Fluorogenic surrogate substrates for toluene-degrading bacteria-Are they useful for activity analysis?

Journal of Microbiological Methods

Volumn 70, Issue 2, 2007, Pages 272-283

  Günther, Susanne ^a   Geyer, Wolfgang ^b   Harms, Hauke ^a   Müller, Susann ^a  

^a HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

^b Department of Analytical Chemistry ^*  (Germany)

Author keywords

Bacterial activity; Flow cytometry; Fluorescent products; Population dynamics; Toluene degradation

Indexed keywords

3 HYDROXYPHENYLACETYLENE; CINNAMONITRILE; FORMALDEHYDE; INDOLE; PHENYLACETYLENE; TOLUENE; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ARTICLE; BACTERIAL GROWTH; BACTERIUM CULTURE; CELL CYCLE; CHROMOSOME NUMBER; CONTROLLED STUDY; FLOW CYTOMETRY; FLUORESCENCE; FLUORESCENCE MICROSCOPY; FLUORESCENCE SPECTROSCOPY; MICROBIAL DEGRADATION; NONHUMAN; PRIORITY JOURNAL; STAINING;

ACETYLENE; BACTERIA; FLOW CYTOMETRY; FLUORESCENT DYES; INDOLES; MICROSCOPY, FLUORESCENCE; NITRILES; SPECTROMETRY, FLUORESCENCE; STAINING AND LABELING; TOLUENE;

BACTERIA (MICROORGANISMS);

EID: 34547575506     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2007.04.016     Document Type: Article

References (48)

1. Achilles J., Harms H., and Müller S. Analysis of living S. cerevisiae cell states-a three color approach. Cytometry, Part A 69A (2006) 173-177
2. Albertini M.C., Accorsi A., Teodore L., Pierfelici L., Uguccioni F., Rocchi M.B.L., Burattini S., and Citterio B. Use of multiparametric analysis for Vibrio alginolyticus viable but nonculturable state determination. Cytometry, Part A 69A (2006) 260-265
3. Arenghi F.L.G., Pinti M., Galli E., and Barbieri P. Identification of the Pseudomonas stutzeri OX1 toluene/o-xylene monooxygenase regulatory gene (touR) and of its cognate promoter. Appl. Environ. Microbiol. 65 (1999) 4057-4063
4. Billinton N., and Knight A.W. Seeing the wood through the trees: a review of techniques for distinguishing Green Fluorescent Protein from endogenous autofluorescence. Anal. Biochem. 291 (2001) 175-197
5. Bondza-Kibangou P., Millot C., Dufer J., and Millot J.M. Modifications of cellular autofluorescence emission spectra under oxidative stress induced by 1α,25dihydroxyvitamin D3 and its analog EB1089. Technol. Cancer Res. Treat. 3 (2004) 383-391
6. Bouzakri K., Zachrisson A., Al-Khalili L., Zhang B.B., Koistinen H.A., Krook A., and Zierath J.R. siRNA based gene silencing reveals specialized roles of IRS-1/Akt2 and IRS-2/Akt1 in glucose and lipid metabolism in human skeletal muscle. Cell. Metab. 4 (2006) 89-96
7. Cafaro V., Izzo V., Scognamiglio R., Notomista E., Capasso P., Casbarra A., Pucci P., and Di Donato A. Phenol hydroxylase and toluene/o-xylene monooxygenase from Pseudomonas stutzeri OX1: interplay between two enzymes. Appl. Environ. Microbiol. 70 (2004) 2211-2219
8. Chan S.M., Olson J.A., and Utz P.J. Single-cell analysis of siRNA-mediated gene silencing using multiparameter flow cytometry. Cytometry, Part A 69A (2006) 59-65
9. Chance B., Schoener B., Oshino R., Itshak F., and Nakase Y. Oxidation-reduction ratio studies of mitochondria in freeze-trapped samples. NADH and flavoprotein fluorescence signals. J. Biol. Chem. 254 (1979) 1764-4771
10. Choi E.N., Cho M.C., Kim Y., Kim C.-K., and Lee K. Expansion of growth substrate range in Pseudomonas putida F1 by mutations in both cymR and todS, which recruit a ring-fission hydrolase CmtE and induce the tod catabolic operon, respectively. Microbiology 149 (2003) 795-805
11. Choi H.S., Kim J.K., Cho E.H., Kim Y.C., Kim J.I., and Kim S.W. A novel flavin-containing monooxygenase from Methylophaga sp. strain SK1 and its indigo synthesis in Escherichia coli. Biochem. Biophys. Res. Commun. 306 (2003) 93093-93096
12. Clingenpeel S.R., Keener W.K., Keller C.R., de Jesus K., Howard M.H., and Watwood M.E. Activity-dependent fluorescent labeling of bacterial cells expressing the TOL pathway. J. Microbiol. Methods 60 (2005) 41-46
13. Couzin J. RNAi shows cracks in its armor. Science 306 (2004) 1124-1125
14. Dinkla I.J.T., Gabor E.M., and Janssen D.B. Effects of iron limitation on the degradation of toluene by Pseudomonas strains carrying the TOL (pWWO) plasmid. Appl. Environ. Microbiol. 67 (2001) 3406-3412
15. Dirks R.W., Molenaar C., and Tanke H.J. Methods for visualizing RNA processing and transport pathways in living cells. Histochem. Cell Biol. 115 (2001) 3-11
16. Fishman A., Tao Y., and Wood T.K. Toluene 3-monooxygenase of Ralstonia pickettii PKO1 is a para-hydroxylating enzyme. J. Bacteriol. 186 (2004) 3117-3123
17. Ho H.Y., Cheng M.L., Wang Y.H., and Chiu D.T.Y. Flow cytometry for assessment of the efficacy of siRNA. Cytometry, Part A 69A (2006) 1054-1061
18. Jacobson M.R., Cao L.G., Wang Y.L., and Pederson T. Dynamic localization of RNase MRP RNA in the nucleolus observed by fluorescent RNA cytochemistry in living cells. J. Cell Biol. 131 (1995) 1649-1658
19. Kauffman M.E., Keener W.K., Clingenpeel S.R., Watwood M.E., Reed D.W., Fujita Y., and Lehman R.M. Use of 3-hydroxyphenylacetylene for activity-dependent, fluorescent labeling of bacteria that degrade toluene via 3-methylcatechol. J. Microbiol. Methods 55 (2003) 801-805
20. Keener W.K., Watwood M.E., and Apel W.A. Activity-dependent Fluorescent labeling of bacteria that degrade toluene via toluene 2,3-dioxygenase. Appl. Microbiol. Biotechnol. 49 (1998) 455-462
21. Keener W.K., Watwood M.E., Schaller K.D., Walton M.R., Partin J.K., Smith W.A., and Clingenpeel S.R. Use of selective inhibitors and chromogenic substrates to differentiate bacteria based on toluene oxygenase activity. J. Microbiol. Methods 46 (2001) 171-185
22. Kleinsteuber S., Riis V., Fetzer I., Harms H., and Müller S. Population dynamics of a microbial consortium during growth on diesel fuel in saline environments. Appl. Environ. Microbiol. 72 (2006) 3531-3542
23. Knemeyer J.P., Herten D.P., and Sauer M. Detection and identification of single molecules in living cells using spectrally resolved fluorescence lifetime imaging microscopy. Anal. Chem. 75 (2003) 2147-2153
24. Lakowicz, J.R., 1999. Principles of fluorescence spectroscopy, 2nd ed. In: Kluwer Academic/Plenum Publishers, New York, pp. 35, 698.
25. Lange C.C., and Wackett L.P. Oxidation of aliphatic olefins by toluene dioxygenase: enzyme rates and product identification. J. Bacteriol. 179 (1997) 3858-3865
26. Masami Y., Daniel G., and Denis M. Monitoring the uptake of protein-derived peptides by Porphyromonas gingivalis with fluorophore-labeled substrates. Curr. Microbiol. 47 (2003) 1-4
27. Meistrich M.L., Göhde W., and White R.A. Resolution of x and y spermatids by pulse cytophotometry. Nature 274 (1978) 821-823
28. Moreno-Ruiz E., Hernaez M.J., Martinez-Perez O., and Santero E. Identification and functional characterization of Sphingomonas macrogolitabida strain TFA genes involved in the first two steps of the tetralin catabolic pathway. J. Bacteriol. 185 (2003) 2026-2030
29. Müller S., and Babel W. Analysis of multiplication activity-an approach for controlling biotechnological processes. J. Microbiol. Methods 55 (2003) 851-858
30. Muthian S., Nithipatikom K., Campbell W.B., and Hillard C.J. Synthesis and characterization of a fluorescent substrate for the N-arachidonoylethanolamine (anandamide) transmembrane carrier. J. Pharmacol. Exp. Ther. 293 (2000) 289-295
31. Parales R.E., Ditty J.L., and Harwood C.S. Toluene-degrading bacteria are chemotactic towards the environmental pollutants benzene, toluene, and trichloroethylene. Appl. Environ. Microbiol. 66 (2000) 4098-4104
32. Pernthaler J., and Amann R. Fate of heterotrophic microbes in pelagic habitats: focus on populations. Microbiol. Mol. Biol. Rev. 69 (2005) 440-461
33. Phoenix P., Keane A., Patel A., Bergeron H., Ghoshal S., and Lau P.C.K. Characterization of a new solvent-responsive gene locus in Pseudomonas putida F1 and its functionalization as a versatile biosensor. Environ. Microbiol. 5 (2003) 1309-1327
34. Pouchert, C.J., 1985. The Aldrich library of FT-IR spectra. In: Aldrich Chemical Company Inc., Milwaukee WI, pp. 653, 946, 493.
35. Reardon K.F., Mosteller D.C., and Bull Rogers J.D. Biodegradation kinetics of benzene, toluene, and phenol as single and mixed substrates for Pseudomonas putida F1. Biotechnol. Bioeng. 69 (2000) 385-400
36. Rojas A., Duque E., Mosqueda G., Golden G., Hurtado A., Ramos J.L., and Segura A. Three efflux pumps are required to provide efficient tolerance to toluene in Pseudomonas putida DOT-T1E. J. Bacteriol. 183 (2001) 3967-3973
37. Shapiro H.M. Practical Flow Cytometry. 4th ed. (2002), WILEY-LISS, New York, NY 376-377
38. Shav-Tal Y. The living test-tube: imaging of real-time gene expression. Soft Matter. 2 (2006) 361-370
39. Shi L., Günther S., Hübschmann T., Wick L.Y., Harms H., and Müller S. Limits of propidium iodide (PI) as a cell viability indicator for environmental bacteria. Cytometry, Part A 71A/7 (2007) (on-line)
40. Sun A.K., and Wood T.K. Trichloroethylene degradation and mineralization by pseudomonads and Methylosinus trichosporium OB3b. Appl. Microbiol. Biotechnol. 45 (1996) 248-256
41. van Herwijnen R., Springael D., Slot P., Govers H.A.J., and Parsons J.R. Degradation of anthracene by Mycobacterium sp. strain LB501T proceeds via a novel pathway, through o-phthalic acid. Appl. Environ. Microbiol. 69 (2003) 186-190
42. Vercellone-Smith P., and Herson D.S. Toluene elicits a carbon starvation response in Pseudomonas putida mt-2 containing the TOL plasmid pWW0. Appl. Environ. Microbiol. 63 (1997) 1925-1932
43. Vogt C., Lösche A., Kleinsteuber S., and Müller S. Population profiles of a stable, commensalistic bacterial culture grown with toluene under sulphate-reducing conditions. Cytometry, Part A 66A (2005) 91-102
44. Wiacek C., Müller S., and Benndorf D. A cytomic approach reveals population heterogeneity of Cupriavidus necator in response to harmful phenol concentrations. Proteomics 6 (2006) 5983-5994
45. Wick L.Y., Colangelo T., and Harms H. Kinetics of mass transfer-limited bacterial growth on solid PAHs. Environ. Sci. Technol. 35 (2001) 354-361
46. Woo H., Sanseverino J., Cox C.D., Robinson K.G., and Sayler G.S. The measurement of toluene dioxygenase in biofilm culture of Pseudomonas putida F1. J. Microbiol. Methods 40 (2000) 181-191
47. Yanagihara K., Tashiro M., Fukuda Y., Ohno H., Higashiyama Y., Miyazaki Y., Hirakata Y., Tomono K., Mizuta Y., Tsukamoto K., and Kohno S. Effects of short interfering RNA against methicillin-resistant Staphylococcus aureus coagulase in vitro and in vivo. J. Antimicrob. Chemother. 57 (2006) 122-126
48. Zylstra G.J., and Gibson D.T. Toluene degradation by Pseudomonas putida F1: nucleotide sequence of the todC1C2BADE genes and their expression in E. coli. J. Biol. Chem. 264 (1989) 14940-14946