Structural basis for phage-mediated activation and repression of bacterial DSR2 anti-phage defense system

Abstract

Silent information regulator 2 (Sir2) proteins typically catalyze NAD⁺-dependent protein deacetylation. The recently identified bacterial Sir2 domain-containing protein, defense-associated sirtuin 2 (DSR2), recognizes the phage tail tube and depletes NAD⁺ to abort phage propagation, which is counteracted by the phage-encoded DSR anti-defense 1 (DSAD1), but their molecular mechanisms remain unclear. Here, we determine cryo-EM structures of inactive DSR2 in its apo form, DSR2-DSAD1 and DSR2-DSAD1-NAD⁺, as well as active DSR2-tube and DSR2-tube-NAD⁺ complexes. DSR2 forms a tetramer with its C-terminal sensor domains (CTDs) in two distinct conformations: CTD^closed or CTD^open. Monomeric, rather than oligomeric, tail tube proteins preferentially bind to CTD^closed and activate Sir2 for NAD⁺ hydrolysis. DSAD1 binding to CTD^open allosterically inhibits tube binding and tube-mediated DSR2 activation. Our findings provide mechanistic insight into DSR2 assembly, tube-mediated DSR2 activation, and DSAD1-mediated inhibition and NAD⁺ substrate catalysis in bacterial DSR2 anti-phage defense systems.