Structural Biochemistry/Nucleic Acid/RNA/Riboswitch
Riboswitches are recently discovered RNA domains that function as gene expression regulators. It is a portion of the mRNA strand that is able to bind small molecules and alter the gene activity. An mRNA which possesses the riboswitch is able to regulate its own activity depending on whether or not a molecule is attached to it. They are located at the 5' end of untranslated regions of messenger RNA. These functional domains exist in bacteria and have also been engineered in the laboratory. Riboswitches are significant because most believe that proteins are primarily responsible for the complexity, specificity, and efficiency of gene control. Most riboswitches exist in bacterias although some have also been found in plants and fungi.
It was first described by Ronald Breaker's lab in 2002 when they utilized in-line probing of Escherichia coli btuB mRNA to show that it could bind a metabolite/substrate and inhibit translation of the strand's product (AdoCbl) -- without proteins.
The original meaning of riboswitch was that messenger RNA can sense small molecules of metabolite. While this is still the use today, others have changed the meaning to include other types of RNA, further expanding the meaning. mRNA that contains a riboswitch can regulate its own activity. This opens many doors in the world of biology because it shows that molecules can evolve to be their own masters, or regulating themselves. These RNA were seen to distinguish between very similar molecules or analogs which shows the intricacy of the method. This fact has opened up a world of RNA because it is now known that the capabilities of RNA were much greater than once known. It is interesting because it illustrates how little we humans know about our very own bodies. Riboswitches allow RNA to respond to different concentrations of molecules almost as though the RNA had a mind of its own determining its actions. Due to the expansion of the definition of a riboswitch, there are many different kinds known to mankind today.
As the mantra of structural biochemistry is that structure determines function, it is not a surprise that the structure of the riboswitch allows for such great function. Most RNA do not need to conform to the strict watson and crick model of DNA allowing for many variations in RNA. The great variation in RNA is responsible for riboswitchs abilities. Riboswitches are made of two parts. the aptamer domain and the expression platform. The aptamer domain essentially acts as a receptor that binds to specific ligands. The expression platform is interesting because it can toggle between two different secondary structures when binding to a ligand, creating a plethora of possible structures. In both parts of a riboswitch there is a switching sequence. This switching sequence directs the expression of the genes. 
Types of Riboswitches
There are several types of riboswitches known, some of which are:
- TPP riboswitch : this riboswitch binds TPP (thiamin pyrophosphate in order to regulate the transport and synthesis of thiamin as well as other metabolites with similar properties.
- Lysine riboswitch : binds to lysine and regulates its biosynthesis, catabolism, and transport.
- Glycine riboswitch : this riboswitch regulates glycine metabolism. This is the only riboswitch known currently to be able to perform cooperative binding.
- FMN riboswitch : this riboswitch binds FMN (flavin mononucleotide) in order to regulate the transport and synthesis of riboflavin.
- Purine riboswitch : binds purines to regulate its transport and metabolism. Different forms of this riboswitch are able to bind either guanine or adenine depending on the pyrimidine in the riboswitch.
- Cobalamin riboswitch : this riboswitch binds adenosylcobalamin, the coenzyme form of B12 vitamin, in order to moderate the synthesis and transport of cobalamin and other similar metabolites.
as well as many others such as SAM riboswitch, PreQ1 riboswitch, SAH riboswitch, glmS riboswitch, and cyclic di-GMP riboswitch.
Riboswitches consist of two functional components, the conserved aptamer region and the highly variable expression platform. Unlike proteins, only four nucleotides are available to generate the specificity required by the riboswitch to bind.
The aptamer domain is usually a single binding site that has a highly conserved primary and secondary RNA structure and forms selective binding pockets for ligands. It essentially acts as a sensor for metabolites within the cell. Since it is located at the 5' end of mRNA, it is usually the first to be transcribed by RNA polymerase.
To improve aptamer-substrate affinity, structural data shows that hydrogen bonds, van der Waals, and other interactions form with the substrate and also adjacent RNA regions. Other aptamers may utilize an induced fit mechanism with deep binding pockets.
The expression platform is commonly located downstream from the aptamer.
Most riboswitches function within feedback pathways by sensing metabolites and turning "off" the ability to express genes that would produce proteins that would continue the production of that metabolite. The aptamer region tends to recognize ligands that are closely related to the gene products downstream from the riboswitch expression platform.
- ^ Wang, J., Lee, E., Morales, D., Lim, J., Breaker, R. "Riboswitches that Sense S-adenosylhomocysteine and Activate Genes Involved in Coenzyme Recycling". Molecular Cell 29, 691–702, March 28, 2008.
- ^ Nahvi, A., Sudarsan, N., Ebert, M., Zou, X., Brown, K., Breaker, R., "Genetic Control by a Metabolite Binding mRNA" Chemistry & Biology, Vol. 9, 1043-1049, September, 2002.
- ^ Coppins, R., Hall, K., Groisman, A. "The intricate world of riboswitches" Current Opinion in Microbiology, Volume 10, Issue 2, April 2007, Pages 176-181.
- ^ Breaker, R. "Complex Riboswitches''Science, Vol. 319, 1795-1797, 28 March 2008.
- Riboswitches, November 14th, 2012.