Alphaproteobacterial gene transfer agent (GTA) represents the most sophisticated system for horizontal gene transfer in prokaryotes discovered to date. Here, we present the near-atomic structure of Rhodobacter capsulatus GTA, first GTA discovered in nature, determined by cryo-EM. Furthermore, we describe the mechanism how GTA particles transfer DNA into the recipient cells. Our results show an evolutionary linkage between families of tailed phages and bring possibilities of controlling the gene transfer in ocean environments, where alphaproteobacteria prevail.

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