Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes.

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.

[1]  Margaret S. Ebert,et al.  An mRNA structure in bacteria that controls gene expression by binding lysine. , 2003, Genes & development.

[2]  M. Gelfand,et al.  Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes* , 2003, Journal of Biological Chemistry.

[3]  R. Breaker,et al.  Genetic Control by Metabolite‐Binding Riboswitches , 2003, Chembiochem : a European journal of chemical biology.

[4]  Andrey A Mironov,et al.  Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. , 2003, RNA.

[5]  Ali Nahvi,et al.  An mRNA structure that controls gene expression by binding S-adenosylmethionine , 2003, Nature Structural Biology.

[6]  Jeffrey E. Barrick,et al.  Metabolite-binding RNA domains are present in the genes of eukaryotes. , 2003, RNA.

[7]  Jeffrey E. Barrick,et al.  Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria , 2003, Cell.

[8]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[9]  M. Gelfand,et al.  Comparative Genomics of Thiamin Biosynthesis in Procaryotes , 2002, The Journal of Biological Chemistry.

[10]  R. Breaker,et al.  An mRNA structure that controls gene expression by binding FMN , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Evgeny Nudler,et al.  Sensing Small Molecules by Nascent RNA A Mechanism to Control Transcription in Bacteria , 2002, Cell.

[12]  Ronald R. Breaker,et al.  Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression , 2002, Nature.

[13]  Ali Nahvi,et al.  Genetic control by a metabolite binding mRNA. , 2002, Chemistry & biology.

[14]  Gary D. Stormo,et al.  Do mRNAs act as direct sensors of small molecules to control their expression? , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[15]  R R Breaker,et al.  Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. , 2001, RNA.

[16]  D. Andersson,et al.  An adenosyl–cobalamin (coenzyme‐B12)‐repressed translational enhancer in the cob mRNA of Salmonella typhimurium , 2001, Molecular microbiology.

[17]  X. Zou,et al.  Thermolysis of coenzymes B12 at physiological temperatures: activation parameters for cobalt-carbon bond homolysis and a quantitative analysis of the perturbation of the homolysis equilibrium by the ribonucleoside triphosphate reductase from Lactobacillus leichmannii. , 1999, Journal of inorganic biochemistry.

[18]  P. Stragier,et al.  Plasmids for ectopic integration in Bacillus subtilis. , 1996, Gene.

[19]  D. Andersson,et al.  Vitamin B12 repression of the cob operon in Salmonella typhimurium: translational control of the cbiA gene , 1994, Molecular microbiology.

[20]  D. Andersson,et al.  Cobalamin (vitamin B12) repression of the Cob operon in Salmonella typhimurium requires sequences within the leader and the first translated open reading frame , 1992, Molecular microbiology.

[21]  R. Kadner,et al.  Transcribed sequences of the Escherichia coli btuB gene control its expression and regulation by vitamin B12. , 1991, Proceedings of the National Academy of Sciences of the United States of America.