Enzymatic initiation of DNA synthesis by yeast DNA polymerases.

Partially purified yeast RNA polymerases (RNA nucleotidyltransferases) initiate DNA synthesis by yeast DNA polymerase (DNA nucleotidyltransferase) I and to a lesser extent yeast DNA polymerase II in the replication of single-stranded DNA. The enzymatic initiation of DNA synthesis on phage fd DNA template occurs with dNTPs alone and is further stimulated by the presence of rNTPs in DNA polymerase I reactions. The presence of rNTPs has no effect on the RNA polymerase initiation of the DNA polymerase II reaction. RNA polymerases I and III are more efficient in initiation of DNA synthesis than RNA polymerase II. Analyses of the products of fd DNA replication show noncovalent linkage between the newly synthesized DNA and the template DNA, and covalent linkage between the newly synthesized RNA and DNA.     

Properties of the Escherichia coli DNA Binding (Unwinding) Protein: Interaction with DNA Polymerase and DNA

The E. coli DNA binding protein reduces the activity of the single-strand-specific nucleases associated with all three DNA polymerases known in E. coli. A slight excess of binding protein over that required to saturate the DNA template leads to total inhibition of activity of the 3' --> 5' nucleases associated with DNA polymerases I and III, but restores maximum activity of the DNA polymerase II-associated nuclease. The binding protein forms a specific complex with DNA polymerase II in the absence of DNA, and it is this complex that degrades a DNA.binding protein complex. Binding protein also facilitates the binding of DNA polymerase II to single-stranded DNA, whereas the binding to DNA of DNA polymerase I is inhibited. These data may explain the specificity with which the binding protein enhances the synthetic ability of DNA polymerase II.     

Sequential stimulation of nuclear RNA polymerase activities in livers from thyroidectomized rats treated with triiodothyronine.

A single ip injection of triiodothyronine (T3; 30 mug/100 g BW) to thyroidectomized rats markedly stimulates RNA synthesis in isolated liver nuclei. The increased level of RNA synthesized in vitro by isolated nuclei does not depend on a reduced degradation of the nascent RNA molecules, since ribonuclease activities are not affected by the administration of T3. In addition, our results have confirmed previous findings of Tata et al. that the increase in nucleolar alpha-amanitin-resistant RNA polymerase I activity at low ionic strength always preceded the rise of the nucleoplasmic alpha-amanitin-sensitive RNA polymerase II activity at high ionic strength. Moreover, it has been found that a significant increase in an alpha-amanitin-resistant activity at high ionic strength occurs as early as 10 h after hormone injection. This enzyme, which forms RNA with a U to G ratio significantly higher than that of RNA synthesized by the nucleolar alpha-amanitin-resistant enzyme, is probably nucleoplasmic RNA polymerase III which is though to synthesize 5S and transfer RNAs. The possible role and the mechanism(s) of the early and concomitant increase in nucleolar and nucleoplasmic alpha-aminitin-resistant activities, and of the subsequent rise of RNA polymerase II activity following T3 administration are discussed.     

Mechanism of Carcinogenesis by RNA Tumor Viruses, III Formation of RNA·DNA Complex and Duplex DNA Molecules by the DNA Polymerase(s) of Avian Myeloblastosis Virus

DNA polymerase activity can be unmasked in avian myeloblastosis virus (AMV) by treatment with the nonionic detergent Nonidet P-40. Two products are formed: (1) RNA.DNA hybrid molecules and (2) duplex DNA molecules. The kinetics of dTTP incorporation into DNA are biphasic: an initial rapid reaction for 4 min at 37 degrees C with a minimal polymerization rate of 10-20 nucleotides per see, and a second reaction at about half the initial rate. Viral RNA.DNA complexes are detected as early as 30 sec after the initiation of DNA synthesis; DNA free of template is formed subsequently. Most of the free AMV DNA forms an RNA.DNA hybrid when annealed with viral RNA. Over half of the free AMV DNA product is inferred to be double-stranded, since it is retained on hydroxyapatite columns after elution with 0.12 M phosphate buffer, and is resistant to Escherichia coli exonuclease I. Adenovirus or calfthymus DNA added to unmasked AMV stimulates DNA synthesis 4-16 times if there is no treatment with RNase, and 40-130 fold if RNase treatment precedes the enzyme assay. It is possible that two polymerases are present, or that a single enzyme forms both the RNA.DNA hybrid and the double-stranded product.     

Action of growth-promoting hormones on macromolecular biosynthesis during lobulo-alveolar development of the entire mammary gland in organ culture.

The entire 2nd thoracic mammary gland of the immature virgin BALB/c mouse was stimulated to full lobulo-alveolar (LA) growth after 120 h organ culture in hormone supplemented medium. The minimal hormonal combination required was insulin (I) + prolactin (Prl) + aldosterone (A). The corticosteroid was replaceable by oestradiol-17beta (E) + progesterone (P). The combination I alone or I + the steroid hormone(s) failed to induce the LA development and similar results were also evident in presence of Prl + the steroids. Incubation of the glands in medium with I + Prl + A activated a sequential rise of RNA, protein and DNA synthesis. A near maximal increase of RNA synthesis was present at 48 h in the medium with I + Prl, addition of the steroid hormones did not show further stimulatory effect. Supplementation of the medium with I + Prl and the adrenal or the ovarian steroids was needed for maximal activation of protein synthesis at 72 h and DNA replication at 96 h. The medium with I alone did not show a substantial rise of macromolecular biosynthesis in the mammary gland in organ culture. The highest level of DNA polymerase activity was observed at 72 h in glands cultivated in medium with I + Prl and A or E + P. Only a modest increase of DNA polymerase activity was present in glands cultivated with I alone or I + Prl. Prior treatment of the glands (cultivated with I + Prl + A) with actinomycin D or puromycin resulted into 44 and 40% reduction of DNA polymerase activity suggesting hormone-induced synthesis of the enzyme before the rise of DNA synthesis in the mammary cells at 96 h in organ culture. Significance of these results with respect to the action of the "growth-promoting" hormones in the mammary gland in organ culture and in the animal has been discussed.     

DNA or RNA priming of bacteriophage G4 DNA synthesis by Escherichia coli dnaG protein.

Escherichia coli dnaG protein is involved in the initiation of DNA synthesis dependent on G4 or ST-1 single-stranded phage DNAs [Bouche, J.-P., Zechel, K & Kornberg, A. (1975) J. Biol. Chem. 250, 5995-6001]. The reaction occurs by the following mechanism: dnaG protein binds to specific sites on the DNA in a reaction requiring E. coli DNA binding protein. An oligonucleotide is synthesized in a reaction involving dnaG protein, DNA binding protein, and DNA. With G4 DNA this reaction requires ADP, dTTP (or UTP), and dGTP (or GTP). Elongation of the oligonucleotide can be catalyzed by DNA polymerase II or III in combination with dnaZ protein and DNA elongation factors I and III, presumably by the mechanism previously reported [Wickner, S. (1976) Proc. Natl. Acad. Sci. USA 73, 3511-3515] or by DNA polymerase I.     

A Novel Form of RNA Polymerase from Escherichia coli

A new form of RNA polymerase, termed RNA polymerase III, has been recognized as a large fraction of the rifampicin-sensitive enzyme in E. coli. It is physically separable from RNA polymerase (holoenzyme, RNA polymerase I) by gel filtration and is distinguished by its capacity to discriminate between M13 and varphiX174 viral DNA templates in priming DNA synthesis. This template specificity is manifested only with saturating levels of DNA unwinding protein and characterizes the priming of DNA synthesis on viral single strands in cell-free extracts and in vivo. RNA polymerase III has less than 5% of the specific activity of RNA polymerase I in transcribing duplex DNA of phages lambda and T4, salmon sperm DNA, and the copolymer poly[d(A-T)]. Rifampicin inactivation of RNA polymerase III releases a factor, presumably a small subunit, which can be isolated and used to confer on RNA polymerase I the properties of III, namely, discrimination between M13 and varphiX174 templates in priming DNA synthesis, and a relative inability to transcribe duplex DNA.     

Glucocorticoid regulation of rat thymus RNA polymerase activity: the role of RNA and protein synthesis.

Treatment of rat thymus cells with the glucocorticoids cortisol and dexamethasone resulted in the stimulation of RNA polymerase B activity within 10 min of steroid addition. This early effect was followed by the inhibition of both RNA polymerase A and B activities. These effects were glucocorticoid-specific and were inhibited by the antiglucocorticoid cortexolone. The inhibitory effect of dexamethasone on RNA polymerase A activity was abolished by prior treatment of the cells with alpha-amanitin, cordycepin or cycloheximide, but cycloheximide was only capable of inhibiting the steroid effect measured at 3 h if added within 10--20 min after steroid addition. Cycloheximide had no effect on the steroid-mediated inhibition of RNA polymerase B activity. Control RNA polymerase A activities were unaffected by the presence of inhibitors of RNA and protein synthesis. It is concluded that the inhibition of ribosomal RNA synthesis by glucocorticoids is dependent on protein synthesis, but that basal RNA polymerase A activity in rat thymus cells is not stringently coupled to protein synthesis.     

Independent Regulation of the Nuclear RNA Polymerases I and II During the Yeast Cell Cycle

The activities of the nuclear RNA polymerases I and II have been investigated in cells of Sacharomyces cerevisiae at G(1), S, early G(2), and late G(2) stages of the cell cycle. The results show that the ratio of the activities of the two enzymes is different at these four stages, indicating that the two RNA polymerases are regulated independently during the cell cycle. The specific activity of the RNA polymerase I remains constant but that of RNA polymerase II increases sharply in cells at the beginning of the G(2) phase. These results are compatible with a pattern of continuous synthesis of the RNA polymerase I and step-wise synthesis of the RNA polymerase II during the yeast cell cycle.     

Comparative Properties of RNA and DNA Templates for the DNA Polymerase of Rous Sarcoma Virus

Several natural RNAs were compared with respect to their template activities for the DNA polymerase of Rous Sarcoma Virus during a 2-hr incubation period. 60-70S viral RNA was found to be a 5- to 10-fold better template than heat-dissociated Rous viral RNA, influenza virus RNA, tobacco mosaic virus RNA, or ribosomal RNA. Denatured salmon DNA is a little better, and poly(dAT) is 2-4 times better as a template for the enzyme than is 60-70S Rous viral RNA. The 60-70S RNAs of different strains of avian tumor viruses have very similar template activities for a given avian tumor virus DNA polymerase. Oligo(dT) or oligo(dC) were found to enhance the template activity of heat-dissociated Rous viral RNA 20- to 30-fold, and that of other natural RNAs tested one- to several-fold. DNA syntheses of 1-24% were obtained during a 2-hour incubation of the enzyme with the above RNA templates. The results suggest that the enzyme prefers partially doublestranded or hybrid regions of RNAs for optimal DNA synthesis, but certain regions of single-stranded RNA can also serve as templates.Poly(dAT) competes with viral RNA for purified DNA polymerase during DNA synthesis, as would be expected if RNA- and DNA-dependent DNA synthesis was performed by at least one common active site of the same enzyme.     

Mitochondrial DNA, RNA and protein synthesis in normal, hypothyroid and mildly hyperthyroid rat liver during cold exposure

We have examined in isolated liver mitochondria the effect of cold exposure on DNA, RNA and protein synthesis in normal, hypothyroid and mildly hyperthyroid rats. In normal rats DNA polymerase activity increased from the first day of cold exposure remaining high up to the fifteenth day. RNA polymerase and protein synthesis were stimulated from the fifth day of cold exposure, maintaining a high level up to the fifteenth day. These activities were related to serum triiodothyronine (T3) levels. Indeed propylthiouracil (PTU) administration to cold-exposed rats drastically depressed the above activities, whereas T3 administration to PTU-treated cold-exposed rats restored them to about the values prevalent in normal cold-exposed rats. The translation products analyzed by gel electrophoresis showed that different effects may be exerted by T3 depending on whether its circulating levels are physiologically or pharmacologically modified. These findings suggest that T3 may be involved in the regulation of the acclimation process by acting, presumably with a permissive role, on those activities which determine a modification of the mitochondrial morphometric features and an increase in mitochondria number and turnover.     

Age-dependent regulation of isoproterenol-stimulated DNA synthesis in rat salivary gland in vivo

In an attempt to determine the initial isoproterenol-stimulated response on which the age-dependent delay in DNA synthesis is based, the time course and magnitude of several previously documented biochemical events within this sequence were examined. An increase in activity of thymidine kinase, and perhaps deoxythymidylate synthesis, is initiated at 12 hr following treatment with isoproterenol, and is delayed nearly 5 hr as rats age from 2 to 12 months. Incorporation of [³H]-uridine into total cellular RNA following isoproterenol injection is initiated at 7 hr in 2-month old rats and occurs as early as 2 hr in 12-month old rats. However, this age-dependent acceleration of apparent RNA synthesis probably is not essential to subsequent synthesis of DNA. The appearance of RNA species required for DNA synthesis, as determined by the time of insensitivity to inhibition by Actinomycin D, occurs at 10 hr following isoproterenol treatment of 2-month old rats, and is delayed nearly 12 hr in 12-month old rats. The possible appearance of protein species required for DNA synthesis, as determined by the time of diminished sensitivity to inhibition by cycloheximide, occurs at 5 hr following isoproterenol treatment of both 2- and 12-month old rats. It is proposed that the initial age dependent modification relates to either the stimulated appearance of crucial RNA species between 5 and 10 hr following isoproterenol treatment, or an early biochemical action of the drug, distinct from its membrane receptor binding which enhances secretion of α-amylase.     

Amino acids and control of nucleolar size, the activity of RNA polymerase I, and DNA synthesis in liver.

The volume of nucleolar material per nucleus and the activity of RNA polymerase I (RNA nucleotidyltransferase I) become doubled in the liver cells of rats that are fed for several days a diet that lacks essential amino acids. Omission of methionine from a fully supplemented diet is equivalent to leaving out all the amino acids, and the responses to a deficiency of tryptophan are about 40% as great. Deprivation of one of the remaining essential amino acids gives either small responses or none at all. Supplementation of the methionine-free diet with cystine blocks the nucleolar enlargement and the enhancement of the polymerase activity that would otherwise take place, but the dispensable amino acid does not affect the responses to a deprivation of one of the other essential amino acids. After deprivation of all the essential amino acids or only methionine, hepatocytes make DNA when the rat is fed a meal with protein. A preparatory diet lacking in tryptophan is much less effective; a deficiency in any of the other indispensable compounds tested fails to prepare the liver for DNA synthesis. The results give hope that elucidation of the means by which methionine deprivation affects the nucleolus will also provide information on the regulation of nuclear DNA replication in liver. One attractive possibility is that the amino acid deficiency acts by producing some imbalance in protein metabolism.     

Initiation of DNA replication at the primary origin of bacteriophage T7 by purified proteins: requirement for T7 RNA polymerase.

The primary origin of bacteriophage T7 DNA replication is located 15% of the distance from the left end of the T7 DNA molecule. This intergenic segment is A + T-rich, contains a single gene 4 protein recognition site, and is preceded by two tandem promoters for T7 RNA polymerase [RNA nucleotidyltransferase (DNA-directed), EC 2.7.7.6]. Analysis by electron microscopy shows that T7 DNA polymerase [DNA nucleotidyltransferase (DNA-directed), EC 2.7.7.7] and gene 4 protein initiate DNA synthesis at randomly located nicks on duplex DNA to produce branched molecules. However, upon the addition of T7 RNA polymerase and ribonucleoside triphosphates 14% of the product molecules have replication bubbles, all of which are located near the primary origin observed in vivo; no such initiation occurs on T7 deletion mutant LG37 DNA, which lacks the primary origin. We have also studied initiation by using plasmids into which fragments of T7 DNA have been inserted. DNA synthesis on these templates is also dependent on the presence of T7 RNA polymerase and ribonucleoside triphosphates. DNA synthesis is specific for plasmids containing the primary origin, provided they are first converted to linear forms.     

Adenovirus DNA replication in vitro: synthesis of full-length DNA with purified proteins.

A protein required for the elongation of replicating intermediates of adenovirus (Ad) DNA to full length has been isolated and characterized. This factor, isolated from nuclear extracts of uninfected HeLa cells, has been designated nuclear factor II. In the presence of Ad DNA with proteins at each 5' end (Ad DNA-protein) and three proteins coded for by the Ad genome [the preterminal protein (pTP), the DNA polymerase (Ad Pol), and the DNA binding protein (Ad DBP)], nuclear factor II complementing activity is detected only in the presence of host nuclear factor I. Highly purified preparations of nuclear factor II that are free of detectable DNA polymerase alpha, beta, and gamma activities contain a DNA topoisomerase activity. Furthermore, type I DNA topoisomerases purified from HeLa cells and calf thymus substitute for nuclear factor II complementing activity in the in vitro Ad DNA replication system. These results indicate that a protein that is involved in higher order DNA structure is required for Ad replication. This protein plus the purified proteins described above carry out the initiation and synthesis of full-length 36,000-base-pair Ad DNA.     

RNA-Primed DNA Synthesis In Vitro

In vitro DNA synthesis on single-stranded circular DNA can be initiated by RNA primers. RNA chains are covalently extended by DNA polymerase II from KB cells and DNA polymerase I from Micrococcus luteus, but not by an RNA-dependent DNA polymerase from avian myeloblastosis virus. The reaction product consists of DNA chains with a piece of RNA at their 5'-ends, hydrogen bonded to the template DNA. The primer RNA is linked to the product DNA via a 3':5'-phosphodiester bond, and can be specifically removed by ribonuclease H. The possible role of ribonuclease H in RNA-primed DNA synthesis in vivo is discussed.