The Riboswitch Explained

Bacterial cells synthesize proteins in the same manner as mammalian cells do. Both cells start synthesis by DNA polymerase transcribing double-stranded DNA into single-stranded messenger RNA (mRNA). The resulting transcript is then translated by ribosomes, another form of RNA into amino acids, the subunits of protein. The resulting proteins in both cells then fold and assume their shapes. Some of the proteins serve as regulators of protein synthesis.
For instance, bacteria maintain levels of lactose by a regulatory protein, the Lac repressor complex. When lactose levels are high lactose metabolites bind to the Lac repressor complex, preventing it from attaching to the DNA. This allows the lactose cleaving enzyme to be made which in turn regulates lactose levels through its cleaving action. However, when lactose is absent the Lac repressor complex binds to the DNA preventing DNA polymerase from making an mRNA transcript of the lactose cleaving enzyme. Thus the enzyme isn’t made allowing lactose levels to rise.
However, it started to become evident by the early 1980’s that many bacteria can also regulate protein synthesis through RNA molecules. This is accomplished by a short segment of the leading end of mRNA termed a riboswitch. A riboswitch has two domains, a sensor (aptamer) to recognize and bind a specific metabolite and an expression platform to prevent synthesis of the same metabolite.
When a specific metabolite is present the aptamer binds to it. This event instructs the expression platform to take actions to prevent its synthesis. When that metabolite is not present the production process continues normally. In this way riboswitches maintain the appropriate levels of a specific metabolite in the bacterial cell.
The expression platform prevents the production of a specific metabolite in one of 3 ways. It can prevent production by either halting transcription or translation. In some instances this is achieved through self cleavage by a ribozyme, an RNA enzyme capable of cleaving mRNA
An example of a riboswitch controlling metabolite levels through transcription is seen in the way bacteria regulate levels of the coenzyme, flavin mononucleotide (FMN). When this coenzyme is sensed a terminator hairpin structure is formed by mRNA. This structure blocks DNA polymerase from transcribing FMN. If the coenzyme isn’t present, then transcription proceeds eventually leading to the production of FMN. The regulation of thiamine pyrophosphate (TPP) is an example of a. riboswitch controlling metabolite levels through translation. When TPP is bound by the aptamer a hairpin structure is formed which blocks translation. Regulation of glucosamine 6-phosphate (GlcN6P) levels shows how riboswiches can control metabolites levels in a third novel way, self-cleavage. A ribozyme, an RNA molecule with enzymatic properties cleaves the mRNA transcript of GlnN6P when GlnN6P is present.
Riboswitches may potentially be used in important medical applications since they play a vital role in the regulation of microbial nutrients and the survival of the microbe. The two most likely areas where riboswitches could be important are fighting pathogens and gene therapy. More than a dozen known microbes from E. coli to Yersinia pestis ( bubonic plague) employ riboswitches. Many researchers are fighting these pathogens by attempting to find molecules that will fool the aptamer into mistaking them for the specific metabolite and thus eliciting a deleterious regulatory response. Riboswiches might also provide a good target for new antibiotics.
Gene therapy may be another area that could benefit from riboswitches. Researchers want to develop an artificial riboswitch which has an on-off switch that could be controlled by a benign drug. This construct would then be incorporated into a therapeutic gene that’s inserted into a person’s cells. A patient would regulate the gene by taking a pill which activates the riboswitch.

The Power of Riboswitches, Jeffrey E. Barrick and Ronald R. Breaker, Scientific American, pp. 50-57, 1/07.