title: A genome-wide screen for site-specific DNA-binding proteins.
abstract: We used a biochemical genomics method of assaying Saccharomyces cerevisiae proteins, derived from a nearly complete set of glutathione S-transferase fusions, to develop an approach that is able to identify proteins that bind to a DNA element. Using the upstream activation sequence (UAS) of the promoter for the invertase gene, SUC2, we identified both specific and nonspecific binding activities, which could be classified based on whether they bound with equivalent affinity to a nonspecific DNA competitor. Three transcription factors, Mig1, Yer028c, and Rgt1, were found to be binding activities specific to the SUC2 UAS. Mig1 and Yer028c had been reported previously to bind to elements within the SUC2 UAS, validating the ability of the method to identify sequence-specific factors. The third activity, Rgt1, had not been reported previously to bind to SUC2. Additional gel shift assays narrowed the Rgt1 binding site to the SUC2-B element within the SUC2 UAS, which is similar to previously identified Rgt1 binding sites present in other genes. In vivo levels of invertase activity in an rgt1Delta strain were reduced relative to an isogenic RGT+ strain when these strains were grown under inducing (low glucose) conditions, suggesting that Rgt1 may have a role in the activated transcription of SUC2. This report demonstrates the feasibility of identifying DNA binding activities by rapidly assaying a large fraction of the predicted open reading frames of an organism for binding to a regulatory DNA motif.
authors.affiliation: Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA. thazbun@u.washington.edu
authors.forename: Tony R
authors.initials: TR
authors.lastname: Hazbun
authors.forename: Stanley
authors.initials: S
authors.lastname: Fields
mesh_terms: D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D016681:Genome, Fungal; D006026:Glycoside Hydrolases / Q000235:genetics* / Q000378:metabolism; D016366:Open Reading Frames; D011485:Protein Binding; D011993:Recombinant Fusion Proteins / Q000235:genetics / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D012097:Repressor Proteins / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D015534:Trans-Activators / Q000378:metabolism; D014157:Transcription Factors; D043324:beta-Fructofuranosidase
chemical_list: D004268:DNA-Binding Proteins; C102114:RGT1 protein, S cerevisiae; D011993:Recombinant Fusion Proteins; D012097:Repressor Proteins; D029701:Saccharomyces cerevisiae Proteins; D015534:Trans-Activators; D014157:Transcription Factors; D006026:Glycoside Hydrolases; D043324:beta-Fructofuranosidase