Evolution of $\textit{Pectobacterium}$ Bacteriophage ΦM1 To Escape Two Bifunctional Type III Toxin-Antitoxin and Abortive Infection Systems through Mutations in a Single Viral Gene.

Some bacteria, when infected by their viral parasites (bacteriophages), undergo a suicidal response that also terminates productive viral replication (abortive infection [Abi]). This response can be viewed as an altruistic act protecting the uninfected bacterial clonal population. Abortive infection can occur through the action of type III protein-RNA toxin-antitoxin (TA) systems, such as ToxIN$_{Pa}$ from the phytopathogen $\textit{Pectobacterium atrosepticum}$ Rare spontaneous mutants evolved in the generalized transducing phage ΦM1, which escaped ToxIN$_{Pa}$- mediated abortive infection in $\textit{P. atrosepticum}$ ΦM1 is a member of the $\textit{Podoviridae}$ and a member of the "KMV-like" viruses, a subset of the T7 supergroup. Genomic sequencing of ΦM1 escape mutants revealed single-base changes which clustered in a single open reading frame. The "escape" gene product, M1-23, was highly toxic to the host bacterium when overexpressed, but mutations in M1-23 that enabled an escape phenotype caused M1-23 to be less toxic. M1-23 is encoded within the DNA metabolism modular section of the phage genome, and when it was overexpressed, it copurified with the host nucleotide excision repair protein UvrA. While the M1-23 protein interacted with UvrA in coimmunoprecipitation assays, a UvrA mutant strain still aborted ΦM1, suggesting that the interaction is not critical for the type III TA Abi activity. Additionally, ΦM1 escaped a heterologous type III TA system (TenpIN$_{Pl}$) from $\textit{Photorhabdus luminescens}$ (reconstituted in $\textit{P. atrosepticum}$) through mutations in the same protein, M1-23. The mechanistic action of M1-23 is currently unknown, but further analysis of this protein may provide insights into the mode of activation of both systems. IMPORTANCE Bacteriophages, the viral predators of bacteria, are the most abundant biological entities and are important factors in driving bacterial evolution. In order to survive infection by these viruses, bacteria have evolved numerous antiphage mechanisms. Many of the studies involved in understanding these interactions have led to the discovery of biotechnological and gene-editing tools, most notably restriction enzymes and more recently the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems. Abortive infection is another such antiphage mechanism that warrants further investigation. It is unique in that activation of the system leads to the premature death of the infected cells. As bacteria infected with the virus are destined to die, undergoing precocious suicide prevents the release of progeny phage and protects the rest of the bacterial population. This altruistic suicide can be caused by type III toxin-antitoxin systems, and understanding the activation mechanisms involved will provide deeper insight into the abortive infection process.This research was funded by support from the Biotechnology and Biological Sciences Research Council, United Kingdom, to G.P.C.S., by a Marsden Fund, Royal Society of New Zealand (RSNZ) award to P.C.F. and G.P.C.S., and by a Rutherford Discovery Fellowship (RSNZ) to P.C.F. B.F.L. was supported by the Wellcome Trust, United Kingdom. Work carried out with P. atrosepticum was under DEFRA license no. 50864/197900/3