Debunking myths on genetics and DNA

Thursday, February 23, 2012

Modifying gene expression through riboswitches

Messenger RNA (mRNA), the RNA transcribed from a DNA template in order to make proteins, contains elements able to sense and bind to specific targeting molecules (metabolites or metal ions). In bacteria, fungi and plants, these binding mechanisms are used to control gene expression, and therefore act as genetic "switches", which is why these RNA elements are called "riboswitches". They are often found at the 5' end of the mRNA, in the untranslated region (the stretch that precedes the start codon): this way, they are the first domain to be synthesized and can therefore influence expression before the entire mRNA is created.

Riboswitches have two components: the domain that binds to the ligand is called "aptamer" and it's highly conserved from an evolutionary point of view, as it has to "sense" a precise type of molecule. The other component, called "expression platform," is what regulates gene expression, and, contrary to the aptamer, it can vary greatly in order to affect the different processes of transcription, translation, and RNA processing.

In order to understand how riboswitches bind to their specific ligands, it is vital to decipher their "secondary structure," in other words, the way they fold and assume a 3-D structure that allows them to "sense" and "capture" the targeting molecules. Common elements of RNA secondary structures are "helices" (similar to those found in DNA), and "hairpins," which take place when the RNA folds back onto itself. "Some riboswitches are surprisingly complex, and they rival protein factors in their structural and functional sophistication [1]."

The following figure, from this Scitable article, illustrates the kind of changes in secondary (3D) structure a riboswitch can undergo before and after binding to a molecule. 

A riboswitch can adopt different secondary structures to effect gene regulation depending on whether ligand is bound. This schematic is an example of a riboswitch that controls transcription. When metabolite is not bound (-M), the expression platform incorporates the switching sequence into an antiterminator stem-loop (AT) and transcription proceeds through the coding region of the mRNA. When metabolite binds (+M), the switching sequence is incorporated into the aptamer domain, and the expression platform folds into a terminator stem-loop (T), causing transcription to abort. aptamer domain (red), switching sequence (purple), and expression platform (blue).

Because they affect gene expression, particularly genes involved in biosynthetic pathways, riboswitches are natural targets for drug development.
"First, many riboswitches repress the expression of genes whose protein products are involved in the transport or biosynthesis of essential metabolites. Therefore, compounds that trick riboswitches by mimicking the natural ligand might inhibit bacterial growth by starving the cells for that essential metabolite. Second, medicinal chemists already have a ‘‘hit’’ compound (the natural ligand) for each validated riboswitch class that they can begin to chemically alter to create new antibiotics. In this regard, riboswitches are almost unique among noncoding RNAs classes because they have evolved pockets to purposefully bind a small molecule, and therefore should be more easily drugged [1]."
From the Scitable article:
"Their role in regulating transcription in bacteria makes them enticing targets for the development of novel antibiotics aimed at stopping bacterial pathogens from flourishing inside the people they infect. Because riboswitches control genes essential for bacterial survival, or genes that control the ability of bacteria to succeed at infection, a drug designed to affect a riboswitch could be a powerful tool for shutting down pathogenic bacteria."
Synthetic riboswitches have been developed and shown to activate or repress gene expression in bacteria [2]. While I couldn't find any studies done in humans yet (though if you guys know of some, please let me know!), I did find a Nature letter reporting the first ever human RNA switch analogous to riboswitches [3].

[1] Breaker, R. (2011). Prospects for Riboswitch Discovery and Analysis Molecular Cell, 43 (6), 867-879 DOI: 10.1016/j.molcel.2011.08.024

[2] Topp, S., Reynoso, C., Seeliger, J., Goldlust, I., Desai, S., Murat, D., Shen, A., Puri, A., Komeili, A., Bertozzi, C., Scott, J., & Gallivan, J. (2010). Synthetic Riboswitches That Induce Gene Expression in Diverse Bacterial Species Applied and Environmental Microbiology, 76 (23), 7881-7884 DOI: 10.1128/AEM.01537-10

[3] Ray, P., Jia, J., Yao, P., Majumder, M., Hatzoglou, M., & Fox, P. (2008). A stress-responsive RNA switch regulates VEGFA expression Nature, 457 (7231), 915-919 DOI: 10.1038/nature07598


  1. Thanks for another really interesting post. I'm soooo curious to see where increased understanding of change at the genome/epigenome etc. level leads in terms of understanding evolution, especially rapid evolution. I never was satisfied with the old slow, small, rare mutation scenario. But now there are so many possibilities! so fun to read and think about.

  2. Thanks so much, Hollis! There have been studies that looked at "short-term" adaptation at the epigenetic level: the induced changes are inherited for 1-2 generations and then ebb off.

    The other thing that strikes me is that it really affects the way we think in term of "causal variants," because so much happens between DNA and proteins...

  3. antisocialbutterflieFebruary 24, 2012 at 3:59 PM

    I saw your title and immediately thought about the various antibiotics that are being developed that target riboswitches but you beat me to it. As an interesting side note the aptamer part of riboswitches are also being developed as drug, explosive, and bioweapon detection systems by the department of defense.

  4. Bioweapons? Oh, that is intriguing, can you tell me more about it? Thanks, that's an awesome side note!! :)

  5. antisocialbutterflieFebruary 24, 2012 at 7:21 PM

    There is a free full text that talks about aptamer protein sensing. Sensors 2008, 8(7), 4296-4307

    I heard about the detection system stuff in a seminar many years ago but a review of the speaker's recent PubMed references is coming up empty so I don't know if the project ever made much forward progress. It seems that he's had some luck with ribozyme mediated mRNA knockdowns of TGF-beta in cell culture (Methods Mol Biol. 2012;820:117-32) and I know they've worked out an mRNA ocular delivery system in rabbit to prevent corneal scarring (Wound Repair Regen. 2008 Sep-Oct;16(5):661-73 <<Most terrifying treatment regime in the history of ever. It's electrophoresis using your eye as a gel *shudder*). I really need to learn to stop remembering random crap people said in a talk five years ago.

  6. No, no, please keep remembering, I love it! :)
    I'll check out those references, thanks!!


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