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characterization of the escherichia coli uracil-dna glycosylase.inhibitor protein complex.the bacillus subtilis bacteriophage pbs2 uracil-dna glycosylase inhibitor (ugi) protein was characterized and shown to form a stable complex with escherichia coli uracil-dna glycosylase (ung). as determined by mass spectrometry, the ugi protein had a molecular weight of 9,474. we confirmed this value by sedimentation equilibrium centrifugation and determined that ugi exists as a monomeric protein in solution. amino acid analysis performed on both ugi and ung proteins was in excellent agreement w ...19921429601
new rna polymerase from bacillus subtilis infected with phage pbs2. 19744215026
bacteriophage pbs2-induced deoxycytidine triphosphate deaminase in bacillus subtilis.the dctp deaminase induced by bacillus subtilis bacteriophage pbs2, whose dna contains uracil instead of thymine, requires metal ion and thiol activators and has a molecular weight of 125,000. the enzyme displays sigmoidal substrate saturation kinetics and inhibition by dutp, consistent with the deaminase's proposed role of providing balanced levels of dutp and dctp for pbs2 uracil-dna synthesis.19744214944
uracil-dna glycosylase inhibitor of bacteriophage pbs2: cloning and effects of expression of the inhibitor gene in escherichia coli.the uracil-dna glycosylase inhibitor gene of bacteriophage pbs2 was cloned, and the effects of this inhibitor on escherichia coli cells that contain uracil-dna glycosylase activity were determined. a pbs2 genomic library was constructed by inserting ecori restriction fragments of pbs2 dna into a plasmid puc19 vector. the library was used to transform wild-type (ung+) e. coli, and the presence of the functional inhibitor gene was determined by screening for colonies that supported growth of m13mp ...19882963806
uracil-dna glycosylase inhibitor gene of bacteriophage pbs2 encodes a binding protein specific for uracil-dna glycosylase.the uracil-dna glycosylase inhibitor gene (ugi) of the bacillus subtilis bacteriophage pbs2 has been subcloned to a 720-base pair dna fragment contained in pzw2-0.7 and its nucleotide sequence determined. using nucleotide deletion analysis, we have located the cloned ugi gene along with potential regulatory elements. a promoter-like region (-10 and -35 consensus sequences) similar to other b. subtilis genes and the shine-dalgarno sequence characteristic of gram-positive bacteria were both identi ...19892492016
use of the pbs2 uracil-dna glycosylase inhibitor to differentiate the uracil-dna glycosylase activities encoded by herpes simplex virus types 1 and 2.the bacteriophage pbs2 encoded uracil-dna glycosylase (ung) inhibitor was examined for its effect upon the nuclear ung activities of kb, hela, and vero cells infected with herpes simplex virus (hsv) type 1 or 2 and mock-infected cells. ung activity from hsv-1 infected cells exhibited the greatest sensitivity to inhibition by the inhibitor, while ung activity from cells infected with hsv-2 exhibited the greatest resistance. this differential effect was dependent upon the virus, cell line, and buf ...19902176221
overproduction and characterization of the uracil-dna glycosylase inhibitor of bacteriophage pbs2.a plasmid expression vector (pzwtac1) was constructed which allowed inducible overexpression of the uracil-dna glycosylase (ung) inhibitor (ugi)-encoding gene (ugi) in escherichia coli. in this plasmid, the ugi gene was under the control of both its own promoter and the tac promoter. constitutive expression of the ugi was observed in the absence of isopropyl-beta-d-thiogalactopyranoside (iptg). in the presence of 1 mm iptg, the ugi protein was overproduced to an approx. 16-fold higher level, and ...19911902430
bacteriophage pbs2-induced inhibition of uracil-containing dna degradation.degradation of uracil-containing dna by bacillus subtilis extracts and its inhibition after infection by the uracil-containing dna phage pbs2 have been investigated to resolve differences between the published reports of tomita and takahashi (1975) and friedberg et al. (1975, 1976). the product of hydrolysis of pbs2 dna, tritium labeled in its uracil and cytosine residues, is solely uracil and not deoxyuridine. the degrading activity is completely inhibited within 7 min after pbs2 infection, bef ...1976824463
enzymatic degradation of uracil-containing dna. ii. evidence for n-glycosidase and nuclease activities in unfractionated extracts of bacillus subtilis.further studies have confirmed our earlier observations that in the presence of edta, degradation of phage pbs2 [3h]uracil-labeled dna is effected by an n-glycosidase activity in extracts of bacillus subtilis that removes free uracil from dna. in addition, such extracts contain a nuclease activity that attacks pbs2 dna in the presence of cacl2. the nuclease activity is not observed under conditions that inactivate n-glycosidase activity but does attack dna that has been preincubated to remove ur ...1976822172
molecular weight of bacteriophage pbs2 dna.the molecular weight of bacteriophage pbs2 dna has been determined by viscoelastic retardation time experiments to be 1.50 x 10(8).1976818409
bacillus subtilis deoxyuridinetriphosphatase and its bacteriophage pbs2-induced inhibitor.extracts of bacillus subtilis contain a deoxyuridinetriphosphatase (dutpase) activity with a molecular weight of approximately 48,000. the enzyme is maximally active at ph 8.5, being stimulated by mg2+ and inhibited by edta. the enzyme is specific for dutp among all the natural nucleotides tested, with an apparent km for dutp of 2 mum. bacteriophage pbs2, whose dna contains uracil instead of thymine, induces upon infection of b. subtilis a new 83,000-dalton protein which inhibits the host's dutp ...1975810487
n-glycosidase activity in extracts of bacillus subtilis and its inhibition after infection with bacteriophage pbs2.we have detected in crude extracts of bacillus subtilis an n-glycosidase activity which catalyzes the release of free uracil from dna of the subtilis phage pbs2 labeled with [3h]uridine. this dna contains deoxyuridine instead of thymidine. the enzyme is active in the presence of 1.0 mm edta and under these conditions escherichia coli or t7 dna labeled with [3h]thymidine is not degraded to labeled acid-soluble products. the activity resembles an n-glycosidase from e. coli which releases free urac ...1975807745
bacteriophage transformation of pbs2 in bacillus subtilis.transformation of temperature-sensitive mutants of bacteriophage pbs2 for bacillus subtilis was demonstrated. the number of transformants was linearly related to the concentration of dna within a range of 0.01 to 1 mug/ml. no transformants were obtained when the dna was pretreated with dnase. pbs2 dna sheared to approximately 1% of the total chromosome length was centrifuged in cs2so4-hg gradients to fractionate the dna according to the base composition. transformation experiments carried out wi ...1975803565
transcriptional specificity of a multisubunit rna polymerase induced by bacillus subtilis bacteriophage pbs2.bacillus subtilis phage pbs2 induced the synthesis of two temporally defined categories of phage-specified transcripts. the transcription of phage "early" genes was induced almost immediately after infection; this rna synthesis did not require phage protein synthesis. phage "late" gene transcription, on the other hand, was induced at an intermediate time in the lytic cycle; this rna synthesis required the production of phage proteins. both classes of transcription were resistant to the drug rifa ...1978413936
rifampicin-resistant bacteriophage pbs2 infection and rna polymerase in bacillus subtilis.bacteriophage pbs2 replication is unaffected by rifampicin and other rifamycin derivatives, which are potent inhibitors of bacillus subtilis rna synthesis. extracts of gently-lysed infected cells contain a dna-dependent rna polymerase activity which is specific for uracil-containing pbs2 dna. the pbs2-induced rna polymerase is insensitive to rifamycin derivatives which inhibit the host's rna polymerase.197410793705
metabolism of uracil-containing dna: degradation of bacteriophage pbs2 dna in bacillus subtilis.when bacillus subtilis is infected by the uracil-containing dna phage pbs2, the parental dna labeled with radioactive uracil and cytosine remains acid insoluble. if the synthesis of the phage-induced uracil-dna n-glycosidase inhibitor is prevented, the parental dna is completely degraded to acid-soluble products beginning at about 6 min after infection. the host n-glycosidase probably initiates the degradation pathway, with nucleases being responsible for the remaining degradation of the dna.1977406424
the effects of substituted pyrimidines in dnas on cleavage by sequence-specific endonucleases.the rates of cleavage of dnas containing substituents at position 5 of thymine or cytosine have been measured for a variety of sequence-specific endonucleases, so as to determine which features in the dna sequence are being probed. phage phi e dna fully substituted with 5-hydroxymethyluracil is cleaved more slowly by enzymes whose recognition sequences contain a-t base pairs than are dnas containing thymine, but both types of dna are cleaved at similar rates by enzymes recognizing sequences comp ...1979372183
bacillus subtilis deoxyribonucleic acid transfer in pbs2 transduction.mahler, i. (brandeis university, waltham, mass.), m. cahoon, and j. marmur. bacillus subtilis deoxyribonucleic acid transfer in pbs2 transduction. j. bacteriol. 87:1423-1428. 1964.-lysates of the general transducing bacteriophage pbs2 grown on bacillus subtilis sb19 were fractionated by preparative cscl density-gradient centrifugation. five distinct and separate bands which varied in their ability to transduce three nutritional markers were obtained by this procedure. deoxyribonucleic acid (dna) ...196414188723
dextran sulfates as a contaminant of dna extracted from concentrated viruses and as an inhibitor of dna polymerases.dextran sulfate is commonly used with polyethylene glycol to concentrate viruses before extraction of their dna. however, dextran slulfate then easily contaminated such dna and acted as a potent inhibitor of dna polymerases from bacillus subtilis (iii), phage pbs2, and phage t4. dextran sulfate only weakly inhibited micrococcus luteus and escherichia coli dna polymerase i preparations.1978357755
inhibition of bacteriophage pbs2 replication in bacillus subtilis by phleomycin.phleomycin is an effective inhibitor of the replication of bacillus subtilis bacteriophage pbs2, whose dna contains uracil instead of thymine. phleomycin does not affect the induction of the known phage enzymes involved in deoxyribonucleotide metabolism. but phage dna synthesis is severely inhibited by phleomycin, and late virion protein synthesis is eliminated. these effects appear to result from a phleomycin-induced degradation of the parental phage dna. similar inhibitory and degradative effe ...1975163361
relationship of bacillus subtilis dna polymerase iii to bacteriophage pbs2-induced dna polymerase and to the replication of uracil-containing dna.in vivo studies of pbs2 phage replication in a temperature-sensitive bacillus subtilis dna polymerase iii (pol iii) mutant and a temperature-resistant revertant of this mutant have suggested the possible involvement of pol iii in pbs2 dna synthesis. previous results with 6-(p-hydroxyphenylazo)-uracil (hpura), a specific inhibitor of pol iii and dna replication in uninfected cells, suggest that pol iii is not involved in phage dna replication, due to its resistance to this drug. experiments were ...1978104052
bacillus subtilis bacteriophage pbs2-induced dna polymerase. its purification and assay characteristics.the dna polymerase induced by bacillus subtilis bacteriophage pbs2 (whose dna contains uracil instead of thymine) has been purified and characterized for its specificity. the enzyme requires a high ionic strength for optimal stability and activity and is sensitive to various anions and to sulfhdryl reagents. both dutp and dttp are incorporated efficiently as substrates and are competitive inhibitors at the same active site. the apparent km and ki values are about 6 micrometers for dttp and 15 mi ...1978101547
characterization of the bacillus subtilis bacteriophage pbs2-induced dna polymerase and its associated exonuclease activity.the dna polymerase induced by bacillus subtilis bacteriophage pbs2 has a stokes radius of 7.2 in buffers of high ioninc strength, suggesting a molecular weight in the range 145,000 to 195,000. the polypeptide bands observed on gel electrophoresis in dodecyl sulfate have apparent molecular weights of 78,000 and 69,000 (and possibly another 27,000) in equimolar amounts. in buffers of low ionic strength, the enzyme appears to form large aggregates and even precipitates, with about 90% loss of activ ...1978101539
bacillus subtilis rna polymerase and its modification in sporulating and phage-infected bacteria.bacillus subtilis rna polymerase holoenzyme consists of the subunits beta', beta, sigma, alpha, delta, and omega. in sporulating bacteria and in bacteria infected with phages sp01 and sp82, this enzyme undergoes changes in subunit composition and transcriptional specificity that could play a regulatory role in gene transcription. sporulating bacteria may contain a specific component that inhibits the activity of the sigma subunit of polymerase probably by interfering with the binding of sigma-p ...197658549
hydroxymethyluracil dna glycosylase in mammalian cells.an activity has been purified 350-fold from extracts of mouse plasmacytoma cells that forms 5-hydroxymethyluracil (alpha-hydroxythymine) and apyrimidinic sites with phage spo1 dna, which contains this base in place of thymine. this dna glycosylase presumably functions to eliminate hydroxymethyluracil, a major thymine-derived dna lesion produced by ionizing radiation and oxidative damage. the enzyme has no cofactor requirement and is active in edta. neither intermediate formation nor hydrolysis o ...19846588376
resistance of bacteriophage pbs2 infection to 6-(p-hydroxyphenylazo)-uracil, an inhibitor of bacillus subtilis deoxyribonucleic acid synthesis.6-(p-hydroxyphenylazo)-uracil (hpura), an inhibitor of semiconservative deoxyribonucleic acid (dna) synthesis in bacillus subtilis, does not prevent (but slightly reduces the rate of) replication of the uracil-containing dna phage pbs2. our observations are consistent with the hypothesis that all b. subtilis phages which are resistant to hpura are able to induce a new dna polymerase activity.19734631841
deoxythymidylate phosphohydrolase induced by bacteriophage pbs2 during infection of bacillus subtilis. 19734631391
perturbations of enzymic uracil excision due to guanine modifications in dna.phage pbs2 dna, which contains uracil in place of thymine, was used as substrate for purified bacillus subtilis uracil:dna glycosylase. incubation of this dna with the ultimate carcinogen n-acetoxy-n-2-acetylaminofluorene resulted in the production of n-(deoxyguanosin-8-yl)acetylaminofluorene. a decreased vmax resulted from the reaction of the glycosylase with this arylamidated substrate. addition of a 2-fold excess of control pbs2 dna following initiation of the reaction with the modified subst ...19846420049
an enzyme activity from escherichia coli that attacks single-stranded deoxyribopolymers and single-stranded deoxyribonucleic acid containing apyrimidinic sites.we have isolated an enzyme activity from extracts of escherichia coli that catalyzes the hydrolysis of phosphodiester bonds in the single-stranded deoxyribopolymer (du.[3h]dt)(2000) containing depyrimidinated sites created by enzymatic removal of uracil with uracil-dna glycosylase. nondepyrimidinated polymer is not degraded by the enzyme, nor is the depyrimidinated polymer degraded after reduction of apyrimidinic sites with sodium borohydride. the enzyme also degrades circular m13 dna containing ...19826284204
inhibition by lipiarmycin of bacteriophage growth in bacillus subtilis.we have used lipiarmycin, a specific inhibitor of initiation of transcription, to study the role of host rna polymerase in the transcription programs of various phages of bacillus subtilis. unlike rifampin, lipiarmycin preferentially inhibits transcription dependent on the sigma subunit of rna polymerase because it inactivates holoenzyme at a much greater rate than it does core enzyme. with phage sp01, addition of lipiarmycin at a middle-to-late time of infection did not inhibit phage production ...19806767859
inhibitor of uracil-dna glycosylase induced by bacteriophage pbs2. purification and preliminary characterization.a pbs2 phage-coded inhibitor of uracil-dna glycosylase activity from bacillus subtilis has been purified extensively and characterized preliminary. the inhibitor has a relative s value of 1.44 +/- 0.08 measured by sedimentation in 15 to 40% glycerol density gradients. it is unusually stable to heating and to the presence of sodium dodecyl sulfate and/or 8 m urea. the inhibitor has no known cofactor requirement and is active in the presence of 10 mm edta. inhibitor activity is sensitive to digest ...19806776115
specificity of the bacteriophage pbs2 induced inhibitor of uracil-dna glycosylase.the purified pbs2 phage-coded inhibitor of uracil-dna glycosylase (ura-dna glycosylase) from bacillus subtilis has been tested for its ability to inhibit this enzyme isolated from other prokaryotic and from eukaryotic sources. in addition, the inhibitor has been assayed for its effect on dna glycosylases specific for other base residues in dna. the data indicate that ura-dna glycosylases from a variety of sources are equally sensitive to inhibition by the inhibitor. dna glycosylases specific for ...19816796110
tertiary structure of uracil-dna glycosylase inhibitor protein.the bacillus subtilis bacteriophage pbs2 uracil-dna glycosylase inhibitor (ugi) is an acidic protein of 84 amino acids that inactivates uracil-dna glycosylase from diverse organisms. the secondary structure of ugi consists of five anti-parallel beta-strands and two alpha-helices (balasubramanian, s., beger, r.d., bennett, s.e., mosbaugh, d.w., and bolton, p.h. (1995) j. biol. chem. 270, 296-303). the tertiary structure of ugi has been determined by solution state multidimensional nuclear magneti ...19957622499
secondary structure of uracil-dna glycosylase inhibitor protein.the bacillus subtilis bacteriophage pbs2 uracil-dna glycosylase inhibitor (ugi) is an acidic protein of 84 amino acids that inactivates uracil-dna glycosylase from diverse organisms (wang, z., and mosbaugh, d. w. (1989) j. biol. chem. 264, 1163-1171). the secondary structure of ugi has been determined by solution state multidimensional nuclear magnetic resonance. the protein adopts a single well defined structure consisting of five anti-parallel beta-strands and two alpha-helices. six loop or tu ...19957814390
uv-catalyzed cross-linking of escherichia coli uracil-dna glycosylase to dna. identification of amino acid residues in the single-stranded dna binding site.photochemical cross-linking of escherichia coli uracil-dna glycosylase (ung) to oligonucleotide dt20 was performed to identify amino acid residues that reside in or near the dna-binding site. uv-catalyzed cross-linking reactions produced a covalent ung x dt20 complex which was resolved from uncross-linked enzyme by sds-polyacrylamide gel electrophoresis. cross-link formation required native ung and was inhibited by increasing concentrations of nacl in a manner characteristics of nacl inhibition ...19948063831
kinetics of the uracil-dna glycosylase/inhibitor protein association. ung interaction with ugi, nucleic acids, and uracil compounds.the bacteriophage pbs2 uracil-dna glycosylase inhibitor (ugi) inactivates escherichia coli uracil-dna glycosylase (ung) by forming an ung.ugi protein complex with 1:1 stoichiometry. stability of the ung.ugi complex was demonstrated by the inability of free ugi to exchange with ugi bound in preformed complex. ung was reacted with fluorescein 5-isothiocyanate to produce fluorescent-ung (f-ung), which retained full uracil-dna glycosylase activity and susceptibility to ugi inactivation. addition of ...19938262921
incorporation of 5-fluorodeoxyuridine into the dna of bacillus subtilis phage pbs2 and its radiobiological consequences. 19674231342
new deoxyribonucleic acid polymerase induced by bacillus subtilis bacteriophage pbs2.the deoxyribonucleic acid (dna) of bacillus subtilis phage pbs2 has been confirmed to contain uracil instead of thymine. pbs2 phage infection of wild-type cells or dna polymerase-deficient cells results in an increase in the specific activity of dna polymerase. this induction of dna polymerase activity is prevented by actinomycin d and chloramphenicol. in contrast to the major b. subtilis dna polymerase, which prefers deoxythymidine triphosphate (dttp) to deoxyuridine triphosphate (dutp), the dn ...19724623224
resistance of bacteriophage pbs2 infection to rifampicin, an inhibitor of bacillus subtilis rna synthesis. 19724404678
identification of specific carboxyl groups on uracil-dna glycosylase inhibitor protein that are required for activity.the bacteriophage pbs2 uracil-dna glycosylase inhibitor (ugi) protein inactivates uracil-dna glycosylase (ung) by forming an exceptionally stable protein-protein complex in which ugi mimics electronegative and structural features of duplex dna (beger, r. d., balasubramanian, s., bennett, s. e., mosbaugh, d. w., and bolton, p. h. (1995) j. biol. chem. 270, 16840-16847; mol, c. d., arvai, a. s., sanderson, r. j., slupphaug, g., kavli, b., krokan, h. e., mosbaugh, d. w., and tainer, j. a. (1995) ce ...19968910574
increased spontaneous mutation frequency in human cells expressing the phage pbs2-encoded inhibitor of uracil-dna glycosylase.the ugi protein inhibitor of uracil-dna glycosylase encoded by bacteriophage pbs2 inactivates human uracil-dna glycosylases (udg) by forming a tight enzyme:inhibitor complex. to create human cells that are impaired for udg activity, the human glioma u251 cell line was engineered to produce active ugi protein. in vitro assays of crude cell extracts from several ugi-expressing clonal lines showed udg inactivation under standard assay conditions as compared to control cells, and four of these udg d ...200010980411
purification and characterization of a cold-adapted uracil-dna glycosylase from atlantic cod (gadus morhua).uracil-dna glycosylase (udg; ung) has been purified 17000-fold from atlantic cod liver (gadus morhua). the enzyme has an apparent molecular mass of 25 kda, as determined by gel filtration, and an isoelectric point above 9.0. atlantic cung is inhibited by the specific ung inhibitor (ugi) from the bacillus subtilis bacteriophage (pbs2), and has a 2-fold higher activity for single-stranded dna than for double-stranded dna. cung has an optimum activity between ph 7.0-9.0 and 25-50 mm nacl, and a tem ...200011126771
overproduction of thymidine by recombinant brevibacterium helvolum amplified with thymidine monophosphate phosphohydrolase gene from bacteriophage pbs2.a microbial fermentation process could be used to produce thymidine biologically but many of the enzymes related to nucleotide biosynthesis are highly regulated. to overcome the complex regulation steps, an analogue mutant of brevibacterium helvolum resistant to fluorouracil, hydroxyurea, and trimethoprim was constructed. this mutant accumulated 380 mg thymidine 1(-1) in 16 h in shake-flask culture. however, the accumulation of thymidine monophosphate (tmp) inside the cells suggested a low activ ...200415055759
fermentative production of thymidine by a metabolically engineered escherichia coli strain.thymidine is an important precursor in the production of various antiviral drugs, including azidothymidine for the treatment of aids. since thymidine-containing nucleotides are synthesized only by the de novo pathway during dna synthesis, it is not easy to produce a large amount of thymidine biologically. in order to develop a host strain to produce thymidine, thymidine phosphorylase, thymidine kinase, and uridine phosphorylase genes were deleted from an escherichia coli bl21 strain to develop b ...200919251902
specific association of cyclin-like uracil-dna glycosylase with the proliferating cell nuclear antigen.we have previously isolated a human gene that encodes a cyclin-like protein with uracil-removing activity (udg2) (muller, s.j., and caradonna, s. 1993. j. biol. chem. 268, 1310-1319). the structural and regulatory similarities shared between this uracil-dna glycosylase and cyclins suggested that it may interact with additional proteins. using a unique affinity purification protocol (ugi-sepharose) and anti-udg2 antibodies, we have identified a physical interaction between the cyclin-like uracil- ...19968806438
site-directed mutagenesis and characterization of uracil-dna glycosylase inhibitor protein. role of specific carboxylic amino acids in complex formation with escherichia coli uracil-dna glycosylase.bacteriophage pbs2 uracil-dna glycosylase inhibitor (ugi) protein inactivates uracil-dna glycosylase (ung) by acting as a dna mimic to bind ung in an irreversible complex. seven mutant ugi proteins (e20i, e27a, e28l, e30l, e31l, d61g, and e78v) were created to assess the role of various negatively charged residues in the binding mechanism. each mutant ugi protein was purified and characterized with respect to inhibitor activity and ung binding properties relative to the wild type ugi. analysis o ...19979261156
fidelity and mutational specificity of uracil-initiated base excision dna repair synthesis in human glioblastoma cell extracts.the fidelity of dna synthesis associated with uracil-initiated base excision repair was measured in human whole cell extracts. an m13mp2 laczalpha dna-based reversion assay was developed to assess the error frequency of dna repair synthesis at a site-specific uracil residue. all three possible base substitution errors were detected at the uracil target causing reversion of opal codon 14 in the escherichia coli laczalpha gene. using human glioblastoma u251 whole cell extracts, approximately 50% o ...19989733786
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