title: Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains.
abstract: Sequence-specific DNA-binding proteins are among the most important classes of gene regulatory proteins, controlling changes in transcription that underlie many aspects of biology. In this work, we identify a transcriptional regulator from the human fungal pathogen Candida albicans that binds DNA specifically but has no detectable homology with any previously described DNA- or RNA-binding protein. This protein, named White-Opaque Regulator 3 (Wor3), regulates white-opaque switching, the ability of C. albicans to switch between two heritable cell types. We demonstrate that ectopic overexpression of WOR3 results in mass conversion of white cells to opaque cells and that deletion of WOR3 affects the stability of opaque cells at physiological temperatures. Genome-wide chromatin immunoprecipitation of Wor3 and gene expression profiling of a wor3 deletion mutant strain indicate that Wor3 is highly integrated into the previously described circuit regulating white-opaque switching and that it controls a subset of the opaque transcriptional program. We show by biochemical, genetic, and microfluidic experiments that Wor3 binds directly to DNA in a sequence-specific manner, and we identify the set of cis-regulatory sequences recognized by Wor3. Bioinformatic analyses indicate that the Wor3 family arose more recently in evolutionary time than most previously described DNA-binding domains; it is restricted to a small number of fungi that include the major fungal pathogens of humans. These observations show that new families of sequence-specific DNA-binding proteins may be restricted to small clades and suggest that current annotations--which rely on deep conservation--underestimate the fraction of genes coding for transcriptional regulators.
authors.affiliation: Departments of Microbiology and Immunology and Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Lohse
authors.forename: Aaron D
authors.initials: AD
authors.lastname: Hernday
authors.forename: Polly M
authors.initials: PM
authors.lastname: Fordyce
authors.forename: Liron
authors.initials: L
authors.lastname: Noiman
authors.forename: Trevor R
authors.initials: TR
authors.lastname: Sorrells
authors.forename: Victor
authors.initials: V
authors.lastname: Hanson-Smith
authors.forename: Clarissa J
authors.initials: CJ
authors.lastname: Nobile
authors.forename: Joseph L
authors.initials: JL
authors.lastname: DeRisi
authors.forename: Alexander D
authors.initials: AD
authors.lastname: Johnson
mesh_terms: D002176:Candida albicans / Q000166:cytology / Q000235:genetics / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism*; D017353:Gene Deletion; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D049452:Green Fluorescent Proteins / Q000378:metabolism; D005810:Multigene Family; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D049452:Green Fluorescent Proteins; D004247:DNA
keywords: epigenetic switch; transcription factor; transcription networks; transcriptional regulation