Sister chromatid cohesion is resolved at anaphase onset when separase, a site-specific protease, cleaves the Scc1 subunit of the chromosomal cohesin complex that is responsible for holding sister chromatids together. This mechanism to initiate anaphase is conserved in eukaryotes from budding yeast to man. Budding yeast separase recognizes and cleaves two conserved peptide motifs within Scc1. In addition, separase cleaves a similar motif in the kinetochore and spindle protein Slk19. Separase may cleave further substrate proteins to orchestrate multiple cellular events that take place during anaphase. To investigate substrate recognition by budding yeast separase we analyzed the sequence requirements at one of the Scc1 cleavage site motifs by systematic mutagenesis. We derived a cleavage site consensus motif (not(FKRWY))(ACFHILMPVWY)(DE)X(AGSV)R/X. This motif is found in 1,139 of 5,889 predicted yeast proteins. We analyzed 28 candidate proteins containing this motif as well as 35 proteins that contain a core (DE)XXR motif. We could so far not confirm new separase substrates, but we have uncovered other forms of mitotic regulation of some of the proteins. We studied whether determinants other than the cleavage site motif mediate separase-substrate interaction. When the separase active site was occupied with a peptide inhibitor covering the cleavage site motif, separase still efficiently interacted with its substrate Scc1. This suggests that separase recognizes both a cleavage site consensus sequence as well as features outside the cleavage site.The segregation of sister chromatids to daughter cells during mitosis requires a complex series of cellular events to be performed faithfully, which has been studied in some detail in the budding yeast Saccharomyces cerevisiae (1). One of the key events is activation of a site-specific protease, separase, which triggers the resolution of sister chromatid cohesion at anaphase onset. Sister chromatids are kept aligned in metaphase by a protein complex, cohesin, which counteracts the pulling force of the mitotic spindle. Cohesion is lost abruptly at anaphase onset when separase cleaves the Scc1 subunit of the cohesin complex. During meiosis Scc1 in cohesin is replaced by a related subunit, Rec8, which is cleaved by separase during the two subsequent rounds of meiotic chromosome segregation. Premature loss of cohesion leads to chromosome missegregation, thus cohesin cleavage by separase is kept under tight cellular control (2).Separase is required for processes in addition to sister chromatid separation. These include anaphase spindle stabilization and the coupling of anaphase to mitotic exit during budding yeast mitosis (3-8) as well as the coordination of the chromosome segregation and spindle cycles during meiosis (9). In fission yeast, separase binds to the mitotic spindle and has been implicated in spindle pole body morphology and positioning (10 -12). In nematode worms separase is required for correct centrosome positioning during the first asymmetric mitotic division (13)...