Terminal Phosphate Residues Research Articles

The Arabidopsis thaliana Poly(ADP-Ribose) Polymerases 1 and 2 Modify DNA by ADP-Ribosylating Terminal Phosphate Residues.

Proteins from the poly(ADP-ribose) polymerase (PARP) family, such as PARP1 and PARP2, use NAD+ as a substrate to catalyze the synthesis of polymeric chains consisting of ADP-ribose units covalently attached to an acceptor molecule. PARP1 and PARP2 are viewed as DNA damage sensors that, upon binding to strand breaks, poly(ADP-ribosyl)ate themselves and nuclear acceptor proteins. The flowering plant Arabidopsis thaliana contains three genes encoding homologs of mammalian PARPs: atPARP1, atPARP2, and atPARP3. Both atPARP1 and atPARP2 contain poly(ADP-ribosyl)ating activity; however, it is unknown whether they could covalently modify DNA by ADP-ribosylating the strand break termini. Here, we report that similar to their mammalian counterparts, the plant atPARP1 and atPARP2 proteins ADP-ribosylate 5′-terminal phosphate residues in duplex DNA oligonucleotides and plasmid containing at least two closely spaced DNA strand breaks. AtPARP1 preferentially catalyzes covalent attachment of ADP-ribose units to the ends of recessed DNA duplexes containing 5′-phosphate, whereas atPARP2 preferentially ADP-ribosylates the nicked and gapped DNA duplexes containing the terminal 5′-phosphate. Similar to their mammalian counterparts, the plant PARP-catalyzed DNA ADP-ribosylation is particularly sensitive to the distance that separates two strand breaks in the same DNA molecule, 1.5 and 1 or 2 turns of helix for atPARP1 and atPARP2, respectively. PAR glycohydrolase (PARG) restored native DNA structure by hydrolyzing the PAR–DNA adducts generated by atPARPs. Biochemical and mass spectrometry analyses of the PAR–DNA adducts showed that atPARPs utilize phosphorylated DNA termini as an alternative to protein acceptor residues to catalyze PAR chain synthesis via phosphodiester bond formation between C1′ of ADP-ribose and a phosphate residue of the terminal nucleotide in DNA fragment. Taken together, these data establish the presence of a new type of DNA-modifying activity in Arabidopsis PARPs, suggesting a possible role of DNA ADP-ribosylation in DNA damage signaling and repair of terrestrial plants.

Insight into DNA substrate specificity of PARP1-catalysed DNA poly(ADP-ribosyl)ation

DNA-dependent poly(ADP-ribose) polymerases (PARPs) PARP1, PARP2 and PARP3 act as DNA break sensors signalling DNA damage. Upon detecting DNA damage, these PARPs use nicotine adenine dinucleotide as a substrate to synthesise a monomer or polymer of ADP-ribose (MAR or PAR, respectively) covalently attached to the acceptor residue of target proteins. Recently, it was demonstrated that PARP1–3 proteins can directly ADP-ribosylate DNA breaks by attaching MAR and PAR moieties to terminal phosphates. Nevertheless, little is still known about the mechanisms governing substrate recognition and specificity of PARP1, which accounts for most of cellular PARylation activity. Here, we characterised PARP1-mediated DNA PARylation of DNA duplexes containing various types of breaks at different positions. The 3′-terminal phosphate residue at double-strand DNA break ends served as a major acceptor site for PARP1-catalysed PARylation depending on the orientation and distance between DNA strand breaks in a single DNA molecule. A preference for ADP-ribosylation of DNA molecules containing 3′-terminal phosphate over PARP1 auto-ADP-ribosylation was observed, and a model of DNA modification by PARP1 was proposed. Similar results were obtained with purified recombinant PARP1 and HeLa cell-free extracts. Thus, the biological effects of PARP-mediated ADP-ribosylation may strongly depend on the configuration of complex DNA strand breaks.

Ribonucleoside-5′-diphosphates (NDPs) support RNA polymerase transcription, suggesting NDPs may have been substrates for primordial nucleic acid biosynthesis

A better understanding of the structural basis for the preferences of RNA and DNA polymerases for nucleoside-5'-triphosphates (NTPs) could help define the catalytic mechanisms for nucleotidyl transfer during RNA and DNA synthesis and the origin of primordial nucleic acid biosynthesis. We show here that ribonucleoside-5'-diphosphates (NDPs) can be utilized as substrates by RNA polymerase (RNAP). We found that NDP incorporation is template-specific and that noncognate NDPs are not incorporated. Compared with the natural RNAP substrates, NTPs, the Km of RNAP for NDPs was increased ∼4-fold, whereas the V max was decreased ∼200-fold. These properties could be accounted for by molecular modeling of NTP/RNAP co-crystal structures. This finding suggested that the terminal phosphate residue in NTP (not present in NDP) is important for positioning the nucleotide for nucleolytic attack in the nucleotidyl transfer reaction. Strikingly, a mutational substitution of the active-center βR1106 side chain involved in NTP positioning also strongly inhibited NDP-directed synthesis, even though this residue does not contact NDP. Substitutions in the structurally analogous side chain in RB69 DNA polymerase (Arg-482) and HIV reverse transcriptase (Lys-65) were previously observed to inhibit dNDP incorporation. The unexpected involvement of these residues suggests that they affect a step in catalysis common for nucleic acid polymerases. The substrate activity of NDPs with RNAP along with those reported for DNA polymerases reinforces the hypothesis that NDPs may have been used for nucleic acid biosynthesis by primordial enzymes, whose evolution then led to the use of the more complex triphosphate derivatives.

Characterization of DNA ADP-ribosyltransferase activities of PARP2 and PARP3: new insights into DNA ADP-ribosylation.

Poly(ADP-ribose) polymerases (PARPs) act as DNA break sensors and catalyze the synthesis of polymers of ADP-ribose (PAR) covalently attached to acceptor proteins at DNA damage sites. It has been demonstrated that both mammalian PARP1 and PARP2 PARylate double-strand break termini in DNA oligonucleotide duplexes in vitro. Here, we show that mammalian PARP2 and PARP3 can PARylate and mono(ADP-ribosyl)ate (MARylate), respectively, 5′- and 3′-terminal phosphate residues at double- and single-strand break termini of a DNA molecule containing multiple strand breaks. PARP3-catalyzed DNA MARylation can be considered a new type of reversible post-replicative DNA modification. According to DNA substrate specificity of PARP3 and PARP2, we propose a putative mechanistic model of PARP-catalyzed strand break–oriented ADP-ribosylation of DNA termini. Notably, PARP-mediated DNA ADP-ribosylation can be more effective than PARPs’ auto-ADP-ribosylation depending on the DNA substrates and reaction conditions used. Finally, we show an effective PARP3- or PARP2-catalyzed ADP-ribosylation of high-molecular-weight (∼3-kb) DNA molecules, PARP-mediated DNA PARylation in cell-free extracts and a persisting signal of anti-PAR antibodies in a serially purified genomic DNA from bleomycin-treated poly(ADP-ribose) glycohydrolase-depleted HeLa cells. These results suggest that certain types of complex DNA breaks can be effectively ADP-ribosylated by PARPs in cellular response to DNA damage.

Unique Structural Modifications Are Present in the Lipopolysaccharide from Colistin-Resistant Strains of Acinetobacter baumannii

Acinetobacter baumannii is a nosocomial opportunistic pathogen that can cause severe infections, including hospital-acquired pneumonia, wound infections, and sepsis. Multidrug-resistant (MDR) strains are prevalent, further complicating patient treatment. Due to the increase in MDR strains, the cationic antimicrobial peptide colistin has been used to treat A. baumannii infections. Colistin-resistant strains of A. baumannii with alterations to the lipid A component of lipopolysaccharide (LPS) have been reported; specifically, the lipid A structure was shown to be hepta-acylated with a phosphoethanolamine (pEtN) modification present on one of the terminal phosphate residues. Using a tandem mass spectrometry platform, we provide definitive evidence that the lipid A isolated from colistin-resistant A. baumannii MAC204 LPS contains a novel structure corresponding to a diphosphoryl hepta-acylated lipid A structure with both pEtN and galactosamine (GalN) modifications. To correlate our structural studies with clinically relevant samples, we characterized colistin-susceptible and -resistant isolates obtained from patients. These results demonstrated that the clinical colistin-resistant isolate had the same pEtN and GalN modifications as those seen in the laboratory-adapted A. baumannii strain MAC204. In summary, this work has shown complete structure characterization including the accurate assignment of acylation, phosphorylation, and glycosylation of lipid A from A. baumannii, which are important for resistance to colistin.

Microwave-assisted sample preparation for rapid and sensitive analysis of H. pylori lipid A applicable to a single colony

The lipid A of Gram-negative bacteria plays a major role in the pathogenesis of bacterial infections. Lipid A diversity is observed both in the number and length of fatty-acid side chains and in the presence of terminal phosphate residues and associated modifications. In this report, we describe a new sample preparation method based on microwave-assisted enzymatic digestion and detergent-free mild hydrolysis, in conjunction with a MALDI-time-of-flight (TOF)/TOF analysis, to determine the structures of lipid A from Helicobacter pylori. The total time for sample preparation and mass spectrometric analysis is within 2 h and applicable to profiling the lipid A structures from dried bacterial cells on as little as 1 microg. The reliability of the technique was further demonstrated through the analysis of the lipid A from bacterial cells of different H. pylori strains. The phosphorylation and acylation patterns of lipid A could be elucidated using material from a single colony. Furthermore, we found unusual heptaacyl lipid A species present in H. pylori mutant that have not been previously reported, although the abundance was relatively low. The present study provides the first characterization of the lipid A component from a single bacterial colony sample by mass spectrometry.

The Wall Teichoic Acid Polymerase TagF Is Non-processive in Vitro and Amenable to Study Using Steady State Kinetic Analysis

Wall teichoic acids are a chemically diverse group of anionic polymers that constitute up to 50% of the Gram-positive cell wall. These polymers play a pivotal role in virulence and have been implicated in a diverse range of physiological functions. The TagF-like family of enzymes has been shown to be responsible for wall teichoic acid priming and polymerization events. Although many such enzymes are well validated therapeutic targets, a mechanistic understanding of this enzyme family has remained elusive. TagF is the prototypical teichoic acid polymerase and uses CDP-glycerol to catalyze synthesis of the linear (1,3)-linked poly(glycerol phosphate) teichoic acid in Bacillus subtilis 168. Here we used a synthetic soluble analog of the natural substrate of the enzyme, Lipid , to conduct the first detailed mechanistic investigation of teichoic acid polymerization. Through the use of a new high pressure liquid chromatography-based assay to monitor single glycerol phosphate incorporations into the Lipid analog, we conducted a detailed analysis of reaction product formation patterns and unequivocally showed TagF to be non-processive in vitro. Furthermore by monitoring the kinetics of polymerization, we showed that Lipid analog species varying in size have the same K(m) value of 2.6 microm and validated use of Bi Bi velocity expressions to model the TagF enzyme system. Initial rate analysis showed that TagF catalyzes a sequential Bi Bi mechanism where both substrates are added to the enzyme prior to product release consistent with a single displacement chemical mechanism.

Determination of the Intrinsic Affinities of Multiple Site-Specific Mg2+Ions Coordinated to Domain 6 of a Group II Intron Ribozyme

Group II introns are large metallo-ribozymes that use divalent metal ions in folding and catalysis. The 3'-terminal domain 6 (D6) contains a conserved adenosine whose 2'-OH group acts as the nucleophile in the first splicing step. In the hierarchy of folding, D6 binds last into the active site. In order to investigate and understand the folding process to the catalytically active intron structure, it is important to know the individual binding affinities of Mg2+ ions to D6. We recently studied the solution structure of a 27 nucleotide long D6 (D6-27) from the mitochondrial yeast group II intron Sc.ai5gamma, also identifying five Mg2+ binding sites including the one at the 5'-terminal phosphate residues. Mg2+ coordination to the 5'-terminal di- and triphosphate groups is strongest (e.g., log KA,TP = 4.55 +/- 0.10) and is evaluated here in detail for the first time. The other four binding sites within D6-27 are filled simultaneously (e.g., log KA,BR = 2.38 +/- 0.06) and thus compete for the free Mg2+ ions in solution, having a distinct influence on the individual affinities of the various sites. For the first time, we take this competition into account to obtain the intrinsic binding constants, describing a method that is generally applicable. Our data illustrates that any RNA molecule undergoing tertiary contacts to a second RNA molecule first needs to be loaded evenly and specifically with metal ions to compensate for the repulsion between the negatively charged RNA molecules.

Synthetic monoacylphospholipids as reactivators of the calcium-dependent ATPase of enzymatically delipidated sarcoplasmic membranes.

1. The reactivating effect of synthetic analogues of natural lysophosphatidylcholines, acyldeoxyglycerophosphocholines, with acyl chain lengths between C10-C18 on enzymatically delipidated sarcoplasmic membranes has been analyzed. 2. The calcium-dependent ATPase is fully restored by myristoyldeoxyglycerophosphocholine. The restoring effect of deoxyglycerophosphocholines declines when the length of the saturated acyl chain becomes shorter or longer. 3. In contrast to the weakly effective palmitoyldeoxyglycerphosphocholine, its cis-9-mono unsaturated analogue oleyldeoxyglycerophosphocholine proved to be a highly effective reactivating compound. 4. The transfer of the terminal phosphate residue of ATP to the transport protein and the phosphate exchange between ADP and ATP displays the same dependence on the acyl chain length of the deoxyglycerophos-phocholines. In contrast to the ATPase activity the ATP-supported phosphoryltransfer reactions can only partially be restored. 5. A significant restoration of the phosphorylation of the protein by inorganic phosphate could be achieved with none of the deoxyglycerophosphocholines. 6. Below 23 degrees C the apparent activation energy of the calcium-dependent ATPase increases with increasing chain length of the deoxyglycerophosphoclines while above 23 degrees C the activation energies were identical for all restituted preparations.

A comparison of enzymatic digestion for the quantitation of an oligonucleotide by liquid chromatography–isotope dilution mass spectrometry

DNA is a universal analyte found in almost every organism. It is the code that dictates our genetic make-up and it provides a vast library of information. DNA sequences can indicate genetic modification of foodstuffs, how we may metabolise pharmaceuticals and the likelihood of suffering particular diseases. The basis for many of these genetic tests would benefit greatly from procedures that can accurately quantitate DNA in an absolute manner. This would then provide a sound and universally consistent foundation for regulatory and diagnostic decision making. This work compares two different enzymatic digestion systems as precursor steps to high accuracy isotope dilution mass spectrometry (IDMS) quantitation of a 20mer oligonucleotide. In the first approach, snake venom phosphodiesterase (SVP) digests the oligonucleotide to its constituent deoxynucleotides (dNMPs), followed by liquid chromatography–IDMS (LC–IDMS) quantitation. The second enzyme digestion approach used a combination of snake venom phosphodiesterase and shrimp alkaline phosphatase (SAP) which reduces the oligonucleotide to its constituent deoxynucleosides (dNs). This was then followed by an alternative LC separation and equivalent IDMS measurements. Total phosphorous content of the 20mer oligonucleotide was measured by inductively coupled plasma optical emission spectroscopy (ICP-OES). This provided independent data for comparison with the two enzyme digestion–IDMS based procedures. The most appropriate method of quantitation was found to be the combined SVP and SAP digestion. This approach negates the need to consider and/or account for the lack of a 5′ terminal phosphate residue. It also enables the use of positive ion mass spectrometry which simplifies the chromatographic requirements. Based on the exact matched IDMS of the adenine deoxynucleoside, the concentration of the original 20mer oligonucleotide was found to be 110 ± 9 μg g −1. This showed good agreement with the ICP-OES data based on the measurement of phosphorus which gave an equivalent value for the original 20mer oligonucleotide of 108 ± 5 μg g −1 (uncertainties at the 95% confidence interval). It is intended that this high accuracy methodology should be used to produce high calibre reference standards. These, in turn, could then be used to underpin the quality and consistency of routine measurements involving a variety of more commonly encountered methodologies. It should be noted that the IDMS procedures are equally applicable to both sequenced and non-sequenced oligonucleotide materials.

Partial characterization of a new nucleotide binding glycoprotein of hepatocyte plasma membrane

Hepatocyte plasma membranes contain a glycosylated 230-kDa Ca 2+-dependent, Mg 2+-stimulated ATPase (pgp230), which consists of two subunits, one of 120 kDa and the other of 110 kDa. pgp230 can be enriched by the use of affinity chromatography on Concanavalin A-Sepharose, wheat germ lectin-Sepharose, and 5′-AMP-Sepharose. It has a high-affinity Ca 2+ binding site. In the presence of Ca 2+, it forms a phosphorylated intermediate by autocatalytic transfer of the terminal phosphate residue from ATP. Maximal Ca 2+-dependent autophosphorylation is observed at pH 5–6. Photoaffinity labeling using 8-azido-[α- 32P]ATP or [y- 32P]ATP confirms the presence of ATP binding sites. Incubation with [α- 32P]ATP leads to a rapid but transient labeling of pgp230. Various nucleotides, nucleotide receptor agonists, or antagonists inhibit Ca 2+-dependent phosphorylation by [y- 32P]ATP. The concentrations of half-maximal inhibition range from 10 −7 M to 10 −3 M. The rank order of inhibitory potency is: ATP > α,β-methylene-ATP > CTP = TTP > y-4-aminophenyl-ATP = 2-methyl-thio-ATP > UTP = GTP > GDP = ADP = β,y-methylene-ATP = β,y-methylene-TTP = β,y-methylene-GTP = adenosine-5′-O-2-thiodiphosphate = CMP = AMP > adenosine > cytidine > guanosine = suramin > Reactive blue 2 > iso-butyl-methyl-xanthine > thymidine > uridine. These data suggest a nucleotide binding capacity of this new hepatocyte membrane glycoprotein. Further investigations should be carried out to reveal its biological function.

Oxygen radical-induced single-strand DNA breaks and repair of the damage in a cell-free system.

Ferric nitrilotriacetate (Fe(3+)-NTA) catalyzes hydrogen peroxide-derived production of hydroxyl radicals, which are known to cause DNA damage. In the present work, Fe(3+)-NTA plus hydrogen peroxide-induced single-strand DNA breaks and repair of the DNA damage were studied in vitro by monitoring DNA damage- and DNA repair-dependent conformational changes of pUC18 plasmid DNA. Single-strand DNA breaks were induced in the pUC18 DNA by Fe(3+)-NTA plus hydrogen peroxide in a dose-dependent fashion. Induction of the DNA damage was inhibited by deferoxamine mesylate (an iron chelator) and by hydroxyl radical scavengers such as dimethyl sulfoxide (DMSO), D-mannitol and ethanol indicating that the DNA damage was caused by hydroxyl radicals which were generated by reaction of Fe(3+)-NTA with hydrogen peroxide. The oxygen radical-induced single-strand DNA breaks were repaired partly (more than 50%) by incubating the damaged DNA at 37 degrees C for 3 h with a partially purified preparation of APEX nuclease (a multifunctional DNA repair enzyme), DNA polymerase beta, four deoxyribonucleoside triphosphates, T4 DNA ligase and ATP. Analyses of the partially purified preparation of APEX nuclease revealed that a 45-kDa protein as well as APEX nuclease in the preparation were involved in the repair of the single-strand DNA breaks. APEX nuclease was suggested to initiate the repair by removing 3' termini blocked by the nucleotide fragments and also by incising the 5' side of AP sites. The 45-kDa protein was suggested to be required for removal of the 5' tags such as 5'-terminal deoxyribose phosphate residues produced by the action of APEX nuclease on AP sites.

Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair.

Eukaryotic DNA polymerase beta (pol beta) can catalyze DNA synthesis during base excision DNA repair. It is shown here that pol beta also catalyzes release of 5'-terminal deoxyribose phosphate (dRP) residues from incised apurinic-apyrimidinic sites, which are common intermediate products in base excision repair. The catalytic domain for this activity resides within an amino-terminal 8-kilodalton fragment of pol beta, which comprises a distinct structural domain of the enzyme. Magnesium is required for the release of dRP from double-stranded DNA but not from a single-stranded oligonucleotide. Analysis of the released products indicates that the excision reaction occurs by beta-elimination rather than hydrolysis.

Determination of Endopolyphosphatase Using Polyphosphate Glucokinase

A method has been developed for determining endopolyphosphatase (polyphosphate depolymerase, EC 3.6.1.10) activity. The enzyme catalyzes the hydrolysis of inorganic polyphosphates [poly(Ps)] by cleaving internal phosphoanhydride bonds without removal of terminal phosphate residues. During the reaction, shorter poly(P) chains are formed and the molar concentration of poly(P) increases. This enzymatic activity is difficult to quantitate, because the substrates and products of the reaction are chemically identical. The commonly used viscometric method lacks sensitivity and cannot be used with shorter poly(P) substrates. The method described here overcomes these problems, and in addition is rapid, simple, and can be used for distinguishing between the endopolyphosphatase and exopolyphosphatase (EC 3.6.1.11) activities. It is based on monitoring the increase in the number of poly(P) chains generated by endopolyphosphatase. For this purpose, the method takes advantage of the specific property of poly(P) glucokinase (EC 2.7.1.63) which utilizes poly(Ps) of different sizes present in the endopolyphosphatase reaction mixture and reduces them to fairly uniform very short-chain product, poly(P)m. The concentration of poly(P)m is expressed in terms of acid-labile phosphorus and is proportional to the duration of the endopolyphosphatase reaction (i.e., the number of original poly(P) chains) and to protein concentration. The increase in the poly(P)m concentration is a relative measure of the endopolyphosphatase activity. Under certain conditions, m equals 3.5 and the activity can be expressed in standard units, since the exact number of poly(P) chains formed by endopolyphosphatase can be calculated from the increase in molar concentration of poly(P)3.5. Accuracy and advantages of the assay are discussed.

Enzymic release of 5'-terminal deoxyribose phosphate residues from damaged DNA in human cells

Activities that catalyze or promote the release of 5'-terminal deoxyribose phosphate residues from DNA abasic sites previously incised by an AP endonuclease have been identified in soluble extracts of several human cell lines and calf thymus. Such excision of base-free sugar phosphate residues from apurinic/apyrimidinic sites is expected to be obligatory prior to repair by gap filling and ligation. The most efficient excision function is due to a DNA deoxyribophosphodiesterase similar to the protein found in Escherichia coli. The human enzyme has been partially purified and freed from detectable exonuclease activity. This DNA deoxyribophosphodiesterase is a Mg(2+)-requiring hydrolytic enzyme with an apparent molecular mass of approximately 47 kDa and is located in the cell nucleus. By comparison, the major nuclear 5'----3' exonuclease, DNase IV, is unable to catalyze the release of 5'-terminal deoxyribose phosphate residues as free sugar phosphates but can liberate them at a slow rate as part of small oligonucleotides. Nonenzymatic removal of 5'-terminal deoxyribose phosphate from DNA by beta-elimination promoted by polyamines and basic proteins is a very slow mechanism of release compared to enzymatic hydrolysis. We conclude that a DNA deoxyribophosphodiesterase acts at an intermediate stage between an AP endonuclease and a DNA polymerase during DNA repair at apurinic/apyrimidinc sites in mammalian cells, but several alternative routes also exist for the excision of deoxyribose phosphate residues.

Reaction mechanism of the calcium-transport ATPase in endoplasmic reticulum of rat liver. Demonstration of different reactive forms of the phosphorylated intermediate.

A calcium-transport ATPase is inserted into the endoplasmic reticulum of rat liver. Catalysis of calcium translocation involves transient covalent binding of the terminal phosphate residue of ATP by the enzyme, resulting in the formation of an alkali- and hydroxylamine-labile phosphorylprotein intermediate. Both MgATP as well as CaATP can be utilized in the phosphorylation reaction which requires calcium as a cofactor. Magnesium accelerates the turnover of the phosphorylprotein intermediate. An ADP-reactive and ADP-unreactive state of the phosphoenzyme could be distinguished. In the ADP-reactive state with tightly bound calcium, the phosphoenzyme can transphosphorylate its phosphate residue to ADP, giving rise to synthesis of ATP. The ADP-reactive phosphoenzyme can be converted into an ADP-unreactive state by prolonged incubation with excess EGTA (ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid). It is suggested that this conversion is brought about by the removal of tightly bound calcium from the phosphoenzyme. A strong homology of the sequential reaction steps during calcium translocation by the calcium-transport ATPases in endoplasmic reticulum from rat liver and sarcoplasmic reticulum from skeletal muscle is suggested.

Substrate specificity and adenosine triphosphatase activity of the ATP-dependent deoxyribonuclease of Bacillus subtilis.

Studies on the specificity of the ATP-dependent DNase of Bacillus subtilis 168, carried out with pure enzyme at the optimal conditions for its action, have shown that the substrate is double-stranded linear DNA. Linear single-stranded DNA (separated strands of B. subtilis DNA and linear phage fd DNA) is not attacked, neither are there any circular forms (supercoiled or nicked simian virus 40 and circular single-stranded fd DNAs). The double-stranded DNA can be completely hydrolysed, the limit products being, almost exclusively, mononucleotides. The presence of terminal phosphate residues in the substrate (either at the 3' or the 5' end) is not necessary for enzyme action. This DNase appears therefore to be an exonuclease processively liberating mononucleotides from both strands of the native linear DNA. ATP (indispensable for the DNase reaction) is also hydrolysed by the enzyme, to ADP and inorganic orthophosphate (Pi) in the presence of DNA. The apparent Km for ATP, in the ATPase reaction, is 0.15 mM. At high ATP concentrations, which inhibit the DNase activity, there is activation of the ATPase reaction. Three molecules of ATP are consumed for each DNA phosphodiester bond split, at optimal conditions for DNase activity.

Mechanism of interferon action: Synthesis and activity of the interferon-mediated low-molecular-weight oligonucleotide from murine and human cells

The interferon-mediated synthesis of the low-molecular-weight 2′,5′-oligoadenylate effectors (LMWE) of endoribonuclease activity and the interaction of the LMWE with components present in extracts prepared from mouse fibroblast and human amnion cells was investigated. The following results were obtained: (1) The LMWE was synthesized by cell-sap fractions prepared from mouse and human cells treated with their homologous interferons. Preincubation of interferon-treated cell-free S-10 extracts increased by about 50-fold the apparent concentration of the LMWE oligonucleotide synthetase observed in the S-100 cell-sap fractions. Mouse and human LMWEs enhanced ribonuclease activity in their heterologous human and mouse cell-free extracts prepared from untreated cells. (2) Degredation of the reovirus [ 3H]mRNA by the LMWE-activated endonuclease was quantitated both by sucrose density gradient centrifugation and by formation of acid-soluble oligonucleotides. (3) Free LMWE was rapidly inactivated ( t 1 2 < 10 min ) by cell-free extracts prepared from untreated L 929 cells. The inactivation of LMWE appeared to involve the cleavage of a 2′,5′-phosphodiester bond of the oligonucleotide rather than removal of the 5′-terminal phosphate residue. (4) In addition to the effect of LMWE on ribonuclease activity, the phosphorylation of a 110,000-dalton protein present in S-10 extracts prepared both from untreated and interferon-treated cells was observed in the presence of [γ- 32P]-LMWE. Increased phosphorylation of a protein of comparable molecular weight was also observed in ribosomal salt-wash fractions that contained an interferon-activated nuclease. The LMWE did not, however, substitute for RNA with double-stranded character in the phosphorylation of either the 38,000-dalton subunit of eIF-2 or the 67,000-dalton ribosome-associated protein P 1.

Polynucleotides. XIX. Synthesis of oligonucleotides by the use of the N-trityl-p-aminophenyl group, a new protecting group for the terminal phosphate residues.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolynucleotides. XIX. Synthesis of oligonucleotides by the use of the N-trityl-p-aminophenyl group, a new protecting group for the terminal phosphate residuesEiko. Ohtsuka, Shigeo. Morioka, and Morio. IkeharaCite this: J. Am. Chem. Soc. 1973, 95, 25, 8437–8440Publication Date (Print):December 1, 1973Publication History Published online1 May 2002Published inissue 1 December 1973https://doi.org/10.1021/ja00806a039RIGHTS & PERMISSIONSArticle Views119Altmetric-Citations8LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (504 KB) Get e-Alerts Get e-Alerts

The occurrence of lipoteichoic acids in the membranes of gram-positive bacteria.

Glycerol teichoic acids have been found associated with the cytoplasmic membrane of all of the Gram-positive bacteria examined and it is believed that, unlike wall teichoic acids which are absent from some organisms, these membrane teichoic acids are characteristically present in all species (for reviews see Archibald, Baddiley &amp; Blumsom, 1968; Baddiley, 1970, 1972). Wall teichoic acid is attached to the peptidoglycan of the wall through its terminal phosphate residue, but although it has been known for some time that membrane teichoic acid is associated with the outer surface of the membrane (Hay, Wicken &amp; Baddiley, 1963; Shockman &amp; Slade, 1964) the nature of this association has only recently been examined.