title: Structural basis of RNA recognition and activation by innate immune receptor RIG-I.
abstract: Retinoic-acid-inducible gene-I (RIG-I; also known as DDX58) is a cytoplasmic pathogen recognition receptor that recognizes pathogen-associated molecular pattern (PAMP) motifs to differentiate between viral and cellular RNAs. RIG-I is activated by blunt-ended double-stranded (ds)RNA with or without a 5'-triphosphate (ppp), by single-stranded RNA marked by a 5'-ppp and by polyuridine sequences. Upon binding to such PAMP motifs, RIG-I initiates a signalling cascade that induces innate immune defences and inflammatory cytokines to establish an antiviral state. The RIG-I pathway is highly regulated and aberrant signalling leads to apoptosis, altered cell differentiation, inflammation, autoimmune diseases and cancer. The helicase and repressor domains (RD) of RIG-I recognize dsRNA and 5'-ppp RNA to activate the two amino-terminal caspase recruitment domains (CARDs) for signalling. Here, to understand the synergy between the helicase and the RD for RNA binding, and the contribution of ATP hydrolysis to RIG-I activation, we determined the structure of human RIG-I helicase-RD in complex with dsRNA and an ATP analogue. The helicase-RD organizes into a ring around dsRNA, capping one end, while contacting both strands using previously uncharacterized motifs to recognize dsRNA. Small-angle X-ray scattering, limited proteolysis and differential scanning fluorimetry indicate that RIG-I is in an extended and flexible conformation that compacts upon binding RNA. These results provide a detailed view of the role of helicase in dsRNA recognition, the synergy between the RD and the helicase for RNA binding and the organization of full-length RIG-I bound to dsRNA, and provide evidence of a conformational change upon RNA binding. The RIG-I helicase-RD structure is consistent with dsRNA translocation without unwinding and cooperative binding to RNA. The structure yields unprecedented insight into innate immunity and has a broader impact on other areas of biology, including RNA interference and DNA repair, which utilize homologous helicase domains within DICER and FANCM.
authors.affiliation: Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, 679 Hoes Lane West, Piscataway, New Jersey 08854, USA.
authors.forename: Fuguo
authors.initials: F
authors.lastname: Jiang
authors.forename: Anand
authors.initials: A
authors.lastname: Ramanathan
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Miller
authors.forename: Guo-Qing
authors.initials: GQ
authors.lastname: Tang
authors.forename: Michael
authors.initials: M
authors.lastname: Gale
authors.forename: Smita S
authors.initials: SS
authors.lastname: Patel
authors.forename: Joseph
authors.initials: J
authors.lastname: Marcotrigiano
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D000071457:DEAD Box Protein 58; D053487:DEAD-box RNA Helicases / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism*; D004789:Enzyme Activation; D005470:Fluorometry; D006801:Humans; D007113:Immunity, Innate / Q000276:immunology*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D018583:Pliability; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D059748:Proteolysis; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000276:immunology / Q000378:metabolism; D011971:Receptors, Immunologic; D053838:Scattering, Small Angle; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D014357:Trypsin / Q000378:metabolism; D014961:X-Ray Diffraction
chemical_list: D012330:RNA, Double-Stranded; D016601:RNA-Binding Proteins; D011971:Receptors, Immunologic; D000255:Adenosine Triphosphate; D014357:Trypsin; D000251:Adenosine Triphosphatases; C452820:RIGI protein, human; D000071457:DEAD Box Protein 58; D053487:DEAD-box RNA Helicases