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

Volumn 128, Issue 4, 2007, Pages 747-761

  Vijayendran, Chandran ^a   Polen, Tino ^b   Wendisch, Volker F ^b   Friehs, Karl ^a   Niehaus, Karsten ^a   Flaschel, Erwin ^a  

^a BIELEFELD UNIVERSITY   (Germany)

^b FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

E. coli; Genomics; MG1655; Proteomics; W3110

Indexed keywords

DNA; ESCHERICHIA COLI; GENES; GROWTH KINETICS; METABOLISM; METABOLITES; PROTEINS;

GENOMICS; PROTEOMICS; RNA POLYMERASE (RPOS);

MOLECULAR BIOLOGY;

ENTEROCHELIN; GLYOXYLIC ACID; SIGMA FACTOR RPOS;

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIUM CULTURE; CITRIC ACID CYCLE; CORRELATION ANALYSIS; CULTURE MEDIUM; ESCHERICHIA COLI; ESCHERICHIA COLI MG1655; ESCHERICHIA COLI W3110; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GLYCOLYSIS; GROWTH RATE; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ESCHERICHIA COLI K12; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENOME, BACTERIAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOME;

ESCHERICHIA COLI;

EID: 33847418713     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2006.12.026     Document Type: Article

References (57)

1. Altuvia S., Almiron M., Huisman G., Kolter R., and Storz G. The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase. Mol. Microbiol. 13 (1994) 265-272
2. Arnow L.E. Colorimetric determination of the components of 3,4-dihydroxyphenylalaninetyrosine mixtures. J. Biol. Chem. 118 (1937) 531-537
3. Arnqvist A., Olsen A., and Normark S. 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. Mol. Microbiol. 13 (1994) 1021-1032
4. Atlung T., Nielsen H.V., and Hansen F.G. Characterisation of the allelic variation in the rpoS gene in thirteen K12 and six other non-pathogenic Escherichia coli strains. Mol. Genet. Genomics 266 (2002) 873-881
5. Barbara J.B. Derivations and genotypes of some mutant derivatives of Escherichia coli K-12. In: Neidhardt F.C. (Ed). Escherichia coli and Salmonella: Cellular and Molecular Biology (1996), ASM Press, Washington, D.C. 2460-2488
6. Barnard T.J., Watson Jr. M.E., and McIntosh M.A. Mutations in the Escherichia coli receptor FepA reveal residues involved in ligand binding and transport. Mol. Microbiol. 41 (2001) 527-536
7. Bernal A., Ear U., and Kyrpides N. Genomes online database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res. 29 (2001) 126-127
8. Blattner F.R., Plunkett III G., Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., and Shao Y. The complete genome sequence of Escherichia coli K-12. Science 277 (1997) 1453-1474
9. Brem R.B., Yvert G., Clinton R., and Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science 296 (2002) 752-755
10. Brickman T.J., and McIntosh M.A. Overexpression and purification of ferric enterobactin esterase from Escherichia coli. Demonstration of enzymatic hydrolysis of enterobactin and its iron complex. J. Biol. Chem. 267 (1992) 12350-12355
11. Castanie-Cornet M.P., Penfound T.A., Smith D., Elliott J.F., and Foster J.W. Control of acid resistance in Escherichia coli. J. Bacteriol. 181 (1999) 3525-3535
12. Charles F.E. In: Neidhardt F.C. (Ed). Uptake and Metabolism of Iron and Molybdenum, Escherichia coli and Salmonella: Cellular and Molecular Biology (1996), ASM Press, Washington, D.C. 1075-1090
13. Cheung V.G., Conlin L.K., Weber T.M., Arcaro M., Jen K.Y., Morley M., and Spielman R.S. Natural variation in human gene expression assessed in lymphoblastoid cells. Nat. Genet. 33 (2003) 422-425
14. Conter A., Menchon C., and Gutierrez C. Role of DNA supercoiling and rpoS sigma factor in the osmotic and growth phase-dependent induction of the gene osmE of Escherichia coli K12. J. Mol. Biol. 273 (1997) 75-83
15. Eisen M.B., Spellman P.T., Brown P.O., and Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 14863-14868
16. Enard W., Khaitovich P., Klose J., Zollner S., Heissig F., Giavalisco P., Nieselt-Struwe K., Muchmore E., Varki A., Ravid R., Doxiadis G.M., Bontrop R.E., and Paabo S. Intra-and interspecific variation in primate gene expression patterns. Science 296 (2002) 340-343
17. Gordia S., and Gutierrez C. Growth-phase-dependent expression of the osmotically inducible gene osmC of Escherichia coli K-12. Mol. Microbiol. 19 (1996) 729-736
18. Gygi S.P., Rochon Y., Franza B.R., and Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19 (1999) 1720-1730
19. Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., and Horiuchi T. Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol. Syst. Biol. 2 (2006) Art. no. 2006 0007
20. Held K.G., and Postle K. ExbB and ExbD do not function independently in TonB-dependent energy transduction. J Bacteriol. 184 (2002) 5170-5173
21. Hengge-Aronis R. Survival of hunger and stress: the role of rpoS in early stationary phase gene regulation in E. coli. Cell 72 (1993) 165-168
22. Hengge-Aronis R. Back to log phase: sigma S as a global regulator in the osmotic control of gene expression in Escherichia coli. Mol. Microbiol. 21 (1996) 887-893
23. Hengge-Aronis R. Regulation of gene expression during entry into stationary phase. In: Neidhardt F.C. (Ed). Escherichia coli and Salmonella: Cellular and Molecular Biology (1996), ASM Press, Washington, D.C. 1497-1512
24. Hengge-Aronis R. Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase. Microbiol. Mol. Biol. Rev. 66 (2002) 373-395 (table of contents)
25. Hengge-Aronis R., Klein W., Lange R., Rimmele M., and Boos W. Trehalose synthesis genes are controlled by the putative sigma factor encoded by rpoS and are involved in stationary-phase thermotolerance in Escherichia coli. J. Bacteriol. 173 (1991) 7918-7924
26. Hengge-Aronis R., Lange R., Henneberg N., and Fischer D. Osmotic regulation of rpoS-dependent genes in Escherichia coli. J. Bacteriol. 175 (1993) 259-265
27. Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., and Watanabe C. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. U.S.A. 90 (1993) 5011-5015
28. Ibanez-Ruiz M., Robbe-Saule V., Hermant D., Labrude S., and Norel F. Identification of RpoS (sigma(S))-regulated genes in Salmonella enterica serovar typhimurium. J. Bacteriol. 182 (2000) 5749-5756
29. Ideker T., Thorsson V., Ranish J.A., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., and Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292 (2001) 929-934
30. Itoh T., Okayama T., Hashimoto H., Takeda J., Davis R.W., Mori H., and Gojobori T. A low rate of nucleotide changes in Escherichia coli K-12 estimated from a comparison of the genome sequences between two different substrains. FEBS Lett. 450 (1999) 72-76
31. Lacour S., and Landini P. SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences. J. Bacteriol. 186 (2004) 7186-7195
32. Liolios K., Tavernarakis N., Hugenholtz P., and Kyrpides N.C. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res. 34 (2006) D332-D334
33. Loewen P.C., and Hengge-Aronis R. The role of the sigma factor sigma S (KatF) in bacterial global regulation. Annu. Rev. Microbiol. 48 (1994) 53-80
34. Loewen P.C., Hu B., Strutinsky J., and Sparling R. Regulation in the rpoS regulon of Escherichia coli. Can. J. Microbiol. 44 (1998) 707-717
35. Oleksiak M.F., Churchill G.A., and Crawford D.L. Variation in gene expression within and among natural populations. Nat. Genet. 32 (2002) 261-266
36. Patten C.L., Kirchhof M.G., Schertzberg M.R., Morton R.A., and Schellhorn H.E. Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Mol. Genet. Genomics 272 (2004) 580-591
37. Petersen C., Moller L.B., and Valentin-Hansen P. The cryptic adenine deaminase gene of Escherichia coli. Silencing by the nucleoid-associated DNA-binding protein, H-NS, and activation by insertion elements. J. Biol. Chem. 277 (2002) 31373-31380
38. Peterson C.N., Carabetta V.J., Chowdhury T., and Silhavy T.J. LrhA regulates rpoS translation in response to the Rcs phosphorelay system in Escherichia coli. J. Bacteriol. 188 (2006) 3175-3181
39. Polen T., Rittmann D., Wendisch V.F., and Sahm H. DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate. Appl. Environ. Microbiol. 69 (2003) 1759-1774
40. Rahman M., Hasan M.R., Oba T., and Shimizu K. 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. Biotechnol. Bioeng. 94 (2006) 585-595
41. Schadt E.E., Monks S.A., Drake T.A., Lusis A.J., Che N., Colinayo V., Ruff T.G., Milligan S.B., Lamb J.R., Cavet G., Linsley P.S., Mao M., Stoughton R.B., and Friend S.H. Genetics of gene expression surveyed in maize, mouse and man. Nature 422 (2003) 297-302
42. Schellhorn H.E., Audia J.P., Wei L.I., and Chang L. Identification of conserved, RpoS-dependent stationary-phase genes of Escherichia coli. J. Bacteriol. 180 (1998) 6283-6291
43. Schnetz K., and Rak B. IS5: a mobile enhancer of transcription in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 89 (1992) 1244-1248
44. Schweder T., Lee K.H., Lomovskaya O., and Matin A. Regulation of Escherichia coli starvation sigma factor (sigma s) by ClpXP protease. J. Bacteriol. 178 (1996) 470-476
45. Schwyn B., and Neilands J.B. Universal chemical assay for the detection and determination of siderophores. Anal. Biochem. 160 (1987) 47-56
46. Serres M.H., and Riley M. MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microb. Comp. Genomics 5 (2000) 205-222
47. Soupene E., van Heeswijk W.C., Plumbridge J., Stewart V., Bertenthal D., Lee H., Prasad G., Paliy O., Charernnoppakul P., and Kustu S. Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. J. Bacteriol. 185 (2003) 5611-5626
48. Steinmetz L.M., Sinha H., Richards D.R., Spiegelman J.I., Oefner P.J., McCusker J.H., and Davis R.W. Dissecting the architecture of a quantitative trait locus in yeast. Nature 416 (2002) 326-330
49. Stephens D.L., Choe M.D., and Earhart C.F. Escherichia coli periplasmic protein FepB binds ferrienterobactin. Microbiology 141 Pt 7 (1995) 1647-1654
50. Strom A.R., and Kaasen I. Trehalose metabolism in Escherichia coli: stress protection and stress regulation of gene expression. Mol. Microbiol. 8 (1993) 205-210
51. Subbarayan P.R., and Sarkar M. A comparative study of variation in codon 33 of the rpoS gene in Escherichia coli K12 stocks: implications for the synthesis of sigma(s). Mol. Genet. Genomics 270 (2004) 533-538
52. Tao H., Bausch C., Richmond C., Blattner F.R., and Conway T. Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J. Bacteriol. 181 (1999) 6425-6440
53. Thimm O., Biasing O., Gibon Y., Nagel A., Meyer S., Kruger P., Selbig J., Muller L.A., Rhee S.Y., and Stitt M. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37 (2004) 914-939
54. Treffry A., Zhao Z., Quail M.A., Guest J.R., and Harrison P.M. How the presence of three iron binding sites affects the iron storage function of the ferritin (EcFtnA) of Escherichia coli. FEBS Lett. 432 (1998) 213-218
55. Weber H., Polen T., Heuveling J., Wendisch V.F., and Hengge R. Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. J. Bacteriol. 187 (2005) 1591-1603
56. Yang W., Ni L., and Somerville R.L. A stationary-phase protein of Escherichia coli that affects the mode of association between the trp repressor protein and operator-bearing DNA. Proc. Natl. Acad. Sci. U.S.A. 90 (1993) 5796-5800
57. Zimmer D.P., Soupene E., Lee H.L., Wendisch V.F., Khodursky A.B., Peter B.J., Bender R.A., and Kustu S. Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc. Natl.Acad. Sci. U.S.A. 97 (2000) 14674-14679