Prokaryotic real-time gene expression profiling for toxicity assessment

Environmental Science and Technology

Volumn 43, Issue 12, 2009, Pages 4574-4581

  Onnis Hayden, Annalisa ^a   Weng, Haifeng ^b   He, Miao ^c   Hansen, Sonja ^b   Ilyin, Valentin ^b   Lewis, Kim ^b   Gu, April Z ^a  

^a Northeastern University   (United States)

^b NORTHEASTERN UNIVERSITY   (United States)

^c TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DAMAGE AND REPAIR; ENVIRONMENTAL POLLUTANTS; ENVIRONMENTAL SAMPLE; GENE CLUSTERING ANALYSIS; GENE EXPRESSION PROFILES; GENE EXPRESSION PROFILING; GLOBAL EFFECTS; GREEN FLUORESCENT PROTEIN; MERCURY CONCENTRATIONS; MERCURY RESISTANCE; MITOMYCIN; P-TYPE; RESISTANCE/SENSITIVITY; SOS RESPONSE; STRESS RESPONSE GENES; TEMPORAL RESPONSE; TIME-DEPENDENT; TOXICITY ASSESSMENT; TRANSCRIPTIONAL ACTIVITY; WATER SAMPLES;

ANTIGENS; BIOACTIVITY; DETOXIFICATION; ESCHERICHIA COLI; GENE EXPRESSION; MERCURY (METAL); MERCURY COMPOUNDS; METABOLITES; METALLIC MATRIX COMPOSITES; NUCLEIC ACIDS; WATER POLLUTION;

TOXICITY;

ADENOSINE TRIPHOSPHATASE; GREEN FLUORESCENT PROTEIN; MERCURY; MITOMYCIN C;

COLIFORM BACTERIUM; DETOXIFICATION; DNA; GENE EXPRESSION; GENOTOXICITY; MERCURY (ELEMENT); PROTEIN; REAL TIME; TOXICITY TEST; TOXIN;

ARTICLE; BACTERIAL STRAIN; DETOXIFICATION; DNA DAMAGE; DNA REPAIR; ESCHERICHIA COLI; GENE CLUSTER; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; NONHUMAN; POLLUTANT; PROKARYOTE; STRESS; TOXICITY TESTING; UPREGULATION; WATER SAMPLING;

ANTIBIOTICS, ANTINEOPLASTIC; DOSE-RESPONSE RELATIONSHIP, DRUG; ENVIRONMENTAL MONITORING; ENVIRONMENTAL POLLUTANTS; ESCHERICHIA COLI K12; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; MERCURY; MITOMYCIN; SENSITIVITY AND SPECIFICITY;

ESCHERICHIA COLI; PROKARYOTA;

EID: 67449119218     PISSN: 0013936X     EISSN: 15205851     Source Type: Journal    
DOI: 10.1021/es803227z     Document Type: Article

References (42)

1. Kawata, K.; Yokoo, H.; Shimazaki, R.; Okabe, S. Classification of heavy-metal toxicity by human DNA microarray analysis. Environ. Sci. Technol. 2007, 41 (10), 3769-3774. (Pubitemid 350067227)
2. Newton, R. K.; Aardema, M.; Aubrecht, J. The utility of DNA microarrays for characterizing genotoxicity. Environ. Health Perspect. 2004, 112 (4), 420-422. (Pubitemid 38404552)
3. Yamanaka, T.; Toyoshiba, H.; Sone, H.; Parham, F. M.; Portier, C. J. The TAO-Gen algorithm for identifying gene interaction networks with application toSOSrepair in E-coli. Environ. Health Perspect. 2004, 112 (16), 1614-1621. (Pubitemid 41309822)
4. Aardema, M. J.; MacGregor, J. T. Toxicology and genetic toxicology in the new era of "toxicogenomics": impact of "-omics" technologies. Mutat. Res. 2002, 499 (1), 13-25.
5. Kim, S. Y.; Min, J. H.; Hong, H. N.; Park, J. H.; Park, K. S.; Gu, M. B. Analysis of the stress effects of endocrine disrupting chemicals (EDCs) on Escherichia coli. J. Microbiol. Biotechnol. 2007, 17 (8), 1390-1393. (Pubitemid 47377406)
6. Phadtare, S.; Kato, I.; 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. 2002, 184 (23), 6725-6729. (Pubitemid 35332578)
7. Belkin, S.; Smulski, D. R.; Vollmer, A. C.; VanDyk, T. K.; LaRossa, R. A. Oxidative stress detection with Escherichia coli harboring a katG′::lux fusion. Appl. Environ. Microbiol. 1996, 62 (7), 2252-2256. (Pubitemid 26231185)
8. Ben-Israel, O.; Ben-Israel, H.; Ulitzur, S. Identification and quantification of toxic chemicals by use of Escherichia coli carrying lux genes fused to stress promoters. Appl. Environ. Microbiol. 1998, 64 (11), 4346-4352. (Pubitemid 28537999)
9. Gu, M. B.; Mitchell, R. J.; Kim, B. C. Whole-cell-based biosensors for environmental biomonitoringandapplication. Adv. Biochem. Eng. Biotechnol. 2004, 87, 269-305.
10. Plaper, A.; Jenko-Brinovec, S.; Premzl, A.; Kos, J.; Raspor, P. Genotoxicity of trivalent chromium in bacterial cells. Possible effects on DNA topology. Chem. Res. Toxicol. 2002, 15 (7), 943-949. (Pubitemid 34774449)
11. Ptitsyn, L. R.; Horneck, G.; Komova, O.; Kozubek, S.; Krasavin, E. A.; Bonev, M.; Rettberg, P. A biosensor for environmental genotoxin screening based on an SOS lux assay in recombinant Escherichia coli cells. Appl. Environ. Microbiol. 1997, 63 (11), 4377-4384. (Pubitemid 27485764)
12. Riether, K. B.; Dollard, M. A.; Billard, P. Assessment of heavy metal bioavailability using Escherichia coli zntAp::lux and copAp::lux-based biosensors. Appl. Microbiol. Biotechnol. 2001, 57 (5-6), 712-716. (Pubitemid 34028268)
13. Van Dyk, T. K.; DeRose, E. J.; Gonye, G. E. LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains. J. Bacteriol. 2001, 183 (19), 5496-5505. (Pubitemid 32880577)
14. Van Dyk, T. K.; Wei, Y.; Hanafey, M. K.; Dolan, M.; Reeve, M. J. G.; Rafalski, J. A.; Rothman-Denes, L. B.; LaRossa, R. A. A genomic approach to gene fusion technology. Proc. Natl. Acad. Sci. U.S.A. 2001, 98 (5), 2555-2560. (Pubitemid 32209520)
15. Vandyk, T. K.; Majarian, W. R.; Konstantinov, K. B.; Young, R. M.; Dhurjati, P. S.; Larossa, R. A. Rapid and sensitive pollutant detection by induction of heat-shock gene-bioluminescence gene fusions. Appl. Environ. Microbiol. 1994, 60 (5), 1414-1420. (Pubitemid 24144794)
16. Vandyk, T. K.; Smulski, D. R.; Reed, T. R.; Belkin, S.; Vollmer, A. C.; Larossa, R. A. Responses to toxicants of an Escherichia coli strain carrying a Uspa′ - Lux genetic fusion and an Escherichia coli strain carrying a Grpe′ - Lux fusion are similar. Appl. Environ. Microbiol. 1995, 61 (11), 4124-4127.
17. Zaslaver, A.; Bren, A.; Ronen, M.; Itzkovitz, S.; Kikoin, I.; Shavit, S.; Liebermeister, W.; Surette, M. G.; Alon, U. A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 2006, 3 (8), 623-628. (Pubitemid 44123429)
18. Kalir, S.; McClure, J.; Pabbaraju, K.; Southward, C.; Ronen, M.; Leibler, S.; Surette, M. G.; Alon, U. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 2001, 292 (5524), 2080-2083. (Pubitemid 32691575)
19. Kim, B. C.; Gu, M. B. Discrimination of toxic impacts of various chemicals using chemical-gene expression profiling of Escherichia coli DNA microarray. Process Biochem. 2007, 42 (3), 392-400. (Pubitemid 46329545)
20. Corbisier, P.; van der Lelie, D.; Borremans, B.; Provoost, A.; de Lorenzo, V.; Brown, N. L.; Lloyd, J. R.; Hobman, J. L.; Csoregi, E.; Johansson, G.; Mattiasson, B. Whole cell- and protein-based biosensors for the detection of bioavailable heavy metals in environmental samples. Anal. Chim. Acta 1999, 387 (3), 235-244. (Pubitemid 29172948)
21. Daunert, S.; Barrett, G.; Feliciano, J. S.; Shetty, R. S.; Shrestha, S.; Smith-Spencer, W. Genetically engineered whole-cell sensing systems: Coupling biological recognition with reporter genes. Chem. Rev. 2000, 100 (7), 2705-2738. (Pubitemid 30903955)
22. Courcelle, J.; Khodursky, A.; Peter, B.; Brown, P. O.; Hanawalt, P. C. Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics 2001, 158 (1), 41-64. (Pubitemid 32428629)
23. Min, J.; Gu, M. B. Adaptive responses of Escherichia coli for oxidative and protein damage using bioluminescence reporters. J. Microbiol. Biotechnol. 2004, 14 (3), 466-469. (Pubitemid 38979423)
24. Karp, P. D.; Keseler, I.; Shearer, A.; Kothari, A.; Paley, S.; Krummenacker, M.; Altman, T.; Paulsen, I.; Nolan, L.; Johnson, A.; Ren, Q.; Collado-Vides, J.; Bonavides-Martinez, C.; Gama-Castro, S.; Peralta, M.; Santos-Zavaleta, A.; Ingraham, J. L.; Gunsalus R. EcoCyc: a comprehensive view of Escherichia coli biology; http://EcoCyc.org.
25. Selifonova, O.; Burlage, R.; Barkay, T. Bioluminescent sensors for detection of bioavailable Hg(II) in the environment. Appl. Environ. Microbiol. 1993, 59 (9), 3083-3090. (Pubitemid 23267107)
26. Saeed, A. I.; Sharov, V.; White, J.; Li, J.; Liang, W.; Bhagabati, N.; Braisted, J.; Klapa, M.; Currier, T.; Thiagarajan, M.; Sturn, A.; Snuffin, M.; Rezantsev, A.; Popov, D.; Ryltsov, A.; Kostukovich, E.; Borisovsky, I.; Liu, Z.; Vinsavich, A.; Trush, V.; Quackenbush, J. TM4: A free, open-source system for microarray data management and analysis. BioTechniques 2003, 34 (2), 374+. (Pubitemid 36184095)
27. Norman, A.; Hansen, L. H.; Sorensen, S. J. Construction of a ColD cda promoter-based SOS-green fluorescent protein whole-cell biosensor with higher sensitivity toward genotoxic compounds than constructs based on recA, umuDC, or sul4 promoters. Appl. Environ. Microbiol. 2005, 71 (5), 2338-2346. (Pubitemid 40646975)
28. Khil, P. P.; Camerini-Otero, R. D. Over 1000 genes are involved in theDNAdamage response of Escherichia coli. Mol. Microbiol. 2002, 44 (1), 89-105. (Pubitemid 34429767)
29. Sener, G.; Sehirli, A. O.; Ayanoglu-Dulger, G. Melatonin protects against mercury(II)-induced oxidative tissue damage in rats. Pharmacol. Toxicol. 2003, 93 (6), 290-296. (Pubitemid 38096108)
30. Walker, G. C. The SOS response of Escherichia coli. In Escherichia coli and Salmonella typhimurium: cellular and molecular biology; Neidhardt, F. C.; Ingraham, J. L.; Low, K. B.; Magasanik, B.; Schaechter, M.; Umbarger, H. E., Eds.; ASM Press: Washington, DC, 1996.
31. Fernandez de Henestrosa, A. R.; Ogi, T.; Aoyagi, S.; Chafin, D.; Hayes, J. J.; Ohmori, H.; Woodgate, R. Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol. Microbiol. 2000, 35 (6), 1560-1572. (Pubitemid 30175530)
32. Ronen, M.; Rosenberg, R.; Shraiman, B. I.; Alon, U. Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (16), 10555-10560. (Pubitemid 34907015)
33. Wei, Y.; Vollmer, A. C.; LaRossa, R. A. In vivo titration of mitomycin C action by four Escherichia coli genomic regions on multicopy plasmids. J. Bacteriol. 2001, 183 (7), 2259-2264. (Pubitemid 32240395)
34. Mitchell, R. J.; Gu, M. B. Construction and characterization of novel dual stress-responsive bacterial biosensors. Biosens. Bioelectron. 2004, 19 (9), 977-985. (Pubitemid 38264481)
35. Rensing, C.; Sun, Y.; Mitra, B.; Rosen, B. P. Pb(II)-translocating P-type ATPases. J. Biol. Chem. 1998, 273 (49), 32614-32617.
36. Sharma, R.; Rensing, C.; Rosen, B. P.; Mitra, B. The ATP hydrolytic activity of purified ZntA, a Pb(II)/Cd(II)/Zn(II)-translocating ATPase from Escherichia coli. J. Biol. Chem. 2000, 275 (6), 3873-3878. (Pubitemid 30094611)
37. Brown, N. L.; Stoyanov, J. V.; Kidd, S. P.; Hobman, J. L. The MerR family of transcriptional regulators. FEMS Microbiol. Rev. 2003, 27 (2-3), 145-163. (Pubitemid 36694653)
38. Chen, P.; He, C. A. A general strategy to convert the MerR family proteins into highly sensitive and selective fluorescent biosensors for metal ions. J. Am. Chem. Soc. 2004, 126 (3), 728-729. (Pubitemid 38114352)
39. Galhardo, R. S.; Almeida, C. E. B.; Leitao, A. C.; Cabral-Neto, J. B. Repair of DNA lesions induced by hydrogen peroxide in the presence of iron chelators in Escherichia coli: Participation of endonuclease IV and Fpg. J. Bacteriol. 2000, 182 (7), 1964-1968. (Pubitemid 30165386)
40. Bradley, T. M.; Hidalgo, E.; Leautaud, V.; Ding, H.; Demple, B. Cysteine-to-alanine replacements in the Escherichia coli SoxR protein and the role of the [2Fe-2S] centers in transcriptional activation. Nucleic Acids Res. 1997, 25 (8), 1469-1475. (Pubitemid 27302902)
41. Stohs, S. J.; Bagchi, D. Oxidative mechanisms in the toxicity of metal-ions. Free Radical Biol. Med. 1995, 18 (2), 321-336.
42. Zaslaver, A.; Mayo, A. E.; Rosenberg, R.; Bashkin, P.; Sberro, H.; Tsalyuk, M.; Surette, M. G.; Alon, U. Just-in-time transcription program in metabolic pathways. Nat. Genet. 2004, 36 (5), 486-491. (Pubitemid 38620033)