Integrating phenotypic and expression profiles to map arsenic-response networks

BackgroundArsenic is a nonmutagenic carcinogen affecting millions of people. The cellular impact of this metalloid in Saccharomyces cerevisiae was determined by profiling global gene expression and sensitivity phenotypes. These data were then mapped to a metabolic network composed of all known biochemical reactions in yeast, as well as the yeast network of 20,985 protein-protein/protein-DNA interactions.ResultsWhile the expression data unveiled no significant nodes in the metabolic network, the regulatory network revealed several important nodes as centers of arsenic-induced activity. The highest-scoring proteins included Fhl1, Msn2, Msn4, Yap1, Cad1 (Yap2), Pre1, Hsf1 and Met31. Contrary to the gene-expression analyses, the phenotypic-profiling data mapped to the metabolic network. The two significant metabolic networks unveiled were shikimate, and serine, threonine and glutamate biosynthesis. We also carried out transcriptional profiling of specific deletion strains, confirming that the transcription factors Yap1, Arr1 (Yap8), and Rpn4 strongly mediate the cell's adaptation to arsenic-induced stress but that Cad1 has negligible impact.ConclusionsBy integrating phenotypic and transcriptional profiling and mapping the data onto the metabolic and regulatory networks, we have shown that arsenic is likely to channel sulfur into glutathione for detoxification, leads to indirect oxidative stress by depleting glutathione pools, and alters protein turnover via arsenation of sulfhydryl groups on proteins. Furthermore, we show that phenotypically sensitive pathways are upstream of differentially expressed ones, indicating that transcriptional and phenotypic profiling implicate distinct, but related, pathways.

[1]  R. Bentley,et al.  The shikimate pathway--a metabolic tree with many branches. , 1990, Critical reviews in biochemistry and molecular biology.

[2]  K. Entian,et al.  Identification and characterization of a Saccharomyces cerevisiae gene (PAR1) conferring resistance to iron chelators. , 1991, European journal of biochemistry.

[3]  A. Smith,et al.  Cancer risks from arsenic in drinking water. , 1992, Environmental health perspectives.

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

[5]  P. Thuriaux,et al.  Suppression of yeast RNA polymerase III mutations by FHL1, a gene coding for a fork head protein involved in rRNA processing , 1994, Molecular and cellular biology.

[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]  L. Penland,et al.  Use of a cDNA microarray to analyse gene expression patterns in human cancer , 1996, Nature Genetics.

[9]  K. Jan,et al.  Arsenite induces apoptosis in chinese hamster ovary cells by generation of reactive oxygen species , 1996, Journal of cellular physiology.

[10]  F. MacIver,et al.  Stationary‐phase induction of GLR1 expression is mediated by the yAP‐1 transcriptional regulatory protein in the yeast Saccharomyces cerevisiae , 1996, Molecular microbiology.

[11]  J. Brown,et al.  Arsenite, but not cadmium, induces ornithine decarboxylase and heme oxygenase activity in rat liver: relevance to arsenic carcinogenesis. , 1996, Cancer letters.

[12]  Wilfred W. Li,et al.  The tumor promoter arsenite stimulates AP‐1 activity by inhibiting a JNK phosphatase. , 1996, The EMBO journal.

[13]  R. Wysocki,et al.  The Saccharomyces cerevisiae ACR3 Gene Encodes a Putative Membrane Protein Involved in Arsenite Transport* , 1997, The Journal of Biological Chemistry.

[14]  A. Goffeau,et al.  Isolation of Three Contiguous Genes, ACR1, ACR2 and ACR3, Involved in Resistance to Arsenic Compounds in the Yeast Saccharomyces cerevisiae , 1997, Yeast.

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

[16]  S. T. Coleman,et al.  Saccharomyces cerevisiae Basic Region-Leucine Zipper Protein Regulatory Networks Converge at the ATR1 Structural Gene* , 1997, The Journal of Biological Chemistry.

[17]  N Jones,et al.  Regulation of yAP‐1 nuclear localization in response to oxidative stress , 1997, The EMBO journal.

[18]  M. Raymond,et al.  AP1-mediated Multidrug Resistance in Saccharomyces cerevisiae Requires FLR1 Encoding a Transporter of the Major Facilitator Superfamily* , 1997, The Journal of Biological Chemistry.

[19]  Michigan.,et al.  Toxicological profile for dichloropropenes , 2008 .

[20]  Wei Tang,et al.  Use of arsenic trioxide (As2O3) in the treatment of acute promyelocytic leukemia (APL): II. Clinical efficacy and pharmacokinetics in relapsed patients. , 1997, Blood.

[21]  P. Bobrowicz,et al.  Arsenical - induced transcriptional activation of the yeast Saccharomyces cerevisiae ACR2 and ACR3 genes requires the presence of the ACR1 gene product , 1998 .

[22]  M Vingron,et al.  Transcriptional profiling on all open reading frames of Saccharomyces cerevisiae , 1998, Yeast.

[23]  Wolfgang Baumeister,et al.  The Proteasome: Paradigm of a Self-Compartmentalizing Protease , 1998, Cell.

[24]  E. Epping,et al.  Yap1p Activates Gene Transcription in an Oxidant-Specific Fashion , 1999, Molecular and Cellular Biology.

[25]  K. Herrmann,et al.  THE SHIKIMATE PATHWAY. , 1999, Annual review of plant physiology and plant molecular biology.

[26]  C. Fonatsch,et al.  Successful treatment with arsenic trioxide of a patient with ATRA-resistant relapse of acute promyelocytic leukemia , 1999, Annals of Hematology.

[27]  S. Johnston,et al.  Subcellular Localization, Stoichiometry, and Protein Levels of 26 S Proteasome Subunits in Yeast* , 1999, The Journal of Biological Chemistry.

[28]  B. Rosen.  Families of arsenic transporters. , 1999, Trends in microbiology.

[29]  P. Zhang.  The use of arsenic trioxide (As2O3) in the treatment of acute promyelocytic leukemia. , 1999, Journal of biological regulators and homeostatic agents.

[30]  B. Rosen,et al.  Pathways of As(III) detoxification in Saccharomyces cerevisiae. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[31]  S. Toyokuni,et al.  The role of oxidative DNA damage in human arsenic carcinogenesis: detection of 8-hydroxy-2'-deoxyguanosine in arsenic-related Bowen's disease. , 1999, The Journal of investigative dermatology.

[32]  H. Feldmann,et al.  Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast , 1999, FEBS letters.

[33]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[35]  M. Hochstrasser,et al.  The Saccharomyces cerevisiae ubiquitin-proteasome system. , 1999, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[36]  J. Garin,et al.  Yap1 and Skn7 Control Two Specialized Oxidative Stress Response Regulons in Yeast* , 1999, The Journal of Biological Chemistry.

[37]  M. Jacquet,et al.  The heat shock response in yeast: differential regulations and contributions of the Msn2p/Msn4p and Hsf1p regulons , 1999, Molecular microbiology.

[38]  D. Raitt,et al.  The Skn7 response regulator of Saccharomyces cerevisiae interacts with Hsf1 in vivo and is required for the induction of heat shock genes by oxidative stress. , 2000, Molecular biology of the cell.

[39]  K. Jan,et al.  NADH oxidase activation is involved in arsenite-induced oxidative DNA damage in human vascular smooth muscle cells. , 2000, Circulation research.

[40]  A. Ciechanover,et al.  Modes of regulation of ubiquitin‐mediated protein degradation , 2000, Journal of cellular physiology.

[41]  F. Estruch.  Stress-controlled transcription factors, stress-induced genes and stress tolerance in budding yeast. , 2000, FEMS microbiology reviews.

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

[43]  J. Mellor,et al.  Cadmium-inducible Expression of the Yeast GSH1 Gene Requires a Functional Sulfur-Amino Acid Regulatory Network* , 2000, The Journal of Biological Chemistry.

[44]  George M. Church,et al.  Regulatory Networks Revealed by Transcriptional Profiling of Damaged Saccharomyces cerevisiae Cells: Rpn4 Links Base Excision Repair with Proteasomes , 2000, Molecular and Cellular Biology.

[45]  E. Lander,et al.  Remodeling of yeast genome expression in response to environmental changes. , 2001, Molecular biology of the cell.

[46]  T. Rossman,et al.  Effects of arsenite on p53, p21 and cyclin D expression in normal human fibroblasts -- a possible mechanism for arsenite's comutagenicity. , 2001, Mutation research.

[47]  Kate Johnson,et al.  MAPS: a microarray project system for gene expression experiment information and data validation , 2001, Bioinform..

[48]  F. Estruch,et al.  Hsf1p and Msn2/4p cooperate in the expression of Saccharomyces cerevisiae genes HSP26 and HSP104 in a gene‐ and stress type‐dependent manner , 2001, Molecular microbiology.

[49]  Pierre R. Bushel,et al.  Inactivation of DNA Mismatch Repair by Increased Expression of Yeast MLH1 , 2001, Molecular and Cellular Biology.

[50]  Ronald W. Davis,et al.  A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[51]  T. Ideker,et al.  A new approach to decoding life: systems biology. , 2001, Annual review of genomics and human genetics.

[52]  K. Kitchin.  Recent advances in arsenic carcinogenesis: modes of action, animal model systems, and methylated arsenic metabolites. , 2001, Toxicology and applied pharmacology.

[53]  S. X. Liu,et al.  Induction of oxyradicals by arsenic: implication for mechanism of genotoxicity. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[54]  R. Wysocki,et al.  Yap1 overproduction restores arsenite resistance to the ABC transporter deficient mutant ycf1 by activating ACR3 expression. , 2001, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[55]  Michel B Toledano,et al.  The control of the yeast H2O2 response by the Msn2/4 transcription factors , 2002, Molecular microbiology.

[56]  Ronald W. Davis,et al.  Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[57]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

[58]  Ioannis Xenarios,et al.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..

[59]  Benno Schwikowski,et al.  Discovering regulatory and signalling circuits in molecular interaction networks , 2002, ISMB.

[60]  Michel Werner,et al.  Sulfur sparing in the yeast proteome in response to sulfur demand. , 2002, Molecular cell.

[61]  C. Afshari,et al.  Coordination of altered DNA repair and damage pathways in arsenite-exposed keratinocytes. , 2002, Toxicological sciences : an official journal of the Society of Toxicology.

[62]  Trey Ideker,et al.  Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. , 2002, Molecular cancer research : MCR.

[63]  G. Church,et al.  Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks. , 2002, Molecular biology of the cell.

[64]  G. Owsianik,et al.  Control of 26S proteasome expression by transcription factors regulating multidrug resistance in Saccharomyces cerevisiae , 2002, Molecular microbiology.

[65]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[66]  J. Finnerty,et al.  The shikimate pathway and its branches in apicomplexan parasites. , 2002, The Journal of infectious diseases.

[67]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[68]  K. Korach,et al.  Estrogen receptor-dependent genomic responses in the uterus mirror the biphasic physiological response to estrogen. , 2003, Molecular endocrinology.

[69]  R. Karp,et al.  Conserved pathways within bacteria and yeast as revealed by global protein network alignment , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[70]  B. Palsson,et al.  Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. , 2003, Genome research.

[71]  E. Estey,et al.  Use of arsenic trioxide (As2O3) in the treatment of patients with acute promyelocytic leukemia , 2003, Cancer.

[72]  B. Birren,et al.  Sequencing and comparison of yeast species to identify genes and regulatory elements , 2003, Nature.

[73]  Xianglin Shi,et al.  Oxidative mechanism of arsenic toxicity and carcinogenesis , 2004, Molecular and Cellular Biochemistry.

[74]  C. Rodrigues-Pousada,et al.  Yap8p activation in Saccharomyces cerevisiae under arsenic conditions , 2004, FEBS letters.

[75]  L. Lazzeroni,et al.  Genome-Wide Identification of Genes Conferring Resistance to the Anticancer Agents Cisplatin, Oxaliplatin, and Mitomycin C , 2004, Cancer Research.

[76]  Markus J. Tamás,et al.  Transcriptional activation of metalloid tolerance genes in Saccharomyces cerevisiae requires the AP-1-like proteins Yap1p and Yap8p. , 2004, Molecular biology of the cell.

[77]  Overexpression of the SNQ3/YAP1 gene confers hyper-resistance to nitrosoguanidine in Saccharomyces cerevisiae via a glutathione-independent mechanism , 1994, Current Genetics.

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