A novel prophage-encoded type III toxin–antitoxin system promotes resistance to phage infection in Streptococcus pyogenes
Toxin-antitoxin (TA) systems have been predicted in many bacteria. However, their experimental characterization in Streptococcus pyogenes (S. pyogenes) remains limited. In this study, we characterized the chromosomal TA landscape of this pathogen, identifying four predicted TA systems. Notably, we found that these systems are located within the four prophage regions of the genome—areas that remain largely unexplored in this organism. We identify and characterize SpytIN as a novel type III TA system. Unlike typical type III systems that require processing of a precursor RNA, SpytN toxin is inhibited by a small non-coding RNA SpytI. We demonstrate that SpytN acts as an endoribonuclease that predominantly cleaves RNA at a conserved A?AU motif. Genome-wide analysis revealed that this toxin targets transcripts encoding essential metabolic pathways, triggering a coordinated shutdown of transcription, translation and core metabolism. Furthermore, expression of this TA system enhances bacterial survival during bacteriophage infection through abortive infection. Our findings identify a unique subtype of type III TA systems and characterize its function in bacterial adaptation to phage-induced stress within prophage regions.