1887

Abstract

cytoplasmic polyhedrosis virus is a segmented dsRNA virus of the family . Segment 2 (S2)-encoded RNA-dependent RNA polymerase (RdRp) helps the virus to propagate its genome in the host cell of the silkworm, . Cloning, expression, purification and functional analysis of individual domains of RdRp have demonstrated that the purified domains interact . The central polymerase domain (PD) shows nucleotide binding properties, but neither the N-terminal domain (NTD) nor the C-terminal domain (CTD). Isolated PD does not exhibit RdRp activity but this activity can be reconstituted when all three domains are included in the reaction mixture. Molecular dynamics simulation suggests that the isolated PD has increased internal motions in comparison to when it is associated with the NTD and CTD. The motions of the separated PD may lead to the formation of a less accessible RNA template-binding channel and, thus, impair RdRp activity.

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2016-07-01
2021-10-24
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References

  1. Biswas P., Kundu A., Ghosh A. K. 2014a; Genome segment 4 of Antheraea mylitta cytoplasmic polyhedrosis virus encodes RNA triphosphatase and methyltransferases. J Gen Virol 96:95–105 [View Article]
    [Google Scholar]
  2. Biswas P., Kundu A., Ghosh A. K. 2014b; Genome segment 5 of Antheraea mylitta cytoplasmic polyhedrosis virus encodes a bona fide guanylyltransferase. Virol J 11:1–13 [View Article]
    [Google Scholar]
  3. Bradford M. M. 1976; A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein dye binding. Anal Biochem 131:499–503
    [Google Scholar]
  4. Chakrabarti M., Ghorai S., Mani S. K. K., Ghosh A. K. 2010; Molecular characterization of genome segments 1 and 3 encoding two capsid proteins of Antheraea mylitta cytoplasmic polyhedrosis virus. Virology J 7:181–191 [View Article]
    [Google Scholar]
  5. Chavali V. R., Ghosh A. K. 2007; Molecular cloning, sequence analysis and expression of genome segment 7 (S7) of Antheraea mylitta cypovirus (AmCPV) that encodes a viral structural protein. Virus Genes 35:433–441 [View Article][PubMed]
    [Google Scholar]
  6. Chavali V. R., Madhurantakam C., Ghorai S., Roy S., Das A. K., Ghosh A. K. 2008; Genome segment 6 of Antheraea mylitta cypovirus encodes a structural protein with ATPase activity. Virology 377:7–18 [View Article][PubMed]
    [Google Scholar]
  7. Davis B. C., Thorpe I. F. 2013; Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase. Proteins 81:40–52 [View Article]
    [Google Scholar]
  8. Ghorai S., Chakrabarti M., Roy S., Chavali V. R., Bagchi A., Ghosh A. K. 2010; Molecular characterization of genome segment 2 encoding RNA dependent RNA polymerase of Antheraea mylitta cytoplasmic polyhedrosis virus. Virology 404:21–31 [View Article][PubMed]
    [Google Scholar]
  9. Ivetac A., McCammon J. A. 2009; Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations. J Mol Biol 388:644–658 [View Article][PubMed]
    [Google Scholar]
  10. Jangam S. R., Chakrabarti M., Ghosh A. K. 2006; Molecular cloning, expression and analysis of Antheraea mylitta cypovirus genome segments 8 and 11. Int J Virol 3:60–72 [CrossRef]
    [Google Scholar]
  11. Jolly M. S., Sen S. K., Ahsan M. M. 1974 Tasar Culture Bombay: Ambika Publishers;
    [Google Scholar]
  12. Jorgensen W. L., Tirado-Rives J. 1988; The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657–1666 [CrossRef]
    [Google Scholar]
  13. Kundu A., Dutta A., Biswas P., Das A. K., Ghosh A. K. 2015; Functional insights from molecular modeling, docking and dynamics study of a cypoviral RNA-dependent RNA polymerase. J Mol Graph Mod 61:160–174 [CrossRef]
    [Google Scholar]
  14. Lakowicz J. R. 2006 Principles of Fluorescence Spectroscopy, 3rd edn. New York: Springer; [CrossRef]
    [Google Scholar]
  15. Liu H., Cheng L. 2015; Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus. Science 349:1347–1350 [View Article][PubMed]
    [Google Scholar]
  16. Liu Y., Jiang W. W., Pratt J., Rockway T., Harris K., Vasavanonda S., Tripathi R., Pithawalla R., Kati W. M. 2006; Mechanistic study of HCV polymerase inhibitors at individual steps of the polymerization reaction. Biochemistry 45:11312–11323 [View Article][PubMed]
    [Google Scholar]
  17. Lu X., McDonald S. M., Tortorici M. A., Tao Y. J., Vasquez-Del Carpio R., Nibert M. L., Patton J. T., Harrison S. C. 2008; Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1. Structure 16:1678–1688 [View Article][PubMed]
    [Google Scholar]
  18. McDonald S. M., Patton J. T. 2009; Rotavirus VP2 core shell regions critical for viral polymerase activation. J Virol 85:3095–4105 [CrossRef]
    [Google Scholar]
  19. McDonald S. M., Tao Y. J., Patton J. T. 2009; The ins and outs of four-tunneled Reoviridae RNA-dependent RNA polymerases. Curr Opin Struct Biol 19:775–782 [View Article][PubMed]
    [Google Scholar]
  20. Mertens P. P. C., Rao S., Zhou Z. H. 2005; Cypovirus. In Virus Taxonomy, 8th Report of the ICTV pp 522–533 Edited by Fauquet C. M., Mayo M. A., Maniloff J., Desselberger U., Ball L. A. Amsterdam: Elsevier;
    [Google Scholar]
  21. Moustafa I. M., Shen H., Morton B., Colina C. M., Cameron C. E. 2011; Molecular dynamics simulations of viral RNA polymerases link conserved and correlated motions of functional elements to fidelity. J Mol Biol 410:159–181 [View Article][PubMed]
    [Google Scholar]
  22. Oh J. W., Ito T., Lai M. M. 1999; A recombinant hepatitis C virus RNA-dependent RNA polymerase capable of copying the full-length viral RNA. J Virol 73:7694–7702[PubMed]
    [Google Scholar]
  23. Qanungo K. R., Kundu S. C., Ghosh A. K. 2000; Characterization of cypovirus isolates from tropical and temperate Indian saturniidae silkworms. Acta Virol 44:349–357[PubMed]
    [Google Scholar]
  24. Qanungo K. R., Kundu S. C., Mullins J. I., Ghosh A. K. 2002; Molecular cloning and characterization of Antheraea mylitta cytoplasmic polyhedrosis virus genome segment 9. J Gen Virol 83:1483–1491 [View Article][PubMed]
    [Google Scholar]
  25. Sali A., Blundell T. L. 1993; Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 243:779–815 [CrossRef]
    [Google Scholar]
  26. Sinha-Datta U., Chavali V. R., Ghosh A. K. 2005; Molecular cloning and characterization of Antheraea mylitta cytoplasmic polyhedrosis virus polyhedrin gene and its variant forms. Biochem Biophys Res Commun 332:710–718 [View Article][PubMed]
    [Google Scholar]
  27. Sullivan S. M., Mishra R., Neubig R. R., Maddock J. R. 2000; Analysis of guanine nucleotide binding and exchange kinetics of the Escherichia coli GTPase Era. J Bacteriol 182:3460–3466[PubMed] [CrossRef]
    [Google Scholar]
  28. Tao Y., Farsetta D. L., Nibert M. L., Harrison S. C. 2002; RNA synthesis in a cage – structural studies of reovirus polymerase lambda3. Cell 111:733–745[PubMed] [CrossRef]
    [Google Scholar]
  29. van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A. E., Berendsen H. J. C. 2005; GROMACS: fast, flexible and free. J Comp Chem 26:1701–1718 [CrossRef]
    [Google Scholar]
  30. Wehrfritz J. M., Boyce M., Mirza S., Roy P. 2007; Reconstitution of bluetongue virus polymerase activity from isolated domains based on a three-dimensional structural model. Biopolymers 86:83–94 [View Article][PubMed]
    [Google Scholar]
  31. Yamashita T., Kaneko S., Shirota Y., Qin W., Nomura T., Kobayashi K., Murakami S. 1998; RNA-dependent RNA polymerase activity of the soluble recombinant hepatitis C virus NS5B protein truncated at the C-terminal region. J Biol Chem 273:15479–15486[PubMed] [CrossRef]
    [Google Scholar]
  32. Zhang X., Ding K., Yu X., Chang W., Sun J., Zhou Z. H. 2015; In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus. Nature 527:531–534 [View Article][PubMed]
    [Google Scholar]
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