Abstract
The RecQ DNA helicases human BLM and yeast Sgs1 interact with DNA
topoisomerase III and are thought to act on stalled replication forks to
maintain genome stability. To gain insight into this mechanism, we previously
identified
SLX1
and
SLX4
as genes that are required for
viability and for completion of rDNA replication in the absence of
SGS1–TOP3
. Here we show that
SLX1
and
SLX4
encode a heteromeric structure-specific endonuclease. The Slx1–Slx4
nuclease is active on branched DNA substrates, particularly simple-Y,
5′-flap, or replication forkstructures. It cleaves the strand bearing
the 5′ nonhomologous arm at the branch junction and generates ligatable
nicked products from 5′-flap or replication fork substrates. Slx1 is the
founding member of a family of proteins with a predicted URI nuclease domain
and PHD-type zinc finger. This subunit displays weakstructure-specific
endonuclease activity on its own, is stimulated 500-fold by Slx4, and requires
the PHD finger for activity in vitro and in vivo. Both subunits are required
in vivo for resistance to DNA damage by methylmethane sulfonate (MMS). We
propose that Sgs1–Top3 acts at the termination of rDNA replication to
decatenate stalled forks, and, in its absence, Slx1–Slx4 cleaves these
stalled forks.