ECB-ART-40014
Dev Biol
2006 Dec 01;3001:366-84. doi: 10.1016/j.ydbio.2006.08.066.
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The chemical defensome: environmental sensing and response genes in the Strongylocentrotus purpuratus genome.
Goldstone JV
,
Hamdoun A
,
Cole BJ
,
Howard-Ashby M
,
Nebert DW
,
Scally M
,
Dean M
,
Epel D
,
Hahn ME
,
Stegeman JJ
.
???displayArticle.abstract???
Metazoan genomes contain large numbers of genes that participate in responses to environmental stressors. We surveyed the sea urchin Strongylocentrotus purpuratus genome for homologs of gene families thought to protect against chemical stressors; these genes collectively comprise the ''chemical defensome.'' Chemical defense genes include cytochromes P450 and other oxidases, various conjugating enzymes, ATP-dependent efflux transporters, oxidative detoxification proteins, and transcription factors that regulate these genes. Together such genes account for more than 400 genes in the sea urchin genome. The transcription factors include homologs of the aryl hydrocarbon receptor, hypoxia-inducible factor, nuclear factor erythroid-derived 2, heat shock factor, and nuclear hormone receptors, which regulate stress-response genes in vertebrates. Some defense gene families, including the ABCC, the UGT, and the CYP families, have undergone expansion in the urchin relative to other deuterostome genomes, whereas the stress sensor gene families do not show such expansion. More than half of the defense genes are expressed during embryonic or larval life stages, indicating their importance during development. This genome-wide survey of chemical defense genes in the sea urchin reveals evolutionary conservation of this network combined with lineage-specific diversification that together suggest the importance of these chemical stress sensing and response mechanisms in early deuterostomes. These results should facilitate future studies on the evolution of chemical defense gene networks and the role of these networks in protecting embryos from chemical stress during development.
???displayArticle.pubmedLink??? 17097629
???displayArticle.pmcLink??? PMC3166225
???displayArticle.link??? Dev Biol
???displayArticle.grants??? [+]
P30-ES06096 NIEHS NIH HHS , 2-P42-ES07381 NIEHS NIH HHS , P42 ES007381 NIEHS NIH HHS , F32 HD047136 NICHD NIH HHS , F32 HD047136-03 NICHD NIH HHS , R01 ES006272 NIEHS NIH HHS , F32-ES012794 NIEHS NIH HHS , Intramural NIH HHS, P30 ES006096 NIEHS NIH HHS , F32 ES012794 NIEHS NIH HHS , F32-HD47136 NICHD NIH HHS , R01ES006272 NIEHS NIH HHS , F32 HD047136-02 NICHD NIH HHS , R01 ES006272-13 NIEHS NIH HHS
Genes referenced: LOC100887844 LOC115925415 LOC115928006 LOC575116 LOC591088 slc35a2
References [+] :
Allikmets,
A human placenta-specific ATP-binding cassette gene (ABCP) on chromosome 4q22 that is involved in multidrug resistance.
1998, Pubmed
Allikmets, A human placenta-specific ATP-binding cassette gene (ABCP) on chromosome 4q22 that is involved in multidrug resistance. 1998, Pubmed
Ambudkar, Biochemical, cellular, and pharmacological aspects of the multidrug transporter. 1999, Pubmed
An, SKN-1 links C. elegans mesendodermal specification to a conserved oxidative stress response. 2003, Pubmed
Andrews, Erythroid transcription factor NF-E2 is a haematopoietic-specific basic-leucine zipper protein. 1993, Pubmed
Annilo, Evolution of the vertebrate ABC gene family: analysis of gene birth and death. 2006, Pubmed
Antebi, daf-12 encodes a nuclear receptor that regulates the dauer diapause and developmental age in C. elegans. 2000, Pubmed
BACKSTROM, Content and distribution of ascorbic acid in sea urchin embryos of different developmental trends. 1957, Pubmed , Echinobase
Barth, The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions. 2004, Pubmed
Barth, Sequence and structure of epoxide hydrolases: a systematic analysis. 2004, Pubmed
Blackburn, Deficiency of glutathione transferase zeta causes oxidative stress and activation of antioxidant response pathways. 2006, Pubmed
Bock, Coordinate regulation of drug metabolism by xenobiotic nuclear receptors: UGTs acting together with CYPs and glucuronide transporters. 2004, Pubmed
Bogarad, Interference with gene regulation in living sea urchin embryos: transcription factor knock out (TKO), a genetically controlled vector for blockade of specific transcription factors. 1998, Pubmed , Echinobase
Boukouvala, Arylamine N-acetyltransferases: what we learn from genes and genomes. 2005, Pubmed
Butler, An aryl hydrocarbon receptor (AHR) homologue from the soft-shell clam, Mya arenaria: evidence that invertebrate AHR homologues lack 2,3,7,8-tetrachlorodibenzo-p-dioxin and beta-naphthoflavone binding. 2001, Pubmed
Calestani, Isolation of pigment cell specific genes in the sea urchin embryo by differential macroarray screening. 2003, Pubmed , Echinobase
Cashman, Human and plant flavin-containing monooxygenase N-oxygenation of amines: detoxication vs. bioactivation. 2002, Pubmed
Cashman, Some distinctions between flavin-containing and cytochrome P450 monooxygenases. 2005, Pubmed
Chan, Reduced oxidative-stress response in red blood cells from p45NFE2-deficient mice. 2001, Pubmed
Chan, Cloning of Nrf1, an NF-E2-related transcription factor, by genetic selection in yeast. 1993, Pubmed
Clemens, Caenorhabditis elegans expresses a functional phytochelatin synthase. 2001, Pubmed
Clemens, Evolution and function of phytochelatin synthases. 2006, Pubmed
Cole, Multidrug resistance mediated by the ATP-binding cassette transporter protein MRP. 1998, Pubmed
Coolen, Phylogenomic analysis and expression patterns of large Maf genes in Xenopus tropicalis provide new insights into the functional evolution of the gene family in osteichthyans. 2005, Pubmed
Cowen, Hsp90 potentiates the rapid evolution of new traits: drug resistance in diverse fungi. 2005, Pubmed
Davidson, Gene regulatory networks and the evolution of animal body plans. 2006, Pubmed
Dean, Evolution of the ATP-binding cassette (ABC) transporter superfamily in vertebrates. 2005, Pubmed
Dean, The human ATP-binding cassette (ABC) transporter superfamily. 2001, Pubmed
Dean, Tumour stem cells and drug resistance. 2005, Pubmed
Denison, Activation of the aryl hydrocarbon receptor by structurally diverse exogenous and endogenous chemicals. 2003, Pubmed
Dickinson, Human glutamate cysteine ligase gene regulation through the electrophile response element. 2004, Pubmed
Dogra, Transcriptional activation of cytochrome P450 genes by different classes of chemical inducers. 1998, Pubmed
Duncan, Phylogenetic analysis of the 5-aminolevulinate synthase gene. 1999, Pubmed , Echinobase
Duncan, Control of distal antennal identity and tarsal development in Drosophila by spineless-aristapedia, a homolog of the mammalian dioxin receptor. 1998, Pubmed
Eddy, Profile hidden Markov models. 1998, Pubmed
Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput. 2004, Pubmed
Eloranta, Coordinate transcriptional regulation of bile acid homeostasis and drug metabolism. 2005, Pubmed
Epel, Protection of DNA during early development: adaptations and evolutionary consequences. 2003, Pubmed , Echinobase
Fahey, The glutathione thiol-disulfide status in the sea urchin egg during fertilization and the first cell division cycle. 1976, Pubmed , Echinobase
Feder, Heat-shock proteins, molecular chaperones, and the stress response: evolutionary and ecological physiology. 1999, Pubmed
Gamage, Human sulfotransferases and their role in chemical metabolism. 2006, Pubmed
Giudice, Studies on heat shock proteins in sea urchin development. 1999, Pubmed , Echinobase
Gong, Nrf2 is increased by CYP2E1 in rodent liver and HepG2 cells and protects against oxidative stress caused by CYP2E1. 2006, Pubmed
Green, The effects of methoxychlor on early sea urchin development. 1997, Pubmed , Echinobase
Griffiths, Seasonal changes in the carotenoids of the sea urchin Strongylocentrotus dröbachiensis. 1976, Pubmed , Echinobase
Griffiths, The carotenoids of the eggs and embryos of the sea urchin Strongylocentrotus purpuratus. 1966, Pubmed , Echinobase
Gu, The PAS superfamily: sensors of environmental and developmental signals. 2000, Pubmed
Guengerich, Cytochrome P-450 3A4: regulation and role in drug metabolism. 1999, Pubmed
Guengerich, Analysis of the kinetic mechanism of haloalkane conjugation by mammalian theta-class glutathione transferases. 2003, Pubmed
Hahn, Unexpected diversity of aryl hydrocarbon receptors in non-mammalian vertebrates: insights from comparative genomics. 2006, Pubmed
Hahn, Aryl hydrocarbon receptors: diversity and evolution. 2002, Pubmed
Hamdoun, Activation of multidrug efflux transporter activity at fertilization in sea urchin embryos (Strongylocentrotus purpuratus). 2004, Pubmed , Echinobase
Handschin, Regulatory network of lipid-sensing nuclear receptors: roles for CAR, PXR, LXR, and FXR. 2005, Pubmed
Hein, Metabolic activation and deactivation of arylamine carcinogens by recombinant human NAT1 and polymorphic NAT2 acetyltransferases. 1993, Pubmed
Heinecke, Superoxide peroxidase activity of ovoperoxidase, the cross-linking enzyme of fertilization. 1990, Pubmed , Echinobase
Henderson, Pi-class glutathione S-transferase: regulation and function. 1998, Pubmed
Hernandez, Organization and evolution of the flavin-containing monooxygenase genes of human and mouse: identification of novel gene and pseudogene clusters. 2004, Pubmed
Howard-Ashby, Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development. 2006, Pubmed , Echinobase
Hu, Differential roles of hypoxia-inducible factor 1alpha (HIF-1alpha) and HIF-2alpha in hypoxic gene regulation. 2003, Pubmed
Huang, The AHR-1 aryl hydrocarbon receptor and its co-factor the AHA-1 aryl hydrocarbon receptor nuclear translocator specify GABAergic neuron cell fate in C. elegans. 2004, Pubmed
Huvet, The identification of genes from the oyster Crassostrea gigas that are differentially expressed in progeny exhibiting opposed susceptibility to summer mortality. 2004, Pubmed
Hyndman, The aldo-keto reductase superfamily homepage. 2003, Pubmed
Ichio, Glutathione reductase in the sea urchin egg. III. Activation of the complex form by proteinases. 1977, Pubmed , Echinobase
Igarashi, The heme-Bach1 pathway in the regulation of oxidative stress response and erythroid differentiation. 2006, Pubmed
Ii, Glutathione reductase in the sea urchin egg. I. Purification and general properties. 1974, Pubmed , Echinobase
Ii, Glutathione reductase in the sea urchin egg. II. Cleavage-associating fluctuation of the activity and its possible regulatory mechanism. 1974, Pubmed , Echinobase
Ioannides, Cytochromes P450 in the bioactivation of chemicals. 2004, Pubmed
Jeanmougin, Multiple sequence alignment with Clustal X. 1998, Pubmed
Jez, The aldo-keto reductase (AKR) superfamily: an update. 2001, Pubmed
Järving, On the evolutionary origin of cyclooxygenase (COX) isozymes: characterization of marine invertebrate COX genes points to independent duplication events in vertebrate and invertebrate lineages. 2004, Pubmed
Kast, Regulation of multidrug resistance-associated protein 2 (ABCC2) by the nuclear receptors pregnane X receptor, farnesoid X-activated receptor, and constitutive androstane receptor. 2002, Pubmed
Kewley, The mammalian basic helix-loop-helix/PAS family of transcriptional regulators. 2004, Pubmed
Klaassen, Regulation of hepatic transporters by xenobiotic receptors. 2005, Pubmed
Kobayashi, Molecular cloning and functional characterization of a new Cap'n' collar family transcription factor Nrf3. 1999, Pubmed
Kontrogianni-Konstantopoulos, A novel sea urchin nuclear receptor encoded by alternatively spliced maternal RNAs. 1996, Pubmed , Echinobase
Krasowski, Evolution of the pregnane x receptor: adaptation to cross-species differences in biliary bile salts. 2005, Pubmed
Kullak-Ublick, Regulation of drug and bile salt transporters in liver and intestine. 2003, Pubmed
Kwong, The CNC basic leucine zipper factor, Nrf1, is essential for cell survival in response to oxidative stress-inducing agents. Role for Nrf1 in gamma-gcs(l) and gss expression in mouse fibroblasts. 1999, Pubmed
LaFleur, Sea urchin ovoperoxidase: oocyte-specific member of a heme-dependent peroxidase superfamily that functions in the block to polyspermy. 1998, Pubmed , Echinobase
Lavista-Llanos, Control of the hypoxic response in Drosophila melanogaster by the basic helix-loop-helix PAS protein similar. 2002, Pubmed
Lee, Identification of mouse liver aldehyde dehydrogenases that catalyze the oxidation of retinaldehyde to retinoic acid. 1991, Pubmed
Lee, Transcriptional regulatory networks in Saccharomyces cerevisiae. 2002, Pubmed
Leslie, Toxicological relevance of the multidrug resistance protein 1, MRP1 (ABCC1) and related transporters. 2001, Pubmed
Lesser, Oxidative stress in marine environments: biochemistry and physiological ecology. 2006, Pubmed
Lesser, Exposure to ultraviolet radiation causes apoptosis in developing sea urchin embryos. 2003, Pubmed , Echinobase
Leung, Deficiency of the Nrf1 and Nrf2 transcription factors results in early embryonic lethality and severe oxidative stress. 2003, Pubmed
Lewis, Substrates of human cytochromes P450 from families CYP1 and CYP2: analysis of enzyme selectivity and metabolism. 2004, Pubmed
Longabaugh, Computational representation of developmental genetic regulatory networks. 2005, Pubmed
Luque, Functional and phylogenetic analyses of a putative Drosophila melanogaster UDP-glycosyltransferase gene. 2002, Pubmed
Luscombe, Genomic analysis of regulatory network dynamics reveals large topological changes. 2004, Pubmed
Ma, The effect of stress withdrawal on gene expression and certain biochemical and cell biological properties of peroxide-conditioned cell lines. 2004, Pubmed
Mackenzie, Nomenclature update for the mammalian UDP glycosyltransferase (UGT) gene superfamily. 2005, Pubmed
McMahon, The Cap'n'Collar basic leucine zipper transcription factor Nrf2 (NF-E2 p45-related factor 2) controls both constitutive and inducible expression of intestinal detoxification and glutathione biosynthetic enzymes. 2001, Pubmed
Miyake, Molecular cloning of cDNAs which are highly overexpressed in mitoxantrone-resistant cells: demonstration of homology to ABC transport genes. 1999, Pubmed
Mohler, Segmentally restricted, cephalic expression of a leucine zipper gene during Drosophila embryogenesis. 1991, Pubmed
Motola, Identification of ligands for DAF-12 that govern dauer formation and reproduction in C. elegans. 2006, Pubmed
Nebert, Proposed role of drug-metabolizing enzymes: regulation of steady state levels of the ligands that effect growth, homeostasis, differentiation, and neuroendocrine functions. 1991, Pubmed
Nebert, Clinical importance of the cytochromes P450. 2002, Pubmed
Nebert, Analysis of the glutathione S-transferase (GST) gene family. 2004, Pubmed
Nebert, Role of aryl hydrocarbon receptor-mediated induction of the CYP1 enzymes in environmental toxicity and cancer. 2004, Pubmed
Nelson, Comparison of P450s from human and fugu: 420 million years of vertebrate P450 evolution. 2003, Pubmed
Nelson, Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants. 2004, Pubmed
Nelson, The P450 superfamily: update on new sequences, gene mapping, accession numbers, early trivial names of enzymes, and nomenclature. 1993, Pubmed
Nemer, Structure, spatial, and temporal expression of two sea urchin metallothionein genes, SpMTB1 and SpMTA. 1991, Pubmed , Echinobase
Ney, Purification of the human NF-E2 complex: cDNA cloning of the hematopoietic cell-specific subunit and evidence for an associated partner. 1993, Pubmed
Nguyen, Regulatory mechanisms controlling gene expression mediated by the antioxidant response element. 2003, Pubmed
Nguyen, Increased protein stability as a mechanism that enhances Nrf2-mediated transcriptional activation of the antioxidant response element. Degradation of Nrf2 by the 26 S proteasome. 2003, Pubmed
Nomura, The primary and higher order structures of sea urchin ovoperoxidase as determined by cDNA cloning and predicted by homology modeling. 1999, Pubmed , Echinobase
Oyake, Bach proteins belong to a novel family of BTB-basic leucine zipper transcription factors that interact with MafK and regulate transcription through the NF-E2 site. 1996, Pubmed
Pearson, Phylogenies of glutathione transferase families. 2005, Pubmed
Pettersson, Human microsomal prostaglandin E synthase 1: a member of the MAPEG protein superfamily. 2005, Pubmed
Powell-Coffman, Caenorhabditis elegans orthologs of the aryl hydrocarbon receptor and its heterodimerization partner the aryl hydrocarbon receptor nuclear translocator. 1998, Pubmed
Puga, Ah receptor signals cross-talk with multiple developmental pathways. 2005, Pubmed
Qin, The Caenorhabditis elegans aryl hydrocarbon receptor, AHR-1, regulates neuronal development. 2004, Pubmed
Queitsch, Hsp90 as a capacitor of phenotypic variation. 2002, Pubmed
Robey, Pheophorbide a is a specific probe for ABCG2 function and inhibition. 2004, Pubmed
Roepke, Estradiol and endocrine disrupting compounds adversely affect development of sea urchin embryos at environmentally relevant concentrations. 2005, Pubmed , Echinobase
Roepke, Maternal exposure to estradiol and endocrine disrupting compounds alters the sensitivity of sea urchin embryos and the expression of an orphan steroid receptor. 2006, Pubmed , Echinobase
Ronquist, MrBayes 3: Bayesian phylogenetic inference under mixed models. 2003, Pubmed
Rosenfeld, Response delays and the structure of transcription networks. 2003, Pubmed , Echinobase
SAKAI, Studies on sulfhydryl groups during cell division of sea urchin egg. I. Glutatione. 1959, Pubmed , Echinobase
Samanta, The transcriptome of the sea urchin embryo. 2006, Pubmed , Echinobase
Sarkadi, ABCG2 -- a transporter for all seasons. 2004, Pubmed
Schmuck, Characterization of the monomethylarsonate reductase and dehydroascorbate reductase activities of Omega class glutathione transferase variants: implications for arsenic metabolism and the age-at-onset of Alzheimer's and Parkinson's diseases. 2005, Pubmed
Schomer, Redox changes during fertilization and maturation of marine invertebrate eggs. 1998, Pubmed , Echinobase
Scortegagna, Multiple organ pathology, metabolic abnormalities and impaired homeostasis of reactive oxygen species in Epas1-/- mice. 2003, Pubmed
Scotti, Pernin: a novel, self-aggregating haemolymph protein from the New Zealand green-lipped mussel, Perna canaliculus (Bivalvia: Mytilidae). 2001, Pubmed
Shapiro, The control of oxidant stress at fertilization. 1991, Pubmed , Echinobase
Shapiro, Ovothiols: biological and chemical perspectives. 1991, Pubmed , Echinobase
Shen, Roles of the HIF-1 hypoxia-inducible factor during hypoxia response in Caenorhabditis elegans. 2005, Pubmed
Shtil, Redundancy of biological regulation as the basis of emergence of multidrug resistance. 2005, Pubmed
Smital, Emerging contaminants--pesticides, PPCPs, microbial degradation products and natural substances as inhibitors of multixenobiotic defense in aquatic organisms. 2004, Pubmed , Echinobase
Snyder, Cytochrome P450 enzymes belonging to the CYP4 family from marine invertebrates. 1998, Pubmed
Sodergren, The genome of the sea urchin Strongylocentrotus purpuratus. 2006, Pubmed , Echinobase
Stoilov, Roles of cytochrome p450 in development. 2001, Pubmed
Sugiura, An evolutionarily conserved N-terminal acetyltransferase complex associated with neuronal development. 2003, Pubmed
Sundberg, Glutathione conjugation of bay- and fjord-region diol epoxides of polycyclic aromatic hydrocarbons by glutathione transferases M1-1 and P1-1. 1997, Pubmed
Surh, Bioactivation of benzylic and allylic alcohols via sulfo-conjugation. 1998, Pubmed
Sweet, The organic anion transporter family: from physiology to ontogeny and the clinic. 2001, Pubmed
Sweet, Organic anion transporter (Slc22a) family members as mediators of toxicity. 2005, Pubmed
Thummel, In vitro and in vivo drug interactions involving human CYP3A. 1998, Pubmed
Trebino, Impaired inflammatory and pain responses in mice lacking an inducible prostaglandin E synthase. 2003, Pubmed
Turner, Ovothiol: a novel thiohistidine compound from sea urchin eggs that confers NAD(P)H-O2 oxidoreductase activity on ovoperoxidase. 1986, Pubmed , Echinobase
Turner, Ovothiol replaces glutathione peroxidase as a hydrogen peroxide scavenger in sea urchin eggs. 1988, Pubmed , Echinobase
Vasiliou, Update of the NAD(P)H:quinone oxidoreductase (NQO) gene family. 2006, Pubmed
Vasiliou, Analysis and update of the human aldehyde dehydrogenase (ALDH) gene family. 2005, Pubmed
Vasák, Metallothioneins: new functional and structural insights. 2000, Pubmed , Echinobase
Vega, Stress-induced apoptosis in sea urchin embryogenesis. 2004, Pubmed , Echinobase
Veraksa, Cap 'n' collar B cooperates with a small Maf subunit to specify pharyngeal development and suppress deformed homeotic function in the Drosophila head. 2000, Pubmed
Verslycke, Isolation and phylogeny of novel cytochrome P450 genes from tunicates (Ciona spp.): a CYP3 line in early deuterostomes? 2006, Pubmed
Walisser, Aryl hydrocarbon receptor-dependent liver development and hepatotoxicity are mediated by different cell types. 2005, Pubmed
Walker, A conserved transcription motif suggesting functional parallels between Caenorhabditis elegans SKN-1 and Cap'n'Collar-related basic leucine zipper proteins. 2000, Pubmed
Waxman, P450 gene induction by structurally diverse xenochemicals: central role of nuclear receptors CAR, PXR, and PPAR. 1999, Pubmed
Wernet, Stochastic spineless expression creates the retinal mosaic for colour vision. 2006, Pubmed
Whitbread, Characterization of the human Omega class glutathione transferase genes and associated polymorphisms. 2003, Pubmed
Whitlock, Induction of cytochrome P4501A1. 1999, Pubmed
Wong, The oxidative burst at fertilization is dependent upon activation of the dual oxidase Udx1. 2004, Pubmed , Echinobase
Wong, Reactive oxygen species and Udx1 during early sea urchin development. 2005, Pubmed , Echinobase
Xie, Orphan nuclear receptors: the exotics of xenobiotics. 2001, Pubmed
Xu, Induction of phase I, II and III drug metabolism/transport by xenobiotics. 2005, Pubmed
Yabe, Multidrug resistance-associated protein MRP-1 regulates dauer diapause by its export activity in Caenorhabditis elegans. 2005, Pubmed
Yang, Two organochlorine pesticides, toxaphene and chlordane, are antagonists for estrogen-related receptor alpha-1 orphan receptor. 1999, Pubmed
Yang, Tumour necrosis factor alpha induces co-ordinated activation of rat GSH synthetic enzymes via nuclear factor kappaB and activator protein-1. 2005, Pubmed
Ziegler, An overview of the mechanism, substrate specificities, and structure of FMOs. 2002, Pubmed
de Torres, Expression profiling of the host response to bacterial infection: the transition from basal to induced defence responses in RPM1-mediated resistance. 2003, Pubmed
von Dassow, The segment polarity network is a robust developmental module. 2000, Pubmed