DDX1, DDX21, and DHX36 helicases form a complex with the adaptor molecule TRIF to sense dsRNA in dendritic cells

Abstract

The innate immune system detects viral infection predominantly by sensing viral nucleic acids. We report the identification of a viral sensor, consisting of RNA helicases DDX1, DDX21, and DHX36, and the adaptor molecule TRIF, by isolation and sequencing of poly I:C-binding proteins in myeloid dendritic cells (mDCs). Knockdown of each helicase or TRIF by shRNA blocked the ability of mDCs to mount type I interferon (IFN) and cytokine responses to poly I:C, influenza A virus, and reovirus. Although DDX1 bound poly I:C via its Helicase A domain, DHX36 and DDX21 bound the TIR domain of TRIF via their HA2-DUF and PRK domains, respectively. This sensor was localized within the cytosol, independent of the endosomes. Thus, the DDX1-DDX21-DHX36 complex represents a dsRNA sensor that uses the TRIF pathway to activate type I IFN responses in the cytosol of mDCs.

Copyright © 2011 Elsevier Inc. All rights reserved.

Figures

Figure 1. Characterization of poly I:C-Binding Proteins in mDCs

(A) Silver staining of poly I:C-biotin-associated proteins purified with NA-beads from D2SC cells without stimulation (N-STM) or stimulated with poly I:C, biotin-poly I:C, biotin, biotin-poly A:U, or poly A:U. Proteins identified by LC-mass spectrometry are indicated. (B) Immunoblot analysis showing the knockdown efficiency of indicated proteins in D2SC cells without treatment (D2SC, first lane), treated with scrambled shRNA (control, second lane), or treated with shRNA for targeting protein (third lane and fourth lane). β-Actin blots are shown as loading controls (lower panel). (C and D) ELISA of type I IFN production by D2SC with the indicated shRNA after 16 hr stimulation with short poly I:C delivered by Lipofectamine 2000 or short poly I:C directly (C), or long poly I:C delivered by Lipofectamine 2000 or long poly I:C directly (D). N-STM, D2SC treated with scrambled shRNA without stimulation. Individual diamond represents the value from each independent experiment. Error bars represent the average value from at least three independent experiments. (E) L929 cells were transfected with 100 ng of the IFN-β promoter luciferase reporter vector (Luc) together with indicated expression vectors to a total of 500 ng of various expression vectors or empty vector. Renilla-luciferase reporter gene (2 ng) was transfected simultaneously for the internal control. Cells were no-stimulated (N), stimulated with 1 μg/ml of short poly I:C (S), or long poly I:C (L) delivered with Lipofectamine 2000. Data represent the mean ± SD of triplicate or quadruplicate measurements. The data shown represent at least three independent experiments. (F and G) ELISA of IFN-β and TNF-α production by DCs with the indicated shRNA upon 16 hr stimulation with flu A (F) or reovirus (G) at a multiplicity of infection (MOI) = 10. N-STM, D2SC treated with scrambled shRNA without stimulation. Individual diamond represents the value from each independent experiment. Error bars represent the average value from at least three independent experiments.

Figure 2. The Helicase A Domain of DDX1 Binds Poly I:C

(A) Pull-down assays were performed by incubating purified HA-DDX1, HA-DHX36, or HA-DDX21 with poly I:C-biotin-NA beads. Bound proteins were analyzed by immunoblotting with anti-HA. (B) The mixture of HA-DDX1 and poly I:C-biotin-NA beads were incubated without polynucleotides or with polynucleotides at 0.5, 5, or 50 μg/ml concentration. Bound proteins were analyzed by immunoblotting with anti-HA. (C) Schematic representations of DDX1 and its serial deletion mutants: (a) DDX1 full size, (b) DDX1 dSPRY, (c) DDX1 dDEAD, (d) DDX1 nDEAD, (e) DDX1 nHELICa, (f) DDX1 cHELICc, and (g) DDX1 SPY. Helicase A, Helicase ATP-binding domain; DEAD, Asp-Glu-Ala-Asp box motif; SPRY, SPla and the RYanodine domain; and Helic C, helicase C-terminal domain. Numbers denote amino acid residues. Truncated HA fusions were purified (middle panel) and individually incubated with poly I:C-biotin along with NA beads. Bound proteins were analyzed by immunoblotting with anti-HA (lower panel). (D) Immunoblot of endogenous DDX1, recombinant HA-DDX1a and HA-DDX1g in D2SC with the indicated antibodies. D2SC treated with scrambled shRNA (control) or with shRNA targeting DDX1 (sh-DDX1). The sh-DDX1 cells were then transfected with HA-DDX1a (sh-X1+HA-X1a) or HA-DDX1g (sh-X1+HA-X1g) expression plasmids. (E) ELISA of IFN-β production by indicated cells stimulated with short or long poly I:C delivered with Lipofectamine 2000 for 16 hr. Individual diamond represents the value from each independent experiment. Error bars represent the average value from at least three independent experiments.

Figure 3. Interactions among DDX1, DDX21, DHX36, and TRIF

(A) HA-DDX1, HA-DHX36, or HA-DDX21 protein was incubated with Myc-DDX1, Myc-DDX21 or Myc-TRIF, then incubated with anti-Myc beads. Bound proteins were analyzed by immunoblotting with anti-HA. (B) Schematic representations of TRIF and its serial truncations (top panel): (a) TRIF full size, (b) TRIF N terminal, (c) TRIF N terminal plus TIR domain, and (d) TRIF C-terminal TIR domain: the Toll and interleukin-1 receptor homology domain. Numbers denote amino acid residues. HEK293T cells were transfected with HA-tagged TRIF full size or truncation expression plasmids. Proteins were purified with anti-HA beads. TRIF truncations were individually incubated with full-size Myc-DDX21 or Myc-DHX36. After incubation with anti-Myc beads, the bound proteins were analyzed by immunoblotting with anti-HA. (C) DDX1 truncations, as illustrated in Figure 2C, were individually incubated with Myc-DDX21. Bound proteins were analyzed by immunoblotting with anti-HA (lower panel). (D) Schematic representations of DHX36 and its serial truncations (top panel): (a) DHX36 full size, (b) DHX36 dCOG, (c) DHX36 dHELICc, (d) DHX36 dHA2, and (e) DHX36 dDUF. PRK, ATP-dependent RNA helicase RhlB; GUCT, GUCT domain; COG, CRISPR-associated helicase Cas3; HA2, Helicase-associated domain; and DUF, domain of unknown function. DHX36 truncations were individually incubated with the full-size Myc-DDX21 or Myc-TRIF. After incubation with anti-Myc beads, the bound proteins were analyzed by immunoblotting with anti-HA. (E) Schematic representations of DDX21 and its serial truncations (top panel): (a) DDX21 full size, (b) DDX21 dDEAD, (c) DDX21 cHELICc, (d) DDX21 dGUCT, and (e) DDX21 dHELICc. DDX21 truncations were individually incubated with full-size Myc-DDX1, DHX36, DDX21 itself, or TRIF. After incubation with anti-Myc beads, the bound proteins were analyzed by immunoblotting with anti-HA.

Figure 4. Identification of the DDX1-DDX21-DHX36-TRIF Complex in Cells

(A) Whole-cell lysates from D2SC cells, with or without poly I:C stimulation, were incubated with the indicated antibodies and protein G beads. Bound proteins were analyzed by immunoblotting with the indicated antibodies. (B) D2SC cells were incubated with bio-poly I:C for 10, 20, or 30 min. Whole-cell lysates from the treated D2SC cells were prepared and subjected to purification with NA-beads. The proteins bound to bio-poly I:C were detected with indicated antibodies. (C) HEK293T cells were cotransfected with indicated expression vectors. Cells were stained with Myc or HA antibodies. (D) HEK293T cells were cotransfected with indicated expression vectors. Twenty-four hours later, cells were stimulated with poly I:C or Alexafluor 488 labeled poly I:C for 4 hr, then stained with Myc antibody or HA antibody. MitoTracker was used to probe the mitochondrion. DAP1 served as the nuclei marker.

Figure 5. DDX1, DDX21, DHX36, or TRIF Knockdown Prevents IκBα Degradation and IRF3 Translocation

Immunoblot (IB) of IκBα (A) and IRF3 (B and C) from protein extracts of D2SC cells treated with indicated shRNA upon stimulation with short poly I:C delivered with Lipofectamine 2000 for indicated time. Scrambled shRNA-treated D2SC cells served as the control. CE, cytoplasmic protein extracts; NE, nuclear protein extracts.

Figure 6. DDX1, DDX21, or DHX36 Knockdown in Bone Marrow Derived DCs Abolishes their Cytokine Responses to poly I:C

(A) Immunoblot (IB) showing the knockdown efficiency of siRNA targeting the indicated genes in BMDCs. Non-targeting siRNA served as a control (first left lane). GAPDH blots are shown as loading controls (lower panel). (B) ELISA of type I IFN production by DCs with the indicated siRNA after 16 hr stimulation with short or long poly I:C delivered by Lipofectamine 2000. N-STM, DCs treated with scrambled siRNA without stimulation. Individual diamond represents the value from each independent experiment. Error bars represent the average value from at least three independent experiments.

Figure 7. The Relationship of DDX1-DDX21-DHX36-TRIF Pathway to TLR3, MyD88, and IPS-1 Pathways

(A–E) BMDCs were prepared from wild-type or indicated knockout mice. ELISA of type I IFN production by DCs stimulated with short poly I:C delivered by Lipofectamine 2000 (A), short poly I:C directly (B), long poly I:C delivered by Lipofectamine 2000 (C), long poly I:C directly (D), or Flu A at a MOI of 10 (E). N-STM, DCs without stimulation. Individual diamond represents the value from each independent experiment. Error bars represent the average value from at least three independent experiments. (F) Whole-cell lysates from D2SC cells, with or without poly I:C stimulation, were incubated with anti-TRIF and Protein G beads. Bound proteins were analyzed by immunoblotting with the indicated antibodies.