Gene expression profiling of Escherichia coli in response to interactions with the lettuce rhizosphere

Journal of Applied Microbiology

Volumn 113, Issue 5, 2012, Pages 1076-1086

  Hou, Z ^a   Fink, R C ^a   Black, E P ^a,b   Sugawara, M ^a   Zhang, Z ^a,c   Diez Gonzalez, F ^a   Sadowsky, M J ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b Ecolab Inc ^*  (United States)

^c Metabolix Inc   (United States)

Author keywords

Attachment; Colonization; Escherichia coli; Lettuce rhizosphere; Microarray

Indexed keywords

ASSAYS; BIOSYNTHESIS; CONFOCAL MICROSCOPY; ESCHERICHIA COLI; GENE EXPRESSION; SOILS;

ASSAY SYSTEM; ATTACHMENT; BACTERIAL GENES; COLONISATION; CURLI PRODUCTION; E. COLI; GENE EXPRESSION PROFILING; LETTUCE RHIZOSPHERE; MICROARRAY ANALYSIS; TRANSCRIPTIONAL CHANGES;

LETTUCE;

BIOFILM; COLIFORM BACTERIUM; COLONIZATION; GENE EXPRESSION; HYDROPONICS; LEAFY VEGETABLE; PATHOGEN; PROTEIN; RHIZOSPHERE;

ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; CELL ADHESION; CONFOCAL LASER MICROSCOPY; CONTROLLED STUDY; CRL GENE; CSGA GENE; DOWN REGULATION; ESCHERICHIA COLI; FLIN GENE; GENE EXPRESSION PROFILING; HYDROPONICS; LETTUCE; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT ROOT; PROTEIN SYNTHESIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RHIZOSPHERE; TRANSCRIPTION REGULATION; UPREGULATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; LACTUCA;

EID: 84867690919     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2012.05412.x     Document Type: Article

References (43)

1. Armstrong, G.L., Hollingsworth, J. and Morris, J.G. (1996) Emerging foodborne pathogens: Escherichia coli O157:H7 as a model of entry of a new pathogen into the food supply of the developed world. Epidemiol Rev 18, 29-51.
2. Arnqvist, A., Olsen, A., Pfeifer, J., Russell, D.G. and Normark, S. (1992) The Crl protein activates cryptic genes for curli formation and fibronectin binding in Escherichia coli Hb101. Mol Microbiol 6, 2443-2452.
3. Austin, J.W., Sanders, G., Kay, W.W. and Collinson, S.K. (1998) Thin aggregative fimbriae enhance Salmonella enteritidis biofilm formation. FEMS Microbiol Lett 162, 295-301.
4. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M. et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2, 2006.0008, doi: 10.1038/msb4100050.
5. Barak, J.D., Gorski, L., Naraghi-Arani, P. and Charkowski, A.O. (2005) Salmonella enterica virulence genes are required for bacterial attachment to plant tissue. Appl Environ Microbiol 71, 5685-5691.
6. Berger, C.N., Sodha, S.V., Shaw, R.K., Griffin, P.M., Pink, D., Hand, P. and Frankel, G. (2010) Fresh fruit and vegetables as vehicles for the transmission of human pathogens. Environ Microbiol 12, 2385-2397.
7. Beuchat, L.R. (1996) Pathogenic microorganisms associated with fresh produce. J Food Prot 59, 204-216.
8. Bloemberg, G.V., Otoole, G.A., Lugtenberg, B.J.J. and Kolter, R. (1997) Green fluorescent protein as a marker for Pseudomonas spp. Appl Environ Microbiol 63, 4543-4551.
9. Bougdour, A., Lelong, C. and Geiselmann, J. (2004) Crl, a low temperature-induced protein in Escherichia coli that binds directly to the stationary phase sigma subunit of RNA polymerase. J Biol Chem 279, 19540-19550.
10. Bowtell, D. and Sambrook, J. (2003) DNA Microarrays: A Molecular Cloning Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
11. Brandl, M.T. (2006) Fitness of human enteric pathogens on plants and implications for food safety. Annu Rev Phytopathol 44, 367-392.
12. Caspersen, S., Sundin, P., Munro, M., Athalsteinsson, S., Hooker, J.E. and Jensen, P. (1999) Interactive effects of lettuce (Lactuca sativa L.), irradiance, and ferulic acid in axenic, hydroponic culture. Plant Soil 210, 115-126.
13. Chang, W.S., Franck, W.L., Cytryn, E., Jeong, S., Joshi, T., Emerich, D.W., Sadowsky, M.J., Xu, D. et al. (2007) An oligonucleotide microarray resource for transcriptional profiling of Bradyrhizobium japonicum. Mol Plant Microbe Interact 20, 1298-1307.
14. Cui, X., Kerr, M.K. and Churchill, G.A. (2003) Transformations for cDNA microarray data. Stat Appl Genet Mol Biol 2, Article 4.
15. Cytryn, E.J., Sangurdekar, D.P., Streeter, J.G., Franck, W.L., Chang, W.S., Stacey, G., Emerich, D.W., Joshi, T. et al. (2007) Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. J Bacteriol 189, 6751-6762.
16. Darrah, P.R. (1991) Models of the rhizosphere.1. Microbial-population dynamics around a root releasing soluble and insoluble carbon. Plant Soil 133, 187-199.
17. Doyle, M.P. and Erickson, M.C. (2008) Summer meeting 2007 - the problems with fresh produce: an overview. J Appl Microbiol 105, 317-330.
18. Fink, R.C., Black, E., Hou, Z., Sugawara, M., Sadowsky, M.J. and Diez-Gonzalez, F. (2012) Transcriptional responses of Escherichia coli K12 and O157:H7 in association with lettuce leaves. Appl Environ Microbiol 78, 1752-1764.
19. Franz, E. and van Bruggen, A.H.C. (2008) Ecology of E. coli O157:H7 and Salmonella enterica in the primary vegetable production chain. Crit Rev Microbiol 34, 143-161.
20. Garg, R.P., Huang, J.Z., Yindeeyoungyeon, W., Denny, T.P. and Schell, M.A. (2000) Multicomponent transcriptional regulation at the complex promoter of the exopolysaccharide I biosynthetic operon of Ralstonia solanacearum. J Bacteriol 182, 6659-6666.
21. Hayashi, T., Makino, K., Ohnishi, M., Kurokawa, K., Ishii, K., Yokoyama, K., Han, C.G., Ohtsubo, E. et al. (2001) Complete genome sequence of enterohemorrhagic Escherichia coli O157: H7 and genomic comparison with a laboratory strain K-12. DNA Res 8, 11-22.
22. Jablasone, J., Warriner, K. and Griffiths, M. (2005) Interactions of Escherichia coli O157:H7, Salmonella typhimurium and Listeria monocytogenes plants cultivated in a gnotobiotic system. Int J Food Microbiol 99, 7-18.
23. Jensen, K.F. (1993) The Escherichia coli K-12 wild types W3110 and MG1655 have and rph frameshift mutation that leads to pyrimidine starvation due to low pyre expression levels. J Bacteriol 175, 3401-3407.
24. Jeter, C. and Matthysse, A.G. (2005) Characterization of the binding of diarrheagenic strains of E. coli to plant surfaces and the role of curli in the interaction of the bacteria with alfalfa sprouts. Mol Plant Microbe Interact 18, 1235-1242.
25. Kerr, M.K., Martin, M. and Churchill, G.A. (2000) Analysis of variance for gene expression microarray data. J Comput Biol 7, 819-837.
26. Li, H. and Sourjik, V. (2011) Assembly and stability of flagellar motor in Escherichia coli. Mol Microbiol 80, 886-899.
27. Lindow, S.E. and Brandl, M.T. (2003) Microbiology of the phyllosphere. Appl Environ Microbiol 69, 1875-1883.
28. Liu, M.Z., Durfee, T., Cabrera, J.E., Zhao, K., Jin, D.J. and Blattner, F.R. (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J Biol Chem 280, 15921-15927.
29. Lugtenberg, B.J.J. and Dekkers, L.C. (1999) What makes Pseudomonas bacteria rhizosphere competent? Environ Microbiol 1, 9-13.
30. Mathusa, E.C., Chen, Y., Enache, E. and Hontz, L. (2010) Non-O157 Shiga Toxin-producing Escherichia coli in foods. J Food Prot 73, 1721-1736.
31. Model, P., Jovanovic, G. and Dworkin, J. (1997) The Escherichia coli phage-shock-protein (psp) operon. Mol Microbiol 24, 255-261.
32. Mora, A., Herrrera, A., Lopez, C., Dahbi, G., Mamani, R., Pita, J.M., Alonso, M.P., Llovo, J. et al. (2011) Characteristics of the Shiga-toxin-producing enteroaggregative Escherichia coli O104:H4 German outbreak strain and of STEC strains isolated in Spain. Int Microbiol 14, 121-141.
33. Ohnishi, M., Tanaka, C., Kuhara, S., Ishii, K., Hattori, M., Kurokawa, K., Yasunaga, T., Makino, K. et al. (1999) Chromosome of the enterohemorrhagic Escherichia coli O157:H7; comparative analysis with K-12 MG1655 revealed the acquisition of a large amount of foreign DNAs. DNA Res 6, 361-368.
34. Olsen, A., Jonsson, A. and Normark, S. (1989) Fibronectin binding mediated by a novel class of surface organelles on Escherichia coli. Nature 338, 652-655.
35. Park, S.Y., Lowder, B., Bilwes, A.M., Blair, D.F. and Crane, B.R. (2006) Structure of FliM provides insight into assembly of the switch complex in the bacterial flagella motor. Proc Nat Acad Sci USA 103, 11886-11891.
36. Paul, K. and Blair, D.F. (2006) Organization of FliN subunits in the flagellar motor of Escherichia coli. J Bacteriol 188, 2502-2511.
37. Solomon, E.B., Yaron, S. and Matthews, K.R. (2002) Transmission of Escherichia coli O157: H7 from contaminated manure and irrigation water to lettuce plant tissue and its subsequent internalization. Appl Environ Microbiol 68, 397-400.
38. Sugawara, M., Cytryn, E.J. and Sadowsky, M.J. (2010) Functional role of Bradyrhizobium japonicum trehalose biosynthesis and metabolism genes during physiological stress and nodulation. Appl Environ Microbiol 76, 1071-1081.
39. Tusher, V.G., Tibshirani, R. and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Nat Acad Sci USA 98, 5116-5121.
40. Vidal, O., Longin, R., Prigent-Combaret, C., Dorel, C., Hooreman, M. and Lejeune, P. (1998) Isolation of an Escherichia coli K-12 mutant strain able to form biofilms on inert surfaces: involvement of a new ompR allele that increases curli expression. J Bacteriol 180, 2442-2449.
41. Yao, J. and Allen, C. (2006) Chemotaxis is required for virulence and competitive fitness of the bacterial wilt pathogen Ralstonia solanacearum. J Bacteriol 188, 3697-3708.
42. Zaslaver, A., Bren, A., Ronen, M., Itzkovitz, S., Kikoin, I., Shavit, S., Liebermeister, W., Surette, M.G. et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3, 623-628.
43. 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.