Enterobactin is required for biofilm development in reduced-genome Escherichia coli

Environmental Microbiology

Volumn 13, Issue 12, 2011, Pages 3149-3162

  May, Thithiwat ^a   Okabe, Satoshi ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; ENTEROCHELIN; ESCHERICHIA COLI PROTEIN; HYDROLASE; ISOCHORISMATASE;

ARTICLE; BACTERIAL GENOME; BIOFILM; DNA MICROARRAY; ESCHERICHIA COLI; ESSENTIAL GENE; GENE DELETION; GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PHENOTYPE; PHYSIOLOGY;

BIOFILMS; DNA, BACTERIAL; ENTEROBACTIN; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENES, ESSENTIAL; GENOME, BACTERIAL; HYDROLASES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; SEQUENCE DELETION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 82555187957     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2011.02607.x     Document Type: Article

References (71)

1. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., etal. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008.
2. Banin, E., Vasil, M.L., and Greenberg, E.P. (2005) Iron and Pseudomonas aeruginosa biofilm formation. Proc Natl Acad Sci USA 102: 11076-11081.
3. Beloin, C., Valle, J., Latour-Lambert, P., Faure, P., Kzreminski, M., Balestrino, D., etal. (2004) Global impact of mature biofilm lifestyle on Escherichia coli K-12 gene expression. Mol Microbiol 51: 659-674.
4. Beloin, C., Roux, A., and Ghigo, J.M. (2008) Escherichia coli biofilms. Curr Top Microbiol Immunol 322: 249-289.
5. Blattner, F.R., Plunkett, G., III, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., etal. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462.
6. Bullen, J.J. (1981) The significance of iron in infection. Rev Infect Dis 3: 1127-1138.
7. Collins, T.J. (2007) ImageJ for microscopy. Biotechniques 43: 25-30.
8. Danese, P.N., Pratt, L.A., Dove, S.L., and Kolter, R. (2000a) The outer membrane protein, Antigen 43, mediates cell-to-cell interactions within Escherichia coli biofilms. Mol Microbiol 37: 424-432.
9. Danese, P.N., Pratt, L.A., and Kolter, R. (2000b) Exopolysaccharide production is required for development of Escherichia coli K-12 biofilm architecture. J Bacteriol 182: 3593-3596.
10. Datsenko, K.A., and Wanner, B.L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97: 6640-6645.
11. De Felice, M., Levinthal, M., Iaccarino, M., and Guardiola, J. (1979) Growth inhibition as a consequence of antagonism between related amino acids: effect of valine in Escherichia coli K-12. Microbiol Mol Biol Rev 43: 42-58.
12. Delgado-Nixon, V.M., Gonzalez, G., and Gilles-Gonzalez, M.-A. (2000) Dos, a heme-binding PAS protein from Escherichia coli, is a direct oxygen sensor. Biochemistry 39: 2685-2691.
13. Diederich, L., Rasmussen, L.J., and Messer, W. (1992) New cloning vectors for integration into the [lambda] attachment site attB of the Escherichia coli chromosome. Plasmid 28: 14-24.
14. Domka, J., Lee, J., Bansal, T., and Wood, T.K. (2007) Temporal gene-expression in Escherichia coli K-12 biofilms. Environ Microbiol 9: 332-346.
15. Feist, A.M., and Palsson, B.O. (2008) The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 26: 659-667.
16. Gehring, A.M., Bradley, K.A., and Walsh, C.T. (1997) Enterobactin biosynthesis in Escherichia coli: isochorismate lyase (EntB) is a bifunctional enzyme that is phosphopantetheinylated by EntD and then acylated by EntE using ATP and 2, 3-dihydroxybenzoate. Biochemistry 36: 8495-8503.
17. Gehring, A.M., Mori, I., and Walsh, C.T. (1998) Reconstitution and characterization of the Escherichia coli enterobactin synthetase from EntB, EntE, and EntF. Biochemistry 37: 2648-2659.
18. Ghigo, J.M. (2001) Natural conjugative plasmids induce bacterial biofilm development. Nature 412: 442-445.
19. González Barrios, A.F., Zuo, R., Hashimoto, Y., Yang, L., Bentley, W.E., and Wood, T.K. (2006) Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022). J Bacteriol 188: 305-316.
20. Guo, Z.-F., Sun, Y., Zheng, S., and Guo, Z. (2009) Preferential hydrolysis of aberrant intermediates by the type IIthioesterase in Escherichia coli nonribosomal enterobactin synthesis: substrate specificities and mutagenic studies on the active-site residues. Biochemistry 48: 1712-1722.
21. Hashimoto, M., Ichimura, T., Mizoguchi, H., Tanaka, K., Fujimitsu, K., Keyamura, K., etal. (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol 55: 137-149.
22. Heydorn, A., Nielsen, A.T., Hentzer, M., Sternberg, C., Givskov, M., Ersboll, B.K., and Molin, S. (2000) Quantification of biofilm structures by the novel computer program comstat. Microbiology 146: 2395-2407.
23. Kato, J., and Hashimoto, M. (2007) Construction of consecutive deletions of the Escherichia coli chromosome. Mol Syst Biol 3: 132.
24. Keseler, I.M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I.T., etal. (2005) EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 33: D334-D337.
25. Kitagawa, M., Ara, T., Arifuzzaman, M., Ioka-Nakamichi, T., Inamoto, E., Toyonaga, H., and Mori, H. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res 12: 291-299.
26. Kolodkin-Gal, I., Romero, D., Cao, S., Clardy, J., Kolter, R., and Losick, R. (2010) d-amino acids trigger biofilm disassembly. Science 328: 627-629.
27. Korea, C.-G., Badouraly, R., Prevost, M.-C., Ghigo, J.-M., and Beloin, C. (2010) Escherichia coli K-12 possesses multiple cryptic but functional chaperone-usher fimbriae with distinct surface specificities. Environ Microbiol 12: 1957-1977.
28. Korea, C.-G., Ghigo, J.-M., and Beloin, C. (2011) The sweet connection: solving the riddle of multiple sugar-binding fimbrial adhesins in Escherichia coli. Bioessays 33: 300-311.
29. Kuchma, S.L., and O'Toole, G.A. (2000) Surface-induced and biofilm-induced changes in gene expression. Curr Opin Biotechnol 11: 429-433.
30. Landini, P. (2009) Cross-talk mechanisms in biofilm formation and responses to environmental and physiological stress in Escherichia coli. Res Microbiol 160: 259-266.
31. Lazazzera, B.A. (2005) Lessons from DNA microarray analysis: the gene expression profile of biofilms. Curr Opin Microbiol 8: 222-227.
32. Lee, J.T., Maeda, T., Hong, S.H., and Wood, T.K. (2009) Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones. Appl Environ Microbiol 75: 1703-1716.
33. Li, C. (2008) Automating dChip: toward reproducible sharing of microarray data analysis. BMC Bioinformatics 9: 231.
34. Li, C., and Wong, W.H. (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98: 31-36.
35. Liu, G., Loraine, A.E., Shigeta, R., Cline, M., Cheng, J., Valmeekam, V., etal. (2003) NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 31: 82-86.
36. Lopez-Campistrous, A., Semchuk, P., Burke, L., Palmer-Stone, T., Brokx, S.J., Broderick, G., etal. (2005) Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth. Mol Cell Proteomics 4: 1205-1209.
37. Maira-Litrán, T., Allison, D.G., and Gilbert, P. (2000) Expression of the multiple antibiotic resistance operon (mar) during growth of Escherichia coli as a biofilm. J Appl Microbiol 88: 243-247.
38. May, T., and Okabe, S. (2008) Escherichia coli harboring a natural IncF conjugative F plasmid develops complex mature biofilms by stimulating synthesis of colanic acid and curli. J Bacteriol 190: 7479-7490.
39. May, T., Ito, A., and Okabe, S. (2009) Induction of multidrug resistance mechanism in Escherichia coli biofilms by interplay between tetracycline and ampicillin resistance genes. Antimicrob Agents Chemother 53: 4628-4639.
40. - phenocopies during Escherichia coli biofilm formation. Mol Genet Genomics 284: 333-342.
41. Monds, R.D., and O'Toole, G.A. (2009) The developmental model of microbial biofilms: ten years of a paradigm up for review. Trends Microbiol 17: 73-87.
42. Mushegian, A. (1999) The minimal genome concept. Curr Opin Genet Dev 9: 709-714.
43. Nadell, C.D., Xavier, J.B., and Foster, K.R. (2009) The sociobiology of biofilms. FEMS Microbiol Rev 33: 206-224.
44. Niba, E., Tabe, E., Naka, Y., Nagase, M., Mori, H., and Kitakawa, M. (2007) A genome-wide approach to identify the genes involved in biofilm formation in E. coli. DNA Res 14: 237-246.
45. Nueda, M.J., Conesa, A., Westerhuis, J.A., Hoefsloot, H.C.J., Smilde, A.K., Talon, M., and Ferrer, A. (2007) Discovering gene expression patterns in time course microarray experiments by anova-sca. Bioinformatics 23: 1792-1800.
46. O'Toole, G., Kaplan, H.B., and Kolter, R. (2000) Biofilm formation as microbial development. Annu Rev Microbiol 54: 49-79.
47. Pinero-Fernandez, S., Chimerel, C., Keyser, U.F., and Summers, D.K. (2011) Indole transport across Escherichia coli membranes. J Bacteriol 193: 1793-1798.
48. Posfai, G., Plunkett, G., III, Feher, T., Frisch, D., Keil, G.M., Umenhoffer, K., etal. (2006) Emergent properties of reduced-genome Escherichia coli. Science 312: 1044-1046.
49. Pratt, L.A., and Kolter, R. (1998) Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili. Mol Microbiol 30: 285-293.
50. Prigent-Combaret, C., Prensier, G., Le Thi, T.T., Vidal, O., Lejeune, P., and Dorel, C. (2000) Developmental pathway for biofilm formation in curli-producing Escherichia coli strains: role of flagella, curli and colanic acid. Environ Microbiol 2: 450-464.
51. Reisner, A., Haagensen, J.A.J., Schembri, M.A., Zechner, E.L., and Molin, S. (2003) Development and maturation of Escherichia coli K-12 biofilms. Mol Microbiol 48: 933-946.
52. Römling, U., Gomelsky, M., and Galperin, M.Y. (2005) C-di-GMP: the dawning of a novel bacterial signalling system. Mol Microbiol 57: 629-639.
53. Saldaña, Z., Xicohtencatl-Cortes, J., Avelino, F., Phillips, A.D., Kaper, J.B., Puente, J.L., and Girón, J.A. (2009) Synergistic role of curli and cellulose in cell adherence and biofilm formation of attaching and effacing Escherichia coli and identification of Fis as a negative regulator of curli. Environ Microbiol 11: 992-1006.
54. Sambrook, J., and Russell, D.W. (2001) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY, USA: Cold Spring Harbor Laboratory Press.
55. Sauer, K. (2003) The genomics and proteomics of biofilm formation. Genome Biol 4: 219.
56. Schaefer, A.L., Greenberg, E.P., Oliver, C.M., Oda, Y., Huang, J.J., Bittan-Banin, G., etal. (2008) A new class of homoserine lactone quorum-sensing signals. Nature 454: 595-599.
57. Schembri, M., Ussery, D., Workman, C., Hasman, H., and Klemm, P. (2002) DNA microarray analysis of fim mutations in Escherichia coli. Mol Genet Genomics 267: 721-729.
58. Schembri, M.A., Kjaergaard, K., and Klemm, P. (2003) Global gene expression in Escherichia coli biofilms. Mol Microbiol 48: 253-267.
59. Seshasayee, A.S.N., Fraser, G.M., Babu, M.M., and Luscombe, N.M. (2009) Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res 19: 79-91.
60. Simm, R., Morr, M., Kader, A., Nimtz, M., and Römling, U. (2004) GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility. Mol Microbiol 53: 1123-1134.
61. Singh, P.K., Parsek, M.R., Greenberg, E.P., and Welsh, M.J. (2002) A component of innate immunity prevents bacterial biofilm development. Nature 417: 552-555.
62. Smalley, D.J., Whiteley, M., and Conway, T. (2003) In search of the minimal Escherichia coli genome. Trends Microbiol 11: 6-8.
63. Surette, M.G., Miller, M.B., and Bassler, B.L. (1999) Quorum sensing in Escherichia coli, Salmonella typhimurium, and Vibrio harveyi: a new family of genes responsible for autoinducer production. Proc Natl Acad Sci USA 96: 1639-1644.
64. Tenorio, E., Saeki, T., Fujita, K., Kitakawa, M., Baba, T., Mori, H., and Isono, K. (2003) Systematic characterization of Escherichia coli genes/ORFs affecting biofilm formation. FEMS Microbiol Lett 225: 107-114.
65. Tremoulet, F., Duche, O., Namane, A., Martinie, B., and Labadie, J. (2002) A proteomic study of Escherichia coli O 157:H 7 NCTC 12900 cultivated in biofilm or in planktonic growth mode. FEMS Microbiol Lett 215: 7-14.
66. Tuckerman, J.R., Gonzalez, G., Sousa, E.H.S., Wan, X., Saito, J.A., Alam, M., and Gilles-Gonzalez, M.-A. (2009) An oxygen-sensing diguanylate cyclase and phosphodiesterase couple for c-di-GMP control. Biochemistry 48: 9764-9774.
67. Valle, J., Da Re, S., Schmid, S., Skurnik, D., D'Ari, R., and Ghigo, J.M. (2008) The amino acid valine is secreted in continuous-flow bacterial biofilms. J Bacteriol 190: 264-274.
68. Van Houdt, R., and Michiels, C.W. (2005) Role of bacterial cell surface structures in Escherichia coli biofilm formation. Res Microbiol 156: 626-633.
69. Wang, X., Preston, J.F., and Romeo, T. (2004) The pgaABCD locus of Escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm formation. J Bacteriol 186: 2724-2734.
70. Wood, T.K. (2009) Insights on Escherichia coli biofilm formation and inhibition from whole-transcriptome profiling. Environ Microbiol 11: 1-15.
71. Zhang, X.S., Garcia-Contreras, R., and Wood, T.K. (2008) Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA). ISME J 2: 615-631.