Essential angiosperm-specific subunits of HDA19 histone deacetylase complexes in Arabidopsis

While both the histone deacetylase HDA19 and its close homolog HDA6 can form SIN3-type histone deacetylase complexes, they display specialized biological roles, with the mechanisms of their functional specificities largely unclear. In this study, we identified three previously uncharacterized homologs designated as HDA19-interacting proteins 1, 2, and 3 (HDIP1/2/3). These homologs not only interact with HDA19 but also with other components of the SIN3-type histone deacetylase complexes, including SNLs, MSI1, and HDC1, thereby facilitating the assembly of HDA19-containing complexes but not HDA6-containing ones. HDIP1/2/3 orthologs are found in angiosperms but are absent in other plant species. The hdip1/2/3 and hda19 mutants exhibit highly similar phenotypes in terms of development, abscisic acid response, and drought tolerance. Omics data indicate that HDIP1/2/3 and HDA19 co-occupy chromatin and co-repress gene transcription, particularly at those genes associated with stress responses. An a-helix motif in HDIP1 is capable of binding to the nucleosome as well as the four-way junction DNA that mimics the DNA entry and exit sites of the nucleosome, and is essential for the function of HDIP1 in Arabidopsis plants. These findings suggest that the HDA19-containing SIN3-type histone deacetylase complexes have incorporated additional subunits in angiosperms to support the intricate regulation of histone deacetylation and gene transcription during plant development and stress responses. Examination of the mRNA expression of 20-day-old wild type and two mutants in Arabidopsis