A General Strategy to Uncover Transcription Factor Properties Identifies a New Regulator of Drug Resistance in Yeast

Abstract

We demonstrate a genomewide approach to determine the physiological role of a putative transcription factor, Ylr266, identified through yeast genome sequencing program. We constructed activated forms of the zinc finger (Zn 2 Cys 6 ) protein Ylr266, and we analyzed the corresponding transcriptomes with DNA microarrays to characterize the up-regulated genes. The direct target genes of Ylr266 were further identified by in vivo chromatin immunoprecipitation procedure. The functions of the genes directly controlled by YLR266c are in agreement with the observed drug-resistance phenotype of the cell expressing an activated form of Ylr266. These target genes code for ATP-binding cassette or major facilitator superfamily transporters such as PDR15, YOR1, or AZR1 or for other proteins such as SNG1, YJL216c, or YLL056c which are already known to be involved in the yeast pleiotropic drug resistance (PDR) phenomenon. YLR266c could thus be named PDR8. Overlaps with the other PDR networks argue in favor of a new specific role for PDR8 in connection with the well known PDR regulators PDR1/PDR3 and YRR1. This strategy to identify the regulatory properties of an anonymous transcription factor is likely to be generalized to all the Zn 2 Cys 6 transcription factors from Saccharomyces cerevisiae and related yeasts.With the advent of postgenomic approaches that provide a nearly complete analysis of the cell transcriptome, it has been disconcerting to discover the complexity of the cell genetic response to apparently simple physiological changes (1). This apparent complexity is likely to reflect the action of underlying regulatory networks that control gene-expression patterns characteristic of many different genetic changes (2). These transcriptional regulatory networks are under the combinatorial action of transcription factors, and dissection of the specific role of each transcription factor offers a good opportunity to decipher the complexity of genome expression (3).One of the main challenge further the understanding of genome functions is to describe the set of genes that are directly regulated by the different specific transcription factors. DNA microarrays are very efficient tools to address such questions, but they have to be coupled with properly designed experiments if one wishes to distinguish direct and indirect effects of the activity of a transcription factor. Such data are already available for several transcription factors (4) that were previously characterized by classical biological approaches. However, it should be kept in mind that even in Saccharomyces cerevisisae, many direct target genes of identified or putative transcription factors are unknown. Any experimental approach to complete these data relies on the possibility to activate the relevant transcription factor. We have recently designed an approach for the artificial activation of yeast Zn 2 Cys 6 transcription factors. The Zn 2 Cys 6 family of transcription factors, exemplified by Gal4, represents more than 25% of the yeast transcription regulators. Our ...

Heterologous carotenoid production in Saccharomyces cerevisiae induces the pleiotropic drug resistance stress response

“…In S. cerevisiae, pleiotropic drug resistance is not solely mediated by Pdr3 but may involve other regulators, viz. Pdr1, Pdr8, Yrr1 and its paralogue Yrm1 (DeRisi et al, 2000;Le Crom et al, 2002;Hikkel et al, 2003;Onda et al, 2004;Lucau-Danila et al, 2005). This response Transcriptional profiling of carotenoid-producing S. cerevisiae 991 C E N .…”

“…We reasoned that carotenoids, which are hydrophobic compounds (Gruszecki and Strzalka, 2005), cannot readily dissolve in the media used for the growth of yeast strains but are more likely to remain attached to cellular membranes. To determine whether carotenoids could be secreted from Orange02 cells during growth in batch cultures, 20% v/v sunflower oil, which is a proper solvent * * * 0 (DeRisi et al, 2000;Le Crom et al, 2002;Devaux et al, 2002;Hikkel et al, 2003;Tuttle et al, 2003;Lucau-Danila et al, 2003;Onda et al, 2004 Nawrocki et al, 2001;Hikkel et al, 2003;Tuttle et al, 2003;Onda et al, 2004) PDR15 2 (Wolfger et al, 1997;DeRisi et al, 2000;Hikkel et al, 2003;Tuttle et al, 2003) YLR346C 3 (DeRisi et al, 2000;do Valle Matta et al, 2001;Le Crom et al, 2002;Devaux et al, 2002;Hikkel et al, 2003;Tuttle et al, 2003;Onda et al, 2004) PDR5 6 (DeRisi et al, 2000Miura et al, 2001;Devaux et al, 2002;Teixeira and Sa-Correia, 2002;Tuttle et al, 2003;Lucau-Danila et al, 2003;Onda et al, 2004;Wehrschutz-Sigl et al, 2004 DeRisi et al, 2000;Le Crom et al, 2002;Devaux et al, 2002;Hikkel et al, 2003;Tuttle et al, 2003;Lucau-Danila et al, 2003;Onda et al, 2...…”

Yeast ABC transporters – A tale of sex, stress, drugs and aging

“…Genomic approaches uncovered another zinc finger regulator, Pdr8p, as involved in the PDR network [70]. Pdr8p mediates resistance to ketoconazole and oligomycin, operating mainly through Yrr1p and its respective target genes.…”

Effect of 21 Different Nitrogen Sources on Global Gene Expression in the YeastSaccharomyces cerevisiae

“…A similar though less pronounced effect was detected on tyrosine medium. All of these genes code for proteins involved in resistance to multiple drugs, and seven of them are known to be targets of Pdr1, Pdr3, Pdr8, Yrr1, and/or Yrm1, i.e., transcription factors involved in pleiotropic-drug resistance (PDR) (34,55,78,96). We used qRT-PCR to measure the expression of the SNQ2 gene on urea with or without added tryptophan or tyrosine.…”