Nucleic Acids Research, Vol 27, Issue 19 3821-3835, Copyright © 1999 by Oxford University Press
CS Richmond, JD Glasner, R Mau, H Jin and FR Blattner
We have established high resolution methods for global monitoring of gene
expression in Escherichia coli. Hybridization of radiolabeled cDNA to spot
blots on nylon membranes was compared to hybridization of
fluorescently-labeled cDNA to glass microarrays for efficiency and
reproducibility. A complete set of PCR primers was created for all 4290
annotated open reading frames (ORFs) from the complete genome sequence of
E.coli K-12 (MG1655). Glass- and nylon-based arrays of PCR products were
prepared and used to assess global changes in gene expression. Full-length
coding sequences for array printing were generated by two- step PCR
amplification. In this study we measured changes in RNA levels after
exposure to heat shock and following treatment with isopropyl-
beta-D-thiogalactopyranoside (IPTG). Both radioactive and fluorescence-
based methods showed comparable results. Treatment with IPTG resulted in
high level induction of the lacZYA and melAB operons. Following heat shock
treatment 119 genes were shown to have significantly altered expression
levels, including 35 previously uncharacterized ORFs and most genes of the
heat shock stimulon. Analysis of spot intensities from hybridization to
replicate arrays identified sets of genes with signals consistently above
background suggesting that at least 25% of genes were expressed at
detectable levels during growth in rich media.
ARTICLES
Genome-wide expression profiling in Escherichia coli K-12
Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA. craig@genetics.wisc.edu
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|
|
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|
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|
|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
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|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
 |
|
 M. M. Riehle, A. F. Bennett, R. E. Lenski, and A. D. Long Evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperature Physiol Genomics, June 24, 2003; 14(1): 47 - 58. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. LI, K. COLE, and S. ALTMAN The effect of a single, temperature-sensitive mutation on global gene expression in Escherichia coli RNA, May 1, 2003; 9(5): 518 - 532. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
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|
|
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|
|
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|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
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|
|
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|
|
|
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|
|
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 S. A. Lesley, J. Graziano, C. Y. Cho, M. W. Knuth, and H. E. Klock Gene expression response to misfolded protein as a screen for soluble recombinant protein Protein Eng. Des. Sel., February 1, 2002; 15(2): 153 - 160. [Abstract] [Full Text] [PDF]
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H. Urakawa, P. A. Noble, S. El Fantroussi, J. J. Kelly, and D. A. Stahl Single-Base-Pair Discrimination of Terminal Mismatches by Using Oligonucleotide Microarrays and Neural Network Analyses Appl. Envir. Microbiol., January 1, 2002; 68(1): 235 - 244. [Abstract] [Full Text] [PDF]
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G. J. Schut, J. Zhou, and M. W. W. Adams DNA Microarray Analysis of the Hyperthermophilic Archaeon Pyrococcus furiosus: Evidence for a New Type of Sulfur-Reducing Enzyme Complex J. Bacteriol., December 15, 2001; 183(24): 7027 - 7036. [Abstract] [Full Text] [PDF]
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L. Wu, D. K. Thompson, G. Li, R. A. Hurt, J. M. Tiedje, and J. Zhou Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment Appl. Envir. Microbiol., December 1, 2001; 67(12): 5780 - 5790. [Abstract] [Full Text] [PDF]
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C. Rosenow, R. M. Saxena, M. Durst, and T. R. Gingeras Prokaryotic RNA preparation methods useful for high density array analysis: comparison of two approaches Nucleic Acids Res., November 15, 2001; 29(22): e112 - e112. [Abstract] [Full Text] [PDF]
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J. W. Campbell and J. E. Cronan Jr. Escherichia coli FadR Positively Regulates Transcription of the fabB Fatty Acid Biosynthetic Gene J. Bacteriol., October 15, 2001; 183(20): 5982 - 5990. [Abstract] [Full Text] [PDF]
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T. K. Van Dyk, E. J. DeRose, and G. E. Gonye LuxArray, a High-Density, Genomewide Transcription Analysis of Escherichia coli Using Bioluminescent Reporter Strains J. Bacteriol., October 1, 2001; 183(19): 5496 - 5505. [Abstract] [Full Text] [PDF]
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S. Karlin, J. Mrazek, A. Campbell, and D. Kaiser Characterizations of Highly Expressed Genes of Four Fast-Growing Bacteria J. Bacteriol., September 1, 2001; 183(17): 5025 - 5040. [Abstract] [Full Text] [PDF]
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J. Comander, G. M. Weber, M. A. Gimbrone Jr., and G. Garcia-Cardena Argus---A New Database System for Web-Based Analysis of Multiple Microarray Data Sets Genome Res., September 1, 2001; 11(9): 1603 - 1610. [Abstract] [Full Text] [PDF]
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P. J. Pomposiello, M. H. J. Bennik, and B. Demple Genome-Wide Transcriptional Profiling of the Escherichia coli Responses to Superoxide Stress and Sodium Salicylate J. Bacteriol., July 1, 2001; 183(13): 3890 - 3902. [Abstract] [Full Text] [PDF]
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D. R. Smulski, L. L. Huang, M. P. McCluskey, M. J. G. Reeve, A. C. Vollmer, T. K. Van Dyk, and R. A. LaRossa Combined, Functional Genomic-Biochemical Approach to Intermediary Metabolism: Interaction of Acivicin, a Glutamine Amidotransferase Inhibitor, with Escherichia coli K-12 J. Bacteriol., June 1, 2001; 183(11): 3353 - 3364. [Abstract] [Full Text]
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S. Lucchini, A. Thompson, and J. C. D. Hinton Microarrays for microbiologists Microbiology, June 1, 2001; 147(6): 1403 - 1414. [Full Text] [PDF]
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H. Tao, R. Gonzalez, A. Martinez, M. Rodriguez, L. O. Ingram, J. F. Preston, and K. T. Shanmugam Engineering a Homo-Ethanol Pathway in Escherichia coli: Increased Glycolytic Flux and Levels of Expression of Glycolytic Genes during Xylose Fermentation J. Bacteriol., May 15, 2001; 183(10): 2979 - 2988. [Abstract] [Full Text]
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J. Qian, B. Stenger, C. A. Wilson, J. Lin, R. Jansen, S. A. Teichmann, J. Park, W. G. Krebs, H. Yu, V. Alexandrov, et al. PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information Nucleic Acids Res., April 15, 2001; 29(8): 1750 - 1764. [Abstract] [Full Text] [PDF]
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Y. Dong, J. D. Glasner, F. R. Blattner, and E. W. Triplett Genomic Interspecies Microarray Hybridization: Rapid Discovery of Three Thousand Genes in the Maize Endophyte, Klebsiella pneumoniae 342, by Microarray Hybridization with Escherichia coli K-12 Open Reading Frames Appl. Envir. Microbiol., April 1, 2001; 67(4): 1911 - 1921. [Abstract] [Full Text]
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C. N. Arnold, J. McElhanon, A. Lee, R. Leonhart, and D. A. Siegele Global Analysis of Escherichia coli Gene Expression during the Acetate-Induced Acid Tolerance Response J. Bacteriol., April 1, 2001; 183(7): 2178 - 2186. [Abstract] [Full Text]
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U. Zuber, K. Drzewiecki, and M. Hecker Putative Sigma Factor SigI (YkoZ) of Bacillus subtilis Is Induced by Heat Shock J. Bacteriol., February 15, 2001; 183(4): 1472 - 1475. [Abstract] [Full Text]
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T. K. Van Dyk, Y. Wei, M. K. Hanafey, M. Dolan, M. J. G. Reeve, J. A. Rafalski, L. B. Rothman-Denes, and R. A. LaRossa A genomic approach to gene fusion technology PNAS, February 8, 2001; (2001) 41620498. [Abstract] [Full Text]
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K.-i. Yoshida, K. Kobayashi, Y. Miwa, C.-M. Kang, M. Matsunaga, H. Yamaguchi, S. Tojo, M. Yamamoto, R. Nishi, N. Ogasawara, et al. Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis Nucleic Acids Res., February 1, 2001; 29(3): 683 - 692. [Abstract] [Full Text] [PDF]
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Y. Wei, J.-M. Lee, C. Richmond, F. R. Blattner, J. A. Rafalski, and R. A. LaRossa High-Density Microarray-Mediated Gene Expression Profiling of Escherichia coli J. Bacteriol., January 15, 2001; 183(2): 545 - 556. [Abstract] [Full Text]
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M. M. Riehle, A. F. Bennett, and A. D. Long Genetic architecture of thermal adaptation in Escherichia coli PNAS, January 5, 2001; (2001) 21448998. [Abstract] [Full Text]
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M.-J. Han, S. S. Yoon, and S. Y. Lee Proteome Analysis of Metabolically Engineered Escherichia coli Producing Poly(3-Hydroxybutyrate) J. Bacteriol., January 1, 2001; 183(1): 301 - 308. [Abstract] [Full Text]
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M. D. Kane, T. A. Jatkoe, C. R. Stumpf, J. Lu, J. D. Thomas, and S. J. Madore Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays Nucleic Acids Res., November 15, 2000; 28(22): 4552 - 4557. [Abstract] [Full Text] [PDF]
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S. Peterson, R. T. Cline, H. Tettelin, V. Sharov, and D. A. Morrison Gene Expression Analysis of the Streptococcus pneumoniae Competence Regulons by Use of DNA Microarrays J. Bacteriol., November 1, 2000; 182(21): 6192 - 6202. [Abstract] [Full Text]
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