified His-tagged EPRS (aa 1–196) (a) or EPRS (aa 1–168) (b) was mixed with the GST-fused PCBP2 KH1 (aa 11-82). After His-tag precipitation, proteins were subjected to SDS-PAGE and stained with Coomassie Brilliant Blue. (c) The purified His-tagged ERS (aa 1-732) and its mutant that is inactive for tRNA glutamylation (MT). Black arrows denote protein fragments derived from ERS during purification (as in Fig. 6j). (d) Aminoacylation assay for ERS (WT) and its mutant (MT). CPM, counts per minute. Ctrl, buffer without protein. (e) IFNB promoter activity in 293T cells transfected with N-RIG-I plus empty vector (EV), Strep-EPRS (WT), or its mutants inactive for tRNA glutamylation only (E-MT), tRNA prolylation only (P-MT), or both (EP-MT). (f) Immunoblot analysis of endogenous EPRS, MAVS, and RIG-I expression in sgEPRS 293T cells or non-targeting control (sgCtrl) cells. (g–k) Non-translational function of EPRS in antiviral immune responses. Virus replication assay (examined by fluorescence microscopy) (g) and plaque assay (h) at 24 h post-infection with VSV-GFP (MOI = 0.0001). Immunoblot analysis of Strep-EPRS or endogenous EPRS expression (i). IFN-β (j) and IL-6 (k) secreted by sgEPRS cells infected with VSV-GFP. sgCtrl or sgEPRS 293T cells were reconstituted with EV, Strep-tagged EPRS (WT), or its catalytic mutant (EP-MT) (g–k). Scale bar, 100 μm (g). *P < 0.01; NS, not significant (Student’s t-test; d,e,h,j,k). Data are representative of two (a-k) independent experiments (mean and s.d. of triplicate in d,e,h,j,k).

Supplementary Figure 7 Infection-specific EPRS phosphorylation is essential for regulating MAVS.

(a,b) In vitro binding assay showing MAVS interaction with PCBP2 KH1 (aa 11–82). (c,d) The precipitation (ppt) assays revealed no interaction between PCBP2 and LRS in 293T cells (c), whereas PCBP2 interacted with MAVS (d). (e) Ubiquitination of exogenous MAVS in non-targeting control (siCtrl) or EPRS-deficient (siEPRS) 293T cells transfected with Ub, ITCH, MAVS, or PCBP2. (f) Ubiquitination of endogenous MAVS in 293T cells transfected with Ub, ITCH, PCBP2, and Strep-empty vector (EV), or with WT EPRS or its mutant (EP-MT, enzymatically inactive for both tRNA glutamylation and prolylation). (g) Expression of endogenous MAVS in 293T cells transfected with PCBP2 and WT EPRS or EP-MT. The histogram shows the intensity of the MAVS band normalized against actin. (h–n) Ubiquitination of endogenous MAVS (h) in non-targeting control (sgCtrl) or sgEPRS 293T cells transfected with HA-Ub and infected with VSV-GFP (MOI = 0.1). (i) Ubiquitination of endogenous MAVS in 293T cells transfected with HA-Ub and infected with VSV-GFP. (j) IFN-β or (k) IL-6 levels in supernatants from cells infected with VSV-GFP. (l) Fluorescence microscopy images and (m) plaque assay at 24 h post-infection with VSV-GFP (MOI = 0.0001). (n) Immunoblot analysis of EPRS-FLAG or endogenous EPRS. sgEPRS 293T cells were reconstituted with a FLAG-EV, WT EPRS, S990A, or S990D (i–n). Scale bar, 100 μm (l). *P < 0.01; NS, not significant (Student’s t-test; j,k,m). Data are representative of two (a-n) independent biological replicates with similar results (mean and s.d. of triplicate in j,k,m).

Supplementary Figure 8 The Tat-Epep is specific to infection with RNA viruses.

(a–c) Tat-Epep has no significant effect on virus replication (a) or IFN-β (b) and IL-6 (c) secretion in RAW264.7 infected with HSV-GFP (MOI = 1) for 12 h. HSV-GFP-infected RAW264.7 cells treated with PBS were used as negative controls. (d) Viability of RAW264.7 cells as measured in an MTS assay after treatment with the indicated doses of Tat-Epep for 12 h. (e) Viability of 293T cells after treatment with Tat-Epep for 12 or 24 h. Ctrl, 293T cells treated with a lytic detergent (digitonin, 30 μg/ml) for 15 min as a positive control. Results are expressed as the mean ± SD of two independent biological replicates incorporating triplicate samples.

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Lee, EY., Lee, HC., Kim, HK. et al. Infection-specific phosphorylation of glutamyl-prolyl tRNA synthetase induces antiviral immunity. Nat Immunol 17, 1252–1262 (2016). https://doi.org/10.1038/ni.3542

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