1887

Abstract

Statistically significant alignment was generated between the amino acid sequences of the (putative) shell (S) domains of the capsid proteins of small RNA plant viruses with icosahedral capsids in the tombusvirus, carmovirus, dianthovirus, sobemovirus and luteovirus groups. Inspection of the alignment showed good correspondence between the experimentally defined β-strands and α-helices of the capsid proteins of tomato bushy stunt, southern bean mosaic and turnip crinkle viruses, allowing prediction of the secondary structure elements in proteins with unresolved tertiary structure. It is concluded that this set of viral capsid proteins forms a tight evolutionary cluster. Comparison of the alignment of the proteins of this family with the sequences of other capsid proteins of icosahedral RNA viruses revealed more distant similarities to the satellites of tobacco necrosis, panicum mosaic, tobacco mosaic and maize white line mosaic viruses, as well as to nepo- and comoviruses. The tentative phylogenetic tree derived from the capsid protein alignment separated into three main lineages: (I) carmo-, tombus- and dianthoviruses, (II) southern bean mosaic, tobacco necrosis and maize chlorotic mottle viruses, and (III) luteoviruses. Comparison of this tree topology with the tentative evolutionary schemes for the respective virus RNA-dependent RNA polymerases suggested that gene shuffling is the universal trend in the evolution of small RNA plant virus genomes.

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1991-07-01
2024-07-24
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References

  1. Argos P., Tsukihara T., Rossmann M. G. 1980; A structural comparison of concanavalin A and tomato bushy stunt virus. Journal of Molecular Evolution 15:169–179
    [Google Scholar]
  2. Bazan J. F., Fletterick R. J. 1989; Comparative analysis of viral cysteine protease structural model. FEBS Letters 249:5–7
    [Google Scholar]
  3. Biou V., Gibrat F., Levin J. M., Robson B., Garnier J. 1988; Secondary structure prediction: combination of three different methods. Protein Engineering 2:185–191
    [Google Scholar]
  4. Brodsky L. I., Drachev A. L., Tatuzov R. L., Chumakov K. G. 1991; GENEBEE: a package of computer programs for biopolymer sequence analysis (in Russian). Biopolimery i Kletka 7 (in press)
    [Google Scholar]
  5. Carrington J. C., Morris T. J., Stockley P. G., Harrison S. C. 1987; Structure and assembly of turnip crinkle virus. IV. Analysis of the coat protein gene and implications of the subunit primary structure. Journal of Molecular Biology 194:265–276
    [Google Scholar]
  6. Carrington J. C., Heaton L. A., Zuidema D., Hillman B. I., Morris T. J. 1989; The genome structure of turnip crinkle virus. Virology 170:219–226
    [Google Scholar]
  7. Chumakov K. M., Yushmanov S. Yu. 1988; Maximum topological similarity principle in molecular taxonomy (in Russian). Molekulamaya Genetika, Mikrobiologiya i Virusologiya 3:3–9
    [Google Scholar]
  8. Dayhoff M. O., Barker W. C., Hunt L. T. 1983; Establishing homologies in protein sequences. Methods in Enzymology 91:524–549
    [Google Scholar]
  9. Dolja V. V., Boyko V. P., Agranovsky A. A., Koonin E. V. 1991; Phylogeny of capsid proteins of rod-shaped and filamentous plant RNA viruses: two families with distinct patterns of sequence and probably structural conservation. Virology (in press)
    [Google Scholar]
  10. Felsenstein J. 1989 PHYLIP 3.2 Manual Berkeley; University of California Herbarium:
    [Google Scholar]
  11. Feng D. F., Johnson M. S., Doolittle R. F. 1985; Aligning amino acid sequence: comparison of commonly used methods. Journal of Molecular Evolution 21:112–125
    [Google Scholar]
  12. Francki R. I. B. (editor) 1985 The Plant Viruses: Polyhedral Virions with Tripartite Genomes vol 1 pp 1–326 New York: Plenum Press;
    [Google Scholar]
  13. Gibbs A. J. 1987; Molecular evolution of viruses:‘trees’, ‘clocks’ and ‘modules’. Journal of Cell Science Supplement 7319–337
    [Google Scholar]
  14. Gibson T. J., Argos P. 1990; Protruding domain of tomato bushy stunt virus coat protein is a hitherto unrecognized class of jellyroll conformation. Journal of Molecular Biology 212:7–9
    [Google Scholar]
  15. Gorbalenya A. E., Koonin E. V. 1989; Viral proteins containing the purine NTP-binding pattern. Nucleic Acids Research 17:8413–8440
    [Google Scholar]
  16. Gorbalenya A. E., Koonin E. V., Blinov V. M., Donchenko A. P. 1988; Sobemovirus genome appears to encode a serine protease related to cysteine proteases of picomaviruses. FEBS Utters 236:287–290
    [Google Scholar]
  17. Gorbalenya A. E., Blinov V. M., Donchenko A. P., Koonin E. V. 1989; An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication. Journal of Molecular Evolution 28:256–268
    [Google Scholar]
  18. Grieco F., Burgyan J., Russo M. 1989; Nucleotide sequence of the 3′-terminal region of cymbidium ringspot virus RNA. Journal of General Virology 70:2533–2538
    [Google Scholar]
  19. Guilley H., Carrington J. C., Balazs E., Jonard G., Richards K., Morris T. J. 1985; Nucleotide sequence and genome organization of carnation mottle virus RNA. Nucleic Acids Research 13:6663–6677
    [Google Scholar]
  20. Habili N., Symons R. H. 1989; Evolutionary relationship between luteoviruses and other RNA plant viruses based on sequence motifs in their putative RNA polymerases and helicases. Nucleic Acids Research 17:9543–9555
    [Google Scholar]
  21. Hillman B. I., Hearne P., Rochon D., Morris T. J. 1989; Organization of the tomato bushy stunt virus genome: characterization of the coat protein gene and 3′ terminus. Virology 169:42–52
    [Google Scholar]
  22. Hirth L., Givord L. 1988; Tymoviruses. In The Plant Viruses: Polyhedral Virions with Monopartite RNA Genomes vol 3 pp. 163–212 Edited by Koenig R. New York: Plenum Press;
    [Google Scholar]
  23. Klmura M. 1983; The Neutral Theory of Molecular Evolution.Cambridge. Cambridge University Press;
    [Google Scholar]
  24. Koonin E. V. 1990; Towards a phylogenetic taxonomy of positive strand RNA viruses. In Abstracts of VIIlth International Congress of Virology Berlin: p 89
    [Google Scholar]
  25. Lau K. F., Dill K. A. 1990; Theory for protein mutability and biogenesis. Proceedings of the National Academy of Sciences, U.S.A 87:638–642
    [Google Scholar]
  26. Liljas L. 1986; The structure of spherical viruses. Progress in Biophysics and Molecular Biology 48:1–36
    [Google Scholar]
  27. Lommel S. A., Weston-Fina M., Xiong Z., Lomonossoff G. P. 1988; The nucleotide sequence and gene organization of red clover necrotic mosaic virus RNA-2. Nucleic Acids Research 16:8587–8602
    [Google Scholar]
  28. Martin R. R., Keese P. K., Young M. J., Waterhouse P. M., Gerlach W. L. 1990; Evolution and molecular biology of luteoviruses. Annual Review of Phytopathology 28:341–363
    [Google Scholar]
  29. Mayo M. A., Robinson D. J., Jolly C. A., Hyman L. 1989; Nucleotide sequence of potato leafroll luteovirus RNA. Journal of General Virology 70:1037–1051
    [Google Scholar]
  30. Meulewaeter F., Seurinck J., Van Emmelo J. 1990; Genome structure of tobacco necrosis virus strain A. Virology \T1699–709
    [Google Scholar]
  31. Miller W. A., Waterhouse P. M., Gerlach W. L. 1988; Sequence and organization of barley yellow dwarf virus genomic RNA. Nucleic Acids Research 16:6097–6111
    [Google Scholar]
  32. Morozov S. Yu., Dolja V. V., Atabekov J. G. 1989; Probable reassortment of genomic elements among elongated RNA-containing plant viruses. Journal of Molecular Evolution 29:52–62
    [Google Scholar]
  33. Nutter R. C., Scheets K., Panganiban L. C., Lommel S. A. 1989; The complete nucleotide sequence of the maize chlorotic mottle virus genome. Nucleic Acids Research 17:3163–3177
    [Google Scholar]
  34. Richardson J. S. 1981; The anatomy and taxonomy of protein structure. Advances in Protein Chemistry 34:167–339
    [Google Scholar]
  35. Riviere C. J., Pot J., Tremaine J. H., Rochon D. M. 1989; Coat protein of melon necrotic spot carmovirus is more similar to those of tombusviruses than those of carmoviruses. Journal of General Virology 70:3033–3042
    [Google Scholar]
  36. Rochon D. M., Tremaine J. H. 1989; Complete nucleotide sequence of the cucumber necrosis virus genome. Virology 169:251–259
    [Google Scholar]
  37. Rossmann M. G., Johnson J. E. 1989; Icosahedral RNA virus structure. Annual Review of Biochemistry 58:533–573
    [Google Scholar]
  38. Rossmann M. G., Abad-Zapatero C., Murthy M. R. N., Liljas L. 1983; Structural comparisons of some small spherical plant viruses. Journal of Molecular Biology 165:711–736
    [Google Scholar]
  39. Sankoff D. 1972; Matching sequences under deletion/insertion constraints. Proceedings of the National Academy of Sciences, U.S.A 69:4–6
    [Google Scholar]
  40. Sneath P. H. A., Sokal R. R. 1973; Numerical Taxonomy. San Francisco: W. H. Freeman;
    [Google Scholar]
  41. Tavazza M., Lucioli A., Ancora G., Benvenuto E. 1989; cDNA cloning of artichoke mottled crinkle virus RNA and localization and sequence of the coat protein gene. Plant Molecular Biology 13:685–692
    [Google Scholar]
  42. Valegaard K., Liljas L., Fridborg K., Unge T. 1990; The three-dimensional structure of the bacterial virus MS2. Nature, London 345:36–41
    [Google Scholar]
  43. Vander Wilk F., Huisman M. J., Cornelissen B. J. C., Huttinga H., Goldbach R. 1989; Nucleotide sequence and organization of potato leafroll virus genomic RNA. FEBS Letters 245:51–56
    [Google Scholar]
  44. Vartapetian A. B., Bogdanov A. A. 1987; Proteins covalently linked to the viral genome. Progress in Nucleic Acids Research and Molecular Biology 34:209–251
    [Google Scholar]
  45. Veidt I., Lot H., Leiser M., Sheidecker D., Guilley H., Richards K., Jonard G. 1988; Nucleotide sequence of beet western yellows virus RNA. Nucleic Acids Research 16:9917–9932
    [Google Scholar]
  46. Wu S., Rinehart C. A., Kaesberg P. 1987; Sequence and organization of southern bean mosaic virus genomic RNA. Virology 161:73–80
    [Google Scholar]
  47. Xiong Z., Lommel S. A. 1989; The complete nucleotide sequence and genome organization of red clover necrotic mosaic virus RNA-1. Virology 171:543–554
    [Google Scholar]
  48. Zimmern D. 1988; Evolution of RNA viruses. In RNA Genetics pp. 211–240 Edited by Holland J. J., Domingo E., Ahlquist P. Boca Raton: CRC Press;
    [Google Scholar]
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