DNA repair studied with molecular precision

Chalmers University of Technology

If DNA breaks and is not correctly repaired it may pose devastating consequences to humans, not only on the cellular level but for the whole body, as the breaks may cause disease, such as cancer. Using a combination of unique methods, researchers at Chalmers have investigated a mechanism for repairing DNA-breaks in bacteria, which can potentially increase the general understanding of DNA repair in human cells.

Fredrik Westerlund, Professor in Chemical Bi​ology at the Department of Biology and Biological Engineering, was in 2019 awarded the European Research Council’s prestigious research grant ERC Consolidator Grant for the project “Next Generation Nanofluidic for Single Molecule Analysis of DNA Repair Dynamics”.

​​His research group has now published a study linked to the project, where they have characterised the bacterial DNA-repair system responsible for so-called Non-Homologous End-Joining (NHEJ).

What is NHEJ and why are you interested in this system?

Photo of Fredrik WesterlundFredrik Westerlund: DNA molecules can break − it happens all the time in all cells – and the consequences of these breaks can be severe. So-called double-strand breaks can, among other things, stall life-sustaining processes in the cell. If the DNA molecule is not correctly repaired, the cell can potentially lose or change genetic information, i.e. the information that controls all the cellular functions. In turn, this can lead to lethality or the initiation of various diseases, such as cancer. It is important that DNA-breaks are repaired as quickly and efficiently as possible, therefore all cells have developed efficient repair systems.

There are two different mechanisms for repairing DNA-breaks; “Homologous Recombination” − where the enzymes involved use an identical copy of the broken DNA molecule as a template − and NHEJ where enzymes join the DNA ends, without using a template.

NHEJ was first discovered in human cells. However, it has also been found to exist in bacteria, which use a smaller set of components. Thus, we realized that the bacterial mechanism might serve as an interesting model system.

What is a model system?

Photo of Robin ÖzRobin Öz, postdoc at the Division of Chemical Biology, and first author of the study: It means that we study a simpler system, in this case the bacterial repair mechanism, with the aim to eventually gain a better understanding of how the more complex human cells, repair broken DNA. Since inaccurate repair of DNA-breaks plays a major role in, for example, cancer, the model system can potentially help us understand how such disease develop and how they can be prevented from further spreading. We use a simpler model, which consists of only two components, to better understand important features of the more complex human system, consisting of at least ten different proteins.

What are the results of the study?

Fredrik Westerlund: In the study, we focused mainly on one of the two proteins that are part of the bacterial NHEJ system. Together with our collaborators in France we have identified important differences between the bacterial and human systems. Previous studies have shown that a protein, called Ku, binds to broken ends of the DNA, and protects them from systems that may destroy free DNA ends in the cell. Ku can bring the DNA strands together and then recruit, Ligase D, which finally repairs the DNA. In our group we have developed a method where the DNA molecules are stretched out in nanochannels, thin glass tubes, without obstructing the ends. This allow us to study processes and interactions that take place at the free ends when different proteins are added to the solution. In this way, we have been able to show previously unknown mechanisms for the interaction between Ku and DNA.

Robin Öz: The study has shown that there are very interesting similarities between DNA-repair systems in bacteria and human cells, while the mechanisms are very different. Previously, it has been unclear what happens to the proteins attached to the DNA after the repair. We have now shown, among other things, that Ku is actually entrapped on the DNA up to several hours after the repair has finished, which means that there are potentially other, currently unknown systems that are involved in the final phase of the repair process.

What is the next step?

Fredrik Westerlund: The next step is to show how the ligase that binds to Ku works. NHEJ in bacteria could be an important target for new antibacterial drugs. Different variants of combined treatments have become very relevant in the fight against antibiotic-resistant bacteria. For example, one can imagine a combination of drugs that damage DNA − and knock out the DNA-break repair system.

Text: Susanne Nilsson Lindh

Photo: Pixabay, Johan Bodell & Martina Butorac

Read the study in Nucleic Acid Research:

Dynamics of Ku and bacterial non-homologous end-joining characterized using single DNA molecule analysis​

/University Release. This material comes from the originating organization and may be of a point-in-time nature, edited for clarity, style and length. View in full here.