Systematic Discovery of Phage Genes that Inactivate Bacterial Immune Systems

Ojima, S.; Azam, A. H.; Kondo, K.; Nie, W.; Wang, S.; Chihara, K.; Tamura, A.; Yamashita, W.; Nakamura, T.; Sugawara, Y.; Sugai, M.; Zhu, B.; Takahashi, Y.; Watashi, K.; Kiga, K.

doi:10.1101/2024.04.14.589459

bioRxiv · 10.1101/2024.04.14.589459

Systematic Discovery of Phage Genes that Inactivate Bacterial Immune Systems

Ojima, S.·Azam, A. H.·Kondo, K.·Nie, W.·Wang, S.·Chihara, K.·Tamura, A.·Yamashita, W.·Nakamura, T.·Sugawara, Y.·Sugai, M.·Zhu, B.·Takahashi, Y.·Watashi, K.·Kiga, K.

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Abstract

Bacteria have developed numerous defense systems to counter phage infections. However, the extent to which phages possess countermeasures against these defense systems remains unclear. In this study, we combined a phage gene knockout library with a defense system library to analyze the mechanisms by which phages counteract bacterial defense systems. After attempting gene deletions of 105 open reading frames (ORFs) in the DruSM1 phage ({Phi}DruSM1), we successfully generated 73 different ORF knockout phages. By infecting this library with bacteria harboring defense system expression plasmids, we identified inactivators of Druantia type I (Druad1), Brex type I, AVAST type III, Sir2+HerA, DUF4297+HerA, and hhe, as well as an activator of Retron Ec86, in a single phage genome. Synthetic phages incorporating Druad1 effectively eradicated Escherichia coli harboring the robust Druantia type I defense system by altering DNA methylation at m6A sites of the phage. This study highlighted the prevalence of various antidefense mechanisms employed by phages to overcome bacterial defense systems.

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Ojima, S., Azam, A. H., Kondo, K., Nie, W., Wang, S., Chihara, K., Tamura, A., Yamashita, W., Nakamura, T., Sugawara, Y., Sugai, M., Zhu, B., Takahashi, Y., Watashi, K., Kiga, K.. 2024-04-15. Systematic Discovery of Phage Genes that Inactivate Bacterial Immune Systems. https://doi.org/10.1101/2024.04.14.589459

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