title: Evolution of alternative transcriptional circuits with identical logic.
abstract: Evolution of gene regulation is an important contributor to the variety of life. Here, we analyse the evolution of a combinatorial transcriptional circuit composed of sequence-specific DNA-binding proteins that are conserved among all eukaryotes. This circuit regulates mating in the ascomycete yeast lineage. We first identify a group of mating genes that was transcriptionally regulated by an activator in a fungal ancestor, but is now transcriptionally regulated by a repressor in modern bakers' yeast. Despite this change in regulatory mechanism, the logical output of the overall circuit remains the same. By examining the regulation of mating in modern yeasts that are related to different extents, we deduce specific, sequential changes in both cis- and trans-regulatory elements that constitute the transition from positive to negative regulation. These changes indicate specific mechanisms by which fitness barriers were traversed during the transition.
authors.affiliation: Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, California 94143-2200, USA.
authors.forename: Annie E
authors.initials: AE
authors.lastname: Tsong
authors.forename: Brian B
authors.initials: BB
authors.lastname: Tuch
authors.forename: Hao
authors.initials: H
authors.lastname: Li
authors.forename: Alexander D
authors.initials: AD
authors.lastname: Johnson
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D005075:Biological Evolution; D002176:Candida albicans / Q000235:genetics; D017124:Conserved Sequence; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D049770:Genes, Mating Type, Fungal / Q000235:genetics; D007716:Kluyveromyces / Q000235:genetics; D026341:Minichromosome Maintenance 1 Protein / Q000378:metabolism; D008969:Molecular Sequence Data; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D026341:Minichromosome Maintenance 1 Protein; D014157:Transcription Factors