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. 1993 Apr;175(7):2026–2036. doi: 10.1128/jb.175.7.2026-2036.1993

Global regulation of gene expression in Escherichia coli.

S E Chuang 1, D L Daniels 1, F R Blattner 1
PMCID: PMC204293  PMID: 8458845

Abstract

Global transcription responses of Escherichia coli to various stimuli or genetic defects were studied by measuring mRNA levels in about 400 segments of the genome. Measuring mRNA levels was done by analyzing hybridization to DNA dot blots made with overlapping lambda clones spanning the genome of E. coli K-12. Conditions examined included isopropyl-beta-D-thiogalactopyranoside (IPTG) induction, heat shock, osmotic shock, starvation for various nutrients, entrance of cells into the stationary phase of growth, anaerobic growth in a tube, growth in the gnotobiotic mouse gut, and effects of pleiotropic mutations rpoH, himA, topA, and crp. Most mapped genes known to be regulated by a particular situation were successfully detected. In addition, many chromosomal regions containing no previously known regulated genes were discovered that responded to various stimuli. This new method for studying globally regulated genetic systems in E. coli combines detection, cloning, and physical mapping of a battery of coregulated genes in one step.

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Selected References

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  1. Adamowicz M., Kelley P. M., Nickerson K. W. Detergent (sodium dodecyl sulfate) shock proteins in Escherichia coli. J Bacteriol. 1991 Jan;173(1):229–233. doi: 10.1128/jb.173.1.229-233.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bachmann B. J. Linkage map of Escherichia coli K-12, edition 8. Microbiol Rev. 1990 Jun;54(2):130–197. doi: 10.1128/mr.54.2.130-197.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Biek D. P., Cohen S. N. Involvement of integration host factor (IHF) in maintenance of plasmid pSC101 in Escherichia coli: mutations in the topA gene allow pSC101 replication in the absence of IHF. J Bacteriol. 1989 Apr;171(4):2066–2074. doi: 10.1128/jb.171.4.2066-2074.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Blum P. H., Jovanovich S. B., McCann M. P., Schultz J. E., Lesley S. A., Burgess R. R., Matin A. Cloning and in vivo and in vitro regulation of cyclic AMP-dependent carbon starvation genes from Escherichia coli. J Bacteriol. 1990 Jul;172(7):3813–3820. doi: 10.1128/jb.172.7.3813-3820.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Botsford J. L., Harman J. G. Cyclic AMP in prokaryotes. Microbiol Rev. 1992 Mar;56(1):100–122. doi: 10.1128/mr.56.1.100-122.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Brissette J. L., Russel M., Weiner L., Model P. Phage shock protein, a stress protein of Escherichia coli. Proc Natl Acad Sci U S A. 1990 Feb;87(3):862–866. doi: 10.1073/pnas.87.3.862. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Craig E. A., Gross C. A. Is hsp70 the cellular thermometer? Trends Biochem Sci. 1991 Apr;16(4):135–140. doi: 10.1016/0968-0004(91)90055-z. [DOI] [PubMed] [Google Scholar]
  8. Csonka L. N., Hanson A. D. Prokaryotic osmoregulation: genetics and physiology. Annu Rev Microbiol. 1991;45:569–606. doi: 10.1146/annurev.mi.45.100191.003033. [DOI] [PubMed] [Google Scholar]
  9. Daniels D. L., Blattner F. R. Mapping using gene encyclopaedias. 1987 Feb 26-Mar 4Nature. 325(6107):831–832. doi: 10.1038/325831a0. [DOI] [PubMed] [Google Scholar]
  10. Eschenlauer A. C., Reznikoff W. S. Escherichia coli catabolite gene activator protein mutants defective in positive control of lac operon transcription. J Bacteriol. 1991 Aug;173(16):5024–5029. doi: 10.1128/jb.173.16.5024-5029.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  12. Friedman D. I. Integration host factor: a protein for all reasons. Cell. 1988 Nov 18;55(4):545–554. doi: 10.1016/0092-8674(88)90213-9. [DOI] [PubMed] [Google Scholar]
  13. Goldberg E. B., Arbel T., Chen J., Karpel R., Mackie G. A., Schuldiner S., Padan E. Characterization of a Na+/H+ antiporter gene of Escherichia coli. Proc Natl Acad Sci U S A. 1987 May;84(9):2615–2619. doi: 10.1073/pnas.84.9.2615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Granston A. E., Alessi D. M., Eades L. J., Friedman D. I. A point mutation in the Nul gene of bacteriophage lambda facilitates phage growth in Escherichia coli with himA and gyrB mutations. Mol Gen Genet. 1988 Apr;212(1):149–156. doi: 10.1007/BF00322458. [DOI] [PubMed] [Google Scholar]
  15. Groat R. G., Schultz J. E., Zychlinsky E., Bockman A., Matin A. Starvation proteins in Escherichia coli: kinetics of synthesis and role in starvation survival. J Bacteriol. 1986 Nov;168(2):486–493. doi: 10.1128/jb.168.2.486-493.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gutierrez C., Barondess J., Manoil C., Beckwith J. The use of transposon TnphoA to detect genes for cell envelope proteins subject to a common regulatory stimulus. Analysis of osmotically regulated genes in Escherichia coli. J Mol Biol. 1987 May 20;195(2):289–297. doi: 10.1016/0022-2836(87)90650-4. [DOI] [PubMed] [Google Scholar]
  17. Hengge-Aronis R., Klein W., Lange R., Rimmele M., 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. 1991 Dec;173(24):7918–7924. doi: 10.1128/jb.173.24.7918-7924.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Karow M., Fayet O., Cegielska A., Ziegelhoffer T., Georgopoulos C. Isolation and characterization of the Escherichia coli htrB gene, whose product is essential for bacterial viability above 33 degrees C in rich media. J Bacteriol. 1991 Jan;173(2):741–750. doi: 10.1128/jb.173.2.741-750.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  20. Komine Y., Adachi T., Inokuchi H., Ozeki H. Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12. J Mol Biol. 1990 Apr 20;212(4):579–598. doi: 10.1016/0022-2836(90)90224-A. [DOI] [PubMed] [Google Scholar]
  21. Kroh H. E., Simon L. D. The ClpP component of Clp protease is the sigma 32-dependent heat shock protein F21.5. J Bacteriol. 1990 Oct;172(10):6026–6034. doi: 10.1128/jb.172.10.6026-6034.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lange R., Hengge-Aronis R. Growth phase-regulated expression of bolA and morphology of stationary-phase Escherichia coli cells are controlled by the novel sigma factor sigma S. J Bacteriol. 1991 Jul;173(14):4474–4481. doi: 10.1128/jb.173.14.4474-4481.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lin E. C., Iuchi S. Regulation of gene expression in fermentative and respiratory systems in Escherichia coli and related bacteria. Annu Rev Genet. 1991;25:361–387. doi: 10.1146/annurev.ge.25.120191.002045. [DOI] [PubMed] [Google Scholar]
  24. Lipinska B., Fayet O., Baird L., Georgopoulos C. Identification, characterization, and mapping of the Escherichia coli htrA gene, whose product is essential for bacterial growth only at elevated temperatures. J Bacteriol. 1989 Mar;171(3):1574–1584. doi: 10.1128/jb.171.3.1574-1584.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lévêque F., Gazeau M., Fromant M., Blanquet S., Plateau P. Control of Escherichia coli lysyl-tRNA synthetase expression by anaerobiosis. J Bacteriol. 1991 Dec;173(24):7903–7910. doi: 10.1128/jb.173.24.7903-7910.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Makino K., Kim S. K., Shinagawa H., Amemura M., Nakata A. Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12. J Bacteriol. 1991 Apr;173(8):2665–2672. doi: 10.1128/jb.173.8.2665-2672.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Matin A., Auger E. A., Blum P. H., Schultz J. E. Genetic basis of starvation survival in nondifferentiating bacteria. Annu Rev Microbiol. 1989;43:293–316. doi: 10.1146/annurev.mi.43.100189.001453. [DOI] [PubMed] [Google Scholar]
  28. Maurizi M. R., Clark W. P., Katayama Y., Rudikoff S., Pumphrey J., Bowers B., Gottesman S. Sequence and structure of Clp P, the proteolytic component of the ATP-dependent Clp protease of Escherichia coli. J Biol Chem. 1990 Jul 25;265(21):12536–12545. [PubMed] [Google Scholar]
  29. Metcalf W. W., Steed P. M., Wanner B. L. Identification of phosphate starvation-inducible genes in Escherichia coli K-12 by DNA sequence analysis of psi::lacZ(Mu d1) transcriptional fusions. J Bacteriol. 1990 Jun;172(6):3191–3200. doi: 10.1128/jb.172.6.3191-3200.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Neidhardt F. C., Bloch P. L., Smith D. F. Culture medium for enterobacteria. J Bacteriol. 1974 Sep;119(3):736–747. doi: 10.1128/jb.119.3.736-747.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Noda A., Courtright J. B., Denor P. F., Webb G., Kohara Y., Ishihama A. Rapid identification of specific genes in E. coli by hybridization to membranes containing the ordered set of phage clones. Biotechniques. 1991 Apr;10(4):474, 476-7. [PubMed] [Google Scholar]
  32. O'Farrell P. H. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975 May 25;250(10):4007–4021. [PMC free article] [PubMed] [Google Scholar]
  33. Roszak D. B., Colwell R. R. Survival strategies of bacteria in the natural environment. Microbiol Rev. 1987 Sep;51(3):365–379. doi: 10.1128/mr.51.3.365-379.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Rudd K. E., Miller W., Ostell J., Benson D. A. Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map. Nucleic Acids Res. 1990 Jan 25;18(2):313–321. doi: 10.1093/nar/18.2.313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Rudd K. E., Miller W., Werner C., Ostell J., Tolstoshev C., Satterfield S. G. Mapping sequenced E.coli genes by computer: software, strategies and examples. Nucleic Acids Res. 1991 Feb 11;19(3):637–647. doi: 10.1093/nar/19.3.637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Schultz J. E., Latter G. I., Matin A. Differential regulation by cyclic AMP of starvation protein synthesis in Escherichia coli. J Bacteriol. 1988 Sep;170(9):3903–3909. doi: 10.1128/jb.170.9.3903-3909.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Shiau S. P., Schneider B. L., Gu W., Reitzer L. J. Role of nitrogen regulator I (NtrC), the transcriptional activator of glnA in enteric bacteria, in reducing expression of glnA during nitrogen-limited growth. J Bacteriol. 1992 Jan;174(1):179–185. doi: 10.1128/jb.174.1.179-185.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Spector M. P., Park Y. K., Tirgari S., Gonzalez T., Foster J. W. Identification and characterization of starvation-regulated genetic loci in Salmonella typhimurium by using Mu d-directed lacZ operon fusions. J Bacteriol. 1988 Jan;170(1):345–351. doi: 10.1128/jb.170.1.345-351.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Takiff H. E., Baker T., Copeland T., Chen S. M., Court D. L. Locating essential Escherichia coli genes by using mini-Tn10 transposons: the pdxJ operon. J Bacteriol. 1992 Mar;174(5):1544–1553. doi: 10.1128/jb.174.5.1544-1553.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wanner B. L. Is cross regulation by phosphorylation of two-component response regulator proteins important in bacteria? J Bacteriol. 1992 Apr;174(7):2053–2058. doi: 10.1128/jb.174.7.2053-2058.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Weiner L., Brissette J. L., Model P. Stress-induced expression of the Escherichia coli phage shock protein operon is dependent on sigma 54 and modulated by positive and negative feedback mechanisms. Genes Dev. 1991 Oct;5(10):1912–1923. doi: 10.1101/gad.5.10.1912. [DOI] [PubMed] [Google Scholar]
  42. Wilson K. H., Freter R. Interaction of Clostridium difficile and Escherichia coli with microfloras in continuous-flow cultures and gnotobiotic mice. Infect Immun. 1986 Nov;54(2):354–358. doi: 10.1128/iai.54.2.354-358.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Wilson K. H., Sheagren J. N., Freter R., Weatherbee L., Lyerly D. Gnotobiotic models for study of the microbial ecology of Clostridium difficile and Escherichia coli. J Infect Dis. 1986 Mar;153(3):547–551. doi: 10.1093/infdis/153.3.547. [DOI] [PubMed] [Google Scholar]
  44. Yerkes J. H., Casson L. P., Honkanen A. K., Walker G. C. Anaerobiosis induces expression of ant, a new Escherichia coli locus with a role in anaerobic electron transport. J Bacteriol. 1984 Apr;158(1):180–186. doi: 10.1128/jb.158.1.180-186.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Zhou Y. N., Kusukawa N., Erickson J. W., Gross C. A., Yura T. Isolation and characterization of Escherichia coli mutants that lack the heat shock sigma factor sigma 32. J Bacteriol. 1988 Aug;170(8):3640–3649. doi: 10.1128/jb.170.8.3640-3649.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]

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