Abstract
Phylogenetic analyses revealed insights into the distribution of riboswitch classes in different microbial groups, and structural analyses led to updated aptamer structure models and insights into the mechanism of these non-coding RNA structures.
Highlights
Riboswitches are noncoding RNA structures that appropriately regulate genes in response to changing cellular conditions
In order to better gauge whether mutual information (MI) scores support proposed base interactions in an RNA alignment, we developed a procedure for empirically estimating their statistical significance (Figure 4)
We find examples of other RNA structure motifs that have not previously been reported in these riboswitch classes
Summary
Riboswitches are noncoding RNA structures that appropriately regulate genes in response to changing cellular conditions. The expression of many proteins involved in fundamental metabolic processes is controlled by riboswitches that sense relevant small molecule ligands. More than a dozen classes of riboswitches that respond to changes in the concentrations of specific small molecule ligands ranging from amino acids to coenzymes are currently known. These metabolite-binding riboswitches are classified according to the architectures of their conserved aptamer domains, which fold into complex three-dimensional structures to serve as precise receptors for their target molecules. Metabolite binding to riboswitch aptamers typically causes an allosteric rearrangement in nearby mRNA structures that results in a gene control response. Certain riboswitches employ more sophisticated mechanisms involving self-cleavage [5], cooperative ligand binding [6], or tandem aptamer arrangements [7]
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