1887

Abstract

The secondary structure of the 3′ untranslated region (3′UTR) of picornaviruses is thought to be important for the initiation of negative-strand RNA synthesis. In this study, genetic and biological analyses of the 3′ terminus of coxsackievirus B2 (CVB2), which differs from other enteroviruses due to the presence of five additional nucleotides prior to the poly(A) tail, is reported. The importance of this extension was investigated using a 3′UTR mutant lacking the five nucleotides prior to the poly(A) tail and containing two point mutations. The predicted secondary structure within the 3′UTR of this mutant was less energetically favourable compared with that of the wild-type (wt) genotype. This mutant clone was transfected into green monkey kidney cells in four parallel experiments and propagated for multiple passages, enabling the virus to establish a stable revertant genotype. Genetic analysis of the virus progeny from these different passages revealed two major types of revertant. Both types showed wt-like growth properties and more stable and wt-like predicted secondary structures than the parent mutant clone. The first type of revertant neutralized the introduced point mutation with a compensatory second-site mutation, whereas the second type of revertant partly compensated for the deletion of the five proximal nucleotides by the insertion of nucleotides that matched the wt sequence. Therefore, the extended 3′ end of CVB2 may be considered to be a stabilizing sequence for RNA secondary structure and an important feature for the virus.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-82-6-1339
2001-06-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jgv/82/6/0821339a.html?itemId=/content/journal/jgv/10.1099/0022-1317-82-6-1339&mimeType=html&fmt=ahah

References

  1. Abrahams J., van den Berg M., van Batenburg E., Pleij C. W. A. 1990; Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Research 18:3035–3044
    [Google Scholar]
  2. Andino R., Rieckhof G. E., Achacoso P. L., Baltimore D. 1993; Poliovirus RNA synthesis utilizes an RNP complex formed around the 5′-end of viral RNA. EMBO Journal 12:3587–3598
    [Google Scholar]
  3. Belsham G. J., Sonenberg N. 2000; Picornavirus RNA translation: roles for cellular proteins. Trends in Microbiology 8:330–335
    [Google Scholar]
  4. Chang K. H., Auvinen A., Hyypiä T., Stanway G. 1989; The nucleotide sequence of coxsackievirus A9; implications for receptor binding and enterovirus classification. Journal of General Virology 70:3269–3280
    [Google Scholar]
  5. Cui T., Porter A. G. 1995; Localization of binding site for encephalomyocarditis virus RNA polymerase in the 3′-noncoding region of the viral RNA. Nucleic Acids Research 23:377–382
    [Google Scholar]
  6. Gamarnik A. V., Andino R. 1998; Switch from translation to RNA replication in a positive-stranded RNA virus. Genes & Development 12:2293–2304
    [Google Scholar]
  7. Gamarnik A. V., Andino R. 2000; Interactions of viral protein 3CD and poly(rC) binding protein with the 5′ untranslated region of the poliovirus genome. Journal of Virology 74:2219–2226
    [Google Scholar]
  8. Goodfellow I., Chaudhry Y., Richardson A., Meredith J., Almond J. W., Barclay W., Evans D. J. 2000; Identification of a cis -acting replication element within the poliovirus coding region. Journal of Virology 74:4590–4600
    [Google Scholar]
  9. Harris K. S., Xiang W., Alexander L., Lane W. S., Paul A. V., Wimmer E. 1994; 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. Journal of Biological Chemistry 269:27004–27014
    [Google Scholar]
  10. Hierholzer J., Killington R. 1996; Quantitation of virus; plaque assay. In Virology Methods Manual pp 38–39 Edited by Mahy B. W., Kangro H. O. London: Academic Press;
    [Google Scholar]
  11. Jang S. K., Kräusslich H.-G., Nicklin M. J. H., Duke G. M., Palmenberg A. C., Wimmer E. 1988; A segment of the 5′ nontranslated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation. Journal of Virology 62:2636–2643
    [Google Scholar]
  12. King A. M. Q., Brown F., Christian P., Hovi T., Hyypiä T., Knowles N. J., Lemon S. M., Minor P. D., Palmenberg A. C., Skern T., Stanway G. 2000; Picornaviridae . In Virus Taxonomy. Seventh Report of the International Committee for the Taxonomy of Viruses. pp 657–673 Edited by van Regenmortel M. H. V., Fauquet C. M., Bishop D. H. L., Calisher C. H., Carsten E. B., Estes M. K., Lemon S. M., Maniloff J., Mayo M. A., McGeoch D. J., Pringle C. R., Wickner R. B. New York: Academic Press;
  13. Klump W. M., Bergmann I., Mueller B. C., Ameis D., Kandolf R. 1990; Complete nucleotide sequence of infectious coxsackievirus B3 cDNA: two initial 5′ uridine residues are regained during plus-strand synthesis. Journal of Virology 64:1573–1583
    [Google Scholar]
  14. Lindberg A. M., Polacek C. 2000; Molecular analysis of the prototype coxsackievirus B5 genome. Archives of Virology 145:205–221
    [Google Scholar]
  15. Lindberg A. M., Crowell R. L., Zell R., Kandolf R., Pettersson U. 1992; Mapping of the RD phenotype of the Nancy strain of coxsackievirus B3. Virus Research 24:187–196
    [Google Scholar]
  16. Lindberg A. M., Polacek C., Johansson S. 1997; Amplification and cloning of complete enterovirus genomes by long distance PCR. Journal of Virological Methods 65:191–199
    [Google Scholar]
  17. Lindberg A. M., Johansson S., Andersson A. 1998; Echovirus 5: infectious transcripts and complete nucleotide sequence from uncloned cDNA. Virus Research 59:75–87
    [Google Scholar]
  18. McKnight K., Lemon S. 1996; Capsid coding sequence is required for efficient replication of human rhinovirus-14 RNA. Journal of Virology 70:1941–1952
    [Google Scholar]
  19. Melchers W. J. G., Hoenderop J. G. J., Bruins Slot H. J., Pleij C. W. A., Pilipenko E. V., Agol V. I., Galama J. M. D. 1997; Kissing of the two predominant hairpin loops in the coxsackie B virus 3′ untranslated region is the essential structural feature of the origin of the replication required for negative-strand RNA synthesis. Journal of Virology 71:686–696
    [Google Scholar]
  20. Melchers W. J. G., Bakkers J. M. J. E., Bruins Slot H. J., Galama J. M. D., Agol V. I., Pilipenko E. V. 2000; Cross-talk between orientation-dependent recognition determinants of a complex control RNA element, the enterovirus ori R. RNA 6:976–987
    [Google Scholar]
  21. Melnick J. L. 1996; Enteroviruses: polioviruses, coxsackieviruses, echoviruses, and newer enteroviruses. In Fields Virology pp 655–712 Edited by Fields B. N., Knipe D. M., Howley P. M. Philadelphia: Lippincott–Raven;
    [Google Scholar]
  22. Meredith J., Rohll J. B., Almond J. W., Evans D. J. 1999; Similar interactions of the poliovirus and rhinovirus 3D polymerase with the 3′ untranslated region of rhinovirus 14. Journal of Virology 73:9952–9958
    [Google Scholar]
  23. Mirmomeni M. H., Hughes P. J., Stanway G. 1997; An RNA tertiary structure in the 3′untranslated region of enteroviruses is necessary for efficient replication. Journal of Virology 71:2363–2370
    [Google Scholar]
  24. Parsley T., Towner J., Blyn L., Ehrenfeld E., Semler B. 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
    [Google Scholar]
  25. Paul A. V., van Boom J. H., Filippov D., Wimmer E. 1998; Protein-primed RNA synthesis by purified poliovirus RNA polymerase. Nature 393:280–284
    [Google Scholar]
  26. Pelletier J., Kaplan G., Racaniello V. R., Sonenberg N. 1988; Cap-independent translation of poliovirus mRNA is conferred by sequence elements within the 5′ noncoding region. Molecular and Cellular Biology 8:1103–1112
    [Google Scholar]
  27. Pilipenko E. V., Maslova S. V., Sinyakov A. N., Agol V. I. 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 Research 20:1739–1745
    [Google Scholar]
  28. Pilipenko E. V., Poperechny K. V., Maslova S. V., Melchers W. J. G., Bruins Slot H. J., Agol V. I. 1996; Cis -element, ori R, involved in the initiation of (−)strand poliovirus RNA: a quasi-globular multi-domain RNA structure maintained by tertiary (‘kissing’) interactions. EMBO Journal 15:5428–5436
    [Google Scholar]
  29. Polacek C., Lundgren A., Andersson A., Lindberg A. M. 1999; Genomic and phylogenetic characterization of coxsackievirus B2 prototype strain Ohio-1 . Virus Research 59:229–238
    [Google Scholar]
  30. Reed L. J., Muench H. 1938; A simple method of estimating fifty per cent endpoints. American Journal of Hygiene 27:493–497
    [Google Scholar]
  31. Rohll J. B., Percy N., Ley R., Evans D. J., Almond J. W., Barclay W. S. 1994; The 5′-untranslated regions of picornavirus RNAs contain-independent functional domains essential for RNA replication and translation. Journal of Virology 68:4384–4391
    [Google Scholar]
  32. Rohll J. B., Moon D. H., Evans D. J., Almond J. W. 1995; The 3′ untranslated region of picornavirus RNA: features required for efficient genome replication. Journal of Virology 69:7835–7844
    [Google Scholar]
  33. Sallés F. J., Richards W. G., Strickland S. 1999; Assaying the polyadenylation state of mRNAs. Methods in Enzymology 17:38–45
    [Google Scholar]
  34. Spector D. H., Baltimore D. 1974; Requirement of 3′-terminal poly(adenylic acid) for the infectivity of poliovirus RNA. Proceedings of the National Academy of Sciences, USA 71:2983–2987
    [Google Scholar]
  35. Spector D. H., Baltimore D. 1975; Polyadenylic acid on poliovirus RNA. IV. Poly(U) in replicative intermediate and soluble-stranded RNA. Virology 67:498–505
    [Google Scholar]
  36. Todd S., Towner J. S., Brown D. M., Semler B. L. 1997; Replication-competent picornaviruses with complete genomic RNA 3′ noncoding region deletions. Journal of Virology 71:8868–8874
    [Google Scholar]
  37. Toyoda H., Yang C.-F., Takeda N., Nomoto A., Wimmer E. 1987; Analysis of RNA synthesis of type 1 poliovirus by using an in vitro molecular genetic approach. Journal of Virology 61:2816–2822
    [Google Scholar]
  38. Trono D., Andino R., Baltimore D. 1988; An RNA sequence of hundreds of nucleotides at the 5′ end of poliovirus RNA is involved in allowing viral protein synthesis. Journal of Virology 62:2291–2299
    [Google Scholar]
  39. Wang J., Bakkers J. M. J. E., Galama J. M. D., Bruins Slot H. J., Pilipenko E. V., Agol V. I., Melchers W. J. G. 1999; Structural requirements of the higher order RNA kissing element in the enteroviral 3′UTR. Nucleic Acids Research 27:485–490
    [Google Scholar]
  40. Yogo Y., Wimmer E. 1972; Polyadenylic acid at the 3′-terminus of poliovirus RNA. Proceedings of the National Academy of Sciences, USA 69:1877–1882
    [Google Scholar]
  41. Zhao J., Hyman L., Moore C. 1999; Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiology and Molecular Biology Reviews 63:405–445
    [Google Scholar]
  42. Zuker M., Mathews D. H., Turner D. H. 1999; Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In RNA Biochemistry and Biotechnology pp 11–43 NATO ASI Series Edited by Clark B. F. C., Barciszewski J. Dordrecht: Kluwer;
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-82-6-1339
Loading
/content/journal/jgv/10.1099/0022-1317-82-6-1339
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error