Environmental and genetic factors that contribute to Escherichia coli K-12 biofilm formation

Archives of Microbiology

Volumn 192, Issue 9, 2010, Pages 715-728

  Prü, Birgit M ^a   Verma, Karan ^a   Samanta, Priyankar ^a   Sule, Preeti ^a   Kumar, Sunil ^a   Wu, Jianfei ^a,b   Christianson, David ^a   Horne, Shelley M ^a   Stafslien, Shane J ^a   Wolfe, Alan J ^c   Denton, Anne ^b  

^a NORTH DAKOTA STATE UNIVERSITY   (United States)

^b North Dakota State University   (United States)

^c LOYOLA UNIVERSITY CHICAGO   (United States)

Author keywords

Acetate metabolism; Biofilm formation; Environmental conditions; Genetic factors; High throughput experimentation; Two component signaling; Vector item pattern mining algorithm

Indexed keywords

ACETIC ACID; ACETYL COENZYME A; MUTANT PROTEIN; PHOSPHATE; PYRUVIC ACID; CULTURE MEDIUM;

ALGORITHM; ARTICLE; BACTERIAL FLAGELLUM; BACTERIAL GENETICS; BACTERIAL GROWTH; BACTERIAL STRAIN; BIOFILM; BIOMASS PRODUCTION; CARBON SOURCE; CELL ORGANELLE; CELL SURFACE; CONTROLLED STUDY; CULTURE MEDIUM; ENVIRONMENTAL FACTOR; ENZYME METABOLISM; ESCHERICHIA COLI K 12; FUNCTIONAL MORPHOLOGY; HIGH THROUGHPUT SCREENING; LIPID METABOLISM; LOW TEMPERATURE PROCEDURES; METABOLIC REGULATION; MICROARRAY ANALYSIS; MICROBIAL ACTIVITY; MICROBIAL BIOMASS; MICROBIAL MORPHOLOGY; NONHUMAN; PHENOTYPIC VARIATION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SCANNING ELECTRON MICROSCOPY; SIGNAL TRANSDUCTION; STRUCTURE ANALYSIS; TEMPERATURE DEPENDENCE; TRANSCRIPTION REGULATION; AUTOMATED PATTERN RECOGNITION; DNA MICROARRAY; ENVIRONMENT; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; TEMPERATURE;

ACETIC ACID; ALGORITHMS; BIOFILMS; CULTURE MEDIA; ENVIRONMENT; ESCHERICHIA COLI K12; GENE EXPRESSION REGULATION, BACTERIAL; MICROSCOPY, ELECTRON, SCANNING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; TEMPERATURE;

ESCHERICHIA COLI K12;

EID: 77956224960     PISSN: 03028933     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00203-010-0599-z     Document Type: Article

References (54)

1. CS Barker BM Prü P Matsumura 2004 Increased motility of Escherichia coli by insertion sequence element integration into the regulatory region of the flhD operon J Bacteriol 186 7529 7537 10.1128/JB.186.22.7529-7537.2004 15516564
2. C Beloin J Valle P Latour-Lambert P Faure M Kzreminski D Balestrino JA Haagensen S Molin G Prensier B Arbeille JM Ghigo 2004 Global impact of mature biofilm lifestyle on Escherichia coli K-12 gene expression Mol Microbiol 51 659 674 10.1046/j.1365-2958.2003.03865.x 14731270
3. P Bertin E Terao EH Lee P Lejeune C Colson A Danchin E Collatz 1994 The H-NS protein is involved in the biogenesis of flagella in Escherichia coli J Bacteriol 176 5537 5540 8071234
4. P Bertin F Hommais E Krin O Soutourina C Tendeng S Derzelle A Danchin 2001 H-NS and H-NS-like proteins in Gram-negative bacteria and their multiple role in the regulation of bacterial metabolism Biochimie 83 235 241 10.1016/S0300-9084(01)01247-0 11278074
5. C Besemann A Denton NJ Carr BM Prü 2006 BISON: Bio-Interface for the Semi-global analysis Of Network patterns Source Code Biol Med 1 8 10.1186/1751-0473-1-8 17147788
6. BR Bochner 2009 Global phenotypic characterization of bacteria FEMS Microbiol Rev 33 191 205 10.1111/j.1574-6976.2008.00149.x 19054113
7. BR Bochner P Gadzinski E Panomitros 2001 Phenotype microarrays for high-throughput phenotypic testing and assay of gene function Genome Res 11 1246 1255 10.1101/gr.186501 11435407
8. BR Bochner L Giovannetti C Viti 2008 Important discoveries from analysing bacterial phenotypes Mol Microbiol 70 274 280 10.1111/j.1365-2958.2008.06383.x 18681942
9. TD Brown MC Jones-Mortimer HL Kornberg 1977 The enzymic interconversion of acetate and acetyl-coenzyme A in Escherichia coli J Gen Microbiol 102 327 336 21941
10. RG Chavez AF Alvarez T Romeo D Georgillis 2010 The physiological stimulus for the BarA sensor kinase J Bacteriol 192 2009 2012 10.1128/JB.01685-09 20118252
11. JW Costerton PS Stewart EP Greenberg 1999 Bacterial biofilms: a common cause of persistent infections Science 284 1318 1322 10.1126/science.284.5418. 1318 10334980
12. DG Davies MR Parsek JP Pearson BH Iglewski JW Costerton EP Greenberg 1998 The involvement of cell-to-cell signals in the development of a bacterial biofilm Science 280 295 298 10.1126/science.280.5361.295 9535661
13. AM Denton J Wu 2009 Data mining of vector-item patterns using neighborhood histograms Knowl Informat Syst 21 173 199 10.1007/s10115-009-0201-7
14. AM Denton J Wu MK Townsend P Sule BM Prü 2008 Relating gene expression data on two-component systems to functional annotations in Escherichia coli BMC Bioinformatics 9 294 10.1186/1471-2105-9-294 18578884
15. J Domka J Lee T Bansal TK Wood 2007 Temporal gene-expression in Escherichia coli K-12 biofilms Environ Microbiol 9 332 346 10.1111/j.1462-2920. 2006.01143.x 17222132
16. CE Fredericks S Shibata SI Aizawa SA Reimann AJ Wolfe 2006 Acetyl phosphate-sensitive regulation of flagellar biogenesis and capsular biosynthesis depends on the Rcs phosphorelay Mol Microbiol 61 734 747 10.1111/j.1365-2958. 2006.05260.x 16776655
17. R Gao AM Stock 2009 Biological insights from structures of two-component proteins Annu Rev Microbiol 63 133 154 10.1146/annurev.micro.091208.073214 19575571
18. P Golby S Davies DJ Kelly JR Guest SC Andrews 1999 Identification and characterization of a two-component sensor-kinase and response-regulator system (DcuS-DcuR) controlling gene expression in response to C4-dicarboxylates in Escherichia coli J Bacteriol 181 1238 1248 9973351
19. CC Goller T Romeo 2008 Environmental influences on biofilm development Curr Top Microbiol Immunol 322 37 66 10.1007/978-3-540-75418-3-3 18453271
20. D Hagiwara M Sugiura T Oshima H Mori H Aiba T Yamashino T Mizuno 2003 Genome-wide analyses revealing a signaling network of the RcsC-YojN-RcsB phosphorelay system in Escherichia coli J Bacteriol 185 5735 5746 10.1128/JB.185.19.5735-5746.2003 13129944
21. A Heydorn AT Nielsen M Hentzer C Sternberg M Givskov BK Ersboll S Molin 2000 Quantification of biofilm structures by the novel computer program COMSTAT Microbiology 146 2395 2407 11021916
22. A Heydorn B Ersboll J Kato M Hentzer MR Parsek T Tolker-Nielsen M Givskov S Molin 2002 Statistical analysis of Pseudomonas aeruginosa biofilm development: impact of mutations in genes involved in twitching motility, cell-to-cell signaling, and stationary-phase sigma factor expression Appl Environ Microbiol 68 2008 2017 10.1128/AEM.68.4.2008-2017.2002 11916724
23. F Hommais E Krin C Laurent-Winter O Soutourina A Malpertuy JP Le Caer A Danchin P Bertin 2001 Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS Mol Microbiol 40 20 36 10.1046/j.1365-2958.2001.02358.x 11298273
24. Hu LI, Lima BP, Wolfe AF (2010) Bacterial protein acetylation: the dawning of a new age. Mol Microbiol. doi: 10.111/j.1365-2958.2010.07204.x
25. M Kanehisa S Goto 2000 KEGG: kyoto encyclopedia of genes and genomes Nucleic Acids Res 28 27 30 10.1093/nar/28.1.27 10592173
26. S Kumari CM Beatty DF Browning SJ Busby EJ Simel G Hovel-Miner AJ Wolfe 2000 Regulation of acetyl coenzyme A synthetase in Escherichia coli J Bacteriol 182 4173 4179 10.1128/JB.182.15.4173-4179.2000 10894724
27. X Liu P Matsumura 1994 The FlhD/FlhC complex, a transcriptional activator of the Escherichia coli flagellar class II operons J Bacteriol 176 7345 7351 7961507
28. RD Monds GA O'Toole 2009 The developmental model of microbial biofilms: ten years of a paradigm up for review Trends Microbiol 17 73 87 10.1016/j.tim.2008.11.001 19162483
29. Myers RH, Montgomery DC (1995) Response surface methodology. Wiley, New York
30. GA O'Toole LA Pratt PI Watnick DK Newman VB Weaver R Kolter 1999 Genetic approaches to study of biofilms Methods Enzymol 310 91 109 10.1016/S0076- 6879(99)10008-9 10547784
31. T Oshima H Aiba Y Masuda S Kanaya M Sugiura BL Wanner H Mori T Mizuno 2002 Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12 Mol Microbiol 46 281 291 10.1046/j.1365-2958.2002.03170.x 12366850
32. LA Pratt R Kolter 1998 Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili Mol Microbiol 30 285 293 10.1046/j.1365-2958.1998.01061.x 9791174
33. BM Prü C Besemann A Denton AJ Wolfe 2006 A complex transcription network controls the early stages of biofilm development by Escherichia coli J Bacteriol 188 3731 3739 10.1128/JB.01780-05 16707665
34. D Ren LA Bedzyk SM Thomas RW Ye TK Wood 2004 Gene expression in Escherichia coli biofilms Appl Microbiol Biotechnol 64 515 524 10.1007/s00253-003-1517-y 14727089
35. K Sauer AK Camper GD Ehrlich JW Costerton DG Davies 2002 Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm J Bacteriol 184 1140 1154 10.1128/jb.184.4.1140-1154.2002 11807075
36. MA Schembri K Kjaergaard P Klemm 2003 Global gene expression in Escherichia coli biofilms Mol Microbiol 48 253 267 10.1046/j.1365-2958.2003. 03432.x 12657059
37. R Shamir A Maron-Katz A Tanay C Linhart I Steinfeld R Sharan Y Shiloh R Elkon 2005 EXPANDER-an integrative program suite for microarray data analysis BMC Bioinform 6 232 10.1186/1471-2105-6-232
38. Silhavy TJ, Berman ML, Enquist LW (1984) Experiments with gene fusions. Cold Spring Harbor Laboratory, Cold Spring Harbor
39. SJ Stafslien JA Bahr JM Feser JC Weisz BJ Chisholm TE Ready P Boudjouk 2006 Combinatorial materials research applied to the development of new surface coatings I: a multiwell plate screening method for the high-throughput assessment of bacterial biofilm retention on surfaces J Comb Chem 8 156 162 10.1021/cc050047m 16529509
40. S Stafslien J Daniels B Chisholm D Christianson 2007 Combinatorial materials research applied to the development of new surface coatings III. Utilisation of a high-throughput multiwell plate screening method to rapidly assess bacterial biofilm retention on antifouling surfaces Biofouling 23 37 44 10.1080/08927010601127311 17453727
41. PS Stewart BM Peyton WJ Drury R Murga 1993 Quantitative observations of heterogeneities in Pseudomonas aeruginosa biofilms Appl Environ Microbiol 59 327 329 8439159
42. P Sule T Wadhawan NJ Carr SM Horne AJ Wolfe BM Prü 2009 A combination of assays reveals biomass differences in biofilms formed by Escherichia coli mutants Lett Appl Microbiol 49 299 304 10.1111/j.1472-765X. 2009.02659.x 19552773
43. BH Sung CH Lee BJ Yu JH Lee JY Lee MS Kim FR Blattner SC Kim 2006 Development of a biofilm production-deficient Escherichia coli strain as a host for biotechnological applications Appl Environ Microbiol 72 3336 3342 10.1128/AEM.72.5.3336-3342.2006 16672475
44. Q Wang Y Zhang C Yang H Xiong Y Lin J Yao H Li L Xie W Zhao Y Yao ZB Ning R Zeng Y Xiong KL Guan S Zhao GP Zhao 2010 Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux Science 19 1004 1007 10.1126/science.1179687
45. Wolfe AJ (2005a) Acetyl phosphate is a global signal. In: Prü BM (ed) Global regulatory networks in enteric bacteria. Research Signpost, Trivandrum, pp 31-44
46. AJ Wolfe 2005 The acetate switch Microbiol Mol Biol Rev 69 12 50 10.1128/MMBR.69.1.12-50.2005 15755952
47. AJ Wolfe 2010 Physiologically relevant small phosphodonors link metabolism to signal transduction Curr Opin Microbiol 13 204 209 10.1016/j.mib.2010.01.002 20117041
48. AJ Wolfe HC Berg 1989 Migration of bacteria in semisolid agar Proc Natl Acad Sci USA 86 6973 6977 10.1073/pnas.86.18.6973 2674941
49. Wolfe AJ, Visick KL (2010) The second messenger cyclic di-GMP. American Society for Microbiology, Washington, DC
50. AJ Wolfe DE Chang JD Walker JE Seitz-Partridge MD Vidaurri CF Lange BM Prü MC Henk JC Larkin T Conway 2003 Evidence that acetyl phosphate functions as a global signal during biofilm development Mol Microbiol 48 977 988 10.1046/j.1365-2958.2003.03457.x 12753190
51. TK Wood 2009 Insights on Escherichia coli biofilm formation and inhibition from whole-transcriptome profiling Environ Microbiol 11 1 15 10.1111/j.1462-2920.2008.01768.x 19125816
52. BJ Yu JA Kim JH Moon SE Ryu JG Pan 2008 The diversity of lysine-acetylated proteins in Escherichia coli J Microbiol Biotechnol 18 1529 1536 18852508
53. J Zhang R Sprung J Pei X Tan S Kim H Zhu CF Liu NV Grishin Y Zhao 2009 Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli Mol Cell Proteomics 8 215 225 18723842
54. D Zheng C Constantinidou JL Hobman SD Minchin 2004 Identification of the CRP regulon using in vitro and in vivo transcriptional profiling Nucleic Acids Res 32 5874 5893 10.1093/nar/gkh908 15520470