Applied Microbiology and Biotechnology

, Volume 64, Issue 4, pp 515–524 | Cite as

Gene expression in Escherichia coli biofilms

  • D. Ren
  • L. A. Bedzyk
  • S. M. Thomas
  • R. W. Ye
  • T. K. WoodEmail author
Original Paper


DNA microarrays were used to study the gene expression profile of Escherichia coli JM109 and K12 biofilms. Both glass wool in shake flasks and mild steel 1010 plates in continuous reactors were used to create the biofilms. For the biofilms grown on glass wool, 22 genes were induced significantly (p≤0.05) compared to suspension cells, including several genes for the stress response (hslS, hslT, hha, and soxS), type I fimbriae (fimG), metabolism (metK), and 11 genes of unknown function (ybaJ, ychM, yefM, ygfA, b1060, b1112, b2377, b3022, b1373, b1601, and b0836). The DNA microarray results were corroborated with RNA dot blotting. For the biofilm grown on mild steel plates, the DNA microarray data showed that, at a specific growth rate of 0.05/h, the mature biofilm after 5 days in the continuous reactors did not exhibit differential gene expression compared to suspension cells although genes were induced at 0.03/h. The present study suggests that biofilm gene expression is strongly associated with environmental conditions and that stress genes are involved in E. coli JM109 biofilm formation.


Glass Wool Continuous Reactor rpoS Mutant Grow Suspension Cell Ribosome Modulation Factor 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Adams JL, McLean RJC (1999) Impact of rpoS deletion on Escherichia coli biofilms. Appl Environ Microbiol 65:4285–4287PubMedGoogle Scholar
  2. Bassler BL (1999) How bacteria talk to each other: regulation of gene expression by quorum sensing. Curr Opin Microbiol 2:582–587CrossRefPubMedGoogle Scholar
  3. Davies DG, Parsek MR, Pearson JP, Iglewski BH, Costerton JW, Greenberg EP (1998) The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science 280:295–298PubMedGoogle Scholar
  4. DeLisa MP, Wu C-F, Wang L, Valdes JJ, Bentley WE (2001) DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli. J Bacteriol 183:5239–5247PubMedGoogle Scholar
  5. Elvers KT, Lappin-Scott HM (2000) Biofilms and biofouling. Academic Press, San DiegoGoogle Scholar
  6. Fawcett P, Eichenberger P, Losick R, Youngman P (2000) The transcriptional profile of early to middle sporulation in Bacillus subtilis. Proc Natl Acad Sci USA 97:8063–8068CrossRefPubMedGoogle Scholar
  7. Ghigo J-M (2001) Natural conjugative plasmids induce bacterial biofilm development. Nature 412:442–445CrossRefGoogle Scholar
  8. Hamon MA, Lazazzera BA (2001) The sporulation transcription factor Spo0A is required for biofilm development in Bacillus subtilis. Mol Microbiol 42:1199–1209CrossRefPubMedGoogle Scholar
  9. Helmann JD, Wu MFW, Kobel PA, Gamo F-J, Wilson M, Morshedi MM, Navre M, Paddon C (2001) Global transcriptional response of Bacillus subtilis to heat shock. J Bacteriol 183:7318–7328CrossRefPubMedGoogle Scholar
  10. Heydorn A, Ersboll B, Kato J, Hentzer M, Parsek MR, Tolker-Nielsen T, Givskov M, Molin S (2002) Statistical analysis of Pseudomonas aeruginosa biofilm development: impact of mutations in genes involved in twitching motility, cell-to-cell signaling, and stationary-phase sigma factor expression. Appl Environ Microbiol 68:2008–2017Google Scholar
  11. Hoffman JA, Badger JL, Zhang Y, Kim KS (2001) Escherichia coli K1 purA and sorC are preferentially expressed upon association with human brain microvascular endothelial cells. Microb Pathog 31:69–79CrossRefPubMedGoogle Scholar
  12. Ishihama A (1997) Adaptation of gene expression in stationary phase bacteria. Curr Opin Genet Dev 7:582–588CrossRefPubMedGoogle Scholar
  13. Jackson DW, Suzuki K, Oadford L, Simecka JW, Hart ME, Romeo T (2002) Biofilm formation and dispersal under the influence of the global regulator CsrA of Escherichia coli. J Bacteriol 184:290–301CrossRefPubMedGoogle Scholar
  14. Jayaraman A, Earthman JC, Wood TK (1997) Corrosion inhibition by aerobic biofilms on SAE1018 steel. Appl Microbiol Biotechnol 47:62–68CrossRefGoogle Scholar
  15. Kievit TRD, Gillis R, Marx S, Brown C, Iglewski BH (2001) Quorum-sensing genes in Pseudomonas aeruginosa biofilms: their role and expression patterns. Appl Environ Microbiol 67:1865–1873CrossRefPubMedGoogle Scholar
  16. Kitagawa M, Matsumura Y, Tsuchido T (2000) Small heat shock proteins, IbpA and IbpB, are involved in heat and superoxide stresses in Escherichia coli. FEMS Microbiol Lett 184:165–171CrossRefPubMedGoogle Scholar
  17. Kjaergaard K, Schembri MA, Ramos C, Molin S, Klemm P (2000) Antigen 43 facilitates formation of multispecies biofilm. Environ Microbiol 2:695–702CrossRefPubMedGoogle Scholar
  18. Kolter R, Losick R (1998) One for all and all for one. Science 280:226–227CrossRefPubMedGoogle Scholar
  19. Kuchma SL, O’Toole GA (2000). Surface-induced and biofilm-induced changes in gene expression. Curr Opin Biotechnol 11:429–433CrossRefPubMedGoogle Scholar
  20. Lagares A, Hozbor DF, Niehaus K, Otero AJLP, Lorenzen J, Arnold W, Puhler A (2001) Genetic characterization of a Sinorhizobium meliloti chromosomal region involved in lipopolysaccharide biosynthesis. J Bacteriol 183:1248–1258CrossRefPubMedGoogle Scholar
  21. Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J (1999) Molecular cell biology. Freeman, New YorkGoogle Scholar
  22. Loewen PC, Hu B, Strutinsky J, Sparling R (1998) Regulation in the rpoS regulon of Escherichia coli. Can J Microbiol 44:707–717CrossRefPubMedGoogle Scholar
  23. Michán C, Manchado M, Peuyo C (2002) SoxRS down-regulation of rob transcription. J Bacteriol 184:4733–4738CrossRefPubMedGoogle Scholar
  24. Moat AG, Foster JW (1995) Microbial physiology. Wiley-Liss, New YorkGoogle Scholar
  25. Mourino M, Madrid C, Balsalobre C, Prenafeta A, Munoa F, Blanco J, Blanco M, Blanco JE, Juarez A (1996) The Hha protein as a modulator of expression of virulence factors in Escherichia coli. Infect Immun 64:2881–2884PubMedGoogle Scholar
  26. Nickel JC, Ruseska I, Wright JB, Costerton JW (1985) Tobramycin resistance of Pseudomonas aeruginosa cells growing as a biofilm on urinary catheter material. Antimicrob Agents Chemother 27:619–624PubMedGoogle Scholar
  27. Oosthuizen MC, Steyn B, Lindsay D, Brözel VS, von Holy A (2001) Novel method for the proteomic investigation of a dairy-associated Bacillus cereus biofilm. FEMS Microbiol Lett 194:47–51CrossRefPubMedGoogle Scholar
  28. Oosthuizen MC, Steyn B, Theron J, Cosette P, Lindsay D, von Holy A, Brözel VS (2002) Proteomic analysis reveals differential protein expression by Bacillus cereus during biofilm formation. Appl Environ Microbiol 68:2770–2780CrossRefPubMedGoogle Scholar
  29. Örnek D, Jayaraman A, Syrett BC, Hsu CH, Mansfeld F, Wood TK (2002) Pitting corrosion inhibition of aluminum 2024 by Bacillus biofilms secreting polyaspartate or γ-polyglutamate. Appl Microbiol Biotechnol 58:651–657CrossRefPubMedGoogle Scholar
  30. O’Toole GA, Kolter R (1998) Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol Microbiol 30:295–304CrossRefPubMedGoogle Scholar
  31. Potera C (1999) Forging a link between biofilms and disease. Science 19:1837–1838CrossRefGoogle Scholar
  32. Pratt LA, Kolter R (1998) Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili. Mol Microbiol 30:285–293PubMedGoogle Scholar
  33. Prigent-Combaret C, Vidal O, Dorel C, Lejeune P (1999) Abiotic surface sensing and biofilm-dependent regulation of gene expression in Escherichia coli. J Bacteriol 181:5993–6002PubMedGoogle Scholar
  34. Purevdorj B, Costerton JW, Stoodley P (2002) Influence of hydrodynamics and cell signaling on the structure and behavior of Pseudomonas aeruginosa biofilms. Appl Environ Microbiol 68:4457–4464CrossRefPubMedGoogle Scholar
  35. Reisner A, Haagensen JAJ, Schembri MA, Zechner EL, Molin S (2003) Development and maturation of Escherichia coli K-12 biofilms. Mol Microbiol 48:933–946CrossRefPubMedGoogle Scholar
  36. Ren D, Bedzyk LA Setlow P, Thomas SM, Ye RW, Wood TK (2004) Gene expression in Bacillus subtilis surface. Biofilms with and without sporulation and the importance of yveR for biofilm maintenance. Biotechnol Bioeng (in press)Google Scholar
  37. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning, a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.Google Scholar
  38. Sauer K, Camper AK (2001) Characterization of phenotypic changes in Pseudomonas putida in response to surface-associated growth. J Bacteriol 183:6579–6589CrossRefPubMedGoogle Scholar
  39. Schembri MA, Kjaergaard K, Klemm P (2003) Global gene expression in Escherichia coli biofilms. Mol Microbiol 48:253–267PubMedGoogle Scholar
  40. Sperandio V, Torres AG, Giron JA, Kaper JB (2001) Quorum sensing is a global regulatory mechanism in enterohemorrhagic Escherichia coli O157:H7. J Bacteriol 183:5187–5197PubMedGoogle Scholar
  41. Stanley NR, Britton RA, Grossman AD, Lazazzera BA (2003) Identification of catabolite repression as a physiological regulator of biofilm formation by Bacillus subtilis by use of DNA microarrays. J Bacteriol 185:1951–1957CrossRefPubMedGoogle Scholar
  42. Steyn B, Oosthuizen MC, MacDonald R, Theron J, Brözel VS (2001) The use of glass wool as an attachment surface for studying phenotypic changes in Pseudomonas aeruginosa biofilms by two-dimensional gel electrophoresis. Proteomics 1:871–879CrossRefPubMedGoogle Scholar
  43. Wada A, Yamazaki Y, Fujita N, Ishihama A (1990) Structure and probable genetic location of a “ribosome modulation factor” associated with 100S ribosomes in stationary-phase. Proc Natl Acad Sci USA 87:2657–2661PubMedGoogle Scholar
  44. Wei Y, Lee J-M, Richmond C, Blattner FR, Rafalski JA, Larossa RA (2001) High-density microarray-mediated gene expression profiling of Escherichia coli. J Bacteriol 183:545–556PubMedGoogle Scholar
  45. Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teltzel GM, Lory S, Greenberg EP (2001) Gene expression in Pseudomonas aeruginosa biofilms. Nature 413:860–864CrossRefPubMedGoogle Scholar
  46. Wilson M, DeRisi J, Kristensen H-H, Imboden P, Rane S, Brown PO, Schoolnik GK (1999) Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Proc Natl Acad Sci USA 96:12833–12838PubMedGoogle Scholar
  47. Yanisch-Perron C, Viera J, Messing J (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103–119PubMedGoogle Scholar
  48. Ye RW, Tao W, Bedzyk L, Young T, Chen M, Li L (2000) Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions. J Bacteriol 182:4458–4465CrossRefPubMedGoogle Scholar
  49. Zheng M, Wang X, Templeton LJ, Smulski DR, LaRossa RA, Storz G (2001) DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J Bacteriol 183:4562–4570PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • D. Ren
    • 1
    • 3
  • L. A. Bedzyk
    • 2
  • S. M. Thomas
    • 2
  • R. W. Ye
    • 2
  • T. K. Wood
    • 1
    Email author
  1. 1.Departments of Chemical Engineering and Molecular and Cell BiologyUniversity of ConnecticutStorrsUSA
  2. 2.Experimental Station E328/B33DuPont Central Research and DevelopmentWilmingtonUSA
  3. 3.Chemical and Biomolecular EngineeringCornell UniversityIthacaUSA

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