Riboswitches

Moco and btuB

riboswitch
riboswitch

Riboswitches are highly conserved sequences in the untranslated regions (UTR) of bacterial mRNAs. Upon binding to their metabolite with high specificity and selectivity they change their three-dimensional structure and are thus promising candidates for understanding gene regulation at the RNA level. Our research focuses on two riboswitches, the Moco and the btuB riboswitch.

The latter is a B12 specific RNA found among other bacteria, especially in E. coli. Upon binding of B12, a conformational switch of the btuB aptamer occurs, thus inhibiting the expression of the cellular B12 transporter (Figure right). We intend to use smFRET to characterize the conformational states and the folding kinetics of the aptamer region. We co-developed a method for fluorescence site-specific internal labeling of the btuB riboswitch. Preliminary folding studies on the bulk level ensure for best in vitro folding conditions. In-line probing experiments proved the switching behaviour.

On the other side several riboswitch candidates are waiting to be identified and fully characterized. Since 2007, a molybdenum-dependent riboswitch is indicated as one of the most promising riboswitch candidates (Figure left), but to date there is no final evidence for this hypothesis. In this context, our research deals with the characterization of the molybdenum-dependent riboswitch structure and functionalities. Especially, we aim at identifying metabolites that interact selectively with the molybdenum-dependent riboswitch. Herein, we use different spectroscopic methods and footprinting assays performed on 32P-radiolabeled RNA.

Literature

[1] Sofia Gallo, Michael Oberhuber, Roland K. O. Sigel*, Bernhard Kräutler*, ChemBioChem, 2008, 9, 1408-1414.
doi:10.1002/cbic.200800099

[2] Sofia Gallo, Stefan Mundwiler, Roger Alberto, Roland K. O. Sigel*, Chem. Commun., 2011, 47, 403-405.
doi:10.1039/c0cc02447c

[3] Pallavi K. Choudhary, Roland K. O. Sigel*, RNA, 2014, 20, 36-45.
doi:10.1261/rna.039909.113

[4] Meng Zhao, Fabio D. Steffen, Richard Börner, Roland K. O. Sigel*, Eva Freisinger*, Nucleic Acids Res., 2017, published online.
doi:10.1093/nar/gkx1100

[5] Pallavi K. Choudhary, Sofia Gallo, Roland K. O. Sigel*, Front. Chem. 2017, 5/10, 1-11.
doi:10.3389/fchem.2017.00010