The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well-studied model organism, Escherichia coli-K12

Vijayendran C, Polen T, Wendisch VF, Friehs K, Niehaus K, Flaschel E (2007)
Journal of Biotechnology 128(4): 747-761.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Vijayendran, Chandran; Polen, Tino; Wendisch, Volker F.UniBi ; Friehs, KarlUniBi; Niehaus, KarstenUniBi; Flaschel, ErwinUniBi
Einrichtung
Fakultät für Biologie > Genetik der Prokaryoten
Centrum für Biotechnologie > Arbeitsgruppe E. Flaschel
Centrum für Biotechnologie > Arbeitsgruppe K. Niehaus
Centrum für Biotechnologie > Arbeitsgruppe V. Wendisch
Centrum für Biotechnologie > Institut für Biochemie und Biotechnik
Centrum für Biotechnologie > Graduate Center
Fakultät für Biologie > Proteom- und Metabolomforschung
Technische Fakultät > AG Fermentationstechnik
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Abstract / Bemerkung
The use of Escherichia coli as a model organism has provided a great deal of basic information in biomolecular sciences. Examining trait differences among closely related strains of the same species addresses a fundamental biological question: how much diversity is there at the single species level? The main aim of our research was to identify significant differences in the activities of groups of genes between two laboratory strains of an organism closely related in genome structure. We demonstrate that despite strict and controlled growth conditions, there is high plasticity in the global proteome and genome expression in two closely related E. coli K12 sub-strains (W3110 and MG1655), which differ insignificantly in genome structure. The growth patterns of these two sub-strains were very similar in a well-equipped bioreactor, and their genome structures were shown to be almost identical by DNA microarray. However, detailed profiling of protein and gene expression by 2-dimensional a gel electrophoresis and microarray analysis showed many differentially expressed genes and proteins, combinations of which were highly correlated. The differentially regulated genes and proteins belonged to the following functional categories: genes regulated by sigma subunit of RNA polymerase (RpoS), enterobactin-related genes, and genes involved in central metabolism. C Genes involved in central cell metabolism - the glycolysis pathway, the tricarboxylic acid cycle and the glyoxylate bypass - were differentially regulated at both the mRNA and proteome levels. The strains differ significantly in central metabolism and thus in the generation of precursor metabolites and energy. This high plasticity probably represents a universal feature of metabolic activities in closely related species, and has the potential to reveal differences in regulatory networks. We suggest that unless care is taken in the choice of strains for any validating experiment, the results might be misleading. (c) 2007 Elsevier B.V. All rights reserved.
Stichworte
MG1655; genomics; W3 110; proteomics; E. coli
Erscheinungsjahr
2007
Zeitschriftentitel
Journal of Biotechnology
Band
128
Ausgabe
4
Seite(n)
747-761
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/1594835

Zitieren

Vijayendran C, Polen T, Wendisch VF, Friehs K, Niehaus K, Flaschel E. The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well-studied model organism, Escherichia coli-K12. Journal of Biotechnology. 2007;128(4):747-761.
Vijayendran, C., Polen, T., Wendisch, V. F., Friehs, K., Niehaus, K., & Flaschel, E. (2007). The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well-studied model organism, Escherichia coli-K12. Journal of Biotechnology, 128(4), 747-761. https://doi.org/10.1016/j.jbiotec.2006.12.026
Vijayendran, Chandran, Polen, Tino, Wendisch, Volker F., Friehs, Karl, Niehaus, Karsten, and Flaschel, Erwin. 2007. “The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well-studied model organism, Escherichia coli-K12”. Journal of Biotechnology 128 (4): 747-761.
Vijayendran, C., Polen, T., Wendisch, V. F., Friehs, K., Niehaus, K., and Flaschel, E. (2007). The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well-studied model organism, Escherichia coli-K12. Journal of Biotechnology 128, 747-761.
Vijayendran, C., et al., 2007. The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well-studied model organism, Escherichia coli-K12. Journal of Biotechnology, 128(4), p 747-761.
C. Vijayendran, et al., “The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well-studied model organism, Escherichia coli-K12”, Journal of Biotechnology, vol. 128, 2007, pp. 747-761.
Vijayendran, C., Polen, T., Wendisch, V.F., Friehs, K., Niehaus, K., Flaschel, E.: The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well-studied model organism, Escherichia coli-K12. Journal of Biotechnology. 128, 747-761 (2007).
Vijayendran, Chandran, Polen, Tino, Wendisch, Volker F., Friehs, Karl, Niehaus, Karsten, and Flaschel, Erwin. “The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well-studied model organism, Escherichia coli-K12”. Journal of Biotechnology 128.4 (2007): 747-761.

14 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

An evolutionary optimization of a rhodopsin-based phototrophic metabolism in Escherichia coli.
Kim HA, Kim HJ, Park J, Choi AR, Heo K, Jeong H, Jung KH, Seok YJ, Kim P, Lee SJ., Microb Cell Fact 16(1), 2017
PMID: 28619035
Testing nanoeffect onto model bacteria: Impact of speciation and genotypes.
Gelabert A, Sivry Y, Gobbi P, Mansouri-Guilani N, Menguy N, Brayner R, Siron V, Benedetti MF, Ferrari R., Nanotoxicology 10(2), 2016
PMID: 26593393
Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.
Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM., Cell Syst 3(3), 2016
PMID: 27667363
Role of L-alanine for redox self-sufficient amination of alcohols.
Klatte S, Wendisch VF., Microb Cell Fact 14(), 2015
PMID: 25612558
Aerobic expression of Vitreoscilla hemoglobin efficiently reduces overflow metabolism in Escherichia coli.
Pablos TE, Sigala JC, Le Borgne S, Lara AR., Biotechnol J 9(6), 2014
PMID: 24677798
The effect of the rpoSam allele on gene expression and stress resistance in Escherichia coli.
Galbiati HF, Taschner NP, Spira B., Arch Microbiol 196(8), 2014
PMID: 24862098
Nitrogen and carbon status are integrated at the transcriptional level by the nitrogen regulator NtrC in vivo.
Schumacher J, Behrends V, Pan Z, Brown DR, Heydenreich F, Lewis MR, Bennett MH, Razzaghi B, Komorowski M, Barahona M, Stumpf MP, Wigneshweraraj S, Bundy JG, Buck M., MBio 4(6), 2013
PMID: 24255125
Assessment of the diversity of dairy Lactococcus lactis subsp. lactis isolates by an integrated approach combining phenotypic, genomic, and transcriptomic analyses.
Tan-a-ram P, Cardoso T, Daveran-Mingot ML, Kanchanatawee S, Loubière P, Girbal L, Cocaign-Bousquet M., Appl Environ Microbiol 77(3), 2011
PMID: 21131529
The evolution of metabolic networks of E. coli.
Baumler DJ, Peplinski RG, Reed JL, Glasner JD, Perna NT., BMC Syst Biol 5(), 2011
PMID: 22044664
Identification of conserved amino acid residues of the Salmonella sigmaS chaperone Crl involved in Crl-sigmaS interactions.
Monteil V, Kolb A, D'Alayer J, Beguin P, Norel F., J Bacteriol 192(4), 2010
PMID: 20008066
Transcriptional effects of CRP* expression in Escherichia coli.
Khankal R, Chin JW, Ghosh D, Cirino PC., J Biol Eng 3(), 2009
PMID: 19703305
The ygaVP genes of Escherichia coli form a tributyltin-inducible operon.
Gueuné H, Durand MJ, Thouand G, DuBow MS., Appl Environ Microbiol 74(6), 2008
PMID: 18245262
Application of proteomics in biotechnology--microbial proteomics.
Josic D, Kovac S., Biotechnol J 3(4), 2008
PMID: 18320565
Comparison between Escherichia coli K-12 strains W3110 and MG1655 and wild-type E. coli B as platforms for xylitol production.
Khankal R, Luziatelli F, Chin JW, Frei CS, Cirino PC., Biotechnol Lett 30(9), 2008
PMID: 18414795

57 References

Daten bereitgestellt von Europe PubMed Central.

The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase.
Altuvia S, Almiron M, Huisman G, Kolter R, Storz G., Mol. Microbiol. 13(2), 1994
PMID: 7984106
Colorimetric determination of the components of 3,4-dihydroxyphenylalaninetyrosine mixtures
Arnow, J. Biol. Chem. 118(), 1937
Sigma S-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by sigma 70 in the absence of the nucleoid-associated protein H-NS.
Arnqvist A, Olsen A, Normark S., Mol. Microbiol. 13(6), 1994
PMID: 7854117
Characterisation of the allelic variation in the rpoS gene in thirteen K12 and six other non-pathogenic Escherichia coli strains.
Atlung T, Nielsen HV, Hansen FG., Mol. Genet. Genomics 266(5), 2001
PMID: 11810263
Derivations and genotypes of some mutant derivatives of Escherichia coli K-12
Barbara, 1996
Mutations in the Escherichia coli receptor FepA reveal residues involved in ligand binding and transport.
Barnard TJ, Watson ME Jr, McIntosh MA., Mol. Microbiol. 41(3), 2001
PMID: 11532122
Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.
Bernal A, Ear U, Kyrpides N., Nucleic Acids Res. 29(1), 2001
PMID: 11125068
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 dissection of transcriptional regulation in budding yeast.
Brem RB, Yvert G, Clinton R, Kruglyak L., Science 296(5568), 2002
PMID: 11923494
Overexpression and purification of ferric enterobactin esterase from Escherichia coli. Demonstration of enzymatic hydrolysis of enterobactin and its iron complex.
Brickman TJ, McIntosh MA., J. Biol. Chem. 267(17), 1992
PMID: 1534808
Control of acid resistance in Escherichia coli.
Castanie-Cornet MP, Penfound TA, Smith D, Elliott JF, Foster JW., J. Bacteriol. 181(11), 1999
PMID: 10348866

Charles, 1996
Natural variation in human gene expression assessed in lymphoblastoid cells.
Cheung VG, Conlin LK, Weber TM, Arcaro M, Jen KY, Morley M, Spielman RS., Nat. Genet. 33(3), 2003
PMID: 12567189
Role of DNA supercoiling and rpoS sigma factor in the osmotic and growth phase-dependent induction of the gene osmE of Escherichia coli K12.
Conter A, Menchon C, Gutierrez C., J. Mol. Biol. 273(1), 1997
PMID: 9367747
Cluster analysis and display of genome-wide expression patterns.
Eisen MB, Spellman PT, Brown PO, Botstein D., Proc. Natl. Acad. Sci. U.S.A. 95(25), 1998
PMID: 9843981
Intra- and interspecific variation in primate gene expression patterns.
Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, Giavalisco P, Nieselt-Struwe K, Muchmore E, Varki A, Ravid R, Doxiadis GM, Bontrop RE, Paabo S., Science 296(5566), 2002
PMID: 11951044
Growth-phase-dependent expression of the osmotically inducible gene osmC of Escherichia coli K-12.
Gordia S, Gutierrez C., Mol. Microbiol. 19(4), 1996
PMID: 8820643
Correlation between protein and mRNA abundance in yeast.
Gygi SP, Rochon Y, Franza BR, Aebersold R., Mol. Cell. Biol. 19(3), 1999
PMID: 10022859
Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.
Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T., Mol. Syst. Biol. 2(), 2006
PMID: 16738553
ExbB and ExbD do not function independently in TonB-dependent energy transduction.
Held KG, Postle K., J. Bacteriol. 184(18), 2002
PMID: 12193634
Survival of hunger and stress: the role of rpoS in early stationary phase gene regulation in E. coli.
Hengge-Aronis R., Cell 72(2), 1993
PMID: 8425216
Back to log phase: sigma S as a global regulator in the osmotic control of gene expression in Escherichia coli.
Hengge-Aronis R., Mol. Microbiol. 21(5), 1996
PMID: 8885260
Regulation of gene expression during entry into stationary phase
Hengge-Aronis, 1996
Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase.
Hengge-Aronis R., Microbiol. Mol. Biol. Rev. 66(3), 2002
PMID: 12208995
Trehalose synthesis genes are controlled by the putative sigma factor encoded by rpoS and are involved in stationary-phase thermotolerance in Escherichia coli.
Hengge-Aronis R, Klein W, Lange R, Rimmele M, Boos W., J. Bacteriol. 173(24), 1991
PMID: 1744047
Osmotic regulation of rpoS-dependent genes in Escherichia coli.
Hengge-Aronis R, Lange R, Henneberg N, Fischer D., J. Bacteriol. 175(1), 1993
PMID: 8416901
Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases.
Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C, Watanabe C., Proc. Natl. Acad. Sci. U.S.A. 90(11), 1993
PMID: 8506346
Identification of RpoS (sigma(S))-regulated genes in Salmonella enterica serovar typhimurium.
Ibanez-Ruiz M, Robbe-Saule V, Hermant D, Labrude S, Norel F., J. Bacteriol. 182(20), 2000
PMID: 11004173
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L., Science 292(5518), 2001
PMID: 11340206
A low rate of nucleotide changes in Escherichia coli K-12 estimated from a comparison of the genome sequences between two different substrains.
Itoh T, Okayama T, Hashimoto H, Takeda J, Davis RW, Mori H, Gojobori T., FEBS Lett. 450(1-2), 1999
PMID: 10350060
SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences.
Lacour S, Landini P., J. Bacteriol. 186(21), 2004
PMID: 15489429
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide.
Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381880
The role of the sigma factor sigma S (KatF) in bacterial global regulation.
Loewen PC, Hengge-Aronis R., Annu. Rev. Microbiol. 48(), 1994
PMID: 7826018
Regulation in the rpoS regulon of Escherichia coli.
Loewen PC, Hu B, Strutinsky J, Sparling R., Can. J. Microbiol. 44(8), 1998
PMID: 9830102
Variation in gene expression within and among natural populations.
Oleksiak MF, Churchill GA, Crawford DL., Nat. Genet. 32(2), 2002
PMID: 12219088
Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12.
Patten CL, Kirchhof MG, Schertzberg MR, Morton RA, Schellhorn HE., Mol. Genet. Genomics 272(5), 2004
PMID: 15558318
The cryptic adenine deaminase gene of Escherichia coli. Silencing by the nucleoid-associated DNA-binding protein, H-NS, and activation by insertion elements.
Petersen C, Moller LB, Valentin-Hansen P., J. Biol. Chem. 277(35), 2002
PMID: 12077137
LrhA regulates rpoS translation in response to the Rcs phosphorelay system in Escherichia coli.
Peterson CN, Carabetta VJ, Chowdhury T, Silhavy TJ., J. Bacteriol. 188(9), 2006
PMID: 16621809
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
Effect of rpoS gene knockout on the metabolism of Escherichia coli during exponential growth phase and early stationary phase based on gene expressions, enzyme activities and intracellular metabolite concentrations.
Rahman M, Hasan MR, Oba T, Shimizu K., Biotechnol. Bioeng. 94(3), 2006
PMID: 16511888
Genetics of gene expression surveyed in maize, mouse and man.
Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH., Nature 422(6929), 2003
PMID: 12646919
Identification of conserved, RpoS-dependent stationary-phase genes of Escherichia coli.
Schellhorn HE, Audia JP, Wei LI, Chang L., J. Bacteriol. 180(23), 1998
PMID: 9829938
IS5: a mobile enhancer of transcription in Escherichia coli.
Schnetz K, Rak B., Proc. Natl. Acad. Sci. U.S.A. 89(4), 1992
PMID: 1311089
Regulation of Escherichia coli starvation sigma factor (sigma s) by ClpXP protease.
Schweder T, Lee KH, Lomovskaya O, Matin A., J. Bacteriol. 178(2), 1996
PMID: 8550468
Universal chemical assay for the detection and determination of siderophores.
Schwyn B, Neilands JB., Anal. Biochem. 160(1), 1987
PMID: 2952030
MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products.
Serres MH, Riley M., Microb. Comp. Genomics 5(4), 2000
PMID: 11471834
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
Dissecting the architecture of a quantitative trait locus in yeast.
Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, McCusker JH, Davis RW., Nature 416(6878), 2002
PMID: 11907579
Escherichia coli periplasmic protein FepB binds ferrienterobactin.
Stephens DL, Choe MD, Earhart CF., Microbiology (Reading, Engl.) 141 ( Pt 7)(), 1995
PMID: 7551033
Trehalose metabolism in Escherichia coli: stress protection and stress regulation of gene expression.
Strom AR, Kaasen I., Mol. Microbiol. 8(2), 1993
PMID: 8391102
A comparative study of variation in codon 33 of the rpoS gene in Escherichia coli K12 stocks: implications for the synthesis of sigma(s).
Subbarayan PR, Sarkar M., Mol. Genet. Genomics 270(6), 2003
PMID: 14618393
Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media.
Tao H, Bausch C, Richmond C, Blattner FR, Conway T., J. Bacteriol. 181(20), 1999
PMID: 10515934
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M., Plant J. 37(6), 2004
PMID: 14996223
How the presence of three iron binding sites affects the iron storage function of the ferritin (EcFtnA) of Escherichia coli.
Treffry A, Zhao Z, Quail MA, Guest JR, Harrison PM., FEBS Lett. 432(3), 1998
PMID: 9720927
Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity.
Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R., J. Bacteriol. 187(5), 2005
PMID: 15716429
A stationary-phase protein of Escherichia coli that affects the mode of association between the trp repressor protein and operator-bearing DNA.
Yang W, Ni L, Somerville RL., Proc. Natl. Acad. Sci. U.S.A. 90(12), 1993
PMID: 8516330
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
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 17331609
PubMed | Europe PMC

Suchen in

Google Scholar