DNA Double‐Strand Breaks and Their Consequences in Bacterial Genomes

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DNA Double‐Strand Breaks and Their Consequences in Bacterial Genomes

Ichizo Kobayashi, University of Tokyo, Tokyo, Japan
Naofumi Handa, University of California, Davis, California, USA
Kohji Kusano, Meiji University, Kanagawa, Japan

Published online: July 2014

DOI: 10.1002/9780470015902.a0000576.pub3

Full Article on Wiley Online Library

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Abstract

Deoxyribonucleic acid (DNA) double‐strand breaks, which are caused by many factors such as chemical treatments, radiations and, often, biological factors, are lethal events in organisms carrying DNA as their genome, which include bacteria. There are various mechanisms that work in the processing of these breaks, sometimes in collaboration or competition with each other. These include exonucleolytic degradation, end joining and recombination repair. These may bring about death, restoration or recombinational/mutational changes in the genome. Intragenomic collaboration and conflict between various pathways can be a force in their genome evolution. Recent analyses suggest that DNA double‐strand breaks switch on the programme of cell death in bacteria. DNA double‐strand breakage and its consequences in bacteria may provide a good model system to analyse the dynamic relationship between life, death and evolution. Understanding these processes in bacteria is important in medicine, environmental studies and industrial application.

Key Concepts:

DNA double‐strand breakage and its consequences in bacteria may provide a model system to analyse the relationship between life, death and evolution.
DNA double‐strand breakage may switch on programmes of cell death in bacteria.
Repair of DNA double‐strand breakage provides accurate products and innacurate products for host genome.
Small and large genome alterations are important in bacterial genome evolution.
The concept of intragenomic conflict may lead to meanings of the generation, processing and consequences of double‐strand breaks.

Keywords: recombination; restriction enzyme; programmed cell death; DNA methylation; genome evolution

	Figure 1. Bacterial cells dying from chromosomal DNA double‐strand breaks made by a restriction enzyme. (a) Escherichia coli cells observed after loss of EcoRI restriction‐modification gene complex (r+m+) placed on a ts plasmid by a temperature shift. Nuclei were stained with 4′,6′‐diamidino‐2‐phenylindole. The loss of the gene complex likely led to exposure of unmethylated recognition sites on the newly replicated chromosomes to lethal attack by the remaining restriction enzyme molecules (see Figure c). Many of the cells became elongated and either became multinucleated, indicating SOS response, or had lost nuclei (white arrow heads). (b) Control E. coli cells losing restriction‐negative EcoRI gene complex (r−m+) placed on a ts plasmid by a temperature shift. White bar indicates 20 μm.
	Figure 2. Multiple routes in the processing of DNA double‐strand breaks in E. coli. A double‐strand break (a–b) may be rejoined by DNA ligase to reconstitute a dsDNA indistinguishable from the starting DNA (accurate type end joining; c). Exonucleolytic degradation may be followed by end joining. It could be between DNA sequences with no or very short sequence identity (inaccurate type end joining; d). This process is classified as ‘illegitimate recombination’ – generating a novel sequence at the joint. It could result in deletion of a part of a genome. As lambdoid bacteriophage recombination function action of RecE (or Red α) exonuclease generates 3′ single‐strand tail (e), which will pair with a homologous DNA. This results in homologous recombination near the break (f). As bacterial homologous recombination DNA degradation by RecBCD exonuclease/helicase from the double‐strand break (g) is attenuated at χ sequence. Near χ, RecA promotes homolgous recombination with a homologous DNA (i). DNA without a χ sequence would be destroyed by extensive DNA degradation (h); DNA with χ would be repaired (j). Single‐strand DNAs generated through degradation by RecBCD enzyme activate RecA protein and induce SOS response and programmed death and then ClpXP proteases affect the ability of RecA to induce the apoptotic phenotypes (k).
	Figure 3. Biological contexts of DNA double‐strand break repair – a few examples. (a) Intron homing. A homing endonuclease gene is inserted at a specific sequence within a gene. The endonuclease introduces a double‐strand break at an unoccupied, homologous site. The break is repaired by copying the endonuclease gene. The net outcome is increased copy number of the endonuclease gene. (b) Recombination repair of restriction breaks. (Right) Invading unmethylated bacteriophage DNA is cleaved by the resident restriction enzyme. The restricted DNA may be degraded by bacterial RecBCD enzyme. (Left) The restriction break may be repaired by homologous recombination functions carried by the bacteriophage or its resident homologous prophage. In this case, the bacteriophage would multiply and kill the host. (c) Postsegregational host killing by a restriction‐modification gene complex. Loss of several Type II restriction‐modification gene complexes leads to chromosome cleavage by restriction enzyme. The host will be killed unless the double‐strand break is somehow repaired.
	Figure 4. Repair of a DNA double‐strand break by illegitimate recombination involving short repeats. DNA double‐strand break occurs between direct repeats. Exonucleolytic degradation from the break exposes complementary single strands, which anneal together at the repeats. The unpaired strands are trimmed, and the gaps are filled. The nicks will be sealed by ligase to complete the recombinant.
	Figure 5. A hypothetical scheme for the steps and consequences of RecBCD/χ‐mediated destruction/repair in E. coli. After a replication fork encounters a nick or a damage, a double‐strand break is made in the chromosome (a–c). A double‐strand break is also made at a terminator sequence. A double‐strand break is made by restriction enzyme after passage of the fork through a hemimethylated restriction site. A double‐strand break is made at unmethylated site on incoming DNA (b). RecBCD enzyme enters duplex DNA from the break and initiates exonucleolytic degradation (d). This would destroy incoming unrelated DNAs (g). In the case of chromosomal DNA, the enzyme encounters a χ sequence (e), which would serve as an identification marker for the chromosome. Then degradation would attenuate, and promotion of recombinational repair with the sister chromosome would occur (f). A replication fork may be created there. In the case of incoming DNA with χ sequence (h), degradation would stop, and there is a chance of homologous recombination incorporating the DNA, if not inhibited by the mismatch recognition system (i). This would result in mosaic polymorphism in the bacterial chromosome within a group sharing χ in the proper configuration and with substantial sequence homology.

Article Title:	DNA Double‐Strand Breaks and Their Consequences in Bacterial Genomes
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