We assembled the genome of the human fungal pathogen Candida albicans into eight chromosomes, and annotated each of its genes. A genome comparison with Saccharomyces cerevisiae revealed an increased number of C. albicans superoxide dismutase genes. We analyzed the expression patterns and the function of one of these genes, SOD5, whose role is to protect the pathogen against extracellularly produced, neutrophil-generated superoxide radicals. Comparative genomics also showed that although many of the C. albicans transcription factors, such as Gal4p and Gcn4p, have homologues in S. cerevisiae, the sequence similarities occur only in the DNA binding motifs of those proteins. Deletion analysis of CaGcn4 and CaGal4 proteins show that the N' and C' termini respectively are needed for their transactivation ability. These two transactivation regions show no sequence similarity to the equivalent domains in their S. cerevisiae homologues, and the two C. albicans transactivatiog domains themselves show little similarity. A comparative analysis of the transcriptional machinery between C. albicans and S. cerevisiae showed low sequence similarity of the mediator complex that bridges activation domains of transcription factors to the RNA polymerase II complex. We performed a comparison of intergenic DNA regions to identify the cis-regulatory elements from Candida and Saccharomyces species to examine the organization of the transcriptional regulatory networks between these two organisms. We observed that the C. albicans GAL genes lack Gal4p binding sites, but that such sites are found upstream of telomeric genes and genes involved in glycolysis, and we show that CaGal4p regulates the expression of those genes. We identified the regulatory DNA sequences in the promoters of GAL genes, including a GAL-specific palindrome necessary for GAL10˛ expression. Cph1p, the C. albicans homolog of the Ste12p transcription factor controlling pheromone-induced gene expression in yeast, acts through this GAL-specific palindrome, functioning as an activator in the presence of galactose. This shows C. albicans and S. cerevisiae can regulate the same process by different regulatory circuits.

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