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Group I Intron Ribozymes

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Ribozymes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 848))

Abstract

Group I intron ribozymes constitute one of the main classes of ribozymes and have been a particularly important model in the discovery of key concepts in RNA biology as well as in the development of new methods. Compared to other ribozyme classes, group I intron ribozymes display considerable variation both in their structure and the reactions they catalyze. The best described pathway is the splicing pathway that results in a spliced out intron and ligated exons. This is paralleled by the circularization pathway that leads to full-length circular intron and un-ligated exons. In addition, the intronic products of these pathways have the potential to integrate into targets and to form various types of circular RNA molecules. Thus, group I intron ribozymes and associated elements found within group I introns is a rich source of biological phenomena. This chapter provides a strategy and protocols for initial characterization of new group I intron ribozymes.

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References

  1. T.R. Cech and B.L. Golden (1999) Building a Catalytic Active Site Using Only RNA. In R.F. Gesteland, T.R. Cech and J.F. Atkins (eds.), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor; New York, pp. 321–349.

    Google Scholar 

  2. Hougland, J.L., Piccirilli, J.A., Forconi, M., Lee, J. and Herschlag, D. (2006) How the Group I Intron Works: A Case Study of RNA Structure and Function. In Gesteland, R.F., Cech, T.R. and Atkins, J.F. (eds.), The RNA World. CSHL Press, pp. 133–205.

    Google Scholar 

  3. Golden, B.L. (2008) Group I Introns:Biochemical and Crystallographic Character­ization of the Active Site Structure. In Lilley, D.M. and Eckstein,F. (eds.), Ribozymes and RNA Catalysis. RSC Publishing, pp. 178–200.

    Google Scholar 

  4. Vicens, Q. and Cech, T.R. (2006) Atomic level architecture of group I introns revealed. Trends Biochem. Sci., 31, 41–51.

    Article  PubMed  CAS  Google Scholar 

  5. Haugen, P., Simon, D.M. and Bhattacharya, D. (2005) The natural history of group I introns. Trends Genet., 21, 111–119.

    Article  PubMed  CAS  Google Scholar 

  6. Nielsen, H. and Johansen, S.D. (2009) Group I introns: Moving in new directions. RNA. Biol., 6, 375–383.

    Article  PubMed  CAS  Google Scholar 

  7. Beckert, B., Nielsen, H., Einvik, C., Johansen, S.D., Westhof, E. and Masquida, B. (2008) Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes. EMBO J., 27, 667–678.

    Article  PubMed  CAS  Google Scholar 

  8. Nielsen, H., Westhof, E. and Johansen, S. (2005) An mRNA is capped by a 2′, 5′ lariat catalyzed by a group I-like ribozyme. Science, 309, 1584–1587.

    Article  PubMed  CAS  Google Scholar 

  9. Vicens, Q. and Cech, T.R. (2009) A natural ribozyme with 3′,5′ RNA ligase activity. Nat. Chem. Biol., 5, 97–99.

    Article  PubMed  CAS  Google Scholar 

  10. Lee, E.R., Baker, J.L., Weinberg, Z., Sudarsan, N. and Breaker, R.R. (2010) An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science, 329, 845–848.

    Article  PubMed  CAS  Google Scholar 

  11. Vaidya, N. and Lehman, N. (2009) One RNA plays three roles to provide catalytic activity to a group I intron lacking an endogenous internal guide sequence. Nucleic Acids Res., 37, 3981–3989.

    Article  PubMed  CAS  Google Scholar 

  12. Fiskaa, T. and Birgisdottir, A.B. (2010) RNA reprogramming and repair based on trans-splicing group I ribozymes. N. Biotechnol., 27, 194–203.

    Article  PubMed  CAS  Google Scholar 

  13. Kruger, K., Grabowski, P.J., Zaug, A.J., Sands, J., Gottschling, D.E. and Cech, T.R. (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 31, 147–157.

    Article  PubMed  CAS  Google Scholar 

  14. Gardner, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R. et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37, D136–D140.

    Article  PubMed  CAS  Google Scholar 

  15. Zhou, Y., Lu, C., Wu, Q.J., Wang, Y., Sun, Z.T., Deng, J.C. and Zhang, Y. (2008) GISSD: Group I Intron Sequence and Structure Database. Nucleic Acids Res., 36, D31-D37.

    Article  PubMed  CAS  Google Scholar 

  16. Cannone, J.J., Subramanian, S., Schnare, M.N., Collett, J.R., D’Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., Muller, K.M. et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC. Bioinformatics., 3, 2.

    Article  PubMed  Google Scholar 

  17. Michel, F. and Westhof, E. (1990) Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol Biol, 216, 585–610.

    Article  PubMed  CAS  Google Scholar 

  18. Suh, S.O., Jones, K.G. and Blackwell, M. (1999) A Group I intron in the nuclear small subunit rRNA gene of Cryptendoxyla hypophloia, an ascomycetous fungus: evidence for a new major class of Group I introns. J. Mol. Evol., 48, 493–500.

    Article  PubMed  CAS  Google Scholar 

  19. Reinhold-Hurek, B. and Shub, D.A. (1993) Experimental approaches for detecting self-splicing group I introns. Methods Enzymol., 224, 491–502.

    Article  PubMed  CAS  Google Scholar 

  20. Vicens, Q., Paukstelis, P.J., Westhof, E., Lambowitz, A.M. and Cech, T.R. (2008) Toward predicting self-splicing and protein-facilitated splicing of group I introns. RNA., 14, 2013–2029.

    Article  PubMed  CAS  Google Scholar 

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Correspondence to Henrik Nielsen .

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Nielsen, H. (2012). Group I Intron Ribozymes. In: Hartig, J. (eds) Ribozymes. Methods in Molecular Biology, vol 848. Humana Press. https://doi.org/10.1007/978-1-61779-545-9_6

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  • DOI: https://doi.org/10.1007/978-1-61779-545-9_6

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-544-2

  • Online ISBN: 978-1-61779-545-9

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