The roles of metal ions in regulation by riboswitches

Abstract

Metal ions are required by all organisms in order to execute an array of essential molecular functions. They play a critical role in many catalytic mechanisms and structural properties. Proper homeostasis of ions is critical; levels that are aberrantly low or high are deleterious to cellular physiology. To maintain stable intracellular pools, metal ion-sensing regulatory (metalloregulatory) proteins couple metal ion concentration fluctuations with expression of genes encoding for cation transport or sequestration. However, these transcriptional-based regulatory strategies are not the only mechanisms by which organisms coordinate metal ions with gene expression. Intriguingly, a few classes of signal-responsive RNA elements have also been discovered to function as metalloregulatory agents. This suggests that RNA-based regulatory strategies can be precisely tuned to intracellular metal ion pools, functionally akin to metal-loregulatory proteins. In addition to these metal-sensing regulatory RNAs, there is a yet broader role for metal ions in directly assisting the structural integrity of other signal-responsive regulatory RNA elements. In this chapter, we discuss how the intimate physicochemical relationship between metal ions and nucleic acids is important for the structure and function of metal ion- and metabolite-sensing regulatory RNAs.

Figure 1

Mg²⁺ ions mediate recognition of phosphate-containing riboswitch ligands. A. TPP is bound to its cognate riboswitch chelated to two Mg²⁺ ions ¹. B. The phosphate group of FMN binds to single Mg²⁺ ion in the binding site of the cognate riboswitch ¹².

Figure 2

Cation-mediated recognition of riboswitch ligands without phosphate groups. A. A K⁺ ion coordinates lysine when the amino acid is bound by its cognate riboswitch ¹⁸. B. The characteristic exocyclic aminomethyl group of preQ1 engages in hydrogen bonding with a water of hydration of a structural Ca²⁺ ion ²⁶.

Figure 3

Genetic regulation by the mgtA riboswitch. A. Secondary structure of the Salmonella enterica mgtA riboswitch. B. Under low Mg²⁺ conditions the PhoP protein activates transcription of the mgtA transcript. Under high Mg²⁺ conditions, a riboswitch located within the 5’ leader region activates destabilization of the mgtA transcript and reduces the efficiency of transcription elongation of the mgtA gene.

Figure 4

Genetic regulation by the M-box riboswitch. A. Classes of genes that are regulated y the M-box riboswitch. B. Shown in this figure is a schematic depiction of genetic regulation by the M-box riboswitch. Under conditions of high Mg²⁺, the P1 helix at the base of the aptamer domain is stabilized, which allows for formation of a downstream termination site. Under conditions of low Mg²⁺, the right half of the P1 helix associates with downstream sequences to prevent terminator formation, and thereby allow for transcription elongation to continue synthesis of downstream genes. C. Secondary structure of the B. subtilis mgtE M-box aptamer. Symbols denote locations of metal ions that form interactions with the RNA, as observed within the crystallographically determined structural model (D). Circled residues denote sites of phosphorothioate interferences, which prevent the compacted metal-bound conformation. E. One of the six RNA-bound Mg²⁺ ions appears to be particular important for the compacted RNA conformation, as evidenced by strong phosphorothioate interference and four inner-sphere metal coordinations.