Slow formation of a pseudoknot structure is rate limiting in the productive co-transcriptional folding of the self-splicing Candida intron

  1. Libin Zhang1,2,5,
  2. Penghui Bao1,2,
  3. Michael J. Leibowitz3,4 and
  4. Yi Zhang1,2
  1. 1State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
  2. 2Department of Biochemistry and Molecular Biology, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
  3. 3Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey–Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
  4. 4Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA
    • 5 Present address: Department of Microbiology, Immunology and Pathology, Colorado State University, 1619 Campus Delivery, Fort Collins, CO 80523, USA.

    Abstract

    Pseudoknots play critical roles in packing the active structure of various functional RNAs. The importance of the P3–P7 pseudoknot in refolding of group I intron ribozymes has been recently appreciated, while little is known about the pseudoknot function in co-transcriptional folding. Here we used the Candida group I intron as a model to address the question. We show that co-transcriptional folding of the active self-splicing intron is twice as fast as refolding. The P3–P7 pseudoknot folds slowly during co-transcriptional folding at a rate constant similar to the folding of the active ribozyme, and folding of both P3–P7 and P1–P10 pseudoknots are inhibited by antisense oligonucleotides. We conclude that when RNA folding is coupled with transcription, formation of pseudoknot structures dominates the productive folding pathway and serves as a rate-limiting step in producing the self-splicing competent Candida intron.

    Keywords

    Footnotes

    • Reprint requests to: Yi Zhang, State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China; e-mail: yizhang{at}whu.edu.cn; fax: 86-27-68754945.

    • Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.1638609.

      • Received March 8, 2009.
      • Accepted July 30, 2009.
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