Memoirs of a fish pathogen: how CRISPR-Cas captures phage encounters in Flavobacterium columnare

Abstract

Bacteria are in constant interaction with their viruses, bacteriophages (phages). To prevent or abort phage infections, a variety of defence mechanisms have evolved. CRISPR-Cas, the only known adaptive bacterial immune system, targets intracellular phage genomes by utilizing genetic memories of past infections. A memory is formed during CRISPR adaptation when a fragment of a phage genome is integrated into a CRISPR array on the bacterial genome. This fragment, called a spacer, is later used in the interference phase to recognize and cleave phage genomes with matching sequences. While these core principles are shared by most CRISPR-Cas systems, many subtypes have not been thoroughly explored, especially in their native hosts or in natural environments. In this thesis, I characterize type II-C and VI-B CRISPR-Cas systems in the fish pathogen Flavobacterium columnare in association with its virulent phage. The first study describes how aquaculture settings can be harnessed for coevolutionary studies in semi-natural settings using bacteria that carry CRISPR-Cas loci. The second study shows F. columnare and its virulent phages evolving for several years in aquaculture, where coevolutionary dynamics were reflected by spacer acquisition in bacteria and genomic and host-range changes in phages. The third study examines the adaptation process of the II-C and VI-B CRISPR-Cas systems in the laboratory. The RNA-targeting VI-B locus was dependent on the spacer acquisition machinery of the II-C locus, leading to characteristic interference patterns for both loci. The fourth study shows how the presence of eukaryotic host signals accelerates spacer acquisition, suggesting that environmental determinants play important roles in phage defence strategies. Together, these studies show that type II-C and VI-B CRISPR-Cas systems are active in natural and laboratory conditions, driving coevolution between F. columnare and its virulent phages. Understanding native functioning of CRISPR-Cas is also important for practical applications such as phage therapy.