Biogenesis of multisubunit RNA polymerases.

Gene transcription in the nucleus of eukaryotic cells is carried out by three related multisubunit RNA polymerases, Pol I, Pol II and Pol III. Although the structure and function of the polymerases have been studied extensively, little is known about their biogenesis and their transport from the cytoplasm (where the subunits are synthesized) to the nucleus. Recent studies have revealed polymerase assembly intermediates and putative assembly factors, as well as factors required for Pol II nuclear import. In this review, we integrate the available data into a model of Pol II biogenesis that provides a framework for future analysis of the biogenesis of all RNA polymerases.

Cellular targets for activation by the E2F1 transcription factor include DNA synthesis- and G1/S-regulatory genes.

Although a number of transfection experiments have suggested potential targets for the action of the E2F1 transcription factor, as is the case for many transcriptional regulatory proteins, the actual targets in their normal chromosomal environment have not been demonstrated. We have made use of a recombinant adenovirus containing the E2F1 cDNA to infect quiescent cells and then measure the activation of endogenous cellular genes as a consequence of E2F1 production. We find that many of the genes encoding S-phase-acting proteins previously suspected to be E2F targets, including DNA polymerase alpha, thymidylate synthase, proliferating cell nuclear antigen, and ribonucleotide reductase, are indeed induced by E2F1. Several other candidates, including the dihydrofolate reductase and thymidine kinase genes, were only minimally induced by E2F1. In addition to the S-phase genes, we also find that several genes believed to play regulatory roles in cell cycle progression, such as the cdc2, cyclin A, and B-myb genes, are also induced by E2F1. Moreover, the cyclin E gene is strongly induced by E2F1, thus defining an autoregulatory circuit since cyclin E-dependent kinase activity can stimulate E2F1 transcription, likely through the phosphorylation and inactivation of Rb and Rb family members. Finally, we also demonstrate that a G1 arrest brought about by gamma irradiation is overcome by the overexpression of E2F1 and that this coincides with the enhanced activation of key target genes, including the cyclin A and cyclin E genes.

The Pole3 bidirectional unit is regulated by MYC and E2Fs.

Pole3 (DPB4/YBL1/CHRAC17) is one of the subunits of the DNA polymerase e. It contains a histone-like domain required for the hererodimerization with its Pole4 (DPB3) partner. In another interaction, Pole3 heterodimerizes with YCL1/CHRAC15 and associates with the ACF1/SNF2H remodelling complex. We find that the Pol3 gene is regulated in starved NIH3T3 fibroblasts upon induction with serum, with a peak at the entry in the S phase. We characterized the Pole3 promoter, which is linked bidirectionally to C9Orf46, a gene of unknown function: it has no CCAAT nor TATA-boxes, and contains an E box and two potential E2F sites. Mutagenesis analysis points to a minimal promoter region as sufficient for activation; the E box and a neighbouring direct repeat are important for regulation. Cell-cycle regulation was reproduced in stable clones and an additional E2F site was found to be important. Chromatin immunoprecipitation analysis indicates that E2F1/4, as well as MYC, are associated with the Pole3 promoter in a phase-specific way. These data highlight coregulation of a histone-like gene with core histones upon DNA synthesis, and represent a first dissection of the interplay between two essential cell-cycle regulators on a bidirectional promoter.

Evaluation of growth fractions with monoclonal antibodies to human alpha-DNA polymerase.

We have established and partially characterized a panel of monoclonal antibodies against alpha-DNA polymerase. One of the hybridomas, clone 5F, has been exploited for cell kinetic studies on three colon cancer cell lines, LOVO, SW 620, and SW 403, which are endowed with different growth patterns and differentiation status. By an immunoperoxidase method, we could demonstrate the specific intranuclear localization of alpha-DNA polymerase during the exponential phase of in vitro growth and contrast it with the diffuse distribution of the enzyme throughout the cytoplasm during the resting state. The percentage of intranuclear staining positive cells, evaluated at successive time points of in vitro growth, changed from 75 to 95% (assayed on Days 3 and 7) to 15 to 25% in confluent and resting populations assayed on Days 12 to 14. In agreement with the assumption that the enzyme moves from nucleus to cytoplasm after entering quiescence, alpha-DNA polymerase was still present in the cytoplasm or in the cytoplasmic perinuclear area of cells in resting phase cultures. Comparisons between traditional kinetic parameters (thymidine labeling index and primer-dependent alpha-DNA polymerase) and proliferative state determined by the monoclonal antibody supported the feasibility of this approach to define the proportion of actively proliferating elements in a tumor cell population. Moreover, parallel flow cytometric analysis performed on Days 5 and 14 of continuous culture showed fluctuations of alpha-DNA polymerase content in relation to exponential and steady-state phases, with a significant increase in the amount of alpha-DNA polymerase in actively proliferating populations and a progressive reduction of the enzyme as the cultures entered the resting stage.

c-myb effects on kinetic events during MEL cell differentiation.

During dimethylsulfoxide (DMSO)-induced differentiation of Friend mouse erythroleukemia (MEL) cells there is a biphasic fall in c-myb mRNA levels. We have previously shown that constitutive expression of c-myb blocks differentiation. To delineate more accurately the point at which Myb blocks differentiation, MEL cells were transfected with a human c-myb construct under the control of the beta-globin promoter and enhancers. In concert with endogenous DMSO-induced globin transcription during MEL cell differentiation, the beta-globin c-myb transcription unit of the transfected plasmid is activated after 3-5 days of culture in media containing DMSO. Here we describe c-myb-transformed MEL clones which undergo delayed expression of the exogenous c-myb following 3-5 days of culture in DMSO. In contrast to wild-type MEL cells, both clones failed to display phenotypic markers of differentiation and continued to proliferate for up to 10 days of culture. These data suggest that the late fall in c-myb levels may be required in order for differentiation to occur. Additionally, we suggest that constitutive expression of c-myb does not block early commitment events such as activation of histone Hl', subsequent chromatin condensation, and alteration of proliferation-related gene expression. Taken together, these results show that c-myb acts very late in the process of differentiation.

Decreased fidelity in one subspecies of DNA polymerase-alpha that appears during N-2-acetylaminofluorene hepatocarcinogenesis.

During the exposure of rat livers to the hepatocarcinogen 2-acetylaminofluorene (N-2-fluorenylacetamide), it was demonstrated that the cytoplasmic DNA polymerase-alpha (E.C. 2.7.7.7) was strikingly error-prone when compared to that of normal liver (Chan, J.Y.H. and Becker, F.F. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 814-818). The fidelity of polymerization of these enzymes was assayed by determining the incorporation of noncomplementary deoxyribonucleotide triphosphates (misincorporation) on a poly(dA-dT) template. To identify the mechanism of infidelity, we modified and extended our purificaton scheme. As a result, a subspecies of polymerase-alpha 1 was identified and separated from the normal component, polymerase-alpha 2. Polymerase-alpha 1 activity eluted from a phosphocellulose column at 0.07-0.12 M NaCl, while polymerase-alpha 2 eluted at 0.15-0.2 M NaCl. Polymerase-alpha 2 demonstrated normal fidelity throughout the various steps of purification while polymerase-alpha 1, despite being purified some 10 250-fold, continued to demonstrate a severe degree of infidelity.

Cloning and complete sequence of the DNA polymerase-encoding gene (BstpolI) and characterisation of the Klenow-like fragment from Bacillus stearothermophilus.

A fragment of the DNA polymerase I-encoding gene (polI) from Bacillus stearothermophilus (Bst) was obtained by PCR. This was used as a probe to obtain a full-length gene from a Bst genomic DNA (gDNA) plasmid library. Comparison of the sequence to B. caldotenax (Bca) showed about 93% homology at the amino acid (aa) level. A Klenow-like (BstpolIk) clone was developed and the recombinant protein displayed DNA polymerase activity similar to the wild-type BstPolI enzyme.

Biosynthesis and activity of DNA polymerase throughout the mitotic cycle of Physarum polycephalum.

Measurements of DNA polymerase protein levels and polymerase activity through the naturally synchronous mitotic cycle of Physarum polycephalum show that active DNA polymerase-alpha is synthesized throughout the G2 phase, in step with the profile of general protein biosynthesis. Three main components of P. poly-cephalum DNA polymerase of 200, 112 and 70 kDa were found to be immunologically related.

SOS-inducible DNA polymerase II of E coli is homologous to replicative DNA polymerase of eukaryotes.

The polB gene of Escherichia coli encodes DNA polymerase II whose role in vivo is not defined. The polB gene has been cloned and shown to be identical to a DNA damage-inducible gene dinA which is regulated by the LexA repressor. Nucleotide sequencing of polB reveals that E coli DNA polymerase II is highly homologous to replicative DNA polymerases of eukaryotes which include human DNA polymerase alpha and Saccharomyces cerevisiae DNA polymerases I, II and III. The polB gene is not required for growth, UV-repair and UV-mutagenesis.

Effects of aging and dietary restriction on DNA polymerase expression in mice.

DNA polymerase alpha was isolated from livers of 6-month-, 16-month-, or 26-month-old mice fed ad libitum, or calorically restricted. The enzymes differed in chromatographic characteristics, binding affinity for DNA, and activity, with both total activity and specific activity of DNA polymerase alpha decreasing as a function of age. A positive correlation was observed between polymerase alpha specific activity and the affinity of enzyme binding to activated DNA template-primer. The age-associated decline in enzyme activity was modified by dietary restriction, with measurably higher activity seen for polymerases from dietary restricted animals compared with ad libitum animals of all ages. The data suggest that dietary restriction could act to delay the age-associated decrease in cellular capacity for DNA synthesis, which may play a significant role in prolonging the onset of age-related diseases in which decreased DNA synthesis is a potential component.

Deoxyribonucleic acid polymerase-alpha activity in hamster follicles during the estrous cycle: roles of follicle stimulating hormone and luteinizing hormone.

In the hamster, DNA polymerase-alpha (Pol-alpha) in follicles at stages 1-4 (1-4 layers granulosa cells and no theca) increased significantly during the proestrous (P) gonadotropin surges, remained high on estrus (E) and then declined to low levels by 09.00 h, proestrus (P). However, Pol-alpha in stages 5-8 (large preantral to small antral stages) remained steady throughout the cycle. Hypophysectomy on metestrus decreased Pol-alpha by 17 h which was reversed by 2.5 micrograms follicle stimulating hormone (FSH) but not by luteinizing hormone (LH) (2.5 micrograms) or human chorionic gonadotropin (hCG) (1 IU). Hypophysectomy on E resulted 72 h later in a fall in Pol-alpha in stages 1-6; FSH (2.5 micrograms) or LH (2 micrograms) restored enzyme activity within 5 h to stages 1-6 and 5-6, respectively. Thus, Pol-alpha in the smallest preantral follicles is induced by FSH; however, for large preantral and antral follicles, steady levels are maintained by tonic FSH and LH resulting in no apparent change in enzyme activity during active DNA synthesis.

Murine cytomegalovirus DNA polymerase: purification, characterization and role in the antiviral activity of acyclovir.

Murine cytomegalovirus (MCMV) neither induces a viral thymidine kinase (TK) nor enhances the activity of a cellular TK. Nevertheless, MCMV is highly susceptible to 9-(2-hydroxyethoxymethyl)guanine (acyclovir, ACV). The cellular TK is neither responsible for phosphorylation of ACV nor its anti-MCMV activity. This is clear from the findings that little ACV triphosphate is formed in MCMV-infected mouse embryo fibroblasts (MEF) and that the replication of MCMV is inhibited equally well by ACV in TK+ and TK- cells. Even if trace amounts of ACV triphosphate would be formed by enzymes other than TK, and ACV triphosphate would be responsible for the anti-MCMV activity of ACV, then the MCMV DNA polymerase ought to be highly sensitive to ACV triphosphate. To examine this possibility, the MCMV DNA polymerase was partially purified and characterized. The apparent Ki value of the MCMV DNA polymerase for ACV triphosphate indicates that the sensitivity of the MCMV DNA polymerase to ACV triphosphate is equivalent to that of the HSV DNA polymerase. Therefore, the trace amounts of ACV triphosphate that are formed in MCMV-infected MEF seem to be insufficient to inhibit MCMV DNA polymerase and may not play a key role in the anti-MCMV activity of ACV.

Prostate-specific antigen promoter driven gene therapy targeting DNA polymerase-alpha and topoisomerase II alpha in prostate cancer.

Attainment of cell type-specific cytotoxicity with minimal side effects is the ultimate goal of cancer therapy. By employing the prostate-specific antigen promoter (PSAP), we investigated (1) whether PSAP-driven antisense genetic constructs targeting DNA polymerase-alpha and topoisomerase II alpha (Top II alpha), designated PSAP-antipol and PSAP-antitop respectively, could induce death of prostate cancer cells, and (2) whether the cytotoxicity is restricted to cells of prostate origin. A PSAP-driven beta-galactosidase gene, PSAP-LacZ, was also used to estimate the expression of the PSAP-driven transcripts. Lipofection-mediated gene transfers were performed with these 3 constructs and a control plasmid, pCDNA3, in 3 human prostate cancer cell lines (LNCaP, DU-145, PC-3) and 5 other cell lines (Cos-1 [monkey kidney], HL-60 [human myeloid leukemia], Hep G2 [human hepatoma], NCI H460 [human lung cancer] and SW 480 [human colon cancer]). On transfection with PSAP-LacZ, LNCaP, DU-145, and PC-3 showed a 10.8, 1.8, and 1.6 fold increase in beta-galactosidase activity, respectively. The remaining 5 cell lines showed no changes after transfection. Corresponding to the levels of the induced beta-galactosidase activity, LNCaP showed the strongest growth inhibition by the antisense constructs: 36% by PSAP-antipol, 39% by PSAP-antitop and 80% by PSAP-antipol+PSAP-antitop. DU-145 and PC-3 had minimal growth inhibition with PSAP-antipol alone or PSAP-antitop alone. However, when cotransfected with PSAP-antipol and PSAP-antitop, DU-145 and PC-3 displayed 42% and 55% growth inhibition, respectively. In contrast, no cytotoxicity was observed in the remaining 5 cell lines when transfected with PSAP-antipol, PSAP-antitop or both. Therefore, PSAP-driven antisense gene therapy targeting DNA polymerase-alpha and Top II alpha inhibits the growth of human prostate cancer cells and the cytotoxic effect is restricted in cells of prostate origin.

Assessing the contribution of the herpes simplex virus DNA polymerase to spontaneous mutations.

BACKGROUND: The thymidine kinase (tk) mutagenesis assay is often utilized to determine the frequency of herpes simplex virus (HSV) replication-mediated mutations. Using this assay, clinical and laboratory HSV-2 isolates were shown to have a 10- to 80-fold higher frequency of spontaneous mutations compared to HSV-1. METHODS: A panel of HSV-1 and HSV-2, along with polymerase-recombinant viruses expressing type 2 polymerase (Pol) within a type 1 genome, were evaluated using the tk and non-HSV DNA mutagenesis assays to measure HSV replication-dependent errors and determine whether the higher mutation frequency of HSV-2 is a distinct property of type 2 polymerases. RESULTS: Although HSV-2 have mutation frequencies higher than HSV-1 in the tk assay, these errors are assay-specific. In fact, wild type HSV-1 and the antimutator HSV-1 PAAr5 exhibited a 2-4 fold higher frequency than HSV-2 in the non-HSV DNA mutatagenesis assay. Furthermore, regardless of assay, HSV-1 recombinants expressing HSV-2 Pol had error rates similar to HSV-1, whereas the high mutator virus, HSV-2 6757, consistently showed significant errors. Additionally, plasmid DNA containing the HSV-2 tk gene, but not type 1 tk or LacZ DNA, was shown to form an anisomorphic DNA structure. CONCLUSIONS: This study suggests that the Pol is not solely responsible for the virus-type specific differences in mutation frequency. Accordingly, it is possible that (a) mutations may be modulated by other viral polypeptides cooperating with Pol, and (b) the localized secondary structure of the viral genome may partially account for the apparently enhanced error frequency of HSV-2.

Age-related changes in expression and activity of DNA polymerase alpha: some effects of dietary restriction.

DNA polymerase alpha (pol alpha) purified from human diploid fibroblasts (HDF) and from livers of C57BL/6N mice showed age-related decreases in: (1) mRNA levels; (2) the amount of enzyme isolated per cell; and (3) enzyme activity (HDF); as well as: a) the amount of enzyme isolated; b) the specific activity; and c) the enzyme fidelity (liver). Hepatic pol alpha from dietary restricted (DR) mice exhibited less of a decline in specific activity and copied synthetic DNA templates with relatively higher fidelity than did enzymes from animals fed ad libitum (AL). Pol alpha from fetal-derived HDF exhibited increased expression compared with aged donor-derived HDF, with both fetal and old cell pol alpha in normal cells being expressed at lower levels than in their transformed cell corollaries. Treatment of human pol alpha from aged donor-derived HDF with a pol alpha accessory protein isolated from log phase murine cells resulted in increased pol alpha binding of DNA and increased pol alpha activity. However, highly active pol alpha isolated from fetal-derived or transformed HDF, or from transformed murine cells, showed little or no activity enhancement in the presence of accessory protein. These data indicate that, as a function of increased age, there is a decrease in pol alpha expression and specific activity in HDF, as well as decreases in specific activity and fidelity of pol alpha in essentially amitotic murine hepatic tissues. Dietary restriction impedes the age-related declines in both activity and fidelity of hepatic pol alpha in mice. The data further indicate that transformation of slowly dividing HDF is associated with increased expression of pol alpha, but suggest that increased expression alone is not sufficient to explain the difference in polymerase activity levels between parental and transformed HDF. Lastly, the data suggest that interaction of pol alpha with an essential accessory protein may be altered as a function of age, an alteration that appears to be correlated with the decline in pol alpha DNA binding and specific activity.

DNA polymerase alpha does not mediate G0-G1 increase in yield of X-ray-induced exchange aberrations in human peripheral blood lymphocytes.

We report experiments to test the hypothesis that the increased yield of dicentric chromosomes observed in human peripheral blood lymphocytes treated with X-rays during the G1 phase of their first cell cycle, as compared with the yield when the cells are treated in their G0 phase prior to phytohemagglutinin stimulation, is a manifestation of the recently-reported conversion of an inactive form of DNA polymerase alpha to its active form as the PHA-stimulated cells pass from G0 into G1 (Sylvia et al., 1988). The specific polymerase alpha inhibitor butylphenyl deoxyguanosine was used as an X-ray post-treatment. The results show that polymerase alpha is not involved.

Synthesis of catalytically active polymerase alpha by in vitro translation of calf RNA.

The cell-free synthesis of DNA polymerase in translation mixtures containing calf thymus total and poly (A+) RNA was examined using activity gel analysis and immunobinding with a monoclonal antibody to calf thymus alpha-polymerase. Activity gel analysis indicated that functional DNA polymerase catalytic polypeptides of Mr = 110,000 to 120,000 and Mr approximately 68,000 were synthesized. Sucrose density gradient centrifugation of total RNA resulted in resolution and partial purification of the mRNAs encoding these two DNA polymerase polypeptides. Immunobinding experiments with the monoclonal antibody to calf alpha-polymerase confirmed that an immunoreactive polypeptide of 110 to 120 kilo-daltons had been formed in vitro. This polypeptide and the 68,000-Mr polypeptide correspond in size to alpha-polymerase catalytic polypeptides observed in crude extracts of calf cells and in purified calf alpha-polymerase.