Metal Ion Homeostasis
Over 20 classes of metabolite-sensing regulatory RNAs ('riboswitches') have been discovered for sensing of enzymatic cofactors, nucleobases, amino acids, glucosamine-6-phosphate, and the second messenger molecule, cyclic di-GMP. Certain riboswitch classes are exceptionally widespread in their phylogenetic distribution, suggesting their presence prior to the divergence of the major bacterial lineages. At least one class has been discovered in algae, fungi and plants, and regulates splicing in response to changing intracellular thiamine levels. Bioinformatics-aided methods have also led to the identification of at least a dozen more convincing categories of riboswitches, although the metabolites that bind to them remain unidentified. These latter 'orphan' riboswitches are likely to regulate expression of a wide variety of genes, including numerous genes of unknown function. In the past several years our research efforts have focused on the detailed analyses of riboswitch mechanisms in general as well as investigation of several classes of 'orphan' riboswitches in particular. One orphan class, renamed as the 'M-box''element, is usually located upstream of putative magnesium transport genes. Using a combination of genetic, biochemical and biophysical approaches, our ongoing data reveals that the M-box RNA structure functions as a direct sensor for divalent ions. Specifically, association of divalent ions couples a global conformational change with control of downstream gene expression. These data expand the riboswitch ligand repertoire to include metals and suggest a simple biochemical model for how an RNA-based metalloregulatory agent can be used to regulate metal homeostasis. We are currently investigating several other classes of riboswitches that regulate other metal ion transporters. We are also exploring a variety of synthetic applications for metalloregulatory RNAs.