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Nucleic Acids Research Advance Access published online on September 18, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl643
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection

Kristian H. Link1,2, Lixia Guo1 and Ronald R. Breaker1,2,3,*

1 Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT 06520, USA 2 Howard Hughes Medical Institute, Yale University New Haven, CT 06520, USA 3 Department of Molecular Biophysics and Biochemistry, Yale University New Haven, CT 06520, USA

*To whom correspondence should be addressed. Tel: +1 203 432 9389; Fax: +1 203 432 0753; Email: ronald.breaker{at}yale.edu

Received April 28, 2006. Revised August 2, 2006. Accepted August 3, 2006.

Self-cleaving ribozymes associated with the glmS genes of many Gram-positive bacteria are activated by binding to glucosamine-6-phosphate (GlcN6P). Representatives of the glmS ribozyme class function as metabolite-sensing riboswitches whose self-cleavage activities down-regulate the expression of GlmS enzymes that synthesizes GlcN6P. As with other riboswitches, natural glmS ribozyme isolates are highly specific for their target metabolite. Other small molecules closely related to GlcN6P, such as glucose-6-phosphate, cannot activate self-cleavage. We applied in vitro selection methods in an attempt to identify variants of a Bacillus cereus glmS ribozyme that expand the range of compounds that induce self-cleavage. In addition, we sought to increase the number of variant ribozymes of this class to further examine the proposed secondary structure model. Although numerous variant ribozymes were obtained that efficiently self-cleave, none exhibited changes in target specificity. These findings are consistent with the hypothesis that GlcN6P is used by the ribozyme as a coenzyme for RNA cleavage, rather than an allosteric effector.


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