The Molecular Diversity of Natural Riboswitch Biosensors
Structured noncoding RNAs are relatively rare in biology compared to their protein competitors, but some of these RNAs perform complex functions such as gene control and biosensor activities. To date, ~50 distinct classes of experimentally validated riboswitches have been discovered. Riboswitches selectively bind ligands and regulate the expression of genes related to these chemical targets. The characteristics of some of these riboswitch classes provide evidence that they might have first existed during a period in evolution before the emergence of proteins. If true, then each new discovery possibly provides an opportunity to look back in time to an era when structured RNAs were predominantly used to catalyze chemical reactions and regulate biological systems. Intriguingly, our latest findings support the hypothesis that many thousands of riboswitch classes remain hidden in the genomes of modern organisms. We have developed and further optimized a computational search pipeline that can reveal the presence of essentially every representative of a structured noncoding RNA from an entire bacterial genome. This approach makes practical the comprehensive analysis of the genomes from thousands of species. Such discovery efforts should reveal numerous new roles for riboswitches and other types of bacterial noncoding RNAs.