doi:10.1016/j.jsb.2006.05.014
Copyright © 2006 Elsevier Inc. All rights reserved.
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Nucleoid organization and the maintenance of DNA integrity in E. coli, B. subtilis and D. radiodurans
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Daphna Frenkiel-Krispin1, a and Abraham Minsky
, a, 
aDepartment of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
Received 4 April 2006;
revised 27 May 2006;
accepted 31 May 2006.
Available online 8 July 2006.
Abstract
For enzymatic activities to be effectively carried out, basic prerequisites must be met. Many enzymatic tasks require continuous consumption and dissipation of energy, sometimes in massive amounts. Some activities, such as DNA replication, transcription, and repair through homologous recombination rely upon templates that provide the information required for these transactions. Yet, circumstances where intracellular energy pools are severely depleted, or where intact templates are not available, frequently occur. Moreover, the fact that in order to reach their targets, enzymes must cope with an extremely crowded and viscous cellular milieu that drastically slows down their diffusion is often neglected. These impediments are particularly evident under stress conditions such as prolonged starvation or continuous exposure to DNA-damaging agents. Here we survey recent studies, which imply that when enzymatically-mediated DNA repair pathways are hindered, alternative strategies are deployed, whose common denominator is the reorganization of bacterial nucleoids into morphologies that promote DNA repair and protection.
Keywords: DNA packaging; Homologous recombination; Non-homologous end joining (NHEJ); RecA; Dps
Article Outline
- 1. Introduction
- 2. Energy depletion and DNA protection in starved bacteria: Dps and biocrystallization
- 3. Energy depletion, lack of template, and DNA repair: SASP, DNA sequestration, and non-homologous end-joining in bacterial spores
- 4. Homologous recombination, restricted diffusion, and energy considerations: RecA-DNA assemblies and bacterial repairosomes
- 4.1. Homologous search and restricted diffusion
- 4.2. Energy considerations
- 5. Multiple double-strand DNA breaks, lack of intact templates, and DNA repair in Deinococcus radiodurans: DNA toroids, manganese ions, and NHEJ
- 5.1. Radioresistance, DNA packaging, and Mn2+ ions
- 6. Chromatin structure and the maintenance of DNA integrity
- References
Fig. 1. DNA–Dps co-crystallization in starved E. coli cells. (A) Transmission electron microscopy of a cell after 48 h of starvation, revealing tightly packed DNA–Dps co-crystals. (B) Tomographic reconstruction of a 24 h-starved E. coli cell showing the ring-like chromatin organization. (C) Tomographic reconstruction of a 36 h-starved cell, showing ring-like DNA structures (red arrows) in close vicinity to a growing DNA–Dps co-crystal (blue arrow). The reconstructions shown in (B and C) are high-magnification images that depict specific volumes within the bacterial cytoplasm. (D) Model of the intracellular DNA–Dps assembly, which depicts the initially formed toroidal morphology that acts as a structural template for epitaxial growth of the DNA–Dps co-crystal. The DNA (red stripe) is localized in between the Dps dodecameric particles (blue spheres). Scale bars are 100 nm (Wolf et al., 1999 and Frenkiel-Krispin et al., 2004a).
Fig. 2. DNA toroids in dormant and germinating bacterial spores. (A) B. subtilis spore. The densely stained particles are ribosomes; ribosome-free spaces in the periphery of the spore core contain chromatin (arrows). (B) Specific DNA staining of a dormant B. subtilis spore, which highlights the ring-like chromatin morphology (arrows). Scale bars, 200 nm (Frenkiel-Krispin et al., 2004b). (C–E) Immunofluorescence of germinating B. megaterium spores stained for the DNA-binding proteins SASP (C, red), and HBsu (D, green). (E) Represents an overlay of the two images. The localization of these two major DNA binding proteins highlights the toroidal chromatin morphology in germinating spores (Ragkousi et al., 2000). (C–E) are courtesy of Dr. P. Setlow.
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Fig. 3. DNA-RecA ‘repairosomes’ in E. coli cells exposed to DNA-damaging agents. (A) Electron microscopy of a E. coli cell exposed to agents that cause double-strand DNA breaks, revealing a bundle-like DNA-RecA lateral assembly (arrow). (B) High magnification of the assembly shown in (A). (C) E. coli cell following prolonged exposure to DNA-damaging agents, showing a crystalline organization of the DNA-RecA complex. The inset depicts the calculated Fourier transform of the intracellular crystal. (D) Cross-section view and calculated Fourier transform of the DNA-RecA co-crystal. (E) Projection map along the z-axis of a RecA crystal obtained in vitro in the absence of DNA. (F) Density map derived from the intracellular crystal shown in (D). The density at the site of the sixfold axis of the intracellular assembly (yellow) represents DNA molecules that are absent in the in vitro RecA assembly. Scale bars, 200 nm in (A and C), 50 nm in (D), and 30 Å in (E and F) (Levin-Zaidman et al., 2000).
Fig. 4. Filamentous RecA structures in B. subtilis cells. Filamentous RecA structures in B. subtilis cells expressing GFP-RecA and stained with specific membrane staining (red), which were exposed to a DNA-damaging agent. The filaments were proposed to perform dynamic search for sequence homology along the sister chromosome (Kidane and Graumann, 2005). Courtesy of Dr. P. Graumann.
Fig. 5. DNA toroids in radioresistant members of the Deinococcaceae family. Transmission electron microscopy of (A) actively growing and (B) six-day old D. radiodurans cells stained with a DNA-specific reagent, revealing tightly packed DNA toroids. Scale bars are 400 nm (Levin-Zaidman et al., 2003). (C) Optical sections of a D. radiodurans tetrad. (D) Optical sections of nucleoids in a pair of D. proteolyticus cells. (E) Optical sections of a pair of D. murrayi tetrads. Images were taken at 100 nm intervals; scale bars are 2 μm in (C and E), and 1 μm in (D). DNA (blue, C–E) is stained with DAPI and the lipid membrane (red, C and E) is stained with FM-4-64 (Zimmerman and Battista, 2005). (C–E) are courtesy of Dr. J. Battista.
Corresponding author.
1 Present address: Department of Structural Biology, Max Plank Institute of Biochemistry, Martinsried D-82152, Germany.
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