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The DNA double-strand break repair system represents a core mechanism for maintaining genomic integrity and is vital for cell survival. However, it remains unknown whether and how these repair systems contribute to phage resistance. This study systematically investigates the role of the non-homologous end joining (NHEJ) during phage infection in Mycobacterium smegmatis. We found that NHEJ deficiency compromises host resistance to phage SWU1, as evidenced by increased plaque counts and reduced bacterial survival. Mechanistically, phages exploit host NHEJ for genomic repair; however, the error-prone nature of NHEJ leads to imperfect repair at phage cos sites, thereby blocking replication. The host modulates the balance between NHEJ and homologous recombination (HR) to control repair fidelity: NHEJ loss shifts the balance toward high-fidelity HR, which in turn promotes phage survival. Furthermore, NHEJ deficiency exacerbates infection-induced oxidative stress, leading to a compromise in bacterial viability. Our findings reveal the multifaceted functions of NHEJ in mycobacterium\u2013phage interactions and provide new insights into how DNA repair systems shape antiphage defense and coevolution.<\/jats:p>","DOI":"10.1093\/nar\/gkag066","type":"journal-article","created":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T12:25:46Z","timestamp":1768911946000},"source":"Crossref","is-referenced-by-count":2,"title":["Mycobacterial non-homologous end joining is required for antiphage defense"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4053-3648","authenticated-orcid":false,"given":"Yu","family":"Huang","sequence":"first","affiliation":[{"name":"Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University , Chongqing 400715 ,","place":["China"]},{"name":"Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai Key Laboratory of Tuberculosis , Shanghai 200433 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongxiang","family":"Xu","sequence":"additional","affiliation":[{"name":"Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University , Chongqing 400715 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianyu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University , Chongqing 400715 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiran","family":"Liao","sequence":"additional","affiliation":[{"name":"Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University , Chongqing 400715 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayue","family":"Hu","sequence":"additional","affiliation":[{"name":"Institute of Modern Biopharmaceuticals, School of Life 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