1887

Journal of General Virology header logo

Volume 76, Issue 5

Prunus necrotic ringspot ilarvirus: nucleotide sequence of RNA3 and the relationship to other ilarviruses based on coat protein comparison Free

Abstract

The RNA3 of prunus necrotic ringspot ilarvirus (PNRSV) has been cloned and its entire sequence determined. The RNA3 consists of 1943 nucleotides (nt) and possesses two large open reading frames (ORFs) separated by an intergenic region of 74 nt. The 5′ proximal ORF is 855 nt in length and codes for a protein of molecular mass 31.4 kDa which has homologies with the putative movement protein of other members of the . The 3′ proximal ORF of 675 nt is the cistron for the coat protein (CP) and has a predicted molecular mass of 24.9 kDa. The sequence of the 3′ noncoding region (NCR) of PNRSV RNA3 showed a high degree of similarity with those of tobacco streak virus (TSV), prune dwarf virus (PDV), apple mosaic virus (ApMV) and also alfalfa mosaic virus (AlMV). In addition it contained potential stem-loop structures with interspersed AUGC motifs characteristic for ilar- and alfamoviruses. This conserved primary and secondary structure in all 3′ NCRs may be responsible for the interaction with homologous and heterologous CPs and subsequent activation of genome replication. The CP gene of an ApMV isolate (ApMV-G) of 657 nt has also been cloned and sequenced. Although ApMV and PNRSV have a distant serological relationship, the deduced amino acid sequences of their CPs have an identity of only 51.8%. The N termini of PNRSV and ApMV CPs have in common a zinc-finger motif and the potential to form an amphipathic helix.

  • Received:
  • Accepted:
  • Published Online:
© Journal of General Virology 1995
Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-76-5-1073
1995-05-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/jgv/76/5/JV0760051073.html?itemId=/content/journal/jgv/10.1099/0022-1317-76-5-1073&mimeType=html&fmt=ahah

References

  1. Agranovsky A. A., Koenig R., Maiss E., Boyko V. P., Casper R., Atabekov J. G. 1994; Expression of the beet yellows clostero-virus capsid protein and p24, a capsid protein homologue, in vitro and in vivo . Journal of General Virology 75:1431–1439
     [Google Scholar]
  2. Ahlquist P., Luckow V., Kaesberg P. 1981; Complete nucleotide sequence of brome mosaic virus RNA3. Journal of Molecular Biologv 153:23–38
     [Google Scholar]
  3. Allison R. F., Janda M., Ahlquist P. 1989; Sequence of cowpea chlorotic mottle virus RNAs 2 and 3 and evidence of a recombination event during bromovirus evolution. Virology 172:321–330
     [Google Scholar]
  4. Argos P. 1981; Secondary structure prediction of plant virus coat proteins. Virology 110:55–62
     [Google Scholar]
  5. Bachman E. J., Scott S. W., Xin G., Vance V. B. 1994; The complete nucleotide sequence of prune dwarf ilarvirus RNA3: implication for coat protein activation of genome replication in ilarviruses. Virology 201:127–131
     [Google Scholar]
  6. Baer M. L., Houser F., Loesch-Fries L. S., Gehrke L. 1994; Specific RNA binding by amino-terminal peptides of alfalfa mosaic virus coat protein. EMBO Journal 13:727–735
     [Google Scholar]
  7. Banerjee A. K. 1980; 5′-Terminal cap structure in eucaryotic messenger ribonucleic acids. Microbiological Reviews 44:175–205
     [Google Scholar]
  8. Barker R. F., Javis N. P., Thompson D. V., Loesch-Fries L. S., Hall T. C. 1983; Complete nucleotide sequence of alfalfa mosaic virus RNA3. Nucleic Acids Research 11:2881–2991
     [Google Scholar]
  9. Berg J. 1986; Potential metal binding domains in nucleic acid binding proteins. Science 232:485–186
     [Google Scholar]
  10. Bol J. F., Van Vloten-Doting L., Jaspars E. M. J. 1971; A functional equivalence of top component a RNA and coat protein in the initiation of infection by alfalfa mosaic virus. Virology 46:73–85
     [Google Scholar]
  11. Bol J. F., Kraal B., Brederode F. T. 1974; Limited proteolysis of alfalfa mosaic virus: influence on the structural and biological function of the coat protein. Virology 58:101–110
     [Google Scholar]
  12. Cornelissen B. J. C., Janssen H., Zuidema D., Bol J. F. 1984; Complete nucleotide sequence of tobacco streak virus RNA3. Nucleic Acids Research 12:2427–2437
     [Google Scholar]
  13. Davies C., Symons R. H. 1988; Further implications for the evolutionary relationships between tripartite plant viruses based on cucumber mosaic virus RNA3. Virology 165:216–224
     [Google Scholar]
  14. Devereux F., Haeberli P., Smithies O. 1984; A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Research 12:387–395
     [Google Scholar]
  15. Erny C., Schoumacher F., Jung C., Gagey M. J., Godefroy-Colburn T., Stussi-Garaud C., Berna A. 1992; An N-proximal sequence of alfalfa mosaic virus movement protein is necessary for association with cell walls in transgenic plants. Journal of General Virology 73:2115–2119
     [Google Scholar]
  16. Fichot O., Girard M. 1990; An improved method for sequencing of RNA templates. Nucleic Acids Research 18:6162
     [Google Scholar]
  17. French R., Ahlquist P. 1988; Characterization and engineering of sequences controlling in vitro synthesis of brome mosaic virus subgenomic RNA. Journal of Virology 62:2411–2420
     [Google Scholar]
  18. Fulton R. W. 1970; Prunus necrotic ringspot virus. CMI/AAB Descriptions of Plant Viruses No 5
     [Google Scholar]
  19. Ge X., Scott S. W. 1994; The nucleotide sequence of citrus leaf rugose ilarvirus RNA-2. Journal of General Virology 75:2841–2846
     [Google Scholar]
  20. Gonsalves D., Fulton R. W. 1977; Activation of Prunus necrotic ringspot virus and rose mosaic virus by RNA4 components of some ilarviruses. Virology 81:398–107
     [Google Scholar]
  21. Gonsalves D., Garnsey S. M. 1975; Infectivity of heterologous RNA-protein mixtures from alfalfa mosaic, citrus leaf rugose, citrus variegation, and tobacco streak viruses. Virology 67:319–326
     [Google Scholar]
  22. Gubler U., Hoffman B. J. 1983; A simple and efficient method for generating cDNA libraries. Gene 25:263–269
     [Google Scholar]
  23. Houser-Scott F., Baer M. L., Liem K. F. Jr, Cai J. M., Gehrke L. 1994; Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein peptides to the 3′ untranslated region of alfalfa mosaic virus RNA 4. Journal of Virology 68:2194–2205
     [Google Scholar]
  24. Houwing C. J., Jaspars E. M. J. 1978; Coat protein binds to the 3′ terminal part of RNA4 of alfalfa mosaic virus. Biochemistry 17:2927–2933
     [Google Scholar]
  25. Houwing C. J., Jaspars E. M. J. 1982; Protein binding sites in nucleation complexes of alfalfa mosaic virus RNA4. Biochemistry 21:3408–3414
     [Google Scholar]
  26. Karasawa A., Nakaho K., Kakutani T., Minobe Y., Ehara Y. 1991; Nucleotide sequence of RNA3 of peanut stunt cucumovirus. Virology 185:464–467
     [Google Scholar]
  27. Koper-Zwarthoff E. C., Bol J. F. 1980; Nucleotide sequence of the putative recognition site for coat protein in the RNAs of alfalfa mosaic virus and tobacco streak virus. Nucleic Acids Research 8:3307–3318
     [Google Scholar]
  28. Langereis K., Mugnier M.-A., Cornelissen B. J. C., Pinck L., Bol J. F. 1986; Variable repeats and poly (A)-stretches in the leader sequence of alfalfa mosaic virus RNA3. Virology 154:409–414
     [Google Scholar]
  29. Lister R. M., Saksena K. N. 1976; Some properties of Tulare apple mosaic and other ilarviruses suggesting grouping with tobacco streak virus. Virology 70:440–450
     [Google Scholar]
  30. Maiss E., Breyel E., Brisske A., Casper R. 1988; Molecular cloning of DNA complementary to the RNA-genome of plum pox virus. Journal of Phytopathology 122:222–231
     [Google Scholar]
  31. Martelli G. P. 1992; Classification and nomenclature of plant viruses: state of the art. Plant Disease 76:436–442
     [Google Scholar]
  32. Mushegian A. R., Koonin E. V. 1993; Cell-to-cell movement of plant viruses. Archives of Virology 133:239–257
     [Google Scholar]
  33. Ong C.-A., Mink G. I. 1989; Evaluation of agarose gel electroresis for resolving nucleoprotein components of Prunus necrotic ringspot virus. Phytopathology 79:613–619
     [Google Scholar]
  34. Reusken C. B. E. M., Neeleman L., Bol J. F. 1994; The 3′-untranslated region of alfalfa mosaic virus RNA3 contains at least two independent binding sites for viral coat protein. Nuleic Acids Research 22:1346–1353
     [Google Scholar]
  35. Sanchez-Navarro J. A., Pallas V. 1994; Nucleotide sequence of apple mosaic ilarvirus RNA 4. Journal of General Virology 75:1441–1445
     [Google Scholar]
  36. Sanger F., Nicklen S., Coulso A. R. 1977; DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, USA 74:5463–5467
     [Google Scholar]
  37. Sehnke P. C., Mason A., Hood S. J., Lister R. M., Johnson J. E. 1989; A ‘zinc-finger’-type binding domain in tobacco streak virus coat protein. Virology 168:48–56
     [Google Scholar]
  38. Shukla D. D., Ward C. W. 1989; Structure of potyvirus coat proteins and its application in the taxonomy of the potyvirus group. Advances in Virus Research 36:273–314
     [Google Scholar]
  39. Smit C. H., Roosien J., Van Vloten-Doting L., Jaspars E. M. J. 1981; Evidence that alfalfa mosaic virus infection starts with three RNA-protein complexes. Virology 112:169–173
     [Google Scholar]
  40. Stussi-Garaud C., Garaud J.-C., Berna A., Godefroy-Colburn T. 1987; In situ location of an alfalfa mosaic virus non-structural protein in plant cell walls: correlation with virus transport. Journal of General Virology 68:1779–1784
     [Google Scholar]
  41. Van Der Kuyl A. C., Neeleman L., Bol J. F. 1991; Deletion analysis of cis- and trans- acting elements involved in replication of alfalfa mosaic virus RNA3 in vivo . Virology 183:687–694
     [Google Scholar]
  42. Van Vloten-Doting L. 1975; Coat protein is required for infectivity of tobacco streak virus: biological equivalence of the coat proteins of tobacco streak and alfalfa mosaic viruses. Virology 65:215–225
     [Google Scholar]
  43. Zuidema D., Jaspars E. M. J. 1984; Comparative investigations on the coat protein binding sites of the genomic RNAs of alfalfa mosaic virus and tobacco streak virus. Virology 135:43–52
     [Google Scholar]
  44. Zuidema D., Bierhuizen M. F. A., Cornelissen B. J. C., Bol J. F., Jaspars E. M. J. 1983a; Coat protein binding sites on RNA1 of alfalfa mosaic virus. Virology 125:361–369
     [Google Scholar]
  45. Zuidema D., Bierhuizen M. F. A., Jaspars E. M. J. 1983b; Removal of the N-terminal part of alfalfa mosaic coat protein interferes with the specific binding to RNA1 and genome activition. Virology 129:255–260
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-76-5-1073
Loading
Prunus necrotic ringspot ilarvirus: nucleotide sequence of RNA3 and the relationship to other ilarviruses based on coat protein comparison
J. Gen. Virol. 76, 1073 (1995); https://doi.org/10.1099/0022-1317-76-5-1073
/content/journal/jgv/10.1099/0022-1317-76-5-1073
/content/journal/jgv/10.1099/0022-1317-76-5-1073
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error