Ultraviolet radiation, but not gamma radiation or etoposide-induced DNA damage, results in the phosphorylation of the murine p53 protein at serine-389

Polyclonal antibodies were produced and purified that selectively react with a p53 epitope containing the murine phosphoserine-389 or the human phosphoserine-392 residue, but not the unphosphorylated epitope. These antibodies, termed alpha-392, were employed to demonstrate that the phosphorylation of this serine-389 residue in the p53 protein occurs in vivo in response to ultraviolet radiation of cells containing the p53 protein. After ultraviolet radiation of cells in culture, p53 levels increase and concomitantly serine-389 is phosphorylated in these cells. By contrast, the serine-389 phosphorylation of the p53 protein was not detected by these antibodies in the increased levels of p53 protein made in response to gamma radiation or the treatment of cells with etoposide. These results demonstrate an ultraviolet responsive and specific phosphorylation site at serine-389 of the mouse or serine-392 of the human p53 protein. Previous studies have demonstrated that this phosphorylation of p53 activates the protein for specific DNA binding. This study demonstrates in vivo a unique phosphorylation site in the p53 protein that responds to a specific type of DNA damage.     

Composition of nucleic acids and concentration of methylated bases in the DNA of Bifidobacterium bifidum var. Tissier

Nucleotide composition of the sum total DNA of B. bifidum, biotype III, was determined by paper chromatography in combination with ultraviolet spectrophotometry. DNA of B. bifidum was referred to the GC-type (GC -- 62.6 mol%). Two additional nitrogen bases were present in the DNA composition; 5-methylcytosine and 6-methylaminopurine -- 0.45 mol% and 0.20 mol%, respectively. Nucleotide composition of the sum total RNA was studied with the aid of high-voltage electrophoresis in combination with ultraviolet spectrophotometry. The sum total RNA was referred to the high GC-type (GC -- 64.9 mol%). These data permit to consider it reasonable to refer bifidobacteria to the Bifidobacterium genus.     

Micrococcus luteus correndonucleases. III. Evidence for involvement in repair in vivo of two endonucleases specific for DNA containing pyrimidine dimers

Involvement of Py pyrimidine dimers Py correnconucleases I and II in repair of ultraviolet radiation damage in vivo by Micrococcus luteus has been demonstrated by their absence in the ultraviolet-sensitive mutant DB-7 derived by treatment of the wild type parent with N-methyl-N'-nitro-N-nitrosoguanidine. The necessity for their combined action in DNA repair in M. luteus is shown by: (a) reactivation of ultraviolet-damaged phiX174 RFI DNA in incision-defective hosts after in vivo treatment with both enzymes, (b) correlation between survival after ultraviolet irradiation and the level of the two enzymes, and (c) increased levels of repair synthesis after ultraviolet irradiation of toluenized cells DB-400 with wild type correndonuclease levels when compared with the transformant DB-200 and the mutant DB-7, which lack one or both enzymes.     

Study of methods of inactivating a concentrated, purified cultured antirabies vaccine]

Two methods of inactivation, with ultraviolet (UV) and gamma (gamma) rays, of the concentrated purified tissue culture rabies vaccine from the Vnukovo-32 strain were studied. Under the optimal conditions of treatment of 100-fold concentrated purified virus-containing suspension, a completely inactivated vaccine with high immunogenicity indices (4.1 to 78) was obtained. Both the inactivation methods were found to be of equal value.     

Characterization of the native and recombinant catalytic subunit of human DNA polymerase gamma: identification of residues critical for exonuclease activity and dideoxynucleotide sensitivity

The human DNA polymerase gamma catalytic subunit was overexpressed in recombinant baculovirus-infected insect cells, and the 136 000 Da protein was purified to homogeneity. Application of the same purification protocol to HeLa mitochondrial lysates permitted isolation of native DNA polymerase gamma as a single subunit, allowing direct comparison of the native and recombinant enzymes without interference of other polypeptides. Both forms exhibited identical properties, and the DNA polymerase and 3' --> 5' exonuclease activities were shown unambiguously to reside in the catalytic polypeptide. The salt sensitivity and moderate processivity of the isolated catalytic subunit suggest other factors could be required to restore the salt tolerance and highly processive DNA synthesis typical of gamma polymerases. To facilitate our understanding of mitochondrial DNA replication and mutagenesis as well as cytotoxicity mediated by antiviral nucleotide analogues, we also constructed two site-directed mutant proteins of the human DNA polymerase gamma. Substituting alanine for two essential acidic residues in the exonuclease motif selectively eliminated the 3' --> 5' exonucleolytic function of the purified mutant polymerase gamma. Replacement of a tyrosine residue critical for sugar recognition with phenylalanine in polymerase motif B reduced dideoxynucleotide inhibition by a factor of 5000 with only minor effects on overall polymerase function.     

Termination within oligo(dT) tracts in template DNA by DNA polymerase gamma occurs with formation of a DNA triplex structure and is relieved by mitochondrial single-stranded DNA-binding protein

Xenopus laevis DNA polymerase gamma (pol gamma) exhibits low activity on a poly(dT)-oligo(dA) primer-template. We prepared a single-stranded phagemid template containing a dT41 sequence to test the ability of pol gamma to extend a primer through a defined oligo(dT) tract. pol gamma terminates in the center of this dT41 sequence. This replication arrest is abrogated by addition of single-stranded DNA-binding protein or by substitution of 7-deaza-dATP for dATP. These features are consistent with the formation of a T.A*T DNA triplex involving the primer stem. Replication arrest occurs under conditions that permit highly processive DNA synthesis by pol gamma. A similar replication arrest occurs for T7 DNA polymerase, which is also a highly processive DNA polymerase. These results suggest the possibility that DNA triplex formation can occur prior to dissociation of DNA polymerase. Primers with 3'-oligo(dA) termini annealed to a template with a longer oligo(dT) tract are not efficiently extended by pol gamma unless single-stranded DNA-binding protein is added. Thus, one of the functions of single-stranded DNA-binding protein in mtDNA maintenance may be to enable pol gamma to successfully replicate through dT-rich sequences.     

Modulation of fluorouracil cytotoxicity by interferon-alpha and -gamma

Because interferons (IFN)-alpha and -gamma individually have increased fluorouracil (FUra) cytotoxicity in several in vitro models, we studied the effects of FUra combined with IFN-alpha + gamma in HT29 colon cancer cells. A 96-hr exposure to IFN-alpha (500 units/ml) plus IFN-gamma (10 units/ml) and a 72-hr exposure to 0. 25-1 microM FUra (hr 24-96) inhibited cell growth and colony formation in an additive or more-than-additive fashion. When cells were exposed to IFN-alpha + gamma and FUra, free FdUMP levels became detectable, whereas [3H]FUra-RNA incorporation decreased. Exposure to IFN-alpha + gamma, FUra, or the combination decreased dTTP pools to 58%, 43%, and 17% of control, respectively. A marked increase in the dATP to dTTP ratio was seen with FUra with or without IFN-alpha + gamma. Thymidylate synthase catalytic activity was reduced to 28% and 24% of control with FUra with or without IFN-alpha + gamma, suggesting that the enhanced dTTP depletion must be due to another mechanism. FUra-mediated thymidylate synthase inhibition was accompanied by a 124-fold increase in total deoxyuridylate immunoreactivity and a 31-fold increase in dUTP pools, but the addition of IFN-alpha + gamma attenuated the accumulation. Treatment with IFN-alpha + gamma and FUra individually interfered with nascent DNA chain elongation, whereas the three-drug combination produced the most striking effects. IFN-alpha + gamma plus FUra produced the greatest amount of single-strand breaks in nascent DNA and dramatically decreased net DNA synthesis. IFN-alpha + gamma with or without FUra produced double-strand breaks in parental DNA. These results suggest that dTTP depletion, dATP/dTTP imbalance, pronounced inhibition of DNA synthesis, and damage to nascent and parental DNA contribute to the enhanced cytotoxicity with the triple combination.     

Artificial background and induced levels of oxidative base damage in DNA from human cells

The pre-mutagenic oxidative DNA base damage of 8-hydroxy-guanine is present in DNA isolated from cells and the amount present increases with exposure of cells to oxidative stress. The oxidative DNA base damage may be present before isolation of DNA or it may be produced during isolation and processing of DNA. We have found that the amount of oxidative base damage measured in DNA can be reduced to a stable lower level by adding increasing concentrations of the antioxidants desferrioxamine, histidine and reduced glutathione immediately before cell lysis. Inclusion of these antioxidants after cell lysis did not affect the level of DNA damage. Oxidative DNA base damage produced by ultraviolet A irradiation of human cells was also reduced by adding antioxidants after irradiation and before cell lysis. Thus, unidentified oxidants induced by ultraviolet A irradiation may damage DNA significantly during extractions of DNA from cells subsequent to ultraviolet A irradiation.     

The internal workings of a DNA polymerase clamp-loading machine

Replicative DNA polymerases are multiprotein machines that are tethered to DNA during chain extension by sliding clamp proteins. The clamps are designed to encircle DNA completely, and they are manipulated rapidly onto DNA by the ATP-dependent activity of a clamp loader. We outline the detailed mechanism of gamma complex, a five-protein clamp loader that is part of the Escherichia coli replicase, DNA polymerase III holoenzyme. The gamma complex uses ATP to open the beta clamp and assemble it onto DNA. Surprisingly, ATP is not needed for gamma complex to crack open the beta clamp. The function of ATP is to regulate the activity of one subunit, delta, which opens the clamp simply by binding to it. The delta' subunit acts as a modulator of the interaction between delta and beta. On binding ATP, the gamma complex is activated such that the delta' subunit permits delta to bind beta and crack open the ring at one interface. The clamp loader-open clamp protein complex is now ready for an encounter with primed DNA to complete assembly of the clamp around DNA. Interaction with DNA stimulates ATP hydrolysis which ejects the gamma complex from DNA, leaving the ring to close around the duplex.     

Effects of Xenopus laevis mitochondrial single-stranded DNA-binding protein on primer-template binding and 3'-->5' exonuclease activity of DNA polymerase gamma

Mitochondrial DNA (mtDNA) is replicated by DNA polymerase gamma by a strand displacement mechanism involving mitochondrial single-stranded DNA-binding protein (mtSSB). mtSSB stimulates the overall rate of DNA synthesis on singly-primed M13 DNA mainly by stimulating the processivity of DNA synthesis rather than by stimulating primer recognition. We used electrophoretic mobility shift methods to study the effects of mtSSB on primer-template recognition by DNA pol gamma. Preliminary experiments showed that single mtSSB tetramers bind tightly to oligo(dT) single strands containing 32 to 48 residues. An oligonucleotide primer-template was designed with an 18-mer primer annealed to the 3'-portion of a 71-mer template containing 40 dT residues at its 5'-end as a binding site for mtSSB. DNA pol gamma bound to this primer-template either in the absence or presence of mtSSB in complexes that remained intact and enzymatically active following native gel electrophoresis. Association of mtSSB with the 5'-dT40-tail in the 18:71-mer primer-template reduced the binding of DNA polymerase gamma and the efficiency of primer extension. Binding of mtSSB to single-stranded DNA was also observed to block the action of the 3'-->5' exonuclease of DNA polymerase gamma. The size of fragments protected from 3'-->5' exonuclease trimming increases with increasing ionic strength in a manner consistent with the known salt dependence of the binding site size of Escherichia coli SSB.     

G-protein beta gamma subunit genes expressed in olfactory receptor neurons

The expression of genes encoding G-protein beta gamma subunits was investigated in isolated olfactory receptor neurons from channel catfish. DNA sequencing of PCR products showed that the beta 1, beta 2, gamma 2 and gamma 3 genes were expressed in the neurons. Western blotting showed that at least three of these subunit proteins were expressed. This first analysis of the expression of beta gamma genes in olfactory receptor neurons suggests that these subunits may be involved in a variety of transduction events in these cells.     

pDUAL: a transposon-based cosmid cloning vector for generating nested deletions and DNA sequencing templates in vivo

We describe a transposon gamma delta-containing cosmid cloning vector, pDUAL (previously called pJANUS), and demonstrate an efficient strategy for isolating nested deletions in both large-scale and small-scale DNA sequencing efforts. This "deletion factory" strategy takes advantage of the ability of gamma delta (Tn1000) to generate deletions that extend from an end of the transposon into adjacent DNA when gamma delta transposes to new sites in the same DNA molecule. pDUAL contains the contraselectable (conditional lethal) sacB+ (sucrose sensitivity) and strA+ (streptomycin sensitivity) genes just outside each end of an engineered gamma delta and selectable kan+ (Kanr) and tet+ (Tetr) genes between the cloning site and sacB and strA, respectively. Selection on sucrose tetracycline medium yields deletions that extend from one gamma delta end for various distances into the cloned DNA, while selection on streptomycin kanamycin medium yields comparable deletions in the other direction. Both types of deletions are recoverable because the essential plasmid replication origin is embedded in the gamma delta component and is thereby retained in each deletion product. Pilot experiments with pDUAL clones showed that deletion end points can be mapped or selected by plasmid size and that both DNA strands of any single clone can be accessed for sequencing by using a pair of universal primers specific for sequences that are just interior to the gamma delta ends.     

Purification and characterization of human endonucleases specific for damaged DNA. Analysis of lesions induced by ultraviolet or x-radiation

1. An endonuclease activity from a cultured human lymphoblast cell line, CCRF-CEM, was further purified by chromatography on phosphocellulose to remove a nonspecific acid endonuclease. 2. The purified enzyme acted quantitatively on apurinic sites in the DNA of PM2 phage. It showed optimum activity over a broad range of pH (7.0--8.5), was absolutely dependent on Mg2+ (optimum concentration 0.5 mM) and did not have detectable activity against intact DNA. 3. This enzyme was used as a probe to estimate the number of apurinic or apyrimidinic lesions induced in PM2 DNA by either ultraviolet or X-ray irradiation. High doses of ultraviolet radiation (2500 to 5000 J/m2) immediately induced 0.2 to 0.4 endonuclease-susceptible lesions per molecule of DNA. The lesions continued to increase for several hours after irradiation, reaching a level more than double that found initially. By contrast, in DNA exposed to 5000 rads of X-ray irradiation, the number of endonuclease-susceptible sites reached a maximum of about 0.6 per molecule immediately after exposure and did not increase further. It thus appears that ultraviolet-irradiated (but not X-ray irradiated) DNA contains damaged bases that are lost spontaneously after irradiation. 4. A second endonuclease was purified and was shown to act on ultraviolet-induced lesions that are distinct from either apurinic or apyrimidinic sites. These new lesions occur about ten times more frequently than ultraviolet-induced apurinic or apyrimidinic sites.     

Expression, purification, and initial kinetic characterization of the large subunit of the human mitochondrial DNA polymerase

Faulty replication of the human mitochondrial genome is thought to be the cause of many diseases; moreover, the low selectivity of the mitochondrial DNA polymerase has been implicated as the cause of many side effects observed in the treatment of viral infections such as HIV. To better understand how the mitochondrial genome is replicated, we cloned a cDNA encoding the large subunit of human DNA polymerase gamma, the enzyme that replicates the mitochondrial genome. The large subunit was recombinantly expressed and purified to near homogeneity. The purified enzyme demonstrated both polymerase and 3'-5' exonuclease activity. The purified protein was examined in single nucleotide incorporation assays, demonstrating that the enzyme had a maximum polymerization rate of 3.5 s-1 and a dissociation rate from the DNA substrate of 0.03 s-1, affording a calculated processivity of 116. The dissociation constants for the enzyme binding to DNA and nucleoside triphosphate were 39 nM and 14 microM, respectively. The 3'-5' exonuclease rate was measured at 0. 18 s-1. Though the slow rate of polymerization suggests that the large subunit of human DNA polymerase gamma may require accessory factors to increase its processivity of polymerization, the kinetic parameters indicate that the large subunit of DNA polymerase gamma could replicate the mitochondrial genome in a physiologically relevant time frame. This study provides the initial characterization of the large subunit of DNA polymerase gamma and establishes the baseline for examination of the effects of accessory proteins such as the putative small subunit.     

A homeobox gene, HLXB9, is the major locus for dominantly inherited sacral agenesis

A 12-year-old girl developed ataxia that gradually progressed. At age 18 the patient presented with mental retardation, cachectic dwarfism, microcephalus, and a progeroid appearance but no photosensitive skin lesions or deafness. On analysis of fibroblasts, unscheduled DNA synthesis was reduced to 50% of normal, but colony-forming ability after ultraviolet irradiation was normal. The symptoms and phenotype of the patient were distinguished from those in Cockayne syndrome and xeroderma pigmentosum. This case is interesting because the defect in DNA repair after ultraviolet irradiation was detected in a patient with neurologic disturbances but without photosensitive skin lesions.     

Excision of ultraviolet and gamma ray products of the 5,6-dihydroxy-dihydrothymine type by nuclear preperations of xeroderma pigmentosum cells

Monomeric products of the 5,6-dihydroxy-dihydrothymine type are produced in the DNA by both ultraviolet and ionizing radiations. The capacity of nuclear preparations from normal and Xeroderma pigmentosum (XP) cells (Complementation groups A, B, C and D) to excise such products from ultraviolet or gamma-irradiated T7DNA was comparable and was independent of radiation induced strand breaks.     

Cleavage by calicheamicin gamma 1I of DNA in a nucleosome formed on the 5S RNA gene of Xenopus borealis

The cleavage by calicheamicin gamma 1I (CLM gamma 1I) of a nucleosome formed on the 5S RNA gene of Xenopus borealis was studied in vitro as a first step toward the understanding of CLM gamma 1I-chromatin interactions within the cell. The drug does not cleave in the region of the dyad axis of the nucleosome. Outside of this region, double-stranded cleavage occurs with a periodicity of 10-11 bp. The sites of cleavage correspond to DNA sequences facing outward in the nucleosome. The drug shows some sequence preference of cleavage within these accessible sites. The predominant cleavage event within this nucleosome occurs at -1 helical turn from the dyad axis. This site constitutes a "hot spot" for CLM gamma 1I cleavage within the 5S nucleosome. We observe an overall footprinting effect whereby the drug preferentially cleaves DNA located outside the nucleosome core (analogous to the linker DNA of chromatin) as compared to cleavage within the nucleosome core. We discuss the importance of accessibility, structural deformations of DNA within the nucleosome, and steric constraints posed by sequence, in the recognition and cleavage of nucleosomal DNA by calicheamicin.     

Isolation of cell cycle-dependent gamma ray-sensitive Chinese hamster ovary cell

A technique for the isolation of gamma ray-sensitive Chinese hamster ovary (CHO) cell mutants is described, which uses nylon cloth replica plating and photography with dark-field illumination to directly monitor colonies for growth after gamma irradiation. Two gamma ray-sensitive mutants were isolated using this method. One of these cells (XR-1) had a two-slope survival curve: an initial steep slope and then a flattening of the curve at about 10% survival. Subsequently, it was found that this cell is sensitive to gamma irradiation in G1, early S, and late G2 phases of the cell cycle, whereas in the resistant phase (late S phase) its survival approaches that of the parental cells. The D37 in the sensitive G1 period is approximately 30 rads, compared with 300 rads of the parental cell. This mutant cell is also sensitive to killing by the DNA breaking agent, bleomycin, but is relatively insensitive to UV light and ethyl methane sulfonate, suggesting that the defect is specific for agents that produce DNA strand breakage.