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. 1987 Sep 11;15(17):7067–7079. doi: 10.1093/nar/15.17.7067

Potential secondary and tertiary structure in the genomic RNA of foot and mouth disease virus.

B E Clarke 1, A L Brown 1, K M Currey 1, S E Newton 1, D J Rowlands 1, A R Carroll 1
PMCID: PMC306193  PMID: 2821491

Abstract

The nucleotide sequence of the 5' untranslated region of foot and mouth disease virus (FMDV), serotype A10 has been determined. This completes the first total genomic sequence for any one serotype of FMDV. Analysis of the sequence to the 3' side of the poly (C) tract reveals the presence of a 24 nucleotide repeated motif which has homologies with a sequence located upstream of the transcriptional initiation site from several mammalian fibrinogen genes. The function of this element in FMDV is unclear. However, computer analysis of this region predicts the presence of a high degree of secondary and tertiary structure in which these repeats form an important part. The implications of these predictions are discussed.

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Selected References

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  1. Arnold E., Luo M., Vriend G., Rossmann M. G., Palmenberg A. C., Parks G. D., Nicklin M. J., Wimmer E. Implications of the picornavirus capsid structure for polyprotein processing. Proc Natl Acad Sci U S A. 1987 Jan;84(1):21–25. doi: 10.1073/pnas.84.1.21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Beck E., Forss S., Strebel K., Cattaneo R., Feil G. Structure of the FMDV translation initiation site and of the structural proteins. Nucleic Acids Res. 1983 Nov 25;11(22):7873–7885. doi: 10.1093/nar/11.22.7873. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Boothroyd J. C., Harris T. J., Rowlands D. J., Lowe P. A. The nucleotide sequence of cDNA coding for the structural proteins of foot-and-mouth disease virus. Gene. 1982 Feb;17(2):153–161. doi: 10.1016/0378-1119(82)90068-3. [DOI] [PubMed] [Google Scholar]
  4. Burroughs J. N., Sangar D. V., Clarke B. E., Rowlands D. J., Billiau A., Collen D. Multiple proteases in foot-and-mouth disease virus replication. J Virol. 1984 Jun;50(3):878–883. doi: 10.1128/jvi.50.3.878-883.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Carroll A. R., Rowlands D. J., Clarke B. E. The complete nucleotide sequence of the RNA coding for the primary translation product of foot and mouth disease virus. Nucleic Acids Res. 1984 Mar 12;12(5):2461–2472. doi: 10.1093/nar/12.5.2461. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chung D. W., Rixon M. W., MacGillivray R. T., Davie E. W. Characterization of a cDNA clone coding for the beta chain of bovine fibrinogen. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1466–1470. doi: 10.1073/pnas.78.3.1466. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Clarke B. E., Sangar D. V., Burroughs J. N., Newton S. E., Carroll A. R., Rowlands D. J. Two initiation sites for foot-and-mouth disease virus polyprotein in vivo. J Gen Virol. 1985 Dec;66(Pt 12):2615–2626. doi: 10.1099/0022-1317-66-12-2615. [DOI] [PubMed] [Google Scholar]
  8. Cohen J. I., Ticehurst J. R., Purcell R. H., Buckler-White A., Baroudy B. M. Complete nucleotide sequence of wild-type hepatitis A virus: comparison with different strains of hepatitis A virus and other picornaviruses. J Virol. 1987 Jan;61(1):50–59. doi: 10.1128/jvi.61.1.50-59.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Currey K. M., Peterlin B. M., Maizel J. V., Jr Secondary structure of poliovirus RNA: correlation of computer-predicted with electron microscopically observed structure. Virology. 1986 Jan 15;148(1):33–46. doi: 10.1016/0042-6822(86)90401-0. [DOI] [PubMed] [Google Scholar]
  10. Evans D. M., Dunn G., Minor P. D., Schild G. C., Cann A. J., Stanway G., Almond J. W., Currey K., Maizel J. V., Jr Increased neurovirulence associated with a single nucleotide change in a noncoding region of the Sabin type 3 poliovaccine genome. Nature. 1985 Apr 11;314(6011):548–550. doi: 10.1038/314548a0. [DOI] [PubMed] [Google Scholar]
  11. Forss S., Strebel K., Beck E., Schaller H. Nucleotide sequence and genome organization of foot-and-mouth disease virus. Nucleic Acids Res. 1984 Aug 24;12(16):6587–6601. doi: 10.1093/nar/12.16.6587. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Fowlkes D. M., Mullis N. T., Comeau C. M., Crabtree G. R. Potential basis for regulation of the coordinately expressed fibrinogen genes: homology in the 5' flanking regions. Proc Natl Acad Sci U S A. 1984 Apr;81(8):2313–2316. doi: 10.1073/pnas.81.8.2313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kozak M. Influences of mRNA secondary structure on initiation by eukaryotic ribosomes. Proc Natl Acad Sci U S A. 1986 May;83(9):2850–2854. doi: 10.1073/pnas.83.9.2850. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kurz C., Forss S., Küpper H., Strohmaier K., Schaller H. Nucleotide sequence and corresponding amino acid sequence of the gene for the major antigen of foot and mouth disease virus. Nucleic Acids Res. 1981 Apr 24;9(8):1919–1931. doi: 10.1093/nar/9.8.1919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Larsen G. R., Semler B. L., Wimmer E. Stable hairpin structure within the 5'-terminal 85 nucleotides of poliovirus RNA. J Virol. 1981 Jan;37(1):328–335. doi: 10.1128/jvi.37.1.328-335.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Makoff A. J., Paynter C. A., Rowlands D. J., Boothroyd J. C. Comparison of the amino acid sequence of the major immunogen from three serotypes of foot and mouth disease virus. Nucleic Acids Res. 1982 Dec 20;10(24):8285–8295. doi: 10.1093/nar/10.24.8285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Mellor E. J., Brown F., Harris T. J. Analysis of the secondary structure of the poly(C) tract in foot-and-mouth disease virus RNAs. J Gen Virol. 1985 Sep;66(Pt 9):1919–1929. doi: 10.1099/0022-1317-66-9-1919. [DOI] [PubMed] [Google Scholar]
  18. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  19. Newton S. E., Carroll A. R., Campbell R. O., Clarke B. E., Rowlands D. J. The sequence of foot-and-mouth disease virus RNA to the 5' side of the poly(C) tract. Gene. 1985;40(2-3):331–336. doi: 10.1016/0378-1119(85)90057-5. [DOI] [PubMed] [Google Scholar]
  20. Palmenberg A. C., Kirby E. M., Janda M. R., Drake N. L., Duke G. M., Potratz K. F., Collett M. S. The nucleotide and deduced amino acid sequences of the encephalomyocarditis viral polyprotein coding region. Nucleic Acids Res. 1984 Mar 26;12(6):2969–2985. doi: 10.1093/nar/12.6.2969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Pelletier J., Sonenberg N. Insertion mutagenesis to increase secondary structure within the 5' noncoding region of a eukaryotic mRNA reduces translational efficiency. Cell. 1985 Mar;40(3):515–526. doi: 10.1016/0092-8674(85)90200-4. [DOI] [PubMed] [Google Scholar]
  22. Pelletier J., Sonenberg N. Photochemical cross-linking of cap binding proteins to eucaryotic mRNAs: effect of mRNA 5' secondary structure. Mol Cell Biol. 1985 Nov;5(11):3222–3230. doi: 10.1128/mcb.5.11.3222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Pleij C. W., Rietveld K., Bosch L. A new principle of RNA folding based on pseudoknotting. Nucleic Acids Res. 1985 Mar 11;13(5):1717–1731. doi: 10.1093/nar/13.5.1717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Racaniello V. R., Baltimore D. Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome. Proc Natl Acad Sci U S A. 1981 Aug;78(8):4887–4891. doi: 10.1073/pnas.78.8.4887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Racaniello V. R., Meriam C. Poliovirus temperature-sensitive mutant containing a single nucleotide deletion in the 5'-noncoding region of the viral RNA. Virology. 1986 Dec;155(2):498–507. doi: 10.1016/0042-6822(86)90211-4. [DOI] [PubMed] [Google Scholar]
  26. Robertson B. H., Grubman M. J., Weddell G. N., Moore D. M., Welsh J. D., Fischer T., Dowbenko D. J., Yansura D. G., Small B., Kleid D. G. Nucleotide and amino acid sequence coding for polypeptides of foot-and-mouth disease virus type A12. J Virol. 1985 Jun;54(3):651–660. doi: 10.1128/jvi.54.3.651-660.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Robertson B. H., Morgan D. O., Moore D. M., Grubman M. J., Card J., Fischer T., Weddell G., Dowbenko D., Yansura D. Identification of amino acid and nucleotide sequence of the foot-and-mouth disease virus RNA polymerase. Virology. 1983 Apr 30;126(2):614–623. doi: 10.1016/s0042-6822(83)80017-8. [DOI] [PubMed] [Google Scholar]
  28. Rowlands D. J., Harris T. J., Brown F. More precise location of the polycytidylic acid tract in foot and mouth disease virus RNA. J Virol. 1978 May;26(2):335–343. doi: 10.1128/jvi.26.2.335-343.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Sangar D. V., Black D. N., Rowlands D. J., Harris T. J., Brown F. Location of the initiation site for protein synthesis on foot-and-mouth disease virus RNA by in vitro translation of defined fragments of the RNA. J Virol. 1980 Jan;33(1):59–68. doi: 10.1128/jvi.33.1.59-68.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Sangar D. V., Newton S. E., Rowlands D. J., Clarke B. E. All foot and mouth disease virus serotypes initiate protein synthesis at two separate AUGs. Nucleic Acids Res. 1987 Apr 24;15(8):3305–3315. doi: 10.1093/nar/15.8.3305. [DOI] [PMC free article] [PubMed] [Google Scholar]

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