Biofilm Matrix-Degrading Enzymes

  • Jeffrey B. KaplanEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1147)


Polymeric substances such as proteins, polysaccharides, and DNA constitute a major component of the biofilm matrix. Enzymes that depolymerize and degrade these components are useful tools for investigating the composition and function of the biofilm matrix. This chapter provides a brief overview of the most commonly used biofilm matrix-degrading enzymes and presents examples of their applications in biofilm research.

Key words

Biofilm Extracellular DNA Dispersin B DNase Matrix PNAG Proteinase K 



The author thanks Eun Sun Lee (New Jersey Dental School) for help with Fig. 3. This work was supported by NIH grant AI097182 and by American University.


  1. 1.
    Flemming H-C, Wingender J (2010) The biofilm matrix. Nat Rev Microbiol 8:623–633PubMedGoogle Scholar
  2. 2.
    Mah TF (2012) Biofilm-specific antibiotic resistance. Future Microbiol 7:1061–1072PubMedCrossRefGoogle Scholar
  3. 3.
    Hymes SR, Randis TM, Sun TY, Ratner AJ (2013) DNase inhibits Gardnerella vaginalis biofilms in vitro and in vivo. J Infect Dis 207:1491–1497PubMedCrossRefGoogle Scholar
  4. 4.
    Kaplan JB (2009) Therapeutic potential of biofilm-dispersing enzymes. Int J Artif Organs 32:545–554PubMedGoogle Scholar
  5. 5.
    Kaplan JB (2010) Biofilm dispersal: mechanisms, clinical implications and potential therapeutic uses. J Dent Res 89:205–218PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Xavier JB, Picioreanu C, Abdul Rani S et al (2005) Biofilm-control strategies based on enzymic disruption of the extracellular polymeric substance matrix—a modelling study. Microbiology 151:3817–3832PubMedCrossRefGoogle Scholar
  7. 7.
    Kaplan JB, LoVetri K, Cardona ST et al (2012) Recombinant human DNase I decreases biofilm and increases antimicrobial susceptibility in staphylococci. J Antibiot 65:73–77PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Izano EA, Wang H, Ragunath C et al (2007) Detachment and killing of Aggregatibacter actinomycetemcomitans biofilms by dispersin B and SDS. J Dent Res 86:618–622PubMedCrossRefGoogle Scholar
  9. 9.
    Lu TK, Collins JJ (2007) Dispersing biofilms with engineered enzymatic bacteriophage. Proc Natl Acad Sci U S A 104:11197–11202PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Venketaraman V, Lin AK, Lea A et al (2008) Both leukotoxin and poly-N-acetylglucosamine surface polysaccharide protect Aggregatibacter actinomycetemcomitans cells from macrophage killing. Microb Pathog 45:173–180PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    Dashiff A, Kadouri DE (2011) Predation of oral pathogens by Bdellovibrio bacteriovorus 109J. Mol Oral Microbiol 26:19–34PubMedCrossRefGoogle Scholar
  12. 12.
    Izano EA, Amarante MA, Kher WB, Kaplan JB (2008) Differential roles of poly-N-acetylglucosamine surface polysaccharide and extracellular DNA in Staphylococcus aureus and Staphylococcus epidermidis biofilms. Appl Environ Microbiol 74:470–476PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Kaplan JB, Velliyagounder K, Chandran R et al (2004) Genes involved in the synthesis and degradation of matrix polysaccharide in Actinobacillus actinomycetemcomitans and Actinobacillus pleuropneumoniae biofilms. J Bacteriol 186:8213–8220PubMedCentralPubMedCrossRefGoogle Scholar
  14. 14.
    Izano EA, Sadovskaya I, Wang H et al (2008) Poly-N-acetylglucosamine mediates biofilm formation and detergent resistance in Aggregatibacter actinomycetemcomitans. Microb Pathog 44:52–60PubMedCentralPubMedCrossRefGoogle Scholar
  15. 15.
    Chen WJ, Liao TH (2006) Structure and function of bovine pancreatic deoxyribonuclease I. Protein Pept Lett 13:447–453PubMedCrossRefGoogle Scholar
  16. 16.
    Nijland R, Hall MJ, Burgess JG (2010) Dispersal of biofilms by secreted, matrix degrading, bacterial DNase. PLoS One 12:e15668CrossRefGoogle Scholar
  17. 17.
    Eckhart L, Fischer H, Barken KB et al (2007) DNase1L2 suppresses biofilm formation by Pseudomonas aeruginosa and Staphylococcus aureus. Br J Dermatol 156:1342–1345PubMedCrossRefGoogle Scholar
  18. 18.
    Ramasubbu N, Thomas LM, Ragunath C, Kaplan JB (2005) Structural analysis of dispersin B, a biofilm-releasing glycoside hydrolase from the periodontopathogen Actinobacillus actinomycetemcomitans. J Mol Biol 349:475–486PubMedCrossRefGoogle Scholar
  19. 19.
    Alkawash MA, Soothill JS, Schiller NL (2006) Alginate lyase enhances antibiotic killing of mucoid Pseudomonas aeruginosa in biofilms. APMIS 114:131–138PubMedCrossRefGoogle Scholar
  20. 20.
    Friedman L, Kolter R (2004) Genes involved in matrix formation in Pseudomonas aeruginosa PA14 biofilms. Mol Microbiol 51:675–690PubMedCrossRefGoogle Scholar
  21. 21.
    Friedman L, Kolter R (2004) Two genetic loci produce distinct carbohydrate-rich structural components of the Pseudomonas aeruginosa biofilm matrix. J Bacteriol 186:4457–4465PubMedCentralPubMedCrossRefGoogle Scholar
  22. 22.
    Wu J, Xi C (2009) Evaluation of different methods for extracting extracellular DNA from the biofilm matrix. Appl Environ Microbiol 75:5390–5395PubMedCentralPubMedCrossRefGoogle Scholar
  23. 23.
    Thallinger B, Prasetyo EN, Nyanhongo GS, Guebitz GM (2013) Antimicrobial enzymes: an emerging strategy to fight microbes and microbial biofilms. Biotechnol J 8:97–109PubMedCrossRefGoogle Scholar
  24. 24.
    Brindle ER, Miller DA, Stewart PS (2011) Hydrodynamic deformation and removal of Staphylococcus epidermidis biofilms treated with urea, chlorhexidine, iron chloride, or dispersin B. Biotechnol Bioeng 108:2968–2977PubMedCrossRefGoogle Scholar
  25. 25.
    Cordeiroa AL, Wernerb C (2012) Enzymes for antifouling strategies. J Adhes Sci Technol 25:2317–2344CrossRefGoogle Scholar
  26. 26.
    Cywes-Bentley C, Skurnik D, Zaidi T et al (2013) Antibody to a conserved antigenic target is protective against diverse prokaryotic and eukaryotic pathogens. Proc Natl Acad Sci U S A 110:E2209–E2218PubMedCentralPubMedCrossRefGoogle Scholar
  27. 27.
    Ali Mohammed MM, Nerland AH, Al-Haroni M, Bakken V (2013) Characterization of extracellular polymeric matrix, and treatment of Fusobacterium nucleatum and Porphyromonas gingivalis biofilms with DNase I and proteinase K. J Oral Microbiol 5: 20015. doi: 10.3402/jom.v5i0.20015
  28. 28.
    Kaplan JB, Ragunath C, Velliyagounder K et al (2004) Enzymatic detachment of Staphylococcus epidermidis biofilms. Antimicrob Agents Chemother 48:2633–2636PubMedCentralPubMedCrossRefGoogle Scholar
  29. 29.
    Izano EA, Sadovskaya I, Vinogradov E et al (2007) Poly-N-acetylglucosamine mediates biofilm formation and antibiotic resistance in Actinobacillus pleuropneumoniae. Microb Pathog 43:1–9PubMedCentralPubMedCrossRefGoogle Scholar
  30. 30.
    Kaplan JB, Izano EA, Gopal P et al (2012) Low levels of β-lactam antibiotics induce extracellular DNA release and biofilm formation in Staphylococcus aureus. MBio 3:e00198–12PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Department of BiologyAmerican UniversityWashingtonUSA

Personalised recommendations