Synthesis of Simple Adenosine Diphosphate Ribose Analogues

The synthesis of analogues of adenosine diphosphate ribose and acetylated adenosine diphosphate ribose, modified at the northern pentose, is reported. The stereochemistry at the acetylated centers was chosen to minimize acetyl migration and dictated the overall synthetic strategy.     

Natural occurence of a biopolymer, poly (adenosine diphosphate ribose).

Evidence for the natural occurrence of poly(adenosine diphosphate ribose) in vivo was obtained using a sensitive radioimmunoassay and poly(adenosine diphosphate ribose) glycohydrolase, which specifically hydrolyzes poly(adenosine diphosphate ribose). Calf thymus, liver, kidney, brain, pancreas and spleen contained poly(adenosine diphosphate ribose). Naturally occurring poly(adenosine diphosphate ribose) in calf thymus is composed of molecules of various chain lengths, like that synthesized by an in vitro system. Calf thymus was estimated to contain about 0.02 microgram/mg DNA of poly(adenosine diphosphate ribose).     

Poly(adenosine diphosphate ribose) glycohydrolase in Physarum polycephalum.

Poly(adenosine diphosphate ribose) glycohydrolase, which has thus far only been found in mammalian tissues, was found for the first time in the primitive eukaryotic slime mold Physarum polycephalum. The hydrolytic product of poly(adenosine diphosphate ribose) with this enzyme was identified as adenosine diphosphate ribose by paper and thin-layer chromatography. It is likely that the enzyme caused exoglycosidic hydrolysis. The optimal pH of this enzyme was 6.0, and the K_m value was 4.3 μm, as adenosine diphosphate ribose residues of polymer. Adenosine diphosphate ribose, ADP and ATP at a concentration of 0.1mm strongly inhibited the enzyme activity. 3′,5′-Cyclic AMP was inhibitory at a concentration of 1mm. The molecular weight of this enzyme was estimated to be 57,000.     

Evidence for two variants of poly(adenosine diphosphate ribose) glycohydrolase in rat testis.

The specific activity of rat poly(adenosine diphosphate ribose) glycohydrolase was higher in the testis than in the liver, brain, spleen or kidney. The enzyme was found primarily in the soluble fraction of the testis. When the soluble enzyme was chromatographed on phosphocellulose, the activity eluted in two peaks, at 0.22 and 0.34 m KCl, respectively, referred to in the present study as enzyme A and B. Enzyme A has an optimal pH of 7.25 and was stimulated by 150 mm KCl. The optimal pH of enyzme B was 6.5, but it was not stimulated by KCl. For maximal activity both enzymes required 10 mm 2-mercaptoethanol, and they were strongly inhibited by 100 μmp-chloromercuribenzoate. The K_m values of enzyme A and B for poly(adenosine diphosphate ribose) were 1.52 and 0.70 μm, respectively. Ribose 5′-phosphate, guanosine 3′,5′-monophosphate, adenosine 3′,5′-monophosphate and adenosine diphosphate ribose inhibited both enzymes. The two latter nucleotides behave as noncompetitive inhibitors. Denatured DNA and the homopolypurines poly(G), poly(I) and poly(A) were very potent inhibitors of both glycohydrolases. The mode of hydrolysis of poly(adenosine diphosphate ribose) by glycohydrolases A and B was exoglycosidic, yielding adenosine diphosphate ribose as the final product.     

Separation of oligo(adenosine diphosphate ribose) fractions with various chain lengths and terminal structures.

Oligo(adenosine diphosphate ribose) preparations with chain lengths of 3 to 10 adenosine diphosphate ribose units were fractionated according to their chain lengths and their terminal structures by hydroxyapatite column chromatography and then polyacrylamide gel electrophoresis. The peak fractions from the hydroxyapatite column were each separated into two distinct subfractions by gel electrophoresis. The two subfractions were found to differ in chain length and terminal structure. A linear correlation was observed between the mobility and the logarithm of the chain length of oligo(adenosine diphosphate ribose) on gel electrophoresis, irrespective of the terminal structure.     

Poly(ADP-ribose) glycohydrolase is present in metaphase chromosomes of HeLa S3 cells

Poly(ADP-ribose) glycohydrolase was found in metaphase chromosomes of HeLa S3 cells. Adenosine diphosphate ribose and 3′, 5′-cyclic AMP inhibited the glycohydrolase activity, whereas ADP, ATP, NAD and 3′,5′-cyclic GMP did not. The hydrolytic product of poly(ADP-ribose) bound to metaphase chromosomes with this enzyme was identified as adenosine diphosphate ribose.     

Poly(adp-ribosylation) in N,N-diethylnitrosamine-treated mice

• 1.1. Liver nuclei isolated from male mice treated with the carcinogen N,N-diethylnitrosamine were examined for the homopolymer poly(adenosine diphosphate ribose) and for the activity of the conjugate polymerase.
• 2.2. At all levels of the carcinogen tested, a concomitant increase in both poly(adenosine diphosphate ribose) content and activity of the enzyme were found.
• 3.3. Both responses were transitory and dose dependent.

     

Characterization of the role of lysine 110 of NADH-cytochrome b5 reductase in the binding and oxidation of NADH by site-directed mutagenesis.

An expression vector for bovine NADH-cytochrome b5 reductase was used for site-directed mutagenesis of lysine 110, the residue previously implicated in NADH interactions with this flavoprotein. Replacement of this basic residue with an uncharged glutamine resulted in an increase of 3 orders of magnitude in the Km for NADH and a decrease in kcat of an order of magnitude, strongly implicating lysine 110 in both binding of NADH to the reductase and the orientation of the reduced nicotinamide group for rapid hydride ion transfer to the flavin. Substitution of lysine 110 by histidine, to provide a pH-sensitive positive charge at this position in the neutral pH range, exhibited only a moderate 25-fold increase in Km and a normal kcat at pH 6.0, whereas at pH 8.5 the Km for NADH rose to 238 microM with a decrease of 45% over unmodified enzyme in the kcat. A similar pH sensitivity in the inhibition constant for adenosine diphosphate ribose, lacking only the nicotinamide moiety of NADH, emphasizes the crucial role of the positive charge at this locus and is consistent with charge-pairing of lysine 110 with the pyrophosphate group of NADH or adenosine diphosphate ribose.     

A 13C NMR study of poly(adenosine diphosphate ribose) and its monomers: evidence of alpha-(1'''' leads to 2'') ribofuranosy1 ribofuranoside risidue.

The 13C NMR spectra of poly(adenosine diphosphate ribose), ribosyl adenosine 5', 5'-bis(phosphate) and related compounds were analyzed. The structure of the ribose-ribose linkage was determined as alpha-(1' leads to 2')ribofuranosyl ribofuranoside, from the 13C chemical shifts of methyl-alpha- and methyl-beta-D-ribofuranosides, and from the downfield displacements of 13C NMR signals by glycosidic bond formation.     

Innate immunity is regulated by CD38, an ecto-enzyme with ADP-ribosyl cyclase activity

Through its production of cyclic adenosine diphosphate ribose, the ecto-enzyme CD38 regulates calcium mobilization in neutrophils responding to some, but not all, chemoattractants. This signaling defect results in reduced chemotaxis of CD38-deficient neutrophils to bacterial peptides and increased susceptibility of CD38-deficient mice to bacterial infections.     

Adenosine diphosphate-ribosyltransferase activity in permeabilized mouse testicular cells

Permeabilized mouse testicular cells and Sertoli cells were incubated with [³H]NAD. The radioactive derivative in the acid-precipitable material extracted by washing the cells was determined to be a composite of monomers of adenosine diphosphate ribose (ADP-ribose). The present results suggest that mammalian cells possess an enzyme system which mediates mono-ADP-ribosylation of proteins.     

Partial purification and characterization of S-adenosylhomocysteine hydrolase isolated from Saccharomyces cerevisiae

S-Adenosylhomocysteine (SAH) hydrolase was purified 25-fold from bakers' yeast by chemical methods and column chromatography. The purified enzyme could readily synthesize SAH from adenosine and homocysteine, but could hydrolyze only negligible amounts of SAH. The purified enzyme showed no activity towards S-adenosylmethionine, methylthioadenosine, or adenosine. Several nucleotides, sulfhydryl compounds, and ribose could not replace adenosine or homocysteine in the reaction mixture. SAH could be hydrolyzed by SAH hydrolase if commercial adenosine deaminase was included in the reaction mixture. Under these conditions l-homocysteine could act as a product inhibitor. A number of compounds structurally similar to adenosine and homocysteine were found to inhibit synthesis of SAH from adenosine and homocysteine. The strongest inhibitors were adenine, adenosine-3'-monophosphate, adenosine-2'-monophosphate, adenosine diphosphate, adenosine triphosphate, and adenosine-5'-monophosphate. The biosynthetic and hydrolytic activity of SAH hydrolase in yeast cell ghosts was similar to the activity of the enzyme in vitro.     

A novel fluorescent cell membrane-permeable caged cyclic ADP-ribose analogue

Cyclic adenosine diphosphate ribose is an endogenous Ca(2+) mobilizer involved in diverse cellular processes. A cell membrane-permeable cyclic adenosine diphosphate ribose analogue, cyclic inosine diphosphoribose ether (cIDPRE), can induce Ca(2+) increase in intact human Jurkat T-lymphocytes. Here we synthesized a coumarin-caged analogue of cIDPRE (Co-i-cIDPRE), aiming to have a precisely temporal and spatial control of bioactive cIDPRE release inside the cell using UV uncaging. We showed that Co-i-cIDPRE accumulated inside Jurkat cells quickly and efficiently. Uncaging of Co-i-cIDPRE evoked Ca(2+) release from endoplasmic reticulum, with concomitant Ca(2+) influx in Jurkat cells. Ca(2+) release evoked by uncaged Co-i-cIDPRE was blocked by knockdown of ryanodine receptors (RyRs) 2 and 3 in Jurkat cells. The associated Ca(2+) influx, on the other hand, was abolished by double knockdown of Stim1 and TRPM2 in Jurkat cells. Furthermore, Ca(2+) release or influx evoked by uncaged Co-i-cIDPRE was recapitulated in HEK293 cells that overexpress RyRs or TRPM2, respectively, but not in wild-type cells lacking these channels. In summary, our results indicate that uncaging of Co-i-cIDPRE incites Ca(2+) release from endoplasmic reticulum via RyRs and triggers Ca(2+) influx via TRPM2.     

A coupled optical enzyme assay for phosphopentomutase

Published assays for phosphopentomutase activity are based on acid lability differences between ribose 1-phosphate and ribose 5-phosphate. The present work describes a new method in which the isomerization of ribose 5-phosphate to ribose 1-phosphate is followed spectrophotometrically at 265 nm by coupling it with the following two-stage enzymatic conversion: ribose 1-phosphate + adenine ? phosphate + adenosine (adenosine phosphorylase); adenosine + H₂O → inosine + NH₃ (adenosine deaminase). The method has been used to show some properties of Escherichia coli phosphopentomutase.     

Release of template restriction for DNA synthesis by poly ADP(ribose) polymerase during the HeLa cell cycle.

The degree of complexing between DNA and chromosomal proteins and the ability of poly adenosine diphosphate ribosylation (ADP-ribosylation) of nuclear proteins to release this template restriction and expose DNA primer site changes during the HeLa cell cycle. Primer site exposure by NAD and poly ADP(ribose) polymerase was assessed with intact nuclei by single deoxynucleotide incorporation into DNA in the presence of saturating bacterial DNA polymerase. The most marked in vitro enhancement of primer site exposure by ADP-ribosylation occurred in early G1 phase, where cellular template restriction was the greatest. Cytoplasmic DNA polymerase also had high activity in early G1 phase of the cell cycle. Streptozotocin reduces NAD pools in HeLa cells; a concomitant stimulation of nuclear poly ADP(ribose) polymerase activity is noted.     

The conformation of acetylated virginiamycin M1 and virginiamycin M1 in explicit solvents

The three-dimensional structure of acetylated virginiamycin M(1) (acetylated VM1) in chloroform and in a water/acetonitrile mixture (83:17 v/v) have been established through 2D high resolution NMR experiments and molecular dynamics modeling and the results compared with the conformation of the antibiotic VM1 in the same and other solvents. The results indicated that acetylation of the C-14 OH group of VM1 caused it to rotate about 90 degrees from the position it assumed in non-acetylated VM1. The conformation of both VM1 and acetylated VM1 appear to flatten in moving from a nonpolar to polar solvent. However, the acetylated form has a more hydrophobic nature. The acetylated VM1 in chloroform and in water/acetonitrile solution had a similar configuration to that of VM1 bound to 50S ribosomes and to the Vat(D) active sites as previously determined by X-ray crystallography. Docking studies of VM1 to the 50S ribosomal binding site and the Vat(D) gave conformations very similar to those derived from X-ray crystallographic studies. The docking studies with acetylated VM1 suggested the possibility of a hydrogen bond from the acetyl carbonyl group oxygen of acetylated VM1 to the 2' hydroxyl group of ribose of adenosine 2538 at the ribosomal VM1 binding site. No hydrogen bonds between acetylated VM1 and the Vat(D) active sites were found; the loss of this binding interaction partly accounts for the release of the product from the active site.     

Demonstration of high molecular weight poly (adenosine diphosphate ribose).

An electrophoretic system was established that resolves poly(adenosine diphosphate ribose), enzymatically synthesized polymer from NAD+, by size difference of one residue on polyacrylamide gel. The existence of a polymer of at least 65 residues was demonstrated by band counting in this system. The polymer showed a heterogeneous size distribution on the electrophoregram, and the molecular weight of the largest polymer was deduced to be more than 4.5 X 10(5) daltons. The discrepancy between the size, estimated by electrophoresis, and the chain length, determined by the ratio of total radioactivity to that derived from the terminus, suggests that the polymer has a branched structure.     

Ribose Utilization by Veillonella alcalescens

The utilization of ribose by Veillonella alcalescens has been further investigated. Nonfermentation of ribose is not a result of a phosphorylation lesion since ribose-phosphorylating activity was measured in cell extracts. Resting cells accumulated ribose-5-phosphate and nucleotides when ¹⁴C-ribose was provided; no other sugar phosphates were detectable. Resting cells that were shifted to growth conditions polymerized rather than degraded the accumulated ribose compounds. Cell extracts contained a fructose diphosphate phosphatase. Ribose-5-phosphate, glucose-6-phosphate, and fructose-6-phosphate were not hydrolyzed. It is postulated that the nonfermentation of ribose is not due to any metabolic lesions, but is a consequence of metabolic control at the fructose diphosphate level of glycolysis.     

Level of photosynthetic intermediates in isolated spinach chloroplasts

The level of intermediates of the photosynthetic carbon cycle was measured in intact spinach chloroplasts in an attempt to determine the cause of the induction lag in CO₂ assimilation. In addition, transient changes in the level of the intermediates were determined as affected by a light-dark period and by the addition of an excess amount of bicarbonate during a period of steady photosynthesis. Assayed enzymically were: ribulose 1,5-diphosphate, pentose monophosphates (mixture of ribose 5-phosphate, ribulose 5-phosphate and xylulose 5-phosphate, hexose monophosphates (mixture of glucose 6-phosphate, glucose 1-phosphate, and fructose 6-phosphate), glyceraldehyde 3-phosphate, dihydroxyacetone phosphate, glycerate acid 3-phosphate, a mixture of fructose 1,6-diphosphate and sedoheptulose 1,7-diphosphate, adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP).     

A relationship between nuclear poly(adenosine diphosphate ribosylation) and acetylation posttranslational modifications. 2. Histone studies

In the accompanying paper [Malik, N., & Smulson, M. (1984) Biochemistry (preceding paper in this issue)], we report that certain acetylated domains of chromatin were selectively retained by an anti-poly(ADP-Rib) antibody column. In this paper, we describe investigations of this phenomenon at the molecular level of protein interactions. We observed that the majority of endogenously hyperacetylated histones have a high affinity toward the polymer antibody column. It is speculated that these proteins were bound to the column via endogenous poly(adenosine diphosphate ribose) [poly(ADP-Rib)] since the binding was reversed upon treatment of the histones with alkali prior to immunofractionation. In order to analyze the distribution of acetate and poly(ADP-Rib) on histone proteins, [3H]acetylated nuclei were incubated in vitro with [32P]NAD. Acetate was incorporated mainly into H3 and H4 while H1 was the major acceptor protein for poly(ADP-Rib). These results suggest that a correlation may exist in vivo between the two posttranslational modification processes and that identical histone molecules may be accessible to both modifications.