Bacterial toxin-antitoxin systems as antiphage mechanisms

Phages are viruses that attack Bacteria. They are widely distributed in different environmental niches populated by their bacterial hosts, such as the human and animal intestine, soil, seawater or wastewater. Bacteria have evolved different defense strategies to protect themselves against phages. However, many underlying defense mechanisms and their influence on bacterial physiology still remain elusive: several recent studies have shown that there are still many unknown antiphage defense systems for protection against well-known phages. In this project, I investigate whether toxin- antitoxin (TA) modules are an effective defense mechanism against phages. TA modules are genetically encoded systems, ubiquitous in different bacterial species, including pathogens. Toxin activation during stressful conditions affects bacterial gene expression and growth, and it has been shown that TA systems collectively help bacteria to withstand stress. In this project, I will combine standard phage assays and microbiology techniques with single-cell microscopy tools. Because TA modules are not conserved among different strains belonging to the same bacterial species, I will investigate TA systems in commonly used non-pathogenic Escherichia coli strains, as well as in pathogenic and commensal E. coli strains. This research will elucidate a hitherto poorly investigated role of bacterial TA systems as antiviral defense mechanisms, and give insights into basic ecological concepts of bacteria-phage interactions.

Phages are viruses that specifically attack Bacteria. Bacteria have evolved different defense strategies to protect themselves against viral attacks. However, most of bacterial antiviral defense mechanisms are largely unknown. This Project employed interdisciplinary approaches - microbiology, biochemistry and microscopy - to investigate interactions between phages and bacterial genetic elements called toxin-antitoxin systems. Toxin-antitoxin systems are widespread in most bacterial species, and frequently involved in different cellular processes that affect bacterial physiology and lifestyle. The results revealed a novel, significant role of toxin-antitoxin systems in the bacterial protection against phages. Escherichia coli strains that harbor specific toxin-antitoxin systems were less susceptible to phage attacks, compared to Escherichia coli strains that do not harbor these systems. This is an important finding with regard to phage therapy, which uses phages to treat bacterial infections. An alarming increase in antimicrobial resistance worldwide has put forward the search for alternatives to antibiotic treatments, such as phage therapy. It is therefore essential to evaluate the ability of phages to kill bacterial pathogens, such as pathogenic Escherichia coli, as well as to understand how bacterial pathogens manage to evade phage attacks. Ultimately, the findings of this Project will lay ground for further applications of phages in biomedical research, and will advance our knowledge on what generally determines the success of phage therapy.