Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid

Abstract

The genome DNA of Escherichia coli is associated with about 10 DNA-binding structural proteins, altogether forming the nucleoid. The nucleoid proteins play some functional roles, besides their structural roles, in the global regulation of such essential DNA functions as replication, recombination, and transcription. Using a quantitative Western blot method, we have performed for the first time a systematic determination of the intracellular concentrations of 12 species of the nucleoid protein in E. coli W3110, including CbpA (curved DNA-binding protein A), CbpB (curved DNA-binding protein B, also known as Rob [right origin binding protein]), DnaA (DNA-binding protein A), Dps (DNA-binding protein from starved cells), Fis (factor for inversion stimulation), Hfq (host factor for phage Qβ), H-NS (histone-like nucleoid structuring protein), HU (heat-unstable nucleoid protein), IciA (inhibitor of chromosome initiation A), IHF (integration host factor), Lrp (leucine-responsive regulatory protein), and StpA (suppressor oftd mutant phenotype A). Intracellular protein levels reach a maximum at the growing phase for nine proteins, CbpB (Rob), DnaA, Fis, Hfq, H-NS, HU, IciA, Lrp, and StpA, which may play regulatory roles in DNA replication and/or transcription of the growth-related genes. In descending order, the level of accumulation, calculated in monomers, in growing E. coli cells is Fis, Hfq, HU, StpA, H-NS, IHF*, CbpB (Rob), Dps*, Lrp, DnaA, IciA, and CbpA* (stars represent the stationary-phase proteins). The order of abundance, in descending order, in the early stationary phase is Dps*, IHF*, HU, Hfq, H-NS, StpA, CbpB (Rob), DnaA, Lrp, IciA, CbpA, and Fis, while that in the late stationary phase is Dps*, IHF*, Hfq, HU, CbpA*, StpA, H-NS, CbpB (Rob), DnaA, Lrp, IciA, and Fis. Thus, the major protein components of the nucleoid change from Fis and HU in the growing phase to Dps in the stationary phase. The curved DNA-binding protein, CbpA, appears only in the late stationary phase. These changes in the composition of nucleoid-associated proteins in the stationary phase are accompanied by compaction of the genome DNA and silencing of the genome functions.

A quorum-sensing regulator controls expression of both the type IV secretion system and the flagellar apparatus of Brucella melitensis

“…Combined with our data, this fact suggests that the activity of VjbR is dependent on IHF which is a bending factor acting on the virB promoter topology to allow transcription to proceed. The timing of expression of virB in late exponential phase could then be related to the increasing expression of IHF‐encoding genes preparing the starvation response of the cells in stationary phase as described in other bacteria (Ali Azam et al ., 1999). This hypothesis is coherent with the observation that in minimal medium virB is expressed in early exponential phase (Boschiroli et al ., 2002; Sieira et al ., 2004) and that the alarmone of the stringent response ppGpp, known to control the expression and the activity of IHF (Aviv et al ., 1994), is crucial for virB expression (M. Dozot and S. Köhler, pers.…”

Single molecule tracking reveals the role of transitory dynamics of nucleoid-associated protein HU in organizing the bacterial chromosome

“…To differentiate these two possibilities, we tracked the diffusion of a chromosomal DNA segment labeled with six tetO operator sites ( tetO 6 ) tightly bound by TetR-mCherry fusion protein molecules under the same cell growth and imaging conditions as HUα-PAmCherry (Figure S6A). Note that compared to other fluorescent repressor-operator systems (FROS) using tandem arrays of hundreds of DNA binding sites 37 , the small footprint of the tetO 6 site (∼200 bp) enabled us to pinpoint the position of the labeled chromosomal DNA with high accuracy and negligible perturbations 38 . We observed that TetR-PAmCherry formed distinct fluorescent spots in cells (Figure S6A), consistent with its specific DNA binding property.…”

“…E. coli HU has two subunits of ∼9 kDa each, α and β, which form either HUα 2 homodimers or HUαβ heterodimers depending on the growth phase (HUβ 2 homodimers were negligible under log-phase growth) 7 . Monomers of HU are not detectable 6, 7 . HU was originally proposed to be the bacterial equivalent to eukaryotic histones due to its small size, lack of sequence specificity, and its in vitro ability to generate condensed plasmid DNA 8 and to induce negative supercoils in relaxed plasmid DNA in the presence of topoisomerase I 9 .…”

“…A group of proteins known as nucleoid-associated proteins (NAPs), such as H-NS, IHF, Fis, and HU have been shown to play important roles (reviewed in 3 ). Among these NAPS, HU is the most conserved across eubacteria and the one of the most abundant in E. coli (∼30,000 copies per cell during middle exponential phase growth 6, 7 ). E. coli HU has two subunits of ∼9 kDa each, α and β, which form either HUα 2 homodimers or HUαβ heterodimers depending on the growth phase (HUβ 2 homodimers were negligible under log-phase growth) 7 .…”

Morphological peculiarities of DNA-protein complexes in dormantEscherichia colicells, subjected to prolonged starvation Condensation of DNA in dormant cells ofEscherichia coli

“…Adaptive molecular strategies ensure the ability of microorganisms to survive in environments significantly different from those, optimal for their growth, and have been the subject of active research over the past years [2][3][4][5][6][7][8]. Such adaptive strategy often launch the increasing synthesis (up to 150-200 thousand copies) of a ferritin-like protein Dps (DNA-binding protein of starved cells) [9][10][11][12]. Dps carries on a regulatory and protective role within Escherichia Coli (E. coli) cells [13].…”