The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition
Recognition of foreign RNA is critical for the innate immune response to viruses. Interferon (IFN)-induced proteins with tetratricopeptide repeats (IFIT) 2 and 3 are highly upregulated following viral infection, but mechanistic insight into their antiviral role is lacking. Here we demonstrate that short 5' untranslated regions (UTRs), a characteristic of many viral mRNAs, can serve as a molecular pattern for innate immune recognition via IFIT2 and IFIT3. Structure determination of the IFIT2-IFIT3 complex at 3.2 Å using cryo-EM reveals a domain-swapped heterodimer that is required for recognition of the viral mRNA 5' end, translation inhibition and antiviral activity. Critically, viral or host 5' UTR lengths less than 50 nucleotides are necessary and sufficient to enable translation inhibition by the IFIT2-IFIT3 complex. Accordingly, diverse viruses whose mRNAs contain short 5' UTRs, such as vesicular stomatitis virus and parainfluenza virus 3, are sensitive to IFIT2-IFIT3-mediated antiviral activity. Our work thus reveals a pattern of antiviral nucleic acid immune recognition that takes advantage of the inherent constraints on viral genome size.
Authors
- Elena Estrada
- B. Cook (ORCID: https://orcid.org/0000-0002-5777-3464)
- Kevin D. Corbett (ORCID: https://orcid.org/0000-0001-5854-2388)
- Eric L. Van Nostrand (ORCID: https://orcid.org/0000-0002-5188-0082)
- Jaxon D. Wagner (ORCID: https://orcid.org/0000-0001-7286-5220)
- Kaori M. Ego
- James Brett Case (ORCID: https://orcid.org/0000-0001-7331-5511)
- Candace Todd
- Brian A. Yee (ORCID: https://orcid.org/0000-0001-5615-8550)
- Dustin R. Glasner (ORCID: https://orcid.org/0000-0001-9821-6683)
- Shivani Khosla (ORCID: https://orcid.org/0000-0003-1788-3930)
- Mason Bartels (ORCID: https://orcid.org/0000-0001-7642-959X)
- Mark A. Herzik (ORCID: https://orcid.org/0000-0001-6653-6682)
- Michael Diamond (ORCID: https://orcid.org/0000-0002-8791-3165)
- Benhur Lee (ORCID: https://orcid.org/0000-0003-0760-1709)
- Matthew D. Daugherty (ORCID: https://orcid.org/0000-0002-4879-9603)
- Kathryn S. Hatch (ORCID: https://orcid.org/0000-0002-8629-0939)
- G Yeo
- Sarah R. Holland
- Qishan Liang (ORCID: https://orcid.org/0000-0003-4351-3140)
- Agustina D’Urso
- Chuan-Tien Hung (ORCID: https://orcid.org/0000-0001-6899-1312)
- Pierce Ford (ORCID: https://orcid.org/0000-0002-6492-593X)
- Jordan Prych
Institutions
- Baylor College of Medicine (US)
- Washington University in St. Louis (US)
- University of California San Diego (US)
- Stem Cell Institute (PA)
- Icahn School of Medicine at Mount Sinai (US)
Publication Details
- Journal
- Nature Microbiology
- Published
- 2025-10-15
- DOI
- https://doi.org/10.1038/s41564-025-02138-w
- Citations
- 2
- Primary Topic
- interferon and immune responses
- Type
- article
- Field-Weighted Citation Impact
- 1.59
Funders
- U.S. Department of Defense
- Yale University
- National Institutes of Health
- Defense Advanced Research Projects Agency