CH391L/S13/Riboswitches

What is a riboswitch and how does it work?

A riboswitch is a region on the mRNA that can act like a switch to turn gene expression on or off. In the presence of a specific ligand, a riboswitch changes shape uncoupling the polymerase of the DNA. Polymerase is no longer able to transcribe thus terminating gene expression. Riboswitches are useful for gene regulation.

The mRNA has the ability to fold and base pair with itself forming different structures, such as those found on the regions that make up a riboswitch. On a basic riboswitch, there are two main regions. One region is more sensitive to ligands, also known as an aptamer. The second region is also known as a terminator hairpin and its existence is dependent on whether or not a ligand is bound to the aptamer. When a ligand binds to an aptamer it causes the aptamer to become more stable. Because a more stable aptamer region forms, the mRNA downstream from the aptamer undergoes a shape change and a terminating hairpin forms via mRNA base pairing with itself. In the event that a ligand has bound to an aptamer and a hairpin has formed, transcription is terminated by the uncoupling of the DNA polymerase. mRNA is transcribed until the polymerase reaches a polyuracil region down stream of the riboswitch. The polyuracil region is also known as a pause site because the polymerase tends to slow down as it passes through. The polymerase is knocked of the DNA by the hairpin as it reaches the polyuracil region and uncouples thus terminating transcription. If a ligand does not bind to the aptamer region, the polymerase will simply continue transcribing down the DNA strand and through the pause site.