Deciphering stringent response proteins and toxin-antitoxin systems in the arms race between bacteria and phages

ongoing

Bacteriophages, viruses of bacteria, are the most abundant life form on Earth. The prospect of using them in the fight against pathogenic bacteria has long been recognised, but their very high specificity and unpredictable reproduction limits their use in medicine. The mechanisms phages use to fight bacteria are attractive candidates for the development of novel antimicrobial applications, but are still very poorly understood. Indirect evidence exists of toxin antitoxin systems (TAS) and stringent response involvement in phage defence. The constant co-evolution of phages and bacteria suggests that phages have a way of overcoming all of the wide variety of bacterial defence systems, yet, no direct phage mechanisms targeting bacterial stringent response have been identified. We hypothesise that as the bacterial toxin-antitoxin systems and stringent response play a part in the arms race between bacteria and phages we can provide direct molecular evidence and identify phage proteins involved in these interactions by (1) creating and characterising, morphologically and molecularly, a novel library of phages infecting Pseudomonas putida PaW85; (2) uncovering the stringent response- and TAS-mediated phenotypic effects and their molecular mechanisms on P. putida phage tolerance; (3) discovering and characterising, functionally and structurally, the anti-TAS and anti-stringent response phage effectors; (4) determining the toxicity and specificity of the identified phage-derived toxins by testing them on different bacterial species. This study will bridge several gaps in the phage-bacteria interaction research, advance the research of phage-tolerant bioremediation strains and give crucial basic knowledge that can lead to the development of novel, efficient phage therapy solutions that target bacterial stress-mechanisms.