Abstract
Mobile genetic elements (MGEs), such as bacterial viruses (phages), archaeal viruses, plasmids and integrative and conjugative elements, can inflict deleterious effects on their host. In particular, the life cycle of a lytic phage or archaeal virus necessarily results in the death of the infected cell. The co-evolution of prokaryotes and MGEs over billions of years has resulted in the emergence of diverse immune/defence systems in bacteria and archaea. Our understanding of the range of defence systems that exist has long been limited to a few families. However, in the last five years, there has been a major resurgence in the discovery of new systems. Despite these new discoveries, there has been a lack of computational tools available to identify defence systems in different genomes.
In this thesis, we discuss our development of a computational tool for defence system identification called the Prokaryotic Antiviral Defence LOCator (PADLOC). To make PADLOC accessible, we developed an accompanying web server where researchers can search the genomes of their organisms of interest and browse a precomputed database of more than 200,000 bacteria and archaea. Importantly, PADLOC has facilitated our discovery of new defence systems. Firstly, we investigated the uncharacterised genes frequently associated with several defence systems. This led to our discovery of six new subtypes of known systems and a putative new defence system comprised of a helicase, methylase and ATPase (Hma). Unusually, the majority of Hma systems had additional genes embedded between the three canonical genes. Some genes encoded other known types of defence systems, but most had unknown function. We hypothesised that many of the uncharacterised Hma-embedded genes could themselves be new defence systems. We subsequently confirmed antiphage activity for seven Hma-embedded gene cassettes, including five new systems belonging to larger families of ABC ATPases, GmrSD proteins, and diverse RNases. Overall, this thesis describes the development of an accessible tool for defence system identification and expands on the known phage defence repertoire of prokaryotes. Advancing our knowledge of bacterial immune systems has important implications for developing effective phage therapies and the discovery of new enzymatic functions for molecular biology and biotechnology applications.