1887

Abstract

Comparative sequence analysis suggests that the left terminal domain of (PSTVd) and other large pospiviroids may assume a branched tertiary structure containing two pseudoknots. To search for evidence of such a structure , the nucleotide sequences proposed to interact were mutagenized, tomato seedlings were inoculated with mixtures of potentially infectious PSTVd RNA transcripts and the resulting progeny were screened for compensatory sequence changes. Positions 6–11 and 330–335 tolerated only limited sequence variation, and compensatory changes consistent with formation of an intact pseudoknot were observed in only two of the plants examined. No variation was detected at positions 14–16 or 29–31. Passage of selected variants in Rutgers tomato led to an increase in virulence only upon reversion to wild-type PSTVd_Intermediate. The ability of the left terminal domain to assume a branched conformation containing pseudoknots does not appear to be an important determinant of PSTVd fitness.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.80869-0
2005-06-01
2019-12-08
Loading full text...

Full text loading...

/deliver/fulltext/jgv/86/6/vir861835.html?itemId=/content/journal/jgv/10.1099/vir.0.80869-0&mimeType=html&fmt=ahah

References

  1. Baumstark, T., Schröder, A. R. W. & Riesner, D. ( 1997; ). Viroid processing: a switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation. EMBO J 16, 599–610.[CrossRef]
    [Google Scholar]
  2. Dingley, A. J., Steger, G., Esters, B., Riesner, D. & Grzesiek, S. ( 2003; ). Structural characterization of the 69 nucleotide potato spindle tuber viroid left-terminal domain by NMR and thermodynamic analysis. J Mol Biol 334, 751–767.[CrossRef]
    [Google Scholar]
  3. Gast, F.-U. ( 2003; ). A new structural motif in the left terminal domain of large viroids identified by covariation analysis. Virus Genes 26, 19–23.[CrossRef]
    [Google Scholar]
  4. Gast, F.-U., Kempe, D., Spieker, R. L. & Sänger, H. L. ( 1996; ). Secondary structure probing of potato spindle tuber viroid (PSTVd) and sequence comparison with other small pathogenic RNA replicons provides evidence for central non-canonical base-pairs, large A-rich loops, and a terminal branch. J Mol Biol 262, 652–670.[CrossRef]
    [Google Scholar]
  5. Góra-Sochacka, A., Kierzek, A., Candresse, T. & Zagórski, W. ( 1997; ). The genetic stability of potato spindle tuber viroid (PSTVd) molecular variants. RNA 3, 68–74.
    [Google Scholar]
  6. Hadidi, A., Flores, R., Randles, J. W. & Semancik, J. S. (editors) ( 2003; ). Viroids. Collingwood, Australia: CSIRO Publishing.
  7. Keese, P. & Symons, R. H. ( 1985; ). Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc Natl Acad Sci U S A 82, 4582–4586.[CrossRef]
    [Google Scholar]
  8. Lück, R., Gräf, S. & Steger, G. ( 1999; ). ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure. Nucleic Acids Res 27, 4208–4217.[CrossRef]
    [Google Scholar]
  9. Matoušek, J., Patzak, J., Orctová, L., Schubert, J., Vrba, L., Steger, G. & Riesner, D. ( 2001; ). The variability of hop latent viroid as induced upon heat treatment. Virology 287, 349–358.[CrossRef]
    [Google Scholar]
  10. Owens, R. A., Thompson, S. M. & Kramer, M. ( 2003; ). Identification of neutral mutants surrounding two naturally occurring variants of Potato spindle tuber viroid. J Gen Virol 84, 751–756.[CrossRef]
    [Google Scholar]
  11. Podleckis, E. V., Hammond, R. W., Hurtt, S. W. & Hadidi, A. ( 1993; ). Chemiluminescent detection of potato and pome fruit viroids by digoxygenin-labeled dot blot and tissue blot hybridization. J Virol Methods 43, 147–158.[CrossRef]
    [Google Scholar]
  12. Qu, F., Heinrich, C., Loss, P., Steger, G., Tien, P. & Riesner, D. ( 1993; ). Multiple pathways of reversion in viroids for conservation of structural elements. EMBO J 12, 2129–2139.
    [Google Scholar]
  13. Stasys, R. A., Dry, I. B. & Rezaian, M. A. ( 1995; ). The termini of a new citrus viroid contain duplications of the central conserved regions from two viroid groups. FEBS Lett 358, 182–184.[CrossRef]
    [Google Scholar]
  14. Steger, G. & Riesner, D. ( 2003; ). Molecular characteristics. In Viroids, pp. 15–29. Edited by A. Hadidi, R. Flores, J. W. Randles & J. S. Semancik. Collingwood, Australia: CSIRO Publishing.
  15. Wang, M.-B., Bian, X.-Y., Wu, L.-M. & 10 other authors ( 2004; ). On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. Proc Natl Acad Sci U S A 101, 3275–3280.[CrossRef]
    [Google Scholar]
  16. Woese, C. R. & Pace, N. R. ( 1993; ). Probing RNA structure, function, and history by comparative analysis. In The RNA World, pp. 91–117. Edited by R. F. Gesteland & J. F. Atkins. Plainview, NY: Cold Spring Harbor Press.
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.80869-0
Loading
/content/journal/jgv/10.1099/vir.0.80869-0
Loading

Data & Media loading...

Most Cited This Month

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