Escherichia coli DNA ligase B may mitigate damage from oxidative stress

Bodine, Truston J.; Evangelista, Michael A.; Chang, Huan Ting; Ayoub, Christopher A.; Samuel, Buck S.; Sucgang, Richard; Zechiedrich, Lynn

doi:10.1371/journal.pone.0180800

Cited by 5 publications

(3 citation statements)

References 60 publications

(90 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Consequently, cells deficient in Nfo are more sensitive in these conditions [ 66 ]. Likewise, mutations affecting gap-filling by PolI and ligase render the cells hypersensitive to ROS [ 67 , 68 , 69 ].…”

Section: Repair Of Dna Lesions By Base Excision Repair Pathwaymentioning

confidence: 99%

Coping with Reactive Oxygen Species to Ensure Genome Stability in Escherichia coli

Mendoza-Chamizo

Løbner-Olesen

Charbon

2018

Genes

View full text Add to dashboard Cite

The facultative aerobic bacterium Escherichia coli adjusts its cell cycle to environmental conditions. Because of its lifestyle, the bacterium has to balance the use of oxygen with the potential lethal effects of its poisonous derivatives. Oxidative damages perpetrated by molecules such as hydrogen peroxide and superoxide anions directly incapacitate metabolic activities relying on enzymes co-factored with iron and flavins. Consequently, growth is inhibited when the bacterium faces substantial reactive oxygen insults coming from environmental or cellular sources. Although hydrogen peroxide and superoxide anions do not oxidize DNA directly, these molecules feed directly or indirectly the generation of the highly reactive hydroxyl radical that damages the bacterial chromosome. Oxidized bases are normally excised and the single strand gap repaired by the base excision repair pathway (BER). This process is especially problematic in E. coli because replication forks do not sense the presence of damages or a stalled fork ahead of them. As consequence, single-strand breaks are turned into double-strand breaks (DSB) through replication. Since E. coli tolerates the presence of DSBs poorly, BER can become toxic during oxidative stress. Here we review the repair strategies that E. coli adopts to preserve genome integrity during oxidative stress and their relation to cell cycle control of DNA replication.

show abstract

Section: Repair Of Dna Lesions By Base Excision Repair Pathwaymentioning

confidence: 99%

Coping with Reactive Oxygen Species to Ensure Genome Stability in Escherichia coli

Mendoza-Chamizo

Løbner-Olesen

Charbon

2018

Genes

View full text Add to dashboard Cite

show abstract

“…Ligase B was identified based upon sequence similarity to Ligase A and possesses a similar catalytic activity, but is nonessential [67]. A report recently suggested Ligase B may contribute to resistance during oxidative stress, but otherwise its cellular function presently remains unknown [68]. Whether Ligase A or B participates in the completion of replication has not yet been examined.…”

Section: Introductionmentioning

confidence: 99%

Ligase A and RNase HI Participate in Completing Replication on the Chromosome in Escherichia coli

Wendel

Hernandez

Courcelle

et al. 2021

DNA

View full text Add to dashboard Cite

In Escherichia coli, several enzymes have been identified that participate in completing replication on the chromosome, including RecG, SbcCD, ExoI, and RecBCD. However, other enzymes are likely to be involved and the precise enzymatic mechanism by which this reaction occurs remains unknown. Two steps predicted to be necessary to complete replication are removal of Okazaki RNA fragments and ligation of the nascent strands at convergent replication forks. E. coli encodes two RNases that remove RNA-DNA hybrids, rnhA and rnhB, as well as two ligases, ligA and ligB. Here, we used replication profiling to show that rnhA and ligA, encoding RNase HI and Ligase A, participate in the completion reaction. Deletion of rnhA impaired the ability to complete replication and resulted in over-replication in the terminus region. It additionally suppressed initiation events from oriC, suggesting a role for the enzyme in oriC-dependent initiation, as has been suggested previously. We also show that a temperature-sensitive mutation in Ligase A led to over-replication at sites where replication completes, and that degradation at these sites occurred upon shifting to the nonpermissive temperature. Deletion of rnhB or ligB did not affect the growth or profile of replication on the genome.

show abstract

“…However, cloning for a stronger constitutive promoter for T4 ligase (Ptac) was unsuccessful and resulted in mutations in the promoter region (not shown), indicating toxicity for high T4 ligase expression. Possible explanation can be that the overexpression of T4 ligase may have a similar effect as LigB, which blocks DNA replication and reduces cell viability if overexpressed (212). Next, T4 ligation of double stranded breaks produced by Cas9 cleavage led to large deletions (>6.9 kbp) in the genome (213).…”

Section: Discussionmentioning

confidence: 99%

Right tool for the right job : Exploring the diversity of type V CRISPR-Cas systems

Wu¹

View full text Add to dashboard Cite

In 1660, the Royal Society was established in London as the first national scientific institution in the world. It was a scientific community consisting of rich, Caucasian, Christian, gentlemen pursuing their curiosity-driven scientific hobby (1). Publications of single authors were published in the Proceedings of the Royal Society. The Royal Society followed the idea of acquiring knowledge through experimental investigation and had a motto: "Nullius in verba" (Latin), which means "Take nobody's word for it" (2).Fast forward to the present day. Scientific institutions have been founded all over the world, generally covering many domains of science. The scientific community has diversified, to include people of different sex, ethnicity and religious believes (3). Scientific findings are now submitted to a scientific journal (one of the thousands), peer-reviewed by non-biased colleagues, and eventually distributed online, making knowledge transfer quick and straightforward. A lot has changed in science, but the basics remain the same. Scientists still are curious about all aspects of life, and for that reason they still conduct "curiosity-driven" research (4). This chapter starts with an introductory story on how curiosity-driven fundamental research can lead to extraordinary discoveries with spectacular applications, the story of CRISPR-Cas (5). Then follows an overview of the classification and mechanism of CRISPR-Cas systems. Eventually a summary is provided of one of the more recently discovered, highly diverse type V CRISPR-Cas systems.

show abstract

Escherichia coli DNA ligase B may mitigate damage from oxidative stress

Cited by 5 publications

References 60 publications

Coping with Reactive Oxygen Species to Ensure Genome Stability in Escherichia coli

Coping with Reactive Oxygen Species to Ensure Genome Stability in Escherichia coli

Ligase A and RNase HI Participate in Completing Replication on the Chromosome in Escherichia coli

Right tool for the right job : Exploring the diversity of type V CRISPR-Cas systems

Contact Info

Product

Resources

About