DNA end recognition by the Mre11 nuclease dimer: Insights into resection and repair of damaged DNA

The Mre11-Rad50-Nbs1 (MRN) complex plays important roles in sensing DNA damage, as well as in resecting and tethering DNA ends, and thus participates in double-strand break repair. An earlier structure of Mre11 bound to a short duplex DNA molecule suggested that each Mre11 in a dimer recognizes one DNA duplex to bridge two DNA ends at a short distance. Here, we provide an alternative DNA recognition model based on the structures of Methanococcus jannaschii Mre11 (MjMre11) bound to longer DNA molecules, which may more accurately reflect a broken chromosome. An extended stretch of B-form DNA asymmetrically runs across the whole dimer, with each end of this DNA molecule being recognized by an individual Mre11 monomer. DNA binding induces rigid-body rotation of the Mre11 dimer, which could facilitate melting of the DNA end and its juxtaposition to an active site of Mre11. The identified Mre11 interface binding DNA duplex ends is structurally conserved and shown to functionally contribute to efficient resection, non-homologous end joining, and tolerance to DNA-damaging agents when other resection enzymes are absent. Together, the structural, biochemical, and genetic findings presented here offer new insights into how Mre11 recognizes damaged DNA and facilitates DNA repair. Synopsis DNA end tethering and nucleolytic resection at double-strand break sites are key functions of the conserved MRN (Mre11-Rad50-Nbs1) complex mediated by its Mre11 subunit. New crystal structures of Mre11-DNA complexes reveal an alternative model for Mre11-DNA complexes, in which Mre11 dimers recognize a single stretch of longer, more physiological DNA substrate. Structures of Mre11 bound to longer DNA molecules show that the Mre11 dimer as a whole recognizes one single molecule of extended B-form DNA. A structurally conserved basic region constituting the DNA binding interface is important for binding and cleavage of substrates, as well as for in vivo repair functions. Mre11 quaternary structural changes may facilitate DNA end melting and guide broken ends to the nuclease active site. DNA end tethering may require further oligomerization of Mre11 dimers. Crystal structures reveal the importance of a novel, conserved interface through which the dimeric MRN complex subunit Mre11 binds a single molecule of longer DNA representing its physiological substrate.