title: Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1.
abstract: Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3' acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein.
authors.affiliation: From the Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078 and.
authors.forename: Niyati
authors.initials: N
authors.lastname: Jain
authors.affiliation: From the Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078 and.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Morgan
authors.affiliation: Department of Pathology, Immunology, and Laboratory of Medicine, College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610-3633.
authors.forename: Brittany D
authors.initials: BD
authors.lastname: Rife
authors.affiliation: Department of Pathology, Immunology, and Laboratory of Medicine, College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610-3633.
authors.forename: Marco
authors.initials: M
authors.lastname: Salemi
authors.affiliation: From the Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078 and bst18@case.edu.
authors.forename: Blanton S
authors.initials: BS
authors.lastname: Tolbert
mesh_terms: D017398:Alternative Splicing; D000595:Amino Acid Sequence; D001483:Base Sequence; D004742:Enhancer Elements, Genetic; D020868:Gene Silencing; D015497:HIV-1 / Q000235:genetics*; D000076245:Heterogeneous Nuclear Ribonucleoprotein A1; D034481:Heterogeneous-Nuclear Ribonucleoprotein Group A-B / Q000235:genetics*; D006801:Humans; D007438:Introns; D009682:Magnetic Resonance Spectroscopy; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D010802:Phylogeny; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D020079:Terminal Repeat Sequences
chemical_list: D000076245:Heterogeneous Nuclear Ribonucleoprotein A1; D034481:Heterogeneous-Nuclear Ribonucleoprotein Group A-B; C000619656:hnRNPA1 protein, human; D012313:RNA
keywords: alternative splicing; calorimetry; heterogeneous nuclear ribonucleoprotein (hnRNP); human immunodeficiency virus (HIV); nuclear magnetic resonance (NMR); phylogenetics