The Corrin Moiety of Coenzyme B₁₂ is the Determinant for Switching the btuB Riboswitch of E. coli

Abstract

Riboswitches are regulatory elements in the 5'-untranslated region (5'-UTR) of bacterial mRNAs that bind certain metabolites with high specificity and affinity. The 202 nucleotide (nt)-long btuB riboswitch RNA of E. coli interacts specifically with coenzyme B12 and its derivatives thereby leading to changes in the RNA structure and hence to an altered expression of the downstream btuB gene. We report the investigations of the rearrangement of the three-dimensional structure of the btuB riboswitch upon binding to four different B12 derivatives: coenzyme B12, vitamin B12, adenosyl factor A and adenosyl-cobinamide. In-line probing experiments have shown that the corrin ring plays the crucial role in switching the three-dimensional riboswitch structure. Instead, the apical ligands influence only the binding affinity of the B12 derivative to the btuB riboswitch.

A Kissing Loop Is Important for btuB Riboswitch Ligand Sensing and Regulatory Control

“…Although peripheral extensions (P6 -P10 helices) are involved in ligand recognition (8,9,18), there is relatively little information about the role of the kissing loop structure in the folding and ligand-induced genetic regulation of the btuB riboswitch. A recent study reported that transcriptional pause sites are present upstream of the kissing loop (C184), RBS (U225), and AUG sequences (U235) (19).…”

Shaping RNA Structures with Metal Ions and Metal Ion Complexes

“…Upon binding to certain metabolites with high specificity and selectivity these RNAs change their three-dimensional structure thus regulating gene expression and metabolite concentration on the translational or transcriptional level. [49] Our research focuses on the Mg 2+ -and coenzyme B 12 -sensitive riboswitches [50,51] whereby the latter is explained in more detail in the following Section.…”

“…[49,[51][52][53][54] Out of the more than 20 riboswitch classes discovered so far, only the TPP-binding riboswitch is known to be present also in archeae, fungi and plants, [55][56][57][58] whereas all others are restricted to bacteria where they are believed to regulate up to 2% of the genes. [59] Due to their overwhelming occurrence in bacteria, riboswitches are of increasing interest as new targets for the design of antimicrobial drugs.…”

“…[50,53,81] Our investigations concentrate currently on the structural basis for the interaction between AdoCbl and the 202 nt long aptamer region of the btuB riboswitch of E. coli. [51] In contrast to VitB 12 , AdoCbl is able to release the lower dimethylbenzimidazol ligand in an intramolecular equilibrium, i.e. leading to a 'base-off' form (Fig.…”

“…missing either the upper (VitB 12 ), the lower (adenosyl cobinamide) or both large apical ligands (dicyanocobinamide), or displaying the 'base-off'-form (adenosyl factor A). [51] The conformational changes of the RNA upon interaction with the different B 12 derivatives was visualized by in-line probing experiments, i.e. structure-dependent selfdegradation of RNA (Fig.…”