B12 cofactors directly stabilize an mRNA regulatory switch

Abstract

Structures of riboswitch receptor domains bound to their effector have revealed how mRNAs recognize diverse small molecules, but mechanistic details into its linkage with regulation of gene expression remain elusive1,2. To address this, we solved crystal structures of two different classes of cobalamin (vitamin B12) binding riboswitches that include the structural switch of the downstream regulatory domain. These classes share a common cobalamin-binding core, but use distinct peripheral extensions to recognize different B12 derivatives. In each case, recognition is accomplished through shape complementarity between the RNA and cobalamin with relatively few hydrogen bonding interactions that typically govern RNA-small molecule recognition. We show that a composite cobalamin/RNA scaffold stabilizes an unusual long-range intramolecular kissing-loop interaction that controls mRNA expression. This is the first riboswitch crystal structure detailing how the receptor and regulatory domains communicate in a ligand-dependent fashion to regulate mRNA expression.

Copper control of bacterial nitrous oxide emission and its impact on vitamin B 12 -dependent metabolism

“…Pathways. Upon interrogation of the remaining up-regulated genes, we observed that many have an association with B 12 -dependent metabolism and may be under the control of B 12 riboswitches, known for their ability to modulate transcription of downstream genes dependent on the presence of the B 12 ligand (13,14,(22)(23)(24). Nine putative gene clusters downstream of B 12 riboswitches had elevated expression in Cu-limited conditions (Fig.…”

“…However, N 2 O exhibits cytotoxicity, as it is known to bind to and inactivate vitamin B 12 (B 12 ), an essential cellular cofactor in B 12 -dependent enzymes involved in methionine and DNA synthesis (11,12). B 12 also acts as a ligand for B 12 riboswitches that modulate gene expression in the absence of this cofactor (13,14). The possible impact of environmental N 2 O emissions on B 12 metabolism in microbiological communities has largely been ignored.…”

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

“…Other B 12 derivatives most commonly include methylcobalamin, cyanocobalamin, and aquocobalamin, which differ in their composition by their corrin ring (13). It was recently shown that methylcobalamin and aquocobalamin are also recognized by different cobalamin riboswitches where various RNA architectures are used to sense these B 12 derivatives (9). As reported for the S-adenosyl-* This work was supported in part by the Canadian Institutes of Health…”

“…Mutagenesis experiments showed that residues forming the kissing loop interaction are important for ligand binding (10), consistent with the kissing loop being involved in genetic control. Recent crystal structures revealed that the bound ligand interacts weakly with the kissing loop ribose-phosphate backbone through van der Waals contacts (8,9). The kissing loop interaction was also shown to form in the absence of ligand at elevated Mg 2ϩ ion concentrations (9).…”

“…Another example is the adenosylcobalamin (AdoCbl)-sensing riboswitch, which represents one of the most intricate and complex riboswitch structures including a kissing loop (KL) interaction (Fig. 1A) (8,9). This riboswitch is involved in the control of the btuB gene, which encodes an outer membrane receptor for transporting B 12 derivatives, as part of the TonB-dependent active transport system (10 -12).…”