New insights into the pleiotropic drug resistance network from genome-wide characterization of the YRR1 transcription factor regulation system

Mol Cell Biol. 2002 Apr;22(8):2642-9. doi: 10.1128/MCB.22.8.2642-2649.2002.


Yrr1p is a recently described Zn(2)Cys(6) transcription factor involved in the pleiotropic drug resistance (PDR) phenomenon. It is controlled in a Pdr1p-dependent manner and is autoregulated. We describe here a new genome-wide approach to characterization of the set of genes directly regulated by Yrr1p. We found that the time-course production of an artificial chimera protein containing the DNA-binding domain of Yrr1p activated the 15 genes that are also up-regulated by a gain-of-function mutant of Yrr1p. Gel mobility shift assays showed that the promoters of the genes AZR1, FLR1, SNG1, YLL056C, YLR346C, and YPL088W interacted with Yrr1p. The putative consensus Yrr1p binding site deduced from these experiments, (T/A)CCG(C/T)(G/T)(G/T)(A/T)(A/T), is strikingly similar to the PDR element binding site sequence recognized by Pdr1p and Pdr3p. The minor differences between these sequences are consistent with Yrr1p and Pdr1p and Pdr3p having different sets of target genes. According to these data, some target genes are directly regulated by Pdr1p and Pdr3p or by Yrr1p, whereas some genes are indirectly regulated by the activation of Yrr1p. Some genes, such as YOR1, SNQ2, and FLR1, are clearly directly controlled by both classes of transcription factor, suggesting an important role for the corresponding membrane proteins.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Binding Sites / genetics
  • Consensus Sequence
  • DNA, Fungal / genetics
  • DNA, Fungal / metabolism
  • Drug Resistance, Multiple, Fungal / genetics*
  • Gene Expression Profiling
  • Gene Expression Regulation, Fungal
  • Genome, Fungal*
  • Models, Biological
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis
  • Promoter Regions, Genetic
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Sequence Homology, Amino Acid
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism


  • DNA, Fungal
  • Recombinant Fusion Proteins
  • Transcription Factors