Bioinformatic and physical characterizations of genome-scale ordered RNA structure in mammalian RNA viruses.
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.
Davis
Matthew
M
Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom.
Sagan
Selena M
SM
Pezacki
John P
JP
Evans
David J
DJ
Simmonds
Peter
P
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
D012367:RNA, Viral
RNA. 2002 Jan;8(1):110-22
11873757
J Gen Virol. 2008 Jan;89(Pt 1):1-47
18089727
J Virol. 2007 Oct;81(19):10460-73
17652401
J Mol Biol. 1996 Dec 20;264(5):919-32
9000621
RNA. 2004 Sep;10(9):1337-51
15273323
Science. 2006 Nov 10;314(5801):994-7
17038590
Bioinformatics. 1999 Jun;15(6):446-54
10383470
J Virol. 2005 Jun;79(11):6631-43
15890901
Cell Mol Life Sci. 2007 Jul;64(14):1785-92
17415516
J Chem Phys. 2006 Nov 21;125(19):194905
17129165
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W577-81
15980540
Nucleic Acids Res. 2008 May;36(8):2530-46
18319285
Biochem Biophys Res Commun. 2004 May 21;318(1):303-10
15110788
Nat Methods. 2005 Apr;2(4):269-76
15782219
Proc Natl Acad Sci U S A. 1996 Dec 24;93(26):15400-4
8986823
Science. 2005 Sep 2;309(5740):1577-81
16141076
Science. 2003 Mar 7;299(5612):1575-8
12624267
J Gen Virol. 1998 Jul;79 ( Pt 7):1725-34
9680136
Nucleic Acids Res. 2003 Jul 1;31(13):3429-31
12824340
Cell. 2007 Jul 13;130(1):101-12
17632058
Nucleic Acids Res. 1981 Jan 10;9(1):133-48
6163133
Cell. 2002 Sep 6;110(5):563-74
12230974
J Virol. 2000 Oct;74(19):9125-33
10982359
J Mol Biol. 1999 May 21;288(5):911-40
10329189
Biochemistry. 2002 Aug 20;41(33):10439-45
12173930
Nucleic Acids Res. 1999 Dec 15;27(24):4816-22
10572183
Org Biomol Chem. 2007 Aug 7;5(15):2380-9
17637957
Semin Virol. 1994 Feb;5(1):39-49
32288439
Gastroenterology. 2003 Dec;125(6):1808-17
14724833
Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17264-9
15563593
J Virol. 2000 May;74(10):4590-600
10775595
Proc Natl Acad Sci U S A. 1990 Nov;87(22):8687-91
2247437
Science. 2006 Nov 10;314(5801):997-1001
17038589
Microbiol Rev. 1996 Sep;60(3):499-511
8840784
Nucleic Acids Res. 1993 Sep 25;21(19):4483-90
7901835
Nat Immunol. 2004 Jul;5(7):730-7
15208624
Nat Immunol. 2006 Jun;7(6):563-7
16715068
Curr Top Microbiol Immunol. 1995;199 ( Pt 2):173-87
7555067
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D101-3
14681368
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W335-8
17452347
J Virol. 1999 Jul;73(7):5787-94
10364330
J Mol Biol. 2005 Mar 18;347(1):41-52
15733916
J Virol. 2003 Sep;77(17):9502-10
12915564
Comp Med. 2006 Aug;56(4):247-51
16941951
RNA. 2001 Nov;7(11):1509-21
11720281
J Microsc. 2003 Dec;212(Pt 3):273-9
14629553
J Virol. 2002 Oct;76(19):9686-94
12208947