Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains
Lohse MB, Hernday AD, Fordyce PM, Noiman L, Sorrells TR, Hanson-Smith V, Nobile CJ, DeRisi JL, Johnson ADPNAS, 2013Abstract:
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.