The DynaTweezers project

In 2018 I have been awarded a Marie Skłodowska-Curie Global Fellowship by the European Union to do research on how certain proteins interact with DNA to silence the expression of genes. Why? Let me back up a little.

For many years doctors have observed an increase in the number of bacterial infections that have become resistant to antibiotics and antimicrobials. This is a big deal as the invention of antibiotics has helped us prevent many preventable diseases and deaths over the years. Without antibiotics many now minor infections can become major problems. Natural selection drives bacteria to become more and more resistant to antibiotics (this video demonstrates the process beautifully).

One of the ways that bacterial resistance spreads is through something called Horizontal Gene Transfer. Pieces of DNA are spread between different bacteria and even to entirely different bacterial species. Most of the time this DNA is useless or even bad for the bacteria, but occasionally something useful like an antimicrobial resistance gene is transferred. By borrowing a ready made piece of DNA another bacterial species can become resistant to antimicrobials. Great for the bacteria, they don’t need to evolve resistance by themselves, but bad news for us.

The pieces of foreign DNA are called Xenogeneic (belonging to another species) DNA. Because this DNA is often not beneficial to the bacteria, they have a system based on proteins that bind to the DNA to silence the expression. These so called ‘Nucleoid Associated Proteins’ (NAPs) often recognize Xenogeneic DNA based on a higher or lower content of certain letters that make up the DNA compared to the rest of the DNA. By initially silencing the DNA the bacteria can first multiply and then start using it over time, increasing the chance that it will work for the bacteria.

Silencing the DNA effectively means that the DNA is not transcribed into RNA, another form of genetic material that is used as a blueprint to make the proteins that fulfill the different functions (such as making it resistant). What is unknown is exactly how NAPs interact with DNA to silence it. There are several theories: the NAPs prevent the transcription machinery from binding to and occluding the piece of DNA that signals that is should be transcribed, the NAPs sit in the way of the transcription machinery and stall its progress or the NAPs reorganize the DNA through the formation of loops such that transcription stops. How exactly the silencing occurs and under which conditions which mechanisms play a role is still largely unknown. In the DynaTweezer project I am trying to figure out how these NAPs interact with DNA to silence DNA expression by studying it at a single molecular level at unprecedented resolution.

The aim is to elucidate how these NAPs function. Understanding how this molecular system works may provide us with invaluable insight into how to design medication that acts on this system to prevent or possibly even revert the spread of antimicrobial resistance.

I use an improved version of Tethered Particle Motion (TPM) to study this system, but more on that later.