Functional overlap between Sgs1-Top3 and the Mms4-Mus81 endonuclease

The RecQ DNA helicases, human BLM and yeast Sgs1, form a complex with topoi somerase III (Top3). and are thought to act during DNA replication to resta rt forks that have paused due to DNA damage or topological stress. We have shown previously that yeast cells lacking SGS1 or TOP3 require MMS4 and MUS 81 for viability. Here we show that Mms4 and Mus81 form a heterodimeric str ucture-specific endonuclease that cleaves branched DNA. Both subunits are r equired for optimal expression, substrate binding, and nuclease activity. M ms4 and Mus81 are conserved proteins related to the Rad1-Rad10 (XPF/ERCC1) endonuclease required for nucleotide excision repair (NER). However, the Mm s4-Mus81 endonuclease is 25 times more active on branched duplex DNA and re plication fork substrates than simple Y-forms, the preferred substrate for the NER complexes. We also present genetic data that indicate a novel role for Mms4-Mus81 in meiotic recombination. Our results suggest that stalled r eplication forks are substrates for Mms4-Mus81 cleavage-particularly in the absence of Sgs1 or BLM. Repair of this double-strand break (DSB) by homolo gous recombination may be responsible for the elevated levels of sister chr omatid exchange (SCE) found in BLM-/- cells.