title: Global RNA structure analysis of poliovirus identifies a conserved RNA structure involved in viral replication and infectivity.
abstract: The genomes of RNA viruses often contain RNA structures that are crucial for translation and RNA replication and may play additional, uncharacterized roles during the viral replication cycle. For the picornavirus family member poliovirus, a number of functional RNA structures have been identified, but much of its genome, especially the open reading frame, has remained uncharacterized. We have now generated a global RNA structure map of the poliovirus genome using a chemical probing approach that interrogates RNA structure with single-nucleotide resolution. In combination with orthogonal evolutionary analyses, we uncover several conserved RNA structures in the open reading frame of the viral genome. To validate the ability of our global analyses to identify functionally important RNA structures, we further characterized one of the newly identified structures, located in the region encoding the RNA-dependent RNA polymerase, 3D(pol), by site-directed mutagenesis. Our results reveal that the structure is required for viral replication and infectivity, since synonymous mutants are defective in these processes. Furthermore, these defects can be partially suppressed by mutations in the viral protein 3C(pro), which suggests the existence of a novel functional interaction between an RNA structure in the 3D(pol)-coding region and the viral protein(s) 3C(pro) and/or its precursor 3CD(pro).
authors: Tetrad Graduate Program, University of California, San Francisco, California, USA.
authors: Cecily P
authors: CP
authors: Burrill
authors: Oscar
authors: O
authors: Westesson
authors: Michael B
authors: MB
authors: Schulte
authors: Vanessa R
authors: VR
authors: Strings
authors: Mark
authors: M
authors: Segal
authors: Raul
authors: R
authors: Andino
mesh_terms: D000086042:3C Viral Proteases; D003546:Cysteine Endopeptidases / Q000235:genetics; D004252:DNA Mutational Analysis; D015684:Gene Products, pol; D006367:HeLa Cells; D006801:Humans; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D017354:Point Mutation; D017955:Poliovirus / Q000737:chemistry* / Q000235:genetics / Q000502:physiology*; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics; D014779:Virus Replication
chemical_list: D015684:Gene Products, pol; D012367:RNA, Viral; D014764:Viral Proteins; C090443:polymerase 3Dpol, poliovirus; D012324:RNA-Dependent RNA Polymerase; D003546:Cysteine Endopeptidases; D000086042:3C Viral Proteases
references: EMBO J. 1996 Oct 1;15(19):5428-36
references: 8895586
references: EMBO J. 1993 Sep;12(9):3587-98
references: 8253083
references: J Virol. 2004 Apr;78(7):3378-86
references: 15016860
references: PLoS One. 2012;7(6):e36898
references: 22693624
references: J Virol. 2000 Mar;74(5):2219-26
references: 10666252
references: Curr Protoc Microbiol. 2013;Chapter 15:Unit 15H.1
references: 23686830
references: Cell. 1990 Oct 19;63(2):369-80
references: 2170027
references: J Virol. 2000 May;74(10):4590-600
references: 10775595
references: Science. 2008 Jun 27;320(5884):1784-7
references: 18583614
references: Biochemistry. 2013 May 7;52(18):3182-90
references: 23614526
references: RNA. 2003 Jan;9(1):124-37
references: 12554882
references: Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14301-7
references: 22886087
references: PLoS Pathog. 2010 Jun 03;6(6):e1000936
references: 20532207
references: Pathol Microbiol (Basel). 1974;41(3-4):143-50
references: 4374677
references: PLoS Pathog. 2013;9(4):e1003294
references: 23593004
references: RNA. 2009 Jul;15(7):1314-21
references: 19458034
references: J Virol. 2000 Jul;74(14):6394-400
references: 10864650
references: Nat Protoc. 2006;1(3):1610-6
references: 17406453
references: Methods Enzymol. 2009;468:67-89
references: 20946765
references: Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92
references: 15123812
references: PLoS One. 2009 Oct 22;4(10):e7468
references: 19847293
references: J Virol. 2006 Apr;80(7):3259-72
references: 16537593
references: Bull Math Biol. 2009 Oct;71(7):1671-92
references: 19459014
references: RNA. 2008 Jun;14(6):1026-36
references: 18426919
references: J Virol. 2007 Jun;81(11):5561-72
references: 17344297
references: Mol Cell Biol. 1988 Mar;8(3):1103-12
references: 2835660
references: Cell. 1986 Jun 6;45(5):761-70
references: 3011278
references: Annu Rev Microbiol. 2005;59:587-635
references: 16153180
references: Acc Chem Res. 2011 Dec 20;44(12):1280-91
references: 21615079
references: Genes Dev. 1998 Aug 1;12(15):2293-304
references: 9694795
references: Methods. 2010 Oct;52(2):150-8
references: 20554050
references: J Virol. 2006 Oct;80(19):9687-96
references: 16973573
references: Science. 1988 Jul 22;241(4864):445-8
references: 2839901
references: Science. 1985 Sep 27;229(4720):1358-65
references: 2994218
references: Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19248-53
references: 20974908
references: PLoS Biol. 2008 Apr 29;6(4):e96
references: 18447581
references: RNA Biol. 2008 Oct-Dec;5(4):263-72
references: 19088502
references: J Am Chem Soc. 2011 Dec 21;133(50):20326-34
references: 22126209
references: J Biol Chem. 2002 Aug 30;277(35):31551-62
references: 12077141
references: Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):97-102
references: 19109441
references: J Virol. 2000 Nov;74(22):10359-70
references: 11044080
references: Proteins. 1996 May;25(1):120-9
references: 8727324
references: J Virol. 2009 Oct;83(19):9957-69
references: 19605476
references: J Virol. 2003 May;77(9):5152-66
references: 12692218
references: J Virol. 2010 Jan;84(2):898-906
references: 19889760
references: RNA. 2008 Oct;14(10):1979-90
references: 18772246
references: J Virol. 2009 Oct;83(19):10129-39
references: 19625405
references: J Virol. 1991 Feb;65(2):913-21
references: 1846205
references: J Virol. 2000 Nov;74(22):10371-80
references: 11044081
references: EMBO J. 2001 Mar 1;20(5):1153-63
references: 11230138
references: J Mol Biol. 2011 Sep 30;412(4):737-50
references: 21839092
references: EMBO J. 2001 Mar 15;20(6):1439-48
references: 11250909
references: Cell Host Microbe. 2012 Nov 15;12(5):623-32
references: 23159052
references: Nature. 2009 Aug 6;460(7256):711-6
references: 19661910
references: Mol Biol Int. 2012;2012:530754
references: 22685659