RNA-Dependent RNA Switches in Bacteria

The versatility of RNA as a regulatory molecule has become increasingly apparent in recent years. RNA elements within a transcript can sense a large variety of physiological signals, resulting in modulation of expression of the gene(s) encoded on that transcript by effects on transcript synthesis, mRNA stability, and translation. The response of the transcript to the signal can result in direct sequestration of elements involved in various steps of gene expression, or promotion of a structural rearrangement of the target mRNA that affects the activity of elements important for expression. The regulatory signal can be as simple as a change in temperature, or as complex as a translating ribosome, the processivity of which is affected by the appropriate cellular parameter. Among these many regulatory mechanisms are those in which the regulatory signal is a specific RNA that binds to the target mRNA. Systems of this type are widespread in bacteria, and they fall into several classes based on the type of RNA that acts as the regulator, and the mode of interaction of the regulatory RNA with its target. These include systems in which the regulatory RNA is encoded on the opposite strand of its target, systems in which the regulatory RNA is encoded elsewhere in the genome, and systems in which RNAs (such as tRNAs) that are normally used for a different cellular process are borrowed for use as regulatory molecules. This review will summarize these classes of regulatory mechanisms and their use in bacterial systems.