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24 reviewsIn the evolutionary arms race between bacteria and viruses, retrons have emerged as distinctive antiphage defense systems. Here,we elucidate the structure and function of Retron-Eco2, which comprises a non-coding RNA (ncRNA) that encodes multicopy singlestranded DNA (msDNA, a DNA‒RNA hybrid) and a fusion protein containing a reverse transcriptase (RT) domain and atopoisomerase-primase-like (Toprim) effector domain. The Eco2 msDNA and RT-Toprim fusion protein form a 1:1 stoichiometricnucleoprotein complex that further assembles into a trimer (msDNA:RT-Toprim ratio of 3:3) with a distinctive triangularconfiguration. The RNA portion of the msDNA in one protomer closely intertwines around the RT domain of an adjacent protomer,mediating the formation of this self-inhibitory assembly. Upon activation, the Toprim effector domain exhibits RNase activity,1234567890();,:degrading RNA to arrest phage replication. We further reveal that phage mutants evading Eco2-mediated defense harbormutations in the endonuclease IV-like protein DenB, underscoring DenB’s critical role in triggering the activation of this system.Together, these findings provide key structural and functional insights into Retron-Eco2, laying the groundwork for harnessing itspotential in biotechnology and synthetic biology applications.Cell Discovery;