Skip to main content
SpringerLink
Log in

A multiple alignment of the capsid protein sequences of nepoviruses and comoviruses suggests a common structure

  • Original Papers
  • Published:
Archives of Virology Aims and scope Submit manuscript

Summary

The amino acid sequences of the regions encoding the structural proteins of eleven nepoviruses and five comoviruses, two genera of the familyComoviridae, have been aligned. The properties predicted by computer analysis (three-dimensional-3D-structure, hydrophobicity) are also correlated along this alignment, and aligned to the experimentally determined 3D structure of two comoviruses. It can thus be assumed that the 3D structure of the unique nepovirus coat protein matches that of the bipartite protomer found in the comovirus particles. In this model, the spatial locations of two amino-acid motifs characteristic of nepoviruses are in close vicinity, at the external surface of the virion. The coat proteins of nepoviruses and comoviruses may thus share a common evolutionary origin. A phylogenetic analysis was made using the multiple alignment, allowing a better understanding of the molecular relationships between these two groups of viruses.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Bacher JW, Warkentin D, Ramsdell D, Hancock JF (1994) Sequence analysis of the 3′ termini of RNA1 and RNA2 of blueberry leaf motle virus. Virus Res 33: 145–156

    Google Scholar 

  2. Block VC, Wardell J, Jolly CA, Manoukian A, Robinson DJ, Edwards ML, Mayo MA (1992) The nucleotide sequence of RNA-2 of raspberry ringspot nepovirus. J Gen Virol 73: 2189–2194

    Google Scholar 

  3. Chen X, Bruening G (1992) Nucleotide sequence and genetic map of cowpea severe mosaic virus RNA-2 and comparisons with RNA-2 of other comoviruses. Virology 187: 682–692

    Google Scholar 

  4. Chen Z, Stauffacher C, Li Y, Schmidt T, Bomu W, Kamer G, Shanks M, Lomonossoff G, Johnson JE (1989) Protein-RNA interactions in an icosahedral virus at 3.0 Å resolution. Science 245: 154–159

    Google Scholar 

  5. Chen Z, Stauffacher CV, Johnson JE (1990) Capsid structure and RNA packaging in comoviruses. Semin Virol 1: 453–466

    Google Scholar 

  6. Daubert SD, Bruening G, Najarian RC (1978) Protein bound to the genome RNAs of cowpea mosaic virus. Eur J Biochem 92: 45–51

    Google Scholar 

  7. Dayhoff MO, Barker WC, Hunt LT (1983) Establishing homologies in protein sequences. Methods Enzymol 91: 524–549

    Google Scholar 

  8. Demangeat G, Hemmer O, Reinbolt J, Mayo MA, Fritsch C (1992) Virus-specific proteins in cells infected with tomato black ring nepovirus: evidence for proteolytic processing in vivo. J Gen Virol 73: 1609–1614

    Google Scholar 

  9. Dolja VV, Boyko VP, Agranovsky AA, Koonin EV (1991) Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation. Virology 184: 79–86

    Google Scholar 

  10. Dolja VV, Koonin EV (1991) Phylogeny of capsid proteins of small icosahedral RNA plant viruses. J Gen Virol 72: 1481–1486

    Google Scholar 

  11. El Manna MM, Bruening G (1973) Polyadenylate sequences in the ribonucleic acids of cowpea mosaic virus. Virology 56: 198–206

    Google Scholar 

  12. Everett KR, Milne KS, Forster RLS (1994) Nucleotide sequence of the coat protein genes of strawberry latent ringspot virus: lack of homology to the nepoviruses and comoviruses. J Gen Virol 75: 1821–1825

    Google Scholar 

  13. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791

    Google Scholar 

  14. Felsenstein J (1989) PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5: 164–166

    Google Scholar 

  15. Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155: 279–284

    Google Scholar 

  16. Fritsch C, Mayo MA, Murant AF (1980) Translation products of genome and satellite RNAs of tomato black ring virus. J Gen Virol 46: 381–389

    Google Scholar 

  17. Goldbach R, Rezelman G, Van Kammen A (1980) Independent replication and expression of B-component RNA of cowpea mosaic virus. Nature 286: 297–300

    Google Scholar 

  18. Goldbach R (1987) Genome similarities between plant and animal RNA viruses. Microbiol Sci 4: 197–202

    Google Scholar 

  19. Goulden MG, Davies JW, Wood KR, Lomonossoff GP (1992) Structure of tobraviral particles: a model suggested from sequence conservation in tobraviral and tobamoviral coat proteins. J Mol Biol 227: 1–8

    Google Scholar 

  20. Greif C, Hemmer O, Fritsch C (1988) Nucleotide sequence of tomato black ring virus RNA-1. J Gen Virol 69: 1517–1529

    Google Scholar 

  21. Harrison BD, Murant AF (1977) Nematode transmissibility of pseudo-recombinant isolates of tomato black ring virus. Ann Appl Biol 86: 209–212

    Google Scholar 

  22. Hellen CUT, Liu YY, Cooper JI (1991) Synthesis and proteolytic processing of arabis mosaic nepovirus, cherry leaf roll nepovirus and strawberry latent ringspot nepovirus proteins in reticulocyte lysate. Arch Virol 120: 19–31

    Google Scholar 

  23. Higgins DG, Bleasby AJ, Fuchs R (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci 8: 189–191

    Google Scholar 

  24. Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24: 946–950

    Google Scholar 

  25. Kyte J, Doolittle RS (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105–132

    Google Scholar 

  26. Le Gall O, Lanneau M, Candresse T, Dunez J (1995) The nucleotide sequence of the RNA-2 of an isolate of the English serotype of tomato black ring virus: RNA recombination in the history of nepoviruses. J Gen Virol 76: 1279–1283

    Google Scholar 

  27. Le Gall O, Candresse T, Dunez J (1995) Transfer of the 3′ non-translated region of grapevine chrome mosaic virus RNA-1 by recombination to tomato black ring virus RNA-2 in pseudorecombinant isolates. J Gen Virol 76: 1285–1289

    Google Scholar 

  28. Levin JM, Garnier J (1987) Improvement in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool. Biochem Biophys Acta 955: 283–295

    Google Scholar 

  29. Martelli GP (1975) Some features of nematode-borne viruses and their relationships with the host plants. In: Lamberti F, Taylor CE, Seinhorst JW (eds) Nematode vectors of plant viruses. Plenum Press, London New York, pp 223–252

    Google Scholar 

  30. Mayo MA, Barker H, Harrison BD (1979) Polyadenylate in the RNA of five nepoviruses. J Gen Virol 43: 603–610

    Google Scholar 

  31. Mayo MA, Barker H, Harrison BD (1982) Specificity and properties of the genome-linked proteins of nepoviruses. J Gen Virol 59: 149–162

    Google Scholar 

  32. Mayo MA, Martelli GP (1993) New families and genera of plant viruses. Arch Virol 133: 496–498

    Google Scholar 

  33. Niblett CL, Semancik JS (1969) Conversion of the electrophoretic forms of cowpea mosaic virus in vivo and in vitro. Virology 38: 685–693

    Google Scholar 

  34. Palmenberg AC (1989) Sequence alignments if picornaviral capsid proteins. In: Semler BL, Ehrenfeld E (eds) Molecular aspects of picornavirus infection and detection. American Society for Microbiology, Washington, pp 211–241

    Google Scholar 

  35. Pelham HRP (1979) Synthesis and proteolytic processing of cowpea mosaic virus proteins in reticulocyte lysates. Virology 96: 463–477

    Google Scholar 

  36. Robinson DJ, Barker H, Harrison BD, Mayo MA (1980) Replication of RNA-1 of tomato black ring virus independently of RNA-2. J Gen Virol 51: 317–326

    Google Scholar 

  37. Rott ME, Tremaine JH, Rochon DM (1991) Nucleotide sequence of tomato ringspot virus RNA-2. J Gen Virol 72: 1505–1514

    Google Scholar 

  38. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425

    Google Scholar 

  39. Serghini MA, Fuchs M, Pinck M, Reinbolt J, Walter B, Pinck L (1990) RNA2 of grapevine fanleaf virus: sequence analysis and coat protein cistron location. J Gen Virol 71: 1433–1441

    Google Scholar 

  40. Steinkellner H, Himmler G, Sagl R, Mattanovich D, Katinger H (1992) Amino-acid sequence comparison of nepovirus coat proteins. Virus Genes 6: 197–202

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Station de Pathologie Végétale, INRA, Villenave d'Ornon Cedex, France

    O. Le Gall, T. Candresse & J. Dunez

Authors
  1. O. Le Gall
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. T. Candresse
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. J. Dunez
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Le Gall, O., Candresse, T. & Dunez, J. A multiple alignment of the capsid protein sequences of nepoviruses and comoviruses suggests a common structure. Archives of Virology 140, 2041–2053 (1995). https://doi.org/10.1007/BF01322691

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF01322691

Keywords

Search

Navigation