University of Dundee

Flicking the switch inside the cell

09 Oct 2017

All living cells make proteins to carry out nearly all the jobs that keep them alive, including the enzymes that speed up chemical reactions and molecular pumps that move molecules from one place to another. All this constant activity is what we call the cell's metabolism. Often scientists seek some kind of Achilles heel in that metabolism to achieve therapeutic intervention.

All that busy chemical activity in the cell is subject to stringent control. Cells should not make something when its not needed, yet in times of need they may need to make a lot more of something. In all cells the machine that makes proteins is programmed by a long molecule called RNA, that acts a bit like computer code. In bacteria an important way of maintaining control over metabolism is by small molecules binding to RNA. When the controlling molecule binds, it changes the local shape of the RNA so that more or less of the protein is made according to the needs of the cell. These sections of RNA are called "riboswitches", because they switch genes on or off. There are many of these, that respond to a variety of chemicals, such as amino acids or vitamins.

The current work concerns two riboswitches that regulate the production of proteins that rid the cell of a very toxic compound called guanidine, that is formed when some key molecules in the cell break down. Until very recently it was not understood that guanidine was produced in cells, but it turns out that it is, and it must be removed from the cell lest it suffer detrimental consequences. So the cell makes proteins that either convert guanidine into something less poisonous, or literally pump it out of the cell. The production of these proteins is under the control of the guanidine riboswitches. In fact there are three of these. To understand their function it is desirable to determine the structure of these RNA molecules.

In the last few months the lab of Professor David Lilley in the School of Life Sciences at Dundee University has used X-ray crystallography to determine the molecular structures of two of the three kinds. The first was published in mid-summer, and the second has just been published, both in the journal Cell Chemical Biology.  This analysis reveals the way the RNA folds up in 3D space to create a site that will bind the small molecule (guanidine), and further shows how the site specifically interacts with the guanidine, and importantly how it excludes very similar-looking molecules that must not flick the molecular switch in the same way.

Comparison of these different structures provides a fascinating insight into how over geological timescales evolution leads to different solutions to a given problem. There is another significance to such work. The reliance of bacteria on this ability of these special riboswitches to bind compounds in a very specific way suggests how chemists might engineer new molecules that might bind to these RNA species to disrupt the metabolism. As resistance to the natural antibiotics increases, these approaches might eventually lead to new classes of antibacterial agents for treating infectious disease.

L. Huang, J. Wang and D. M. J. Lilley The structure of the guanidine-II riboswitch Cell Chem. Biol. 24, 695–702 (2017).

L. Huang, J. Wang, T. J. Wilson and D. M. J. Lilley Structure of the guanidine-III riboswitch Cell Chem. Biol. in the press.

For background : D. M. J. Lilley The guanidine riboswitch - a poor orphan no longer. Cell Chem. Biol. 24, 130-131 (2017)

Image: The heart of the guanidine-III riboswitch, where it binds the metabolite (shown in magenta). This is guanidine, a toxic substance produced in the breakdown of proteins and DNA in the cell.