A phage-derived reconfigurable effector associated with an actinobacterial contractile nanomachine tailors bacterial responses to competition

Contractile injection systems (CISs) are derivatives of phage tails and widely distributed in prokaryotes. CISs load cognate effectors and eject them through contractile actions resembling those of phage tails. Ejected effectors play central roles in CIS functionality by acting on target cells and mediating various biological processes. Here, we report a novel group of CIS effectors related to phage tapemeasure protein, the transmembrane component of the phage infection machinery. This group is broadly distributed within the class actinobacteria, one of the bacterial classes in which CIS gene clusters are highly conserved, and is represented by Sle1, a cognate effector of the intracellularly localised Streptomyces lividans phage tail-like nanoparticle (SLP). This effector is associated with Sle2, which contains a CIS effector core domain and interacts with the SLP core component. Sle1 is packaged inside SLP and is translocated to lipid membranes along with SLPs. The functional domain of Sle1, probably through interactions with ribosome-containing subcellular fractions, upregulates the membrane-associated proteome in S. lividans and E. coli . This effect modifies the physiological properties of S. lividans , ultimately enhancing its adaptation to microbial competition. In addition, we revealed that Sle1-type effectors conserved among actinobacterial species are structurally and functionally diverse in their functional domains. One of them from Micromonospora eburnea constitutes a novel toxin-antitoxin system and introducing its functional domain into Sle1 reprogrammes the phenotypic responsiveness of S. lividans to neighbouring bacteria. Our findings illustrate that phage elements can be incorporated into CISs as reconfigurable platforms for bacterial adaptation to various environmental conditions.