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Volume 153, Issue 5

Differential gene expression profiling of cultured under biofilm and planktonic conditions Free

Abstract

often adopts a sessile biofilm lifestyle that differs greatly from that of free-living cells. Biofilm formation represents a protected mode of growth that allows cells to survive in hostile environments. In this study, comparative transcriptome analysis was carried out to identify genes that are differentially expressed in biofilm of compared with free-living cells. DNA-microarray analyses indicated that about 12 % of genes showed significant differential expression: 139 were activated and 104 were repressed in biofilm vs the planktonic environment. The differential expression of 20 selected genes was confirmed by real-time RT-PCR. In addition, regulation of expression of these genes during biofilm development was tested in 100 and 400 μm deep biofilms. Direct comparison of optical images consistently demonstrated that changes in biofilm thickness are accompanied by significant shifts in cell viability. From evaluation of gene expression patterns, it was shown that the majority of the genes tested were significantly down-regulated in 400 vs 100 μm deep biofilms. This study provides a genome-scale synopsis and adds important insights into gene expression in biofilm development processes of , which are strongly associated with the pathogenesis of dental diseases.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): BHI, brain heart infusion , CDFF, constant-depth film fermenter , CLSM, confocal laser scanning microscope , PTFE, polytetrafluoroethylene and TIGR, The Institute for Genomic Research
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2007-05-01
2024-04-19
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References

  1. Ajdic D., McShan W. M., McLaughlin R. E., Savic G., Chang J., Carson M. B., Primeaux C., Tian R., Kenton S. other authors 2002; Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen. Proc Natl Acad Sci U S A 99:14434–14439 [CrossRef]
     [Google Scholar]
  2. Biswas S., Biswas I. 2006; Regulation of the glucosyltransferase ( gtfBC ) operon by CovR in Streptococcus mutans. J Bacteriol 188:988–998 [CrossRef]
     [Google Scholar]
  3. Bowden G. H., Hamilton I. R. 1998; Survival of oral bacteria. Crit Rev Oral Biol Med 9:54–85 [CrossRef]
     [Google Scholar]
  4. Bowden G. H., Li Y. H. 1997; Nutritional influences on biofilm development. Adv Dent Res 11:81–99 [CrossRef]
     [Google Scholar]
  5. Browngardt C. M., Wen Z. T., Burne R. A. 2004; RegM is required for optimal fructosyltransferase and glucosyltransferase gene expression in Streptococcus mutans. FEMS Microbiol Lett 240:75–79 [CrossRef]
     [Google Scholar]
  6. Burne R. A., Chen Y. Y., Wexler D. L., Kuramitsu H., Bowen W. H. 1996; Cariogenicity of Streptococcus mutans strains with defects in fructan metabolism assessed in a program-fed specific-pathogen-free rat model. J Dent Res 75:1572–1577 [CrossRef]
     [Google Scholar]
  7. Burne R. A., Chen Y. Y., Penders J. E. 1997; Analysis of gene expression in Streptococcus mutans in biofilms in vitro. Adv Dent Res 11:100–109 [CrossRef]
     [Google Scholar]
  8. Bustin S. A. 2000; Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25:169–193 [CrossRef]
     [Google Scholar]
  9. Davidson A. L., Chen J. 2004; ATP-binding cassette transporters in bacteria. Annu Rev Biochem 73:241–268 [CrossRef]
     [Google Scholar]
  10. Gilmore K. S., Srinivas P., Akins D. R., Hatter K. L., Gilmore M. S. 2003; Growth, development, and gene expression in a persistent Streptococcus gordonii biofilm. Infect Immun 71:4759–4766 [CrossRef]
     [Google Scholar]
  11. Graham M. R., Smoot L. M., Migliaccio C. A., Virtaneva K., Sturdevant D. E., Porcella S. F., Federle M. J., Adams G. J., Scott J. R., Musser J. M. 2002; Virulence control in group A Streptococcus by a two-component gene regulatory system: global expression profiling and in vivo infection modeling. Proc Natl Acad Sci U S A 99:13855–13860 [CrossRef]
     [Google Scholar]
  12. Hall-Stoodley L., Costerton J. W., Stoodley P. 2004; Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol 2:95–108 [CrossRef]
     [Google Scholar]
  13. Hamilton I. R. 2000; Ecological basis for dental caries. In Oral Bacterial Ecology: the Molecular Basis pp 219–264 Edited by Kuramitsu H. K., Ellen R. P. Wymondham, UK: Horizon Scientific Press;
     [Google Scholar]
  14. Henke J. M., Bassler B. L. 2004; Three parallel quorum-sensing systems regulate gene expression in Vibrio harveyi. J Bacteriol 186:6902–6914 [CrossRef]
     [Google Scholar]
  15. Kolenbrander P. E. 2000; Oral microbial communities: biofilms, interactions, and genetic systems. Annu Rev Microbiol 54:413–437 [CrossRef]
     [Google Scholar]
  16. Liljemark W. F., Bloomquist C. 1996; Human oral microbial ecology and dental caries and periodontal diseases. Crit Rev Oral Biol Med 7:180–198 [CrossRef]
     [Google Scholar]
  17. Lonnstedt I., Speed T. 2002; Replicated microarray data. Statistica Sinica 12:31–46
     [Google Scholar]
  18. Marsh P. D. 2003; Are dental diseases examples of ecological catastrophes?. Microbiology 149:279–294 [CrossRef]
     [Google Scholar]
  19. Marsh P. D. 2005; Dental plaque: biological significance of a biofilm and community life-style. J Clin Periodontol 32 (Suppl. 6:7–15 [CrossRef]
     [Google Scholar]
  20. Merritt J., Kreth J., Shi W., Qi F. 2005; LuxS controls bacteriocin production in Streptococcus mutans through a novel regulatory component. Mol Microbiol 57:960–969 [CrossRef]
     [Google Scholar]
  21. Munson M. A., Banerjee A., Watson T. F., Wade W. G. 2004; Molecular analysis of the microflora associated with dental caries. J Clin Microbiol 42:3023–3029 [CrossRef]
     [Google Scholar]
  22. O'Toole G., Kaplan H. B., Kolter R. 2000; Biofilm formation as microbial development. Annu Rev Microbiol 54:49–79 [CrossRef]
     [Google Scholar]
  23. Pratten J., Wilson M. 1999; Antimicrobial susceptibility and composition of microcosm dental plaques supplemented with sucrose. Antimicrob Agents Chemother 43:1595–1599
     [Google Scholar]
  24. Quivey R. G., Jr., Kuhnert W. L., Hahn K. 2000; Adaptation of oral streptococci to low pH. Adv Microb Physiol 42:239–274
     [Google Scholar]
  25. Reiner A., Yekutieli D., Benjamini Y. 2003; Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19:368–375 [CrossRef]
     [Google Scholar]
  26. Rozen R., Bachrach G., Bronshteyn M., Gedalia I., Steinberg D. 2001; The role of fructans on dental biofilm formation by Streptococcus sobrinus , Streptococcus mutans , Streptococcus gordonii and Actinomyces viscosus. FEMS Microbiol Lett 195:205–210 [CrossRef]
     [Google Scholar]
  27. Senadheera M. D., Guggenheim B., Spatafora G. A., Huang Y. C., Choi J., Hung D. C., Treglown J. S., Goodman S. D., Ellen R. P., Cvitkovitch D. G. 2005; A VicRK signal transduction system in Streptococcus mutans affects gtfBCD , gbpB , and ftf expression, biofilm formation, and genetic competence development. J Bacteriol 187:4064–4076 [CrossRef]
     [Google Scholar]
  28. Shemesh M., Steinberg D. 2006; Surface plasmon resonance for real-time evaluation of immobilized fructosyltransferase activity. J Microbiol Methods 64:411–415 [CrossRef]
     [Google Scholar]
  29. Shemesh M., Tam A., Feldman M., Steinberg D. 2006; Differential expression profiles of Streptococcus mutans ftf , gtf and vicR genes in the presence of dietary carbohydrates at early and late exponential growth phases. Carbohydr Res 341:2090–2097 [CrossRef]
     [Google Scholar]
  30. Smyth G. K. 2004; Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article 3
     [Google Scholar]
  31. Smyth G. K., Speed T. 2003; Normalization of cDNA microarray data. Methods 31:265–273 [CrossRef]
     [Google Scholar]
  32. Smyth G. K., Michaud J., Scott H. S. 2005; Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21:2067–2075 [CrossRef]
     [Google Scholar]
  33. Steinberg D. 2000; Studying plaque biofilms on various dental surfaces. In Handbook of Bacterial Adhesion: Principles, Methods, and Applications pp 353–370 Edited by An Y. H., Friedman R. J. Totowa, NJ: Humana Press;
     [Google Scholar]
  34. Stewart P. S., Costerton J. W. 2001; Antibiotic resistance of bacteria in biofilms. Lancet 358:135–138 [CrossRef]
     [Google Scholar]
  35. Stock A. M., Robinson V. L., Goudreau P. N. 2000; Two-component signal transduction. Annu Rev Biochem 69:183–215 [CrossRef]
     [Google Scholar]
  36. Tam A., Shemesh M., Wormser U., Sintov A., Steinberg D. 2006; Effect of different iodine formulations on the expression and activity of Streptococcus mutans glucosyltransferase and fructosyltransferase in biofilm and planktonic environments. J Antimicrob Chemother 57:865–871 [CrossRef]
     [Google Scholar]
  37. Wen Z. T., Burne R. A. 2002; Functional genomics approach to identifying genes required for biofilm development by Streptococcus mutans. Appl Environ Microbiol 68:1196–1203 [CrossRef]
     [Google Scholar]
  38. Wen Z. T., Baker H. V., Burne R. A. 2006; Influence of BrpA on critical virulence attributes of Streptococcus mutans. J Bacteriol 188:2983–2992 [CrossRef]
     [Google Scholar]
  39. Whiteley M., Bangera M. G., Bumgarner R. E., Parsek M. R., Teitzel G. M., Lory S., Greenberg E. P. 2001; Gene expression in Pseudomonas aeruginosa biofilms. Nature 413:860–864 [CrossRef]
     [Google Scholar]
  40. Wilson M. 2001; Bacterial biofilms and human disease. Sci Prog 84:235–254 [CrossRef]
     [Google Scholar]
  41. Yoshida A., Kuramitsu H. K. 2002; Multiple Streptococcus mutans genes are involved in biofilm formation. Appl Environ Microbiol 68:6283–6291 [CrossRef]
     [Google Scholar]
  42. Zhang Y., Lei Y., Khammanivong A., Herzberg M. C. 2004; Identification of a novel two-component system in Streptococcus gordonii V288 involved in biofilm formation. Infect Immun 72:3489–3494 [CrossRef]
     [Google Scholar]
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Differential gene expression profiling of Streptococcus mutans cultured under biofilm and planktonic conditions
Microbiology 153, 1307 (2007); https://doi.org/10.1099/mic.0.2006/002030-0
/content/journal/micro/10.1099/mic.0.2006/002030-0
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