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

doi:10.1016/j.celrep.2022.110434

The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity

Cell Rep. 2022 Mar 8;38(10):110434. doi: 10.1016/j.celrep.2022.110434.

Authors

Adam Hage¹, Preeti Bharaj¹, Sarah van Tol¹, Maria I Giraldo¹, Maria Gonzalez-Orozco¹, Karl M Valerdi¹, Abbey N Warren², Leopoldo Aguilera-Aguirre¹, Xuping Xie³, Steven G Widen³, Hong M Moulton⁴, Benhur Lee⁵, Jeffrey R Johnson⁵, Nevan J Krogan⁶, Adolfo García-Sastre⁷, Pei-Yong Shi⁸, Alexander N Freiberg⁹, Ricardo Rajsbaum¹⁰

Affiliations

¹ Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
² Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.
³ Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
⁴ Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA.
⁵ Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁶ 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.
⁷ 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.
⁸ 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.
⁹ 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.
¹⁰ 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. Electronic address: rirajsba@utmb.edu.

Abstract

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.

Keywords: DHX16; RIG-I; SARS-CoV-2; TRIM6; influenza A virus; innate immunity; splicing; tripartite motif (TRIM) protein; type I interferon; unanchored ubiquitin.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

COVID-19
DEAD Box Protein 58* / immunology
Humans
Immunity, Innate
Interferon Type I* / immunology
RNA Helicases* / immunology
RNA, Viral*
Receptors, Immunologic* / immunology
SARS-CoV-2
Tripartite Motif Proteins
Zika Virus Infection* / immunology
Zika Virus* / genetics

Substances

Interferon Type I
RNA, Viral
Receptors, Immunologic
Tripartite Motif Proteins
DHX16 protein, human
RIGI protein, human
DEAD Box Protein 58
RNA Helicases

Abstract

Publication types

MeSH terms

Substances

Grants and funding