Structure and function analysis of the poliovirus cis-acting replication element (CRE)

RNA

Volumn 9, Issue 1, 2003, Pages 124-137

  Goodfellow, Ian G ^a   Kerrigan, David ^a   Evans, David J ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

Enterovirus; Picornavirus; Polymerase; Protease; Replication; Uridylylation; VPg

Indexed keywords

CIS ACTING ELEMENT; NUCLEOTIDE;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; GENOME; HUMAN; HUMAN CELL; HUMAN RHINOVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLIOMYELITIS VIRUS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TRANSPORT; REPLICON; RNA BINDING; STRUCTURE ANALYSIS; VIRUS REPLICATION;

BASE SEQUENCE; ELECTROPHORETIC MOBILITY SHIFT ASSAY; HELA CELLS; HUMANS; MOLECULAR SEQUENCE DATA; MUTAGENESIS; NUCLEIC ACID CONFORMATION; POLIOVIRUS; RNA, VIRAL; STRUCTURE-ACTIVITY RELATIONSHIP;

ENTEROVIRUS; HUMAN RHINOVIRUS SP.; PICORNAVIRIDAE; POLIOVIRUS; RHINOVIRUS;

EID: 0037276580     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.2950603     Document Type: Article

References (48)

1. Andino, R., Böddeker, N., Silvera, D., and Gamarnik, A.V. 1999. Intracellular determinants of picornavirus replication. Trends Microbiol. 7: 76-82.
2. Andino, R., Rieckhof, G.E., and Baltimore, D. 1990. A functional ribonucleoprotein complex forms around the 5′ end of poliovirus RNA. Cell 63: 369-380.
3. Andino, R., Rieckhof, G.E., Achacoso, P.L., and Baltimore, D. 1993. Poliovirus RNA synthesis utilizes an RNP complex formed around the 5′-end of viral RNA. EMBO J. 12: 3587-3598.
4. Barclay, W., Li, Q., Hutchinson, G., Moon, D., Richardson, A., Percy, N., Almond, J., and Evans, D. 1998. Encapsidation studies of poliovirus subgenomic replicons. J. Gen. Virol, 79: 1725-1734.
5. Barton, D.J., Black, E.P., and Flanegan, J.B. 1995. Complete replication of poliovirus in vitro: Preinitiation RNA replication complexes require soluble cellular factors for the synthesis of VPg-linked RNA. J. Virol. 69: 5516-5527.
6. Barton, D.J., O'Donnell, B.J., and Flanegan, J.B. 2001. 5′ cloverleaf in poliovirus RNA is a cis-acting replication element required for negative-strand synthesis. EMBO J. 20: 1439-1448.
7. Cammack, N., Phillips, A., Dunn, G., Patel, V., and Minor, P.D. 1988. Intertypic genomic rearrangements of poliovirus strains in vaccinees. Virology 167: 507-514.
8. Crawford, N.M. and Baltimore, D. 1983. Genome-linked protein VPg of poliovirus is present as free VPg and VPg-pUpU in poliovirus-infected cells. Proc. Natl. Acad. Sci. 80: 7452-7455.
9. Earle, J.A., Skuce, R.A., Fleming, C.S., Hoey, E.M., and Martin, S.J. 1988. The complete nucleotide sequence of a bovine enterovirus. J. Gen. Virol. 69: 253-263.
10. Evans, D.J. 1999. Reverse genetics of picornaviruses. Adv. Virus Res. 53: 209-228.
11. Evans, D.J. and Almond, J.W. 1991. Design, construction and characterization of poliovirus antigen chimeras. Methods Enzymol. 203: 387-400.
12. Flanegan, J.B., Petterson, R.F., Ambros, V., Hewlett, M.J., and Baltimore, D. 1977. Covalent linkage of a protein to a defined nucleotide sequence at the 5′-terminus of virion and replicative intermediate RNAs of poliovirus. Proc. Natl. Acad. Sci. 74: 961-965.
13. Gamarnik, A.V. and Andino, R. 1997. Two functional complexes formed by KH domain containing proteins with the 5′ noncoding region of poliovirus RNA. RNA 3: 882-892.
14. Gerber, K., Wimmer, E., and Paul, A.V. 2001a. Biochemical and genetic studies of the initiation of human rhinovirus 2 RNA replication: Identification of a cis-replicating element in the coding sequence of 2A(pro). J. Virol. 75: 10979-10990.
15. -. 2001b. Biochemical and genetic studies of the initiation of human rhinovirus 2 RNA replication: Purification and enzymatic analysis of the RNA-dependent RNA polymerase 3D(pol). J. Virol. 75: 10969-10978.
16. Goodfellow, I.G., Chaudhry, Y., Richardson, A., Meredith, J.M., Almond, J.W., Barclay, W.S., and Evans, D.J. 2000. Identification of a cis-acting replication element (CRE) within the poliovirus coding region. J. Virol. 74: 4590-4600.
17. Herold, J. and Andino, R. 2001. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol. Cell 7: 581-591.
18. Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, L.S., Tacker, M., and Schuster, P. 1994. Fast folding and comparison of RNA secondary structures. Monatshefte Chem. 125: 167-188.
19. Kirkegaard, K. and Baltimore, D. 1986. The mechanism of RNA recombination in poliovirus. Cell 47: 433-443.
20. Kitamura, N., Aider, C., Martinko, J., Nathenson, S.G., and Wimmer, E. 1980. The genome-linked protein ofpicornaviruses. VII. Genetic mapping of poliovirus VPg by protein and RNA sequence studies. Cell 21: 295-302.
21. Kuge, S., Saito, I., and Nomoto, A. 1986. Primary structure of poliovirus defective-interfering particle genomes and possible generation mechanisms of the particles. J. Mol. Biol. 192: 473-487.
22. Kuhn, R.J., Tada, H., Ypma Wong, M.F., Semler, B.L., and Wimmer, E. 1988. Mutational analysis of the genome-linked protein VPg of poliovirus. J. Virol. 62: 4207-4215.
23. Lobert, P.E., Escriou, N., Ruelle, J., and Michiels, T. 1999. A coding RNA sequence acts as a replication signal in cardioviruses. Proc. Natl. Acad. Sci. 96: 11560-11565.
24. Mason, P.W., Bezborodova, S.V., and Henry, T.M. 2002. Identification and characterization of a cis-acting replication element (cre) adjacent to the internal ribosome entry site of foot-and-mouth disease virus. J. Virol. 76: 9686-9694.
25. McKnight, K.L. and Lemon, S.M. 1998. The rhinovirus type 14 genome contains an internally located RNA structure that is required for viral replication. RNA 4: 1569-1584.
26. Melchers, W.J.G., Hoenderop, J.G.J., Slot, H.J.B., Pleij, C.W.A., Pilipenko, E.V., Agol, V.I., and Galama, J.M.D. 1997. Kissing of the 2 predominant hairpin loops in the coxsackie-b virus 3′-untranslated region is the essential structural feature of the origin of replication required for negative-strand rna-synthesis. J. Virol. 71: 686-696.
27. Mellits, K.H., Meredith, J.M., Rohll, J.B., Evans, D.J., and Almond, J.W. 1998. Binding of a cellular factor to the 3′ untranslated region of the RNA genomes of entero- and rhinoviruses plays a role in virus replication. J. Gen. Virol. 79: 1715-1723.
28. Meredith, J.M., Rohll, J.B., Almond, J.W., and Evans, D.J. 1999. Similar interactions of the poliovirus and rhinovirus 3D polymerase with the 3′ untranslated region of rhinovirus 14. J. Virol. 73: 9952-9958.
29. Moss, E.G., O'Neill, R.E., and Racaniello, V.R. 1989. Mapping of attenuating sequences of an avirulent poliovirus type 2 strain. J. Virol. 63: 1884-1890.
30. Nomoto, A., Kitamura, N., Golini, F., and Wimmer, E. 1977. The 5′ terminal structures of poliovirus RNA and poliovirus mRNA differ only in the genome-linked protein VPg. Proc. Natl. Acad. Sci. 77: 5345-5349.
31. Nomoto, A., Jacobson, A., Lee, Y.F., Dunn, J., and Wimmer, E. 1979. Defective interfering particles of poliovirus: Mapping of the deletion and evidence that the deletions in the genomes of DI(1), (2) and (3) are located in the same region. J. Mol. Biol. 128: 179-196.
32. Parsley, T.B., Towner, J.S., Blyn, L.B., Ehrenfeld, E., and Semler, B.L. 1997. Poly (rC) binding protein 2 forms a ternary complex with the 5′-terminal sequences of poliovirus RNA and the viral 3CD proteinase. RNA 3:1124-1134.
33. Paul, A.V., vanBoom, J.H., Filippov, D., and Wimmer, E. 1998. Protein-primed RNA synthesis by purified poliovirus RNA polymerase. Nature 393: 280-284.
34. Paul, A.V., Rieder, E., Kim, D.W., van Boom, J.H., and Wimmer, E. 2000. Identification of an RNA hairpin in poliovirus RNA that serves as the primary template in the in vitro uridylylation of VPg. J. Virol. 74: 10359-10370.
35. Pelletier, J. and Sonenberg, N. 1988. Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature 334: 320-325.
36. Pelletier, J., Flynn, M.E., Kaplan, G., Racaniello, V., and Sonenberg, N. 1988. Mutational analysis of upstream AUG codons of poliovirus RNA. J. Virol. 62: 4486-4492.
37. Percy, N., Barclay, W.S., Sullivan, M., and Almond, J.W. 1992. A poliovirus replicon containing the chloramphenicol Acetyltransferase gene can be used to study the replication and encapsidation of poliovirus RNA. J. Virol. 66: 5040-5046.
38. Pilipenko, E.V., Poperechny, K.V., Maslova, S.V., Melchers, W.J., Slot, H.J., and Agol, V.I. 1996. cis-Element, oriR, involved in the initiation of (-) strand poliovirus RNA: A quasi-globular multi-domain RNA structure maintained by tertiary ("kissing") interactions. EMBO J. 15: 5428-5436.
39. Pollard, S.R., Dunn, G., Cammack, N., Minor, P.D., and Almond, J.W. 1989. Nucleotide sequence of a neurovirulent variant of the type 2 oral poliovirus vaccine. J. Virol. 63: 4949-4951.
40. Racaniello, V.R. and Baltimore, D. 1981. Cloned poliovirus complementary DNA is infectious in mammalian cells. Science 214: 916-919.
41. Rieder, E., Paul, A.V., Kim, D.W., van Boom, J.H., and Wimmer, E. 2000. Genetic and biochemical studies of poliovirus cis-acting replication element cre in relation to VPg uridylylation. J. Virol. 74: 10371-10380.
42. Rohll, J.B., Moon, D.H., Evans, D.J., and Almond, J.W. 1995. The 3′-untranslated region of picornavirus RNA - Features required for efficient genome replication. J. Virol. 69: 7835-7844.
43. Salas, M., Miller, J.T., Leis, J., and DePamphilis, M. 1996. Mechanisms of priming DNA synthesis. In DNA replication in eukaryotic cells (ed. M.L. DePamphilis), pp. 131-176. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
44. Skinner, M.A., Racaniello, V.R., Dunn, G., Cooper, J., Minor, P.D., and Almond, J.W. 1989. New model for the secondary structure of the 5′ non-coding RNA of poliovirus is supported by biochemical and genetic data that also show that RNA secondary structure is important in neurovirulence. J. Mol. Biol. 207: 379-392.
45. Todd, S., Towner, J.S., Brown, D.M., and Semler, B.L. 1997. Replication-competent picornaviruses with complete genomic RNA 3′ noncoding region deletions. J. Virol. 71: 8868-8874.
46. Wang, J., Bakkers, J.M., Galama, J.M., Bruins Slot, H.J., Pilipenko, E.V., Agol, V.I., and Melchers, W.J. 1999. Structural requirements of the higher order RNA kissing element in the enteroviral 3′UTR. Nucleic Acids Res. 27: 485-490.
47. Yang, Y., Rijnbrand, R., McKnight, K.L., Wimmer, E., Paul, A., Martin, A., and Lemon, S.M. 2002. Sequence requirements for viral RNA replication and VPg uridylylation directed by the internal cis-acting replication element (cre) of human rhinovirus type 14. J. Virol. 76: 7485-7494.
48. Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52.