An end-joining repair mechanism in
            <i>Escherichia coli</i>

Chayot, Romain; Montagne, Benjamin; Mazel, Didier; Ricchetti, Miria

doi:10.1073/pnas.0906355107

Cited by 142 publications

(144 citation statements)

References 36 publications

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“…For example, transformation frequencies at different genomic loci of Acinetobacter baylyi, which lacks the NHEJ proteins, were shown to vary up to 10,000-fold (Ray et al 2009). Moreover, Chayot et al (2010) recently showed that DNA acquisition in E. coli can be mediated in vitro by a mechanism that is independent of homologous recombination. E. coli, which lacks the NHEJ pathway, possesses an alternative end-joining mechanism (A-EJ) for DNA double-strand break repair (Chayot et al 2010).…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, Chayot et al (2010) recently showed that DNA acquisition in E. coli can be mediated in vitro by a mechanism that is independent of homologous recombination. E. coli, which lacks the NHEJ pathway, possesses an alternative end-joining mechanism (A-EJ) for DNA double-strand break repair (Chayot et al 2010). The A-EJ mechanism recruits the RecBCD complex for end-restriction and Ligase A for DNA ligation.…”

Section: Discussionmentioning

confidence: 99%

“…The A-EJ mechanism recruits the RecBCD complex for end-restriction and Ligase A for DNA ligation. Chayot et al (2010) showed that an acquisition of antibiotic resistance gene in E. coli can be mediated by the A-EJ proteins, demonstrating the possible role of DSBR end-joining mechanisms in LGT. This suggests the existence of yet unexplored roles of DNA repair mechanisms for integrating acquired DNA into prokaryotic genomes.…”

Section: Discussionmentioning

confidence: 99%

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Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Popa

Hazkani‐Covo²,

Landan³

et al. 2011

Genome Res.

227

204

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Lateral gene transfer (LGT) plays a major role in prokaryote evolution with only a few genes that are resistant to it; yet the nature and magnitude of barriers to lateral transfer are still debated. Here, we implement directed networks to investigate donor-recipient events of recent lateral gene transfer among 657 sequenced prokaryote genomes. For 2,129,548 genes investigated, we detected 446,854 recent lateral gene transfer events through nucleotide pattern analysis. Among these, donor-recipient relationships could be specified through phylogenetic reconstruction for 7% of the pairs, yielding 32,028 polarized recent gene acquisition events, which constitute the edges of our directed networks. We find that the frequency of recent LGT is linearly correlated both with genome sequence similarity and with proteome similarity of donor-recipient pairs. Genome sequence similarity accounts for 25% of the variation in gene-transfer frequency, with proteome similarity adding only 1% to the variability explained. The range of donor-recipient GC content similarity within the network is extremely narrow, with 86% of the LGTs occurring between donor-recipient pairs having #5% difference in GC content. Hence, genome sequence similarity and GC content similarity are strong barriers to LGT in prokaryotes. But they are not insurmountable, as we detected 1530 recent transfers between distantly related genomes. The directed network revealed that recipient genomes of distant transfers encode proteins of nonhomologous end-joining (NHEJ; a DNA repair mechanism) far more frequently than the recipient lacking that mechanism. This implicates NHEJ in genes spread across distantly related prokaryotes through bypassing the donor-recipient sequence similarity barrier.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Popa

Hazkani‐Covo²,

Landan³

et al. 2011

Genome Res.

227

204

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“…Some species (e.g., Bacillus subtilis) also possess a rudimentary analog to the eukaryotic nonhomologous end-joining pathway (NHEJ) (34), and a modified version of NHEJ, named alternative end joining (A-EJ), exists in E. coli (35). Recently, genome condensation under stress conditions was suggested as an additional DSB repair mechanism that operates in E. coli (36).…”

Section: Discussionmentioning

confidence: 99%

DNA Double-Strand Break Repair at −15°C

Dieser

Battista

Christner

2013

Appl Environ Microbiol

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The survival of microorganisms in ancient glacial ice and permafrost has been ascribed to their ability to persist in a dormant, metabolically inert state. An alternative possibility, supported by experimental data, is that microorganisms in frozen matrices are able to sustain a level of metabolic function that is sufficient for cellular repair and maintenance. To examine this experimentally, frozen populations of Psychrobacter arcticus 273-4 were exposed to ionizing radiation (IR) to simulate the damage incurred from natural background IR sources in the permafrost environment from over ϳ225 kiloyears (ky). High-molecularweight DNA was fragmented by exposure to 450 Gy of IR, which introduced an average of 16 double-strand breaks (DSBs) per chromosome. During incubation at ؊15°C for 505 days, P. arcticus repaired DNA DSBs in the absence of net growth. Based on the time frame for the assembly of genomic fragments by P. arcticus, the rate of DNA DSB repair was estimated at 7 to 10 DSBs year ؊1 under the conditions tested. Our results provide direct evidence for the repair of DNA lesions, extending the range of complex biochemical reactions known to occur in bacteria at frozen temperatures. Provided that sufficient energy and nutrient sources are available, a functional DNA repair mechanism would allow cells to maintain genome integrity and augment microbial survival in icy terrestrial or extraterrestrial environments. The results from decades of studying the stability of DNA in bacteria may be summarized in two uncomplicated axioms. First, genomic DNA is not inert; the genetic material will degrade with time, and damage will accumulate unless that degradation is repaired. And second, if this degradation is not reversed, the cell will die. The repair processes that cope with DNA damage are integral to life, and it is assumed that all species express means of maintaining genetic integrity.The importance of DNA repair to cell viability motivated extensive study of the biochemistry and molecular biology of these repair processes in model organisms such as Escherichia coli (1). Although the advantages of using this species for such studies are well documented, there is a question as to whether detailed knowledge of DNA repair in E. coli as observed under standard laboratory conditions adequately represents the full spectrum of bacterial responses to DNA damage. For instance, DNA repair is an energy-intensive activity (2, 3), but microbial species in nature rarely experience optimal conditions for growth or have access to nutrient excess. Without a generous supply of energy, cells may need to generate a more measured response, rationing available resources in a manner that prioritizes the most important tasks for survival. Moreover, viability in the absence of cellular reproduction is sustained only by cells that do not accumulate a level of damage (e.g., to DNA) that exceeds a threshold beyond which effective repair is no longer possible.Genomic DNA and viable bacteria are preserved in ancient ice and permafrost for hun...

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“…Illegitimate recombination occurring during DNA synthesis can be responsible for local sequence conversion, deletion, or duplication. It can arise during DNA replication (336,337), transposition (91, 338), or gyrase-and topoisomerase I-mediated strand cleavage (339-341); as a consequence of UV or gamma irradiation (342-344); or following the transformation of cells with linear DNA sequences under circumstances where homologous recombination is not possible (345,346). Single-strand annealing following a DNA break can occur after DNA degradation, leading to a local deletion.…”

Section: Mechanisms Of Homologous and Illegitimate Recombinationmentioning

confidence: 99%

Bacterial Genome Instability

Darmon

Leach

2014

Microbiol Mol Biol Rev

348

289

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SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.

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An end-joining repair mechanism in Escherichia coli

Cited by 142 publications

References 36 publications

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

DNA Double-Strand Break Repair at −15°C

Bacterial Genome Instability

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