Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: EC:2.7.7.7 (DNA polymerase)
 17,007 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Caffeine inhibited DNA synthesis in toluene-treated Escherichia coli K12 strains to the same extent as in intact cells using the incorporation of [3H]thymidine as a measure of DNA synthesis. The inhibition was found to be competitive with ATP, and it was not influenced by the concentrations of deoxynucleoside triphosphates to any extent. When caffeine was added together with other DNA synthesis inhibitors such as novobiocin, nalidixic acid or actinomycin D, the inhibition in all cases was non-additive. It is suggested that caffeine inhibits one of the ATP-requiring enzymes in the DNA replication machinery, possibly DNA polymerase III or one of the DNA helicases.
 ...
PMID:Mechanism of caffeine-induced inhibition of DNA synthesis in escherichia coli. 633 73

A double mutant of Escherichia coli K12 which carries a conditional lethal mutator mutation, dnaQ49 (Horiuchi et al. 1978), and a DNA polymerase III-deficient mutation, dnaE486 (Wechsler and Gross 1971), was found to be more thermolabile than was either of the dnaQ49 or dnaE486 single mutants. The double mutant is able to grow at 28 degrees C but not at 30 degrees C. Under the restrictive conditions DNA synthesis, but not protein synthesis, of the double mutant was suppressed. All the other combinations of dnaQ and dnaE mutation alleles tested so far rendered the cells thermolabile. A dnaZ mutation exerted a similar effect on the dnaQ strain. However, when non-specific temperature-sensitive growth mutations were combined with the dnaQ49 mutation, no such increase in thermosensitivity was observed. There is a possibility that the product of the dnaQ gene interacts directly with the DNA replicating enzyme complex.
 ...
PMID:Conditional lethality of Escherichia coli strains carrying dnaE and dnaQ mutations. 701 48

The primary sequence of DNA polymerase I from Escherichia coli K12 as derived from the DNA sequence (Joyce, C. M., Kelley, W. S., and Grindley, N. D. F. (1982) J. Biol. Chem. 257, 1958-1964) has been verified. Protein sequencing through eight cycles of the Klenow large fragment yields a unique sequence corresponding to residues 324 to 331 from the translated DNA sequence and defines the subtilisin cleavage site for formation of the large and small fragments as Thr323-Val324. Site-specific cleavage of whole enzyme and large fragment at cysteines and sizing of the resulting fragments verify the location of the two cysteines at residues 262 and 907 as assigned by the DNA sequencing. Isolation of tryptic peptides derived from DNA polymerase I yielded unique peptides whose composition exactly corresponded to theoretical tryptic peptides derived from the translated DNA sequence. Identification of the expected carboxyl-terminal tryptic peptide and carboxypeptidase digestion of whole enzyme and large fragment confirm histidine-928 as the carboxylterminus. A secondary structure prediction is made using the available primary sequence data. The model contains 43% alpha helix, 17% beta-structure, 58 beta-turns, and several interesting super-secondary structure elements.
 ...
PMID:Escherichia coli DNA polymerase I. Sequence characterization and secondary structure prediction. 703 56

DNA polymerase III', a new form of DNA polymerase III, has been purified 15,000-fold to 90% homogeneity from an Escherichia coli K12 strain. DNA polymerase III's is a subassembly of four subunits of the DNA polymerase III holoenzyme; it has functional and physical properties intermediate between the core DNA polymerase III and holoenzyme. Polyacrylamide gel electrophoresis performed under denaturing conditions indicates DNA polymerase III' to be a complex of the alpha, epsilon, and theta subunits of DNA polymerase III and a newly assigned subunit of the DNA polymerase III holoenzyme, tau (Mr = 83,000). Both gel filtration and phosphocellulose chromatography separate DNA polymerase III from DNA polymerase III'. All enzyme forms can utilize a duplex template containing short gaps. DNA polymerase III', like the DNA polymerase III holoenzyme, can synthesize DNA on a long single-stranded template in the presence of 5 mM spermidine; DNA polymerase III cannot. Alone, DNA polymerase III' is inert in the G4 natural replicative system in which the DNA polymerase III holoenzyme is active. Molecular weight and subunit stoichiometry determinations suggest that DNA polymerase III' contains two units of core DNA polymerase III and two tau subunits.
 ...
PMID:Purification and characterization of DNA polymerase III'. Identification of tau as a subunit of the DNA polymerase III holoenzyme. 703 70

Ultraviolet-radiation-induced DNA-repair replication was measured in wild-type, polA1, uvrD3, and polA1 uvrD3 strains of Escherichia coli K12. A large stimulation of repair replication was observed in the uvrD3 strain, compared to the wild-type and polA1 strains. This enhanced repair replication was reduced in the polA1 uvrD3 strain. Therefore, uvrD3 mutation appears to affect the amount of repair replication performed by DNA polymerase I. In the polA1 strain, there also appears to be an effect of the uvrD3 mutation on the amount of repair replication performed by DNA polymerase III (and/or II). The enhanced repair replication observed for the uvrD3 strains appears to be in response to the enhanced DNA degradation observed for these strains.
 ...
PMID:Effect of the uvrD3 mutation on ultraviolet radiation-induced DNA-repair replication in Escherichia coli K12. 703 52

Purified T7 phage, treated with methyl methanesulfonate, was assayed on four Escherichia coli K12 host cells: (1) AB1157, wild-type; (2) PK432-1, lacking 3-methyladenine-DNA glycosylase (tag); (3) NH5016, lacking apurinic endonuclease VI (xthA); (4) p3478, lacking DNA polymerase I (polA), the latter three strains being deficient in enzymes of the base excision repair pathway. For inactivation measured immediately after alkylation, phage survival was lowest on strains PK432-1 and p3478; for delayed inactivation, measured after partial depurination of alkylated phage, survival was much lower on strain p3478 than on PK432-1. These results demonstrate the important role played by 3-methyladenine-DNA glycosylase in the survival of methylated T7 phage. Quantitative analysis of the data, using the results of Verly et al. (Verly, W.G., Crine, P., Bannon, P. and Forget, A. (1974) Biochim. Biophys. Acta 349, 204-213) to correlate the dose with the number of methyl groups introduced into phage DNA, revealed that 5-10 3-methyladenine residues per T7 DNA constituted an inactivation hit for the tag mutant. Thus, 3-methyladenine may be as toxic a lesion as an apurinic site.
 ...
PMID:Role of 3-methyladenine-DNA glycosylase in host-cell reactivation of methylated T7 bacteriophage. 705 30

We have used thymine glycol and dihydrothymine as representative ring saturation products resulting from free-radical interaction with DNA pyrimidines, and urea glycosides and beta-ureidoisobutyric acid (UBA) as models for pyrimidine-ring fragmentation products. We have shown that thymine glycol and the ring-fragmentation products urea and beta-ureidoisobutyric acid, as well as abasic sites, are strong blocks to DNA polymerases in vitro. In contrast, dihydrothymine is not a block to any of the polymerases tested. For thymine glycol, termination sites were observed opposite the putative lesions, whereas for the ring-fragmentation products, the termination sites were primarily one base prior to the lesion. These and other data have suggested that thymine glycol codes for an A, and that a base is stably inserted opposite the damage, whereas when a base is inserted opposite the non-coding lesions, it is removed by the 3-->5 exonuclease activity of DNA polymerase I. Despite their efficiency as blocking lesions, thymine glycol, urea and UBA can be bypassed at low frequency in certain specific sequence contexts. When the model lesions were introduced individually into single-stranded biologically active DNA, we found that thymine glycol, urea, beta-ureidoisobutyric acid, and abasic sites were all lethal lesions having an activation efficiency of 1, whereas dihydrothymine was not. Thus the in vitro studies predicted the in vivo results. When the survival of biologically active single-stranded DNA was examined in UV-induced Escherichia coli cells where the block to replication was released, no increase in survival was observed for DNA containing urea or abasic sites, suggesting inefficient bypass of these lesions. In contrast, beta-ureidoisobutyric acid survival was slightly enhanced, and transfecting DNA containing thymine glycols was significantly reactivated. When mutation induction by unique lesions was measured using f1-K12 hybrid DNA containing an E. coli target gene, thymine glycols and dihydrothymine were found to be inefficient as premutagenic lesions, suggesting that in vivo, as in vitro, they primarily code for A. In contrast, urea and beta-ureidoisobutyric acid were efficient premutagenic lesions, with beta-ureidoisobutyric acid being about 4-5-fold more effective than urea glycosides, which have approximately the same rate of mutation induction as abasic sites from purines. Sequence analysis of the mutations resulting from these ring-fragmentation products shows that the mutations produced are both lesion and sequence context dependent. The possible roles that bypass efficiency and lesion-directed misinsertion might play in mutagenesis are discussed.
 ...
PMID:Thymine ring saturation and fragmentation products: lesion bypass, misinsertion and implications for mutagenesis. 768 83

Free radicals produce a broad spectrum of damages to DNA, a major proportion of which includes ring fragmentation and contraction products of DNA bases as well as abasic sites. In this study, the mutagenic potential fo two pyrimidine ring fragmentation products, urea and beta-ureidoisobutyric acid (UBA), was analyzed using the i-d region of the Escherichia coli lacI gene contained in a single-stranded f1-K12 phage hybrid vector. Single-stranded DNA was used so that the in vivo interactions between the damage and the DNA polymerase could be assessed in the absence of excision repair. The i-d region contains 20 mutable thymine sites so that 20 separate sequence contexts containing a unique lesion at a position of thymine can be analyzed simultaneously. Urea and UBA residues were uniquely introduced into f1-K12 DNA by chemical and enzymatic methods and primer extension and piperidine analysis of the damage-containing template molecules demonstrated that the potential mutable thymine sites contained randomly distributed lesions. Both fragmentation products were poorly bypassed by DNA polymerases in vitro and in the cell; although in the presence of SOS-induction, UBA was bypassed more efficiently than urea. UBA was a potent premutagenic lesion with a rate of mutation induction more than sixfold above that observed with abasic sites derived from purines. Urea residues were about as mutagenic as abasic sites derived from purines, which in turn were more mutagenic than abasic sites derived from thymine. Mutations derived from urea, UBA and abasic sites were all dependent on SOS-induction of the host cells. Since both urea and UBA were derived from DNA thymine, these data demonstrate that adenine is not routinely inserted opposite products that no longer retain the structural integrity of the pyrimidine ring. Sequence analysis showed that the mutations were targeted at thymine with 62% of the urea-derived mutations being T to C transitions and 62% of the UBA derived mutations being T to A transversions. Thus, the two fragmentation products appeared to direct specific misinsertions. The mutations were not randomly distributed over the i-d region for either fragmentation product and hotspots were observed for both damages. The presence of hotspots suggests that in addition to lesion structure, sequence context plays an important role in base selectivity by DNA polymerases opposite DNA lesions. Energy minimization calculations were used to model the urea and UBA lesions at two contrasting hotspot sites. In both cases, there was significant agreement between the computational and biological data sets.
 ...
PMID:Pyrimidine ring fragmentation products. Effects of lesion structure and sequence context on mutagenesis. 810 37

Postreplication DNA repair (PRR) in UV-irradiated Escherichia coli WP2 uvrA (tryptophan-dependent strain) and K12 AB1886 uvrA6 pre-irradiated by gamma-rays in low doses (radioadaptation, the first stress effect) has been investigated. PRR was found to be more effective after incubation in the growth medium (for 45-60 min) than in non-radioadapted cells: the repair of postreplication gaps increased by 6-15%. If cells of WP2 uvrA strain were incubated after UV-irradiation in media lacking tryptophan or casamin acids (the second stress effect), PRR was seen to increase as early as within 15 min of incubation and it is more effective than at the first stress. After a 30-60 min incubation the double stress effect leads to an increase in postreplication gap repair by 23-45%. In this case almost all the gaps prove to be repaired. The second stress alone exerts no influence on PPR efficiency. It is supposed that a preliminary radioadaptation may stimulate synthesis of a protein (proteins) of the SOS-response (presumably DNA polymerase V). The second stress effect apparently induces synthesis of an unknown factor (or depreesses synthesis of a MmrA-like protein), and this in cooperation with a protein newly synthesized during radioadaptation significantly increases the efficiency of PPR.
 ...
PMID:[Radioadaptive enhancement of the repair of UV-induced postreplication gaps in Escherichia coli DNA]. 1188 Nov 56

The capacity of DNA macroarrays that contain all 4290 predicted open reading frames of the E. coli K12 genome was evaluated by measuring changes in gene expression in response to irradiation by ultraviolet light (UV). UV and other DNA damaging agents are known to trigger the induction of the SOS response. This is a coordinated increase in the level of expression of a set of approximately 30 unlinked genes, the SOS genes, negatively regulated by the LexA repressor. The analysis was performed on a set of isogenic strains with mutations that affect expression of genes of the SOS system: (i) the lexA+ strain, in which the SOS system can be induced after DNA damage, (ii) lexAind- mutants in which the SOS system cannot be induced, and (iii) lexAdef mutants in which the SOS system is induced constitutively. We found that a large set of genes appeared to be either upregulated or downregulated following UV irradiation. Among the genes which appeared to be upregulated in a LexA-dependent manner, we correctly identified 9 out of 27 SOS genes printed on the arrays and one gene containing a LexA binding site. One gene, dnaN, encoding the beta subunit of DNA polymerase III holoenzyme, was identified as an upregulated gene in a LexA-independent manner. Our results were compared to those of similar studies previously published. Although the SOS response as a whole could not be illustrated by using DNA arrays, the data suggest that regulation of some SOS genes might be more complex than previously thought.
 ...
PMID:DNA array analysis of gene expression in response to UV irradiation in Escherichia coli. 1452 57


<< Previous 1 2 3