Microbial responses to xenobiotic compounds. Identification of genes that allow Pseudomonas putida KT2440 to cope with 2,4,6-trinitrotoluene

Microbial Biotechnology

Volumn 2, Issue 2 SPEC. ISS., 2009, Pages 287-294

  Fernández, Matilde ^a   Duque, Estrella ^b   Pizarro Tobías, Paloma ^a   Van Dillewijn, Pieter ^b   Wittich, Rolf Michael ^b   Ramos, Juan L ^b  

^a Bio Iliberis Research and Development   (Spain)

^b CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

1 AMINO 1,3 CYCLOPENTANEDICARBOXYLIC ACID; AROMATIC NITRO COMPOUND; DNA; ENZYME; GLUCOSE; ISOQUINOLINE; NITROREDUCTASE; OXIDOREDUCTASE; PNRA ENZYME; TRINITROTOLUENE; UNCLASSIFIED DRUG; XEND ENZYME; XENOBIOTIC AGENT;

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DETOXIFICATION; DNA MICROARRAY; DOWN REGULATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE INDUCTION; MEXE GENE; MEXEF GENE; MICROBIOLOGY; MUTANT; NONHUMAN; OPRN GENE; PSEUDOMONAS PUTIDA; REGULATORY MECHANISM; SCREENING; STRESS; TOXICITY; UPREGULATION;

BACTERIAL PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; PSEUDOMONAS PUTIDA; TRANSCRIPTION, GENETIC; TRINITROTOLUENE; XENOBIOTICS;

PSEUDOMONAS PUTIDA;

EID: 70350708933     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/j.1751-7915.2009.00085.x     Document Type: Article

References (53)

1. Bore, E., Langsrud, S., Langsrud, Ø., Rode, T.M., and Holck, A. (2007) Acid-shock responses in staphylococcus aureus investigated by global gene expression analysis. Microbiology 153: 289-303.
2. Bouskill, N.J., Barnhart, E.P., Galloway, T.S., Handy, R.D., and Ford, T.E. (2007) Quantification of changing Pseudomonas aeruginosa sodA, htpX and mt gene abundance in response to trace metal toxicity: a potential in situ biomarker of environmental health. FEMS Microbiol Ecol 60: 276-286.
3. Bryant, C., and DeLuca, M. (1991) Purification and characterization of an oxygen-insensitive NAD(P)H nitroreductase from Enterobacter cloacae. J Biol Chem 266: 4119-4125.
4. Caballero, A., Lázaro, J.J., Ramos, J.L., and Esteve-Nuñez, A. (2005) PnrA, a new nitroreductase-family enzyme in the TNT-degrading strain Pseudomonas putida JLR11. Environ Microbiol 7: 1211-1219.
5. Claus, H., Bausinger, T., Lehmler, I., Fels, G., Dehner, U., Preuss, J., and Köning, H. (2007) Transformation of 2,4,6- trinitrotoluene (TNT) by Raoultella terrigena. Biodegradation 18: 27-35.
6. Duque, E., Molina-Henares, A.J., de la Torre, J., Molina- Henares, M.A., del Castillo, T., Lam, J., and Ramos, J.L. (2007a) Towards a genome-wide mutant library of Pseudomonas strain KT2440. In Pseudomonas: A Model System in Biology. Vol.V. Ramos, J.L., and Filloux, A. (eds). Dorchester, the Netherlands: Springer, pp: 227-251.
7. Duque, E., Rodríguez-Herva, J.J., de la Torre, J., Domínguez-Cuevas, P., Muñoz-Rojas, J., and Ramos, J.L. (2007b) The RpoT regulon of Pseudomonas putida DOTT1E and its role in stress endurance against solvents. J Bacteriol 189: 207-219.
8. van Dillewijn, P., Wittich, R.M., Caballero, A., and Ramos, J.L. (2008a) Subfunctionalization of hydride transferases of the Old Yellow Enzyme family of flavoproteins of Pseudomonas putida. Appl Environ Microbiol 74: 6703-6708.
9. van Dillewijn, P., Wittich, R.M., Caballero, A., and Ramos, J.L. (2008b) Type II hydride transferases from different microorganisms yield nitrite and diarylamines from polynitroaromatic compounds. Appl Environ Microbiol 74: 6820-6823.
10. Esteve-Núñez, A., Caballero, A., and Ramos, J.L. (2001) Biological degradation of 2,4,6-trinitrotoluene. Microb Mo Biol Rev 65: 335-352.
11. Fitzpatrick, T.B., Amrhein, N., and Macheroux, P. (2003) Characterization of YqjM, an old yellow enzyme homolog from Bacillus subtilis involved in the oxidative stress response. J Biol Chem 278: 19891-19897.
12. Fortin, P.D., Horsman, G.P., Yang, H.M., and Eltis, L.D. (2006) A glutathione S-transferase catalyzes the dehalogenation of inhibitory metabolites of polychlorinated biphenyls. J Bacteriol 188: 4424-4430.
13. Fraga-Muller, J., Stevens, A.M., Craig, J., and Love, N.G. (2007) Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress. Appl Environ Microbiol 73: 4550-4558.
14. Garmendia, J., de las Heras, A., Calcagno Galvão, T., and de Lorenzo, V. (2008) Tracing explosives in soil with transcriptional regulators of Pseudomonas putida evolved for responding to nitrotoluenes. Microb Biotechnol 1: 236-246.
15. George, I., Eyers, L., Stenuit, B., and Aghatos, S.N. (2008) Effect of 2,4,6-trinitrotoluene on soil bacterial communities. J Ind Microbiol Biotechnol 35: 225-236.
16. González-Pérez, M.M., van Dillewijn, P., Wittich, R.M., and Ramos, J.L. (2007) Escherichia coli has multiple enzymes that attack TNT and release nitrogen for growth. Environ Microbiol 9: 1535-1540.
17. Goodwin, A., Kersulyte, D., Sisson, G., Veldhuyzen van Zanten, S.J., Berg, D.E., Haynes, C.A., et al. (2002) Structures of nitroreductase in three states: effects of inhibitor binding and reduction. J Biol Chem 277: 11513-11520.
18. Ho, E.M., Chang, H.W., Kim, S.I., Kahng, H.Y., and Oh, K.H. (2004) Analysis of TNT (2,4,6-trinitrotoluene) inducible cellular responses and stress shock proteome in Stenotrophomonas sp. O.K-5. Curr Microbiol 49: 346-352.
19. Jiménez, J.I., Miñambres, B., García, J.L., and Díaz, E. (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4: 824-841.
20. Kiefer, P.M., Jr. and Copley, S.D. (2002) Characterization of the initial steps in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry 41: 1315-1322.
21. Kornitzer, D., Teff, D., Altuvia, S., and Oppenheim, A.B. (1991) Isolation, characterization, and sequence of an Escherichia coli heat shock gene, htpX. J Bacteriol 173: 2944-2953.
22. Kutty, R., and Bennett, G.N. (2005) Biochemical characterization of nitrotoluene transforming oxygen-insensitive nitroreductases from Clostridium acetobutylicum ATCC 824. Arch Microbiol 184: 158-167.
23. Köhler, T., Michéa-Hamzehpour, M., Henze, U., Gotoh, N., Curty, L.K., and Pechère, J.C. (1997) Characterization of MexE-MexF-OprN, a positively regulated multidrug efflux system of Pseudomonas aeruginosa. Mol Microbiol 23: 345-354.
24. Lewis, A.T., Newcombe, D.A., and Crawford, R.L. (2004) Bioremediation of soils contaminated with explosives. J Environ Manage 70: 291-307.
25. Li, X.Z., Zhang, L., and Poole, K. (1998) Role of the multidrug efflux systems of Pseudomonas aeruginosa in organic solvent tolerance. J Bacteriol 180: 2987-2991.
26. Liu, G., Zhou, J., Lv, H., Xiang, X., Wang, J., Zhou, M., and Qv, Y. (2007) Azoreductase from Rhodobacter sphaeroides AS1.1737 is a flavodoxin that also functions as nitroreductase and flavin mononucleotide reductase. Appl Microbiol Biotechnol 76: 1271-1279.
27. Marsch-Moreno, R., Hernández-Guzmán, G., and Alvarez- Morales, A. (1998) pTn5cat: a Tn5-derived genetic element to facilitate insertion mutagenesis, promoter probing, physical mapping, cloning, and marker exchange in phytopathogenic and other gram-negative bacteria. Plasmid 39: 205-214.
28. Maseda, H., Kitao, M., Eda, S., Yoshihara, E., and Nakae, T. (2002) A novel assembly process of the multicomponent xenobiotic efflux pump in Pseudomonas aeruginosa. Mol Microbiol 43: 677-686.
29. Miura, K., Tomioka, Y., Suzuki, H., Yonezawa, M., Hishinuma, T., and Mizugaki, M. (1997) Molecular cloning of the nemA gene encoding N-ethylmaleimide reductase from Escherichia coli. Biol Pharm Bull 20: 110-112.
30. Molina, L., Ramos, C., Duque, E., Ronchel, M.C., Garcia, J.M., Wyke, L., and Ramos, J.L. (2000) Survival of Pseudomonas putida KT2440 in soil and in the rhizosphere of plants under greenhouse and environmental conditions. Soil Biol Biochem 32: 315-321.
31. Nelson, K.E., Weinel, C., Paulsen, I.T., Dodson, R.J., Hilbert, H. Martins dos Santos, V.A., et al. (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Env Microbiol 4: 799-808.
32. Nokhbeh, M.R., Boroumandi, S., Pokorny, N., Koziarz, P., Paterson, E.S., and Lambert, I.B. (2002) Identification and characterization of SnrA, an inducible oxygen-insensitive nitroreductase in Salmonella enterica serovar Typhimurium TA1535. Mutant Res 508: 59-70.
33. Pak, J.W., Knoke, K.L., Noguera, D.R., Fox, B.G., and Chambliss, G.H. (2000) Transformation of 2,4,6-trinitrotoluene by purified xenobiotic reductase B from Pseudomonas fluorescens I-C. Appl Environ Microbiol 66: 4742-4750.
34. Park, H.S., and Kim, H.S. (2000) Identification and characterization of the nitrobenzene catabolic plasmid pNB1 and pNB2 in Pseuomonas putida HS12. J Bacteriol 182: 573-580.
35. Patel, N., Cardoza, V., Christensen, E., Rekapalli, B., Ayalew, M., and Stewart, C.N., Jr (2004) Differential gene expression of Chlamydomonas reinhardtii in response to 2,4,6- trinitrotoluene (TNT) using microarray analysis. Plant Sci 167: 1109-1122.
36. Reid, A.N., Pandey, R., Palyada, K., Naikare, H., and Stintzi, A. (2008) Identification of Campylobacter jejuni genes involved in the response to acidic pH and stomach transit. Appl Environ Microbiol 74: 1583-1597.
37. Reva, O.N., Weinel, C., Weinel, M., Böhm, K., Stjepandic, D., Hoheisel, J.D., and Tümmler, B. (2006) Functional genomics of stress response in Pseudomonas putida KT2440. J Bacteriol 188: 4079-4092.
38. Riefler, R.G., and Smets, B.F. (2002) NAD(P)H:flavin mononucleotide oxidoreductase inactivation during 2,4,6- trinitrotoluene reduction. Appl Environ Microbiol 68: 1690-1696.
39. Roca, A. Rodríguez-Herva, J.J., Duque, E., and Ramos, J.L. (2008) Physiological responses of Pseudomonas putida to formaldehyde during detoxification. Microbial Biotechnol 1: 158-169.
40. Rui, L., Kwon, Y.M., Reardon, K.F., and Wood, T.K. (2004) Metabolic pathway engineering to enhance aerobic degradation of chlorinated ethenes and to reduce their toxicity by cloning a novel glutathione S-transferase, an evolved toluene o-monooxygease, and γ-glutamylcysteine synthetase. Environ Microbiol 4: 491-500.
41. Sakoh, M., Ito, K., and Akiyama, Y. (2005) Proteolytic activity of HtpX, a membrane-bound and stress-controlled protease from Escherichia coli. J Biol Chem 280: 33305-33310.
42. Segura, A., Godoy, P., van Dillewijn, P., Hurtado, A., Arroyo, N., Santacruz, S., and Ramos, J.L. (2005) Proteomic analysis reveals the participation of energy- and stress-related proteins in the response of Pseudomonas putida DOT-T1E to toluene. J Bacteriol 187: 5937-5945.
43. Siddiqui, A.A., Jalah, R., and Sharma, Y.D. (2007) Expression and purification of HtpX-like small heat shock integral membrane protease of an unknown organism related to Methylobacillus flagellatus. J Biochem Biophys Methods 70: 539-546.
44. Smets, B.F., Yin, H., and Esteve-Nuñez, A. (2007) TNT biotransformation: when chemistry confronts mineralization. Appl Microbiol Biotechnol 76: 267-277.
45. Timmis, K.N. (2002) Pseudomonas putida: a cosmopolitan opportunist par excellence. Environ Microbiol 4: 779-781.
46. Vuilleumier, S., and Pagni, M. (2002) The elusive roles of bacterial glutathione S-transferases: new lessons from genomes. Appl Microbiol Biotechnol 58: 138-146.
47. Williams, R.E., Rathbone, D.A., Scrutton, N.S., and Bruce, N.C. (2004) Biotransformation of explosives by the Old Yellow Enzyme family of flavoproteins. Appl Environ Microbiol 7: 3566-3574.
48. Williams, R.E., and Bruce, N.C. (2002) 'New uses for an old enzyme' - the Old Yellow Enzyme family of flavoenzymes. Microbiology 148: 1607-1614.
49. Wittich, R.-M., Haïdour, A., van Dillewijn, P., and Ramos, J.L. (2008) OYE Flavoprotein reductases initiate the condensation of TNT-derived intemediates to secondary diarylamines and nitrite. Environ Sci Technol 42: 734-739.
50. Yuste, L., Hervás, A.B., Canosa, I., Tobes, R., Jiménez, J.I., Nogales, J., Pérez-Pérez, M.M., Santero, E., Diaz, E., Ramos, J.L., de Lorenzo, V., and Rojo, F. (2006) Growthphase dependent expression of Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray. Environ Microbiol 8: 165-177.
51. Zenno, S., Saigo, K., Kanoh, H., and Inouye, S. (1994) Identification of the gene encoding the major NAD(P)H-flavin oxidoreductase of the bioluminescent bacterium Vibrio fischeri ATCC 7744. J Bacteriol 176: 3536-3543.
52. Zenno, S., Koike, H., Tanokura, M., and Saigo, K. (1996a) Conversion of NfsB, a minor Escherichia coli nitroreductase, to a flavin reductase similar in biochemical properties to FRase I, the major flavin reductase in Vibrio fischeri, by a single amino acid substitution. J Bacteriol 178: 4731-4733.
53. Zenno, S., Koike, H., Kumar, A., Jayaraman, R., Tanokura, M., and Saigo, K. (1996b) Biochemical characterization of NfsA, the Escherichia coli major nitroreductase exhibiting a high amino acid sequence homology to Frp, a Vibrio harvey flavin oxidoreductase. J Bacteriol 178: 4508-4514.