Five histone deacetylase genes (HDA1, RPD3, HOS1, HOS2, and HOS3) have been cloned from Candida albicans and characterized. Sequence analysis and comparison with 17 additional deacetylases resulted in a phylogenetic tree composed of three major groups. Transcription of the deacetylases HDA1 and RPD3 is downregulated in the opaque phase of the white-opaque transition in strain WO-1. HOS3 is selectively transcribed as a 2.5-kb transcript in the white phase and as a less-abundant 2.3-kb transcript in the opaque phase. HDA1 and RPD3 were independently deleted in strain WO-1, and both switching between the white and opaque phases and the downstream regulation of phase-specific genes were analyzed. Deletion of HDA1 resulted in an increase in the frequency of switching from the white phase to the opaque phase, but had no effect on the frequency of switching from the opaque phase to the white phase. Deletion of RPD3 resulted in an increase in the frequency of switching in both directions. Deletion of HDA1 resulted in reduced white-phase-specific expression of the EFG1 3.2-kb transcript, but had no significant effect on white-phase-specific expression of WH11 or opaque-phase-specific expression of OP4, SAP1, and SAP3. Deletion of RPD3 resulted in reduced opaquephase-specific expression of OP4, SAP1, and SAP3 and a slight reduction of white-phase-specific expression of WH11 and 3.2-kb EFG1. Deletion of neither HDA1 nor RPD3 affected the high level of white-phase expression and the low level of opaque-phase expression of the MADS box protein gene MCM1, which has been implicated in the regulation of opaque-phase-specific gene expression. In addition, there was no effect on the phase-regulated levels of expression of the other deacetylase genes. These results demonstrate that the two deacetylase genes HDA1 and RPD3 play distinct roles in the suppression of switching, that the two play distinct and selective roles in the regulation of phase-specific genes, and that the deacetylases are in turn regulated by switching.Most strains of Candida albicans and related species switch, or can be induced to switch, between two or more general phenotypes distinguishable by colony morphology (14,41,42,44,48). Switching regulates a number of phenotypic characteristics, including putative virulence traits, and for that reason, it has been considered a higher-order virulence factor (42). Switching has been demonstrated to occur at sites of commensalism (21) and infection (48-50) and to occur at higher frequencies in strains causing infections than in commensal strains (21, 24, 61). Therefore, it has been proposed that switching provides colonizing populations with phenotypic variants for rapid adaptation in response to environmental challenges, such as drug therapy and the immune response, as well as changes in host physiology, the competing microflora, and anatomical locale (34,45).By using the simple white-opaque transition in C. albicans strain WO-1 (42) as a model system, it has been demonstrated that switching involves the transcription...