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Published online 2 January 2004

Nucleic Acids Research, 2004, Vol. 32, No. 1 143-150
© 2004 Oxford University Press

Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes

Ali Nahvi, Jeffrey E. Barrick and Ronald R. Breaker*,1

Department of Molecular Biophysics and Biochemistry and 1 Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA

*To whom correspondence should be addressed. Tel: +1 203 432 9389; Fax: +1 203 432 6604; Email: ronald.breaker{at}yale.edu

Recent studies have begun to reveal that numerous fundamental metabolic pathways in bacteria are regulated by riboswitches residing within certain messenger RNAs. These riboswitches selectively bind metabolites and modulate gene expression in response to changing ligand concentrations. Previously, we provided evidence that the btuB mRNAs of Escherichia coli and Salmonella typhimurium each carry a coenzyme B12-dependent riboswitch that causes repressed translation of the encoded cobalamin-transport protein at elevated coenzyme concentrations. Herein, we use a phylogenetic analysis to define a consensus sequence and secondary structure model for the ligand- binding domain of this riboswitch class. RNA structures that conform to this model are widespread in both Gram-positive and Gram-negative organisms. In addition, we find that the 5'-untranslated region (5'-UTR) of the cobalamin biosynthesis (cob) operon of S.typhimurium carries an RNA motif that matches this consensus sequence. Biochemical and genetic characterization of this motif confirms that the RNA directly binds coenzyme B12, and that it likely serves as a genetic control element for regulating expression of the 25-gene operon for cobalamin production in this pathogen.


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