Ligase ribozymes

Case Study Conformational Transition in the LI Ligase Ribozyme... 

The authors obtained an RNA ligase ribozyme using the method of in vitro evolution . Here, macromolecules are allowed to go through a series of synthetic cycles, which are followed by a proliferation phase, mutation and selection. As in Darwinian evolution, the goal is to carry out laboratory selection of molecules with certain required properties. 

Fig. 6. A Secondary structure of the class I ligase. B Template-directed RNA polymerization of up to six nucleotides catalyzed by the class I ligase (Ribozyme)...

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. 

Paul, N. and Joyce, G. F. (2002). A self-replicating ligase ribozyme. Proc. Natl. Acad. 

Teramoto, N., Imanishi, Y, and Yoshihiro, I. (2000). In vitro selection of a ligase ribozyme carrying alkylamino groups in the side chains. Bioconjugate Chem., 11, 744-8. 

In July 2000 Bartel and coworkers published the impressive example of a single RNA sequence that can adopt either of two ribozyme (Box 22) folds and catalyze two different reactions (Figure 1.1.1) [8]. One reaction is cleavage of RNA catalyzed by the hepatitis delta vims (HDV) ribozyme, which assists the replication of HDV viral RNA. The other is RNA ligation catalyzed by the class III ligase ribozyme, an activity obtained in the laboratory in in-vitro selection experiments. The two ribozyme folds are completely different and do not have a single base pair in common. Importantly, minor variants of this sequence are highly active for one or other catalytic activity and can be accessed from the prototype by a few nucleotide mutations only. 

Figure 5 RNA ligation and poiymerization. A schematic representation, based on the Class I RNA ligase ribozyme, iiiustrating that the difference between a iigase and a poiymerase iies primariiy in the substrates utilized and not in the chemistry of the reactions.

Keywords RNA catalysis molecular simulation hammerhead ribozyme LI ligase ribozyme Mg2 ions... 

Bagby, S.C., Bergman, N.H., Shechner, D.M., Yen, C., Bartel, D.P. A class I ligase ribozyme with reduced Mg2+ dependence Selection, sequence analysis, and identification of functional tertiary interactions. RNA 2009,15, 2129-46. 

Glasner ME, Bergman NH, Bartel DP Metal ion requirements for struca ure and catalysis of an RNA ligase ribozyme. Biochemistry 2002, 4l(25) 8103—8112. 

Evidence supporting this theory first came from Tom Cech and Sidney Altman s groups, which showed that extant RNAs can function as enzymes, termed ribozymes [8, 9]. Both synthetic and naturally-occurring ribozymes have been shown to make (ligate) and break phosphodiester bonds (the polyanionic backbone of nucleic acids) [10-12], and a derivative of the Class I ligase ribozyme [13] can polymerize up to 95 nucleotides on an RNA primer [14], In addition, RNAs can fold into structures that bind to specific targets. Such RNAs are known as aptamers (from the Latin aptus, meaning to fit ). Many people believe that RNA should be able to direct its own replication. 

Of the RNA crystal structures reported there is the structure of the known RNA ligase ribozyme, an RNA aptamer binding to its bacterial protein target Hfq, myotonic dystrophy type 1 (DMl) RNA that showed internal UU loop structures, and the structure of the CUG helix from DMl, and a structure of the Fragile X syndrome repeating r(CGG) transcript/ " A number of crystal structures of riboswitches have been reported, including dG, cyclic-di-GMP, glycine, and M-box ° riboswitches. 

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