Kissing of the Two 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

Journal of Virology

Volumn 71, Issue 1, 1997, Pages 686-696

  Melchers, Willem J G ^a   Hoenderop, Joost G J ^a   Bruins Slot, Hilbert J ^a   Pleij, Cornelis W A ^b   Pilipenko, Evgeny V ^c   Agol, Vadim I ^c   Galama, Joep M D ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^b LEIDEN UNIVERSITY   (Netherlands)

^c CHUMAKOV INSTITUTE OF POLIOMYELITIS AND VIRAL ENCEPHALITIDES   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; RNA POLYMERASE; VIRUS PROTEIN; VIRUS RNA;

ANIMAL CELL; ARTICLE; COMPUTER PROGRAM; COXSACKIE VIRUS B; COXSACKIE VIRUS B3; GENE MUTATION; GENETIC TRANSFECTION; MOLECULAR CLONING; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROCESSING; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; RNA SYNTHESIS; VERO CELL; VIRUS REPLICATION; VIRUS TRANSCRIPTION;

BASE SEQUENCE; ENTEROVIRUS B, HUMAN; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; REPLICATION ORIGIN; RNA, VIRAL; VIRUS REPLICATION;

EID: 0031060472     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.71.1.686-696.1997     Document Type: Article

References (50)

1. Abrahams, J. P., M. van den Berg, E. van Batenburg, and C. Pleij. 1990. Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res. 18:3035-3044.
2. Andino, R., G. E. Rieckhof, and D. Baltimore. 1990. A functional ribonucleoprotein complex forms around the 5′-end of poliovirus RNA. Cell 63:369-380.
3. Andino, R., G. E. Rieckhof, P. L. Achacoso, and D. Baltimore. 1993. Poliovirus RNA synthesis utilizes an RNP complex formed around the 5′-end of viral RNA. EMBO J. 12:3587-3598.
4. Arnott, S., D. W. L. Hukins, and S. D. Dover. 1972. Optimised parameters for RNA double-helices. Biochem. Biophys. Res. Commun. 48:1392-1399.
5. Auvinen, P., G. Stanway, and T. Hyypiä. 1989. Genetic diversity of enterovirus subgroups. Arch. Virol. 104:175-186.
6. Bienz, K., D. Egger, T. Pfister, and M. Troxler. 1992. Structural and functional characterization of the poliovirus replication complex. J. Virol. 66:2740-2747.
7. Bienz, K., D. Egger, M. Troxler, and L. Pasamontes. 1990. Structural organization of poliovirus RNA replication is mediated by viral proteins of the P2 genomic region. J. Virol. 64:1156-1163.
8. Chang, K.-Y., and I. Tinoco. 1995. Characterization of a "kissing" hairpin complex derived from the human immunodeficiency virus genome. Proc. Natl. Acad. Sci. USA 91:8705-8709.
9. Chomczynski, P., and N. Sacchi. 1987. Single step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162:156-159.
10. Cui, T., and A. G. Porter. 1995. Localization of binding site for encephalomyocarditis virus RNA polymerase in the 3′-noncoding region of the viral RNA. Nucleic Acids Res. 23:377-382.
11. Frankel, A. D., I. W. Mattaj, and D. C. Rio. 1991. RNA-protein interactions. Cell 67:1041-1046.
12. pro with the 5′ and 3′ termini of the poliovirus genome. J. Biol. Chem. 269:27004-27014.
13. Jacobson, S. J., D. A. M. Konings, and P. Sarnow. 1993. Biochemical and genetic evidence for a pseudoknot structure at the 3′ terminus of the poliovirus RNA genome and its role in viral amplification. J. Virol. 67:2961-2971.
14. Kaine, B. P. 1990. Structure of the archaebacterial 7S RNA molecule. Mol. Gen. Genet. 221:315-321.
15. Klump, W. M., I. Bergmann, B. C. Muller. D. Ameis, and R. Kandolf. 1990. Complete nucleotide sequence of infectious coxsackievirus B3 cDNA: two initial 5′ uridine residues are regained during plus-strand RNA synthesis. J. Virol. 64:1573-1583.
16. Ladner, J. E., A. Jack, J. D. Robertus, R. Brown, D. Rhodes, B. F. C. Clark, and A. Klug. 1975. Structure of yeast phenylalanine transfer RNA at 2.5 A resolution. Proc. Natl. Acad. Sci. USA 72:4414-4418.
17. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature (London) 227:680-685.
18. Lama, J., M. A. Sanz, and P. L. Rodriguez. 1995. A role of 3AB protein in poliovirus genome replication. J. Biol. Chem. 270:14430-14438.
19. Mans, R. M. W., C. W. A. Pleij, and L. Bosch. 1991. tRNA-like structures. Structure, function and evolutionary significance. Eur. J. Biochem. 201:303-324.
20. Marino, J. P., R. S. Gregorian, G. Csankovski, and D. M. Crothers. 1995. Bent helix formation between RNA hairpins with complementary loops. Science 268:1448-1454.
21. Persson, C., E. Gerhart, H. Wagner, and K. Nordström. 1990. Control of replication of plasmid R1: structures and sequences of the antisense RNA, CopA, required for its binding to the target RNA, CopT. EMBO J. 9:3767-3775.
22. Persson, C., E. Gerhart, H. Wagner, and K. Nordström. 1990. Control of replication of plasmid R1: formation of an initial transient complex is rate-limiting for antisense RNA-target RNA pairing. EMBO J. 9:3777-3785.
23. Philippe, C., F. Eyermann, L. Bernard, C. Portier, B. Ehresmann, and C. Ehresmann. 1993. Ribosomal protein S15 from Escherichia coli modulates its own translation by trapping the ribosome on the mRNA initiation loading site. Proc. Natl. Acad. Sci. USA 90:4394-4398.
24. Pierangeli, A., M. Bucci, P. Pagnotti, A. M. Degener, and R. P. Bercoff. 1995. Mutational analysis of the 3′-terminal extra-cistronic region of poliovirus RNA: secondary structure is not the only requirement for minus strand RNA replication. FEBS Lett. 374:327-332.
25. Pilipenko, E. V., V. M. Blinov, B. K. Chernov, T. M. Dmitrieva, and V. I. Agol. 1989. Conservation of the secondary structure elements of the 5′-untranslated region of cardio- and aphtovirus RNAs. Nucleic Acids Res. 17:5701-5711.
26. Pilipenko, E. V., A. P. Gmyl, S. V. Maslova, A. P. Belov, A. N. Sinyakov, M. Huang, T. D. K. Brown, and V. I. Agol. 1994. Starting window, a distinct element in the Cap-dependent internal initiation of translation on picornaviral RNA. J. Mol. Biol. 241:398-414.
27. Pilipenko, E. V., S. V. Maslova, A. N. Sinyakov, and V. I. Agol. 1992. Towards identification of cis-acting elements involved in the replication of enterovirus and rhinovirus RNAs: a proposal for the existence of tRNA-like terminal structures. Nucleic Acids Res. 20:1739-1745.
28. Pilipenko, E. V., K. V. Poperechny, S. V. Maslova, W. J. G. Melchers, H. J. Bruins Slot, and V. I. Agol. Cis-element, oriR, involved in the initiation of (-)strand poliovirus RNA: a quasi-globular multi-domain RNA structure maintained by tertiary ("kissing") interactions. Submitted for publication.
29. Pleij, C. W. A. 1990. Pseudoknots: a new motif in the RNA game. Trends Biochem. Sci. 15:143-147.
30. pol. J. Virol. 69:7169-7179.
31. Reed, L. J., and H. Muench. 1938. A simple method of estimating fifty percent endpoints. Am. J. Hyg. 27:493-497.
32. Rietveld, K., K. Linschooten, C. W. A. Pleij, and L. Bosch. 1984. The three-dimensional folding of the tRNA-like structure of tobacco mosaic virus RNA. A new building principle applied twice. EMBO J. 3:2613-2619.
33. Rietveld, K., R. van Poelgeest, C. W. A. Pleij, J. H. van Boom, and L. Bosch. 1982. The tRNA-like structure at the 3′ terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA. Nucleic Acids Res. 10:1929-1946.
34. Rohll, J. B., D. H. Moon, D. J. Evans, and J. W. Almond. 1995. The 3′ untranslated region of picornavirus RNA: features required for efficient genome replication. J. Virol. 69:7835-7844.
35. Rohll, J. B., N. Percy, E. Ley, D. J. Evans, J. W. Almond, and W. S. Barclay. 1994. The 5′ untranslated regions of picornavirus RNAs contain independent functional domains essential for RNA replication and translation. J. Virol. 68:4384-4391.
36. Sarnow, P., H. D. Bernstein, and D. Baltimore. 1986. A poliovirus temperature-sensitive RNA synthesis mutant located in a noncoding region of the genome. Proc. Natl. Acad. Sci. USA 83:571-575.
37. Schmidt, N. J. 1979. Cell culture techniques for diagnostic virology, p. 65-139. In E. H. Lennette, and N. J. Schmidt (ed.), Diagnostic procedures for viral, rickettsial and chlamydial infections. American Public Health Association, Washington, D.C.
38. Struck, J. C. R., and V. A. Erdmann. 1990. Phylogenetic and biochemical evidence for a secondary structure model of a small cytoplasmic RNA from Bacilli. Eur. J. Biochem. 192:17-24.
39. Sugimoto, N., R. Kierzek, S. M. Freier, and D. H. Turner. 1986. Energetics of internal GU mismatches in ribo-oligonucleotide helixes. Biochemistry 25:5755-5759.
40. Sussman, J. L., and S.-H. Kim. 1976. Three-dimensional structure of a transfer RNA in two crystal forms. Analysis of three sets of atomic coordinates of yeast phenylalanine tRNA establishes common features. Science 192:853-858.
41. Takeda, N., R. J. Kuhn, C.-F. Yang, T. Takegami, and E. Wimmer. 1986. Initiation of poliovirus plus-strand RNA synthesis in a membrane complex of infected HeLa cells. J. Virol. 60:43-53.
42. Tang, C. K., and D. E. Draper. 1989. Unusual mRNA pseudoknot structure is recognized by a protein translation repressor. Cell 59:511-536.
43. Todd, S., J. H. C. Nguyen, and B. L. Semler. 1995. RNA-protein interactions directed by the 3′ end of human rhinovirus genomic RNA. J. Virol. 69:3605-3614.
44. Toyoda, H., C. F. Yang, N. Takeda, A. Nomoto, and E. Wimmer. 1987. Analysis of RNA synthesis of type 1 poliovirus by using an in vitro molecular genetic approach. J. Virol. 61:2816-2822.
45. van Kuppeveld, F. J. M., J. M. D. Galama, J. Zoll, and W. J. G. Melchers. 1995. Genetic analysis of a hydrophobic domain of coxsackie B3 virus protein 2B: a moderate degree of hydrophobicity is required for a cis-acting function in viral RNA synthesis. J. Virol. 69:7782-7790.
46. Weiner, S. J., P. A. Kollman, D. T. Nguyen, and D. A. Case. 1986. An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7:230-252.
47. Wimmer, E., C. U. T. Hellen, and X. Cao. 1993. Genetics of poliovirus. Annu. Rev. Genet. 27:353-436.
48. Zoll, J., P. Jongen, J. Galama, F. van Kuppeveld, and W. Melchers. 1993. Coxsackievirus B1-induced murine myositis: no evidence for viral persistence. J. Gen. Virol. 74:2071-2076.
49. Zoll, J., J. Galama, and W. Melchers. 1994. Intratypic genome variability of the coxsackievirus B1 2A protease region. J. Gen. Virol. 75:687-692.
50. Zwieb, C. 1989. Structure and function of signal recognition particle RNA. Prog. Nucleic Acid Res. Mol. Biol. 37:207-234.