Lessons from DNA microarray analysis: The gene expression profile of biofilms

Current Opinion in Microbiology

Volumn 8, Issue 2, 2005, Pages 222-227

  Lazazzera, Beth A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME PROTEIN; TRANSCRIPTION FACTOR;

BIOFILM; DNA MICROARRAY; FLAGELLUM; GENE EXPRESSION PROFILING; GENE REPRESSION; NONHUMAN; PLANKTON; PROTEIN ANALYSIS; REGULATORY MECHANISM; REVIEW;

EID: 15744396567     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2005.02.015     Document Type: Review

References (34)

1. L. Hall-Stoodley, J.W. Costerton, and P. Stoodley Bacterial biofilms: from the natural environment to infectious diseases Nat Rev Microbiol 2 2004 95 108
2. M.E. Davey, and G.A. O'Toole Microbial biofilms: from ecology to molecular genetics Microbiol Mol Biol Rev 64 2000 847 867
3. C.A. Fux, J.W. Costerton, P.S. Stewart, and P. Stoodley Survival strategies of infectious biofilms Trends Microbiol 13 2005 34 40
4. J.W. Costerton, P.S. Stewart, and E.P. Greenberg Bacterial biofilms: a common cause of persistent infections Science 284 1999 1318 1322
5. D. Davies Understanding biofilm resistance to antibacterial agents Nat Rev Drug Discov 2 2003 114 122
6. P.S. Stewart Mechanisms of antibiotic resistance in bacterial biofilms Int J Med Microbiol 292 2002 107 113
7. G.A. O'Toole, L.A. Pratt, P.I. Watnick, D.K. Newman, V.B. Weaver, and R. Kolter Genetic approaches to study of biofilms Methods Enzymol 310 1999 91 109
8. D.G. Davies, M.R. Parsek, J.P. Pearson, B.H. Iglewski, J.W. Costerton, and E.P. Greenberg The involvement of cell-to-cell signals in the development of a bacterial biofilm Science 280 1998 295 298
9. L.A. Pratt, and R. Kolter Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili Mol Microbiol 30 1998 285 293
10. G.A. O'Toole, and R. Kolter Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development Mol Microbiol 30 1998 295 304
11. C. Heilmann, C. Gerke, F. Perdreau-Remington, and F. Götz Characterization of Tn917 insertion mutants of Staphylococcus epidermidis affected in biofilm formation Infect Immun 64 1996 277 282
12. G. O'Toole, H.B. Kaplan, and R. Kolter Biofilm formation as microbial development Annu Rev Microbiol 54 2000 49 79
13. P. Stoodley, K. Sauer, D.G. Davies, and J.W. Costerton Biofilms as complex differentiated communities Annu Rev Microbiol 56 2002 187 209
14. H. Tao, C. Bausch, C. Richmond, F.R. Blattner, and T. Conway Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media J Bacteriol 181 1999 6425 6440
15. C.S. Richmond, J.D. Glasner, R. Mau, H. Jin, and F.R. Blattner Genome-wide expression profiling in Escherichia coli K-12 Nucleic Acids Res 27 1999 3821 3835
16. C. Beloin, J. Valle, P. Latour-Lambert, P. Faure, M. Kzreminski, D. Balestrino, J.A. Haagensen, S. Molin, G. Prensier, and B. Arbeille Global impact of mature biofilm lifestyle on Escherichia coli K-12 gene expression Mol Microbiol 51 2004 659 674 This study demonstrates that many biofilm-required genes are not specific to biofilms, but are also expressed in stationary phase, planktonic cells.
17. M.A. Schembri, K. Kjaergaard, and P. Klemm Global gene expression in Escherichia coli biofilms Mol Microbiol 48 2003 253 267 This DNA microarray study revealed that many genes controlled by the stationary phase, transcription factor RpoS were hyper-expressed in biofilms as compared to exponential phase, planktonic cells and were under-expressed as compared to stationary phase, planktonic cells. These data suggest that the average physiology of these biofilm cells is somewhere between exponential and stationary phase.
18. K.E. Beenken, P.M. Dunman, F. McAleese, D. Macapagal, E. Murphy, S.J. Projan, J.S. Blevins, and M.S. Smeltzer Global gene expression in Staphylococcus aureus biofilms J Bacteriol 186 2004 4665 4684 The transcription factor SarA of Staphylococcus aureus is required for biofilm formation, but this study demonstrates how the involvement of this transcription factor could be missed by DNA microarray analysis. While genes controlled by SarA are differentially expressed in biofilms, they do not show a consistent pattern of expression.
19. A.A. de Souza, M.A. Takita, H.D. Coletta-Filho, C. Caldana, G.M. Yanai, N.H. Muto, R.C. de Oliveira, L.R. Nunes, and M.A. Machado Gene expression profile of the plant pathogen Xylella fastidiosa during biofilm formation in vitro FEMS Microbiol Lett 237 2004 341 353
20. M.A. Pysz, S.B. Conners, C.I. Montero, K.R. Shockley, M.R. Johnson, D.E. Ward, and R.M. Kelly Transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium Thermotoga maritima Appl Environ Microbiol 70 2004 6098 6112
21. S. Garcia-Sanchez, S. Aubert, I. Iraqui, G. Janbon, J.M. Ghigo, and C. d'Enfert Candida albicans biofilms: a developmental state associated with specific and stable gene expression patterns Eukaryot Cell 3 2004 536 545 This study is particularly noteworthy for having compared biofilms grown under five different conditions to planktonic cells grown under four different conditions.
22. D. Ren, L.A. Bedzyk, P. Setlow, S.M. Thomas, R.W. Ye, and T.K. Wood Gene expression in Bacillus subtilis surface biofilms with and without sporulation and the importance of yveR for biofilm maintenance Biotechnol Bioeng 86 2004 344 364
23. D. Ren, L.A. Bedzyk, S.M. Thomas, R.W. Ye, and T.K. Wood Gene expression in Escherichia coli biofilms Appl Microbiol Biotechnol 64 2004 515 524
24. M. Whiteley, M.G. Bangera, R.E. Bumgarner, M.R. Parsek, G.M. Teitzel, S. Lory, and E.P. Greenberg Gene expression in Pseudomonas aeruginosa biofilms Nature 413 2001 860 864
25. N.R. Stanley, R.A. Britton, A.D. Grossman, and B.A. Lazazzera Identification of catabolite repression as a physiological regulator of biofilm formation by Bacillus subtilis by use of DNA microarrays J Bacteriol 185 2003 1951 1957 This is the only DNA microarray study to analyze more than one time point during the formation of a biofilm. This study compares the genes differentially expressed in biofilms to genes differentially expressed in other DNA microarray studies of genes controlled by transcription factors.
26. E. Werner, F. Roe, A. Bugnicourt, M.J. Franklin, A. Heydorn, S. Molin, B. Pitts, and P.S. Stewart Stratified growth in Pseudomonas aeruginosa biofilms Appl Environ Microbiol 70 2004 6188 6196 This study beautifully demonstrates the heterogeneous nature of biofilm cells, a property that complicates DNA microarray studies that average gene expression across the population.
27. C. Sternberg, B.B. Christensen, T. Johansen, A. Toftgaard Nielsen, J.B. Andersen, M. Givskov, and S. Molin Distribution of bacterial growth activity in flow-chamber biofilms Appl Environ Microbiol 65 1999 4108 4117
28. T. Yu, C. de la Rosa, and R. Lu Microsensor measurement of oxygen concentration in biofilms: from one dimension to three dimensions Water Sci Technol 49 2004 353 358
29. C. Prigent-Combaret, O. Vidal, C. Dorel, and P. Lejeune Abiotic surface sensing and biofilm-dependent regulation of gene expression in Escherichia coli J Bacteriol 181 1999 5993 6002
30. J.M. Ghigo Are there biofilm-specific physiological pathways beyond a reasonable doubt? Res Microbiol 154 2003 1 8
31. J. Errington Regulation of endospore formation in Bacillus subtilis Nat Rev Microbiol 1 2003 117 126
32. R. Milo, S. Itzkovitz, N. Kashtan, R. Levitt, S. Shen-Orr, I. Ayzenshtat, M. Sheffer, and U. Alon Superfamilies of evolved and designed networks Science 303 2004 1538 1542
33. P.J. Piggot, and D.W. Hilbert Sporulation of Bacillus subtilis Curr Opin Microbiol 7 2004 579 586
34. W.K. Huh, J.V. Falvo, L.C. Gerke, A.S. Carroll, R.W. Howson, J.S. Weissman, and E.K. O'Shea Global analysis of protein localization in budding yeast Nature 425 2003 686 691