1887

Microbiology Society logo

Volume 153, Issue 8

Temporal analysis of gene expression during biofilm development Free

Abstract

Microarrays were used to identify changes in gene expression associated with biofilm development. Two biofilm substrates (denture and catheter), and two strains for each substrate, were tested to remove model- and strain-dependent variability from the overall dataset. Three biofilm developmental phases were examined: early (6 h), intermediate (12 h), and mature (48 h). Planktonic specimens were collected at the same time points. Data analysis focused primarily on gene expression changes over the time-course of biofilm development. Glycolytic and non-glycolytic carbohydrate assimilation, amino acid metabolism, and intracellular transport mechanisms were important during the early phase of biofilm formation. These early events increase intracellular pools of pyruvate, pentoses and amino acids, which prepare the biofilm for the large biomass increase that begins around 12 h of development. This developmental stage demands energy and utilizes specific transporters for amino acids, sugars, ions, oligopeptides and lactate/pyruvate. At mature phase (48 h), few genes were differentially expressed compared with the 12 h time point, suggesting a relative lack of initiation of new metabolic activity. Data analysis to assess biofilm model-specific gene expression showed more dynamic changes in the denture model than in the catheter model. Data analysis to identify gene expression changes that are associated with each strain/substrate combination identified the same types of genes that were identified in the analysis of the entire dataset. Collectively, these data suggest that genes belonging to different, but interconnected, functional categories regulate the morphology and phenotype of biofilm.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): CT, crossing threshold , ECM, extracellular matrix and IMD, indwelling medical device
SGM
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2007/006163-0
2007-08-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/micro/153/8/2373.html?itemId=/content/journal/micro/10.1099/mic.0.2007/006163-0&mimeType=html&fmt=ahah

References

  1. Al-Fattani M. A., Douglas L. J. 2006; Biofilm matrix of Candida albicans and Candida tropicalis : chemical composition and role in drug resistance. J Med Microbiol 55:999–1008
     [Google Scholar]
  2. Andes D., Nett J., Oschel P., Albrecht R., Marchillo K., Pitula A. 2004; Development and characterization of an in vivo central venous catheter Candida albicans biofilm model. Infect Immun 72:6023–6031
     [Google Scholar]
  3. Baillie G. S., Douglas L. J. 1999; Candida biofilms and their susceptibility to antifungal agents. Methods Enzymol 310:644–656
     [Google Scholar]
  4. Braun B. R., van Het Hoog M., d'Enfert C., Martchenko M., Dungan J., Kuo A., Inglis D. O., Uhl M. A., Hogues H. other authors 2005; A human-curated annotation of the Candida albicans genome . PLoS Genet 1:
     [Google Scholar]
  5. Budtz-Jorgensen E. 1990a; Histopathology, immunology, and serology of oral yeast infections. Diagnosis of oral candidosis. Acta Odontol Scand 48:37–43
     [Google Scholar]
  6. Budtz-Jorgensen E. 1990b; Etiology, pathogenesis, therapy, and prophylaxis of oral yeast infections. Acta Odontol Scand 48:61–69
     [Google Scholar]
  7. Cao Y. Y., Cao Y. B., Xu Z., Ying K., Li Y., Xie Y., Zhu Z. Y., Chen W. S., Jiang Y. Y. 2005; cDNA microarray analysis of differential gene expression in Candida albicans biofilm exposed to farnesol. Antimicrob Agents Chemother 49:584–589
     [Google Scholar]
  8. Chandra J., Mukherjee P. K., Leidich S. D., Faddoul F. F., Hoyer L. L., Douglas L. J., Ghannoum M. A. 2001; Antifungal resistance of candidal biofilms formed on denture acrylic in vitro. J Dent Res 80:903–908
     [Google Scholar]
  9. Churchill G. A. 2002; Fundamentals of experimental design for cDNA microarrays. Nat Genet 32:Suppl490–495
     [Google Scholar]
  10. Collart M. A., Oliviero S. 1993; Preparation of yeast RNA. In Current Protocols in Molecular Biology vol 2 pp 13.12.1–13.12.5 Edited by Ausubel F. M. New York: Wiley;
     [Google Scholar]
  11. Costerton J. W., Cheng K. J., Geesey G. G., Ladd T. I., Nickel J. C., Dasgupta M., Marrie T. J. 1987; Bacterial biofilms in nature and disease. Annu Rev Microbiol 41:435–464
     [Google Scholar]
  12. Costerton J. W., Lewandowski Z., Caldwell D. E., Korber D. R., Lappin-Scott H. M. 1995; Microbial biofilms. Annu Rev Microbiol 49:711–745
     [Google Scholar]
  13. Donlan R. M. 2002; Biofilms: microbial life on surfaces. Emerg Infect Dis 8:881–890
     [Google Scholar]
  14. Donlan R. M., Costerton J. W. 2002; Biofilms: survival mechanisms of clinically relevant microorganisms. Clin Microbiol Rev 15:167–193
     [Google Scholar]
  15. Douglas L. J. 2003; Candida biofilms and their role in infection. Trends Microbiol 11:30–36
     [Google Scholar]
  16. Dudoit S., Yang Y. H., Callow M. J., Speed T. P. 2002; Statistical methods for identifying genes with differential expression in replicated cDNA microarray experiments. Stat Sinica 12:111–139
     [Google Scholar]
  17. Edmond M. B., Wallace S. E., McClish D. K., Pfaller M. A., Jones R. N., Wenzel R. P. 1999; Nosocomial bloodstream infections in United States hospitals: a three-year analysis. Clin Infect Dis 29:239–244
     [Google Scholar]
  18. Elledge S. J., Zhou Z., Allen J. B., Navas T. A. 1993; DNA damage and cell cycle regulation of ribonucleotide reductase. Bioessays 15:333–339
     [Google Scholar]
  19. Garcia-Sanchez S., Aubert S., Iraqui I., Janbon G., Ghigo J.-M., d'Enfert C. 2004; Candida albicans biofilms: a developmental state associated with specific and stable gene expression patterns. Eukaryot Cell 3:536–545
     [Google Scholar]
  20. Ghannoum M. A., O'Toole G. A. 2004 Microbial Biofilms Washington, DC: American Society for Microbiology Press;
  21. Ghannoum M. A., Rice L. B. 1999; Antifungal agents: mode of action, mechanisms of resistance, and correlation of these mechanisms with bacterial resistance. Clin Microbiol Rev 12:501–517
     [Google Scholar]
  22. Gillum A. M., Tsay E. Y. H., Kirsch D. R. 1984; Isolation of the Candida albicans genes for orotidine-5′-phosphate decarboxylase by complementation of S. cerevisiae ura3 and E. coli pyrF mutations. Mol Gen Genet 198:179–182
     [Google Scholar]
  23. Granger B. L., Flenniken M. L., Davis D. A., Mitchell A. P., Cutler J. E. 2005; Yeast wall protein 1 of Candida albicans . Microbiology 151:1631–1644
     [Google Scholar]
  24. Green C. B., Zhao X., Yeater K. M., Hoyer L. L. 2005; Construction and real-time RT-PCR validation of Candida albicans PALS-GFP reporter strains and their use in flow cytometry analysis of ALS gene expression in budding and filamenting cells. Microbiology 151:1051–1060
     [Google Scholar]
  25. Gudlaugsson O., Gillespie S., Lee K., Vande B. J., Hu J., Messer S., Herwaldt L., Pfaller M., Diekema D. 2003; Attributable mortality of nosocomial candidemia, revisited. Clin Infect Dis 37:1172–1177
     [Google Scholar]
  26. Hawser S. P., Douglas L. J. 1995; Resistance of Candida albicans biofilms to antifungal agents in vitro. Antimicrob Agents Chemother 39:2128–2131
     [Google Scholar]
  27. Jabra-Rizk M. A., Falkler W. A., Meiller T. F. 2004; Fungal biofilms and drug resistance. Emerg Infect Dis 10:14–19
     [Google Scholar]
  28. Jones T., Federspiel N. A., Chibana H., Dungan J., Kalman S., Magee B. B., Newport G., Thorstenson Y. R., Agabian N. other authors 2004; The diploid genome sequence of Candida albicans . Proc Natl Acad Sci U S A 101:7329–7334
     [Google Scholar]
  29. Kelly M. T., MacCallum D. M., Clancy S. D., Odds F. C., Brown A. J. P., Butler G. 2004; The Candida albicans CaACE2 gene affects morphogenesis, adherence and virulence. Mol Microbiol 53:969–983
     [Google Scholar]
  30. Kojic E. M., Darouiche R. O. 2004; Candida infections of medical devices. Clin Microbiol Rev 17:255–267
     [Google Scholar]
  31. Krueger K. E., Ghosh A. K., Krom B. P., Cihlar R. L. 2004; Deletion of the NOT4 gene impairs hyphal development and pathogenicity in Candida albicans . Microbiology 150:229–240
     [Google Scholar]
  32. Kuhn D. M., Chandra J., Mukherjee P. K., Ghannoum M. A. 2002; Comparison of biofilms formed by Candida albicans and Candida parapsilosis on bioprosthetic surfaces. Infect Immun 70:878–888
     [Google Scholar]
  33. Kumamoto C. A. 2005; A contact-activated kinase signals Candida albicans invasive growth and biofilm development. Proc Natl Acad Sci U S A 102:5576–5581
     [Google Scholar]
  34. Littell R. C., Milliken G. A., Stroup W. W., Wolfinger R. D. 1996 SAS System for Mixed Models Cary, NC: SAS Institute;
  35. Livak K. J., Schmittgen T. D. 2001; Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔ C T method. Methods 25:402–408
     [Google Scholar]
  36. MacEntee M. I. 1985; The prevalence of edentulism and diseases related to dentures – a literature review. J Oral Rehabil 12:195–207
     [Google Scholar]
  37. Mackenzie D. J., Mclean M. A., Mukerji S., Green M. 1997; Improved RNA extraction from woody plants for the detection of viral pathogens by reverse transcription–polymerase chain reaction. Plant Dis 81:222–226
     [Google Scholar]
  38. MANMADA 2002
  39. Mukherjee P. K., Chandra J. 2004; Candida biofilm resistance. Drug Resist Updat 7:301–309
     [Google Scholar]
  40. Mukherjee P. K., Chandra J., Kuhn D. M., Ghannoum M. A. 2003; Mechanism of fluconazole resistance in Candida albicans biofilms: phase-specific role of efflux pumps and membrane sterols. Infect Immun 71:4333–4340
     [Google Scholar]
  41. Mukherjee P. K., Mohamed S., Chandra J., Kuhn D., Liu S., Antar O. S., Munyon R., Mitchell A. P., Andes D. other authors 2006; Alcohol dehydrogenase restricts the ability of the pathogen Candida albicans to form a biofilm on catheter surfaces through an ethanol-based mechanism. Infect Immun 74:3804–3816
     [Google Scholar]
  42. Murillo L. A., Newport G., Lan C.-Y., Habelitz S., Dungan J., Agabian N. M. 2005; Genome-wide transcription profiling of the early phase of biofilm formation by Candida albicans . Eukaryot Cell 4:1562–1573
     [Google Scholar]
  43. Nailis H., Coeyne T., Van Nieuwerburgh F., Deforce D., Nelis H. J. 2006; Development and evaluation of different normalization strategies for gene expression studies in Candida albicans biofilms by real-time PCR. BMC Mol Biol 7:25
     [Google Scholar]
  44. Nobile C. J., Mitchell A. P. 2005; Regulation of cell-surface genes and biofilm formation by the C. albicans transcription factor Bcr1p. Curr Biol 15:1150–1155
     [Google Scholar]
  45. Nobile C. J., Andes D. R., Nett J. E., Smith F. J. Jr, Yue F., Phan Q.-T., Edwards J. E. Jr, Filler S. G., Mitchell A. P. 2006a; Critical role of Bcr1-dependent adhesins in C. albicans biofilm formation in vitro and in vivo. PLoS Pathog 2:e63
     [Google Scholar]
  46. Nobile C. J., Nett J. E., Andes D. R., Mitchell A. P. 2006b; Function of Candida albicans adhesin Hwp1 in biofilm formation. Eukaryot Cell 5:1604–1610
     [Google Scholar]
  47. O'Connor L., Lahiff S., Casey F., Glennon M., Cormican M., Maher M. 2005; Quantification of ALS1 gene expression in Candida albicans biofilms by RT-PCR using hybridization probes on the LightCycler. Mol Cell Probes 19:153–162
     [Google Scholar]
  48. Peltroche-Llacsahuanga H., Goyard S., d'Enfert C., Prill S. K.-H., Ernst J. F. 2006; Protein O-mannosylation isoforms regulate biofilm formation in Candida albicans . Antimicrob Agents Chemother 50:3488–3491
     [Google Scholar]
  49. Perez A., Pedros B., Murgui A., Casanova M., Lopez-Ribot J. L., Martinez J. P. 2006; Biofilm formation by Candida albicans mutants for genes coding fungal proteins exhibiting the eight-cysteine-containing CFEM domain. FEMS Yeast Res 6:1074–1084
     [Google Scholar]
  50. Ramage G., VandeWalle K., Lopez-Ribot J. L., Wickes B. L. 2002; The filamentation pathway controlled by the Efg1 regulator protein is required for normal biofilm formation and development in Candida albicans . FEMS Microbiol Lett 214:95–100
     [Google Scholar]
  51. Richard M. L., Nobile C. J., Bruno V. M., Mitchell A. P. 2005; Candida albicans biofilm-defection mutants. Eukaryot Cell 4:1493–1502
     [Google Scholar]
  52. Rupp M. E. 2005; Microbial biofilms. N Engl J Med 352:846
     [Google Scholar]
  53. SAS Institute 2000 SAS/STAT Software , Version 8 Cary, NC: SAS Institute;
     [Google Scholar]
  54. Schwank S., Rajacic Z., Zimmerli W., Blaser J. 1998; Impact of bacterial biofilm formation on in vitro and in vivo activities of antibiotics. Antimicrob Agents Chemother 42:895–898
     [Google Scholar]
  55. Stewart P. S., Mukherjee P. K., Ghannoum M. A. 2004; Biofilm antimicrobial resistance. In Microbial Biofilms pp 250–268 Edited by Ghannoum M. A., O'Toole G. A. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  56. Tanaka T. S., Jaradat S. A., Lim M. K., Kargul G. J., Wang X., Grahovac M. J., Pantano S., Sano Y., Piao Y. other authors 2000; Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA Microarray. Proc Natl Acad Sci U S A 97:9127–9132
     [Google Scholar]
  57. Wey S. B., Mori M., Pfaller M. A., Woolson R. F., Wenzel R. P. 1988; Hospital-acquired candidemia. The attributable mortality and excess length of stay. Arch Intern Med 148:2642–2645
     [Google Scholar]
  58. White T. C. 1997; Increased mRNA levels of ERG16, CDR , and MDR1 correlate with increases in azole resistance in Candida albicans isolates from a patient infected with human immunodeficiency virus. Antimicrob Agents Chemother 41:1482–1487
     [Google Scholar]
  59. Wilson M. 1996; Susceptibility of oral bacterial biofilms to antimicrobial agents. J Med Microbiol 44:79–87
     [Google Scholar]
  60. Wolfinger R. D., Gibson G., Wolfinger E. D., Bennett L., Hamadeh H., Bushel P., Afshari C., Paules R. S. 2001; Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8:625–637
     [Google Scholar]
  61. Zhao X., Oh S.-H., Cheng G., Green C. B., Nuessen J. A., Yeater K., Leng R. P., Brown A. J. P., Hoyer L. L. 2004; ALS3 and ALS8 represent a single locus that encodes a Candida albicans adhesin; functional comparisons between Als3p and Als1p. Microbiology 150:2415–2428
     [Google Scholar]
  62. Zhao X., Oh S.-H., Yeater K. M., Hoyer L. L. 2005; Analysis of the Candida albicans Als2p and Als4p adhesins suggests the potential for compensatory function within the Als family. Microbiology 151:1619–1630
     [Google Scholar]
  63. Zhao X., Daniels K. J., Oh S.-H., Green C. B., Yeater K. M., Soll D. R., Hoyer L. L. 2006; Candida albicans Als3p is required for wild-type biofilm formation on silicone elastomer surfaces. Microbiology 152:2287–2299
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2007/006163-0
Loading
Temporal analysis of Candida albicans gene expression during biofilm development
Microbiology 153, 2373 (2007); https://doi.org/10.1099/mic.0.2007/006163-0
/content/journal/micro/10.1099/mic.0.2007/006163-0
/content/journal/micro/10.1099/mic.0.2007/006163-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL

Supplementary material 2

EXCEL

Supplementary material 3

EXCEL

Supplementary material 4

EXCEL

Supplementary material 5

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error