Function of adenovirus terminal protein in the initiation of DNA replication

An early event in the initiation of adenovirus DNA replication is the formation of a covalent complex between the 87,000-dalton adenovirus terminal protein precursor and 5'- dCMP (pTP-dCMP complex). Nuclear extracts prepared from adenovirus-infected HeLa cells catalyzed complex formation in the presence of ATP, Mg2+, and adenovirus DNA-protein complex but were not active when Pronase-treated DNA was used as template. The activity has been partially purified by chromatography on denatured DNA-cellulose and used to examine whether the 55,000-dalton terminal protein on adenovirus DNA is required for pTP-dCMP complex formation. Results obtained with either DNA-protein complex or Pronase-treated DNA were identical to those obtained using crude nuclear extracts. However, after treatment with piperidine to remove residual peptides. Pronase-treated DNA supported complex formation with the partially purified activity but not with the crude extracts. In addition, when a plasmid containing an origin of adenovirus DNA replication was used as template, the pTP-dCMP complex was formed provided the plasmid was linearized in such a way that the origin was located at the end of the molecule. Neither linearized plasmid DNA with an internal origin nor supercoiled plasmid DNA supported complex formation. Furthermore, after heat denaturation, the linear plasmid DNA still supported complex formation, again provided that the origin was located at the end of the molecule. The partially purified protein fraction supported a limited amount of DNA chain elongation, which permitted exact positioning of the initiation site. These results suggest that enzymes responsible for complex formation recognize a DNA sequence at the origin and that the terminal protein on the template DNA plays a subordinate role.

CMP-dependent incorporation of [14C]Glycerol 3-phosphate into phosphatidylglycerol and phosphatidylglycerol phosphate by rabbit lung microsomes

Rabbit lung microsomes were found to catalyze CMP-dependent incorporation of [14C]glycerol 3-phosphate into a total lipid extract. The radioactively labeled products in the lipid extract were identified as phosphatidylglycerol and phosphatidylglycerol phosphate. CMP-dependent incorporation of [14C]glycerol 3-phosphate by lung microsomes proceeded optimally at pH 7.4 and required Mn2+. The apparent Km value for CMP in this reaction was calculated to be 0.19 mM. No other cytidine nucleotide could substitute completely for CMP in supporting [14C]glycerol 3-phosphate incorporation into lipid. Cytosine-beta-D-arabinofuranoside-5'-monophosphate-dependent incorporation of [14C]glycerol 3-phosphate was observed at pH 8.5 but not at pH 6.8 CMP-dependent incorporation of [14C]glycerol 3-phosphate by microsomes was inhibited by inositol. The optimal in vitro rates of CMP-dependent and CDP diacylglycerol-dependent incorporation of [14C]glycerol 3-phosphate into lipid were similar (approximately 1 nmol . mg-1 protein . h-1) and were not additive. Both CMP -dependent and CDP diacylglycerol-dependent incorporation of [14C]glycerol 3-phosphate by lung microsomes appeared to involve CDPdiacylglycerol:glycerol-3-phosphate phosphatidyltransferase. However, the specific activity of this enzyme in a particular subcellular fraction did not relate directly in the extent of CMP-dependent [14C]glycerol 3-phosphate incorporation in that fraction. Preincubation of lung microsomes with 5 mM CMP plus 3 mM phosphatidylinositol increased CMP-dependent incorporation of [14C]glycerol 3-phosphate. When lung microsomes were depleted specifically of phosphatidylinositol by incubating with a phosphatidylinositol-specific phospholipase C, CMP-dependent incorporation was diminished. The Mn2+ requirement for CMP-dependent incorporation of [14C] glycerol 3-phosphate, its phosphatidylinositol requirement and its inhibition by Triton X-100 (0.2%) were not features shared by CDPdiacylglycerol-dependent incorporation of [14C]glycerol 3-phosphate but were characteristics of the reverse reaction catalyzed by CDPdiacylglycerol: inositol phosphatidyltransferase. Together with the previous finding of a developmental increase in the CMP content of fetal rabbit lung, these observations are consistent with a role for CMP in the regulation of the phosphatidylinositol and phosphatidylglycerol content of lung surfactant during lung maturation.

Competition of rifampicin with binding of substrate and RNA to RNA polymerase

The rate of formation of dinucleoside tetraphosphate, pppApU, from ATP and UTP by RNA polymerase on the A1 promoter of the mutant D111 of bacteriophage T7 is distinctly and specifically reduced not only by the third template-directed nucleotide, CTP, but also by CMP. The inhibitory effect of CMP is not changed when the enzyme contains prebound rifampicin. The synthesis of pppApU is also strongly reduced after preincubation of the enzyme with RNA. This inhibitory effect of RNA is, however, distinctly diminished by rifampicin bound to the enzyme prior to the addition of RNA. On the other hand RNA can suppress the specific binding of the antibiotic to the RNA polymerase subassembly alpha 2 beta.

Solubilization of microsomal-associated phosphatidylserine synthase and phosphatidylinositol synthase from Saccharomyces cerevisiae

Membrane-associated cytidine 5'-diphospho-1,2-diacyl-sn-glycerol (CDP-diacylglycerol):L-serine O-phosphatidyltransferase (phosphatidylserine synthase, EC2.7.8.8.) and CDP-diacylglycerol:myo-inositol phosphatidyltransferase (phosphatidylinositol synthase, EC 2.7.8.11) were solubilized from the microsomal fraction of Saccharomyces cerevisiae. A variety of detergents were examined for their ability to release phosphatidylserine synthase and phosphatidylinositol synthase activities from the microsome fraction. Both enzymes were solubilized from the microsome fraction with Renex 690 in yield over 80% with increase to specific activity of 1.6-fold. Both solubilized enzymatic activities were dependent on manganese ions and Triton X-100 for maximum activity. The pH optimum for each reaction was 8.0. The apparent Km values for CDP-diacylglycerol and serine for the phosphatidylserine synthase reaction were 0.1 and 0.25 mM, respectively. The apparent Km values for CDP-diacylglycerol and inositol for the phosphatidylinositol synthase reaction were 70 microM and 0.1 mM, respectively. Thioreactive agents inhibited both enzymatic activities. Both solubilized enzymatic activities were thermally inactivated at temperatures above 30 degrees C.

The reverse reaction of cholinephosphotransferase in rat brain microsomes. A new pathway for degradation of phosphatidylcholine

The synthesis of phosphatidylcholine is catalyzed by cholinephosphotransferase (EC 2.7.8.2) which is known to be reversible in liver. The reversibility of cholinephosphotransferase in rat brain in demonstrated in this paper. Labeled microsomes were prepared from young rats which had been given an intracerebral injection of labeled choline or oleate 2 h before killing. During incubation of choline-labeled microsomes with CMP, label was lost from ;choline glycerophospholipids and labeled CDPcholine was produced. The Km for CMP was 0.35 mM and V was 3.3 nmol/min per mg protein. Neither AMP nor UMP could substitute for CMP. Oleate-labeled microsomes were pretreated with e mM diisopropylfluorophosphate (lipase inhibitor). During incubation with CMP, label was lost from choline, and ethanolamine glycerophospholipid and labeled diacylglycerols were produced. When the lipase was not inhibited, labeled oleate was produced. We propose that a principal pathway for degradation of phosphatidylcholine, particularly during brain ischemia, is by reversal of cholinephosphotransferase, followed by hydrolysis of diacylglycerols by the lipase.

Some properties of human erythrocyte pyrimidine 5'-nucleotidase

In haemolysates human erythrocyte pyrimidine 5'-nucleotidase had a single optimum at pH 7.2 with CMP and 6.75 with UMP as substrate. The purified enzyme showed two pH optima at pH 6.25 and 7.2 with UMP as substrate. The enzyme was inhibited by both its products - inorganic phosphate and pyrimidine nucleoside. The inhibition by inorganic phosphate appeared to be non-competitive with Ki = 1.5 mM. Contrary to previous reports adenosine and inosine did not inhibit the enzyme.

Dissection of the active site of rabbit liver tRNA nucleotidyltransferase. Specificity and properties of subsites for donor nucleotide triphosphates

tRNA nucleotidyltransferase incorporates both AMP and CMP into tRNA acceptors. Studies of the effects of nucleoside triphosphates, nucleotide analogues, and affinity reagents on AMP and CMP incorporation indicate that these residues are donated from different subsites. However, neither of these sites is completely specific for nucleoside triphosphate binding, and CMP can actually be incorporated from the AMP-donating site, although at a slow rate. The two donor subsites interact with each other, such that binding of a ligand to the ATP site stimulates incorporation from the CMP-donating site. This interaction accounts for the biphasic CTP saturation curve and the unusual effects of nucleoside triphosphates on CMP incorporation observed earlier. In addition to donating CMP, the CTP subsite also serves as the position of binding of the terminal C residue of tRNA-C-C and, in the absence of CTP, for binding of the terminal residue of tRNA-C. These results, together with those in the accompanying paper, have defined multiple accepting and donating subsites within the active site of tRNA nucleotidyltransferase, as predicted from our previous model for enzyme action (Deutscher, M. P. (1972) J. Biol. Chem. 247, 459-468). However, since we have been unable to obtain definitive evidence for two CMP-donating sites, we have considered a modification of this earlier model which utilizes only a single CMP-donating site. Using these models, we discuss how the specificity of the donor and acceptor subsites ensures the accurate synthesis of the -C-C-A sequence of tRNA.

Thermodynamic studies on the hydrolysis of cytidine 2':3'-phosphate by bovine pancreatic ribonuclease A. A possible effect of the change of the structure of water

The temperature-dependence of the ribonuclease A-catalysed hydrolysis of cytidine 2':3'-phosphate was studied in the range of temperatures 0--40 degrees C. A break at 4 degrees C was found both in the Arrhenius and the van't Hoff plots. It is likely that the transition observed is due to the change in the structure of water.

Multienzyme complex for metabolic channeling in mammalian DNA replication

In the DNA-synthesizing phase (S phase) of CHEF/18 Chinese hamster embryo fibroblast cells, six enzymes associated with DNA metabolism, including DNA polymerase (deoxynucleoside triphosphate:DNA deoxynucleotidyl-transferase, EC 2.7.7.7), were largely localized in the nuclear region (karyoplasts). By contrast, in quiescent and G1 phase cells these enzymatic activites were mainly absent from the nucleus and were recovered in the cytoplasmic portion (cytoplasts). These nuclear (but not cytoplasmic) enzymatic activities cosedimented rapidly on sucrose density gradients. Further, the rapidly sedimenting enzyme activities were unique to cells in S phase. An organized supramolecular structure that allows channeling of metabolites into DNA was demonstrated by kinetics of nucleotide incorporation. "Permeabilized" cells selectively channeled incorporation of ribonucleoside diphosphates into DNA in preference to deoxyribonucleoside triphosphates. Deoxyribonucleoside triphosphate incorporation occurred when ribonucleoside-diphosphate reductase (2'-deoxyribonucleoside-diphosphate: oxidized-thioredoxin 2'-oxidoreductase, EC 1.17.4.1) activity was abolished by hydroxyurea. Our interpretation is that during DNA replication, the nucleus contains a complex of DNA precursor-synthesizing enzymes juxtaposed with the "replication apparatus" comprising DNA polymerase, other enzymes, and structural proteins. Functional integrity of this structure is impaired when one of its essential components is inactivated. We propose the name "replitase" for this multienzyme complex for DNA replication and suggest that it incorporates precursors rapidly and efficiently. Possibly its assembly signals the initiation of the S phase of the cell cycle.

Purification of a base-specific ribonuclease Ru from Rhizopus niveus

A base-specific ribonuclease (RNase) Ru (EC 3.1.27.5) was isolated and purified from Rhizopus niveus in a yield of 17% by the procedures of acetone precipitation, column chromatography on Duolite A-2, DEAE-cellulose, CM-cellulose, and 2'(3')-aminohexyl-5'-UMP-agarose. The enzyme was shown to be homogeneous by polyacrylamide disc electrophoresis. The amino- and carboxyl-terminal amino acids of the enzyme were determined to be an arginine and an aspartic acid, respectively. The enzyme has a base specificity: it released only 3'-UMP from yeast RNA or poly(U) and, in addition, small amounts of 3'-CMP from poly(C).

Purification and characterization of a mutant tRNA nucleotidyltransferase

tRNA nucleotidyltransferase has been extensively purified from a mutant strain of Escherichia coli which displays greatly decreased AMP incorporation, but normal CMP incorporation. The defect in AMP incorporation is retained throughout the purification of the mutant protein. The mutant protein behaves identically to the wild-type protein with regard to elution position on various chromatographic columns, and both have similar molecular weights of about 50000. The defect in the mutant protein is accentuated by the use of yeast tRNA rather than E. coli tRNA-C--C as substrate, by decreased pH, by increased ionic strength and by decreased divalent cation concentration. Substitution of MN2+ for Mg2+ greatly increases the relative activity of the mutant enzyme. In all these cases, CMP incorporation by the mutant enzyme remains the same as the wild-type enzyme. The Km values of the mutant enzyme for its tRNA and triphosphate substrates are unchanged, and the mutant protein is as stable as the wild type with respect to temperature inactivation. These results strongly suggest that the mutation is in the structural gene for tRNA nucleotidyltransferase, and that the mutation probably does not affect the overall structure of the mutant protein, but only a localized region near the AMP-incorporating site.

Kinetics and equilibria of pyrimidine nucleoside monophosphate kinase from human erythrocytes

The common type of pyrimidine nucleoside monophosphate kinase (ATP:CMP phosphotransferase, EC 2.7.4.14), purified 50 000-fold from human erythrotes, reacted with a wide variety of nucleotides, but only ATP, dATP, UMP and CMP were good substrates. The optimum Mg2+ concentration, 2-3 mM, was generally independent of substrate concentration, of the nature of the substrate, and of the direction of the reaction. Kinetic studies indicated that a ternary complex was formed, that the substrates were bound at two unlike sites, and that the order of addition of substrates was random. Equilibrium constants were ATP + UMP 0.98, ATP + CMP 1.59, dATP + UMP 1.13, and ATP + AMP 1.20.

Electrophoretic and kinetic studies of a mutant red cell pyrimidine 5'-nucleotidase

Human red cell pyrimidine 5'-nucleotidase (P5N) was studied by partial purification and condensation in a patient with an extremely low red cell P5N activity and chronic hemolytic anemia. The residual P5N in the red cell of the patient was characterized by an increased Michaelis constant for cytidine 5'-monophosphate, a marked shift of the pH optimum to the acidic side, normal electrophoretic mobility and normal heat stability. These data indicate that, in this patient, severe enzyme deficiency is caused by a structural gene mutation. This variant is clearly distinguished from a previously reported case and it is designated P5N Kagoshima.

The mechanism of modification by propranolol of the metabolism of phosphatidyl-CMP (CDP-diacylglycerol) and other lipids in the rat pineal gland

The mechanism underlying the alteration of phospholipid metabolism in rat pineal gland in vitro produced by propranolol and tertiary amine local anesthetics was investigated. 0.1 mM propranolol did not affect either the levels or specific activity of [32P]ATP in glands. In the presence of the drug, the incorporation of cytidine, but not of inorganic phosphate, into phosphatidyl-CMP (CDP-diacylglycerol) was dependent on the cytidine concentration. The incorporation of glycerol into phosphatidyl-CMP, phosphatidylinositol and phosphatidylglycerol was enhanced by propranolol, whereas labeling of phosphatidylcholine was decreased. When both 1 mM propranolol and 1 mM inositol were present, labeling of phosphatidylinositol was further increased, stimulation of phosphatidyl-CMP and phosphatidylglycerol labeling was reduced and incorporation into phosphatidylcholine and triacylglycerol was depressed. The incorporation of [3H]inositol into pineal lipids was also enhanced by propranolol. 10 microM propranolol inhibited rat liver phosphatidic acid phosphohydrolase by 50%, while local anesthetics were less potent in the decreasing order: dibucaine greater than tetracaine greater than lidocaine greater than procaine. The propranolol-induced accumulation of phosphatidyl-CMP was prevented by supplying adequate freely diffusible inositol in the medium. The phosphatidyl-CMP which accumulated was not utilized for the enhanced formation of phosphatidylinositol brought about by norepinephrine. The results indicate that propranolol and local anesthetics redirect pineal phospholipid metabolism in part by inhibition of phosphatidic acid phosphohydrolase.

Reversible inactivation of tRNA nucleotidyltransferase from baker's yeast by tRNAPhe containing iodoacetamide-alkylated 2-thiocytidine in normal and additional positions

2-Thiocytidine 5'-triphosphate, s2CTP, is able to replace CTP as a substrate for tRNA nucleotidyltransferase. s2CMP can be incorporated into both cytidine sites of the C-C-A terminus common to all tRNAs, and in the absence of ATP into at least two additional positions. This was shown by alkylation of the 2-thiocytidine residues with iodo[14C]acetamide, total nucleoside analysis, microgel electrophoresis and analysis of RNase T1 fragments of these tRNAs. The incorporation of the 3'-terminal AMP is not influenced by the additional s2CMP residues at pH 9.0. However, at pH 7.6 the additional s2CMP residues are hydrolysed and AMP can be incorporated into the normal position. Two different tRNAs with terminal 2-thiocytidine alkylated by iodoacetamide inhibit tRNA nucleotidyltransferase. This inhibition is significantly slower if an elongated species is used compared to a tRNA with alkylated 2-thiocytidine in the normal position 75. The addition of 2-mercaptoethanol reactivates the enzyme and leads to a cytidine containing tRNA. This reaction identifies the attacking nucleophile of the enzyme as cysteine residue, which is probably identical to a cysteine residue found in a similar experiment reported previously. The mechanism of the enzymatic and chemical reactions is discussed.

Evidence for compartmentation of uridine nucleotide pools in rat hepatoma cells

Interaction between the de novo and salvage pathways of pyrimidine metabolism was studied in a line of rat hepatoma cells by co-labelling with [14C]-uridine and [3H]orotate. A difference in the ratio of 14C/3H between CTP and UTP in acid-soluble nucleotide pool was reflected in the corresponding ratios in CMP and UMP in RNA, with uridine labelling cytidine nucleotides relatively more effectively than orotate. These results are not compatible with the concept of a single UTP pool, and a new model for pyrimidine anabolic pathways, based on compartmentation of de novo from salvage pathways, is proposed.

Transcription of rat liver deoxyribonucleic acid in vitro at low ionic strength

1. When RNA polymerase is in excess over DNA, the single-stranded breaks of DNA can be recognized as initiation sites for the ezyme. On the other hand stabel initiation complexes (resistant to inhibition by heparin) are the most abundant under these conditions. The formation of these complexes needs double-stranded DNA. It seems that RNA sequences rich in cytidine are preferentially synthesized; since rat liver DNA is A + T-rich, the transcription thus appears not to be random with respect to the base composition of DNA. 2. When the template is in excess over the polymerase, the single-stranded gaps of DNA are preferentially transcribed by rat liver RNA polymerase B and native DNA regions by Escherichia coli RNA polymerase. 3. With a large excess of DNA over the polymerase, the enzyme activity is markedly inhibited. This inhibition is proportional to the concentration of double-stranded DNA ends, but it also depends on the presence of a contaminant of DNA, removed when DNA is banded in a CsCl gradient. This contaminant could be polyphosphates. Low concentrations of spermine completely reverse this inhibition, by enhancing the rate of RNA chain elongation. 4. Double-stranded RNA is synthesized in great abundance when RNA polymerase is in excess over native DNA. Besides a majority of symmetrical sequences, stable 'hairpins' can be found. Whereas the synthesis of symmetrical sequences is more prevalent in polymerase excess, it seems that the proportion of stable 'hairpins' in RNA is independent of the polymerase/DNA ratio.

Preparation of allosteric ribonuclease

A method for the preparation of allosteric ribonuclease from bovine pancreas is described. The effects of freeze-drying ribonuclease from acid and alkaline solutions on plots of velocity versus substrate concentration for the hydrolysis of 2':3'-cyclic CMP are examined. Comparison of these plots with the plots obtained with severeal commercial enzyme preparations indicates that the conformation of the enzyme is dependent on the method of preparation. Aging experiments demonstrate that further conformational changes occur at different rates, depending on the methods of storage. Results suggest that the allosteric behaviour of ribonuclease has not always been observed with commercial preparations, owing to variations in methods of preparation and storage of the enzyme.

How much is secondary structure responsible for resistance of double-stranded RNA to pancreatic ribonuclease A?

1. Double-stranded f2 sus11 or Qbeta RNAs, resistant to bovine pancreatic RNAase A in 0.15 M NaCl/0.015 M sodium citrate (SSC), are quickly and completely degraded at 10-fold lower ionic strength (0.1 X SSC) under otherwise similar conditions. At this ionic strength the secondary structure of double-stranded RNA is maintained, as judged by the following: (a) the unchanged resistance of double-stranded RNA and DNA, under similar low ionic strength conditions, to nuclease S1 from Aspergillus oryzae, in contrast with the sensitivity of the corresponding denatured nucleic acids to this enzyme, specific for single-stranded RNA and DNA; (b) the co-operative pattern of the thermal-transition profile of double-stranded RNA (with a Tm of 89 degrees C) in 0.1 X SSC. 2. Whereas in SSC bovine seminal RNAase (RNAase BS-1) and whale pancreatic RNAase show an activity on double-stranded RNA significantly higher than that of RNAase A, in 0.1 X SSC the activity of the latter enzyme on this substrate becomes distinctly higher than that of RNAase BS-1, and similar to that of whale RNAase. 3. From these results it is deduced that the secondary structure is probably not the only nor the most important variable in determining the susceptibility double-stranded RNA to ribonuclease. Other factors, such as the effect of ionic strength on the enzyme and/or the binding of enzyme to nucleic acids, may play an important role in the process of double-stranded RNA degradation by ribonucleases specific for single-stranded RNA.

Partial purification and properties of an acid nucleotidase from the postmicrosomal supernatant of rat spleen

1. The dephosphorylation of 3'-AMP, 3'-dAMP, 3'-CMP and 3'-dCMP was studied in the postmicrosomal supernatant of rat spleen and liver. In both organs 3'-AMP and 3'-dAMP were dephosphorylated at an appreciable rate, in both the presence and the absence of Mg(2+). The pH optimum for this dephosphorylation was in the range 4.5-5.0. 3'-CMP and 3'-dCMP were very slowly degraded, though the activity towards 3'-dCMP increased somewhat in the presence of Mg(2+). The optimum pH for this Mg(2+)-dependent dephosphorylation was 5.5-6.0. 2. The rate of dephosphorylation of 3'-AMP and 3'-dAMP per mg of protein was about 5 times as high in spleen as in liver. 3. The dephosphorylation of 3'-AMP could be ascribed to a single enzyme with pH optimum about 4.5. The activity towards 3'-dAMP could be resolved into one component coinciding with the 3'-dAMP-degrading enzyme, and one Mg(2+)-requiring component probably identical with the soluble deoxyinosine-activated nucleotidase. The dephosphorylation of 3'-dCMP seemed to be performed only by the latter enzyme. 4. The enzyme dephosphorylating 3'-AMP was purified 200-fold from the postmicrosomal supernatant and its physical and catalytic properties were compared with those of acid nucleotidase (EC 3.1.3.31) purified from rat liver lysosomes. The two enzymes were identical in all properties tested (substrate specificity, K(m), molecular weight, response to phosphatase inhibitors), but some of the data differed from earlier reports on the acid nucleotidase. 5. The subcellular localization of the acid nucleotidase, its relationship to the acid phosphatase(s) and its role in the breakdown of nucleic acid constituents are discussed.

The association between mutagenicity and adduct formation of 1,2,7,8-diepoxyoctane and 1,2,5,6-diepoxycyclooctane

The mutagenicity of 1,2,5,6-diepoxycyclooctane (DECO) and 1,2,7,8-diepoxyoctane (DEO) was investigated using diploid Chinese hamster lung cells. 6-thioguanine (6-TG) resistance was used as the marker for mutagenicity testing: DEO was found to be genetically active; DECO, on the contrary, totally inactive. DEO readily formed adducts with radiolabeled nucleotides, while DECO failed to do so, as demonstrated through thin-layer chromatography (TLC) and the shift of the ultraviolet absorption maximum in DEO/nucleotide mixtures. The difference between the two compounds in chemical and genetic activities was attributed to their molecular conformations and the resulting differential flexibilities and adduct-forming abilities. Association between mutagenicity and adduct formation was conclusive.