Different types of maize histone deacetylases are distinguished by a highly complex substrate and site specificity

Enzymes involved in histone acetylation have been identified as important transcriptional regulators. Maize embryos contain three histone deacetylase families: RPD3-type deacetylases (HD1-B), nucleolar phosphoproteins of the HD2 family, and a third form unrelated to RPD3 and HD2 (HD1-A). Here we first report on the specificity of deacetylases for core histones, acetylated histone H4 subspecies, and acetylated H4-lysine residues. HD1-A, HD1-B, and HD2 deacetylate all four core histones, although with different specificity. However, experiments with histones from different sources (hyperacetylated MELC and chicken histones) using antibodies specific for individually acetylated H4-lysine sites indicate that the enzymes recognize highly distinct acetylation patterns. Only RPD3-type deacetylase HD1-B is able to deacetylate the specific H4 di-acetylation pattern (position 12 and 5) introduced by the purified cytoplasmic histone acetyltransferase B after incubation with pure nonacetylated H4 subspecies. HD1-A and HD2 exist as phosphorylated forms. Dephosphorylation has dramatic, but opposite effects; whereas HD2 loses enzymatic activity upon dephosphorylation, HD1-A is activated with a change of specificity against acetylated H4 subspecies. The data suggest that different types of deacetylases interact with different and highly specific acetylation patterns on nucleosomes.