Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks.

Ohno [Ohno, S. (1970) in Evolution by Gene Duplication, Springer, New York] proposed that gene duplication with subsequent divergence of paralogs could be a major force in the evolution of new gene functions. In practice the functional differences between closely related homologues produced by duplications can be subtle and difficult to separate experimentally. Here we show that DNA microarrays can distinguish the functions of two closely related homologues from the yeast Saccharomyces cerevisiae, Yap1p and Yap2p. Although Yap1p and Yap2p are both bZIP transcription factors involved in multiple stress responses and are 88% identical in their DNA binding domains, our work shows that these proteins activate nonoverlapping sets of genes. Yap1p controls a set of genes involved in detoxifying the effects of reactive oxygen species, whereas Yap2p controls a set of genes over represented for the function of stabilizing proteins. In addition we show that the binding sites in the promoters of the Yap1p-dependent genes differ from the sites in the promoters of Yap2p-dependent genes and we validate experimentally that these differences are important for regulation by Yap1p. We conclude that while Yap1p and Yap2p may have some overlapping functions they are clearly not redundant and, more generally, that DNA microarray analysis will be an important tool for distinguishing the functions of the large numbers of highly conserved genes found in all eukaryotic genomes.

[1]  T. D. Schneider,et al.  Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. , 1982, Nucleic acids research.

[2]  J. Davies,et al.  Molecular Biology of the Cell , 1983, Bristol Medico-Chirurgical Journal.

[3]  T. D. Schneider,et al.  Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.

[4]  L. Fernandes,et al.  Overexpression of YAP2, coding for a new yAP protein, and YAP1 in Saccharomyces cerevisiae alleviates growth inhibition caused by 1,10-phenanthroline. , 1993, The Journal of biological chemistry.

[5]  M. Goebl,et al.  Yeast bZip proteins mediate pleiotropic drug and metal resistance. , 1993, The Journal of biological chemistry.

[6]  W S Moye-Rowley,et al.  GSH1, which encodes gamma-glutamylcysteine synthetase, is a target gene for yAP-1 transcriptional regulation. , 1994, Molecular and cellular biology.

[7]  S. Kuge,et al.  YAP1 dependent activation of TRX2 is essential for the response of Saccharomyces cerevisiae to oxidative stress by hydroperoxides. , 1994, The EMBO journal.

[8]  D. Thiele,et al.  Cadmium tolerance mediated by the yeast AP-1 protein requires the presence of an ATP-binding cassette transporter-encoding gene, YCF1. , 1994, The Journal of biological chemistry.

[9]  D W Stephen,et al.  The role of the YAP1 and YAP2 genes in the regulation of the adaptive oxidative stress responses of Saccharomyces cerevisiae , 1995, Molecular microbiology.

[10]  C. Grant,et al.  Yeast glutathione reductase is required for protection against oxidative stress and is a target gene for yAP‐1 transcriptional regulation , 1996, Molecular microbiology.

[11]  G. Mickisch Multidrug Resistance , 1996, Der Urologe A.

[12]  K. Struhl,et al.  Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions , 1997, Molecular and cellular biology.

[13]  L. Wodicka,et al.  Genome-wide expression monitoring in Saccharomyces cerevisiae , 1997, Nature Biotechnology.

[14]  J. Boeke,et al.  Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR‐mediated gene disruption and other applications , 1998, Yeast.

[15]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..

[16]  G. Church,et al.  Systematic determination of genetic network architecture , 1999, Nature Genetics.

[17]  A. Dudley,et al.  Specific components of the SAGA complex are required for Gcn4- and Gcr1-mediated activation of the his4-912delta promoter in Saccharomyces cerevisiae. , 1999, Genetics.

[18]  Laurie J. Heyer,et al.  Exploring expression data: identification and analysis of coexpressed genes. , 1999, Genome research.

[19]  Yudong D. He,et al.  Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.

[20]  Ken Chen,et al.  Gene-target recognition among members of the Myc superfamily and implications for oncogenesis , 2000, Nature Genetics.

[21]  D. Botstein,et al.  Genomic expression programs in the response of yeast cells to environmental changes. , 2000, Molecular biology of the cell.

[22]  G. Church,et al.  Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.

[23]  G. Church,et al.  A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression , 2000, Nature Genetics.

[24]  D. Hirata,et al.  Stress-induced transcriptional activation mediated by YAP1 and YAP2 genes that encode the Jun family of transcriptional activators in Saccharomyces cerevisiae , 1994, Molecular and General Genetics MGG.

[25]  D. Hirata,et al.  Saccharomyces cerevisiae YDR1, which encodes a member of the ATP-binding cassette (ABC) superfamily, is required for multidrug resistance , 1994, Current Genetics.

[26]  Karl-Dieter Entian,et al.  The PAR1 (YAP1/SNQ3) gene of Saccharomyces cerevisiae, ac-jun homologue, is involved in oxygen metabolism , 1992, Current Genetics.