A phage-derived reconfigurable effector associated with an actinobacterial contractile nanomachine tailors bacterial...

Contractile injection systems (CISs) are derivatives of phage tails and are 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 tape measure 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 localized 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 enriches the membrane-associated subproteome 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 reprograms the phenotypic responsiveness of S. lividans to neighboring bacteria. Our findings illustrate that phage elements can be incorporated into CISs as reconfigurable platforms for bacterial adaptation to various environmental conditions.IMPORTANCEBacterial CISs have attracted interest for their importance in microbial ecology and potential in biotechnological applications. However, understanding of their functional diversity is currently limited because many CIS effectors remain unannotated due to a lack of inferable structural and genetic signatures. Our findings on Sle1 and its relatives illuminate a previously unidentified class of CIS effectors with phage tape measure protein-related modular architecture, association with the CIS effector core domain, and wide distribution within the major class of Actinobacteria, substantially expanding the known repertoire of effector classes. The impact of Sle1 on S. lividans suggests a link between CIS effectors and bacterial adaptation to environmental conditions, highlighting unexplored functional diversity of CIS effectors as tuners of bacterial phenotypes in communities.