2,882
Views
4
CrossRef citations to date
0
Altmetric
Original Articles

Mathematical modelling of CRISPR-Cas system effects on biofilm formation

&
Pages 264-284 | Received 16 Mar 2016, Accepted 26 Mar 2017, Published online: 20 Apr 2017

References

  • S.T. Abedon, Bacteriophage Ecology, Advances in Molecular and Cellular Microbiology, Cambridge University Press, Cambridge, UK, 2008.
  • S.T. Abedon, Phage evolution and ecology, Adv. App. Microbiol. 67 (2009), pp. 1–45. doi: 10.1016/S0065-2164(08)01001-0
  • S.T. Abedon, Bacterial ‘immunity’ against bacteriophages, Bacteriophage 2 (2012), pp. 50–54. doi: 10.4161/bact.18609
  • A.F. Andersson and J.F. Banfield, Virus population dynamics and acquired virus resistance in natural microbial communities, Science 320 (2008), pp. 1047–1050. doi: 10.1126/science.1157358
  • S. Bachellier, J.M. Clément, M. Hofnung, and E. Gilson, Bacterial interspersed mosaic elements (bimes) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence, Genetics 145 (1997), pp. 551–562.
  • M. Ballyk, D. Jones, and H.L. Smith, The biofilm model of freter: A review, in Structured Population Models in Biology and Epidemiology, P. Magal and S. Ruan, eds., Springer, Berlin, 2008, pp. 265–302.
  • L. Barksdale and S.B. Arden, Persisting bacteriophage infections, lysogeny, and phage conversions, Ann. Rev. Microbiol. 28 (1974), pp. 265–300. doi: 10.1146/annurev.mi.28.100174.001405
  • R. Barrangou, C. Fremaux, H. Deveau, M. Richards, P. Boyaval, S. Moineau, D.A. Romero, and P. Horvath, CRISPR provides acquired resistance against viruses in prokaryotes, Science 315 (2007), pp. 1709–1712. doi: 10.1126/science.1138140
  • A. van Belkum, S. Scherer, L. van Alphen, and H. Verbrugh, Short-sequence DNA repeats in prokaryotic genomes, Microbiol. Mol. Bio. Rev. 62 (1998), pp. 275–293.
  • E. Bester, E.A. Edwards, and G.M. Wolfaardt, Planktonic cell yield is linked to biofilm development, Can. J. Microbiol. 55 (2009), pp. 1195–1206. doi: 10.1139/W09-075
  • D. Bhaya, M. Davison, and R. Barrangou, CRISPR-Cas systems in bacteria and archaea: Versatile small RNAs for adaptive defense and regulation, Ann. Rev. Gen. 45 (2011), pp. 273–297. doi: 10.1146/annurev-genet-110410-132430
  • R. Capparelli, M. Parlato, G. Borriello, P. Salvatore, and D. Iannelli, Experimental phage therapy against Staphylococcus aureus in mice, Antimicrob. Agents Chemo. 51 (2007), pp. 2765–2773. doi: 10.1128/AAC.01513-06
  • S. Chibani-Chennoufi, A. Bruttin, M.L. Dillmann, and H. Brüssow, Phage-host interaction: An ecological perspective, J. Bact. 186 (2004), pp. 3677–3686. doi: 10.1128/JB.186.12.3677-3686.2004
  • L.M. Childs, N.L. Held, M.J. Young, R.J. Whitaker, and J.S. Weitz, Multiscale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin, Evolution 66 (2012), pp. 2015–2029. doi: 10.1111/j.1558-5646.2012.01595.x
  • J.W. Costerton, P.S. Stewart, and E.P. Greenberg, Bacterial biofilms: A common cause of persistent infections, Science 284 (1999), pp. 1318–1322. doi: 10.1126/science.284.5418.1318
  • L. Deng, R.A. Garrett, S.A. Shah, X. Peng, and Q. She, A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus, Mol. Microb. 87 (2013), pp. 1088–1099. doi: 10.1111/mmi.12152
  • H. Deveau, J.E. Garneau, and S. Moineau, CRISPR-Cas system and its role in phage-bacteria interactions, Ann. Rev. Microbiol. 64 (2010), pp. 475–493. doi: 10.1146/annurev.micro.112408.134123
  • H. Echols, Developmental pathways for the temperate phage: Lysis vs lysogeny, Ann. Rev. Gen. 6 (1972), pp. 157–190. doi: 10.1146/annurev.ge.06.120172.001105
  • R. Edgar and U. Qimron, The Escherichia coli CRISPR system protects from λ lysogenization, lysogens, and prophage induction, J. Bact. 192 (2010), pp. 6291–6294. doi: 10.1128/JB.00644-10
  • B.O. Emerenini, B.A. Hense, C. Kuttler, H.J. Eberl, and C. Forestier, A mathematical model of quorum sensing induced biofilm detachment, PLoS ONE 10 (2015), pp. e0132385. doi: 10.1371/journal.pone.0132385
  • R. Freter, H. Brickner, J. Fekete, M.M. Vickerman, and K.E. Carey, survival and implantation of Escherichia coli in the intestinal tract, Inf. Immun. 39 (1983), pp. 686–703.
  • J.E. Garneau, M.-È. Dupuis, M. Villion, D.A. Romero, R. Barrangou, P. Boyaval, C. Fremaux, P. Horvath, A.H. Magadán, and S. Moineau, The CRISPR-Cas bacterial immune system cleaves bacteriophage and plasmid DNA, Nature 468 (2010), pp. 67–71. doi: 10.1038/nature09523
  • J.O. Haerter and K. Sneppen, Spatial structure and Lamarckian adaptation explain extreme genetic diversity at CRISPR locus, mBio 3 (2012), pp. e00126-12 12. doi: 10.1128/mBio.00126-12
  • C.R. Hale, P. Zhao, S. Olson, M.O. Duff, B.R. Graveley, L. Wells, R.M. Terns, and M.P. Terns, RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex, Cell 139 (2009), pp. 945–956. doi: 10.1016/j.cell.2009.07.040
  • J. He and M.W. Deem, Heterogeneous diversity of spacers within CRISPR (clustered regularly interspaced short palindromic repeats), Phy. Rev. Lett. 105 (2010), p. 128102.
  • S. Heilmann, K. Sneppen, and S. Krishna, Sustainability of virulence in a phage-bacterial ecosystem, J. Virol. 84 (2010), pp. 3016–3022. doi: 10.1128/JVI.02326-09
  • N.L. Held, A. Herrera, H. Cadillo-Quiroz, R.J. Whitaker, and P.J. Planet, CRISPR associated diversity within a population of sulfolobus islandicus, PLoS ONE 5 (2010), p. e12988. doi: 10.1371/journal.pone.0012988
  • N.L. Held, L.M. Childs, M. Davison, J.S. Weitz, R.J. Whitaker, and D. Bhaya, CRISPR-Cas systems to probe ecological diversity and host–viral interactions, in CRISPR-Cas systems, R. Barrangou and J. Van Der Oost, eds., Springer, Berlin, 2013, pp. 221–250.
  • G.E. Heussler, K.C. Cady, K. Koeppen, S. Bhuju, B.A. Stanton, and G.A. O'Toole, Clustered regularly interspaced short palindromic repeat-dependent, biofilm-specific death of Pseudomonas aeruginosa mediated by increased expression of phage-related genes, mBio 6 (2015), pp. e00129-15 15. doi: 10.1128/mBio.00129-15
  • Y. Ishino, H. Shinagawa, K. Makino, M. Amemura, and A. Nakata, Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product, J. Bact. 169 (1987), pp. 5429–5433. doi: 10.1128/jb.169.12.5429-5433.1987
  • R. Jansen, J.D.A. van Embden, W. Gaastra, and L.M. Schouls, Identification of genes that are associated with DNA repeats in prokaryotes, Mol. Microb. 43 (2002), pp. 1565–1575. doi: 10.1046/j.1365-2958.2002.02839.x
  • D.A. Jones and H.L. Smith, Bacteriophage and bacteria in a flow reactor, Bull. Math. Biol. 73 (2011), pp. 2357–2383. doi: 10.1007/s11538-010-9626-0
  • D.A. Jones, H.V. Kojouharov, D. Le, and H.L. Smith, The Freter model: A simple model of biofilm formation, J. Math. Biol. 47 (2003), pp. 137–152. doi: 10.1007/s00285-003-0202-1
  • H. Kawaji and Y. Hayashizaki, Exploration of small RNAs, PLoS Gen. 4 (2008), p. e22. doi: 10.1371/journal.pgen.0040022
  • E.V. Koonin and Y.I. Wolf, Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: Models and observations on virus-host coevolution, Mol. Biosys. 11 (2015), pp. 20–27. doi: 10.1039/C4MB00438H
  • E. Kutter and H. Brussow, Phage ecology, in Bacteriophages: Biology and Applications, E. Kutter and A. Sulakvelidze, eds., CRC Press, Boca Raton, FL, 2004.
  • S.J. Labrie, J.E. Samson, and S. Moineau, Bacteriophage resistance mechanisms, Nat. Rev. Micro. 8 (2010), pp. 317–327. doi: 10.1038/nrmicro2315
  • B.R. Levin, S. Moineau, M. Bushman, R. Barrangou, and D. Hughes, The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity, PLoS Gen. 9 (2013), p. e1003312. doi: 10.1371/journal.pgen.1003312
  • J.R. Lupski, J.R. Roth, and G.M. Weinstock, Chromosomal duplications in bacteria, fruit flies, and humans, Am. J. Hum. Gen. 58 (1996), pp. 21–27.
  • A. Mašić and H.J. Eberl, Persistence in a single species CSTR model with suspended flocs and wall attached biofilms, Bull. Math. Biol. 74 (2012), pp. 1001–1026. doi: 10.1007/s11538-011-9707-8
  • J.K. Miller, J.S. Brantner, C. Clemons, K.L. Kreider, A. Milsted, P. Wilber, Y.H. Yun, W.J. Youngs, G. Young, H.T. Badawy, A. Milsted, C. Clemons, K.L. Kreider, P. Wilber, G. Young, Y.H. Yun, P.O. Wagers, and W.J. Youngs, Mathematical modelling of Pseudomonas aeruginosa biofilm growth and treatment in the cystic fibrosis lung, Math. Med. Biol. (2014), pp. 179–204. doi: 10.1093/imammb/dqt003
  • F.J.M. Mojica and R.A. Garrett, Discovery and seminal developments in the CRISPR field, in CRISPR-Cas Systems, R. Barrangou and J. Van Der Oost, eds., Springer, Berlin, 2013, pp. 1–31.
  • C.D. Nadell, K. Drescher, and K.R. Foster, Spatial structure, cooperation and competition in biofilms, Nat. Rev. Microbiol. 14 (2016), pp. 589–600. doi: 10.1038/nrmicro.2016.84
  • G. O'Toole, H.B. Kaplan, and R. Kolter, Biofilm formation as microbial development, Ann. Rev. Microbiol. 54 (2000), pp. 49–79. doi: 10.1146/annurev.micro.54.1.49
  • V. Paul, S. Sundarrajan, S. Rajagopalan, S. Hariharan, N. Kempashanaiah, S. Padmanabhan, B. Sriram, and J. Ramachandran, Lysis-deficient phages as novel therapeutic agents for controlling bacterial infection, BMC Microbiol. 11 (2011), p. 195. doi: 10.1186/1471-2180-11-195
  • D.P. Pires, D. Vilas Boas, S. Sillankorva, J. Azeredo, and S.P. Goff, Phage therapy: A step forward in the treatment of Pseudomonas aeruginosa infections, J. Virol. 89 (2015), pp. 7449–7456. doi: 10.1128/JVI.00385-15
  • M.F. Rollins, J.T. Schuman, K. Paulus, H.S.T. Bukhari, and B. Wiedenheft, Mechanism of foreign DNA recognition by a CRISPR RNA-guided surveillance complex from Pseudomonas aeruginosa, Nuc. Acids Res. 43 (2015), pp. 2216–2222. doi: 10.1093/nar/gkv094
  • K.D. Seed and J.J. Dennis, Experimental bacteriophage therapy increases survival of Galleria mellonella larvae infected with clinically relevant strains of the Burkholderia cepacia complex, Antimic. Agents Chemo. 53 (2009), pp. 2205–2208. doi: 10.1128/AAC.01166-08
  • P.K. Singh, A.L. Schaefer, M.R. Parsek, T.O. Moninger, M.J. Welsh, and E.P. Greenberg, Quorum-sensing signals indicate that cystic fibrosis lungs are infected with bacterial biofilms, Nature 407 (2000), pp. 762–764. doi: 10.1038/35037627
  • M. Skurnik and E. Strauch, Phage therapy: Facts and fiction, Int. J. Med. Microbiol. 296 (2006), pp. 5–14. doi: 10.1016/j.ijmm.2005.09.002
  • R. Sorek, C.M. Lawrence, and B. Wiedenheft, CRISPR-mediated adaptive immune systems in bacteria and archaea, Ann. Rev. Biochem. 82 (2013), pp. 237–266. doi: 10.1146/annurev-biochem-072911-172315
  • F.M. Stewart and B.R. Levin, The population biology of bacterial viruses: Why be temperate, Theoret. Pop. Biol. 26 (1984), pp. 93–117. doi: 10.1016/0040-5809(84)90026-1
  • N. Takeuchi, Y.I. Wolf, K.S. Makarova, and E.V. Koonin, Nature and intensity of selection pressure on CRISPR-associated genes, J. Bact. 194 (2012), pp. 1216–1225. doi: 10.1128/JB.06521-11
  • G.W. Tyson and J.F. Banfield, Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses, Env. Microbiol. 10 (2008), pp. 200–207.
  • K.G. Vandervoort and G. Brelles-Mariño, Plasma-mediated inactivation of Pseudomonas aeruginosa biofilms grown on borosilicate surfaces under continuous culture system, PLoS ONE 9 (2014), p. e108512. doi: 10.1371/journal.pone.0108512
  • J.S. Webb, L.S. Thompson, S. James, T. Charlton, T. Tolker-Nielsen, B. Koch, M. Givskov, and S. Kjelleberg, Cell death in Pseudomonas aeruginosa biofilm development, J. Bact. 185 (2003), pp. 4585–4592. doi: 10.1128/JB.185.15.4585-4592.2003
  • M.G. Weinbauer, Ecology of prokaryotic viruses, FEMS Microbiol. Rev. 28 (2004), pp. 127–181. doi: 10.1016/j.femsre.2003.08.001
  • B. Wiedenheft, S.H. Sternberg, and J.A. Doudna, RNA-guided genetic silencing systems in bacteria and archaea, Nature 482 (2012), pp. 331–338. doi: 10.1038/nature10886
  • S.S. Yoon, R.F. Hennigan, G.M. Hilliard, U.A. Ochsner, K. Parvatiyar, M.C. Kamani, H.L. Allen, T.R. DeKievit, P.R. Gardner, U. Schwab, J.J. Rowe, B.H. Iglewski, T.R. McDermott, R.P. Mason, D.J. Wozniak, R.E.W. Hancock, M.R. Parsek, T.L. Noah, R.C. Boucher, and D.J. Hassett, Pseudomonas aeruginosa anaerobic respiration in biofilms: Relationships to Cystic fibrosis pathogenesis, Develop. Cell 3 (2002), pp. 593–603. doi: 10.1016/S1534-5807(02)00295-2
  • M.E. Zegans, J.C. Wagner, K.C. Cady, D.M. Murphy, J.H. Hammond, and G.A. O'Toole, Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa, J. Bact. 191 (2009), pp. 210–219. doi: 10.1128/JB.00797-08