Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Owen, Jennifer ^a   Ann, B Ann ^b   Svendsen, Claus ^c   Wren, Jodie ^a,c   Jonker, Martijs J ^d   Hankard, Peter K ^c   Lister, Linsey J ^c   Stürzenbaum, Stephen R ^e   Morgan, A John ^a   Spurgeon, David J ^c   Blaxter, Mark L ^b   Kille, Peter ^a  

^a CARDIFF UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

^d UNIVERSITY OF AMSTERDAM   (Netherlands)

^e Pharmaceutical Science Research Div   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ATRAZINE; CADMIUM; FLUORANTHENE; XENOBIOTIC AGENT; FLUORENE DERIVATIVE; HERBICIDE;

ARTICLE; DNA FINGERPRINTING; DNA MICROARRAY; DOSE RESPONSE; EARTHWORM; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SOIL POLLUTION; ANIMAL; ANNELID WORM; CHEMISTRY; DRUG EFFECT; ENVIRONMENTAL EXPOSURE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; GROWTH, DEVELOPMENT AND AGING; REPRODUCIBILITY; SOIL; SOIL POLLUTANT;

ANIMALIA; ANNELIDA; INVERTEBRATA; LUMBRICUS RUBELLUS;

ANIMALS; ATRAZINE; CADMIUM; ENVIRONMENTAL EXPOSURE; EXPRESSED SEQUENCE TAGS; FLUORENES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE LIBRARY; HERBICIDES; OLIGOCHAETA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; SOIL; SOIL POLLUTANTS; XENOBIOTICS;

EID: 45449085563     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-266     Document Type: Article

References (73)

1. Darwin C The formation of vegtable Mould through the action of Worms with observations on their habitats London: John Murray 1883
2. Lavelle P Spain A Soil Ecology Amsterdam: Kluwer Academic Publishers 1 2001
3. Spurgeon DJ Weeks JM Van Gestel CAM A summary of eleven years progress in earthworm ecotoxicology Pedobiologia 2003, 47(5-6):588-606
4. Bundy JG Osborn D Weeks JM Lindon JC Nicholson JK An NMR-based metabonomic approach to the investigation of coelomic fluid biochemistry in earthworms under toxic stress Febs Letters 2001, 500(1-2):31-35 10.1016/S0014-5793(01)02582-0 11434921
5. Bundy JG Spurgeon DJ Svendsen C Hankard PK Weeks JM Osborn D Lindon JC Nicholson JK Environmental metabonomics: Applying combination biomarker analysis in earthworms at a metal contaminated site Ecotoxicology 2004, 13(8):797-806 10.1007/s10646-003-4477-1 15736850
6. Harper GL Cesarini S Casey SP Morgan AJ Kille P Bruford MW Microsatellite markers for the earthworm Lumbricus rubellus Molecular Ecology Notes 2006, 6(2):325-327 10.1111/j.1471-8286.2005.01219.x
7. Kille P Sturzenbaum SR Galay M Winters C Morgan AJ Molecular diagnosis of pollution impact in earthworms - Towards integrated biomonitoring Pedobiologia 1999, 43(6):602-607
8. Morgan AJ Sturzenbaum SR Kille P A short overview of molecular biomarker strategies with particular regard to recent developments in earthworms Pedobiologia 1999, 43(6):574-584
9. Morgan AJ Sturzenbaum SR Winters C Kille P Cellular and molecular aspects of metal sequestration and toxicity in earthworms Invertebrate Reproduction & Development 1999, 36(1-3):17-24
10. Sturzenbaum SR Kille P Morgan AJ Heavy metal-induced molecular responses in the earthworm, Lumbricus rubellus genetic fingerprinting by directed differential display Applied Soil Ecology 1998, 9(1-3):495-500 10.1016/ S0929-1393(98)00111-5
11. Sturzenbaum SR Cater S Morgan AJ Kille P Earthworm pre-procarboxypeptidase: A copper responsive enzyme Biometals 2001, 14(1):85-94 10.1023/A:1016698907653 11368280
12. Sturzenbaum SR Kille P Morgan AJ Identification of heavy metal induced changes in the expression patterns of the translationally controlled tumour protein (TCTP) in the earthworm Lumbricus rubellus Biochimica et Biophysica Acta Gene Structure and Expression 1998, 1398(3):294-304 10.1016/S0167-4781(98)00077-3 9655922
13. Sturzenbaum SR Georgiev O Morgan AJ Kille P Cadmium detoxification in earthworms: From genes to cells Environmental Science & Technology 2004, 38(23):6283-6289 10.1021/es049822c 15597883
14. Sturzenbaum SR Kille P Morgan AJ The identification, cloning and characterization of earthworm metallothionein Febs Letters 1998, 431(3):437-442 10.1016/S0014-5793(98)00809-6 9714559
15. Sturzenbaum SR Winters C Galay M Morgan AJ Kille P Metal ion trafficking in earthworms - Identification of a cadmium-specific metallothionein Journal of Biological Chemistry 2001, 276(36):34013-34018 10.1074/ jbc.M103605200 11418603
16. Sturzenbaum SR Parkinson J Blaxter M Morgan AJ Kille P Georgiev O The earthworm Expressed Sequence Tag project Pedobiologia 2003, 47(5-6):447-45
17. Parkinson J Anthony A Wasmuth J Schmid R Hedley A Blaxter M PartiGene - constructing partial genomes Bioinformatics 2004, 20(9):1398-1404 10.1093/bioinformatics/bth101 14988115
18. Wasmuth JD Blaxter ML Prot4EST: Translating Expressed Sequence Tags from neglected genomes Bmc Bioinformatics 2004:5 543579 15571632
19. Earthworms.org: Home of the Lumbricus rubellus genome project http://www.earthworms.org
20. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Gene Ontology: Tool for the unification of biology Nature Genetics 2000, 25(1):25-29 10.1038/75556 10802651
21. Martin DM Berriman M Barton GJ GOtcha: A new method for prediction of protein function assessed by the annotation of seven genomes BMC Bioinformatics 2004, 5:178 535938 15550167 10.1186/1471-2105-5-178
22. Sochova I Hofman J Holoubek I Using nematodes in soil ecotoxicology Environment International 2006, 32(3):374-383 10.1016/ j.envint.2005.08.031 16213020
23. Harris TW Chen N Cunningham F Tello-Ruiz M Antoshechkin I Bastiani C Bieri T Blasiar D Bradnam K Chan J WormBase: A multi-species resource for nematode biology and genomics Nucleic Acids Res 2004:32 Database D411-417 308800 14681445 10.1093/nar/gkh066
24. Dudoit S Yang YH Callow MJ Speed TP Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments Statistica Sinica 2002, 12(1):111-139
25. Beyersmann D Hechtenberg S Cadmium, gene regulation, and cellular signalling in mammalian cells Toxicology and Applied Pharmacology 1997, 144(2):247-261 10.1006/taap.1997.8125
26. Waisberg M Joseph P Hale B Beyersmann D Molecular and cellular mechanisms of cadmium carcinogenesis Toxicology 2003, 192(2-3):95-117 10.1016/S0300-483X(03)00305-6 14580780
27. Giaginis C Gatzidou E Theocharis S DNA repair systems as targets of cadmium toxicity Toxicology and Applied Pharmacology 2006, 213(3):282-290 10.1016/j.taap.2006.03.008
28. Wang YD Fang J Leonard S Demchuk E Rao KMK Cadmium inhibits the activity of Complexes II and III of respiratory chain and induces ROS production in mitochondria Faseb Journal 2004, 18(5):A1196-A1196 10.1096/ fj.04-2047com
29. Wiseman A Avoidance of oxidative-stress perturbation in yeast bioprocesses by proteomic and genomic biostrategies Letters in Applied Microbiology 2005, 40(1):37-43 10.1111/j.1472-765X.2004.01624.x 15613000
30. Casalino E Sblano C Calzaretti G Landriscina C Acute cadmium intoxication induces alpha-class glutathione S-transferase protein synthesis and enzyme activity in rat liver Toxicology 2006, 217(2-3):240-245 10.1016/j.tox.2005.09.020 16297521
31. Stewart D Killeen E Naquin R Alam S Alam J Degradation of transcription factor Nrf2 via the ubiquitin-proteasome pathway and stabilization by cadmium Journal of Biological Chemistry 2003, 278(4):2396-2402 10.1074/ jbc.M209195200 12441344
32. Filipic M Fatur T Vudrag M Molecular mechanisms of cadmium induced mutagenicity Human & Experimental Toxicology 2006, 25(2):67-77 10.1191/0960327106ht590oa 16539211
33. Mladenov E Anachkova B Tsaneva I Sub-nuclear localization of Rad51 in response to DNA damage Genes to Cells 2006, 11(5):513-524 10.1111/ j.1365-2443.2006.00958.x 16629903
34. Yang ZG Liu Y Mao LY Zhang JT Zou Y Dimerization of human XPA and formation of XPA(2)-RPA protein complex Biochemistry 2002, 41(43):13012-13020 1450105 12390028 10.1021/bi026064z
35. Martelli A Moulis JM Zinc and cadmium specifically interfere with RNA-binding activity of human iron regulatory protein 1 Journal of Inorganic Biochemistry 2004, 98(8):1413-1420 10.1016/ j.jinorgbio.2004.04.011 15271519
36. Sabolic I Herak-Kramberger CM Brown D Subchronic cadmium treatment affects the abundance and arrangement of cytoskeletal proteins in rat renal proximal tubule cells Toxicology 2001, 165(2-3):205-216 10.1016/ S0300-483X(01)00450-4 11522379
37. Walker CH Organic Pollutants: An Ecotoxicological Perspective London Taylor and Francis 2001
38. Rubin H Synergistic mechanisms in carcinogenesis by polycyclic aromatic hydrocarbons and by tobacco smoke: A bio-historical perspective with updates Carcinogenesis 2001, 22(12):1903-1930 10.1093/carcin/22.12.1903 11751421
39. Miller KP Ramos KS Impact of cellular metabolism on the biological effects of benzo[a]pyrene and related hydrocarbons Drug Metabolism Reviews 2001, 33(1):1-35 10.1081/DMR-100000138 11270659
40. Burstyn I Kromhout H Partanen T Svane O Langard S Ahrens W Kauppinen T Stucker I Shaham J Heederik D Polycyclic aromatic hydrocarbons and fatal ischemic heart disease Epidemiology 2005, 16(6):744-750 10.1097/ 01.ede.0000181310.65043.2f 16222163
41. Hennig B Oesterling E Toborek M Environmental toxicity, nutrition, and gene interactions in the development of atherosclerosis Nutrition Metabolism and Cardiovascular Diseases 2007, 17(2):162-169 10.1016/ j.numecd.2006.01.003
42. Ma Q Induction of CYP1A1. The AhR/DRE paradigm: Transcription, receptor regulation, and expanding biological roles Current Drug Metabolism 2001, 2(2):149-164 10.2174/1389200013338603 11469723
43. Nebert DW Roe AL Dieter MZ Solis WA Yang Y Dalton TP Role of the aromatic hydrocarbon receptor and [Ah] gene battery in the oxidative stress response, cell cycle control, and apoptosis Biochemical Pharmacology 2000, 59(1):65-85 10.1016/S0006-2952(99)00310-X 10605936
44. AliOsman F Akande O Antoun G Mao JX Buolamwini J Molecular cloning, characterization, and expression in Escherichia coli of full-length cDNAs of three human glutathione S-transferase Pi gene variants - Evidence for differential catalytic activity of the encoded proteins Journal of Biological Chemistry 1997, 272(15):10004-10012 10.1074/ jbc.272.15.10004 9092542
45. Martinez JM Baek SJ Mays DM Tithof PK Eling TE Walker NJ EGR1 is a novel target for AhR agonists in human lung epithelial cells Toxicological Sciences 2004, 82(2):429-435 10.1093/toxsci/kfh272 15342960
46. Kim JH Yamaguchi K Lee SH Tithof PK Sayler GS Yoon JH Baek SJ Evaluation of polycyclic aromatic hydrocarbons in the activation of early growth response-1 and peroxisome proliferator activated receptors Toxicological Sciences 2005, 85(1):585-593 10.1093/toxsci/kfi118 15716483
47. Leonard SS Wang SW Shi XL Jordan BS Castranova V Dubick MA Wood smoke particles generate free radicals and cause lipid peroxidation, DNA damage, NF kappa B activation and TNF-alpha release in macrophages Toxicology 2000, 150(1-3):147-157 10.1016/S0300-483X(00)00256-0 10996671
48. Achazi RK Flenner C Livingstone DR Peters LD Schaub K Scheiwe E Cytochrome P450 and dependent activities in unexposed and PAH-exposed terrestrial annelids Comparative Biochemistry and Physiology C-Pharmacology Toxicology & Endocrinology 1998, 121(1-3):339-350 10.1016/S0742-8413(98)10055-5 9972476
49. Brown PJ Long SM Spurgeon DJ Svendsen C Hankard PK Toxicological and biochemical responses of the earthworm Lumbricus rubellus to pyrene, a non-carcinogenic polycyclic aromatic hydrocarbon Chemosphere 2004, 57(11):1675-1681 10.1016/j.chemosphere.2004.05.041 15519413
50. Livingstone DR Lemaire P Matthews A Peters LD Porte C Fitzpatrick PJ Forlin L Nasci C Fossato V Wootton N Assessment of the impact of organic pollutants on Goby (Zosterisessor ophiocephalus) and Mussel (Mytilus galloprovincialis) from the Venice lagoon, Italy - biochemical studies Marine Environmental Research 1995, 39(1-4):235-240 10.1016/ 0141-1136(94)00055-T
51. Peters LD Shaw JP Nott M O'Hara SCM Livingstone DR Development of cytochrome P450 as a biomarker of organic pollution in Mytilus sp.: field studies in United Kingdom ('Sea Empress' oil spill) and the Mediterranean Sea Biomarkers 1999, 4(6):425-441 10.1080/135475099230598
52. PAN Pesticides Database http://www.pesticideinfo.org
53. Morgan MK Scheuerman PR Bishop CS Pyles RA Teratogenic potential of atrazine and 2,4-D using FETAX Journal of Toxicology and Environmental Health 1996, 48(2):151-168 10.1080/009841096161401 8642623
54. Pfister K Steinback KE Gardner G Arntzen CJ Photoaffinity-labeling of an herbicide receptor protein in chloroplast membranes Proceedings of the National Academy of Sciences of the United States of America-Biological Sciences 1981, 78(2):981-985 10.1073/pnas.78.2.981
55. Kee Y Huibregtse JM Regulation of catalytic activities of HECT ubiquitin ligases Biochemical and Biophysical Research Communications 2007, 354(2):329-333 10.1016/j.bbrc.2007.01.025 17240353
56. Philippe H Lartillot N Brinkmann H Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia Molecular Biology and Evolution 2005, 22(5):1246-1253 10.1093/molbev/msi111 15703236
57. Jones M Blaxter M Evolutionary biology - Animal roots and shoots Nature 2005, 434(7037):1076-1077 10.1038/4341076a 15858555
58. Cho SJ Cho PY Lee MS Na Y Lee JH Koh KS Choo JK Park SC Up-regulation of multiple serine proteinases during earthworm tail regeneration Invertebrate Reproduction & Development 2001, 40(2-3):103-108
59. Cooper EL Kauschke E Cossarizza A Digging for innate immunity since Darwin and Metchnikoff Bioessays 2002, 24(4):319-333 10.1002/bies.10077 11948618
60. Spurgeon DJ Svendsen C Weeks JM Hankard PK Stubberud HE Kammenga JE Quantifying copper and cadmium impacts on intrinsic rate of population increase in the terrestrial oligochaete Lumbricus rubellus Environmental Toxicology and Chemistry 2003, 22(7):1465-1472 10.1897/ 1551-5028(2003)22<1465:QCACIO>2.0.CO;2 12836970
61. Chomczynski P Sacchi N Single-step method of RNA isolation by acid guanidinium thiocyanate phenol chloroform extraction Analytical Biochemistry 1987, 162(1):156-159 10.1016/0003-2697(87)90021-2 2440339
62. Galay-Burgos M Spurgeon DJ Weeks JM Sturzenbaum SR Morgan AJ Kille P Developing a new method for soil pollution monitoring using molecular genetic biomarkers Biomarkers 2003, 8(3-4):229-239 10.1080/ 354750031000138685 12944175
63. Whitton C Daub J Thompson M Blaxter M Expressed sequence tags: medium-throughput protocols Methods Mol Biol 2004, 270:75-92 15153623
64. Parkinson J Guiliano DB Blaxter M Making sense of EST sequences by CLOBBing them Bmc Bioinformatics 200:3 137596 12398795
65. Wu CH Apweiler R Bairoch A Natale DA Barker WC Boeckmann B Ferro S Gasteiger E Huang H Lopez R The Universal Protein Resource (UniProt): An expanding universe of protein information Nucleic Acids Res 2006:34 Database D187-191 1347523 16381842 10.1093/nar/gkj161
66. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic Local Alignment Search Tool Journal of Molecular Biology 1990, 215(3):403-410 2231712
67. Quevillon E Silventoinen V Pillai S Harte N Mulder N Apweiler R Lopez R InterProScan: Protein domains identifier Nucleic Acids Research 2005, 33:W116-W120 1160203 15980438 10.1093/nar/gki442
68. Horton P Nakai K Better prediction of protein cellular localization sites with the k nearest neighbors classifier Proceedings International Conference on Intelligent Systems for Molecular Biology 1997, 5:147-152
69. Bendtsen JD Nielsen H von Heijne G Brunak S Improved prediction of signal peptides: SignalP 3.0 Journal of Molecular Biology 2004, 340(4):783-795 10.1016/j.jmb.2004.05.028 15223320
70. Gasteiger E Gattiker A Hoogland C Ivanyi I Appel RD Bairoch A ExPASy: the proteomics server for in-depth protein knowledge and analysis Nucleic Acids Research 2003, 31(13):3784-3788 168970 12824418 10.1093/ nar/gkg563
71. Ausubel F Brent R Kingston R Moore D Seidman J Smith J Struhl K Nucleic Acid Arrays Wiley 2000
72. Dennis G Sherman BT Hosack DA Yang J Gao W Lane HC Lempicki RA DAVID: Database for annotation, visualization, and integrated discovery Genome Biology 2003, 4(9):3 10.1186/gb-2003-4-5-p3
73. Sturzenbaum SR Kille P Control genes in quantitative molecular biological techniques: The variability of invariance Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology 2001, 130(3):281-289 10.1016/S1096-4959(01)00440-7 11567890