title: A Random Screen Using a Novel Reporter Assay System Reveals a Set of Sequences That Are Preferred as the TATA or TATA-Like Elements in the CYC1 Promoter of Saccharomyces cerevisiae.
abstract: In Saccharomyces cerevisiae, the core promoters of class II genes contain either TATA or TATA-like elements to direct accurate transcriptional initiation. Genome-wide analyses show that the consensus sequence of the TATA element is TATAWAWR (8 bp), whereas TATA-like elements carry one or two mismatches to this consensus. The fact that several functionally distinct TATA sequences have been identified indicates that these elements may function, at least to some extent, in a gene-specific manner. The purpose of the present study was to identify functional TATA sequences enriched in one particular core promoter and compare them with the TATA or TATA-like elements that serve as the pre-initiation complex (PIC) assembly sites on the yeast genome. For this purpose, we conducted a randomized screen of the TATA element in the CYC1 promoter by using a novel reporter assay system and identified several hundreds of unique sequences that were tentatively classified into nine groups. The results indicated that the 7 bp TATA element (i.e., TATAWAD) and several sets of TATA-like sequences are preferred specifically by this promoter. Furthermore, we find that the most frequently isolated TATA-like sequence, i.e., TATTTAAA, is actually utilized as a functional core promoter element for the endogenous genes, e.g., ADE5,7 and ADE6. Collectively, these results indicate that the sequence requirements for the functional TATA or TATA-like elements in one particular core promoter are not as stringent. However, the variation of these sequences differs significantly from that of the PIC assembly sites on the genome, presumably depending on promoter structures and reflecting the gene-specific function of these sequences.
authors.affiliation: Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan.
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Watanabe
authors.affiliation: Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan.
authors.forename: Makoto
authors.initials: M
authors.lastname: Yabe
authors.affiliation: Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Kasahara
authors.affiliation: Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan.
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Kokubo
mesh_terms: D001483:Base Sequence; D045304:Cytochromes c / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics; D015966:Gene Expression Regulation, Fungal; D017930:Genes, Reporter / Q000235:genetics; D016681:Genome, Fungal / Q000235:genetics; D018832:Molecular Chaperones / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D016385:TATA Box / Q000235:genetics*; D024363:Transcription Initiation Site; D061785:Transcription Initiation, Genetic; D033921:Vesicular Transport Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: C014059:CYC1 protein, S cerevisiae; D004271:DNA, Fungal; D018832:Molecular Chaperones; D029701:Saccharomyces cerevisiae Proteins; C499587:VTC1 protein, S cerevisiae; D033921:Vesicular Transport Proteins; D045304:Cytochromes c