Dual fluorescence system for flow cytometric analysis of Escherichia coli transcriptional response in multi-species context

Journal of Microbiological Methods

Volumn 76, Issue 2, 2009, Pages 109-119

  Miao, Huang ^a   Ratnasingam, Shalini ^a   Pu, Chui San ^a   Desai, Malan Manish ^a   Sze, Chun Chau ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

Bacterial interaction; Flow cytometry; Interspecies interaction; Multi species systems; Transcriptional response

Indexed keywords

ARABINOSE; ARABINOSE B; GREEN FLUORESCENT PROTEIN; RED FLUORESCENT PROTEIN; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; DUAL FLUORESCENCE SYSTEM; ENTEROCOCCUS FAECALIS; ESCHERICHIA COLI; FLOW CYTOMETRY; FLUORESCENCE; FLUORESCENCE ACTIVATED CELL SORTING; GENETIC HETEROGENEITY; KLEBSIELLA PNEUMONIAE; MICROMORPHOLOGY; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; SPECIES COMPARISON; TRANSCRIPTOMICS;

BACTERIOLOGICAL TECHNIQUES; COENZYME A LIGASES; ENTEROCOCCUS FAECALIS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FLOW CYTOMETRY; GENE EXPRESSION REGULATION, BACTERIAL; GENES, REPORTER; GENETIC HETEROGENEITY; GREEN FLUORESCENT PROTEINS; KLEBSIELLA PNEUMONIAE; LUMINESCENT AGENTS; LUMINESCENT PROTEINS; PROMOTER REGIONS, GENETIC; RECOMBINANT FUSION PROTEINS; SIGMA FACTOR; SPECIES SPECIFICITY; TRANSCRIPTIONAL ACTIVATION;

BACTERIA (MICROORGANISMS); ENTEROCOCCUS FAECALIS; ESCHERICHIA COLI; KLEBSIELLA PNEUMONIAE;

EID: 58349101277     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2008.09.015     Document Type: Article

References (52)

1. Al-Bakri A.G., Gilbert P., and Allison D.G. Immigration and emigration of Burkholderia cepacia and Pseudomonas aeruginosa between and within mixed biofilm communities. J. Appl. Microbiol. 96 (2004) 455-463
2. An D., and Parsek M.R. The promise and peril of transcriptional profiling in biofilm communities. Curr. Opin. Microbiol. 10 (2007) 292-296
3. Andersen J.B., Sternberg C., Poulsen L.K., Bjorn S.P., Givskov M., and Molin S. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol. 64 (1998) 2240-2246
4. Bartilson M., Marra A., Christine J., Asundi J.S., Schneider W.P., and Hromockyj A.E. Differential fluorescence induction reveals Streptococcus pneumoniae loci regulated by competence stimulatory peptide. Mol. Microbiol. 39 (2001) 126-135
5. Bi E., and Lutkenhaus J. Cell division inhibitors SulA and MinCD prevent formation of the FtsZ ring. J. Bacteriol. 175 (1993) 1118-1125
6. Casamayor E.O., Ferrera I., Cristina X., Borrego C.M., and Gasol J.M. Flow cytometric identification and enumeration of photosynthetic sulfur bacteria and potential for ecophysiological studies at the single-cell level. Environ. Microbiol. 9 (2007) 1969-1985
7. Castanie-Cornet M.P., and Foster J.W. Escherichia coli acid resistance: cAMP receptor protein and a 20 bp cis-acting sequence control pH and stationary phase expression of the gadA and gadBC glutamate decarboxylase genes. Microbiology. 147 (2001) 709-715
8. Christensen B.B., Haagensen J.A., Heydorn A., and Molin S. Metabolic commensalism and competition in a two-species microbial consortium. Appl. Environ. Microbiol. 68 (2002) 2495-2502
9. Cormack B.P., Valdivia R.H., and Falkow S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene. 173 (1996) 33-38
10. da Silva T.L., Reis A., Kent C.A., Roseiro J.C., and Hewitt C.J. The use of multi-parameter flow cytometry to study the impact of limiting substrate, agitation intensity, and dilution rate on cell aggregation during Bacillus licheniformis CCMI 1034 aerobic continuous culture fermentations. Biotechnol Bioeng. 92 (2005) 568-578
11. Darwin A.J. The phage-shock-protein response. Mol. Microbiol. 57 (2005) 621-628
12. Davey H.M., and Kell D.B. Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses. Microbiol. Rev. 60 (1996) 641-696
13. Dojka M.A., Hugenholtz P., Haack S.K., and Pace N.R. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64 (1998) 3869-3877
14. Donlan R.M. Biofilms: microbial life on surfaces. Emerg Infect Dis. 8 (2002) 881-890
15. Duan K., Dammel C., Stein J., Rabin H., and Surette M.G. Modulation of Pseudomonas aeruginosa gene expression by host microflora through interspecies communication. Mol. Microbiol. 50 (2003) 1477-1491
16. Dubnau D., and Losick R. Bistability in bacteria. Mol. Microbiol. 61 (2006) 564-572
17. Farewell A., Diez A.A., DiRusso C.C., and Nyström T. Role of the Escherichia coli FadR regulator in stasis survival and growth phase-dependent expression of the uspA, fad, and fab genes. J. Bacteriol. 178 (1996) 6443-6450
18. Fux C.A., Costerton J.W., Stewart P.S., and Stoodley P. Survival strategies of infectious biofilms. Trends Microbiol. 13 (2005) 34-40
19. Gay P., Le Coq D., Steinmetz M., Berkelman T., and Kado C.I. Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J. Bacteriol. 164 (1985) 918-921
20. Glascock C.B., and Weickert M.J. Using chromosomal lacIQ1 to control expression of genes on high-copy-number plasmids in Escherichia coli. Gene. 223 (1998) 221-231
21. Gunther S., Geyer W., Harms H., and Muller S. Fluorogenic surrogate substrates for toluene-degrading bacteria-are they useful for activity analysis?. J Microbiol Methods. 70 (2007) 272-283
22. Haagensen J.A., Klausen M., Ernst R.K., Miller S.I., Folkesson A., Tolker-Nielsen T., et al. Differentiation and distribution of colistin- and sodium dodecyl sulfate-tolerant cells in Pseudomonas aeruginosa biofilms. J. Bacteriol. 189 (2007) 28-37
23. Hansen S.K., Haagensen J.A., Gjermansen M., Jorgensen T.M., Tolker-Nielsen T., and Molin S. Characterization of a Pseudomonas putida rough variant evolved in a mixed-species biofilm with Acinetobacter sp. strain C6. J. Bacteriol. 189 (2007) 4932-4943
24. Hansen S.K., Rainey P.B., Haagensen J.A., and Molin S. Evolution of species interactions in a biofilm community. Nature. 445 (2007) 533-536
25. Kuramitsu H.K., He X., Lux R., Anderson M.H., and Shi W. Interspecies interactions within oral microbial communities. Microbiol. Mol. Biol. Rev. 71 (2007) 653-670
26. Lee J., Jayaraman A., and Wood T.K. Indole is an inter-species biofilm signal mediated by SdiA. BMC Microbiol. 7 (2007) 42
27. Little J.W., and Mount D.W. The SOS regulatory system of Escherichia coli. Cell. 29 (1982) 11-22
28. Lopilato J.E., Garwin J.L., Emr S.D., Silhavy T.J., and Beckwith J.R. d-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport. J. Bacteriol. 158 (1984) 665-673
29. Marra A., Asundi J., Bartilson M., Lawson S., Fang F., Christine J., et al. Differential fluorescence induction analysis of Streptococcus pneumoniae identifies genes involved in pathogenesis. Infect. Immun. 70 (2002) 1422-1433
30. Milton D.L., O'Toole R., Horstedt P., and Wolf-Watz H. Flagellin A is essential for the virulence of Vibrio anguillarum. J. Bacteriol. 178 (1996) 1310-1319
31. Moller S., Sternberg C., Andersen J.B., Christensen B.B., Ramos J.L., Givskov M., et al. In situ gene expression in mixed-culture biofilms: evidence of metabolic interactions between community members. Appl. Environ. Microbiol. 64 (1998) 721-732
32. Moskovitz J., Rahman M.A., Strassman J., Yancey S.O., Kushner S.R., Brot N., et al. Escherichia coli peptide methionine sulfoxide reductase gene: regulation of expression and role in protecting against oxidative damage. J. Bacteriol. 177 (1995) 502-507
33. Ottesen E.A., Hong J.W., Quake S.R., and Leadbetter J.R. Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science 314 (2006) 1464-1467
34. Pawar S., and Schulz H. The structure of the multienzyme complex of fatty acid oxidation from Escherichia coli. J. Biol. Chem. 256 (1981) 3894-3899
35. Rani S.A., Pitts B., Beyenal H., Veluchamy R.A., Lewandowski Z., Davison W.M., et al. Spatial patterns of DNA replication, protein synthesis, and oxygen concentration within bacterial biofilms reveal diverse physiological states. J. Bacteriol. 189 (2007) 4223-4233
36. Rault A., Beal C., Ghorbal S., Ogier J.C., and Bouix M. Multiparametric flow cytometry allows rapid assessment and comparison of lactic acid bacteria viability after freezing and during frozen storage. Cryobiology. 55 (2007) 35-43
37. Regnier P., and Arraiano C.M. Degradation of mRNA in bacteria: emergence of ubiquitous features. Bioessays. 22 (2000) 235-244
38. Riedel K., Hentzer M., Geisenberger O., Huber B., Steidle A., Wu H., et al. N-acylhomoserine-lactone-mediated communication between Pseudomonas aeruginosa and Burkholderia cepacia in mixed biofilms. Microbiology. 147 (2001) 3249-3262
39. Rosenberg E.Y., Bertenthal D., Nilles M.L., Bertrand K.P., and Nikaido H. Bile salts and fatty acids induce the expression of Escherichia coli AcrAB multidrug efflux pump through their interaction with Rob regulatory protein. Mol. Microbiol. 48 (2003) 1609-1619
40. Rouviere P.E., De Las Penas A., Mecsas J., Lu C.Z., Rudd K.E., and Gross C.A. rpoE, the gene encoding the second heat-shock sigma factor, sigma E, in Escherichia coli. EMBO J. 14 (1995) 1032-1042
41. Ruiz-Perez F., Sheikh J., Davis S., Boedeker E.C., and Nataro J.P. Use of a continuous-flow anaerobic culture to characterize enteric virulence gene expression. Infect. Immun. 72 (2004) 3793-3802
42. Saijo-Hamano Y., Uchida N., Namba K., and Oosawa K. In vitro characterization of FlgB, FlgC, FlgF, FlgG, and FliE, flagellar basal body proteins of Salmonella. J. Mol. Biol. 339 (2004) 423-435
43. Sambrook J., and Russell D.W. Molecular Cloning: A Laboratory Manual (2001), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
44. Shah D., Zhang Z., Khodursky A., Kaldalu N., Kurg K., and Lewis K. Persisters: a distinct physiological state of E. coli. BMC Microbiol. 6 (2006) 53
45. Siemering K.R., Golbik R., Sever R., and Haseloff J. Mutations that suppress the thermosensitivity of green fluorescent protein. Curr Biol. 6 (1996) 1653-1663
46. Temmerman R., Vervaeren H., Noseda B., Boon N., and Verstraete W. Necrotrophic growth of Legionella pneumophila. Appl. Environ. Microbiol. 72 (2006) 4323-4328
47. Truant A.L. Manual of Commercial Methods in Clinical Microbiology (2002), ASM Press, Washington, DC
48. Valdivia R.H., and Falkow S. Flow cytometry and bacterial pathogenesis. Curr. Opin. Microbiol. 1 (1998) 359-363
49. Veening J.W., Smits W.K., Hamoen L.W., and Kuipers O.P. Single cell analysis of gene expression patterns of competence development and initiation of sporulation in Bacillus subtilis grown on chemically defined media. J Appl Microbiol. 101 (2006) 531-541
50. Willey J.M., Sherwood L.M., and Woolverton C.J. Biogeochemical cycling and introductory microbial ecology. In: Willey J.M., Sherwood L.M., and Woolverton C.J. (Eds). Prescott, Harley, and Klein's microbiology (2008), The McGraw-Hill Companies, Inc, New York, NY 643-666
51. Wilmes P., and Bond P.L. Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol. 14 (2006) 92-97
52. Xavier K.B., and Bassler B.L. Interference with AI-2-mediated bacterial cell-cell communication. Nature. 437 (2005) 750-753