Mapping studies of the Peach latent mosaic viroid reveal novel structural features

Molecular Plant Pathology

Volumn 12, Issue 7, 2011, Pages 688-701

  Dubé, Audrey ^a   Bolduc, François ^a   Bisaillon, Martin ^a   Perreault, Jean Pierre ^a  

^a UNIVERSITY OF SHERBROOKE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA;

ARTICLE; CHEMISTRY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PRUNUS; VIROID; VIROLOGY;

BASE SEQUENCE; MOLECULAR SEQUENCE DATA; PRUNUS; RNA, VIRAL; VIROIDS;

PEACH LATENT MOSAIC VIROID; PRUNUS PERSICA; VIROIDS;

EID: 79960439622     PISSN: 14646722     EISSN: 13643703     Source Type: Journal    
DOI: 10.1111/j.1364-3703.2010.00703.x     Document Type: Article

References (23)

1. Ambros, S., Hernandez, C., Desvignes, J.C. and Flores, R. (1998) Genomic structure of three phenotypically different isolates of peach latent mosaic viroid: implications of the existence of constraints limiting the heterogeneity of viroid quasispecies. J. Virol. 72, 7397-7406.
2. Bussière, F., Lafontaine, D. and Perreault, J.P. (1996) Compilation and analysis of viroid and viroid-like RNA sequences. Nucleic Acids Res. 24, 1793-1798.
3. Bussière, F., Ouellet, J., Cote, F., Levesque, D. and Perreault, J.P. (2000) Mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex, branched secondary structure. J. Virol. 74, 2647-2654.
4. Domdey, H., Jank, P., Sanger, L. and Gross, H.J. (1978) Studies on the primary and secondary structure of potato spindle tuber viroid: products of digestion with ribonuclease A and ribonuclease T1, and modification with bisulfite. Nucleic Acids Res. 5, 1221-1236.
5. Dubé, A., Baumstark, T., Bisaillon, M. and Perreault, J.P. (2010) The RNA strands of the plus and minus polarities of peach latent mosaic viroid fold into different structures. RNA, 16, 463-473.
6. Duncan, C.D. and Weeks, K.M. (2008) SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA. Biochemistry, 47, 8504-8513.
7. Fekih Hassen, I., Massart, S., Motard, J., Roussel, S., Parisi, O., Kummert, J., Fakhfakh, H., Marrakchi, M., Perreault, J.P. and Jijakli, M.H. (2007) Molecular features of new Peach Latent Mosaic Viroid variants suggest that recombination may have contributed to the evolution of this infectious RNA. Virology, 360, 50-57.
8. Flores, R., Hernandez, C., Martinez de Alba, A.E., Daros, J.A. and Di Serio, F. (2005) Viroids and viroid-host interactions. Annu. Rev. Phytopathol. 43, 117-139.
9. Gross, H.J., Domdey, H., Lossow, C., Jank, P., Raba, M., Alberty, H. and Sanger, H.L. (1978) Nucleotide sequence and secondary structure of potato spindle tuber viroid. Nature, 273, 203-208.
10. Laederach, A., Das, R., Vicens, Q., Pearlman, S.M., Brenowitz, M., Herschlag, D. and Altman, R.B. (2008) Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nat. Protoc. 3, 1395-1401.
11. Low, J.T. and Weeks, K.M. (2010) SHAPE-directed RNA secondary structure prediction. Methods, 52, 150-158.
12. Malfitano, M., Di Serio, F., Covelli, L., Ragozzino, A., Hernandez, C. and Flores, R. (2003) Peach latent mosaic viroid variants inducing peach calico (extreme chlorosis) contain a characteristic insertion that is responsible for this symptomatology. Virology, 313, 492-501.
13. Misra, V.K. and Draper, D.E. (2002) The linkage between magnesium binding and RNA folding. J. Mol. Biol. 317, 507-521.
14. Mortimer, S.A. and Weeks, K.M. (2009) Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution. Nat. Protoc. 4, 1413-1421.
15. Pelchat, M., Levesque, D., Ouellet, J., Laurendeau, S., Levesque, S., Lehoux, J., Thompson, D.A., Eastwell, K.C., Skrzeczkowski, L.J. and Perreault, J.P. (2000) Sequencing of peach latent mosaic viroid variants from nine North American peach cultivars shows that this RNA folds into a complex secondary structure. Virology, 271, 37-45.
16. Rehmsmeier, M., Steffen, P., Hochsmann, M. and Giegerich, R. (2004) Fast and effective prediction of microRNA/target duplexes. RNA, 10, 1507-1517.
17. Riesner, D., Henco, K., Rokohl, U., Klotz, G., Kleinschmidt, A.K., Domdey, H., Jank, P., Gross, H.J. and Sanger, H.L. (1979) Structure and structure formation of viroids. J. Mol. Biol. 133, 85-115.
18. Rocheleau, L. and Pelchat, M. (2006) The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research. BMC Microbiol. 6, 24.
19. Sanger, H.L., Klotz, G., Riesner, D., Gross, H.J. and Kleinschmidt, A.K. (1976) Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc. Natl. Acad. Sci. USA, 73, 3852-3856.
20. 2+ ions. Biochemistry, 46, 2973-2983.
21. Steger, G., Hofmann, H., Fortsch, J., Gross, H.J., Randles, J.W., Sanger, H.L. and Riesner, D. (1984) Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data. J. Biomol. Struct. Dyn. 2, 543-571.
22. Wilkinson, K.A., Gorelick, R.J., Vasa, S.M., Guex, N., Rein, A., Mathews, D.H., Giddings, M.C. and Weeks, K.M. (2008) High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol. 6, e96.
23. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415.