scholarly journals Escherichia coli Responses to a Single DNA Adduct

2000 ◽  
Vol 182 (23) ◽  
pp. 6598-6604 ◽  
Author(s):  
Gagan A. Pandya ◽  
In-Young Yang ◽  
Arthur P. Grollman ◽  
Masaaki Moriya
Keyword(s):  
Escherichia Coli ◽  
Dna Synthesis ◽  
Plasmid Dna ◽  
Excision Repair ◽  
Dna Adduct ◽  
Translesion Dna Synthesis ◽  
E Coli ◽  
Quantitative Measurements ◽  
Recombination Repair ◽  
Damage Avoidance

ABSTRACT To study the mechanisms by which Escherichia colimodulates the genotoxic effects of DNA damage, a novel system has been developed which permits quantitative measurements of various E. coli pathways involved in mutagenesis and DNA repair. Events measured include fidelity and efficiency of translesion DNA synthesis, excision repair, and recombination repair. Our strategy involves heteroduplex plasmid DNA bearing a single site-specific DNA adduct and several mismatched regions. The plasmid replicates in a mismatch repair-deficient host with the mismatches serving as strand-specific markers. Analysis of progeny plasmid DNA for linkage of the strand-specific markers identifies the pathway from which the plasmid is derived. Using this approach, a single 1,N 6-ethenodeoxyadenosine adduct was shown to be repaired inefficiently by excision repair, to inhibit DNA synthesis by approximately 80 to 90%, and to direct the incorporation of correct dTMP opposite this adduct. This approach is especially useful in analyzing the damage avoidance-tolerance mechanisms. Our results also show that (i) progeny derived from the damage avoidance-tolerance pathway(s) accounts for more than 15% of all progeny; (ii) this pathway(s) requires functional recA, recF,recO, and recR genes, suggesting the mechanism to be daughter strand gap repair; (iii) the ruvABC genes or the recG gene is also required; and (iv) the RecG pathway appears to be more active than the RuvABC pathway. Based on these results, the mechanism of the damage avoidance-tolerance pathway is discussed.

Rapid and apparently error-prone excision repair of nonreplicating UV-irradiated plasmids in Xenopus laevis oocytes

1990 ◽  
Vol 10 (7) ◽  
pp. 3505-3511
Author(s):  
J B Hays ◽  
E J Ackerman ◽  
Q S Pang
Keyword(s):  
Escherichia Coli ◽  
Homologous Recombination ◽  
Plasmid Dna ◽  
Excision Repair ◽  
Xenopus Laevis Oocytes ◽  
Marked Contrast ◽  
Repair Synthesis ◽  
Error Frequency ◽  
Repair Activity ◽  
Good Agreement

Repair of UV-irradiated plasmid DNA microinjected into frog oocytes was measured by two techniques: transformation of repair-deficient (delta uvrB delta recA delta phr) bacteria, and removal of UV endonuclease-sensitive sites (ESS). Transformation efficiencies relative to unirradiated plasmids were used to estimate the number of lethal lesions; the latter were assumed to be Poisson distributed. These estimates were in good agreement with measurements of ESS. By both criteria, plasmid DNA was efficiently repaired, mostly during the first 2 h, when as many as 2 x 10(10) lethal lesions were removed per oocyte. This rate is about 10(6) times the average for removal of ESS from repair-proficient human cells. Repair was slower but still significant after 2 h, but some lethal lesions usually remained after overnight incubation. Most repair occurred in the absence of light, in marked contrast to differentiated frog cells, previously shown to possess photoreactivating but no excision repair activity. There was no increase in the resistance to DpnI restriction of plasmids (methylated in Escherichia coli at GATC sites) incubated in oocytes; this implies no increase in hemimethylated GATC sites, and hence no semiconservative DNA replication. Plasmid substrates capable of either intramolecular or intermolecular homologous recombination were not recombined, whether UV-irradiated or not. Repair of Lac+ plasmids was accompanied by a significant UV-dependent increase in the frequency of Lac- mutants, corresponding to a repair synthesis error frequency on the order of 10(-4) per nucleotide.

One-Step Preparation of Competent E. coli: Transformation and Storage of Bacterial Cells in the Same Solution

2021 ◽  
Vol 2021 (11) ◽  
pp. pdb.prot101212 ◽  
Author(s):  
Michael R. Green ◽  
Joseph Sambrook
Keyword(s):  
Escherichia Coli ◽  
Convenient Method ◽  
Plasmid Dna ◽  
Transformation Efficiency ◽  
Bacterial Cells ◽  
E Coli ◽  
One Step ◽  
And Storage

This protocol describes a convenient method for the preparation, use, and storage of competent Escherichia coli. The reported transformation efficiency of this method is ∼5 × 107 transformants/µg of plasmid DNA.

scholarly journals Alleviation of C⋅C Mismatches in DNA by the Escherichia coli Fpg Protein

2021 ◽  
Vol 12 ◽  
Author(s):  
Almaz Nigatu Tesfahun ◽  
Marina Alexeeva ◽  
Miglė Tomkuvienė ◽  
Aysha Arshad ◽  
Prashanna Guragain ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Excision Repair ◽  
Dna Lesions ◽  
Base Pairs ◽  
E Coli ◽  
Thymine Glycol ◽  
Base Excision ◽  
The Cost ◽  
Primary Substrate

DNA polymerase III mis-insertion may, where not corrected by its 3′→ 5′ exonuclease or the mismatch repair (MMR) function, result in all possible non-cognate base pairs in DNA generating base substitutions. The most thermodynamically unstable base pair, the cytosine (C)⋅C mismatch, destabilizes adjacent base pairs, is resistant to correction by MMR in Escherichia coli, and its repair mechanism remains elusive. We present here in vitro evidence that C⋅C mismatch can be processed by base excision repair initiated by the E. coli formamidopyrimidine-DNA glycosylase (Fpg) protein. The kcat for C⋅C is, however, 2.5 to 10 times lower than for its primary substrate 8-oxoguanine (oxo8G)⋅C, but approaches those for 5,6-dihydrothymine (dHT)⋅C and thymine glycol (Tg)⋅C. The KM values are all in the same range, which indicates efficient recognition of C⋅C mismatches in DNA. Fpg activity was also exhibited for the thymine (T)⋅T mismatch and for N4- and/or 5-methylated C opposite C or T, Fpg activity being enabled on a broad spectrum of DNA lesions and mismatches by the flexibility of the active site loop. We hypothesize that Fpg plays a role in resolving C⋅C in particular, but also other pyrimidine⋅pyrimidine mismatches, which increases survival at the cost of some mutagenesis.

scholarly journals Natural Transformation of Plasmid DNA in Escherichia coli in Sterilized Soil Column

1970 ◽  
Vol 25 (1) ◽  
pp. 49-52
Author(s):  
M Mahabub-Uz-Zaman ◽  
Zia Uddin Ahmed
Keyword(s):  
Escherichia Coli ◽  
Plasmid Dna ◽  
Natural Transformation ◽  
Soil Column ◽  
Limiting Factor ◽  
Broad Host Range ◽  
E Coli ◽  
Competent Cells ◽  
Broad Host Range Plasmid ◽  
Plasmid Puc18

The present study was carried out to assess transformability of natural and laboratory strains of Escherichia coli by plasmid DNA under different transformation conditions in sterilized soil column. Transformation experiments were carried out in laboratory conditions and in sterile soil columns with CaCl2-treated competent cells and non-competent cells at log phase and stationary phase of growth using the broad host range plasmid pUC18. In soil column experiments, transformants were obtained after CaCl2 induced competence in both E. coli K12 DH5α and strain BM09 in the frequency of 10-8 to 10-9. In natural transformation assays, transformants appeared only in log phase cells of strain DH5α at a lower frequency (5.0 x 10-9), and in CaCl2-competent BM09 cells, but not in fresh cells. Thus the major limiting factor for natural transformation in environmental E. coli in soil column is probably the absence of a competent state. The significance of this finding has been discussed with respect to generally observed lower antibiotic resistance in environmental E. coli isolates from aquatic sources. Keywords: Natural transformation; Plasmid DNA; Escherichia coli; Competent stateDOI: http://dx.doi.org/10.3329/bjm.v25i1.4856 Bangladesh J Microbiol, Volume 25, Number 1, June 2008, pp 49-52

Core-Shell Structured Fe3O4/PPy Microspheres with High Magnetization for Purification of Plasmid DNA

2013 ◽  
Vol 716 ◽  
pp. 314-319 ◽  
Author(s):  
Hai Hui Jiang ◽  
Yan Zhou ◽  
Xiao Yun Han ◽  
Xin Cheng Chen ◽  
Yun Hua Hou ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Drug Delivery ◽  
Plasmid Dna ◽  
Magnetic Particles ◽  
Interfacial Polymerization ◽  
Core Shell ◽  
Magnetic Composite ◽  
Amino Group ◽  
High Quality ◽  
E Coli

Amino group-functionalized magnetic particles have wide applications in enzyme immobilization, DNA extraction, drug delivery, water purification, catalysis, and sensor. In this paper, Fe3O4/PPy microspheres with a well-defined coreshell structure have been prepared through an interfacial polymerization approach without surfactant. The magnetic composite spheres were characterized with XRD, FTIR, SEM, TEM, and magnetometry techniques, and further tested as the adsorbent to isolate plasmid DNA from Escherichia coli (E. coli) DH5α cells. The magnetic separation yields high-quality plasmid DNA in satisfying productivity as compared to the conventional phenolchloroform extraction.

scholarly journals Cell Death in Escherichia coli dnaE(Ts) Mutants Incubated at a Nonpermissive Temperature Is Prevented by Mutation in the cydA Gene

2004 ◽  
Vol 186 (7) ◽  
pp. 2147-2155 ◽  
Author(s):  
Bernard Strauss ◽  
Kemba Kelly ◽  
Toros Dincman ◽  
Damian Ekiert ◽  
Theresa Biesieda ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cell Death ◽  
Dna Synthesis ◽  
Dna Content ◽  
Electrophoretic Pattern ◽  
Luria Bertani ◽  
E Coli ◽  
Viable Cells ◽  
Rna And Protein Synthesis ◽  
Transformation Activity

ABSTRACT Cells of the Escherichia coli dnaE(Ts) dnaE74 and dnaE486 mutants die after 4 h of incubation at 40°C in Luria-Bertani medium. Cell death is preceded by elongation, is inhibited by chloramphenicol, tetracycline, or rifampin, and is dependent on cell density. Cells survive at 40°C when they are incubated at a high population density or at a low density in conditioned medium, but they die when the medium is supplemented with glucose and amino acids. Deletion of recA or sulA has no effect. We isolated suppressors which survived for long periods at 40°C but did not form colonies. The suppressors protected against hydroxyurea-induced killing. Sequence and complementation analysis indicated that suppression was due to mutation in the cydA gene. The DNA content of dnaE mutants increased about eightfold in 4 h at 40°C, as did the DNA content of the suppressed strains. The amount of plasmid pBR322 in a dnaE74 strain increased about fourfold, as measured on gels, and the electrophoretic pattern appeared to be normal even though the viability of the parent cells decreased 2 logs. Transformation activity also increased. 4′,6′-Diamidino-2-phenylindole staining demonstrated that there were nucleoids distributed throughout the dnaE filaments formed at 40°C, indicating that there was segregation of the newly formed DNA. We concluded that the DNA synthesized was physiologically competent, particularly since the number of viable cells of the suppressed strain increased during the first few hours of incubation. These observations support the view that E. coli senses the rate of DNA synthesis and inhibits septation when the rate of DNA synthesis falls below a critical level relative to the level of RNA and protein synthesis.

scholarly journals Nucleotide Excision Repair or Polymerase V-Mediated Lesion Bypass Can Act To Restore UV-Arrested Replication Forks in Escherichia coli

2005 ◽  
Vol 187 (20) ◽  
pp. 6953-6961 ◽  
Author(s):  
Charmain T. Courcelle ◽  
Jerilyn J. Belle ◽  
Justin Courcelle
Keyword(s):  
Dna Synthesis ◽  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Translesion Synthesis ◽  
Replication Forks ◽  
Repair Capacity ◽  
Translesion Dna Synthesis ◽  
Pol V ◽  
Nucleotide Excision ◽  
Translesion Dna

ABSTRACT Nucleotide excision repair and translesion DNA synthesis are two processes that operate at arrested replication forks to reduce the frequency of recombination and promote cell survival following UV-induced DNA damage. While nucleotide excision repair is generally considered to be error free, translesion synthesis can result in mutations, making it important to identify the order and conditions that determine when each process is recruited to the arrested fork. We show here that at early times following UV irradiation, the recovery of DNA synthesis occurs through nucleotide excision repair of the lesion. In the absence of repair or when the repair capacity of the cell has been exceeded, translesion synthesis by polymerase V (Pol V) allows DNA synthesis to resume and is required to protect the arrested replication fork from degradation. Pol II and Pol IV do not contribute detectably to survival, mutagenesis, or restoration of DNA synthesis, suggesting that, in vivo, these polymerases are not functionally redundant with Pol V at UV-induced lesions. We discuss a model in which cells first use DNA repair to process replication-arresting UV lesions before resorting to mutagenic pathways such as translesion DNA synthesis to bypass these impediments to replication progression.

scholarly journals Differential Effects of Myeloperoxidase-Derived Oxidants on Escherichia coli DNA Replication

1998 ◽  
Vol 66 (6) ◽  
pp. 2655-2659 ◽  
Author(s):  
Henry Rosen ◽  
Bryce R. Michel ◽  
Donald R. vanDevanter ◽  
James P. Hughes
Keyword(s):  
Escherichia Coli ◽  
Dna Replication ◽  
Dna Synthesis ◽  
Dna Sequences ◽  
Regression Line ◽  
Chromosomal Dna ◽  
Chloride System ◽  
E Coli ◽  
Total Dna ◽  
Cell Envelopes

ABSTRACT The microbicidal myeloperoxidase (MPO)-H2O2-chloride system strongly inhibitsEscherichia coli DNA synthesis. Also, cell envelopes from MPO-treated E. coli cells lose their ability to interact with hemimethylated DNA sequences of oriC, the chromosomal origin of replication, raising the prospect that suppression of DNA synthesis involves impairment of oriC-related functions (H. Rosen, et al. Proc. Natl. Acad. Sci. USA, 87:10048–10052, 1990). To evaluate whether origin-specific DNA sequences play a role in the MPO effect on E. coli DNA synthesis, plasmid DNA replication was compared to total (chromosomal) DNA replication for six plasmids with three distinct origins of replication. Plasmid pCM700 replication, replicating from oriC, was as sensitive to MPO-mediated inhibition as was total (chromosomal) DNA replication. A regression line describing this relationship had a slope of 0.90, and ther 2 was 0.89. In contrast, the replication activities of three of four non-oriC plasmids, pUC19, pACYC184, and pSC101, demonstrated significant early resistance to inhibition by MPO-derived oxidants. The exception to this resistance pattern was plasmid pSP102, which has an origin derived from P1 phage. pSP102 replication declined similarly to that of total DNA synthesis. The regression line for pSP102 replication versus total DNA synthesis had a slope of 0.95, and the r 2 was 0.92. The biochemical requirements for P1-mediated replication are strikingly similar to those for oriC-mediated replication. It is proposed that one of these requirements, common to oriC and the P1 origin but not critical to the replication of the other non-oriC plasmids, is an important target for MPO-mediated oxidations that mediate the initial decline in E. colichromosomal DNA synthesis.

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