Specific phosphorylase from euglena gracilis splits diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A and diadenosine 5',5'''-P1,P3-triphosphate (Ap3A

Enzymatic synthesis of mono and dinucleoside polyphosphates

BACKGROUND

Mono and dinucleoside polyphosphates (p(n)Ns and Np(n)Ns) exist in living organisms and induce diverse biological effects through interaction with intracellular and cytoplasmic membrane proteins. The source of these compounds is associated with secondary activities of a diverse group of enzymes.

SCOPE OF REVIEW

Here we discuss the mechanisms that can promote their synthesis at a molecular level. Although all the enzymes described in this review are able to catalyse the in vitro synthesis of Np(n)Ns (and/or p(n)N), it is not clear which ones are responsible for their in vivo accumulation.

MAJOR CONCLUSIONS

Despite the large amount of knowledge already available, important questions remain to be answered and a more complete understanding of p(n)Ns and Np(n)Ns synthesis mechanisms is required. With the possible exception of (GTP:GTP guanylyltransferase of Artemia), all enzymes able to catalyse the synthesis of p(n)Ns and Np(n)Ns are unspecific and the factors that can promote their synthesis relative to the canonical enzyme activities are unclear.

GENERAL SIGNIFICANCE

The fact that p(n)Ns and Np(n)Ns syntheses are promiscuous activities of housekeeping enzymes does not reduce its physiological or pathological importance. Here we resume the current knowledge regarding their enzymatic synthesis and point the open questions on the field.

Specific and nonspecific enzymes involved in the catabolism of mononucleoside and dinucleoside polyphosphates

This review concerns enzymes that can degrade nucleoside 5'-tetra- and pentaphosphates (p(4)N and p(5)N) and those that can degrade various dinucleoside polyphosphates (Np(3-6)N'). Most of these enzymes are hydrolases, and they occur in all types of organisms. Certain fungi and protozoa also possess specific Np(n)N' phosphorylases. Specific p(4)N hydrolases have been demonstrated in mammals and in plants. In yeast, p(4)N and p(5)N are hydrolyzed by exopolyphosphatases. Among other hydrolases that can degrade these minor mononucleotides are phosphatases, apyrase, and (asymmetrical) Np(4)N' hydrolase, as well as the nonspecific adenylate deaminase. Np(n)N's are good substrates for Type I phosphodiesterases and nucleotide pyrophosphatases, and diadenosine polyphosphates are easily deaminated to diinosine polyphosphates by nonspecific adenylate deaminases. Specific Np(3)N' hydrolases occur in both prokaryotes and eukaryotes. Interestingly, the human fragile histidine triad (Fhit) tumor suppressor protein appears to be a typical Np(3)N' hydrolase. Among the specific Np(4)N' hydrolases are asymmetrically cleaving ones, which are typical of higher eukaryotes, and symmetrically cleaving enzymes found in Physarum polycephalum and in many bacteria. An enzyme that hydrolyzes both diadenosine tetraphosphate and diadenosine triphosphate has been found in the fission yeast Schizosaccharomyces pombe. Its amino acid sequence is similar to that of the human Fhit/Np(3)N' hydrolase. Very recently, a typical (asymmetrical) Np(4)N' hydrolase has been demonstrated for the first time in a bacterium-the pathogenic Bartonella bacilliformis. Another novelty is the discovery of diadenosine 5', 5"'-P(1),P 6-hexaphosphate hydrolases in budding and fission yeasts and in mammalian cells. These enzymes and the (asymmetrical) Np(4)N' hydrolases have the amino acid motif typical of the MutT (or Nudix hydrolase) family. In contrast, the Schizosaccharomyces pombe Ap(4)A/Ap(3)A hydrolase, the human Fhit protein, and the yeast Np(n)N' phosphorylases belong to a superfamily GAFH, which includes the histidine triad proteins.

P1,P3-bis(5'-adenosyl)triphosphate (Ap3A) as a substrate and a product of mammalian tryptophanyl-tRNA synthetase

Bovine tryptophanyl-tRNA synthetase (TrpRS, E.C.6.1.1.2) is unable to catalyze in vitro formation of Ap4A in contrast to some other aminoacyl-tRNA synthetases. However, in the presence of L-tryptophan, ATP-Mg2+ and ADP the enzyme catalyzes the Ap3A synthesis via adenylate intermediate. Ap3A (not Ap4A) may serve as a substrate for TrpRS in the reaction of E.(Trp approximately AMP) formation and in the tRNA(Trp) charging. The Km value for Ap3A was higher than the Km for ATP (approx. 1.00 vs. 0.22 mM) and Vmax was 3 times lower than for ATP. The Zn(2+)-deficient enzyme catalyzes Ap3A synthesis in the absence of exogenous ADP due to ATPase activity of Zn(2+)-deprived TrpRS. The inability of mammalian TrpRS to synthesize Ap4A, might be considered as a molecular tool preventing the removal of Zn2+ due to chelation by Ap4A and therefore preserving the enzyme activity.

Regiospecificity of the hydrolysis of diadenosine polyphosphates catalyzed by three specific pyrophosphohydrolases

The different patterns of enzymatic cleavage of diadenosine polyphosphates, ApnAs, where n = 3-5, have been established by fast atom bombardment mass spectrometry, FAB MS, of the nucleotide products formed in the presence of H2(18)O. The three specific pyrophosphohydrolases, Ap3A hydrolase (EC 3.6.1.29) and (asymmetrical) Ap4A hydrolase (EC 3.6.1.17) from lupin and the (symmetrical) Ap4A hydrolase (EC 3.6.1.41) from Escherichia coli, manifest three different regiospecificities. The Ap3A hydrolase cleaves all four substrates tested, Ap3A, Ap4A, ApCH2ppA, and ApCHFppA, to give [18O]AMP and the corresponding unlabeled adenosine nucleotide. In each case, the enzyme cleaves at the phosphate proximate to the bound adenosine moiety. The (asymmetrical) Ap4A hydrolase cleaves both Ap4A and Ap5A to give unlabeled ATP plus [18O]AMP and [18O]ADP, respectively, and is thus seen to add water at the fourth phosphate from the bound adenosine moiety. Lastly, the (symmetrical) Ap4A hydrolase from E. coli gives beta-[18O]ADP from Ap3A, Ap4A, and Ap5A along with the unlabeled nucleotide coproducts. In addition, with Ap4A alpha S (ApspppA) as substrate for the bacterial enzyme, the products are beta-[18O]ADP and unlabeled ADP alpha S. This symmetrical enzyme is thus characterized as cleaving the polyphosphate chain at the second phosphate from the bound adenosine moiety.

Isolation and characterization of diadenosine tetraphosphate (Ap4A) hydrolase from Schizosaccharomyces pombe

An enzyme that catalyzes the asymmetric hydrolysis of Ap4A has been partially purified from the fission yeast, Schizosaccharomyces pombe. The crude supernatant fraction from log-phase cells was fractionated by (NH4)2SO4 precipitation followed by chromatography on DEAE-cellulose, Red A dye-ligand and QAE-Sepharose resins. Two peaks of Ap4A hydrolase activity, designated major and minor, were separated on the Red A dye-ligand resin. Both the major and minor Ap4A hydrolase have an apparent molecular mass of 49 kDa based on gel filtration chromatography. On a SDS polyacrylamide gel, a protein of 22 kDa exhibited Ap4A hydrolase activity. Both forms of the enzyme have a Km value in the range of 22 to 36 microM for Ap4A. Both forms of the enzyme asymmetrically hydrolyze Ap4A to AMP and ATP as determined by HPLC. Ap4A is the optimal substrate among several nucleotides and dinucleoside polyphosphates tested at 10 microM. A divalent metal cation is required for activity. Concentrations of Pi below 30 mM stimulate Ap4A hydrolase while higher concentrations inhibit the activity. Pi is not a substrate for this Ap4A-degradative enzyme. Fluoride, from 50 microM to 20 mM, has no significant effect on Ap4A hydrolase activity.

Isolation and characterization of a dinucleoside triphosphatase from Saccharomyces cerevisiae

An enzyme able to cleave dinucleoside triphosphates has been purified 3,750-fold from Saccharomyces cerevisiae. Contrary to the enzymes previously shown to catabolize Ap4A in yeast, this enzyme is a hydrolase rather than a phosphorylase. The dinucleoside triphosphatase molecular ratio estimated by gel filtration is 55,000. Dinucleoside triphosphatase activity is strongly stimulated by the presence of divalent cations. Mn2+ displays the strongest stimulating effect, followed by Mg2+, Co2+, Cd2+, and Ca2+. The Km value for Ap3A is 5.4 microM (50 mM Tris-HCl [pH 7.8], 5 mM MgCl2, and 0.1 mM EDTA; 37 degrees C). Dinucleoside polyphosphates are substrates of this enzyme, provided that they contain more than two phosphates and that at least one of the two bases is a purine (Ap3A, Ap3G, Ap3C, Gp3G, Gp3C, m7Gp3A, m7Gp3G, Ap4A, Ap4G, Ap4C, Ap4U, Gp4G, and Ap5A are substrates; AMP, ADP, ATP, Ap2A, and Cp4U are not). Among the products, a nucleoside monophosphate is always formed. The specificity of cleavage of methylated dinucleoside triphosphates and the molecular weight of dinucleoside triphosphatase indicate that this enzyme is different from the mRNA decapping enzyme previously characterized (A. Stevens, Mol. Cell. Biol. 8:2005-2010, 1988).

Particulate diadenosine 5',5"'-P1,P3-triphosphate hydrolases in rat brain: two specific dinucleoside triphosphatases and two phosphodiesterase I-like hydrolases

Rat liver and brain differ in the distribution pattern of the total hydrolytic activity on diadenosine 5',5"'-P1,P3-triphosphate (Ap3A) between the soluble and particulate fractions. The Ap3A-hydrolase activity in both the soluble and particulate liver fractions and in the brain soluble fraction had been previously studied in detail. We report now on the brain particulate fraction which, unlike liver, showed a low unspecific phosphodiesterase I-like (PDEaseI, EC 3.1.4.1) activity relative to the specific dinucleoside triphosphatase (Ap3Aase, EC 3.6.1.29). Two PDEaseI-like forms (PDEaseI-A and PDEaseI-B), with different apparent Mrs and kinetic properties, and two Ap3Aases (Ap3Aase-alpha and Ap3Aase-beta) were solubilized with 0.5% Triton X-100 from the particulate fraction. Ap3Aase-alpha resembled the cytosolic Ap3Aase (Ap3Aase-c), a known situation in liver. Comparative to Ap3Aase-alpha, Ap3Aase-beta showed a slightly higher Km (35 vs. 15 micron) and lower isoelectric point (5.25 vs. 5.45); Ap3Aase-beta was absent from the soluble fraction, and its recovery was unaffected by proteinase inhibitors, strongly arguing for distinct soluble and particulate turnover pathways for dinucleoside polyphosphates.

Fluoride is a strong and specific inhibitor of (asymmetrical) Ap4A hydrolases

Fluoride acts as a noncompetitive, strong inhibitor of (asymmetrical) Ap4A hydrolases (EC 3.6.1.17). The Ki values estimated for the enzymes isolated from seeds of some higher plants (yellow lupin, sunflower and marrow) are in the range of 2-3 microM and I50 for the hydrolase from a mammalian tissue (beef liver) is 20 microM. The anion, up to 25 mM, does not affect the following other enzymes which are able to degrade the bis(5'-nucleosidyl)-oligophosphates: Escherichia coli (symmetrical) Ap4A hydrolase (EC 3.6.1.41), yeast Ap4A phosphorylase (EC 2.7.7.53), yellow lupin Ap3A hydrolase (EC 3.6.1.29) and phosphodiesterase (EC 3.1.4.1). None of halogenic anions but fluoride affects the activity of (asymmetrical) Ap4A hydrolases. Usefulness of the fluoride effect for the in vivo studies on the Ap4A metabolism is shortly discussed.

Isolation, characterization, and inactivation of the APA1 gene encoding yeast diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase

The gene encoding diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) phosphorylase from yeast was isolated from a lambda gt11 library. The DNA sequence of the coding region was determined, and more than 90% of the deduced amino acid sequence was confirmed by peptide sequencing. The Ap4A phosphorylase gene (APA1) is unique in the yeast genome. Disruption experiments with this gene, first, supported the conclusion that, in vivo, Ap4A phosphorylase catabolizes the Ap4N nucleotides (where N is A, C, G, or U) and second, revealed the occurrence of a second Ap4A phosphorylase activity in yeast cells. Finally, evidence is provided that the APA1 gene product is responsible for most of the ADP sulfurylase activity in yeast extracts.

Synthesis of diadenosine 5',5'''-P1,P4-tetraphosphate by organellar and cytoplasmic phenylalanyl-tRNA synthetases of Euglena gracilis

Purified phenylalanyl-tRNA synthetases present in chloroplasts, mitochondria and cytoplasm of green and bleached Euglena gracilis strains, respectively, are able to synthesize diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A). Ap4A synthesis is strictly dependent on zinc ions. This is the first evidence that chloroplasts should be able to synthesize Ap4A. Synthesis of Ap4A by phenylalanyl-tRNA synthetases of the three compartments of a plant cell or by other enzymes such as Ap4A phosphorylase is discussed.