Research
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Phage therapy in medical and agricultural applications
Phages were discovered almost a century ago and are the most abundant and also potentially most diverse entities on Earth. Almost immediately, their potential as antibacterial agents was recognized, since ‘phage therapy’ can combat pathogenic bacteria by directly applying the phages to the site of infection. Currently, our phage research forms the base of phage therapy in human patients, in collaboration with the Military Hospital Queen Astrid (Neder-Over-Heembeek) and UZ Leuven.
In the food industry or agriculture, these regulatory problems do not exist. Industrial applications of phages, approved by the FDA and Europe, exist for treatment of meat products and cheese. We also work on the application of phage biocontrol in leek and cabbage infections caused by Pseudomonas syringae pv. porri and Xanthomonas campestris pv. campestris, respectively. This is done in collaboration with ILVO, Inagro, PSKW and PCG (VLAIO LA-traject 150914). More recently, we started working on Agrobacterium biovar 1 causing crazy roots in tomato and cucumber (H2020 VIROPLANT). In regard of these projects, we are part of the KU Leuven Plant Institute.
Phages as inspiration for synthetic biology
As nature’s first bioengineers, bacteriophages have evolved to modify, adapt and control their bacterial hosts through billions of years of interactions. Indeed, like modern synthetic biologists aspire to do, bacteriophages already evade bacterial silencing of their xenogeneic DNA, subvert host gene expression, and co-opt both the central and peripheral metabolisms of their hosts. Studying these key insights from a molecular systems biology perspective, inspired us to develop these evolutionary fully-adapted phage mechanisms as a next-level layer of synthetic biology tools. In our research, we are providing conceptual novel synthetic biology tools that allow direct manipulation of specific protein activity, post-translational modifications, RNA stability, and metabolite concentrations.
Protein-protein interaction analysis between phages and their host
Considering the current poor rate of release of novel antibiotics, let alone entirely novel classes of antibiotics, it is a worrying indication that we may soon run out of treatment options. Therefore, the development of innovative antibiotics targeting (not yet exploited) essential bacterial pathways will be crucial in the near future.
Strictly lytic bacteriophages, bacteria’s natural enemies, rely completely on the bacterial metabolism for their propagation. Over a billion years of co-evolutionary struggle with an estimated number of 1023 phage infections per second, phages have evolved an incredible number of highly diverse proteins that either inhibit or adapt bacterial metabolic processes to their own benefit. Although not all of these intracellular phage-host interactions are detrimental to the host cell, many of them do indeed lead to cell-cycle arrest or even host lethality. As such, a novel source of Gram-negative antibacterials might originate from mining the thousands of available sequenced phage genomes. At our laboratory, we particularly focus on Pseudomonas aeruginosa and its phages to identify new Pseudomonas drug targets.
Artilysin®s as a novel enzyme-based approach to kill drug-resistant bacteria
Endolysins are bacteriophage enzymes, produced within infected bacterial cells at the end of the viral cycle. They digest the peptidoglycan layer which surrounds every bacterium, resulting in cell burst and the release of newly produced viral particles. The nice thing about endolysins is that purified endolysins are also active when you add them from the outside. This is particularly appealing for Gram-positive bacteria that have a peptidoglycan layer which is immediately accessible from the outside. Addition of purified endolysin to these bacteria results in a rapid cell death through peptidoglycan degradation, irrelative of the presence of existing resistance mechanisms. Endolysins can thus be used as antibiotics and their efficacy has meanwhile been shown for the treatment of mucosal and systemic Gram-positive infections in diverse animal models and food applications.
A major hurdle in the expansion of endolysins as antibiotics against Gram-negative pathogens was their outer membrane that shields the peptidoglycan layer and made them insensitive to lysis by exogenously applied endolysins. To tackle this barrier, endolysins were modified using protein-engineering to combine the self-promoted uptake mechanism of outer membrane permeabilizing peptides and peptidoglycan-degrading activity of endolysins to broaden the use of endolysins. These research efforts resulted in a novel class of engineered endolysins, called Artilysin®s. They are able to eradicate multi-drug resistant Gram-negative bacteria. A well characterized Artilysin is Art-175, which kills the notorious multidrug resistant bacterium Pseudomonas aeruginosa upon contact, indifferent of the presence of any existing antibiotic resistance mechanism. Strains resistant against Art-175 could not be selected. Case studies with dogs suffering otitis support potential applicability of Art-175 against topical, drug-resistant infections.
For more information on this topic, check out From endolysins to Artilysin®s: novel enzyme-based approaches to kill drug-resistant bacteria by Gerstmans H, Rodríguez-Rubio L, Lavigne R and Briers Y.
Elucidation of the biosynthesis of secondary metabolites
Secondary metabolites are produced via a multi-enzyme biosynthesis pathway present in bacteria, fungi, plants and even insects. They provide their producers with a selective advantage e.g. antimicrobial dominance. This natural benefit, together with their chemical diversity, led to the use of secondary metabolites is many applications, ranging from antibiotics and fungicides to cholesterol lowering agents.
In our laboratory, we want to broaden the potential of these natural products as future medicines. Our research focuses on the elucidation and characterization of newly discovered metabolites and their complex pathways. Another topic focuses on the identification of protein interactions between the biosynthesis enzymes in order to optimize the pathway, leading to improved antimicrobial compounds.