Pyrophosphate Linkage Research Articles

Nucleosides and Nucleotides. 192. Toward the Total Synthesis of Cyclic ADP-Carbocyclic-Ribose. Formation of the Intramolecular Pyrophosphate Linkage by a Conformation-Restriction Strategy in a Syn-form Using a Halogen Substitution at the 8-Position of the Adenine Ring

The synthesis of cyclic ADP-carbocyclic-ribose (2), as a stable mimic for cyclic ADP-ribose, was investigated. Construction of the 18-membered backbone structure was successfully achieved by condensation of the two phosphate groups of 19, possibly due to restriction of the conformation of the substrate in a syn-form using an 8-chloro substituent at the adenine moiety. SN2 reactions between an optically active carbocyclic unit 8, which was constructed by a previously developed method, and 8-bromo-N 6-trichloroacetyl-2′,3′-O-isopropylideneadenosine 9c gave N-1-carbocyclic derivative, which was deprotected to give 5′,5′-diol derivatives 18. When 18 was treated with POCl3 in PO(OEt)3, the bromo group at the 8-position was replaced to give N-1-carbocyclic-8-chloroadenosine 5′,5′-diphosphate derivative 19 in 43% yield. Treatment of 19 with 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride gave the desired intramolecular condensation product 20 in 10% yield. This is the first chemical construction of the 18-membered backbone structure containing an intramolecular pyrophosphate linkage of a cADPR-related compound with an adenine base.

Conformational analysis of three pyrophosphate model species: Diphosphate, methyl diphosphate, and triphosphate

Whereas theoretical investigations of the energetic origin of hydrolyzing a pyrophosphate linkage abound, few studies have focused on the energetics of the rotation of this linkage. This less-studied property of the pyrophosphate linkage was investigated here by use of ab initio calculations to characterize the conformational space of three model species of pyrophosphate anions: diphosphate (P2O), methyl diphosphate (CH3P2O), and triphosphate (P3O). By carefully selecting conformationally distinct rotational isomers of the three model compounds, their potential surfaces were thoroughly explored. In addition to showing that a terminal phosphate group is indeed very flexible in accordance with the general perception of free rotation, a number of intriguing features of this linkage emerged from the ab initio calculations, which include an influential sp3-hybridized CHO intramolecular hydrogen bond in methyl diphosphate, and a highly restricted rotational space pertaining to the central pyrophosphate linkage of the triphosphate anion. These ab initio findings were then evaluated by, and proved insightful in, follow-up examinations of experimentally determined complex structures of proteins and their dinucleotide or adenine and guanine triphosphate ligands. © 1999 John Wiley & Sons, Inc. J Comput Chem 20: 1702–1715, 1999

Potent Inhibition of Mammalian Ribonucleases by 3′,5′-Pyrophosphate-linked Nucleotides

Molecular modeling based on the crystal structure of the complex of bovine pancreatic RNase A with the inhibitor 5'-diphosphoadenosine 3'-phosphate (ppAp) (Leonidas, D. D., Shapiro, R., Irons, L. I., Russo, N., and Acharya, K. R. (1997) Biochemistry 36, 5578-5588) was used to design new inhibitors that extend into unoccupied regions of the enzyme active site. These compounds are dinucleotides that contain an unusual 3',5'-pyrophosphate linkage and were synthesized in solution by a combined chemical and enzymatic procedure. The most potent of them, 5'-phospho-2'-deoxyuridine 3'-pyrophosphate, P' --> 5'-ester with adenosine 3'-phosphate (pdUppAp), binds to RNase A with Ki values of 27 and 220 nM at pH 5.9 and 7, respectively. These values are 6-9-fold lower than those for ppAp and 50-fold lower than that for the transition state analogue, uridine vanadate. pdUppAp has broad specificity; it is an effective inhibitor of at least two other members of the pancreatic RNase superfamily, human RNase-2 (eosinophil-derived neurotoxin) and RNase-4, which share only 36-44% sequence identity with the pancreatic enzyme. The potency of pdUppAp and the other inhibitors described here depends critically on the extended internucleotide linkage; the pyrophosphate group enhances dinucleotide binding to the three RNases by 2.1-2.9 orders of magnitude, as compared with a monophosphate. These data give further insight into the organization of the catalytic centers of the various RNases. Moreover, the new class of inhibitors provides a useful means by which to probe the biological actions of these and other related enzymes.

The Gene, ialA, Associated with the Invasion of Human Erythrocytes by Bartonella bacilliformis, Designates a Nudix Hydrolase Active on Dinucleoside 5′-Polyphosphates

ialA, one of two genes associated with the invasion of human red blood cells by Bartonella bacilliformis, the causative agent of several diseases, has been cloned and expressed in Escherichia coli. The protein, IalA, contains an amino acid array characteristic of a family of enzymes, the Nudix hydrolases, active on a variety of nucleoside diphosphate derivatives. IalA has been purified, identified, and characterized as an enzyme catalyzing the hydrolysis of members of a class of signaling nucleotides, the dinucleoside polyphosphates, with its highest activity on adenosine 5'-tetraphospho-5'-adenosine (Ap4A), but also hydrolyzing Ap5A, Ap6A, Gp4G, and Gp5G. In each case, a pyrophosphate linkage is cleaved yielding a nucleoside triphosphate and the remaining nucleotide moiety.

Chemical cross-linking of the human immunodeficiency virus type 1 Tat protein to synthetic models of the RNA recognition sequence TAR containing site-specific trisubstituted pyrophosphate analogues.

A chemical ligation procedure has been developed for the synthesis of oligoribonucleotides carrying a trisubstituted pyrophosphate (tsp) linkage in place of a single phosphodiester. Good yields of tsp were obtained when a single 2'-deoxynucleoside 5' to the tsp was used in the ligation reaction. A tsp linkage was found to be reasonably stable to hydrolysis but cleaved by treatment with ethylenediamine or lysine to give phosphoamidate adducts. A model human immunodeficiency virus type 1 (HIV-1) TAR RNA duplex containing an activated tsp was able to bind to HIV-1 Tat protein with only 3-fold reduced affinity and to a Tat peptide (residues 37-72) with identical affinity compared to that of an unmodified duplex. Tsps incorporated at sites previously identified as being in close proximity to Tat protein were able to cross-link to Tat peptide (37-72) to form a covalent phosphoamidate conjugate. Endopeptidase cleavage followed by MALDI-TOF (matrix-assisted laser desorption ionization time of flight) mass spectrometric analysis provided strong evidence that a TAR duplex containing a tsp replacing the phosphate at 38-39 had reacted specifically with Lys51 in the basic region of Tat peptide (37-72). The new chemical cross-linking method may be generally useful for identifying lysines in close proximity to phosphates in basic RNA-binding domains of proteins.

Isolation of a ribozyme with 5′-5′ ligase activity

Background: Many new ribozymes, including sequence-specific nucleases, ligases and kinases, have been isolated by in vitro selection from large pools of random-sequence RNAs. We are attempting to use in vitro selection to isolate new ribozymes that have, or can be evolved to have, RNA polymerase-like activities. As phosphorimidazolide-activated nucleosides are extensively used to study non-enzymatic RNA replication, we wished to select for a ribozyme that would accelerate the template-directed ligation of 5′-phosphorimidazolide-activated oligonucleotides. Results: Ribozymes selected to perform the desired template-directed ligation reaction instead ligated themselves to the activated substrate oligonucleotide via their 5′-triphosphate, generating a 5′-5′ P 1,P 4-tetraphosphate linkage. Deletion analysis of one of the selected sequences revealed that a 54-nucleotide RNA retained activity; this small ribozyme folds into a pseudoknot secondary structure with an internal binding site for the substrate oligonucleotide. The ribozyme can also synthesize 5′-5′ triphosphate and 5′-5′ pyrophosphate linkages. Conclusions: The emergence of ribozymes that accelerate an unexpected 5′-5′ ligation reaction from a selection designed to yield template-dependent 3′-5′ ligases suggests that it may be much easier for RNA to catalyze the synthesis of 5′-5′ linkages than 3′-5′ linkages. 5′-5′ linkages are found in a variety of contexts in present-day biology. The ribozyme-catalyzed synthesis of such linkages raises the possibility that these 5′-5′ linkages originated in the biochemistry of the RNA world.

Is ligation the only solution to the pyrophosphate problem?

Pyrophosphate linkages are easily formed during the nonenzymatic oligomerization of activated nucleotides. They often form ‘caps’ which terminate an oligonucleotide with a 5′-5′ pyrophosphate. Owing to their structural resemblance to the intermediates in enzymatic ligation reactions, it has been suggested that pyrophosphate caps might have been capable of acting as activating groups in chain elongation processes. We argue that an alternative possibility would have been the specific hydrolysis of pyrophosphates.

The structure of the 5' terminal cap of the respiratory syncytial virus mRNA

The 5' terminal cap structure of the mRNAs of human respiratory syncytial virus synthesized in vitro in the presence of S-adenosyl-L-methionine consists of a 7-methyl guanosine linked to an unmethylated guanosine through a 5'-5' pyrophosphate linkage formed by using the alpha and beta phosphates of GTP. The complete cap structure is m7G (5')ppp(5')Gp ... which is devoid of ribose 2'-O-methylation. Capping, including methylation, is coupled to transcription. These results constitute the first report of a pneumoviral mRNA cap structure.

A new affinity reagent for the site-specific, covalent attachment of DNA to active-site nucleophiles: application to the EcoRI and RsrI restriction and modification enzymes.

A modified oligodeoxyribonucleotide duplex containing an unnatural internucleotide trisubstituted 3' to 5' pyrophosphate bond in one strand [5'(oligo1)3'-P(OCH3)P-5'(oligo2) 3'] reacts with nucleophiles in aqueous media by acting as a phosphorylating affinity reagent. When interacted with a protein, a portion of the oligonucleotide [--P-5'(oligo2)3'] becomes attached to an amino acid nucleophilic group through a phosphate of the O-methyl-modified pyrophosphate linkage. We demonstrate the affinity labeling of nucleophilic groups at the active sites of the EcoRI and RsrI restriction and modification enzymes with an oligodeoxyribonucleotide duplex containing a modified scissile bond in the EcoRI recognition site. With the EcoRI and RsrI endonucleases in molar excess approximately 1% of the oligonucleotide becomes attached to the protein, and with the companion methyltransferases the yield approaches 40% for the EcoRI enzyme and 30% for the RsrI methyltransferase. Crosslinking proceeds only upon formation of a sequence-specific enzyme-DNA complex, and generates a covalent bond between the 3'-phosphate of the modified pyrophosphate in the substrate and a nucleophilic group at the active site of the enzyme. The reaction results in the elimination of an oligodeoxyribonucleotide remnant that contains the 3'-O-methylphosphate [5'(oligo1)3'-P(OCH3)] derived from the modified phosphate of the pyrophosphate linkage. Hydrolysis properties of the covalent protein-DNA adducts indicate that phosphoamide (P-N) bonds are formed with the EcoRI endonuclease and methyltransferase.

Selective cleavage of pyrophosphate linkages.

Pyrophosphate linkages have a number of important roles in biology and are also formed chemically with great ease. They often are unwanted products, such as in the nonenzymatic oligomerization of mononucleotides. We have found that Zr(4+)- and Th(4+)-ions catalyze the symmetrical hydrolysis of pyrophosphate linkages. Oligonucleotide analogs linked by pyrophosphate bonds are substantially degraded in the presence of these metals, even at 0 degrees C. Conditions are described which permit the decapping of a pyrophosphate capped oligonucleotide. Oligodeoxynucleotides can be decapped by this procedure without cleavage of phosphodiester linkages. Oligoribonucleotides are susceptible to partial hydrolysis and require purification by HPLC after decapping.

Structure of the sugar-phosphate moiety of lipid A from lipooligosaccharide of Neisseria meningitidis group B, strain BC5S No. 125. Hydrolytic stability of phosphate and pyrophosphate substituents.

On the basis of chemical and NMR data the partial structure of lipid A from lipooligosaccharide (LOS) of Neisseria meningitidis group B, strain BC5S No 125 was established. Lipid A consisted of disaccharide 2-deoxy-6-O-[2-deoxy-2-(3-hydroxytetradecanoylamino)- beta-gluco-pyranosyl]-2-(3-hydroxytetradecanoylamino)- alpha-glucopyranose carrying the beta-(2-aminoethyl)pyrophosphate residue at 0-4' and the pyrophosphate or phosphate residue at 0-1. On hydrolysis of the acidic form of LOS with 1% acetic acid the substituent at 0-1 was practically completely removed whereas that at 0-4' was stable. The analogous hydrolysis of the Mg-salt of LOS was accompanied by splitting off the pyrophosphate linkage in the substituent at 0-4'. Hydrolysis of LOS at pH 4.5 in the presence of SDS led mainly to a lipid A preparation retaining both pyrophosphate residues.

Comparative Affinity Labeling with Reactive UDP-Glucose Analogues: Possible Locations of Five Lysyl Residues around the Substrate Bound to Potato Tuber UDP-Glucose Pyrophosphorylase1

By using two reactive analogues of UDP-Glc, uridine di- and triphosphopyridoxals, we have recently probed the substrate-binding site in potato tuber UDP-Glc pyrophosphorylase [EC 2.7.7.9]. In this work, pyridoxal diphospho-alpha-D-glucose was used for the same purpose. This compound is also a reactive UDP-Glc analogue but having its reactive group on the opposite side of the pyrophosphate linkage to those of the above two compounds. The enzyme was rapidly inactivated when incubated with the compound at very low concentrations followed by reduction with sodium borohydride. The inactivation was almost completely prevented by UDP-Glc and UTP. Complete inactivation correspond to the incorporation of 1.0 mol of the reagent per mol of enzyme monomer. The label was found to be distributed in five lysyl residues (Lys-263, Lys-329, Lys-367, Lys-409, and Lys-40. All of these results were similar to those obtained previously with the other compounds, suggesting the presence of a cluster of five lysyl residues at or near the substrate-binding site of this enzyme. However, the incorporations of labels into each lysyl residue differed depending on the compounds used. The substrate retarded the incorporations in different manners. Based on the combined results of the present and previous studies, a hypothetical model is presented for the possible locations of the five lysyl residues around the substrate bound to the enzyme. This model is consistent with the kinetic properties of mutant enzymes in which the five lysyl residues were individually replaced by glutamine via site-directed mutagenesis.

Molybdenum cofactor biosynthesis in Escherichia coli. Requirement of the chlB gene product for the formation of molybdopterin guanine dinucleotide

The chlorate-resistant mutants of Escherichia coli are affected in the biosynthesis of the molybdenum cofactor and show pleiotropic loss of the activities of those enzymes which require the cofactor. The molybdenum cofactor in all molybdoenzymes other than nitrogenase is a complex of the metal with a unique pterin termed molybdopterin. The molybdenum cofactor in a number of E. coli enzymes has been shown to contain GMP in addition to the metal-molybdopterin complex, with the GMP appended in pyrophosphate linkage to the terminal phosphate ester on the molybdopterin side chain. In this paper, we have examined the biochemistry of the chlB mutant and show that the gene product of the chlB locus is essential for the addition of the GMP moiety to form molybdopterin guanine dinucleotide, a step which occurs late in the cofactor biosynthetic pathway in E. coli. Sensitive techniques were developed for the identification of fluorescent derivatives of molybdopterin and of molybdopterin guanine dinucleotide in extracts of E. coli cells. Wild type cells were shown to contain both molybdopterin and molybdopterin guanine dinucleotide, while cells of chlB mutants were found to contain elevated levels of molybdopterin but no detectable molybdopterin guanine dinucleotide.

ChemInform Abstract: Sequence Dependence of Template‐Directed Syntheses of Hexadeoxynucleotide Derivatives with 3′‐5′ Pyrophosphate Linkage.

ChemInform Abstract: Sequence Dependence of Template‐Directed Syntheses of Hexadeoxynucleotide Derivatives with 3′‐5′ Pyrophosphate Linkage.

Sequence Dependence of Template‐Directed Syntheses of Hexadeoxynucleotide Derivatives with 3′–5′ Pyrophosphate Linkage

Self‐replication in a minimal chemical system represents both a goal and a challenge for bioorganic chemistry, which concerns itself, among other things, with trying to understand the origin of life. A partial success can now be reported in the creation of a model system consisting of nucleic acid building blocks and capable of self replication under replicase‐free conditions. This article presents evidence that a self complementary template can accelerate—in a highly selective way—the further incorporation of subunits into sequentially homologous oligonucleotides.

Base-catalyzed reactivation of glucogen phosphorylase reconstituted with a coenzyme-substrate conjugate and its analogues

Glycogen phosphorylase reconstituted with pyridoxal (5′)diphospho(1)-α-D-glucose (PLDP-Glc) is catalytically inactive but slowly converted to the active enzyme through the cleavage of the pyrophosphate linkage. A similar reaction occurs more rapidly on PLDP-Gal and -Xyl but not on PLDP-Man. Values of p K a for all the reactions are about 8.3, suggesting the participation of a common basic residue in these reactions. Based on the present and other results, it is presumed that Tyr-573 or Lys-574 acts as the base abstracting the proton from 2-hydroxyl group of the glucosyl moiety of PLDP-Glc.

Biosynthetic studies on N-acetylmannosaminuronic acid containing teichuronic acid in Bacillus megaterium.

The particulate enzymes obtained from four strains of Bacillus megaterium AHU 1240, AHU 1373, AHU 1375, and T catalyzed the synthesis of a polysaccharide and glycolipids from UDP-N-acetylmannosaminuronic acid, UDP-N-acetylglucosamine, and UDP-glucose. Chemical studies involving Smith degradation, acid hydrolysis, and N-acetylation revealed that the polysaccharide product has a backbone made up of trisaccharide repeating units comprising glucose, N-acetylmannosaminuronic acid, and N-acetylglucosamine and that the main oligosaccharide moieties of the glycolipids were identical with N-acetylmannosaminuronosyl-N-acetylglucosamine and glucosyl-N-acetylmannosaminuronosyl-N-acetylglucosamine. Incubation of the disaccharide-linked lipid with each particulate enzyme in the presence of UDP-glucose produced the trisaccharide-linked lipid and a polysaccharide. It is therefore suggested that in this polysaccharide-synthesizing system the repeating unit is formed on a carrier lipid from appropriate nucleotide derivatives first and the polymerization of the units then occurs to synthesize the backbone while the growing chain remains in pyrophosphate linkage to the carrier lipid presumed to be undecaprenol.

A novel coenzymatic function of pyridoxal 5'-phosphate.

AbstractPyridoxal 5′‐phosphate, the vitamin B6 derivative, acts as the coenzyme of many enzymes involved in amino acid metabolism. Exceptionally, this compound was found covalently bound to glycogen phosphorylase, the key enzyme in the regulation of glycogen metabolism. Although it is essential for the function of phosphorylase, its direct role has remained an enigma. We have recently found that the glucose moiety of pyridoxal (5′)diphospho (1)‐α‐D‐glucose, a conjugate of pyridoxal 5′‐phosphate and glucose 1‐phosphate through a pyrophosphate linkage, is transferred to the nonreducing end of glycogen, forming a new α‐1,4‐glucosidic linkage. This finding emphasizes the importance of the direct phosphate‐phosphate interaction between the coenzyme and the substrate in the phosphorylase catalytic reaction. We have proposed a catalytic mechanism for phosphorylase in which the phosphate group of pyridoxal 5′‐phosphate acts as an electrophile to the phosphate group of glucose 1‐phosphate. This appears to represent the first instance of the direct involvement of a phosphate group in catalysis by enzymes.

Proteolysis of poly(ADPribose) polymerase by a pyrophosphate- and nucleotide-stimulated system dependent on two different classes of proteinase

We have identified a system in human lymphocytes which proteolytically cleaves poly(ADPribose) polymerase to specific fragments of molecular weight 96 000, 79 000 and 62 000–60 000. This proteolytic processing is dependent on two different classes of proteinase. One of these proteinases is a serine proteinase, since the processing is inhibited by phenylmethylsulfonyl fluoride, antipain, soybean trypsin inhibitor and diisopropylfluorophosphate, the other is a cathepsin D-like proteinase, since processing is also inhibited by pepstatin A. The processing that occurs in permeabilized cells can be simulated in vitro by treating purified poly(ADPribose) polymerase with trypsin, but not by treating the polymerase with cathepsin D. Since processing at the cellular level is blocked by inhibitors of either of the two proteinases, but only trypsin could cleave the purified polymerase, this suggests that in the cell the action of the cathepsin D-like proteinase is a prerequisite for cleavage of poly(ADPribose) polymerase by the serine proteinase. Thus, a pathway involving sequential action of these proteinases may exist. Proteolysis in permeabilized human lymphocytes is stimulated by nucleotides containing a pyrophosphate group, such as 5′,5′″'- P 1, P 4-tetraphosphate and ATP, or by pyrophosphate itself. In contrast, nucleotides containing only a single phosphate, such as AMP and cyclic AMP, or inorganic sodium phosphate, do not show this stimulation of proteolysis. These results suggest that a pyrophosphate linkage is the minimum molecular requirement for stimulation of proteolytic processing of poly(ADPribose) polymerase. Proteolytic processing of poly(ADPribose) polymerase is independent of ADPribosylation. Following proteolysis, specific fragments of the polymerase, particularly the 62 000–60 000 molecular weight fragment(s), are still capable of being ADPribosylated.

Template-directed synthesis of novel, nucleic acid-like structures.

In studying the origins of life, it is important to examine reactions of substrate mixtures that could plausibly have accumulated on the primitive earth. Nucleoside diphosphates would probably have been synthesized along with the standard nucleotides under prebiotic conditions. For these reasons, the template-directed reactions of activated derivatives of these diphosphates, alone or mixed with activated nucleotides, were investigated. An activated derivative of deoxyguanosine 3',5'-diphosphate condensed efficiently on a polycytidylate template to give oligonucleotide analogues in which each 3',5'-phosphodiester bond was replaced by a pyrophosphate linkage. Oligomers were formed even in the absence of a template, but much more slowly. Template-directed condensation occurred also with an analogous deoxyadenosine derivative on polyuridylic acid and with an analogous acycloguanosine derivative on polycytidylic acid.