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

Authors

  • WENXING XU,

    Corresponding author
    1. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
    2. Key Laboratory of Plant Pathology of Hubei Province, Wuhan, Hubei 430070, China
    3. National Indoor Conservation Center of Virus-free Germplasms of Fruit Crops, Wuhan, Hubei 430070, China
    4. RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada, J1H 5N4
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  • FRANÇOIS BOLDUC,

    1. RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada, J1H 5N4
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  • NI HONG,

    1. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
    2. Key Laboratory of Plant Pathology of Hubei Province, Wuhan, Hubei 430070, China
    3. National Indoor Conservation Center of Virus-free Germplasms of Fruit Crops, Wuhan, Hubei 430070, China
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  • JEAN-PIERRE PERREAULT

    Corresponding author
    1. RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada, J1H 5N4
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Email: jean-pierre.perreault@usherbrooke.ca; xuwenxing@mail.hzau.edu.cn

SUMMARY

The elucidation of the structures of viroids, noncoding infectious RNA species, is paramount to obtain an understanding of the various aspects of their life cycles (including replication, transport and pathogenesis). In general, the secondary structures of viroids have been predicted using computer software programs which have been shown to possess several important limitations. Clearly, the predicted structure of a viroid needs to receive physical support prior to its use in the accurate interpretation of any mechanistic studies. Here, SHAPE probing coupled to computer-assisted structure prediction using the RNAstructure software program was employed to determine the structures of five viroids. These species belong to four genera of the Pospiviroidae family, and none have had their structure characterized in solution. In addition, several interesting questions were addressed by either studying various sequence variants or varying the SHAPE conditions. More importantly, this approach is novel in the study of viroids, and should be of significant aid in the determination of the structures of other RNA species.

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