title: Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2'-O methylations.
abstract: IFIT1 (IFN-induced protein with tetratricopeptide repeats-1) is an effector of the host innate immune antiviral response that prevents propagation of virus infection by selectively inhibiting translation of viral mRNA. It relies on its ability to compete with the translation initiation factor eIF4F to specifically recognize foreign capped mRNAs, while remaining inactive against host mRNAs marked by ribose 2'-O methylation at the first cap-proximal nucleotide (N1). We report here several crystal structures of RNA-bound human IFIT1, including a 1.6-Å complex with capped RNA. IFIT1 forms a water-filled, positively charged RNA-binding tunnel with a separate hydrophobic extension that unexpectedly engages the cap in multiple conformations (synandanti) giving rise to a relatively plastic and nonspecific mode of binding, in stark contrast to eIF4E. Cap-proximal nucleotides encircled by the tunnel provide affinity to compete with eIF4F while allowing IFIT1 to select against N1 methylated mRNA. Gel-shift binding assays confirm that N1 methylation interferes with IFIT1 binding, but in an RNA-dependent manner, whereas translation assays reveal that N1 methylation alone is not sufficient to prevent mRNA recognition at high IFIT1 concentrations. Structural and functional analysis show that 2'-O methylation at N2, another abundant mRNA modification, is also detrimental for RNA binding, thus revealing a potentially synergistic role for it in self- versus nonself-mRNA discernment. Finally, structure-guided mutational analysis confirms the importance of RNA binding for IFIT1 restriction of a human coronavirus mutant lacking viral N1 methylation. Our structural and biochemical analysis sheds new light on the molecular basis for IFIT1 translational inhibition of capped viral RNA.
authors.affiliation: Department of Biochemistry and Groupe de Recherche Axe sur la Structure des Proteines, McGill University, Montreal, QC, Canada H3G 0B1.
authors.forename: Yazan M
authors.identifier: 0000-0001-5625-1034
authors.initials: YM
authors.lastname: Abbas
authors.affiliation: Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, 82152 Martinsried/Munich, Germany.
authors.forename: Beatrice Theres
authors.initials: BT
authors.lastname: Laudenbach
authors.affiliation: Department of Chemistry, McGill University, Montreal, QC, Canada H3A 0B8.
authors.forename: Saúl
authors.initials: S
authors.lastname: Martínez-Montero
authors.affiliation: Department of Biochemistry, McGill University, Montreal, QC, Canada H3G 1Y6.
authors.forename: Regina
authors.initials: R
authors.lastname: Cencic
authors.affiliation: Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, 82152 Martinsried/Munich, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Habjan
authors.affiliation: Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, 82152 Martinsried/Munich, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Pichlmair
authors.affiliation: Department of Chemistry, McGill University, Montreal, QC, Canada H3A 0B8.
authors.forename: Masad J
authors.initials: MJ
authors.lastname: Damha
authors.affiliation: Department of Biochemistry, McGill University, Montreal, QC, Canada H3G 1Y6.|The Rosalind and Morris Goodman Cancer Research Center, Montreal, QC, Canada H3A 1A3.|Department of Oncology, McGill University, Montreal, QC, Canada H3G 1Y6.
authors.forename: Jerry
authors.initials: J
authors.lastname: Pelletier
authors.affiliation: Department of Biochemistry and Groupe de Recherche Axe sur la Structure des Proteines, McGill University, Montreal, QC, Canada H3G 0B1; bhushan.nagar@mcgill.ca.
authors.forename: Bhushan
authors.initials: B
authors.lastname: Nagar
mesh_terms: D048868:Adaptor Proteins, Signal Transducing; D020816:Amino Acid Motifs; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008745:Methylation; D051379:Mice; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D056510:Position-Specific Scoring Matrices; D011485:Protein Binding; D014176:Protein Biosynthesis; D012315:RNA Caps / Q000737:chemistry*; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D013329:Structure-Activity Relationship
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D002352:Carrier Proteins; C484290:IFIT1 protein, human; D012315:RNA Caps; D012333:RNA, Messenger; D012367:RNA, Viral; D016601:RNA-Binding Proteins
keywords: 2′-O methylation; IFIT1 crystal structure; innate immunity; mRNA cap recognition; self vs. nonself