Rad53 directly phosphorylates Swi6 in an MMS-inducible manner. Recombinant Swi6 purified from E. coli was incubated in the presence of [γ-32P]ATP and Rad53 immunoprecipitated from MMS-treated rad53-11 (BY2007) cells (A), untreated (B) or MMS-treated (C) wild-type (BY2006) cells, or with the baculovirus-expressed Rad53 purified from insect cells (D). Kinase-treated Swi6 was resolved on an SDS-polyacrylamide gel, excised, digested with trypsin, and resolved in two dimensions to generate phosphopeptide maps. Major Rad53-dependent phosphopeptides are numbered.