Paving the way for phage research

Nadiia Pozhydaieva-Weber wins the MarBiNa Prize 2024

In her PhD thesis at the Max Planck Institute in Marburg, Dr. Nadiia Pozhydaieva-Weber has developed a method which facilitates the study of bacteriophages. This opens up new possibilities for biotechnological and medical applications. In recognition of this achievement, she has been awarded the Marburg Prize for Biotechnology and Nanotechnology 2024.

When bacteriophages attack their bacterial host, they reprogram its cellular machinery in a complex way. As a result, the bacterium is hijacked to produce a large number of viral progeny. When the bacterium dies, the viruses are released and the cycle begins again. In this way, a bacteriophage can kill a bacterial cell faster than an antibiotic.

Phage research is not only interesting in terms of medical applications; a precise understanding of the infection process could also provide important insights into the regulation of cellular processes. However, little is still known about the infection process because the DNA of phages is difficult to access using molecular methods: molecular tags protect it like a ‘write protection’ against bacterial defences.

In her doctoral thesis at Prof. Dr Katharina Höfer's research group, Dr Nadiia Pozhydaieva-Weber, developed a method to overcome this barrier in the T4 phage. Using an enzyme that is also found in human cells, she was able to remove the write protection without disrupting the infection process. With her method, researchers around the world can now use molecular methods such as CRISPR-Cas gene scissors more successfully to study the infection process of bacteriophages. For this achievement, the researcher has now been awarded the MarBiNa Prize, the Marburg Biotechnology and Nanotechnology Award 2024 of the Initiative for Bio- and Nanotechnology e.V. (IBiNa).

This research success is the result of a long journey - with a few setbacks along the way. At the beginning of her work, Nadiia Pozhydaieva-Weber also wanted to use the CRISPR-Cas gene scissors to elucidate the role of a particular enzyme in the infection process through genetic modification. In many organisms, CRISPR-Cas works efficiently, but in phages, the success rate was disappointingly low," she recalls.

A Solution from the Eukaryotic Cell

The research team developed a new approach: instead of removing the sugar coat directly, for which no suitable enzyme could be found, the researchers focused on a molecular basis of sugar coat formation, namely the attachment of methyl groups to DNA. They took inspiration from eukaryotic cells, where TET dioxygenases regulate DNA methylation. Using this enzyme, Nadiia Pozhydaieva-Weber was able to prevent DNA methylation and thus make the phage DNA accessible for CRISPR-Cas mutagenesis for the first time. ‘When it finally worked, it was an incredible moment,’ says the researcher.

In parallel, she and her colleagues used a 'multi-omics' approach to study the infection process in precise temporal resolution. The team was able to profile all proteins (= proteomics) and transcripts (= transcriptomics) over the course of the infection.

The PhD was funded by the German Research Foundation (DFG) as part of a priority programme on phage research (SPP 2330), which also helped her develop an interest in the field and build a network for the future. Looking back, the awardee is also thankful for the teamwork and mentoring she received: "Thanks to my supervisor Katharina Höfer and our great group, I never lost my motivation. I had to learn a lot of new things at the beginning of my PhD. I am incredibly grateful to Katharina Höfer for her support and guidance. The team spirit, the mutual support, the lively exchange and also the great work of my students - many people have contributed to this success."

Beyond CRISPR-Cas-based editing, the new method offers a non-invasive way to study the effects of DNA modifications on phage biology. Scientists can now analyse phage-bacteria interactions in more detail and modify phage genomes with unprecedented efficiency. "The response from the scientific community has been positive. Our work has already sparked the interest of researchers who are using our method to study the role of DNA modifications in phage infections ' says Nadiia Pozhydaieva-Weber, who is now a postdoctoral researcher in Prof. Dr. Stan Brouns' group at Delft University of Technology.

Using Phage Research to Combat Antibiotic Resistance

Phages are still her topic, but the focus is now more on bacterial immunity and thus more on potential applications. In the context of 'phage therapy', bacteriophages are seen as a promising alternative to antibiotics, especially against antibiotic-resistant bacteria. Phage therapy is not easy to use because bacteria have their own defence mechanisms and can develop resistance,' explains Nadiia Pozhydaieva-Weber. But if we understand how bacteria naturally defend themselves against phages, we can develop better strategies to overcome their immunity."

 

The Marburg-based funding initiative IBiNa e.V. has been holding an annual competition for young scientists since 2014. Prizes are awarded to work that
• are linked to Marburg and the surrounding region
• are based on biotechnological or nanoscale components
• have fundamental technical and economic feasibility
• contribute to improving the quality of life.
More information at https://www.initiative-biotechnologie.de/marbina-foerderpreis.html