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Comparative analysis of the large fragment of the 5′ untranslated region (LF-5′ UTR) of serotype A foot-and-mouth disease virus field isolates from India

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Abstract

India is endemic for foot-and-mouth disease (FMD) and in recent years a unique group within serotype A, carrying a codon deletion at an antigenically critical site in capsid protein VP3 has emerged (VP359-deletion group). This tempted us to analyze the noncoding region, which is an under represented area, though critically associated with virus biology and pathogenesis. Analysis of the large fragment of 5′ untranslated region (LF-5′ UTR) of type A FMD virus revealed discrepancy in the overall tree topology between LF-5′ UTR and 1D region possibly due to independent evolution of coding and noncoding regions. The VP359-deletion group maintained its phylogenetic distinctness even at the LF-5′ UTR. Eighteen lineage specific signatures detected here support independent evolutionary paths for the lineages. Extensive deletions of 45 and 89 nucleotides corresponding to the pseudoknot region were noticed. Conservation pattern in the ‘A253AACA’ motif in the cre/bus stem-loop indicates the importance of first three ‘A’ residues in VPg uridylylation. Of the three polypyrimidine tract binding protein (PTB) binding sites mapped on the internal ribosome entry site (IRES), the pyrimidine tract (Py tract) in the loop of domain 2 was found to be maximally conserved and it might be the major PTB binding site. Strikingly, a deletion group lineage specific transversion was noticed in the Py tract at the 3′ end of IRES without significantly affecting its in vitro infectious titer. Hence, we presume that for efficient cap-independent viral translation, either a minimum number of pyrimidine residues rather than a complete Py tract or a Py tract tolerating transversions only at specific locations and a core motif ‘CUUU’ within the Py tract is essential.

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References

  1. R.K. Jangra, C. Tosh, A. Sanyal, D. Hemadri, S.K. Bandyopadhyay, Virus Res. 112, 52–59 (2005). doi:https://doi.org/10.1016/j.virusres.2005.03.021

    Article  CAS  Google Scholar 

  2. C. Tosh, A. Sanyal, D. Hemadri, R. Venkataraman, Arch. Virol. 147, 493–513 (2002). doi:https://doi.org/10.1007/s007050200002

    Article  CAS  Google Scholar 

  3. J.K. Mohapatra, D. Hemadri, T.V.S. Rao, B.P. Sreenivasa, S. Subramaniam, A. Sanyal, T.R. Periyasamy, N.K. Singh, B. Pattnaik, R. Venkataramanan, Vet. Microbiol. 131, 65–72 (2008). doi:https://doi.org/10.1016/j.vetmic.2008.02.020

    Article  CAS  Google Scholar 

  4. S. Forss, K. Strebel, E. Beck, H. Schaller, Nucleic Acids Res. 12, 6587–6601 (1984). doi:https://doi.org/10.1093/nar/12.16.6587

    Article  CAS  Google Scholar 

  5. B.E. Clarke, A.L. Brown, K.M. Currey, S.E. Newton, D.J. Rowlands, A.R. Carroll, Nucleic Acids Res. 15, 7067–7079 (1987). doi:https://doi.org/10.1093/nar/15.17.7067

    Article  CAS  Google Scholar 

  6. P.W. Mason, S.V. Bezborodova, T.M. Henry, J. Virol. 76, 9686–9694 (2002). doi:https://doi.org/10.1128/JVI.76.19.9686-9694.2002

    Article  CAS  Google Scholar 

  7. G.J. Belsham, J.K. Brangwyn, J. Virol. 64, 5389–5395 (1990)

    CAS  PubMed  PubMed Central  Google Scholar 

  8. R. Kuhn, N. Luz, E. Beck, J. Virol. 64, 4625–4631 (1990)

    CAS  PubMed  PubMed Central  Google Scholar 

  9. E.V. Pilipenko, V.M. Blinov, B.K. Chernov, T.M. Dmitrieva, V.I. Agol, Nucleic Acids Res. 17, 5701–5711 (1989). doi:https://doi.org/10.1093/nar/17.14.5701

    Article  CAS  Google Scholar 

  10. A. Nayak, I.G. Goodfellow, K.E. Woolaway, J. Birtley, S. Curry, G.J. Belsham, J. Virol. 80, 9865–9875 (2006). doi:https://doi.org/10.1128/JVI.00561-06

    Article  CAS  Google Scholar 

  11. N. Luz, E. Beck, FEBS Lett. 269, 311–314 (1990). doi:https://doi.org/10.1016/0014-5793(90)81182-N

    Article  CAS  Google Scholar 

  12. S.R. Stewart, B.L. Semler, Semin. Virol. 8, 242–255 (1997). doi:https://doi.org/10.1006/smvy.1997.0127

    Article  CAS  Google Scholar 

  13. S. Lopez de Quinto, E. Lafuente, E. Martinez-Salas, RNA 7, 1213–1226 (2001). doi:https://doi.org/10.1017/S1355838201010433

    Article  CAS  Google Scholar 

  14. R. Ramos, E. Martinez-Salas, RNA 5, 1374–1383 (1999). doi:https://doi.org/10.1017/S1355838299991240

    Article  CAS  Google Scholar 

  15. S. Biswas, A. Sanyal, D. Hemadri, C. Tosh, J.K. Mohapatra, R. Manoj Kumar, S.K. Bandyopadhaya, Arch. Virol. 150, 2217–2239 (2005). doi:https://doi.org/10.1007/s00705-005-0576-z

    Article  CAS  Google Scholar 

  16. C. Carrillo, E.R. Tulman, G. Delhon, Z. Lu, A. Carreno, A. Vagnozzi, G.F. Kutish, D.L. Rock, J. Virol. 79, 6487–6504 (2005). doi:https://doi.org/10.1128/JVI.79.10.6487-6504.2005

    Article  CAS  Google Scholar 

  17. J.K. Mohapatra, A. Sanyal, D. Hemadri, C. Tosh, S. Biswas, T.J. Rasool, S.K. Bandyopadhyay, B. Pattnaik, Virus Res. 136, 16–29 (2008). doi:https://doi.org/10.1016/j.virusres.2008.04.010

    Article  CAS  Google Scholar 

  18. E.V. Pilipenko, E.G. Victorova, S.T. Guest, V.I. Agol, R.P. Roos, EMBO J. 20, 6899–6908 (2001). doi:https://doi.org/10.1093/emboj/20.23.6899

    Article  CAS  Google Scholar 

  19. C.E. Malnou, T.A. Poyry, R.J. Jackson, K.M. Kean, J. Virol. 76, 10617–10626 (2002). doi:https://doi.org/10.1128/JVI.76.21.10617-10626.2002

    Article  CAS  Google Scholar 

  20. E. Martinez-Salas, J.C. Saiz, M. Davila, G.J. Belsham, E. Domingo, J. Virol. 67, 3748–3755 (1993)

    CAS  PubMed  PubMed Central  Google Scholar 

  21. N.J. Knowles, A.R. Samuel, in Rpt. Sess. Res. Gp. Stand. Tech. Comm. Eur. Comm. Control of FMD (FAO), Vienna, Austria, September 1994, p. 45–53 (1995)

  22. J.D. Thompson, D.G. Higgins, T.J. Gibson, Nucleic Acids Res. 22, 4673–4680 (1994). doi:https://doi.org/10.1093/nar/22.22.4673

    Article  CAS  Google Scholar 

  23. K. Tamura, J. Dudley, M. Nei, S. Kumar, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. (2007). doi: https://doi.org/10.1093/molbev/msm092

    Article  CAS  Google Scholar 

  24. N. Saitou, M. Nei, Mol. Biol. 4, 406–425 (1987)

    CAS  Google Scholar 

  25. P.H.A. Sneath, R.R. Sokal, Numerical Taxonomy (Freeman, San Francisco, 1973)

    Google Scholar 

  26. J. Felsenstein, Evol. Int. J. Org. Evol. 39, 783–791 (1985). doi:https://doi.org/10.2307/2408678

    Article  Google Scholar 

  27. K. Tamura, M. Nei, Mol. Biol. Evol. 10, 512–526 (1993)

    CAS  PubMed  Google Scholar 

  28. K. Tamura, S. Kumar, Mol. Biol. Evol. 19, 1727–1736 (2002)

    Article  CAS  Google Scholar 

  29. S.C. Ray, SimPlot for Windows 95, version 2.5 (1999), www.med.jhu.edu/deptmed/sray/download. Accessed 15 Nov 2008.

  30. J. Reeder, R. Giegerich, BMC Bioinformatics 5, 104 (2004). doi:https://doi.org/10.1186/1471-2105-5-104

    Article  Google Scholar 

  31. L. Heath, E. van der Walt, A. Varsani, D.P. Martin, J. Virol. 80, 11827–11832 (2006). doi:https://doi.org/10.1128/JVI.01100-06

    Article  CAS  Google Scholar 

  32. C. Escarmis, J. Dopazo, M. Davila, E.L. Palma, E. Domingo, Virus Res. 35, 155–167 (1995). doi:https://doi.org/10.1016/0168-1702(94)00091-P

    Article  CAS  Google Scholar 

  33. S. Lopez de Quinto, E. Martinez-Salas, J. Virol. 71, 4171–4175 (1997)

    CAS  PubMed  PubMed Central  Google Scholar 

  34. O. Fernandez-Miragall, S. Lopez de Quinto, E. Martinez-Salas. Virus Res. 139, 172–182 (2009). doi:https://doi.org/10.1016/j.virusres.2008.07.009

    Article  CAS  Google Scholar 

  35. S. Lopez de Quinto, E. Martinez-Salas, RNA 6, 1380–1392 (2000). doi:https://doi.org/10.1017/S1355838200000753

    Article  CAS  Google Scholar 

  36. E.V. Pilipenko, T.V. Pestova, V.G. Kolupaeva, E.V. Khitrina, A.N. Poperechnaya, V.I. Agol, C.U.T. Hellen, Genes Dev. 14, 2028–2045 (2000)

    CAS  PubMed  PubMed Central  Google Scholar 

  37. C. Escarmis, M. Toja, M. Medina, E. Domingo, Virus Res. 26, 113–125 (1992). doi:https://doi.org/10.1016/0168-1702(92)90151-X

    Article  CAS  Google Scholar 

  38. Q. Feng, H. Yu, Y. Liu, C. He, J. Hu, H. Sang, N. Ding, M. Ding, Y.W. Fung, L. Lau, A.C. Yu, J. Chen, Biochem. Biophys. Res. Commun. 323, 254–263 (2004). doi:https://doi.org/10.1016/j.bbrc.2004.08.086

    Article  CAS  Google Scholar 

  39. P.W. Mason, M.J. Grubman, B. Baxt, Virus Res. 91, 9–32 (2003). doi:https://doi.org/10.1016/S0168-1702(02)00257-5

    Article  CAS  Google Scholar 

  40. A.V. Paul, J. Yin, J. Mugavero, E. Rieder, Y. Liu, E. Wimmer, J. Biol. Chem. 278, 43951–43960 (2003). doi:https://doi.org/10.1074/jbc.M307441200

    Article  CAS  Google Scholar 

  41. O. Fernandez-Miragall, E. Martinez-Salas, RNA 9, 1333–1344 (2003). doi:https://doi.org/10.1261/rna.5950603

    Article  CAS  Google Scholar 

  42. P. Serrano, J. Gomez, E. Martinez-Salas, RNA 13, 849–859 (2007). doi:https://doi.org/10.1261/rna.506607

    Article  CAS  Google Scholar 

  43. B.L. Walter, J.H. Nguyen, E. Ehrenfeld, B.L. Semler, RNA 5, 1570–1585 (1999). doi:https://doi.org/10.1017/S1355838299991483

    Article  CAS  Google Scholar 

  44. I.A. Stassinopoulos, G.J. Belsham, RNA 7, 114–122 (2001). doi:https://doi.org/10.1017/S1355838201001170

    Article  CAS  Google Scholar 

  45. E. Martinez-salas, S. Lopez de Quinto, R. Ramos, O. Fernandez-Miragall, Biochimie 84, 755–763 (2002). doi:https://doi.org/10.1016/S0300-9084(02)01408-6

    Article  CAS  Google Scholar 

  46. O. Fernandez-Miragall, R. Ramos, J. Ramajo, E. Martinez-Salas, RNA 12, 223–234 (2006). doi:https://doi.org/10.1261/rna.2153206

    Article  CAS  Google Scholar 

  47. P. Nissen, J.A. Ippolito, N. Ban, P.B. Moore, T.A. Steitz, Proc. Natl. Acad. Sci. USA 98, 4899–4903 (2001). doi:https://doi.org/10.1073/pnas.081082398

    Article  CAS  Google Scholar 

  48. E. Martinez-Salas, M.P. Regalado, E. Domingo, J. Virol. 70, 992–998 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  49. L. Saleh, C.R. Rust, R. Fullkrug, E. Beck, G. Bassili, K. Ochs, M. Niepman, J. Gen. Virol. 82, 757–763 (2001)

    Article  CAS  Google Scholar 

  50. O. Hagenbuchle, M. Santer, J.A. Steitz, Cell 13, 551–563 (1978). doi:https://doi.org/10.1016/0092-8674(78)90328-8

    Article  CAS  Google Scholar 

  51. V.G. Kolupaeva, C.U. Hellen, I.N. Shatsky, RNA 2, 1199–1212 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  52. N. Luz, E. Beck, J. Virol. 65, 6486–6494 (1991)

    CAS  PubMed  PubMed Central  Google Scholar 

  53. C.R. Rust, K. Ochs, K. Meyer, E. Beck, M. Niepmann, J. Virol. 73, 6111–6113 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  54. A. Kaminski, G.J. Belsham, R.J. Jackson, EMBO J. 13, 1673–1681 (1994)

    Article  CAS  Google Scholar 

  55. R. Nicholson, J. Pelletier, S.Y. Le, N. Sonenberg, J. Virol. 65, 5886–5894 (1991)

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Y. Kaku, L.S. Chard, T. Inoue, G.J. Belsham, J. Virol. 76, 11721–11728 (2002). doi:https://doi.org/10.1128/JVI.76.22.11721-11728.2002

    Article  CAS  Google Scholar 

  57. G.J. Belsham, N. Sonenberg, Microbiol. Rev. 60, 499–511 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  58. G.J. Belsham, R.J. Jackson, in Translational Control of Gene Expression, ed. by N. Sonenberg, J.W.B. Hershey, M.B. Mathews (Cold Spring Harbor, New York, 2000), pp. 869–900

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Acknowledgments

This work was supported by the Indian Council of Agricultural Research. We sincerely thank all the past and continuing scientists of PD on FMD who have been instrumental in maintaining the National FMD Virus Repository. Efforts of Dr G. K. Sharma in formatting the references is appreciated.

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  1. Project Directorate on Foot and Mouth Disease, Indian Veterinary Research Institute Campus, Mukteswar-Kumaon, Nainital, 263138, Uttarakhand, India

    Jajati K. Mohapatra, Abhipsa Sahu, Sushanta K. Barik, Aniket Sanyal & Bramhadev Pattnaik

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  1. Jajati K. Mohapatra
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  2. Abhipsa Sahu
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Correspondence to Jajati K. Mohapatra.

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Mohapatra, J.K., Sahu, A., Barik, S.K. et al. Comparative analysis of the large fragment of the 5′ untranslated region (LF-5′ UTR) of serotype A foot-and-mouth disease virus field isolates from India. Virus Genes 39, 81–89 (2009). https://doi.org/10.1007/s11262-009-0366-x

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