Group I ribozymes

Cate J FI, Gooding A R, Podell E, Zhou K, Golden B L, Kundrot C E, Cech T R and Doudna J A 1996 Crystal structure of a group i ribozyme domain principles of RNA packing Science 273 1678-85... 

Cate, J. H., et al., 1996. Crystal structure of a group I ribozyme domain Principles of RNA packing. Science 273 1678. 

Cecil, T. R., et al., 1992. RNA catalysis by a group I ribozyme Developing a model for transition-state stabilization. Journal of Biological Chemistry... 

The ribozymes were widely modified and can be further subdivided according to their structural features in group I ribozymes, hammerhaed ribozymes, hairpin ribozymes, ribonucelase P (RNase P), and hepatitis delta virus ribozymes. 

Figure 10.13 Phosphoryl-transfer reactions. The figure shows (a) nucleotide polymerization, (b) nucleic acid hydrolysis, (c) first cleavage of an exon-intron junction by group I ribozyme (d) and by a group II ribozyme, (e) strand transfer during transposition and (f) exon ligation during RNA splicing. (From Yang et al., 2006. Copyright 2006, with permission from Elsevier.)...

The intron group I ribozymes feature common secondary structure and reaction pathways. Active sites capable of catalyzing consecutive phosphodi-ester reactions produce properly spliced and circular RNAs. Ribozymes fold into a globular conformation and have solvent-inaccessible cores as quantified by Fe(II)-EDTA-induced free-radical cleavage experiments. The Tetrahy-mem group I intron ribozyme catalyzes phosphoryl transfer between guanosine and a substrate RNA strand—the exon. This ribozyme also has been proposed to use metal ions to assist in proper folding, to activate the nucleophile, and to stabilize the transition state. ... 

Jaeger L, Michel E, Westhof E (1996) The structure of group I ribozymes, p 33-51. In Eckstein E, LUley DMJ (ed), Nucleic Acids and Molecular Biology, vol 10. Springer, Berlin Heidelberg New York... 

Fig. 1A-F The two-dimensional structures of various ribozymes. The ribozyme or intron portion is printed in black. The substrate or exon portion is printed in gray. Arrows indicate sites of cleavage by ribozymes A (left) the two-dimensional structure of a hammerhead ribozyme and its substrate. Outlined letters are conserved bases that are involved in catalysis right) The y-shaped structure of the hammerhead ribozyme-sub-strate complex B-F the two-dimensional structures of a hairpin ribozyme, the genomic HDV ribozyme, a group I ribozyme from Tetrahymena, a group II ribozyme from S. cer-evisiae (aiy5), and the ribozyme of RNase P from E. coli...

Cech TR, Herschlag D (1996) Group I ribozyme substrate recognition, catalytic strategies and comparative mechanistic analysis. In Eckstein F, Lilley DMJ (eds) Nucleic acids and molecular biology, vol 10, catalytic RNA. Springer, Berlin Heidelberg New York, P 1... 

Enzymes that probably require three metal ions for full activity include the Tetrahymena group I ribozyme, a Mn " -activated bifimctional enzyme with inositol monophosphatase and fructose 1,6-bisphosphatase activities described belowand some endonucleases. " Inorganic pyrophosphatases from E. coli and S. cerevisiae are well characterized both structurally and mechanistically. Both Mg " " and Mn + are activating metal ions and the enzyme from E. coli is most active with just three metal ions in the active site. These enzymes have been described in Section 5.1.8.2.4. 

Jager, L., Wright, M. C., and Joyce, G. F. (1999). A complex ligase ribozyme evolved in vitro from a group I ribozymes domain, Proc. Natl. Acad. Sci., 96, 14712-17. 

This chapter will focus on the use of native PAGE to investigate folding of the Tetrahymena group I ribozyme. However, these protocols are easily adapted to other ribozymes and structured RNAs (e.g., Adilakshmi et ah, 2005 Lafontaine et ah, 2002 Pinard et ah, 2001 Severcan et ah, 2009). Detailed discussions of gel mobility shift methods for measuring protein—... 

Rangan, P., Masquida, B., Westhof, E., and Woodson, S. A. (2003). Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc. Natl. Acad. Sci. USA 100, 1574-1579. 

Perez-Salas, U. A., Rangan, P., et al. (2004). Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. Biochemistry 43(6), 1746—1753. 

Figure 14.3 The Telrahymena group I ribozyme and its PI duplex. The PI duplex consists of an internal guide sequence (IGS) and an oligonucleotide substrate, which can be conveniently labeled with 6-MI.

Shan S, Yoshida A, Sun S, Piccirilli JA, Herschlag D. Three metal ions at the active site of the Tetrahymena group I ribozyme. Proc. Natl. Acad. Sci.U.S.A. 1999 96 12299-12304. 

Szewczak AA, Kosek AB, Piccirilli JA, Strobel SA, Identification of an active site ligand for a group I ribozyme catalytic metal ion. Biochemistry 2002 41 2516-2525. 

J.F. Wang, W.D. Downs, and T.R. Cech. 1993. Movement of the guide sequence during RNA catalysis by a group I ribozyme Science 260 504-508. (PubMed)... 

Replacement of all uridine residues in the Tetrahymena group I ribozyme with 5-bromouridine results in a 13-fold reduction in catalytic efficiency. " Using a library of 10 ribozymes with 5-bromouridine instead of uridine gave after 5 rounds of selection a 27-fold increase in catalytic efficiency compared to the uridine ribozyme. 

Group I ribozymes require au external guanosine for reactivity. Group II ribozymes do not have this requirement. They carry out catalysis via a lariat mechanism. 

U. Von Ahsen, J. Davies, and R. Schroeder, Antibiotic inhibition of group I ribozyme function, Nature, 353 (1991) 368-370. 

Wan T, Suh H, Russell R, Herschlag D. Multiple unfolding events during native folding of the Tetrahynnena group I ribozyme. J Mol BioL 2010 400 1067-77. 

Weinstein LB, Jones BC, Cosstick R, Cech TRr A second catalytic metal ion in group I ribozyme. Nature 1997, 388(6644) 805—808. 

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