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J Virol. 1997 Jan; 71(1): 686–696.
PMCID: PMC191101

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.


Higher-order RNA structures in the 3' untranslated region (3'UTR) of enteroviruses are thought to play a pivotal role in viral negative-strand RNA synthesis. The structure of the 3'UTR was predicted by thermodynamic calculations using the STAR (structural analysis of RNA) computer program and experimentally verified using chemical and enzymatic probing of in vitro-synthesized RNA. A possible pseudoknot interaction between the 3D polymerase coding sequence and domain Y and a "kissing" interaction between domains X and Y was further studied by mutational analysis, using an infectious coxsackie B3 virus cDNA clone (domain designation as proposed by E. V. Pilipenko, S. V. Maslova, A. N. Sinyakov, and V.I. Agol (Nucleic Acids Res. 20:1739-1745, 1992). The higher-order RNA structure of the 3'UTR appeared to be maintained by an intramolecular kissing interaction between the loops of the two predominant hairpin structures (X and Y) within the 3'UTR. Disturbing this interaction had no effect on viral translation and processing of the polyprotein but exerted a primary effect on viral replication, as was demonstrated in a subgenomic coxsackie B3 viral replicon, in which the capsid P1 region was replaced by the luciferase gene. Mutational analysis did not support the existence of the pseudoknot interaction between hairpin loop Y and the 3D polymerase coding sequence. Based on these experiments, we constructed a three-dimensional model of the 3'UTR of coxsackie B virus that shows the kissing interaction as the essential structural feature of the origin of replication required for its functional competence.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Abrahams JP, van den Berg M, van Batenburg E, Pleij C. Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res. 1990 May 25;18(10):3035–3044. [PMC free article] [PubMed]
  • Andino R, Rieckhof GE, Baltimore D. A functional ribonucleoprotein complex forms around the 5' end of poliovirus RNA. Cell. 1990 Oct 19;63(2):369–380. [PubMed]
  • Andino R, Rieckhof GE, Achacoso PL, Baltimore D. Poliovirus RNA synthesis utilizes an RNP complex formed around the 5'-end of viral RNA. EMBO J. 1993 Sep;12(9):3587–3598. [PMC free article] [PubMed]
  • Arnott S, Hukins DW, Dover SD. Optimised parameters for RNA double-helices. Biochem Biophys Res Commun. 1972 Sep 26;48(6):1392–1399. [PubMed]
  • Auvinen P, Stanway G, Hyypiä T. Genetic diversity of enterovirus subgroups. Arch Virol. 1989;104(3-4):175–186. [PubMed]
  • Bienz K, Egger D, Pfister T, Troxler M. Structural and functional characterization of the poliovirus replication complex. J Virol. 1992 May;66(5):2740–2747. [PMC free article] [PubMed]
  • Bienz K, Egger D, Troxler M, Pasamontes L. Structural organization of poliovirus RNA replication is mediated by viral proteins of the P2 genomic region. J Virol. 1990 Mar;64(3):1156–1163. [PMC free article] [PubMed]
  • Chang KY, Tinoco I., Jr Characterization of a "kissing" hairpin complex derived from the human immunodeficiency virus genome. Proc Natl Acad Sci U S A. 1994 Aug 30;91(18):8705–8709. [PMC free article] [PubMed]
  • Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987 Apr;162(1):156–159. [PubMed]
  • Cui T, Porter AG. Localization of binding site for encephalomyocarditis virus RNA polymerase in the 3'-noncoding region of the viral RNA. Nucleic Acids Res. 1995 Feb 11;23(3):377–382. [PMC free article] [PubMed]
  • Frankel AD, Mattaj IW, Rio DC. RNA-protein interactions. Cell. 1991 Dec 20;67(6):1041–1046. [PubMed]
  • Harris KS, Xiang W, Alexander L, Lane WS, Paul AV, Wimmer E. Interaction of poliovirus polypeptide 3CDpro with the 5' and 3' termini of the poliovirus genome. Identification of viral and cellular cofactors needed for efficient binding. J Biol Chem. 1994 Oct 28;269(43):27004–27014. [PubMed]
  • Jacobson SJ, Konings DA, Sarnow P. Biochemical and genetic evidence for a pseudoknot structure at the 3' terminus of the poliovirus RNA genome and its role in viral RNA amplification. J Virol. 1993 Jun;67(6):2961–2971. [PMC free article] [PubMed]
  • Kaine BP. Structure of the archaebacterial 7S RNA molecule. Mol Gen Genet. 1990 May;221(3):315–321. [PubMed]
  • Klump WM, Bergmann I, Müller BC, Ameis D, Kandolf R. Complete nucleotide sequence of infectious Coxsackievirus B3 cDNA: two initial 5' uridine residues are regained during plus-strand RNA synthesis. J Virol. 1990 Apr;64(4):1573–1583. [PMC free article] [PubMed]
  • Ladner JE, Jack A, Robertus JD, Brown RS, Rhodes D, Clark BF, Klug A. Structure of yeast phenylalanine transfer RNA at 2.5 A resolution. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4414–4418. [PMC free article] [PubMed]
  • Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. [PubMed]
  • Lama J, Sanz MA, Rodríguez PL. A role for 3AB protein in poliovirus genome replication. J Biol Chem. 1995 Jun 16;270(24):14430–14438. [PubMed]
  • Mans RM, Pleij CW, Bosch L. tRNA-like structures. Structure, function and evolutionary significance. Eur J Biochem. 1991 Oct 15;201(2):303–324. [PubMed]
  • Marino JP, Gregorian RS, Jr, Csankovszki G, Crothers DM. Bent helix formation between RNA hairpins with complementary loops. Science. 1995 Jun 9;268(5216):1448–1454. [PubMed]
  • Persson C, Wagner EG, Nordström K. 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. 1990 Nov;9(11):3767–3775. [PMC free article] [PubMed]
  • Persson C, Wagner EG, Nordström K. Control of replication of plasmid R1: formation of an initial transient complex is rate-limiting for antisense RNA--target RNA pairing. EMBO J. 1990 Nov;9(11):3777–3785. [PMC free article] [PubMed]
  • Philippe C, Eyermann F, Bénard L, Portier C, Ehresmann B, Ehresmann C. Ribosomal protein S15 from Escherichia coli modulates its own translation by trapping the ribosome on the mRNA initiation loading site. Proc Natl Acad Sci U S A. 1993 May 15;90(10):4394–4398. [PMC free article] [PubMed]
  • Pierangeli A, Bucci M, Pagnotti P, Degener AM, Perez Bercoff R. 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. 1995 Nov 6;374(3):327–332. [PubMed]
  • Pilipenko EV, Blinov VM, Chernov BK, Dmitrieva TM, Agol VI. Conservation of the secondary structure elements of the 5'-untranslated region of cardio- and aphthovirus RNAs. Nucleic Acids Res. 1989 Jul 25;17(14):5701–5711. [PMC free article] [PubMed]
  • Pilipenko EV, Gmyl AP, Maslova SV, Belov GA, Sinyakov AN, Huang M, Brown TD, Agol VI. Starting window, a distinct element in the cap-independent internal initiation of translation on picornaviral RNA. J Mol Biol. 1994 Aug 19;241(3):398–414. [PubMed]
  • Pilipenko EV, Maslova SV, Sinyakov AN, Agol VI. 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. 1992 Apr 11;20(7):1739–1745. [PMC free article] [PubMed]
  • Pleij CW. Pseudoknots: a new motif in the RNA game. Trends Biochem Sci. 1990 Apr;15(4):143–147. [PubMed]
  • Plotch SJ, Palant O. Poliovirus protein 3AB forms a complex with and stimulates the activity of the viral RNA polymerase, 3Dpol. J Virol. 1995 Nov;69(11):7169–7179. [PMC free article] [PubMed]
  • Rietveld K, Linschooten K, Pleij CW, Bosch L. The three-dimensional folding of the tRNA-like structure of tobacco mosaic virus RNA. A new building principle applied twice. EMBO J. 1984 Nov;3(11):2613–2619. [PMC free article] [PubMed]
  • Rietveld K, Van Poelgeest R, Pleij CW, Van Boom JH, Bosch L. The tRNA-like structure at the 3' terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA. Nucleic Acids Res. 1982 Mar 25;10(6):1929–1946. [PMC free article] [PubMed]
  • Rohll JB, Moon DH, Evans DJ, Almond JW. The 3' untranslated region of picornavirus RNA: features required for efficient genome replication. J Virol. 1995 Dec;69(12):7835–7844. [PMC free article] [PubMed]
  • Rohll JB, Percy N, Ley R, Evans DJ, Almond JW, Barclay WS. The 5'-untranslated regions of picornavirus RNAs contain independent functional domains essential for RNA replication and translation. J Virol. 1994 Jul;68(7):4384–4391. [PMC free article] [PubMed]
  • Sarnow P, Bernstein HD, Baltimore D. A poliovirus temperature-sensitive RNA synthesis mutant located in a noncoding region of the genome. Proc Natl Acad Sci U S A. 1986 Feb;83(3):571–575. [PMC free article] [PubMed]
  • Struck JC, Erdmann VA. Phylogenetic and biochemical evidence for a secondary structure model of a small cytoplasmic RNA from Bacilli. Eur J Biochem. 1990 Aug 28;192(1):17–24. [PubMed]
  • Sugimoto N, Kierzek R, Freier SM, Turner DH. Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry. 1986 Sep 23;25(19):5755–5759. [PubMed]
  • Sussman JL, Kim S. Three-dimensional structure of a transfer rna in two crystal forms. Science. 1976 May 28;192(4242):853–858. [PubMed]
  • Takeda N, Kuhn RJ, Yang CF, Takegami T, Wimmer E. Initiation of poliovirus plus-strand RNA synthesis in a membrane complex of infected HeLa cells. J Virol. 1986 Oct;60(1):43–53. [PMC free article] [PubMed]
  • Tang CK, Draper DE. Unusual mRNA pseudoknot structure is recognized by a protein translational repressor. Cell. 1989 May 19;57(4):531–536. [PubMed]
  • Todd S, Nguyen JH, Semler BL. RNA-protein interactions directed by the 3' end of human rhinovirus genomic RNA. J Virol. 1995 Jun;69(6):3605–3614. [PMC free article] [PubMed]
  • Toyoda H, Yang CF, Takeda N, Nomoto A, Wimmer E. Analysis of RNA synthesis of type 1 poliovirus by using an in vitro molecular genetic approach. J Virol. 1987 Sep;61(9):2816–2822. [PMC free article] [PubMed]
  • van Kuppeveld FJ, Galama JM, Zoll J, Melchers WJ. 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. 1995 Dec;69(12):7782–7790. [PMC free article] [PubMed]
  • Wimmer E, Hellen CU, Cao X. Genetics of poliovirus. Annu Rev Genet. 1993;27:353–436. [PubMed]
  • Zoll J, Jongen P, Galama J, van Kuppeveld F, Melchers W. Coxsackievirus B1-induced murine myositis: no evidence for viral persistence. J Gen Virol. 1993 Oct;74(Pt 10):2071–2076. [PubMed]
  • Zoll J, Galama J, Melchers W. Intratypic genome variability of the coxsackievirus B1 2A protease region. J Gen Virol. 1994 Mar;75(Pt 3):687–692. [PubMed]
  • Zwieb C. Structure and function of signal recognition particle RNA. Prog Nucleic Acid Res Mol Biol. 1989;37:207–234. [PubMed]

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