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Chapter 7 : Stationary-Phase Chromosomes

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Abstract:

One of the most remarkable features of prokaryotes is their ability to remain viable for very long periods under conditions that are not propitious for growth. The intrinsic chemical and physical vulnerability of DNA molecules and the lethal effects caused by unrepaired DNA lesions, even if they occur at low frequency, highlight the need for particularly efficient DNA protection mechanisms. The chapter presents a concise survey of data derived from light and electron microscopy techniques on the architecture of the chromosome in actively growing bacteria. It proceeds to briefly describe phase transitions that characterize DNA molecules. The chapter considers these two issues a prerequisite for a deeper understanding of the factors that determine the structure of chromatin in stationarystate bacteria. The organization of the chromosome within bacterial cells and the factors that dictate and modulate this organization remain less thoroughly understood than the structure of eukaryotic chromosomes. Several factors conspired to bring about this situation. These include the small size of the prokaryotic cell that restricts the effectiveness of light microscopy, the relatively low content of DNA-binding proteins associated to the bacterial chromosome which resulted in severe artifacts in conventional electron microscopic studies, as well as the apparent absence of structural order and architectural hierarchy within the nucleoid. Although this survey is concerned with stationary-phase chromosomes, a sideways glance at sporulating bacteria seems to be in place.

Citation: Minsky A, Kolter R. 2005. Stationary-Phase Chromosomes, p 155-166. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch7
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Figures

Image of Figure 1
Figure 1

Electron microscopy of cryofixed cells. (A) Actively growing wild-type cell at mid-logarithmic phase. The dark particles are ribosomes. The ribosome-free spaces contain chromatin. (B) at mid-logarithmic phase, stained solely with the DNA-specific reagent osmium-amine-SO. The irregular spreading of the chromatin over large parts of the cytoplasm is indicated. Scale bars, 400 nm.

Citation: Minsky A, Kolter R. 2005. Stationary-Phase Chromosomes, p 155-166. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch7
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Image of Figure 2
Figure 2

Electron microscopy of Dps-DNA cocrystals. (A) Purified Dps (50 µg/ml), incubated with closed circular supercoiled DNA molecules (Dps/DNA ratio, 1:5 [wt/wt]). Multiple crystals of dimensions and morphology similar to those revealed by the crystal depicted in this panel are detected following several seconds of incubation of the protein with linear, nickedcircular, and supercoiled DNA, as well as with single-stranded RNA molecules. Fluorescence studies using labeled DNA molecules indicate that DNA is incorporated within the crystals. (B) Higher magnification of the crystal shown in panel A. Scale bars, 100 nm (A) and 40 nm (B).

Citation: Minsky A, Kolter R. 2005. Stationary-Phase Chromosomes, p 155-166. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch7
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Figure 3

Electron microscopy of starved cryofixed cells. (A and B) Sections of Dps-overproducing cells induced to express Dps at mid-logarithmic phase and then incubated for 48 h. The two different morphologies of the intracellular Dps- DNA crystals correspond to sections that are parallel (A) or perpendicular (B) to the layered structure of the cocrystal (see Fig. 4B). (C) Wild-type cells incubated for 48 h after the onset of the stationary phase. A clear demixing of the ribosomes, located in the periphery of the cytoplasm, and the DNA at the center, is detected. (D) Wild-type incubated for 48 h after the onset of the stationary phase, and stained solely with the DNA-specific reagent osmium-amine-SO. The localization of DNA in the center, as opposed to DNA spreading during active growth (Fig. 1B), is clearly indicated. Scale bars, 50 nm (A) and 150 nm (C and D).

Citation: Minsky A, Kolter R. 2005. Stationary-Phase Chromosomes, p 155-166. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch7
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Figure 4

Dps-DNA cocrystal. (A) X-ray scattering patterns from intact wild-type cells, presented as a difference profile that is obtained by subtracting the scattering curve of mid-logarithmic-phase bacteria, in which no bands are discerned, from the scattering profile of cells incubated for 48 h following the onset of stationary phase. (B) A proposed schematic model of the Dps-DNA cocrystal. Dps dodecamers are depicted as spheres, and DNA molecules are represented as rods. The layered structure is consistent with the cocrystal morphology detected within Dps-overproducing cells (Fig. 3A and B), as well as with the X-ray scattering patterns exhibited by starved wild-type cells.

Citation: Minsky A, Kolter R. 2005. Stationary-Phase Chromosomes, p 155-166. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch7
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Figure 5

Electron microscopy of a ¯ cell. ¯ cells from cultures incubated for 6 days following the onset of a stationary phase are shown. A salient demixing of the DNA in the center and ribosomes at the periphery is detected. The nested arcs revealed by the DNA are characteristic of a cholesteric liquid crystalline organization. Scale bar, 150 nm.

Citation: Minsky A, Kolter R. 2005. Stationary-Phase Chromosomes, p 155-166. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch7
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