Fig. 4: Individual TIR defense systems can be sensitive to the same components of different phages.

a–c Plaque assays showed that the TIR-IV (a), TIR-Retron (b), and Thoeris-II (c) systems are sensitive to major capsid proteins, DNA primase-helicases, and tail proteins of different phages, respectively. The empty vector lacking the TIR system was used as a negative control. Tenfold serial dilutions of phage were used for infection. Mutation sites in the proteins were indicated by black arrows. d Structural analysis of the major capsid proteins of phages #41 and #45. Structures were modeled using AlphaFold2 and analyzed using PyMOL. The mutation sites were highlighted in red. e Electron micrographs of purified WT and escaped phage virions. Assays were performed in triplicate and the representative results were shown. f Infection kinetics of WT (green lines) and escaped phages (blue lines) #45, #41, #75, and #106 on E. coli MG1655 expressing the inactivated TIR-IV mutant. E. coli MG1655 cells expressing the WT TIR-IV system were used as controls, and the data were shown in Supplementary Fig. 5. The dashed lines indicated that the escaped phages lysed cultures about 20–70 min slower than the WT phages. g One-step growth curve of WT and escaped phages #45, #41, #75, and #106 on E. coli MG1655. Data were presented as the mean of three biological replicates ± S.D. Source data are provided as a Source data file.