Unwanted Invaders or Welcomed Guests: Impact of Prophage Integration Sites on Host Genomic Integrity and Evolution

ongoing

Bacteriophages are found in over two-thirds of sequenced bacterial genomes, with phage DNA making up an estimated 10% of these genomes. Recent studies suggest that phage DNA integration, during so called lysogeny, can lead to interactions with bacterial hosts that are more complex than once thought. There are phages which very specifically and reversibly integrate into host genes, modulating host development. Altering bacterial behaviours can have detrimental consequences in microbial communities, such as those found in the human gut. However, it is unclear how specific phage integration mechanisms evolve, or if integration specificity influences regulation during lysogeny. I hypothesise that phage integration components are a key factor in phage-host interactions, with attachment sites (att) and phage integrases under strong evolutionary pressure. This project's goal is to examine the consequences of specific phage integration for the host and for the phage and to understand how integration components are directed by evolution. This will be fulfilled via three research objectives: 1) bioinformatics analysis of phage integration components, capitalizing on newly built prophage database and focusing on conservation of host att genes and phage integrases; 2) investigation of the effects of integrase specificity on phage-host interactions and fitness via combining engineered phages and trackable host with high-throughput imaging and RNA sequencing. 3) testing the long-term effect of specific att sites on host genome evolution in ecological context to Bacillus subtilis was selected as the model host due to its tractability, biotechnological importance, and susceptibility to phages with highly specific integrases. Understanding the impacts of phage integration specificity and its evolution will reveal new phage roles in host genome editing and gene transfer, improve our knowledge of phage-bacteria coevolution and it will pave new ways to engineering of bacterial genomes.