Genomic analysis of the response of Arabidopsis thaliana to trinitrotoluene as revealed by cDNA microarrays

Plant Science

Volumn 168, Issue 6, 2005, Pages 1409-1424

  Mentewab, Ayalew ^a   Cardoza, Vinitha ^a,b   Stewart Jr , C Neal ^a  

^a UNIVERSITY OF TENNESSEE   (United States)

^b UNIVERSITY OF VERMONT   (United States)

Author keywords

Arabidopsis thaliana; Microarrays; Motif; Promoter; RDX; TNT; Xenobiotic

Indexed keywords

BIODIVERSITY; DNA; GENETIC ENGINEERING; PLANTS (BOTANY); TOLUENE;

MICROARRAY ANALYSIS; TRANSCRIPTION; TRINITROTOLUENE (TNT); XENOBIOTIC SUBSTANCES;

GENES;

BIODIVERSITY; GENES; GENETIC ENGINEERING; NUCLEIC ACIDS; PLANTS; TOLUENE;

ANIMALIA; ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 18844417155     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2004.10.021     Document Type: Article

References (62)

1. J. Venulet, and R.L. Van Etten Biochemistry and pharmacology of the nitro and nitroso groups H. Feuer The Chemistry of Nitro and Nitroso Groups 1970 Interscience New York 201 289
2. P.P. Fu Metabolic activation of nitro-polycyclic aromatic hydrocarbons Drug Metab. Rev. 22 1990 209 268
3. D.H. Rosenblatt Toxicology of explosives and propellants S.M. Kaye Encyclopedia of Explosives and Related Items, 1980 US Army Armament Research Development Command, Large Caliber Weapons System Laboratory Dover, New Jersey 322 336
4. S.G. Pavlostathis, K.K. Comstock, M.E. Jacobson, and F.M. Saunders Transformation of 2,4,6-trinitrotoluene by the aquatic plant Myriophyllum spicatum Environ. Toxicol. Chem. 17 1998 2266 2273
5. S.J. Rosser, C.E. French, and N.C. Bruce Engineering plants for the phytodetoxification of explosives In Vitro Cell Dev. Biol. Plant 37 2001 330 333
6. C.E. French, S.J. Rosser, G.J. Davies, S. Nicklin, and N.C. Bruce Biodegradation of explosives by transgenic plants expressing pentaerythritol tetranitrate reductase Nat. Biotechnol. 17 1999 491 494
7. N.K. Hannink, S.J. Rosser, C.E. French, A. Basran, J.A.H. Murray, S. Nicklin, and N.C. Bruce Phytodetoxification of TNT by transgenic plants expressing a bacterial nitroreductase Nat. Biotechnol. 19 2001 1168 1172
8. N.K. Hannink, S.J. Rosser, and N.C. Bruce Phytoremediation of explosives Crit. Rev. Plant Sci. 21 2002 511 538
9. J.B. Hughes, J. Shanks, M. Vanderford, J. Lauritzen, and R. Bhadra Transformation of TNT by aquatic plants and plant tissue cultures Environ. Sci. Technol. 31 1997 266 271
10. R. Rivera, V.F. Medina, S.L. Larson, and S.C. McCutcheon Phytotreatment of TNT-contaminated groundwater J. Soil Contam. 7 1998 511 529
11. R. Bhadra, R.J. Spanggord, D.G. Wayment, J.B. Hughes, and J.V. Shanks Characterization of oxidation products of TNT metabolism in aquatic phytoremediation systems of Myriophllum aquaticum Environ. Sci. Technol. 33 1999 3354 3361
12. E. Wisman, and J. Ohlrogge Arabidopsis microarray service facilities J. Plant Physiol. 124 2000 1468 1471
13. T.L. Bailey, and C. Elkan Fitting a mixture model by expectation maximization to discover motifs in biopolymers Proc Int. Conf. Intell. Syst. Mol. Biol. 2 1994 28 36
14. T.L. Bailey, and M. Gribskov Combining evidence using p-values: application to sequence homology searches Bioinformatics 14 1998 48 54
15. K. Higo, Y. Ugawa, M. Iwamoto, and T. Korenaga Plant cis-acting regulatory DNA elements (PLACE) database: 1999 Nucleic Acids Res. 27 1999 297 300
16. S. Rozen, and H. Skaletsky Primer 3 on the www for general users and for biologist programmers Methods Mol. Biol. 132 2000 365 386
17. M.W. Pfaffl A new mathematical model for relative quantification in real-time RT-PCR Nucleic Acids Res. 29 2001 e45
18. L.C. Davis, and N.C. Chou Metabolism of TNT associated with roots of higher plants. Proceedings of the 1996 HSRC-WERC Joint Conference on Environment Albuquerque, NM, 21-23 May 1996
19. H. Shinshi, S. Usami, and M. Ohme-Takagi Identification of an ethylene-responsive region in the promoter of a tobacco class I chitinase gene Plant Mol. Biol. 27 1995 923 932
20. M. Ohta, M. Ohme-Takagi, and H. Shinshi Three ethylene-responsive transcription factors in tobacco with distinct transactivation functions Plant J. 22 2000 29 38
21. S.Y. Fujimoto, M. Ohta, A. Usui, H. Shinshi, and M. Ohme-Takagi Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression Plant Cell 12 2000 393 404
22. X. Qin, and J.A. Zeevaart The 9-cis-epoxycarotenoid cleavage reaction is the key regulatory step of abscisic acid biosynthesis in water-stressed bean Proc. Natl. Acad. Sci. U.S.A. 96 1999 15354 15361
23. H. Ikai, and S. Yamamoto Identification and analysis of a gene encoding l-2,4-diaminobutyrate: 2-ketoglutarate 4-aminotransferase involved in the 1,3-diaminopropane production pathway in Acinetobacter baumannii J. Bacteriol. 179 1997 5118 5125
24. R. Goldberg, C. Morvan, A. Jauneau, and M.C. Jarvis Methyl- esterification, de-esterification and gelation of pectins in the primary cell wall J. Visser A.G.J. Voragen Pectins and Pectinases 1996 Elsevier Science Publishers Amsterdam 151 172
25. F. Wen, Y. Zhu, and M.C. Hawes Effect of pectin methylesterase gene expression on pea root development Plant Cell 11 1999 1129 1140
26. J. Pilling, L. Willmitzer, and J. Fisahn Expression of a Petunia inflata pectin methyl esterase in Solanum tuberosum L. enhances stem elongation and modifies cation distribution Planta 210 2000 391 399
27. R. Meech, and P.I. Mackenzie Structure and function of uridine diphosphate glucuronosyltransferases Clin. Exp. Pharmacol. Physiol. 24 1997 907 915
28. O. Yang, K. Reinhard, E. Schiltz, and U. Matern Characterization and heterologous expression of hydroxycinnamoyl/benzoyl-CoA: anthranilate N-hydroxycinnamoyl/benzoyltransferase from elicited cell cultures of carnation Dianthus caryophyllus L. Plant Mol Biol. 35 1997 777 789
29. J.D. Allen, R.F. Brinkhuis, J. Wijnholds, and A.H. Schinkel The mouse Bcrp1/Mxr/Abcp gene: amplification and overexpression in cell lines selected for resistance to topotecan, mitoxantrone, or doxorubicin Cancer Res. 59 1999 4237 4241
30. D.J. Cosgrove Expansive growth of plant cell walls Plant Physiol. Biochem. 38 2000 109 124
31. J.H. Kim, H.T. Cho, and H. Kende Alpha-expansins in the semiaquatic ferns Marsilea quadrifolia and Regnellidium diphyllum: evolutionary aspects and physiological role in rachis elongation Planta 212 2000 85 92
32. J. Huang, T. Takano, and S. Akita Expression of alpha-expansin genes in young seedlings of rice (Oryza sativa L.) Planta 211 2000 467 473
33. W.H. Vriezen, B. De Graaf, C. Mariani, and L.A. Voesenek Submergence induces expansin gene expression in flooding-tolerant Rumex palustris and not in flooding-intolerant R. acetosa Planta 210 2000 956 963
34. N. Patel, V. Cardoza, E. Christensen, B. Rekapalli, A. Mentewab, and C.N. Stewart Jr. Differential gene expression of Chlamydomonas reinhardtii in response to 2,4,6-trinitrotoluene (TNT) using microarray analysis. Plant Sci. 167 2004 1109 1122
35. T. Werner Target gene identification from expression array data by promoter analysis Biomol. Eng. 17 2001 87 94
36. R. Foster, T. Izawa, and N.H. Chua Plant bZIP proteins gather at ACGT elements FASEB J. 8 1994 192 200
37. W.B. Terzaghi, and A.R. Cashmore Photomorphogenesis: seeing the light in plant development Curr. Biol. 5 1995 466 468
38. S. Klinedinst, P. Pascuzzi, J. Redman, M. Desai, and J. Arias A xenobiotic-stress-activated transcription factor and its cognate target genes are preferentially expressed in root tip meristems Plant Mol. Biol. 42 2000 679 688
39. J. Redman, J. Whitcraft, C. Johnson, and J. Arias Abiotic and biotic stress differentially stimulate as-1 element activity in Arabidopsis Plant Cell Rep. 21 2002 180 185
40. T.H. Rushmore, M.R. Morton, and C.B. Pickett The antioxidant responsive element activation by oxidative stress and identification of the DNA consensus sequence required for functional activity J. Biol. Chem. 266 1991 11632 11639
41. B. Piechulla, N. Merforth, and B. Rudolph Identification of tomato Lhc promoter regions necessary for circadian expression Plant Mol. Biol. 38 1998 655 662
42. S. Yanagisawa, and R.J. Schmidt Diversity and similarity among recognition sequences of Dof transcription factors Plant J. 17 1999 209 214
43. S. Yanagisawa Dof1 and Dof2 transcription factors are associated with expression of multiple genes involved in carbon metabolism in maize Plant J. 21 2000 281 288
44. 2-inducible, Arabidopsis glutathione S-transferase gene contains closely linked OBF- and OBP1-binding sites Plant J. 10 1996 955 966
45. N. Ngai, F.Y. Tsai, and G. Coruzzi Light-induced transcriptional repression of the pea AS1 gene: identification of cis-elements and trans-factors Plant J. 12 1997 1021 1034
46. N. Bate, and D. Twell Functional architecture of a late pollen promoter: pollen-specific transcription is developmentally regulated by multiple stage-specific and co-dependent activator elements Plant Mol. Biol. 37 1998 859 869
47. K. Haralampidis, D. Milioni, S. Rigas, and P. Hatzopoulos Combinatorial interaction of cis elements specifies the expression of the Arabidopsis AtHsp90-1 gene Plant Physiol. 129 2002 1138 1149
48. J. Le Gourrierec, Y.F. Li, and D.X. Zhou Transcriptional activation by Arabidopsis GT-1 may be through interaction with TFIIA-TBP-TATA complex Plant J. 18 1999 663 668
49. A.S. Buchel, F.T. Brederode, J.F. Bol, and H.J. Linthorst Mutation of GT-1 binding sites in the Pr-1A promoter influences the level of inducible gene expression in vivo Plant Mol. Biol. 40 1999 387 396
50. E. Grotewold, B.J. Drummond, B. Bowen, and T. Peterson The myb-homologous P gene controls phlobaphene pigmentation in maize floral organs by directly activating a flavonoid biosynthetic gene subset Cell 76 1994 543 553
51. B. Boyle, and N. Brisson Repression of the defense gene PR-10a by the single-stranded DNA binding protein SEBF Plant Cell 13 2001 2525 2537
52. D. Gidoni, P. Brosio, D. Bond-Nutter, J. Bedbrook, and P. Dunsmuir Novel cis-acting elements in Petunia Cab gene promoters Mol. Gen. Genet. 215 1989 337 344
53. H.J. Rogers, N. Bate, J. Combe, J. Sullivan, J. Sweetman, C. Swan, D.M. Lonsdale, and D. Twell Functional analysis of cis-regulatory elements within the promoter of the tobacco late pollen gene g10 Plant Mol. Biol. 45 2001 577 585
54. Y. Kagaya, K. Ohmiya, and T. Hattori RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants Nucleic Acids Res. 27 1999 470 478
55. N. Chaubet, M. Flenet, B. Clement, P. Brignon, and C. Gigot Identification of cis-elements regulating the expression of an Arabidopsis histone H4 gene Plant J. 10 1996 425 435
56. E.P. Best, M.E. Zappi, H.L. Fredrickson, S.L. Sprecher, S.L. Larson, and M. Ochman Screening of aquatic and wetland plant species for phytoremediation of explosives-contaminated groundwater from the Iowa Army Ammunition Plant Ann. N. Y. Acad. Sci. 829 1997 179 194
57. M.E. Lucero, W. Mueller, J. Hubstenberger, G.C. Phillips, and M. O'Connell Tolerance to nitrogenous explosives and metabolism of TNT by cell suspensions of Datura innoxia In Vitro Cell Dev. Biol. Plant. 35 1999 480 486
58. P.L. Thompson, L.A. Ramer, A.P. Guffey, and J.L. Schnoor Hexahydro-1,3,5-trinitro-1,3,5-triazine translocation in poplar trees Environ. Toxicol. Chem. 18 1999 279 284
59. H. Sandermann Jr. Plant metabolism of xenobiotics Trends Biochem. Sci. 17 1992 82 84
60. D.R. Ekman, W.W. Lorenz, A.E. Przybyla, N.L. Wolfe, and J.F.D. Dean SAGE Analysis of transcriptome responses in Arabidopsis roots exposed to 2,4,6-trinitrotoluene Plant Physiol. 133 2003 1397 1406
61. W.H. Sun, G.L. Horst, R.A. Drijber, and T.E. Elthon Fate of 2,4,6-trinitrotoluene in axenic sand culture systems containing smooth bromegrass Environ. Toxicol. Chem. 19 2000 2038 2046
62. E.P. Best, S.L. Sprecher, S.L. Larson, H.L. Fredrickson, and D.F. Bader Environmental behavior of explosives in groundwater from the Milan Army Ammunition Plant in aquatic and wetland plant treatments uptake and fate of TNT and RDX in plants Chemosphere 39 1999 2057 2072