Metabolite Regulation by Riboswitches: The Role of Metal Ions in Folding, Ligand Binding and Functionality

Metal ions in association with RNA fulfill numerous functions and are vital for structure formation and functionality. K+ and Mg2+ are the most crucial, being the most abundant freely available metal ions in the cell. These ions not only shield the negative charges derived from the phosphate sugar backbone, but also allow the formation of highly complex, functional structures by mediating specific tertiary interactions. In ribozymes, specifically bound Mg2+ additionally promotes catalytic activity by metal ion-assisted RNA self-cleavage. In the context of riboswitches, metal ions take up further roles. Riboswitches are natural RNA aptamers involved in gene regulation by directly binding cellular metabolites or ions. In addition to their role in RNA folding, metal ions are often the key element for ligand binding allowing negatively charged moieties like phosphates, carboxylates, or even the single atomic fluoride to be recognized and bound by the RNA. Additionally, some riboswitch classes respond to metal ion-containing cofactors like molybdenum cofactor or cobalamins, while others are sensitive to single metal ions. For the latter, the RNA needs to discriminate between the correct metal ion and other, more abundant metal ions, a very difficult task to achieve in a cellular environment. For all these purposes riboswitches evolved elaborate binding pockets exploiting the different properties and binding strategies metal ions (and their ligands) can offer: size, softness/hardness, inner- and outer-sphere binding through an intricate H-bond pattern of coordinated water molecules as well as the inclusion of all functional moieties of the binding ligand. In this chapter, we discuss the different roles executed by metal ions for the proper functioning of riboswitches. Besides the general role during structure formation, we present different metal ion-dependent recognition modes, as well as metallo cofactor- and metal ion-binding riboswitches in more detail. In this chapter, the authors discuss the different roles executed by metal ions for the proper functioning of riboswitches. They present different metal ion-dependent recognition modes, as well as metallo cofactor- and metal ion-binding riboswitches in more detail besides the general role during structure formation. Riboswitches binding a metabolite with the same core structure are categorized as a class. The binding of a specific metabolite by the aptamer induces a structural change of the expression platfor