The use of a combination of computer-assisted structure prediction and SHAPE probing to elucidate the secondary structures of five viroids

Molecular Plant Pathology

Volumn 13, Issue 7, 2012, Pages 666-676

  Xu, Wenxing ^a,b,c   Bolduc, François ^c   Hong, Ni ^a,b   Perreault, Jean Pierre ^c  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b Key Laboratory of Plant Pathology of Hubei Province   (China)

^c UNIVERSITY OF SHERBROOKE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; DNA TEMPLATE; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; RNA PROBE; VIROID;

BASE SEQUENCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RNA PROBES; RNA, VIRAL; SOFTWARE; TEMPLATES, GENETIC; VIROIDS;

POSPIVIROIDAE; VIROIDS;

EID: 84864377848     PISSN: 14646722     EISSN: 13643703     Source Type: Journal    
DOI: 10.1111/j.1364-3703.2011.00776.x     Document Type: Article

References (39)

1. Ashulin, L., Lachman, O., Hadas, R. and Bar-Joseph, M. (1991) Nucleotide sequence of a new viroid species, citrus bent leaf viroid (CBLVd) isolated from grapefruit in Israel. Nucleic Acids Res. 19, 4767.
2. Beaudry, D., Bussière, F., Lareau, F., Lessard, C. and Perreault, J.P. (1995) The RNA of both polarities of the peach latent mosaic viroid self-cleaves in vitro solely by single hammerhead structures. Nucleic Acids Res. 23, 745-752.
3. 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.
4. Bussière, F., Ouellet, J., Côté, F., Lévesque, 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.
5. Chaffai, M., Serra, P., Gandia, M., Hernandez, C. and Duran-Vila, N. (2007) Molecular characterization of CEVd strains that induce different phenotypes in Gynura aurantiaca: structure-pathogenicity relationships. Arch. Virol. 152, 1283-1294.
6. Deigan, K.E., Li, T.W., Mathews, D.H. and Weeks, K.M. (2009) Accurate SHAPE-directed RNA structure determination. Proc. Natl. Acad. Sci. USA, 106, 97-102.
7. 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.
8. 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.
9. Dubé, A., Bolduc, F., Bisaillon, M. and Perreault, J.P. (2011) Mapping studies of the Peach latent mosaic viroid reveal novel structural features. Mol. Plant. Pathol. 12, 688-701.
10. Elena, S.F., Dopazo, J., de la Pena, M., Flores, R., Diener, T.O. and Moya, A. (2001) Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment. J. Mol. Evol. 53, 155-159.
11. Fadda, Z., Daros, J.A., Fagoaga, C., Flores, R. and Duran-Vila, N. (2003) Eggplant latent viroid, the candidate type species for a new genus within the family Avsunviroidae (hammerhead viroids). J. Virol. 77, 6528-6532.
12. Flores, R., Randles, J.W., Owens, R.A., Bar-Joseph, M. and Diener, T.O. (2005) Viroids. In: Virus Taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses (Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U. and Ball, A.L., eds), pp. 1145-1159. San Diego: CA: Elsevier Academic Press.
13. Francis, M.I., Szychowski, J.A. and Semancik, J.S. (1995) Structural sites specific to citrus viroid groups. J. Gen. Virol. 76, 1081-1089.
14. Gast, F.U., Kempe, D., Spieker, R.L. and Sanger, 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.
15. 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.
16. Gross, H.J., Krupp, G., Domdey, H., Raba, M., Jank, P., Lossow, C., Alberty, H., Ramm, K. and Sanger, H.L. (1982) Nucleotide sequence and secondary structure of citrus exocortis and chrysanthemum stunt viroid. Eur. J. Biochem. 121, 249-257.
17. Keese, P. and Symons, R.H. (1985) Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc. Natl. Acad. Sci. USA, 82, 4582-4586.
18. Kladwang, W., VanLang, C.C., Cordero, P. and Das, R. (2011) Understanding the errors of SHAPE-directed RNA structure modeling. Biochemistry, 50, 8049-8056.
19. 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.
20. Low, J.T. and Weeks, K.M. (2010) SHAPE-directed RNA secondary structure prediction. Methods, 52, 150-158.
21. Masquida, B., Beckert, B. and Jossinet, F. (2010) Exploring RNA structure by integrative molecular modelling. New Biotechnol. 27, 170-183.
22. Mortimer, S.A. and Weeks, K.M. (2008) Time-resolved RNA SHAPE chemistry. J. Am. Chem. Soc. 130, 16178-16180.
23. Murcia, N., Bernad, L., Duran-Vila, N. and Serra, P. (2011) Two nucleotide positions in the Citrus exocortis viroid RNA associated with symptom expression in Etrog citron but not in experimental herbaceous hosts. Mol. Plant. Pathol. 12, 203-208.
24. Navarro, B. and Flores, R. (1997) Chrysanthemum chlorotic mottle viroid: unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes. Proc. Natl. Acad. Sci. USA, 94, 11262-11267.
25. Reuter, J.S. and Mathews, D.H. (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics, 11, 129.
26. 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.
27. Skoric, D., Conerly, M., Szychowski, J.A. and Semancik, J.S. (2001) CEVd-induced symptom modification as a response to a host-specific temperature-sensitive reaction. Virology, 280, 115-123.
28. Stasys, R.A., Dry, I.B. and 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.
29. Steen, K.A., Malhotra, A. and Weeks, K.M. (2010) Selective 2′-hydroxyl acylation analyzed by protection from exoribonuclease. J. Am. Chem. Soc. 132, 9940-9943.
30. 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.
31. Symons, R.H. (1981) Avocado sunblotch viroid: primary sequence and proposed secondary structure. Nucleic Acids Res. 9, 6527-6537.
32. Szychowski, J.A., Vidalakis, G. and Semancik, J.S. (2005) Host-directed processing of Citrus exocortis viroid. J. Gen. Virol. 86, 473-477.
33. Takeda, R., Petrov, A.I., Leontis, N.B. and Ding, B. (2011) A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana. Plant Cell, 23, 258-272.
34. Visvader, J.E. and Symons, R.H. (1985) Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity. Nucleic Acids Res. 13, 2907-2920.
35. Visvader, J.E. and Symons, R.H. (1986) Replication of in vitro constructed viroid mutants: location of the pathogenicity-modulating domain of citrus exocortis viroid. EMBO J. 5, 2051-2055.
36. Wiesyk, A., Candresse, T., Zagorski, W. and Gora-Sochacka, A. (2011) Use of randomly mutagenized genomic cDNA banks of potato spindle tuber viroid to screen for viable versions of the viroid genome. J. Gen. Virol. 92, 457-466.
37. Wilkinson, K.A., Merino, E.J. and Weeks, K.M. (2006) Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc. 1, 1610-1616.
38. Zhong, X., Archual, A.J., Amin, A.A. and Ding, B. (2008) A genomic map of viroid RNA motifs critical for replication and systemic trafficking. Plant Cell, 20, 35-47.
39. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415.