Template requirements for recognition and copying by Sindbis virus RNA-dependent RNA polymerase

Virology

Volumn 358, Issue 1, 2007, Pages 221-232

  Thal, Melissa A ^a   Wasik, Brian R ^a   Posto, Jessica ^a   Hardy, Richard W ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

RNA dependent RNA polymerase; Sindbis virus; Template recognition

Indexed keywords

MESSENGER RNA; NUCLEOTIDE DERIVATIVE; POLYADENYLIC ACID; RNA DIRECTED RNA POLYMERASE; SINDBIS VIRUS NONSTRUCTURAL PROTEIN 4; VIRUS RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; GEL MOBILITY SHIFT ASSAY; GENE MUTATION; GENE REPLICATION; MOLECULAR RECOGNITION; NONHUMAN; NORTHERN BLOTTING; PRIORITY JOURNAL; PROTEIN ISOLATION; RNA SYNTHESIS; RNA TRANSCRIPTION; SINDBIS VIRUS; VIRUS GENOME; VIRUS REPLICATION; WESTERN BLOTTING;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ANIMALS; BINDING SITES; CELL LINE; CRICETINAE; MUTATION; NUCLEOTIDES; RNA, VIRAL; SINDBIS VIRUS; TEMPLATES, GENETIC; TRANSCRIPTION, GENETIC; VIRAL NONSTRUCTURAL PROTEINS;

SINDBIS VIRUS;

EID: 33845999513     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2006.08.022     Document Type: Article

References (40)

1. 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
2. Behrens S.E., Tomei L., and De Francesco R. Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus. EMBO J. 15 1 (1996) 12-22
3. 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
4. Craig A.W., Haghighat A., Yu A.T., and Sonenberg N. Interaction of polyadenylate-binding protein with the eIF4G homologue PAIP enhances translation. Nature 392 (1998) 520-523
5. de Groot R.J., Hardy W.R., Shirako Y., and Strauss J.H. Cleavage-site preferences of Sindbis virus polyproteins containing the nonstructural proteinase: evidence for temporal regulation of polyprotein processing in vivo. EMBO J. 9 (1990) 2631-2638
6. Ding M., and Schlesinger M.J. Evidence that Sindbis virus nsP2 is an autoprotease which processes the virus nonstructural polyprotein. Virology 171 (1989) 280-284
7. Frey T.K., and Strauss J.H. Replication of Sindbis virus: VI. Poly(A) and poly(U) in virus-specific RNA species. Virology 86 (1978) 494-506
8. Frey T.K., Gard D.L., and Strauss J.H. Biophysical studies on circle formation by Sindbis virus 49S RNA. J. Mol. Biol. 132 (1979) 1-18
9. 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
10. Frolova E., Gorchakov R., Garmashova N., Atasheva S., Vergara L.A., and Frolov I. Formation of nsP3-specific protein complexes during Sindbis virus replication. J. Virol. 80 8 (2006) 4122-4134
11. 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
12. 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
13. Hardy R.W. The role of the 3′ terminus of the Sindbis virus genome in minus-strand initiation site selection. Virology 345 (2006) 520-531
14. 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
15. Hardy W.R., and Strauss J.H. Processing of the nonstructural polyproteins of Sindbis virus: study of the kinetics in vivo using monospecific antibodies. J. Virol. 62 (1988) 998-1007
16. Hardy W.R., and Strauss J.H. Processing the nonstructural polyproteins of Sindbis virus: nonstructural proteinase is in the C-terminal half of nsP2 and functions both in cis and trans. J. Virol. 63 (1989) 4653-4664
17. Herold J., and Andino R. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol. Cell 7 (2001) 581-591
18. Imataka H., Gradi A., and Sonenberg N. A newly identified N-terminal amino acid sequence of human eIF4G binds poly(A)-binding protein and functions in poly(A)-dependent translation. EMBO J. 17 (1998) 7480-7489
19. Kuhn R.J., Hong Z., and Strauss J.H. Mutagenesis of 3′ nontranslated region of Sindbis virus RNA. J. Virol. 64 (1990) 1465-1476
20. Lemm J.A., Rümenapf 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 (1994) 2925-2934
21. 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
22. 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
23. 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
24. Li M.L., and Stollar V. Identification of the amino acid sequence in Sindbis virus nsP4 that binds to the promoter for synthesis of subgenomic RNA. Proc. Natl. Acad. Sci. U.S.A. 101 25 (2004) 9429-9434
25. Li M.L., and Stollar V. A cell-free system for the synthesis of Sindbis virus subgenomic RNA: the importance of the concentration of the initiating nucleotide. Virology 341 1 (2005) 24-33
26. 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
27. Niesters H.G.M., and Strauss J.H. Mutagenesis of the conserved 51 nucleotide region of Sindbis virus. J. Virol. 64 (1990) 1639-1647
28. Raju R., Hajjou M., Hill K.R., Botta V., and Botta S. In vivo addition of poly(A) tail and AU-rich sequences to the 3′ terminus of the Sindbis virus RNA genome: a novel 3′-end repair pathway. J. Virol. 73 (1999) 2410-2419
29. Sawicki D.L., and Gomatos P.J. Replication of Semliki Forest virus: polyadenylate in plus-strand and polyuridylate in minus-strand RNA. J. Virol. 20 2 (1976) 446-464
30. Sawicki D.L., Silverman R.H., Williams B.R., and Sawicki S.G. Alphavirus minus-strand synthesis and persistence in mouse embryo fibroblasts derived from mice lacking RNase L and protein kinase R. J. Virol. 77 3 (2003) 1801-1811
31. Sawicki D.L., Perri S., Polo J.M., and Sawicki S.G. Role for nsP2 proteins in the cessation of alphavirus minus-strand synthesis by host cells. J. Virol. 80 1 (2006) 360-371
32. Schlesinger S., and Schlesinger M.J. Togaviridae: the viruses and their replication. In: Knipe D.M., and Howley P.M. (Eds). Fields Virology. 4th ed. vol. 1 (2001), Lippincott Williams and Wilkins, Philadelphia 895-916 2 vols
33. 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
34. Shirako Y., Strauss E.G., and Strauss J.H. Modification of the 5′ terminus of Sindbis Virus genomic RNA allows nsP4 RNA polymerase with nonaromatic amino acids at the N terminus to function in RNA replication. J. Virol. 77 4 (2003) 2301-2309
35. 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
36. 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
37. 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
38. Tomar, S., Hardy, R.W., Smith, J.L., Kuhn, R.J., in press. Catalytic core of alphavirus nonstructural protein nsP4 possesses terminal adenylyl transferase activity. J. Virol.
39. Wengler G., Wengler G., and Gross H.S. Replicative form of Semliki Forest virus RNA contains an unpaired guanosine. Nature 282 5740 (1979) 754-756
40. 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