The intimate interactions between bacteriophages and bacteria

PhD Student: Veronika Theresa Lutz

Bacteriophages are possible alternatives to antibiotics since they specifically infect and kill bacteria. Elucidating how phages selectively target their host bacteria by binding to the bacterial surface is particularly important for developing phages for therapy.

The projcet and the results
In this thesis we are focusing on a family of phages, the Straboviridae phages. These phages are known to express two different 
receptor-binding proteins that allow the phages to bind to the bacteria. The first, called Gp38, has an unusual protein structure containing a highly variable part responsible for binding to the receptor. The second, called Gp37, forms a long fiber protein that is well characterized, but not much is known about its distribution across the Straboviridae phage family. The objective of the
Ph.D. thesis was to elucidate the molecular determinants of phage binding and the evolution of receptor-binding proteins.

In the first part of the thesis, we isolated phages belonging to the Straboviridae family that specifically use Gp38 variants for binding to their host bacterium. These phages were shown to use three different outer membrane proteins as their receptors. In addition, they had diverse host ranges, meaning that they infect and kill different bacterial hosts, suggesting diverse specificity
of the binding between the different Gp38 variants and their receptors. With the help of AlphaFold, a bioinformatics tool revealing protein structure and interaction, we could predict how the different Gp38 variants bind to the receptors.

By combining our results, we could pinpoint that Gp38 of the phages binds to specific loop structures of the receptors displayed on the bacterial surface. We further discovered that phages expressing Gp38 variants that bind to more than one of these loops can infect a wider range of bacterial strains. In summary, we elucidated the molecular determinants for Gp38 binding to the receptor, which is important for the choice and design of phage cocktails for therapy.

In the second part of the project, we analyzed two phages expressing Gp37 and compared them to phages in two genera of the Straboviridae phages. Hereby, we discovered that Gp37 diversity is mainly located in the tip of the long fiber protein performing host binding, which displays a mutational hotspot. We furthermore showed that the phages expressing Gp37 are often
phylogenetically clustered together, allowing us to hypothesize that Gp37 evolved through linear descent and not through mosaicism, an evolutionary process otherwise very common among phages. Overall, this expanded our understanding of how the important phage-binding process has evolved.