Yeast HOS3 forms a novel trichostatin A-insensitive homodimer with intrinsic histone deacetylase activity

Histone deacetylases such as human HDAC1 and yeast RPD3 are trichostatin A (TSA)-sensitive enzymes that are members of large, multiprotein complexes. These contain specialized subunits that help target the catalytic protein t o histones at the appropriate DNA regulatory element where the enzyme repre sses transcription. To date, no deacetylase catalytic subunits have been sh own to have intrinsic activity, suggesting that noncatalytic subunits of th e deacetylase complex are required for their enzymatic function. In this pa per we describe a novel yeast histone deacetylase HOS3 that is relatively i nsensitive to the histone deacetylase inhibitor TSA, forms a homodimer when expressed ectopically both in yeast and Escherichia coil, and has intrinsi c activity when produced in the bacterium. Most HOS3 protein can be found a ssociated with a larger complex in partially purified yeast nuclear extract s, arguing that the HOS3 homodimer may be dissociated from a very large nuc lear structure during purification. We also demonstrate, using a combinatio n of mass spectrometry, tandem mass spectrometry, and proteolytic digestion , that recombinant HOS3 has a distinct specificity in vitro for histone H4 sites K5 and K8, H3 sites K14 and K23, H2A site K7, and H2B site K11. We pr opose that while factors that interact with HOS3 may sequester the catalyti c subunit at specific cellular sites, they are not required for HOS3 histon e deacetylase activity.