Salmonella Outer Membrane Vesicles contain tRNA Fragments (tRFs) that Inhibit Bacteriophage P22 infection

Abstract Salmonella Outer Membrane Vesicles (OMVs) were recently shown to inhibit P22 bacteriophage infection. Interestingly, we identify 31 recurrent tRFs abundantly expressed by Salmonella enterica serovar Typhimurium and find these tRFs are highly complementary to known Salmonella enterica-infecting bacteriophage (17 averaging 97.4% complementarity over 22.9 nt) and specifically enriched in S. Typhimurium OMVs. Most notably, tRNA-Thr-CGT-1-1, 44-73, bears 100% complementary over its entire 30 nt length to 29 distinct Salmonella enterica-infecting bacteriophage including P22. Importantly, we find inhibiting this tRF in secreted OMVs improves P22 infectivity in a dose dependent manner whereas raising OMV tRF levels conversely inhibits P22. Furthermore, we find P22 pre-incubation with OMVs isolated from naïve S. Typhimurium, rescues the ability of S. Typhimurium depleted of tRNA-Thr-CGT-1-1, 44-73 tRF to defend against P22. Collectively, these experiments confirm tRFs secreted in S. Typhimurium OMVs are directly involved with and required for the ability of OMVs to defend against bacteriophage predation. As we find the majority of OMV tRFs are highly complementary to an array of known Salmonella enterica-infecting bacteriophage, we suggest OMV tRFs may primarily function as a broadly acting, previously uncharacterized ancient antiviral defense.