The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity
Adam Hage,
Preeti Bharaj,
Sarah van Tol,
Maria I. Giraldo,
Maria Gonzalez-Orozco,
Karl M. Valerdi,
Abbey N. Warren,
Leopoldo Aguilera-Aguirre,
Xuping Xie,
Steven G. Widen,
Hong M. Moulton,
Benhur Lee,
Jeffrey R. Johnson,
Nevan J. Krogan,
Adolfo García-Sastre,
Pei-Yong Shi,
Alexander N. Freiberg,
Ricardo Rajsbaum
Affiliations
Adam Hage
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
Preeti Bharaj
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
Sarah van Tol
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
Maria I. Giraldo
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
Maria Gonzalez-Orozco
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
Karl M. Valerdi
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
Abbey N. Warren
Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
Leopoldo Aguilera-Aguirre
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
Xuping Xie
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
Steven G. Widen
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
Hong M. Moulton
Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA
Benhur Lee
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Jeffrey R. Johnson
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Nevan J. Krogan
Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), University of California at San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158, USA
Adolfo García-Sastre
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Pei-Yong Shi
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
Alexander N. Freiberg
Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA; Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
Ricardo Rajsbaum
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA; Corresponding author
Summary: Type I interferons (IFN-I) are essential to establish antiviral innate immunity. Unanchored (or free) polyubiquitin (poly-Ub) has been shown to regulate IFN-I responses. However, few unanchored poly-Ub interactors are known. To identify factors regulated by unanchored poly-Ub in a physiological setting, we developed an approach to isolate unanchored poly-Ub from lung tissue. We identified the RNA helicase DHX16 as a potential pattern recognition receptor (PRR). Silencing of DHX16 in cells and in vivo diminished IFN-I responses against influenza virus. These effects extended to members of other virus families, including Zika and SARS-CoV-2. DHX16-dependent IFN-I production requires RIG-I and unanchored K48-poly-Ub synthesized by the E3-Ub ligase TRIM6. DHX16 recognizes a signal in influenza RNA segments that undergo splicing and requires its RNA helicase motif for direct, high-affinity interactions with specific viral RNAs. Our study establishes DHX16 as a PRR that partners with RIG-I for optimal activation of antiviral immunity requiring unanchored poly-Ub.
