title: Bioinformatic and physical characterizations of genome-scale ordered RNA structure in mammalian RNA viruses.
abstract: By the analysis of thermodynamic RNA secondary structure predictions, we previously obtained evidence for evolutionarily conserved large-scale ordering of RNA virus genomes (P. Simmonds, A. Tuplin, and D. J. Evans, RNA 10:1337-1351, 2004). Genome-scale ordered RNA structure (GORS) was widely distributed in many animal and plant viruses, much greater in extent than RNA structures required for viral translation or replication, but in mammalian viruses was associated with host persistence. To substantiate the existence of large-scale RNA structure differences between viruses, a large set of alignments of mammalian RNA viruses and rRNA sequences as controls were examined by thermodynamic methods (to calculate minimum free energy differences) and by algorithmically independent RNAz and Pfold methods. These methods produced generally concordant results and identified substantial differences in the degrees of evolutionarily conserved, sequence order-dependent RNA secondary structure between virus genera and groups. A probe hybridization accessibility assay was used to investigate the physical nature of GORS. Transcripts of hepatitis C virus (HCV), hepatitis G virus/GB virus-C (HGV/GBV-C), and murine norovirus, which are predicted to be structured, were largely inaccessible to hybridization in solution, in contrast to the almost universal binding of probes to a range of unstructured virus transcripts irrespective of G+C content. Using atomic force microscopy, HCV and HGV/GBV-C RNA was visualized as tightly compacted prolate spheroids, while under the same experimental conditions the predicted unstructured poliovirus and rubella virus RNA were pleomorphic and had extensively single-stranded RNA on deposition. Bioinformatic and physical characterization methods both identified fundamental differences in the configurations of viral genomic RNA that may modify their interactions with host cell defenses and their ability to persist.
authors.affiliation: Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom.
authors.forename: Matthew
authors.initials: M
authors.lastname: Davis
authors.forename: Selena M
authors.initials: SM
authors.lastname: Sagan
authors.forename: John P
authors.initials: JP
authors.lastname: Pezacki
authors.forename: David J
authors.initials: DJ
authors.lastname: Evans
authors.forename: Peter
authors.initials: P
authors.lastname: Simmonds
mesh_terms: D019295:Computational Biology; D029407:GB virus C / Q000235:genetics; D016679:Genome, Viral; D016174:Hepacivirus / Q000235:genetics; D018625:Microscopy, Atomic Force; D029322:Norovirus / Q000235:genetics; D009693:Nucleic Acid Hybridization; D012328:RNA Viruses / Q000235:genetics*; D012367:RNA, Viral / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012367:RNA, Viral
references.citation: RNA. 2002 Jan;8(1):110-22
references.pmid: 11873757
references.citation: J Gen Virol. 2008 Jan;89(Pt 1):1-47
references.pmid: 18089727
references.citation: J Virol. 2007 Oct;81(19):10460-73
references.pmid: 17652401
references.citation: J Mol Biol. 1996 Dec 20;264(5):919-32
references.pmid: 9000621
references.citation: RNA. 2004 Sep;10(9):1337-51
references.pmid: 15273323
references.citation: Science. 2006 Nov 10;314(5801):994-7
references.pmid: 17038590
references.citation: Bioinformatics. 1999 Jun;15(6):446-54
references.pmid: 10383470
references.citation: J Virol. 2005 Jun;79(11):6631-43
references.pmid: 15890901
references.citation: Cell Mol Life Sci. 2007 Jul;64(14):1785-92
references.pmid: 17415516
references.citation: J Chem Phys. 2006 Nov 21;125(19):194905
references.pmid: 17129165
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W577-81
references.pmid: 15980540
references.citation: Nucleic Acids Res. 2008 May;36(8):2530-46
references.pmid: 18319285
references.citation: Biochem Biophys Res Commun. 2004 May 21;318(1):303-10
references.pmid: 15110788
references.citation: Nat Methods. 2005 Apr;2(4):269-76
references.pmid: 15782219
references.citation: Proc Natl Acad Sci U S A. 1996 Dec 24;93(26):15400-4
references.pmid: 8986823
references.citation: Science. 2005 Sep 2;309(5740):1577-81
references.pmid: 16141076
references.citation: Science. 2003 Mar 7;299(5612):1575-8
references.pmid: 12624267
references.citation: J Gen Virol. 1998 Jul;79 ( Pt 7):1725-34
references.pmid: 9680136
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3429-31
references.pmid: 12824340
references.citation: Cell. 2007 Jul 13;130(1):101-12
references.pmid: 17632058
references.citation: Nucleic Acids Res. 1981 Jan 10;9(1):133-48
references.pmid: 6163133
references.citation: Cell. 2002 Sep 6;110(5):563-74
references.pmid: 12230974
references.citation: J Virol. 2000 Oct;74(19):9125-33
references.pmid: 10982359
references.citation: J Mol Biol. 1999 May 21;288(5):911-40
references.pmid: 10329189
references.citation: Biochemistry. 2002 Aug 20;41(33):10439-45
references.pmid: 12173930
references.citation: Nucleic Acids Res. 1999 Dec 15;27(24):4816-22
references.pmid: 10572183
references.citation: Org Biomol Chem. 2007 Aug 7;5(15):2380-9
references.pmid: 17637957
references.citation: Semin Virol. 1994 Feb;5(1):39-49
references.pmid: 32288439
references.citation: Gastroenterology. 2003 Dec;125(6):1808-17
references.pmid: 14724833
references.citation: Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17264-9
references.pmid: 15563593
references.citation: J Virol. 2000 May;74(10):4590-600
references.pmid: 10775595
references.citation: Proc Natl Acad Sci U S A. 1990 Nov;87(22):8687-91
references.pmid: 2247437
references.citation: Science. 2006 Nov 10;314(5801):997-1001
references.pmid: 17038589
references.citation: Microbiol Rev. 1996 Sep;60(3):499-511
references.pmid: 8840784
references.citation: Nucleic Acids Res. 1993 Sep 25;21(19):4483-90
references.pmid: 7901835
references.citation: Nat Immunol. 2004 Jul;5(7):730-7
references.pmid: 15208624
references.citation: Nat Immunol. 2006 Jun;7(6):563-7
references.pmid: 16715068
references.citation: Curr Top Microbiol Immunol. 1995;199 ( Pt 2):173-87
references.pmid: 7555067
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D101-3
references.pmid: 14681368
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W335-8
references.pmid: 17452347
references.citation: J Virol. 1999 Jul;73(7):5787-94
references.pmid: 10364330
references.citation: J Mol Biol. 2005 Mar 18;347(1):41-52
references.pmid: 15733916
references.citation: J Virol. 2003 Sep;77(17):9502-10
references.pmid: 12915564
references.citation: Comp Med. 2006 Aug;56(4):247-51
references.pmid: 16941951
references.citation: RNA. 2001 Nov;7(11):1509-21
references.pmid: 11720281
references.citation: J Microsc. 2003 Dec;212(Pt 3):273-9
references.pmid: 14629553
references.citation: J Virol. 2002 Oct;76(19):9686-94
references.pmid: 12208947