Exonuclease VII is involved in “reckless” DNA degradation in UV-irradiated Escherichia coli

Repar, Jelena; Briški, Nina; Buljubašić, Maja; Zahradka, Ksenija; Zahradka, Davor

doi:10.1016/j.mrgentox.2012.10.005

Cited by 21 publications

(18 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The gel was then stained with SYBR Gold Nucleic Acid Gel Stain (Life Technologies) and quantified using Genetool (Syngene) software with the rolling disc method for background subtraction. SYBR Gold Nucleic Acid Gel Stain (Life Technologies) gives a linear relationship between fluorescence intensity and DNA content over at least two orders of magnitude (48), as also applied previously (49). The percentage of chromosomal fragmentation was found by first measuring the DNA present in the well and directly beneath the well (non-fragmented DNA and most likely chromosomes with a single nick, respectively) and then measuring the DNA in the rest of the lane.…”

Section: Methodsmentioning

confidence: 99%

SeqA structures behind Escherichia coli replication forks affect replication elongation and restart mechanisms

Pedersen

Helgesen

Flåtten

et al. 2017

Nucleic Acids Research

View full text Add to dashboard Cite

The SeqA protein binds hemi-methylated GATC sites and forms structures that sequester newly replicated origins and trail the replication forks. Cells that lack SeqA display signs of replication fork disintegration. The broken forks could arise because of over-initiation (the launching of too many forks) or lack of dynamic SeqA structures trailing the forks. To confirm one or both of these possible mechanisms, we compared two seqA mutants with the oriCm3 mutant. The oriCm3 mutant over-initiates because of a lack of origin sequestration but has wild-type SeqA protein. Cells with nonfunctional SeqA, but not oriCm3 mutant cells, had problems with replication elongation, were highly dependent on homologous recombination, and exhibited extensive chromosome fragmentation. The results indicate that replication forks frequently break in the absence of SeqA function and that the broken forks are rescued by homologous recombination. We suggest that SeqA may act in two ways to stabilize replication forks: (i) by enabling vital replication fork repair and restarting reactions and (ii) by preventing replication fork rear-end collisions.

show abstract

Section: Methodsmentioning

confidence: 99%

SeqA structures behind Escherichia coli replication forks affect replication elongation and restart mechanisms

Pedersen

Helgesen

Flåtten

et al. 2017

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…ExoVII is a nuclease enzyme hydrolyzing singlestranded DNA and involved in degrading damaged DNA upon UV irradiation (Repar et al, 2013). ExoVII consists of a large subunit XseA and a small subunit XseB.…”

Section: Gene Content Analysis Of the Sar11 Clade Populationmentioning

confidence: 99%

Evolution and adaptation of SAR11 and Cyanobium in a saline Tibetan lake

Zhang

et al. 2016

Environ Microbiol Rep

View full text Add to dashboard Cite

Lake Qinghai is a unique lacustrine ecosystem located on the Tibetan Plateau and exhibits oligotrophic, alkaline, and saline conditions. Previous studies have focused on the community phylogenetic diversity of bacterioplankton in the ecosystem. This study aimed to address the ecotype diversity of bacterioplankton populations in the unique microbial habitat, using metagenomic sequencing and analysis. Phylogenetic analysis revealed two major bacterial populations: SAR11 IIIa (14% of the total) and Cyanobium (14%). Although the two populations shared high 16S rRNA gene sequence identity (> 98% identity) with their closest marine counterparts, they displayed substantial genomic divergence (≤ 80% average amino acid sequence identity). Comparative genomic analysis identified conservation of carbon and energy storage metabolism (biosynthesis of polyphosphate and polyhydroxyalkanoate) gene operons in the SAR11 IIIa and a cyanate (potential nitrogen source in alkaline conditions) transporter gene operon in the Cyanobium. We further identified genetic signature of positive selection acting on an exodeoxyribonuclease gene of the SAR11 IIIa population, which is potentially associated with DNA repair responsive to strong UV radiation on the high altitude mountain. Taken together, our results revealed the ecosystem-specific gene content of the bacterioplankton populations and provided new insights into their adaptations unique to the Tibetan lake.

show abstract

“…51 It has recently been shown that RecBCD-catalyzed DNA degradation in the recA mutant is dependent on 3′-5′ ssExos ExoI, SbcCD, and ExoVII. 52,53 Genetic evidence suggests that these ssExos are required for loading and/or reloading of the main DSB processing machine RecBCD to dsDNA ends in recA cells ( Figure 1E). 52,53 And since RecBCD loading to DNA is not dependent on ExoI, SbcCD, and ExoVII in wild-type cells, 52,53 one can conclude that dsDNA ends in recA cells, unlike those in wild-type bacteria, contain long 3′-overhangs that prevent RecBCD loading ( Figure 1E).…”

Section: ′-5′ Ssexos Control Dsb Processing In a Reca Mutantmentioning

confidence: 99%

“…52,53 Genetic evidence suggests that these ssExos are required for loading and/or reloading of the main DSB processing machine RecBCD to dsDNA ends in recA cells ( Figure 1E). 52,53 And since RecBCD loading to DNA is not dependent on ExoI, SbcCD, and ExoVII in wild-type cells, 52,53 one can conclude that dsDNA ends in recA cells, unlike those in wild-type bacteria, contain long 3′-overhangs that prevent RecBCD loading ( Figure 1E). Two sources for such ends occurring in recA cells are proposed: a regressed replication fork would give rise to a dsDNA end with a long 3′-tail in the absence of the RecA protein; and/or a post-Chi 3′ tail created by RecBCD in recA bacteria is not covered by the RecA protein and is therefore not immobilized in a HR intermediate, nor is it protected from degradation by ExoI, and possibly other 3′-5′ ssExos.…”

Section: ′-5′ Ssexos Control Dsb Processing In a Reca Mutantmentioning

confidence: 99%

“…Two sources for such ends occurring in recA cells are proposed: a regressed replication fork would give rise to a dsDNA end with a long 3′-tail in the absence of the RecA protein; and/or a post-Chi 3′ tail created by RecBCD in recA bacteria is not covered by the RecA protein and is therefore not immobilized in a HR intermediate, nor is it protected from degradation by ExoI, and possibly other 3′-5′ ssExos. 52,53 The aforementioned role of the SbcCD exonuclease in enabling loading of the main DSB processing machine to DSBs is especially interesting, as it mimics the role of SbcC and SbcD eukaryotic orthologs, Rad50 and Mre11, respectively, in bringing about recruitment of the main DSB processing proteins that perform long-range DSB end resection. 3 This, in turn, directs DSB repair toward HR and, to a lesser extent, microhomology-mediated end joining repair pathways, and away from NHEJ.…”

Section: ′-5′ Ssexos Control Dsb Processing In a Reca Mutantmentioning

confidence: 99%

See 1 more Smart Citation

Double-strand break repair mechanisms in Escherichia coli: recent insights

Đermić

2015

AGG

View full text Add to dashboard Cite

In order to survive, all organisms must repair the continuous appearance of double-strand breaks (DSBs) in their DNA. Escherichia coli does this by RecA-dependent homologous recombination (HR), during which the RecA protein is assembled on a 3′-terminated overhang that is created by a process called DNA end resection. The RecA nucleoprotein filament searches for and invades an intact homologous DNA sequence, creating a central HR intermediate. This review describes recent insights into HR and DSB repair in E. coli, especially the processes that precede the formation of a RecA nucleoprotein filament, with an emphasis on the regulation of 3′-tail metabolism. Since HR is a highly conserved process, the parallels to DSB repair in eukaryotic systems are discussed, bearing in mind that the lessons learned from studies in simpler bacterial models may be useful for studying DSB repair and the maintenance of genome stability in eukaryotes.

show abstract

Exonuclease VII is involved in “reckless” DNA degradation in UV-irradiated Escherichia coli

Cited by 21 publications

References 58 publications

SeqA structures behind Escherichia coli replication forks affect replication elongation and restart mechanisms

SeqA structures behind Escherichia coli replication forks affect replication elongation and restart mechanisms

Evolution and adaptation of SAR11 and Cyanobium in a saline Tibetan lake

Double-strand break repair mechanisms in Escherichia coli: recent insights

Contact Info

Product

Resources

About