Structural and functional analyses of stem-loop 1 of the Sindbis virus genome

Virology

Volumn 370, Issue 1, 2008, Pages 158-172

  Nickens, David G ^a   Hardy, Richard W ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

Minus_strand; RNA structure; Translation

Indexed keywords

ARTICLE; CHEMICAL ANALYSIS; CONTROLLED STUDY; GENOME; NONHUMAN; PRIORITY JOURNAL; RNA STRUCTURE; SINDBIS VIRUS; VIROGENESIS; VIRUS MORPHOLOGY;

5' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CELL LINE; CRICETINAE; CULICIDAE; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; REGULATORY SEQUENCES, NUCLEIC ACID; RNA, VIRAL; SINDBIS VIRUS; STRUCTURE-ACTIVITY RELATIONSHIP;

ALPHAVIRUS; SINDBIS VIRUS;

EID: 36549060100     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2007.08.006     Document Type: Article

References (50)

1. Alvarez D.E., Lodeiro M.F., Luduena S.J., Pietrasanta L.I., and Gamarnik A.V. Long-range RNA-RNA interactions circularize the dengue virus genome. J. Virol. 79 (2005) 6631-6643
2. Andino R., Rieckhof G.E., and Baltimore D. A functional ribonucleoprotein complex forms around the 5′ end of poliovirus RNA. Cell 63 (1990) 369-380
3. Auron P.E., Weber L.D., and Rich A. Comparison of transfer ribonucleic acid structures using cobra venom and S1 endonucleases. Biochemistry 21 (1982) 4700-4706
4. Barton D.J., Morasco B.J., and Flanegan J.B. Translating ribosomes inhibit poliovirus negative-strand RNA synthesis. J. Virol. 73 (1999) 10104-10112
5. Barton D.J., O'Donnell B.J., and Flanegan J.B. 5′ Cloverleaf in poliovirus RNA is a cis-acting replication element required for negative-strand synthesis. EMBO J. 20 6 (2001) 1439-1448
6. Bedard K.M., and Semler B.L. Regulation of picornavirus gene expression. Microbes Infect. 6 7 (2004) 702-713
7. Brown T.S., and Bevilacqua P.C. Method for assigning double-stranded RNA structures. BioTechniques 38 (2005) 368-372
8. Brunel C., and Romby P. Probing RNA structure and RNA-ligand complexes with chemical probes. Methods Enzymol. 318 (2000) 3-21
9. Chen J., Noueiry A., and Ahlquist P. Brome mosaic virus protein 1a recruits viral RNA2 to RNA replication through a 5′ proximal RNA2 signal. J. Virol. 75 7 (2001) 3207-3219
10. Ehresmann C., Baudin F., Marylene M., Romby P., Ebel J.P., and Ehresmann B. Probing the structure of RNAs in solution. Nucleic Acids Res. 15 22 (1987) 9109-9128
11. Frolov I., Hardy R., and Rice C.M. Cis-acting RNA elements at the 5′ end of Sindbis virus genome RNA regulate minus- and plus-strand RNA synthesis. RNA 7 (2001) 1638-1651
12. Frolova E.I., Fayzulin R.Z., Cook S.H., Griffin D.E., Rice C.M., and Frolov I. Roles of nonstructural protein nsP2 and Alpha/Beta interferons in determining the outcome of Sindbis virus infection. J. Virol. 76 22 (2002) 11254-11264
13. Fuerst T.R., Niles E.G., Studier F.W., and Moss B. Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 83 (1986) 8122-8126
14. Gale Jr. M., and Katze M.G. Molecular mechanisms of interferon resistance mediated by viral-directed inhibition of PKR, the interferon-induced protein kinase. Pharmacol. Ther. 78 (1998) 29-46
15. Galiana-Arnoux D., Dostert C., Schneemann A.A.H.J., and Imler J.-L. Essential function in vivo for Dicer-2 in host defense against RNA viruses in Drosophila. Nat. Immunol. 7 6 (2006) 590-597
16. Gamarnik A.V., and Andino R. Switch from translation to RNA replication in a positive-stranded RNA virus. Genes Dev. 12 (1998) 2293-2304
17. Gorchakov R., Hardy R., Rice C.M., and Frolov I. Selection of functional 5′ cis-acting elements promoting efficient Sindbis virus genome replication. J. Virol. 78 1 (2004) 61-75
18. Griffin D.E. Alphaviruses. In: Knipe D.M., and Howley P.M. (Eds). Fields Virology. 4th ed. vol. 1 (2001), Lippincott Williams and Wilkins, Philadelphia 917-962 2 vols
19. Hardy R.W., and Rice C.M. Requirements at the 3′ end of the Sindbis virus genome for efficient synthesis of minus-strand RNA. J. Virol. 79 8 (2005) 4630-4639
20. Herold J., and Andino R. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol. Cell 7 (2001) 581-591
21. Hofacker I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 31 13 (2003) 3429-3431
22. Hu B., Pillai-Nair N., and Hemenway C. Long-distance RNA-RNA interactions between terminal elements and the same subset of internal elements on the potato virus X genome mediate minus- and plus-strand RNA synthesis. RNA 13 2 (2007) 267-280
23. Knapp G. Enzymatic approaches to probing of RNA secondary and tertiary structure. Methods Enzymol. 180 (1989) 192-212
24. Lemm J.A., Durbin R.K., Stollar V., and Rice C.M. Mutations which alter the level or structure of nsP4 can affect the efficiency of Sindbis virus replication in a host-dependent manner. J. Virol. 64 (1990) 3001-3011
25. Lemm J.A., Rumenapf T., Strauss E.G., Strauss J.H., and Rice C.M. Polypeptide requirements for assembly of functional Sindbis virus replication complexes: a model for the temporal regulation of minus- and plus-strand RNA synthesis. EMBO J. 13 12 (1994) 2925-2934
26. Lemm J.A., Bergqvist A., Read C.M., and Rice C.M. Template-dependent initiation of Sindbis virus replication in vitro. J. Virol. 72 (1998) 6546-6553
27. Li G., and Rice C.M. Mutagenesis of the in-frame opal termination codon preceding nsP4 of Sindbis virus: studies of translational readthrough and its effect on virus replication. J. Virol. 63 (1989) 1326-1337
28. Li G., and Rice C.M. The signal for translational readthrough of a UGA codon in Sindbis virus RNA involves a single cytidine residue immediately downstream of the termination codon. J. Virol. 67 (1993) 5062-5067
29. Lindenbach B.D., Sgro J.Y., and Ahlquist P. Long-distance base pairing in flock house virus RNA1 regulates subgenomic RNA3 synthesis and RNA2 replication. J. Virol. 76 (2002) 3905-3919
30. Lowman H.B., and Draper D.E. On the recognition of helical RNA by cobra venom V1 nuclease. J. Biol. Chem. 261 12 (1986) 5396-5403
31. Lustig S., Jackson A., Hahn C.S., Griffin D.E., Strauss E.G., and Strauss J.H. Molecular basis of Sindbis virus neurovirulence in mice. J. Virol. 62 (1988) 2329-2336
32. McKnight K.L., and Lemon S.M. Capsid coding sequence is required for efficient replication of human rhinovirus 14 RNA. J. Virol. 70 (1996) 1941-1952
33. McKnight K.L., Simpson D.A., Lin S.C., Knott T.A., Polo J.M., Pence D.F., Johannsen D.B., Heidner H.W., Davis N.L., and Johnston R.E. Deduced consensus sequence of Sindbis Virus strain AR339: mutations contained In laboratory strains which affect cell culture and in vivo phenotypes. J. Virol. 70 3 (1996) 1981-1989
34. Niesters H.G.M., and Strauss J.H. Defined mutations in the 5′ nontranslated sequence of Sindbis virus RNA. J. Virol. 64 (1990) 4162-4168
35. Pfefferkorn E.R., and Hunter H.S. Purification and partial chemical analysis of Sindbis virus. Virology 20 (1963) 422-445
36. Pleij C.W.A., and Bosch L. RNA pseudoknots: structure, detection, and prediction. Methods Enzymol. 180 (1989) 289-303
37. Pleij C.W.A., Rietveld K., and Bosch L. A new principle of RNA folding based on pseudoknotting. Nucleic Acids Res. 13 5 (1985) 1717-1731
38. Shirako Y., and Strauss J.H. Regulation of Sindbis virus RNA replication: uncleaved P123 and nsP4 function in minus strand RNA synthesis whereas cleaved products from P123 are required for efficient plus strand RNA synthesis. J. Virol. 185 (1994) 1874-1885
39. Strauss E.G., Rice C.M., and Strauss J.H. Sequence coding for the alphavirus nonstructural proteins is interrupted by an opal termination codon. Proc. Natl. Acad. Sci. U. S. A. 80 (1983) 5271-5275
40. Strauss E.G., Rice C.M., and Strauss J.H. Complete nucleotide sequence of the genomic RNA of Sindbis virus. Virology 133 (1984) 92-110
41. Teterina N.L., Egger D., Bienz K., Brown D.M., Semler B.L., and Ehrenfeld E. Requirements for assembly of poliovirus replication complexes and negative-strand RNA synthesis. J. Virol. 75 8 (2001) 3841-3850
42. Thal M.A., Wasik B.R., Posto J., and Hardy R.W. Template requirements for recognition and copying by the Sindbis virus RNA-dependent RNA polymerase. Virology 358 (2006) 221-232
43. Vary C.P.H., and Vournakis J.N. RNA structure analysis using T2 ribonuclease: detection of pH and metal ion induced conformational changes in yeast tRNA. Nucleic Acids Res. 12 17 (1984) 6763-6778
44. Walter B.L., Parsley T.B., Ehrenfeld E., and Semler B.L. Distinct poly(rC) binding protein KH determinants for poliovirus translation initiation and viral RNA replication. J. Virol. 76 23 (2002) 12008-12022
45. Weeks K.M., and Crothers D.M. Major groove accessibility of RNA. Science 261 (1993) 1574-1577
46. Xayaphoummine A., Bucher T., Thalmann F., and Isambert H. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc. Natl. Acad. Sci. 100 26 (2003) 15310-15315
47. You S., and Padmanabhan R. A novel in vitro replication system for Dengue virus. Initiation of RNA synthesis at the 3′-end of exogenous viral RNA templates requires 5′- and 3′-terminal complementary sequence motifs of the viral RNA. J. Biol. Chem. 274 47 (1999) 33714-33722
48. You S., Falgout B., Markoff L., and Padmanabhan R. In vitro RNA synthesis from exogenous dengue viral RNA templates requires long range interactions between 5′- and 3′-terminal regions that influence RNA structure. J. Biol. Chem. 276 (2001) 15581-15591
49. Zuker M. Mfold server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 13 (2003) 3406-3415
50. Zuker M., Mathews D.H., and Turner D.H. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: Barciszewski J., and Clark B.F.C. (Eds). RNA Biochemistry and Biotechnology (1999), Kluwer Academic Publishers