DNA Double‐Strand Breaks and Their Consequences in Bacterial Genomes

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.

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References

Alm RA, Ling LS, Moir DT et al. (1999) Genomic‐sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397: 176–180.

Arnoldi E, Pan X‐S and Fisher LM (2013) Functional determinants of gate‐DNA selection and cleavage by bacterial type II topoisomerases. Nucleic Acids Research 41(20): 9411–9423.

Asai T and Kogoma T (1994) The RecF pathway of homologous recombination can mediate the initiation of DNA damage‐inducible replication of the E. coli chromosome. Journal of Bacteriology 176: 7113–7114.

Asakura Y and Kobayashi I (2009) From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction‐modification gene complex. Nucleic Acids Research 37: 3021–3031.

Blattner FR, PlunkettG III, Bloch CA et al. (1997) The complete genome sequence of E. coli K‐12. Science 277: 1453–1462.

Chédin F and Kowalczykowski SC (2002) A novel family of regulated helicases/nucleases from Gram‐positive bacteria: insights into the initiation of DNA recombination. Molecular Microbiology 43: 823–834.

Cox MM (1998) A broadening view of recombinational DNA repair in bacteria. Genes to Cells 3: 65–78.

De Septenville AL, Duigou S, Boubakri H and Michel B (2012) Replication fork reversal after replication–transcription collision. PLoS Genetics 8(4): e1002622.

Dillingham MS and Kowalczykowski SC (2008) RecBCD enzyme and the repair of double‐stranded DNA breaks. Microbiology and Molecular Biology Reviews 72: 642–671.

Doolittle WF and Zhaxybayeva O (2009) On the origin of prokaryotic species. Genome Research 19: 744–756.

Drlica K, Malik M, Kerns RJ and Zhao X (2008) Quinolone‐mediated bacterial death. Antimicrobial Agents and Chemotherapy 52: 385–392.

Dwyer DJ, Camacho DM, Kohanski MA, Callura JM and Collins JJ (2012) Antibiotic‐induced bacterial cell death exhibits physiological and biochemical hallmarks of apoptosis. Molecular Cell 46(5): 561–572.

Fukuda E, Kaminska KH, Bujnicki JM and Kobayashi I (2008) Cell death upon epigenetic genome methylation: a novel function of methyl‐specific deoxyribonucleases. Genome Biology 9: R163.

Fukuyo M, Sasaki A and Kobayashi I (2012) Success of a suicidal defense strategy against infection in a structured habitat. Scientific Reports 2(238). doi:10.1038/srep00238.

Furuta Y and Kobayashi I (2013) Restriction-modification systems as mobile epigenetic elements. In: Roberts A and Mullany P (eds) Bacterial Integrative Mobile Genetic Elements, pp. 85–103. Austin, TX: Landes Bioscience. http://www.landesbioscience.com/curie/chapter/5294/

Gelfand MS and Koonin EV (1997) Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. Nucleic Acids Research 25: 2430–2439.

Grove JI, Harris L, Buckman C and Lloyd RG (2008) DNA double strand break repair and crossing over mediated by RuvABC resolvase and RecG translocase. DNA Repair 7: 1517–1530.

Handa N, Ichige A, Kusano K and Kobayashi I (2000) Cellular responses to postsegregational killing by restriction‐modification genes. Journal of Bacteriology 182: 2218–2229.

Handa N, Yang L, Dillingham MS et al. (2012) Molecular determinants responsible for recognition of the single‐stranded DNA regulatory sequence, χ, by RecBCD enzyme. Proceedings of the National Academy of Sciences of the USA 109(23): 8901–8906.

Ishikawa K, Handa N and Kobayashi I (2009) Cleavage of a model DNA replication fork by a Type I restriction endonuclease. Nucleic Acids Research 37: 3531–3544.

Kaldalu N, Mei R and Lewis K (2004) Killing by ampicillin and ofloxacin induces overlapping changes in E. coli transcription profile. Antimicrobial Agents and Chemotherapy 48: 890–896.

Kidane D, Sanchez H, Alonso JC and Graumann PL (2004) Visualization of DNA double‐strand break repair in live bacteria reveals dynamic recruitment of Bacillus subtilis RecF, RecO and RecN proteins to distinct sites on the nucleoids. Molecular Microbiology 52: 1627–1639.

Kleanthous C, James R, Hemmings AM and Moore GR (1999) Protein antibiotics and their inhibitors. Biochemical Society Transactions 27: 63–67.

Kusano K, Takahashi NK, Yoshikura H and Kobayashi I (1994) Involvement of RecE exonuclease and RecT annealing protein in DNA double‐strand break repair by homologous recombination. Gene 138(1–2): 17–25.

Lesterlin C, Ball G, Schermelleh L and Sherratt DJ (2014) RecA bundles mediate homology pairing between distant sisters during DNA break repair. Nature 506(7487): 249–253.

Liu J, Xu L, Sandler SJ and Marians KJ (1999) Replication fork assembly at recombination intermediates is required for bacterial growth. Proceedings of the National Academy of Sciences of the USA 96: 3552–3555.

Lloyd RG and Low KB (1996) Homologous recombination. In: Neidhardt FC, Curtiss R III, Ingraham JL et al. (eds) E. coli and Salmonella: Cellular and Molecular Biology, pp. 2236–2255. Washington, DC: ASM Press.

Marsin S, Mathieu A, Kortulewski T, Guérois R and Radicella JP (2008) Unveiling novel RecO distant orthologues involved in homologous recombination. PLoS Genetics 4: e1000146.

Michel B, Ehrlich SD and Uzest M (1997) DNA double‐strand breaks caused by replication arrest. EMBO Journal 16: 430–438.

Miyazono K, Furuta Y, Watanabe‐Matsui M et al. (2014) A sequence‐specific DNA glycosylase mediates restriction‐modification in Pyrococcus abyssi. Nature Communications 5(3178). doi:10.1038/ncomms4178.

Mochizuki A, Yahara K, Kobayashi I and Iwasa Y (2006) Genetic addiction: selfish gene's strategy for symbiosis in the genome. Genetics 172: 1309–1323.

Morimatsu K and Kowalczykowski SC (2003) RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair. Molecular Cell 11: 1337–1347.

Mosberg JA, Lajoie MJ and Church GM (2010) Lambda red recombineering in Escherichia coli occurs through a fully single‐stranded intermediate. Genetics 186(3): 791–799.

Muyrers JP, Zhang Y, Testa G and Stewart AF (1999) Rapid modification of bacterial artificial chromosomes by ET‐recombination. Nucleic Acids Research 27(6): 1555–1557.

Naito T, Kusano K and Kobayashi I (1995) Selfish behavior of restriction‐modification systems. Science 267: 897–899.

Narumi I, Satoh K, Cui S et al. (2004) PprA: a novel protein from Deinococcus radiodurans that stimulates DNA ligation. Molecular Microbiology 54: 278–285.

Ponder RG, Fonville NC and Rosenberg SM (2005) A switch from high‐fidelity to error‐prone DNA double‐strand break repair underlies stress‐induced mutation. Molecular Cell 19: 791–804.

Povirk LF (1996) DNA damage and mutagenesis by radiomimetic DNA‐cleaving agents: bleomycin, neocarzinostatin and other enediynes. Mutation Research 355: 71–89.

Rocha EP, Cornet E and Michel B (2005) Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genetics 1: e15.

Stelter M, Acajjaoui S, McSweeney S and Timmins J (2013) Structural and mechanistic insight into DNA unwinding by Deinococcus radiodurans UvrD. PLoS One 8(10): e77364.

Takahashi N and Kobayashi I (1990) Evidence for the double‐strand break repair model of bacteriophage lambda recombination. Proceedings of the National Academy of Sciences of the USA 87: 2790–2794.

Takahashi NK, Yamamoto K, Kitamura Y et al. (1992) Nonconservative recombination in E. coli. Proceedings of the National Academy of Sciences of the USA 89: 5912–5916.

de Vega M (2013) The minimal Bacillus subtilis nonhomologous end joining repair machinery. PLoS One 8(5): e64232.

Wimberly H, Shee C, Thornton PC et al. (2013) R‐loops and nicks initiate DNA breakage and genome instability in non‐growing Escherichia coli. Nature Communications 4(2115). doi:10.1038/ncomms3115.

Zahradka K, Slade D, Bailone A et al. (2006) Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature 443: 569–573.

Further Reading

Böck A, CurtissR III and Kaper J (eds) (2008) E. coli and Salmonella, Cellular and Molecular Biology. Washington DC: ASM Press. http://www.ecosal.org/ecosal/.

Craig N, Craigie R, Gellert M and Lambowitz A (eds) (2002) Mobile DNA II. Washington DC: ASM Press.

Friedberg EC, Walker GC, Siede W et al. (2005) DNA Repair and Mutagenesis, 2nd edn. Washington DC: ASM Press.

Funnell BE and Phillips GJ (eds) (2004) Plasmid Biology. Washington DC: ASM Press.

Kobayashi I (2004) Restriction‐modification systems as minimal forms of life. In: Pingoud A (ed.) Restriction Endonucleases, pp. 19–62. Berlin: Springer.

Leach DRF (1996) Genetic Recombination. Oxford: Blackwell.

Loenen WA, Dryden DT, Raleigh EA, Wilson GG and Murray NE (2014) Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Research 42: 3–19. http://nar.oxfordjournals.org/content/42/1/3

Yarmolinsky MB (1995) Programmed cell death in bacterial populations. Science 267: 836–837.

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Kobayashi, Ichizo, Handa, Naofumi, and Kusano, Kohji(Jul 2014) DNA Double‐Strand Breaks and Their Consequences in Bacterial Genomes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000576.pub3]