Human IFIT3 Modulates IFIT1 RNA Binding Specificity and Protein Stability

• Published in: Immunity (Cambridge, Mass.) Mass.), 2018-03, Vol.48 (3), p.487-499.e5
• Main Authors: Johnson, Britney, VanBlargan, Laura A., Xu, Wei, White, James P., Shan, Chao, Shi, Pei-Yong, Zhang, Rong, Adhikari, Jagat, Gross, Michael L., Leung, Daisy W., Diamond, Michael S., Amarasinghe, Gaya K.
• Format: Article
• Language: English
• Subjects: Adaptor Proteins, Signal Transducing; Animals; antiviral; Antiviral drugs; BASIC BIOLOGICAL SCIENCES; Binding; Carrier Proteins - chemistry; Carrier Proteins - genetics; Carrier Proteins - metabolism; Crystal structure; crystallography; flavivirus; Gene Expression Regulation; Genes; host defense; Host-Pathogen Interactions - genetics; Humans; Infections; Influenza; innate immunity; Interferon; interferon stimulated genes; Intracellular Signaling Peptides and Proteins - chemistry; Intracellular Signaling Peptides and Proteins - genetics; Intracellular Signaling Peptides and Proteins - metabolism; Methylation; Mice; Models, Molecular; Molecular Conformation; Orthomyxoviridae; pathogen associated molecular patterns; Protein Binding; Protein Interaction Domains and Motifs; Protein Stability; Proteins; Regulatory mechanisms (biology); Ribonucleic acid; RNA; RNA - chemistry; RNA - genetics; RNA - metabolism; RNA viruses; RNA-binding protein; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; self/non-self RNA recognition; Species Specificity; Structure-Activity Relationship; Viral infections; Viruses; X-ray; Zika virus
• ISSN: 1074-7613; 1097-4180
• DOI: 10.1016/j.immuni.2018.01.014

Although interferon-induced proteins with tetratricopeptide repeats (IFIT proteins) inhibit infection of many viruses by recognizing their RNA, the regulatory mechanisms involved remain unclear. Here we report a crystal structure of cap 0 (m7GpppN) RNA bound to human IFIT1 in complex with the C-terminal domain of human IFIT3. Structural, biochemical, and genetic studies suggest that IFIT3 binding to IFIT1 has dual regulatory functions: (1) extending the half-life of IFIT1 and thereby increasing its steady-state amounts in cells; and (2) allosterically regulating the IFIT1 RNA-binding channel, thereby enhancing the specificity of recognition for cap 0 but not cap 1 (m7GpppNm) or 5′-ppp RNA. Mouse Ifit3 lacks this key C-terminal domain and does not bind mouse Ifit1. The IFIT3 interaction with IFIT1 is important for restricting infection of viruses lacking 2′-O methylation in their RNA cap structures. Our experiments establish differences in the regulation of IFIT1 orthologs and define targets for modulation of human IFIT protein activity. [Display omitted] •A 2.55 Å X-ray crystal structure of cap 0 RNA-bound human IFIT1-IFIT3CTD is presented•Human IFIT3CTD binding to IFIT1 facilitates IFIT1 binding to cap 0 RNA•Human IFIT3 binding to IFIT1 stabilizes expression of IFIT1 in cells•Human IFIT1 inhibition of viruses lacking 2′-O methylation requires IFIT3 Prior studies have suggested that human IFIT1, unlike its mouse ortholog, might not recognize viral RNA molecules lacking 2′-O methylation on their cap structures. Johnson et al. report a crystal structure between cap 0 (m7GpppN) RNA bound to human IFIT1 in complex with the C-terminal domain (CTD) of human IFIT3. The CTD of IFIT3 bound to IFIT1 and allosterically regulated the IFIT1 RNA-binding channel and promoted selective recognition of cap 0 RNA. Functional studies demonstrated that IFIT3 interaction with IFIT1 was important for stabilizing IFIT1 expression and was required for restricting infection of viruses lacking 2′-O methylation in their RNA cap structures