Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase

Xia, Jun; Chen, Li Tzu; Mei, Qian; Hui, Chien; Halliday, Jennifer A.; Lin, Hsin Yu; Magnan, David; Pribis, John P.; Fitzgerald, Devon M.; Hamilton, Holly M.; Richters, Megan M.; Nehring, Ralf B.; Shen, Xi; Li, Lei; Bates, David; Hastings, P. J.; Herman, Christophe; Jayaram, Makkuni; Rosenberg, Susan M.

doi:10.1126/sciadv.1601605

Cited by 39 publications

(136 citation statements)

References 119 publications

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“…Captured images for analysis were chosen randomly. The images were taken with Z-stacks (0.15-μm intervals) and then deconvoluted (DeltaVision SoftWoRx software) to visualize the whole cell for precise and accurate quantification of foci per (Xia et al, 2016; Xia et al, 2018). For each experiment, >400 cells were counted using ImageJ software (NIH) with visual inspection from each independent experiment.…”

Section: Methods Detailsmentioning

confidence: 99%

Gamblers: an Antibiotic-induced Evolvable Cell Subpopulation Differentiated by Reactive-oxygen-induced General Stress Response

Pribis¹,

Garcı́a-Villada²,

Zhen³

et al. 2018

Preprint

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32Antibiotics can induce mutations that cause antibiotic resistance. Yet, despite their importance, 33 mechanisms of antibiotic-promoted mutagenesis remain elusive. We report that the 34 fluoroquinolone antibiotic ciprofloxacin (cipro) induces mutations that cause drug resistance by 35 triggering differentiation of a mutant-generating cell subpopulation, using reactive oxygen species 36 (ROS) to signal the sigma-S (σ S ) general-stress response. Cipro-generated DNA breaks activate 37 the SOS DNA-damage response and error-prone DNA polymerases in all cells. However, 38 mutagenesis is restricted to a cell subpopulation in which electron transfer and SOS induce ROS, 39 which activate the σ S response, allowing mutagenesis during DNA-break repair. When sorted, 40 this small σ S -response-"on" subpopulation produces most antibiotic cross-resistant mutants. An 41FDA-approved drug prevents σ S induction specifically inhibiting antibiotic-promoted mutagenesis. 42 Furthermore, SOS-inhibited cell division, causing multi-chromosome cells, is required for 43 mutagenesis. The data support a model in which within-cell chromosome cooperation together 44 with development of a "gambler" cell subpopulation promote resistance evolution without risking 45 most cells. 46 47 48 49 51 break repair, reactive oxygen species (ROS), RpoS (σ S ) stress response, SOS response, 52 starvation stress response, stress-induced mutagenesis, transient differentiation 53 54 100 once antibiotics have gone (Lewis, 2010). Persister formation can occur stochastically, leaving 101 populations ready for a stress that they have not encountered (Balaban et al., 2004), and can also 102 be induced responsively via stress-response regulons including the SOS- (Dorr et al., 2009) and 103 σ S -response (Radzikowski et al., 2016) regulons. It is unknown whether antibiotics induce 104 4 transient differentiation that could promote resistance through mutagenesis, e.g., (Frenoy and 105 Bonhoeffer, 2018). 106Here we show that low, sub-inhibitory doses of cipro induce transient differentiation of a 107 small cell subpopulation with high ROS and σ S -response activity, that generates mutants, 108 including cross-resistant mutants: a "gambler" subpopulation. We show that the ROS promote 109 mutagenesis in gamblers by activating the σ S response, which allows mutagenic repair of cipro-110 triggered DSBs-a novel signaling/differentiating role of ROS in mutagenesis. We elaborate the 111 regulatory chain from cipro to ROS to σ S response to mutant production, and also discover a 112 requirement for SOS-induced inhibition of cell division, causing multiple chromosomes per cell. 113Mathematical analysis supports a model in which multiple chromosomes allow sharing of cellular 114 resources (e.g., recombination, complementation), avoiding deleterious consequences of some 115 mutations during mutagenesis and repair. Thus, multiple chromosomes allow higher mutation 116 rates to be maintained -resulting in faster adaptation. The findings imply a highly regulated, novel 117 transie...

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Section: Methods Detailsmentioning

confidence: 99%

Gamblers: an Antibiotic-induced Evolvable Cell Subpopulation Differentiated by Reactive-oxygen-induced General Stress Response

Pribis¹,

Garcı́a-Villada²,

Zhen³

et al. 2018

Preprint

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“…The length of mutagenesis is also limited by an oncoming replication fork (Mayle et al 2015). Second, the D-loop might migrate with the replication fork as a replication bubble that pulls a Holliday junction (Motamedi et al 1999; Hastings et al 2009a; Saini et al 2013; Xia et al 2016) as shown in Fig. 1i.…”

Section: Mechanisms Of Bir Mutagenesismentioning

confidence: 99%

“…1i. This migration proceeds possibly to the telomere in yeast (Saini et al 2013) and is shown to reach the replication terminus in E. coli , megabases away from the DSB at which it was initiated (Xia et al 2016). The mutagenicity of this mode of BIR has been postulated to result in E. coli from the loss of direction of mismatch repair by the distinction between old and new DNA that results from conservative distribution of new material behind the migrating D-loop bubble (Kuzminov 1995).…”

Section: Mechanisms Of Bir Mutagenesismentioning

confidence: 99%

Oxygen and RNA in stress-induced mutation

et al. 2018

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Mechanisms of mutation upregulated by stress responses have been described in several organisms from bacteria to human. These mechanisms might accelerate genetic change specifically when cells are maladapted to their environment. Stress-induced mutation mechanisms differ in their genetic requirements from mutation in growing cells, occurring by different mechanisms in different assay systems, but having in common a requirement for the induction of stress-responses. Here, we review progress in two areas relevant to stress-response-dependent mutagenic DNA break repair mechanisms in Escherichia coli. First, we review evidence that relates mutation to transcription. This connection might allow mutagenesis in transcribed regions, including those relevant to any stress being experienced, opening the possibility that mutations could be targeted to regions where mutation might be advantageous under conditions of a specific stress. We review the mechanisms by which replication initiated by transcription can lead to mutation. Second, we review recent findings that, although stress-induced mutation does not require exogenous DNA-damaging agents, it does require the presence of damaged bases in DNA. For starved E. coli, endogenous oxygen radicals cause these altered bases. We postulate that damaged bases stall the replisome, which, we suggest, is required for DNA-polymerase exchange, allowing the action of low-fidelity DNA polymerases that promote mutation.

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“…Belonging to the RecF pathway, it was proposed that RecQ helicase and RecJ nuclease participate to the process by widening the gaps (28)(29)(30). RecJ exonuclease possesses a 5'3' polarity (31) that combined with the action of RecQ helicase can resect the newly synthesized DNA at the previous Okazaki fragment on the lagging, or at the reprimed fragment downstream the lesion on the leading strand if repriming has occurred.…”

Section: ' End Resection By Recj Exonuclease Modulates the Length Ofmentioning

confidence: 99%

“…Daughter strand gaps repair occurs through the RecF pathway where RecFOR mediates the loading of RecA protein onto SSB-coated ssDNA (20). Belonging to the RecF pathway, RecQ helicase and RecJ nuclease participate to the process by widening the gaps (21)(22)(23). RecJ exonuclease possesses a 5'3' polarity (24) that combined with the action of RecQ helicase can resect the newly synthesized DNA that had reprimed downstream the lesion.…”

Section: ' End Resection By Recj Exonuclease Modulates the Length Ofmentioning

confidence: 99%

DNA lesions proximity modulates damage tolerance pathways inEscherichia coli

Chrabaszcz

Laureti

Pagès

2017

Preprint

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The genome of all organisms is constantly threatened by numerous agents that cause DNA damages. When the replication fork encounters an unrepaired DNA lesion, two DNA damage tolerance pathways are possible: error-prone translesion synthesis (TLS) that requires specialized DNA polymerases, and error-free Damage Avoidance (DA) that relies on homologous recombination. The balance between these two mechanisms is essential since it defines the level of mutagenesis during lesion bypass, allowing genetic variability and adaptation to the environment, but also introducing the risk of generating genome instability. Here we report that the mere proximity of replication-blocking lesions that arise in Escherichia coli's genome during a genotoxic stress, leads to a strong increase in the use of the error-prone TLS. We show that this increase is caused by the local inhibition of homologous recombination due to the overlapping of single-stranded DNA regions generated downstream the lesions. This increase in TLS is independent of SOS activation, but its mutagenic effect is additive with the one of SOS. Hence, the combination of SOS induction and lesions proximity leads to a strong increase in TLS that becomes the main lesion tolerance pathway used by the cell during a genotoxic stress.

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Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase

Abstract: Freeze-frame synthetic proteins trap DNA reaction intermediates in single live cells, revealing origins of genome instability.

Cited by 39 publications

References 119 publications

Gamblers: an Antibiotic-induced Evolvable Cell Subpopulation Differentiated by Reactive-oxygen-induced General Stress Response

Gamblers: an Antibiotic-induced Evolvable Cell Subpopulation Differentiated by Reactive-oxygen-induced General Stress Response

Oxygen and RNA in stress-induced mutation

DNA lesions proximity modulates damage tolerance pathways inEscherichia coli

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