Discrimination of toxic impacts of various chemicals using chemical-gene expression profiling of Escherichia coli DNA microarray

Process Biochemistry

Volumn 42, Issue 3, 2007, Pages 392-400

  Kim, Byoung Chan ^a   Gu, Man Bock ^b  

^a Gwangju Institute of Science and Technology (GIST)   (South Korea)

^b Korea University   (South Korea)

Author keywords

Bio monitoring; cDNA microarray; Chemical gene expression profiling; Escherichia coli; Toxic impacts; Toxicity

Indexed keywords

BIOASSAY; DNA SEQUENCES; ESCHERICHIA COLI; GENES; PRINCIPAL COMPONENT ANALYSIS; TOXICITY;

BIOMONITORING; CHEMICAL-GENE EXPRESSION PROFILING; HIERARCHICAL CLUSTERING ANALYSIS; PHYSIOLOGICAL CHANGES; TOXIC CHEMICALS; TOXIC IMPACTS;

GENETIC ENGINEERING;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 33847283654     PISSN: 13595113     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.procbio.2006.09.021     Document Type: Article

References (46)

1. Henry C.M. DNA microarrays in toxicology: gene expression analysis promise to change toxicology. Anal Chem (1999) 462A-464A
2. Neumann N.F., and Galvez F. DNA microarrays and toxicogenomics: applications for ecotoxicology?. Biotechnol Adv 20 (2002) 391-419
3. Kapanen A., and Itavaara M. Ecotoxicity tests for compost applications. Ecotoxicol Environ Saf 49 (2001) 1-16
4. Serra-Wittling C., Houot S., and Barriuso E. Modification of soil water retention and biological properties by municipal solid waste compost. Compost Sci Util 4 (1996) 44-52
5. Boon J.P., van Zanden J.J., Lewis W.E., Zegers B.N., Goksoyr A., and Arukwe A. The expression of CYP1A, vitellogenin and zona radiata proteins in Atlantic salmon (Salmo salar) after oral dosing with two commercial PBDE flame retardant mixtures: absence of short-term responses. Mar Environ Res 54 (2002) 719-724
6. Fish F., Lampert I., Halachmi A., and Riesenfeld G. The SOS Chromotest Kit: a rapid method for the detection of genotoxicity. Toxicity Assess 2 (1987) 135-147
7. Kool H.J., van Kreyl C.F., and Persad S. Mutagenic activity in groundwater in relation to mobilization of organic mutagens in soil. Sci Total Environ 84 (1989) 185-199
8. Lin T.C., and Chao M.R. Assessing the influence of methanol-containing additive on biological characteristics of diesel exhaust emissions using microtox and mutatox assays. Sci Total Environ 284 (2002) 61-74
9. Afshari C.A., Nuwaysir E.F., and Barrett J.C. Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation. Cancer Res 59 (1999) 4759-4760
10. Snell T.W., Brogdon S.E., and Morgan M.B. Gene expression profiling in ecotoxicology. Ecotoxicology 12 (2003) 475-483
11. Meneses-Lorente G., de Longueville F., Dos Santos-Mendes S., Bonnert T.P., Jack A., Evrard S., et al. An evaluation of a low-density DNA microarray using cytochrome P450 inducers. Chem Res Toxicol 16 (2003) 1070-1077
12. de Longueville F., Surry D., Meneses-Lorente G., Bertholet V., Talbot V., Evrard S., et al. Gene expression profiling of drug metabolism and toxicology markers using a low-density DNA microarray. Biochem Pharmacol 64 (2002) 137-149
13. Hong Y., Muller U.R., and Lai F. Discriminating two classes of toxicants through expression analysis of HepG2 cells with DNA arrays. Toxicol In Vitro 17 (2003) 85-92
14. Hoyt P.R., Doktycz M.J., Beattie K.L., and Greeley Jr. M.S. DNA microarrays detect 4-nonylphenol-induced alterations in gene expression during zebrafish early development. Ecotoxicology 12 (2003) 469-474
15. Larkin P., Sabo-Attwood T., Kelso J., and Denslow N.D. Analysis of gene expression profiles in largemouth bass exposed to 17-beta-estradiol and to anthropogenic contaminants that behave as estrogens. Ecotoxicology 12 (2003) 463-468
16. Waring J.F., Ciurlionis R., Jolly R.A., Heindel M., and Ulrich R.G. Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol Lett 120 (2001) 359-368
17. Kitagawa E., Momose Y., and Iwahashi H. Correlation of the structures of agricultural fungicides to gene expression in Saccharomyces cerevisiae upon exposure to toxic doses. Environ Sci Technol 37 (2003) 2788-2793
18. Phadtare S., Kato I., and Inouye M. DNA microarray analysis of the expression profile of Escherichia coli in response to treatment with 4,5-dihydroxy-2-cyclopenten-1-one. J Bacteriol 184 (2002) 6725-6729
19. Kim B.C., Youn C.H., Ahn J.M., and Gu M.B. Screening of target-specific stress responsive genes for the development of cell-based biosensors using a DNA microarray. Anal Chem 77 (2005) 8020-8026
20. McDowell S.A., Gammon K., Bachurski C.J., Wiest J.S., Leikauf J.E., Prows D.R., et al. Differential gene expression in the initiation and progression of nickel-induced acute lung injury. Am J Respir Cell Mol Biol 23 (2000) 466-474
21. Yoo S.M., Keum K.C., Yoo S.Y., Choi J.Y., Chang K.H., Yoo N.C., et al. Development of DNA microarray for pathogen detection. Biotechnol Bioprocess Eng 9 (2004) 93-99
22. Eisen M.B., Spellman P.T., Brown P.O., and Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95 (1998) 14863-14868
23. Knudsen S. A biologist's guide to analysis of DNA microarray data. 1st ed. (2002), John Wiley & Sons Inc., New York
24. Raychaudhuri S., Stuart J.M., and Altman R.B. Principal component analysis to summarize microarray experiments: application to sporulation time series. Pac Symp Biocomput (2000) 455-466
25. Sirisattha S., Momose Y., Kitagawa E., and Iwahashi H. Toxicity of anionic detergents determined by Saccharomyces cerevisiae microarray analysis. Water Res 38 (2004) 61-70
26. Roman G., Isnard P., and Jouany J. Critical analysis of methods for assessment of predicted no-effect concentration. Ecotoxicol Environ Saf 43 (1999) 117-125
27. McKenna D.J., Gallus M., McKeown S.R., Downes C.S., and McKelvey-Martin V.J. Modification of the alkaline Comet assay to allow simultaneous evaluation of mitomycin C-induced DNA cross-link damage and repair of specific DNA sequences in RT4 cells. DNA Repair (Amst) 2 (2003) 879-890
28. Begley T.J., and Samson L.D. Molecular biology: a fix for RNA. Nature 421 (2003) 795-796
29. Breitkreutz B.J., Stark C., and Tyers M. Osprey: a network visualization system. Genome Biol 4 (2003) R22
30. Day III R.S., Ziolkowski C.H., Scudiero D.A., Meyer S.A., Lubiniecki A.S., Girardi A.J., et al. Defective repair of alkylated DNA by human tumour and SV40-transformed human cell strains. Nature 288 (1980) 724-727
31. Maillard K.I., Benedik M.J., and Willson R.C. Rapid detection of mutagens by induction of luciferase bearing prophage in Escherichia coli. Environ Sci Technol 30 (1996) 2478-2483
32. Khil P.P., and Camerini-Otero R.D. Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol Microbiol 44 (2002) 89-105
33. Lee M., Kwon J., Kim S.N., Kim J.E., Koh W.S., Kim E.J., et al. cDNA microarray gene expression profiling of hydroxyurea, paclitaxel, and p-anisidine, genotoxic compounds with differing tumorigenicity results. Environ Mol Mutagen 42 (2003) 91-97
34. Cruz-Ramos H., Crack J., Wu G.G., Hughes M.N., Scott C., Thomson A.J., et al. NO sensing by FNR: regulation of the Escherichia coli NO-detoxifying flavohaemoglobin Hmp. EMBO J 21 (2002) 3235-3244
35. Choi S.H., and Gu M.B. Phenolic toxicity-detection and classification through the use of a recombinant bioluminescent Escherichia coli. Environ Toxicol Chem 20 (2001) 248-255
36. Sikkema J., de Bont J.A., and Poolman B. Mechanisms of membrane toxicity of hydrocarbons. Microbiol Rev 59 (1995) 201-222
37. Hassan H.M., and Fridovich I. Superoxide radical and the oxygen enhancement of the toxicity of paraquat in Escherichia coli. J Biol Chem 253 (1978) 8143-8148
38. Pomposiello P.J., and Demple B. Redox-operated genetic switches: the SoxR and OxyR transcription factors. Trends Biotechnol 19 (2001) 109-114
39. Belkin S., Smulski D.R., Vollmer A.C., Van Dyk T.K., and LaRossa R.A. Oxidative stress detection with Escherichia coli harboring a katG':lux fusion. Appl Environ Microbiol 62 (1996) 2252-2256
40. Mitchell R.J., and Gu M.B. An Escherichia coli biosensor capable of detecting both genotoxic and oxidative damage. Appl Microbiol Biotechnol 64 (2004) 46-52
41. Wu J., and Weiss B. Two divergently transcribed genes, soxR and soxS, control a superoxide response regulon of Escherichia coli. J Bacteriol 173 (1991) 2864-2871
42. Storz G., Tartaglia L.A., and Ames B.N. Transcriptional regulator of oxidative stress-inducible genes: direct activation by oxidation. Science 248 (1990) 189-194
43. Tao K. oxyR-dependent induction of Escherichia coli grx gene expression by peroxide stress. J Bacteriol 179 (1997) 5967-5970
44. Loewen P.C., and Switala J. Purification and characterization of catalase HPII from Escherichia coli K12. Biochem Cell Biol 64 (1986) 638-646
45. Zheng M., Wang X., Templeton L.J., Smulski D.R., LaRossa R.A., and Storz G. DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J Bacteriol 183 (2001) 4562-4570
46. Eggen R.I., Behra R., Burkhardt-Holm P., Escher B.I., and Schweigert N. Challenges in ecotoxicology. Environ Sci Technol 38 (2004) 58A-64A