Zexin Li - Institutionen för experimentell medicinsk vetenskap

Title: Characterisation and discovery of conflict-associated systems in plant-associated prophages

Main supervisor: Gemma C. Atkinson

Reviewers: Catherine Paul, Dag Ahren, Jeovanis Gil Valdés

Abstract

(Bacterio)phages, viruses that infect bacteria, play an important role in cellular and molecular evolution and microbial ecology. In the lysogenic life cycle, phages integrate their DNA into bacterial genomes as prophages. Prophages often carry cargo genes that influence host fitness. Many of these cargo genes are involved in inter-species biological conflict, such as anti-phage defence systems and toxins. Phage defence systems protect bacteria against phage infection, but when encoded on prophages can be seen as phage weapons to inhibit competing phages. These anti-phage defence systems often contain toxins that inhibit bacterial growth to limit spread of the viral infection. In the case of symbionts and pathogens, toxins can be bacterial effector proteins that mediate interactions with eukaryotic hosts. Here, we investigated the anti-phage defence systems in the plant pathogenic bacteria Ralstonia solanacearum species complex, and aim to discover previously unknown anti-phage defence systems. To address this, we mined Ralstonia prophage hotspots and identified putative anti-phage defence systems, in which a representative candidate was further validated for defensive activity by phage assay. We next analysed anti-eukaryote toxin cassettes carried by APSE phages, which reside in insect symbiont bacteria Candidatus Hamiltonella defensa and contribute to aphid protection against parasitoid wasps, revealing extensive structural and functional diversity among APSE-encoded toxins. Together, our findings highlighted that the prophage hotspots are important reservoirs of adaptive genes, particularly those involved in biological conflict.