Conflict between bacteriophages and a mobile genetic element in bacterial immunity

Abstract

Bacteriophages (phages) are the most abundant biological entities on the planet. They are ubiquitous and numerous across the many environments bacteria are found. To combat phage predation, bacteria have evolved numerous immune strategies, so-called anti-phage defense systems. Likewise, phages encode counter-defenses that prevent the function of anti-phage defense systems. Many anti-phage defense systems are found within mobile genetic elements, like plasmids, temperate bacteriophages, and integrative and conjugative elements (ICEs). In this thesis, I show how an ICE in the bacterium Bacillus subtilis, called ICEBs1, protects populations of cells from phage predation by phages in the SPβ family. ICEBs1 has a phage defense system, spbK, which, upon phage infection, causes cell death prior to generating phage progeny. This mechanism of phage defense is considered abortive infection and protects populations of cells via altruistic cell death of infected cells. I show that during SpbK-mediated abortive infection, cells experience NAD⁺ depletion dependent on the Toll-interleukin-1 receptor (TIR) domain of SpbK. Depletion of NAD⁺ likely starves both the cell and infecting phage of energy, killing the cell and preventing the generation of phage progeny. I found that SpbK recognizes phage infection by recognizing and binding to the phage portal protein, YonE, through an interaction between the N-terminus of SpbK and the clip domain of YonE. Furthermore, I show that a gene in the SPβ-like phage Φ3T, nip, was necessary and sufficient to prevent SpbK-mediated anti-phage defense. I found that Nip binds to the TIR domain of SpbK and inhibits NADase activity to prevent abortive infection and enable viable phage production. These findings highlight the conflicts that occur between mobile genetic elements and the co-evolutionary arms race between bacteria and phages.