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Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid
- Talukder Ali Azam, A. Iwata, A. Nishimura, S. Ueda, A. Ishihama
- Biology, MedicineJournal of bacteriology
- 15 October 1999
Using a quantitative Western blot method, this work has performed for the first time a systematic determination of the intracellular concentrations of 12 species of the nucleoid protein in E. coli, finding that changes in the composition of nucleoid-associated proteins in the stationary phase are accompanied by compaction of the genome DNA and silencing of the genomes functions.
Functional modulation of Escherichia coli RNA polymerase.
- A. Ishihama
- Biology, MedicineAnnual review of microbiology
The promoter recognition specificity of Escherichia coli RNA polymerase is modulated by replacement of the sigma subunit in the first step and by interaction with transcription factors in the second step, and the prediction of the expression hierarchy of approximately 4000 genes on the E. coli genome can be estimated.
Functional Characterization in Vitro of All Two-component Signal Transduction Systems from Escherichia coli*
- Kaneyoshi Yamamoto, K. Hirao, T. Oshima, H. Aiba, R. Utsumi, A. Ishihama
- Biology, MedicineJournal of Biological Chemistry
- 14 January 2005
Using the phosphorylated HKs, trans-phosphorylation in vitro of RRs for all possible combinations was examined, raising the possibility that the cross-talk in signal transduction takes place between two-component systems.
A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase.
Results suggest that UP elements comprise a third promoter recognition region (in addition to the -10, -35 recognition hexamers, which interact with the sigma subunit) and may account for the presence of (A+T)-rich DNA upstream of many prokaryotic promoters.
Twelve Species of the Nucleoid-associated Protein from Escherichia coli
The sequence specificity of DNA binding was determined for all the purified nucleoid proteins using gel-mobility shift assays and four proteins, CbpA, Hfq, H-NS, and IciA, showed the binding preference for the curved DNA.
Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions
Results indicated that the levels of sigma 54 and sigma 28 are maintained at 10 and 50%, respectively, of the level of s Sigma 70 in both strains growing at both exponential and stationary phases, but in agreement with the previous measurement for strain MC4100.
Transcriptional response of Escherichia coli to external copper
Transcriptional response of Escherichia coli upon exposure to external copper was studied using DNA microarray and in vivo and in vitro transcription assays, concluding that the copper‐responsive genes are organized into a hierarchy of the regulation network, forming at least four regulons, i.e. CueR, Cus R, CpxR and YedW regulons.
A Regulatory Trade-Off as a Source of Strain Variation in the Species Escherichia coli
- Thea King, A. Ishihama, A. Kori, T. Ferenci
- Biology, MedicineJournal of bacteriology
- 1 September 2004
It is demonstrated that variation in genome usage underpins intraspecific variability in transcription patterns, resistance to external stresses, and the choice of beneficial mutations under nutrient limitation and the evolutionary principle driving strain variation is proposed to be a conceptually novel trade-off that is named SPANC (for "self-preservation and nutritional competence").
A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase.
- M. Jishage, A. Ishihama
- Biology, MedicineProceedings of the National Academy of Sciences…
- 28 April 1998
It is proposed that Rsd is a stationary phase E. coli protein with regulatory activity of the sigma70 function, which binds at or downstream of region 4, the promoter -35 recognition domain.
Characterization of Copper-Inducible Promoters Regulated by CpxA/CpxR in Escherichia coli
- Kaneyoshi Yamamoto, A. Ishihama
- Biology, MedicineBioscience, biotechnology, and biochemistry
- 23 July 2006
The copper stimulon in E. coli mutants defective in cpxRA showed higher sensitivity to copper than the wild type, and a conserved tandem repeat of pentanucleotide sequence, GTAAA(N)4–8GTAAA, was identified to be the CpxR-binding site.