scholarly journals Replication versus Repair Pathways for E. coli and T. aquaticus Pol I DNA Polymerases

2009 ◽  
Vol 23 (S1) ◽  
Author(s):  
Yanling Yang ◽  
Vince J. LiCata
Keyword(s):  
Dna Polymerases ◽  
E Coli ◽  
Pol I ◽  
Repair Pathways

scholarly journals Water Release upon DNA Binding by E. coli and T. aquaticus Pol I DNA Polymerases

2009 ◽  
Vol 23 (S1) ◽  
Author(s):  
John T. Baker ◽  
Daniel J. Deredge ◽  
Kausiki Datta ◽  
Vince J. LiCata
Keyword(s):  
Dna Binding ◽  
Dna Polymerases ◽  
Water Release ◽  
E Coli ◽  
Pol I

The Mechanism of Replication of Single-Stranded DNA. VI. Requirements for Ribonucleoside Triphosphates and DNA Polymerase III

1973 ◽  
Vol 51 (12) ◽  
pp. 1588-1597 ◽  
Author(s):  
David T. Denhardt ◽  
Makoto Iwaya ◽  
Grant McFadden ◽  
Gerald Schochetman
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerases ◽  
Temperature Sensitive ◽  
Restrictive Temperature ◽  
Dna Polymerase Iii ◽  
Single Stranded Dna ◽  
E Coli ◽  
Polymerase Iii

Evidence is presented that in Escherichia coli made permeable to nucleotides by exposure to toluene, the synthesis of a DNA chain complementary to the infecting single-stranded DNA of bacteriophage [Formula: see text] requires ATP as well as the four deoxyribonucleoside triphosphates. This synthesis results in the formation of the parental double-stranded replicative-form (RF) molecule. The ATP is not required simply to prevent degradation of the ribonucleoside or deoxyribonucleoside triphosphates; it can be partially substituted for by other ribonucleoside triphosphates.No single one of the known E. coli DNA polymerases appears to be uniquely responsible in vivo for the formation of the parental RF. Since [Formula: see text] replicates well in strains lacking all, or almost all, of the in-vitro activities of DNA polymerases I and II, neither of these two enzymes would seem essential; and in a temperature-sensitive E. coli mutant (dnaEts) deficient in DNA polmerase-I activity and possessing a temperature-sensitive DNA polymerase III, the viral single-stranded DNA is efficiently incorporated into an RF molecule at the restrictive temperature. In contrast, both RF replication and progeny single-stranded DNA synthesis are dependent upon DNA polymerase III activity.

scholarly journals The Glutamate Effect on the Functionality of Pol I DNA Polymerases

2012 ◽  
Vol 102 (3) ◽  
pp. 282a
Author(s):  
Mytrang H. Do ◽  
Hiromi S. Brown ◽  
Vince J. LiCata
Keyword(s):  
Dna Polymerases ◽  
Pol I

Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis

Nature ◽  
2000 ◽  
Vol 404 (6781) ◽  
pp. 1014-1018 ◽  
Author(s):  
Mengjia Tang ◽  
Phuong Pham ◽  
Xuan Shen ◽  
John-Stephen Taylor ◽  
Mike O'Donnell ◽  
...  
Keyword(s):  
Dna Polymerases ◽  
E Coli ◽  
Sos Mutagenesis

Interaction of 5-Methoxymethyl-2′-Deoxyuridine Triphosphate with DNA Polymerases: Effects of the 5-Substituent and Comparison with the Deoxycytidine Derivative

1992 ◽  
Vol 3 (4) ◽  
pp. 243-247 ◽  
Author(s):  
P. J. Aduma ◽  
S. V. Gupta ◽  
A. L. Stuart
Keyword(s):  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Competitive Inhibitor ◽  
E Coli ◽  
The Difference ◽  
Simplex Virus ◽  
Selective Activity ◽  
Hsv 1

5-Methoxymethyl-2′-deoxyuridine (MMdUrd) is a selective anti-herpes agent that is dependent upon initial phosphorylation by Herpes simplex virus-induced deoxythymidine kinase. In order to determine its mechanism of action, MMdUrd was converted to the 5′-triphosphate (MMdUTP) and the nature of interaction of MMdUTP and dTTP with DNA polymerase of E. coli, HSV-1, and human α was investigated. The order of utilization of deoxyuridine analogues by bacterial and HSV-1 DNA polymerases for DNA synthesis was: dTTP > MMdUTP. In contrast, 5-methoxymethyl-2′-deoxycytidine-5′-triphosphate (MMdCTP) was a better substrate for HSV DNA polymerase compared to dCTP. MMdUTP is a competitive inhibitor of HSV-1 DNA polymerase with respect to dTTP incorporation (Ki = 2.9 × 10−6M). The IC50 values of MMdUTP for both HSV and human αDNA polymerases were 4.5 × 10 −6M. These data suggest that the selective activity of MMdUrd is due to its preferential phosphorylation by viral thymidine kinase and not at the DNA polymerase level. These results may also account for the difference in anti-HSV activity between MMdUrd and its deoxycytidine analogue.

scholarly journals Ada protein– and sequence context–dependent mutagenesis of alkyl phosphotriester lesions in Escherichia coli cells

2020 ◽  
Vol 295 (26) ◽  
pp. 8775-8783
Author(s):  
Jiabin Wu ◽  
Jun Yuan ◽  
Nathan E. Price ◽  
Yinsheng Wang
Keyword(s):  
Escherichia Coli ◽  
Dna Replication ◽  
Adaptive Response ◽  
Dna Polymerases ◽  
Replication Machinery ◽  
Sequence Context ◽  
E Coli ◽  
Highly Efficient ◽  
Escherichia Coli Cells ◽  
Ada Protein

Alkyl phosphotriester (alkyl-PTE) lesions are frequently induced in DNA and are resistant to repair. Here, we synthesized and characterized methyl (Me)- and n-butyl (nBu)-PTEs in two diastereomeric configurations (Sp and Rp) at six different flanking dinucleotide sites, i.e. XT and TX (X = A, C, or G), and assessed how these lesions impact DNA replication in Escherichia coli cells. When single-stranded vectors contained an Sp-Me-PTE in the sequence contexts of 5′-AT-3′, 5′-CT-3′, or 5′-GT-3′, DNA replication was highly efficient and the replication products for all three sequence contexts contained 85–90% AT and 5–10% TG. Thus, the replication outcome was largely independent of the identity of the 5′ nucleotide adjacent to an Sp-Me-PTE. Furthermore, replication across these lesions was not dependent on the activities of DNA polymerases II, IV, or V; Ada, a protein involved in adaptive response and repair of Sp-Me-PTE in E. coli, however, was essential for the generation of the mutagenic products. Additionally, the Rp diastereomer of Me-PTEs at XT sites and both diastereomers of Me-PTEs at TX sites exhibited error-free replication bypass. Moreover, Sp-nBu-PTEs at XT sites did not strongly impede DNA replication, and other nBu-PTEs displayed moderate blockage effects, with none of them being mutagenic. Taken together, these findings provide in-depth understanding of how alkyl-PTE lesions are recognized by the DNA replication machinery in prokaryotic cells and reveal that Ada contributes to mutagenesis of Sp-Me-PTEs in E. coli.

scholarly journals δ-elimination in the repair of AP (apurinic/apyrimidinic) sites in DNA

1989 ◽  
Vol 261 (3) ◽  
pp. 707-713 ◽  
Author(s):  
V Bailly ◽  
M Derydt ◽  
W G Verly
Keyword(s):  
Mammalian Cells ◽  
Nuclear Dna ◽  
Replicative Form ◽  
Dna Polymerization ◽  
E Coli ◽  
Polynucleotide Kinase ◽  
Ap Sites ◽  
Beta Elimination ◽  
Repair Pathways ◽  
Hydrolysis Of

[5′-32P]pdT8d(-)dT7, containing an AP (apurinic/apyrimidinic) site in the ninth position, and [d(-)-1′,2′-3H, 5′-32P]DNA, containing AP sites labelled with 3H in the 1′ and 2′ positions of the base-free deoxyribose [d(-)] and with 32P 5′; to this deoxyribose, were used to investigate the yields of the beta-elimination and delta-elimination reactions catalysed by spermine, and also the yield of hydrolysis, by the 3′-phosphatase activity of T4 polynucleotide kinase, of the 3′-phosphate resulting from the beta delta-elimination. Phage-phi X174 RF (replicative form)-I DNA containing AP (apurinic) sites has been repaired in five steps: beta-elimination, delta-elimination, hydrolysis of 3′-phosphate, DNA polymerization and ligation. Spermine, in one experiment, and Escherichia coli formamidopyrimidine: DNA glycosylase, in another experiment, were used to catalyse the first and second steps (beta-elimination and delta-elimination). These repair pathways, involving a delta-elimination step, may be operational not only in E. coli repairing its DNA containing a formamido-pyrimidine lesion, but also in mammalian cells repairing their nuclear DNA containing AP sites.

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