Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays

Wendisch VF, Zimmer DP, Khodursky A, Peter B, Cozzarelli N, Kustu S (2001)
Analytical Biochemistry 290(2): 205-213.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
Autor*in
Wendisch, Volker F.UniBi ; Zimmer, D. P.; Khodursky, A.; Peter, B.; Cozzarelli, N.; Kustu, S.
Einrichtung
Fakultät für Biologie > Genetik der Prokaryoten
Abstract / Bemerkung
Bacterial messenger RNA (mRNA) is not coherently polyadenylated, whereas mRNA of Eukarya can be separated from stable RNAs by virtue of polyadenylated 3 ' -termini, We have developed a method to isolate Escherichia coil mRNA by polyadenylating it in crude cell extracts with E. coil poly(A) polymerase I and purifying it by oligo(dT) chromatography. Differences in lacZRNA levels were similar with purified mRNA and total RNA in dot blot hydridizations for cultures grown with or without gratuitous induction of the lactose operon, More broadly, changes in gene expression upon induction were similar when cDNAs primed from mRNA or total RNA with random hexanucleotides were hydridized to DNA microarrays for the E. coil genome. Comparable signal intensities were obtained with only 1% as much oligo(dT)-purified mRNA as total RNA, and hence in vitro poly(A) tailing appears to be selective for mRNA. These and additional studies of genome-wide expression with DNA microarrays provide evidence that in vitro poly(A) tailing works universally for E. coil mRNAs, (C) 2001 Academic Press.
Stichworte
polyadenylation; genome; yeast; sequence; lactose operon; messenger-rna; gene-expression; poly(a) polymerase; polyadenylation; messenger rna; DNA microarrays; escherichia coli; polymerase; bacteria; protein
Erscheinungsjahr
2001
Zeitschriftentitel
Analytical Biochemistry
Band
290
Ausgabe
2
Seite(n)
205-213
ISSN
0003-2697
Page URI
https://pub.uni-bielefeld.de/record/1895392

Zitieren

Wendisch VF, Zimmer DP, Khodursky A, Peter B, Cozzarelli N, Kustu S. Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays. Analytical Biochemistry. 2001;290(2):205-213.
Wendisch, V. F., Zimmer, D. P., Khodursky, A., Peter, B., Cozzarelli, N., & Kustu, S. (2001). Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays. Analytical Biochemistry, 290(2), 205-213. https://doi.org/10.1006/abio.2000.4982
Wendisch, Volker F., Zimmer, D. P., Khodursky, A., Peter, B., Cozzarelli, N., and Kustu, S. 2001. “Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays”. Analytical Biochemistry 290 (2): 205-213.
Wendisch, V. F., Zimmer, D. P., Khodursky, A., Peter, B., Cozzarelli, N., and Kustu, S. (2001). Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays. Analytical Biochemistry 290, 205-213.
Wendisch, V.F., et al., 2001. Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays. Analytical Biochemistry, 290(2), p 205-213.
V.F. Wendisch, et al., “Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays”, Analytical Biochemistry, vol. 290, 2001, pp. 205-213.
Wendisch, V.F., Zimmer, D.P., Khodursky, A., Peter, B., Cozzarelli, N., Kustu, S.: Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays. Analytical Biochemistry. 290, 205-213 (2001).
Wendisch, Volker F., Zimmer, D. P., Khodursky, A., Peter, B., Cozzarelli, N., and Kustu, S. “Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays”. Analytical Biochemistry 290.2 (2001): 205-213.

37 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Effects of Kasugamycin on the Translatome of Escherichia coli.
Lange C, Lehr M, Zerulla K, Ludwig P, Schweitzer J, Polen T, Wendisch VF, Soppa J., PLoS One 12(1), 2017
PMID: 28081129
Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes.
Petrova OE, Garcia-Alcalde F, Zampaloni C, Sauer K., Sci Rep 7(), 2017
PMID: 28117413
Use of Metatranscriptomics in Microbiome Research.
Bashiardes S, Zilberman-Schapira G, Elinav E., Bioinform Biol Insights 10(), 2016
PMID: 27127406
Dynamic transcriptional response of Escherichia coli to inclusion body formation.
Baig F, Fernando LP, Salazar MA, Powell RR, Bruce TF, Harcum SW., Biotechnol Bioeng 111(5), 2014
PMID: 24338599
Ribonucleic acid purification.
Martins R, Queiroz JA, Sousa F., J Chromatogr A 1355(), 2014
PMID: 24951289
Comparative community gene expression analysis of Aquificales-dominated geothermal springs.
Hamamura N, Meneghin J, Reysenbach AL., Environ Microbiol 15(4), 2013
PMID: 23279131
Lessons learned and unlearned in periodontal microbiology.
Teles R, Teles F, Frias-Lopez J, Paster B, Haffajee A., Periodontol 2000 62(1), 2013
PMID: 23574465
Extraction of bacterial RNA from soil: challenges and solutions.
Wang Y, Hayatsu M, Fujii T., Microbes Environ 27(2), 2012
PMID: 22791042
Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq.
Yi H, Cho YJ, Won S, Lee JE, Jin Yu H, Kim S, Schroth GP, Luo S, Chun J., Nucleic Acids Res 39(20), 2011
PMID: 21880599
Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity.
Sorek R, Cossart P., Nat Rev Genet 11(1), 2010
PMID: 19935729
Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics.
Stewart FJ, Ottesen EA, DeLong EF., ISME J 4(7), 2010
PMID: 20220791
The TetR-type transcriptional regulator FasR of Corynebacterium glutamicum controls genes of lipid synthesis during growth on acetate.
Nickel J, Irzik K, van Ooyen J, Eggeling L., Mol Microbiol 78(1), 2010
PMID: 20923423
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column.
Shi Y, Tyson GW, DeLong EF., Nature 459(7244), 2009
PMID: 19444216
In vivo labeling and specific magnetic bead separation of RNA for biofilm characterization and stress-induced gene expression analysis in bacteria.
Stankiewicz N, Gold A, Yüksel Y, Berensmeier S, Schwartz T., J Microbiol Methods 79(3), 2009
PMID: 19837116
Microbial community gene expression in ocean surface waters.
Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF., Proc Natl Acad Sci U S A 105(10), 2008
PMID: 18316740
Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.
Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I., PLoS One 3(8), 2008
PMID: 18725995
Global gene expression analysis of glucose overflow metabolism in Escherichia coli and reduction of aerobic acetate formation.
Veit A, Polen T, Wendisch VF., Appl Microbiol Biotechnol 74(2), 2007
PMID: 17273855
Improving lysine production by Corynebacterium glutamicum through DNA microarray-based identification of novel target genes.
Sindelar G, Wendisch VF., Appl Microbiol Biotechnol 76(3), 2007
PMID: 17364200
Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor.
Marincs F, Manfield IW, Stead JA, McDowall KJ, Stockley PG., Biochem J 396(2), 2006
PMID: 16515535
DNA microarray technology for the microbiologist: an overview.
Ehrenreich A., Appl Microbiol Biotechnol 73(2), 2006
PMID: 17043830
The global gene expression response of Escherichia coli to L-phenylalanine.
Polen T, Krämer M, Bongaerts J, Wubbolts M, Wendisch VF., J Biotechnol 115(3), 2005
PMID: 15639085
Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses.
Gyaneshwar P, Paliy O, McAuliffe J, Popham DL, Jordan MI, Kustu S., J Bacteriol 187(3), 2005
PMID: 15659685
Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation.
Gyaneshwar P, Paliy O, McAuliffe J, Jones A, Jordan MI, Kustu S., Proc Natl Acad Sci U S A 102(9), 2005
PMID: 15716358
Bacterial mRNA purification by magnetic capture-hybridization method.
Pang X, Zhou D, Song Y, Pei D, Wang J, Guo Z, Yang R., Microbiol Immunol 48(2), 2004
PMID: 14978333
Genome image programs: visualization and interpretation of Escherichia coli microarray experiments.
Zimmer DP, Paliy O, Thomas B, Gyaneshwar P, Kustu S., Genetics 167(4), 2004
PMID: 15342544
Simultaneous analysis of host and pathogen interactions during an in vivo infection reveals local induction of host acute phase response proteins, a novel bacterial stress response, and evidence of a host-imposed metal ion limited environment.
Motley ST, Morrow BJ, Liu X, Dodge IL, Vitiello A, Ward CK, Shaw KJ., Cell Microbiol 6(9), 2004
PMID: 15272866
Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis.
Netzer R, Krause M, Rittmann D, Peters-Wendisch PG, Eggeling L, Wendisch VF, Sahm H., Arch Microbiol 182(5), 2004
PMID: 15375646
Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection.
Möker N, Brocker M, Schaffer S, Krämer R, Morbach S, Bott M., Mol Microbiol 54(2), 2004
PMID: 15469514
DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate.
Polen T, Rittmann D, Wendisch VF, Sahm H., Appl Environ Microbiol 69(3), 2003
PMID: 12620868
Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine.
Lange C, Rittmann D, Wendisch VF, Bott M, Sahm H., Appl Environ Microbiol 69(5), 2003
PMID: 12732517
The phosphate starvation stimulon of Corynebacterium glutamicum determined by DNA microarray analyses.
Ishige T, Krause M, Bott M, Wendisch VF, Sahm H., J Bacteriol 185(15), 2003
PMID: 12867461
Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression.
Soupene E, van Heeswijk WC, Plumbridge J, Stewart V, Bertenthal D, Lee H, Prasad G, Paliy O, Charernnoppakul P, Kustu S., J Bacteriol 185(18), 2003
PMID: 12949114
Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays.
Wendisch VF., J Biotechnol 104(1-3), 2003
PMID: 12948645
Impact of genomic technologies on studies of bacterial gene expression.
Rhodius V, Van Dyk TK, Gross C, LaRossa RA., Annu Rev Microbiol 56(), 2002
PMID: 12142487
LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli.
Lehnen D, Blumer C, Polen T, Wackwitz B, Wendisch VF, Unden G., Mol Microbiol 45(2), 2002
PMID: 12123461
Characterization of phenotypic changes in Pseudomonas putida in response to surface-associated growth.
Sauer K, Camper AK., J Bacteriol 183(22), 2001
PMID: 11673428
Applications of DNA microarrays in microbial systems.
Ye RW, Wang T, Bedzyk L, Croker KM., J Microbiol Methods 47(3), 2001
PMID: 11714516

34 References

Daten bereitgestellt von Europe PubMed Central.

Quantitative monitoring of gene expression patterns with a complementary DNA microarray.
Schena M, Shalon D, Davis RW, Brown PO., Science 270(5235), 1995
PMID: 7569999
Exploring the new world of the genome with DNA microarrays.
Brown PO, Botstein D., Nat. Genet. 21(1 Suppl), 1999
PMID: 9915498
Exploring the metabolic and genetic control of gene expression on a genomic scale.
DeRisi JL, Iyer VR, Brown PO., Science 278(5338), 1997
PMID: 9381177
The transcriptional program of sporulation in budding yeast.
Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I., Science 282(5389), 1998
PMID: 9784122

Neidhardt, 1996
Last but not least: regulated poly(A) tail formation.
Barabino SM, Keller W., Cell 99(1), 1999
PMID: 10520989
Number and distribution of polyadenylated RNA sequences in yeast.
Hereford LM, Rosbash M., Cell 10(3), 1977
PMID: 321129
Polyadenylic acid sequences in E. coli messenger RNA.
Nakazato H, Venkatesan S, Edmonds M., Nature 256(5513), 1975
PMID: 1097936
Polyadenylation of mRNA in prokaryotes.
Sarkar N., Annu. Rev. Biochem. 66(), 1997
PMID: 9242905
Specific polyadenylation and purification of total messenger RNA from Escherichia coli.
Amara RR, Vijaya S., Nucleic Acids Res. 25(17), 1997
PMID: 9254705
X-ray crystal structures of 70S ribosome functional complexes.
Cate JH, Yusupov MM, Yusupova GZ, Earnest TN, Noller HF., Science 285(5436), 1999
PMID: 10497122

Miller, 1972
Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes.
Studier FW, Moffatt BA., J. Mol. Biol. 189(1), 1986
PMID: 3537305

Sambrook, 1989
Global regulation of gene expression in Escherichia coli.
Chuang SE, Daniels DL, Blattner FR., J. Bacteriol. 175(7), 1993
PMID: 8458845
Poly(A)- and poly(U)-specific RNA 3' tail shortening by E. coli ribonuclease E.
Huang H, Liao J, Cohen SN., Nature 391(6662), 1998
PMID: 9422514
The phosphorylated form of the enhancer-binding protein NTRC has an ATPase activity that is essential for activation of transcription.
Weiss DS, Batut J, Klose KE, Keener J, Kustu S., Cell 67(1), 1991
PMID: 1833069
Characterization of λglnA+ phages used as templates for in vitro synthesis of glutamine synthetase
McFarland, Mol. Gen. Genet. 185(), 1982
A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes.
Tabor S, Richardson CC., Proc. Natl. Acad. Sci. U.S.A. 82(4), 1985
PMID: 3156376
Compounds which serve as the sole source of carbon or nitrogen for Salmonella typhimurium LT-2.
Gutnick D, Calvo JM, Klopotowski T, Ames BN., J. Bacteriol. 100(1), 1969
PMID: 4898986
Mutant strains (nit) of Salmonella typhimurium with a pleiotropic defect in nitrogen metabolism.
Broach J, Neumann C, Kustu S., J. Bacteriol. 128(1), 1976
PMID: 10275
Genome-wide expression profiling in Escherichia coli K-12.
Richmond CS, Glasner JD, Mau R, Jin H, Blattner FR., Nucleic Acids Res. 27(19), 1999
PMID: 10481021
The complete genome sequence of Escherichia coli K-12.
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y., Science 277(5331), 1997
PMID: 9278503
Genetic regulatory mechanisms in the synthesis of proteins.
JACOB F, MONOD J., J. Mol. Biol. 3(), 1961
PMID: 13718526
Physiological role for the GlnK protein of enteric bacteria: relief of NifL inhibition under nitrogen-limiting conditions.
He L, Soupene E, Ninfa A, Kustu S., J. Bacteriol. 180(24), 1998
PMID: 9852012
Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation.
Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S., Proc. Natl. Acad. Sci. U.S.A. 97(26), 2000
PMID: 11121068
Messenger RNA translation state: the second dimension of high-throughput expression screening.
Zong Q, Schummer M, Hood L, Morris DR., Proc. Natl. Acad. Sci. U.S.A. 96(19), 1999
PMID: 10485877
Messenger RNA stability and its role in control of gene expression in bacteria and phages.
Grunberg-Manago M., Annu. Rev. Genet. 33(), 1999
PMID: 10690408
Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization.
Wilson M, DeRisi J, Kristensen HH, Imboden P, Rane S, Brown PO, Schoolnik GK., Proc. Natl. Acad. Sci. U.S.A. 96(22), 1999
PMID: 10536008

AUTHOR UNKNOWN, 0
DNA sequence of the lactose operon: the lacA gene and the transcriptional termination region.
Hediger MA, Johnson DF, Nierlich DP, Zabin I., Proc. Natl. Acad. Sci. U.S.A. 82(19), 1985
PMID: 3901000
Intermediates in the degradation of mRNA from the lactose operon of Escherichia coli.
McCormick JR, Zengel JM, Lindahl L., Nucleic Acids Res. 19(10), 1991
PMID: 1710346
Cloning and promoter identification of the iron-regulated cir gene of Escherichia coli.
Griggs DW, Tharp BB, Konisky J., J. Bacteriol. 169(12), 1987
PMID: 3316180
Nucleotide sequence of the gene for the ferrienterochelin receptor FepA in Escherichia coli. Homology among outer membrane receptors that interact with TonB.
Lundrigan MD, Kadner RJ., J. Biol. Chem. 261(23), 1986
PMID: 3015941
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