ChIP-Seq and RNA-Seq Reveal an AmrZ-Mediated Mechanism for Cyclic di-GMP Synthesis and Biofilm Development by Pseudomonas aeruginosa

PLoS Pathogens

Volumn 10, Issue 3, 2014, Pages

  Jones, Christopher J ^a,b   Newsom, David ^c   Kelly, Benjamin ^c   Irie, Yasuhiko ^d   Jennings, Laura K ^e   Xu, Binjie ^b   Limoli, Dominique H ^b   Harrison, Joe J ^f   Parsek, Matthew R ^e   White, Peter ^c   Wozniak, Daniel J ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b OHIO STATE UNIVERSITY   (United States)

^c THE RESEARCH INSTITUTE AT NATIONWIDE CHILDREN S HOSPITAL   (United States)

^d University of Bath   (United Kingdom)

^e UNIVERSITY OF WASHINGTON   (United States)

^f UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC DIGUANYLATE GUANOSINE PHOSPHATE; CYCLIC GMP; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AMRZ; UNCLASSIFIED DRUG;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BIOFILM; CHROMATIN IMMUNOPRECIPITATION; CONFOCAL LASER MICROSCOPY; CONTROLLED STUDY; DNA SEQUENCE; FLOW RATE; GEL MOBILITY SHIFT ASSAY; GENE EXPRESSION; GENE LIBRARY; GENETIC ASSOCIATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOUSE; NONHUMAN; PROTEIN FUNCTION; PROTEIN STRUCTURE; PSEUDOMONAS AERUGINOSA; RNA ISOLATION; RNA SEQUENCE;

ANIMALS; BACTERIAL PROTEINS; BIOFILMS; CHROMATIN IMMUNOPRECIPITATION; CHROMATOGRAPHY, LIQUID; CYCLIC GMP; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GENE EXPRESSION REGULATION, BACTERIAL; MASS SPECTROMETRY; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PSEUDOMONAS AERUGINOSA; RNA, BACTERIAL; TRANSCRIPTION FACTORS; VIRULENCE;

EID: 84897424003     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.1003984     Document Type: Article

References (102)

1. Wisplinghoff H, Bischoff T, Tallent SM, Seifert H, Wenzel RP, et al. (2004) Nosocomial bloodstream infections in US hospitals: analysis of 24,179 cases from a prospective nationwide surveillance study. Clin Infect Dis 39: 309-317 doi:10.1086/421946.
2. Richards MJ, Edwards JR, Culver DH, Gaynes RP, (1999) Nosocomial infections in medical intensive care units in the United States. Crit Care Med 27: 887.
3. Hall-Stoodley L, Costerton JW, Stoodley P, (2004) Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol 2: 95-108 doi:10.1038/nrmicro821.
4. Tart AH, Wozniak DJ, (2008) Shifting paradigms in Pseudomonas aeruginosa biofilm research. Curr Top Microbiol Immunol 322: 193-206.
5. Evans DJ, Brown MRW, Allison DG, Gilbert P, (1990) Susceptibility of bacterial biofilms to tobramycin: role of specific growth rate and phase in the division cycle. J Antimicrob Chemother 25: 585-591 doi:10.1093/jac/25.4.585.
6. Hentzer M, Teitzel GM, Balzer GJ, Heydorn A, Molin S, et al. (2001) Alginate overproduction affects Pseudomonas aeruginosa biofilm structure and function. J Bacteriol 183: 5395-5401.
7. Alkawash MA, Soothill JS, Schiller NL, (2006) Alginate lyase enhances antibiotic killing of mucoid Pseudomonas aeruginosa in biofilms. APMIS 114: 131-138 doi:_10.1111/j.1600-0463.2006.apm_356.x.
8. Davies DG, Parsek MR, Pearson JP, Iglewski BH, Costerton JW, et al. (1998) The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science 280: 295-298.
9. O'Toole GA, Kolter R, (1998) Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis. Mol Microbiol 28: 449-461.
10. Webb JS, Thompson LS, James S, Charlton T, Tolker-Nielsen T, et al. (2003) Cell death in Pseudomonas aeruginosa biofilm development. J Bacteriol 185: 4585-4592.
11. Shrout JD, Chopp DL, Just CL, Hentzer M, Givskov M, et al. (2006) The impact of quorum sensing and swarming motility on Pseudomonas aeruginosa biofilm formation is nutritionally conditional. Mol Microbiol 62: 1264-1277 doi:10.1111/j.1365-2958.2006.05421.x.
12. O'Toole GA, Kolter R, (1998) Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol Microbiol 30: 295-304.
13. Worlitzsch D, Tarran R, Ulrich M, Schwab U, Cekici A, et al. (2002) Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients. J Clin Invest 109: 317-325 doi:10.1172/JCI13870.
14. Hassett DJ, Sutton MD, Schurr MJ, Herr AB, Caldwell CC, et al. (2009) Pseudomonas aeruginosa hypoxic or anaerobic biofilm infections within cystic fibrosis airways. Trends Microbiol 17: 130-138 doi:10.1016/j.tim.2008.12.003.
15. Drenkard E, Ausubel FM, (2002) Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation. Nature 416: 740-743 doi:10.1038/416740a.
16. Leid JG, Willson CJ, Shirtliff ME, Hassett DJ, Parsek MR, et al. (2005) The exopolysaccharide alginate protects Pseudomonas aeruginosa biofilm bacteria from IFN-gamma-mediated macrophage killing. J Immunol 175: 7512-7518.
17. Nguyen D, Joshi-Datar A, Lepine F, Bauerle E, Olakanmi O, et al. (2011) Active Starvation Responses Mediate Antibiotic Tolerance in Biofilms and Nutrient-Limited Bacteria. Science 334: 982-986 doi:10.1126/science.1211037.
18. Waligora EA, Ramsey DM, Pryor EE, Lu H, Hollis T, et al. (2010) AmrZ beta-sheet residues are essential for DNA binding and transcriptional control of Pseudomonas aeruginosa virulence genes. J Bacteriol 192: 5390-5401 doi:10.1128/JB.00711-10.
19. Jones CJ, Ryder CR, Mann EE, Wozniak DJ, (2013) AmrZ modulates Pseudomonas aeruginosa biofilm architecture by directly repressing transcription of the psl operon. J Bacteriol 195: 1637-1644 doi:10.1128/JB.02190-12.
20. Tart AH, Wolfgang MC, Wozniak DJ, (2005) The alternative sigma factor AlgT represses Pseudomonas aeruginosa flagellum biosynthesis by inhibiting expression of fleQ. J Bacteriol 187: 7955-7962 doi:10.1128/JB.187.23.7955-7962.2005.
21. Tart AH, Blanks MJ, Wozniak DJ, (2006) The AlgT-dependent transcriptional regulator AmrZ (AlgZ) inhibits flagellum biosynthesis in mucoid, nonmotile Pseudomonas aeruginosa cystic fibrosis isolates. J Bacteriol 188: 6483-6489 doi:10.1128/JB.00636-06.
22. Ramsey DM, Baynham PJ, Wozniak DJ, (2005) Binding of Pseudomonas aeruginosa AlgZ to sites upstream of the algZ promoter leads to repression of transcription. J Bacteriol 187: 4430-4443 doi:10.1128/JB.187.13.4430-4443.2005.
23. Pryor EE, Waligora EA, Xu B, Dellos-Nolan S, Wozniak DJ, et al. (2012) The transcription factor AmrZ utilizes multiple DNA binding modes to recognize activator and repressor sequences of Pseudomonas aeruginosa virulence genes. PLoS Pathog 8: e1002648 doi:10.1371/journal.ppat.1002648.
24. Baynham PJ, Wozniak DJ, (1996) Identification and characterization of AlgZ, an AlgT-dependent DNA-binding protein required for Pseudomonas aeruginosa algD transcription. Mol Microbiol 22: 97-108.
25. Baynham PJ, Brown AL, Hall LL, Wozniak DJ, (1999) Pseudomonas aeruginosa AlgZ, a ribbon-helix-helix DNA-binding protein, is essential for alginate synthesis and algD transcriptional activation. Mol Microbiol 33: 1069-1080.
26. Baynham PJ, Ramsey DM, Gvozdyev BV, Cordonnier EM, Wozniak DJ, (2006) The Pseudomonas aeruginosa ribbon-helix-helix DNA-binding protein AlgZ (AmrZ) controls twitching motility and biogenesis of type IV pili. J Bacteriol 188: 132-140 doi:10.1128/JB.188.1.132-140.2006.
27. Davies BW, Bogard RW, Mekalanos JJ, (2011) Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation. Proc Natl Acad Sci U S A 108: 12467-12472 doi:10.1073/pnas.1107894108.
28. Galagan J, Lyubetskaya A, Gomes A, (2013) ChIP-Seq and the complexity of bacterial transcriptional regulation. Curr Top Microbiol Immunol 363: 43-68 doi:__10.1007/82_2012_257.
29. Starkey M, Hickman JH, Ma L, Zhang N, De Long S, et al. (2009) Pseudomonas aeruginosa rugose small-colony variants have adaptations that likely promote persistence in the cystic fibrosis lung. J Bacteriol 191: 3492-3503 doi:10.1128/JB.00119-09.
30. Borlee BR, Goldman AD, Murakami K, Samudrala R, Wozniak DJ, et al. (2010) Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix. Mol Microbiol 75: 827-842 doi:10.1111/j.1365-2958.2009.06991.x.
31. Boyd CD, O'Toole GA, (2012) Second messenger regulation of biofilm formation: breakthroughs in understanding c-di-GMP effector systems. Annu Rev Cell Dev Biol 28: 439-462 doi:10.1146/annurev-cellbio-101011-155705.
32. Hickman JW, Tifrea DF, Harwood CS, (2005) A chemosensory system that regulates biofilm formation through modulation of cyclic diguanylate levels. Proc Natl Acad Sci U S A 102: 14422-14427 doi:10.1073/pnas.0507170102.
33. Christensen LD, van Gennip M, Rybtke MT, Wu H, Chiang WC,et al. (2013) Clearance of Pseudomonas aeruginosa foreign-body biofilm infections through reduction of the c-di-GMP level in the bacteria. Infect Immun [epub ahead of print]. doi:10.1128/IAI.00332-13.
34. Haussler S, (2003) Highly adherent small-colony variants of I in cystic fibrosis lung infection. J Med Microbiol 52: 295-301 doi:10.1099/jmm.0.05069-0.
35. Kirisits MJ, Prost L, Starkey M, Parsek MR, (2005) Characterization of colony morphology variants isolated from Pseudomonas aeruginosa biofilms. Appl Environ Microbiol 71: 4809-4821 doi:10.1128/AEM.71.8.4809-4821.2005.
36. Malone JG, Williams R, Christen M, Jenal U, Spiers AJ, et al. (2007) The structure-function relationship of WspR, a Pseudomonas fluorescens response regulator with a GGDEF output domain. Microbiology 153: 980-994 doi:10.1099/mic.0.2006/002824-0.
37. Hickman JW, Harwood CS, (2008) Identification of FleQ from Pseudomonas aeruginosa as a c-di-GMP-responsive transcription factor. Mol Microbiol 69: 376-389 doi:10.1111/j.1365-2958.2008.06281.x.
38. Baraquet C, Murakami K, Parsek MR, Harwood CS, (2012) The FleQ protein from Pseudomonas aeruginosa functions as both a repressor and an activator to control gene expression from the pel operon promoter in response to c-di-GMP. Nucleic Acids Res 40: 7207-7218 doi:10.1093/nar/gks384.
39. Irie Y, Borlee BR, O'Connor JR, Hill PJ, Harwood CS, et al. (2012) Self-produced exopolysaccharide is a signal that stimulates biofilm formation in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 109: 20632-20636 doi:10.1073/pnas.1217993109.
40. Moscoso JA, Mikkelsen H, Heeb S, Williams P, Filloux A, (2011) The Pseudomonas aeruginosa sensor RetS switches type III and type VI secretion via c-di-GMP signalling. Environ Microbiol 13: 3128-3138 doi:10.1111/j.1462-2920.2011.02595.x.
41. Frangipani E, Visaggio D, Heeb S, Kaever V, Cámara M,et al. (2013) The Gac/Rsm and cyclic-di-GMP signalling networks coordinately regulate iron uptake in Pseudomonas aeruginosa. Environ Microbiol [epub ahead of print] doi:10.1111/1462-2920.12164.
42. Römling U, Galperin MY, Gomelsky M, (2013) Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 77: 1-52 doi:10.1128/MMBR.00043-12.
43. Yu H, Mudd M, Boucher JC, Schurr MJ, Deretic V, (1997) Identification of the algZ gene upstream of the response regulator algR and its participation in control of alginate production in Pseudomonas aeruginosa. J Bacteriol 179: 187-193.
44. Castang S, McManus HR, Turner KH, Dove SL, (2008) H-NS family members function coordinately in an opportunistic pathogen. Proc Natl Acad Sci U S A 105: 18947-18952 doi:10.1073/pnas.0808215105.
45. Gilbert KB, Kim TH, Gupta R, Greenberg EP, Schuster M, (2009) Global position analysis of the Pseudomonas aeruginosa quorum-sensing transcription factor LasR. Mol Microbiol 73: 1072-1085 doi:10.1111/j.1365-2958.2009.06832.x.
46. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, et al. (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. MolCell 38: 576-589 doi:10.1016/j.molcel.2010.05.004.
47. Anders S, Huber W, (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106 doi:10.1186/gb-2010-11-10-r106.
48. Stites SW, Walters B, O'Brien-Ladner AR, Bailey K, Wesselius LJ, (1998) Increased iron and ferritin content of sputum from patients with cystic fibrosis or chronic bronchitis. Chest 114: 814-819.
49. Stites SW, Plautz MW, Bailey K, O'Brien-Ladner AR, Wesselius LJ, (1999) Increased concentrations of iron and isoferritins in the lower respiratory tract of patients with stable cystic fibrosis. Am J Respir Crit Care Med 160: 796-801 doi:10.1164/ajrccm.160.3.9811018.
50. Palmer KL, Aye LM, Whiteley M, (2007) Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum. J Bacteriol 189: 8079-8087 doi:10.1128/JB.01138-07.
51. Oglesby AG, Farrow JM, Lee JH, Tomaras AP, Greenberg EP, et al. (2008) The Influence of Iron on Pseudomonas aeruginosa Physiology: A REGULATORY LINK BETWEEN IRON AND QUORUM SENSING. J Biol Chem 283: 15558-15567 doi:10.1074/jbc.M707840200.
52. Jimenez PN, Koch G, Thompson JA, Xavier KB, Cool RH, et al. (2012) The multiple signaling systems regulating virulence in Pseudomonas aeruginosa. Microbiol Mol Biol Rev 76: 46-65 doi:10.1128/MMBR.05007-11.
53. Mougous JD, Cuff ME, Raunser S, Shen A, Zhou M, et al. (2006) A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus. Science 312: 1526-1530 doi:10.1126/science.1128393.
54. Lesic B, Starkey M, He J, Hazan R, Rahme LG, (2009) Quorum sensing differentially regulates Pseudomonas aeruginosa type VI secretion locus I and homologous loci II and III, which are required for pathogenesis. Microbiology 155: 2845-2855 doi:10.1099/mic.0.029082-0.
55. Hood RD, Singh P, Hsu F, Güvener T, Carl MA, et al. (2010) A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe 7: 25-37 doi:10.1016/j.chom.2009.12.007.
56. Russell AB, Hood RD, Bui NK, LeRoux M, Vollmer W, et al. (2011) Type VI secretion delivers bacteriolytic effectors to target cells. Nature 475: 343-347 doi:10.1038/nature10244.
57. Frisk A, Jyot J, Arora SK, Ramphal R, (2002) Identification and Functional Characterization of flgM, a Gene Encoding the Anti-Sigma 28 Factor in Pseudomonas aeruginosa. J Bacteriol 184: 1514-1521 doi:10.1128/JB.184.6.1514-1521.2002.
58. Dötsch A, Eckweiler D, Schniederjans M, Zimmermann A, Jensen V, et al. (2012) The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing. PLoS ONE 7: e31092 doi:10.1371/journal.pone.0031092.s006.
59. Potvin E, Sanschagrin F, Levesque RC, (2008) Sigma factors in Pseudomonas aeruginosa. FEMS Microbiol Rev 32: 38-55 doi:10.1111/j.1574-6976.2007.00092.x.
60. Kulasakara H, Lee V, Brencic A, Liberati N, Urbach J, et al. (2006) Analysis of Pseudomonas aeruginosa diguanylate cyclases and phosphodiesterases reveals a role for bis-(3"-5")-cyclic-GMP in virulence. Proc Natl Acad Sci U S A 103: 2839-2844 doi:10.1073/pnas.0511090103.
61. Qiu D, Damron FH, Mima T, Schweizer HP, Yu HD, (2008) PBAD-based shuttle vectors for functional analysis of toxic and highly regulated genes in Pseudomonas and Burkholderia spp. and other bacteria. Appl Environ Microbiol 74: 7422-7426 doi:10.1128/AEM.01369-08.
62. Johnson DS, Mortazavi A, Myers RM, Wold B, (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502 doi:10.1126/science.1141319.
63. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349 doi:10.1126/science.1158441.
64. Perkins TT, Davies MR, Klemm EJ, Rowley G, Wileman T, et al. (2012) ChIP-seq and transcriptome analysis of the OmpR regulon of Salmonella enterica serovars Typhi and Typhimurium reveals accessory genes implicated in host colonization. Mol Microbiol 87: 526-538 doi:10.1111/mmi.12111.
65. Liao J, Schurr MJ, Sauer K, (2013) The MerR-like regulator BrlR confers biofilm tolerance by activating multidrug-efflux pumps in Pseudomonas aeruginosa biofilms. J Bacteriol 195(15): 3352-63 doi:10.1128/JB.00318-13.
66. Balasubramanian D, Kumari H, Jaric M, Fernandez M, Turner KH, et al. (2013) Deep sequencing analyses expands the Pseudomonas aeruginosa AmpR regulon to include small RNA-mediated regulation of iron acquisition, heat shock and oxidative stress response. Nucleic Acids Res 42(2): 979-98 doi:10.1093/nar/gkt942.
67. Galagan JE, Minch K, Peterson M, Lyubetskaya A, Azizi E, et al. (2013) The Mycobacterium tuberculosis regulatory network and hypoxia. Nature 499: 178-183 doi:10.1038/nature12337.
68. Lee VT, Matewish JM, Kessler JL, Hyodo M, Hayakawa Y, et al. (2007) A cyclic-di-GMP receptor required for bacterial exopolysaccharide production. Mol Microbiol 65: 1474-1484 doi:10.1111/j.1365-2958.2007.05879.x.
69. Stoltz DA, Meyerholz DK, Pezzulo AA, Ramachandran S, Rogan MP, et al. (2010) Cystic fibrosis pigs develop lung disease and exhibit defective bacterial eradication at birth. Sci Transl Med 2: 29ra31 doi:10.1126/scitranslmed.3000928.
70. Hengge R, (2009) Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7: 263-273 doi:10.1038/nrmicro2109.
71. Sondermann H, Shikuma NJ, Yildiz FH, (2012) You've come a long way: c-di-GMP signaling. Curr Opin Microbiol 15: 140-146 doi:10.1016/j.mib.2011.12.008.
72. Hecht GB, Newton A, (1995) Identification of a novel response regulator required for the swarmer-to-stalked-cell transition in Caulobacter crescentus. J Bacteriol 177: 6223-6229.
73. Paul R, Abel S, Wassmann P, Beck A, Heerklotz H, et al. (2007) Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization. J Biol Chem 282: 29170-29177 doi:10.1074/jbc.M704702200.
74. Guvener ZT, Harwood CS, (2007) Subcellular location characteristics of the Pseudomonas aeruginosa GGDEF protein, WspR, indicate that it produces cyclic-di-GMP in response to growth on surfaces. Mol Microbiol 66: 1459-1473 doi:10.1111/j.1365-2958.2007.06008.x.
75. Huangyutitham V, Guvener ZT, Harwood CS, (2013) Subcellular clustering of the phosphorylated WspR response regulator protein stimulates its diguanylate cyclase activity. MBio 4: e00242-13 doi:10.1128/mBio.00242-13.
76. Paul R, Weiser S, Amiot NC, Chan C, Schirmer T, et al. (2004) Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. Genes Dev 18: 715-727 doi:10.1101/gad.289504.
77. Klausen M, Heydorn A, Ragas P, Lambertsen L, Aaes-Jørgensen A, et al. (2003) Biofilm formation by Pseudomonas aeruginosa wild type, flagella and type IV pili mutants. Mol Microbiol 48: 1511-1524.
78. Klausen M, Aaes-Jørgensen A, Molin S, Tolker-Nielsen T, (2003) Involvement of bacterial migration in the development of complex multicellular structures in Pseudomonas aeruginosa biofilms. Mol Microbiol 50: 61-68.
79. Overhage J, Schemionek M, Webb JS, Rehm BHA, (2005) Expression of the psl operon in Pseudomonas aeruginosa PAO1 biofilms: PslA performs an essential function in biofilm formation. Appl Environ Microbiol 71: 4407-4413 doi:10.1128/AEM.71.8.4407-4413.2005.
80. Toutain CM, Caizza NC, Zegans ME, O'Toole GA, (2007) Roles for flagellar stators in biofilm formation by Pseudomonas aeruginosa. Res Microbiol 158: 471-477 doi:10.1016/j.resmic.2007.04.001.
81. Byrd MS, Pang B, Mishra M, Swords WE, Wozniak DJ (2010) The Pseudomonas aeruginosa exopolysaccharide Psl facilitates surface adherence and NF-kappaB activation in A549 cells. MBio 1 pii: e00140-10. doi:10.1128/mBio.00140-10.
82. Byrd MS, Pang B, Hong W, Waligora EA, Juneau RA, et al. (2011) Direct evaluation of Pseudomonas aeruginosa biofilm mediators in a chronic infection model. Infect Immun 79: 3087-3095 doi:10.1128/IAI.00057-11.
83. Yang L, Hu Y, Liu Y, Zhang J, Ulstrup J, et al. (2011) Distinct roles of extracellular polymeric substances in Pseudomonas aeruginosa biofilm development. Environ Microbiol 13: 1705-1717 doi:10.1111/j.1462-2920.2011.02503.x.
84. Yang L, Hengzhuang W, Wu H, Damkiær S, Jochumsen N, et al. (2012) Polysaccharides serve as scaffold of biofilms formed by mucoid Pseudomonas aeruginosa. FEMS Immunol Med Microbiol 65: 366-376 doi:10.1111/j.1574-695X.2012.00936.x.
85. Wang S, Parsek MR, Wozniak DJ, Ma LZ, (2013) A spider web strategy of type IV pili-mediated migration to build a fibre-like Psl polysaccharide matrix in Pseudomonas aeruginosa biofilms. Environ Microbiol 15(8): 2238-53 doi:10.1111/1462-2920.12095.
86. Goodman AL, Kulasekara B, Rietsch A, Boyd D, Smith RS, et al. (2004) A signaling network reciprocally regulates genes associated with acute infection and chronic persistence in Pseudomonas aeruginosa. Dev Cell 7: 745-754 doi:10.1016/j.devcel.2004.08.020.
87. Goodman AL, Merighi M, Hyodo M, Ventre I, Filloux A, et al. (2009) Direct interaction between sensor kinase proteins mediates acute and chronic disease phenotypes in a bacterial pathogen. Genes Dev 23: 249-259 doi:10.1101/gad.1739009.
88. Burrowes E, Baysse C, Adams C, O'Gara F, (2006) Influence of the regulatory protein RsmA on cellular functions in Pseudomonas aeruginosa PAO1, as revealed by transcriptome analysis. Microbiology 152: 405-418 doi:10.1099/mic.0.28324-0.
89. Mann EE, Wozniak DJ, (2011) Pseudomonas biofilm matrix composition and niche biology. FEMS Microbiol Rev 36: 893-916 doi:10.1111/j.1574-6976.2011.00322.x.
90. Walker TS, Tomlin KL, Worthen GS, Poch KR, Lieber JG, et al. (2005) Enhanced Pseudomonas aeruginosa biofilm development mediated by human neutrophils. Infect Immun 73: 3693-3701 doi:10.1128/IAI.73.6.3693-3701.2005.
91. Mishra M, Byrd MS, Sergeant S, Azad AK, Parsek MR, et al. (2012) Pseudomonas aeruginosa Psl polysaccharide reduces neutrophil phagocytosis and the oxidative response by limiting complement-mediated opsonization. Cell Microbiol 14: 95-106 doi:10.1111/j.1462-5822.2011.01704.x.
92. Young RL, Malcolm KC, Kret JE, Caceres SM, Poch KR, et al. (2011) Neutrophil extracellular trap (NET)-mediated killing of Pseudomonas aeruginosa: evidence of acquired resistance within the CF airway, independent of CFTR. PLoS ONE 6: e23637 doi:10.1371/journal.pone.0023637.
93. Govan JR, Deretic V, (1996) Microbial pathogenesis in cystic fibrosis: mucoid Pseudomonas aeruginosa and Burkholderia cepacia. Microbiol Rev 60: 539-574.
94. Learn DB, Brestel EP, Seetharama S, (1987) Hypochlorite scavenging by Pseudomonas aeruginosa alginate. Infect Immun 55: 1813-1818.
95. Pedersen SS, Kharazmi A, Espersen F, Høiby N, (1990) Pseudomonas aeruginosa alginate in cystic fibrosis sputum and the inflammatory response. Infect Immun 58: 3363-3368.
96. Mai GT, Seow WK, Pier GB, McCormack JG, Thong YH, (1993) Suppression of lymphocyte and neutrophil functions by Pseudomonas aeruginosa mucoid exopolysaccharide (alginate): reversal by physicochemical, alginase, and specific monoclonal antibody treatments. Infect Immun 61: 559-564.
97. Hoang TT, Karkhoff-Schweizer RR, Kutchma AJ, Schweizer HP, (1998) A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants. Gene 212: 77-86.
98. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Laboratory Press. 2028 p.
99. Winsor GL, Lam DKW, Fleming L, Lo R, Whiteside MD, et al. (2011) Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res 39: D596-D600 doi:10.1093/nar/gkq869.
100. Kelley LA, Sternberg MJE, (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 4: 363-371 doi:10.1038/nprot.2009.2.
101. Heydorn A, Nielsen AT, Hentzer M, Sternberg C, Givskov M, et al. (2000) Quantification of biofilm structures by the novel computer program COMSTAT. Microbiology 146 (Pt 10): 2395-2407.
102. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406: 959-964 doi:10.1038/35023079.