Interaction of phenosafranine with nucleic acids and model polyphosphates. I. Self-aggregation and complex formation with inorganic polyphosphates

Aggregation or phenosafranine in concentrated aqueous solutions and its interaction with polyphosphates was Studied by absorption and fluorescence spectroscopy. At concentrations > 10(-3) M phenosafranine forms dimers (Kd = 3.8 x 10(2) l.mole(-1)), which are characterized by a hypsochromic shift of the visible and near ultraviolet absorption maxima accompanied by a hypochromic effect. No fluorescence could be detected from phenosafranine dimers. Analogous spectral changes were observed when a polyphosphate was titrated with phenusafranine, which indicated that with increasing saturation of the polyphosphate binding sites phenosafranine gradually became bound in the aggregated form. Full saturation of the polyphosphate binding sites with phenosafranine was reached only when an excess of free dye was present. The cooperative binding of phenosafranine to a polyphosphate could be evaluated by means of a theory proposed by Schwarz et al. At the zero ionic strength and at 25 degrees C the binding was characterized by cooperative binding constant K = 6.2 x 10(5) l.mole(-1), number of binding sites per monomeric phosphate residue g = 0.4, and cooperativity parameter q reverse similar 30. Spectroscopic properties of phenosafranine in the aggregated and poly phosphate-bound stotes were compared with those of ethidium bromide.     

Synthesis of dinucleoside polyphosphates catalyzed by firefly luciferase.

In the presence of ATP, luciferin (LH2), Mg2+ and pyrophosphatase, the firefly (Photinus pyralis) luciferase synthesizes diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A) through formation of the E-LH2-AMP complex and transfer of AMP to ATP. The maximum rate of the synthesis is observed at pH 5.7. The Km values for luciferin and ATP are 2-3 microM and 4 mM, respectively. The synthesis is strictly dependent upon luciferin and a divalent metal cation. Mg2+ can be substituted with Zn2+, Co2+ or Mn2+, which are about half as active as Mg2+, as well as with Ni2+, Cd2+ or Ca2+, which, at 5 mM concentration, are 12-20-fold less effective than Mg2+. ATP is the best substrate of the above reaction, but it can be substituted with adenosine 5'-tetraphosphate (p4A), dATP, and GTP, and thus the luciferase synthesizes the corresponding homo-dinucleoside polyphosphates:diadenosine 5',5"'-P1,P5-pentaphosphate (Ap5A), dideoxyadenosine 5',5"'-P1,P4-tetraphosphate (dAp4dA) and diguanosine 5',5"'-P1,P4-tetraphosphate (Gp4G). In standard reaction mixtures containing ATP and a different nucleotide (p4A, dATP, adenosine 5'-[alpha,beta-methylene]-triphosphate, (Ap[CH2]pp), (S')-adenosine-5'-[alpha-thio]triphosphate [Sp)ATP[alpha S]) and GTP], luciferase synthesizes, in addition to Ap4A, the corresponding hetero-dinucleoside polyphosphates, Ap5A, adenosine 5',5"'-P1,P4-tetraphosphodeoxyadenosine (Ap4dA), diadenosine 5',5"'-P1,P4-[alpha,beta-methylene] tetraphosphate (Ap[CH2]pppA), (Sp-diadenosine 5',5"'-P1,P4-[alpha-thio]tetraphosphate [Sp)Ap4A[alpha S]) and adenosine-5',5"'-P1,P4-tetraphosphoguanosine (Ap4G), respectively. Adenine nucleotides, with at least a 3-phosphate chain and with an intact alpha-phosphate, are the preferred substrates for the formation of the enzyme-nucleotidyl complex. Nucleotides best accepting AMP from the E-LH2-AMP complex are those which contain at least a 3-phosphate chain and an intact terminal pyrophosphate moiety. ADP or other NDP are poor adenylate acceptors as very little diadenosine 5',5"'-P1,P3-triphosphate (Ap3A) or adenosine-5',5"'-P1,P3-triphosphonucleosides (Ap3N) are formed. In the presence of NTP (excepting ATP), luciferase is able to split Ap4A, transferring the resulting adenylate to NTP, to form hetero-dinucleoside polyphosphates. In the presence of PPi, luciferase is also able to split Ap4A, yielding ATP. The cleavage of Ap4A in the presence of Pi or ADP takes place at a very low rate. The synthesis of dinucleoside polyphosphates, catalyzed by firefly luciferase, is compared with that catalyzed by aminoacyl-tRNA synthetases and Ap4A phosphorylase.     

Selective splitting of 3'-adenylated dinucleoside polyphosphates by specific enzymes degrading dinucleoside polyphosphates

Several 3'-[(32)P]adenylated dinucleoside polyphosphates (Np(n)N'p*As) were synthesized by the use of poly(A) polymerase (Sillero MAG et al., 2001, Eur J Biochem.; 268: 3605-11) and three of them, ApppA[(32)P]A or ApppAp*A, AppppAp*A and GppppGp*A, were tested as potential substrates of different dinucleoside polyphosphate degrading enzymes. Human (asymmetrical) dinucleoside tetraphosphatase (EC 3.6.1.17) acted almost randomly on both AppppAp*A, yielding approximately equal amounts of pppA + pAp*A and pA + pppAp*A, and GppppGp*, yielding pppG + pGp*A and pG + pppGp*A. Narrow-leafed lupin (Lupinus angustifolius) tetraphosphatase acted preferentially on the dinucleotide unmodified end of both AppppAp*A (yielding 90% of pppA + pAp*A and 10 % of pA + pppAp*A) and GppppGp*A (yielding 89% pppG + pGp*A and 11% of pG + pppGp*A). (Symmetrical) dinucleoside tetraphosphatase (EC 3.6.1.41) from Escherichia coli hydrolyzed AppppAp*A and GppppGp*A producing equal amounts of ppA + ppAp*A and ppG + ppGp*A, respectively, and, to a lesser extent, ApppAp*A producing pA + ppAp*A. Two dinucleoside triphosphatases (EC 3.6.1.29) (the human Fhit protein and the enzyme from yellow lupin (Lupinus luteus)) and dinucleoside tetraphosphate phosphorylase (EC 2.7.7.53) from Saccharomyces cerevisiae did not degrade the three 3'-adenylated dinucleoside polyphosphates tested.     

Ectoenzymatic breakdown of diadenosine polyphosphates by Xenopus laevis oocytes.

Xenopus laevis oocytes exhibit ectoenzymatic activity able to hydrolytically cleave extracellular diadenosine polyphosphates (Ap(n)A). The basic properties of this ectoenzyme were investigated using as substrates di-(1,N(6)-ethenoadenosine) 5',5"'-P(1),P(4)-tetraphospate [epsilon-(Ap(4)A)] and di-(1,N(6)-ethenoadenosine) 5',5"'-P(1),P(5)-pentaphospate [epsilon-(Ap(5)A)], fluorogenic derivatives of Ap(4)A and Ap(5)A, respectively. epsilon-(Ap(4)A) and epsilon-(Ap(5)A) are hydrolysed by folliculated oocytes according to hyperbolic kinetics with K(m) values of 13.4 and 12.0 microM and Vmax values of 4.8 and 5.5 pmol per oocyte per min, respectively. The ectoenzyme is activated by Ca(2+) and Mg(2+), reaches maximal activity at pH 8--9 and is inhibited by suramin. Defolliculated oocytes also hydrolyse both substrates with similar K(m) values but V(max) values are approximately doubled with respect to folliculated controls. Chromatographic analysis indicates that extracellular epsilon-(Ap(4)A) and epsilon-(Ap(5)A) are first cleaved into 1,N(6)-ethenoAMP (epsilon-AMP) + 1,N(6)-ethenoATP (epsilon-ATP) and epsilon-AMP + 1,N(6)-ethenoadenosine tetraphosphate (epsilon-Ap(4)), respectively, which are catabolized to 1,N(6)-ethenoadenosine (epsilon-Ado) as the end product by folliculated oocytes. Denuded oocytes, however, show a drastically reduced rate of epsilon-Ado production, epsilon-AMP being the main end-product of extracellular epsilon-(Ap(n)A) catabolism. Results indicate that, whereas the Ap(n)A-cleaving ectoenzyme appears to be located mainly in the oocyte, ectoenzymes involved in the dephosphorylation of mononucleotide moieties are located mainly in the follicular cell layer.     

Inorganic polyphosphates in mitochondria

Current data concerning the crucial role of inorganic polyphosphates (polyP) in mitochondrial functions and dysfunctions in yeast and animal cells are reviewed. Biopolymers with short chain length (∼15 phosphate residues) were found in the mitochondria of Saccharomyces cerevisiae. They comprised 7–10% of the total polyP content of the cell. The polyP are located in the membranes and intermembrane space of mitochondria. The mitochondrial membranes possess polyP/Ca²⁺/polyhydroxybutyrate complexes. PolyP accumulation is typical of promitochondria but not of functionally active mitochondria. Yeast mitochondria possess two exopolyphosphatases splitting P_i from the end of the polyP chain. One of them, encoded by the PPX1 gene, is located in the matrix; the other one, encoded by the PPN1 gene, is membrane-bound. Formation of well-developed mitochondria in the cells of S. cerevisiae after glucose depletion is accompanied by decrease in the polyP level and the chain length. In PPN1 mutants, the polyP chain length increased under glucose consumption, and the formation of well-developed mitochondria was blocked. These mutants were defective in respiration functions and consumption of oxidizable carbon sources such as lactate and ethanol. Since polyP is a compound with high-energy bonds, its metabolism vitally depends on the cell bioenergetics. The maximal level of short-chain acid-soluble polyP was observed in S. cerevisiae under consumption of glucose, while the long-chain polyP prevailed under ethanol consumption. In insects, polyP in the mitochondria change drastically during ontogenetic development, indicating involvement of the polymers in the regulation of mitochondrial metabolism during ontogenesis. In human cell lines, specific reduction of mitochondrial polyP under expression of yeast exopolyphosphatase PPX1 significantly modulates mitochondrial bioenergetics and transport.     

Hydrolysis of diadenosine polyphosphates by nucleotide pyrophosphatases/phosphodiesterases.

Diadenosine polyphosphates (ApnAs) act as extracellular signaling molecules in a broad variety of tissues. They were shown to be hydrolyzed by surface-located enzymes in an asymmetric manner, generating AMP and Apn-1 from ApnA. The molecular identity of the enzymes responsible remains unclear. We analyzed the potential of NPP1, NPP2, and NPP3, the three members of the ecto-nucleotide pyrophosphatase/phosphodiesterase family, to hydrolyze the diadenosine polyphosphates diadenosine 5',5"'-P1,P3-triphosphate (Ap3A), diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A), and diadenosine 5',5"'-P1,P5-pentaphosphate, (Ap5A), and the diguanosine polyphosphate, diguanosine 5',5"'-P1,P4-tetraphosphate (Gp4G). Each of the three enzymes hydrolyzed Ap3A, Ap4A, and Ap5A at comparable rates. Gp4G was hydrolyzed by NPP1 and NPP2 at rates similar to Ap4A, but only at half this rate by NPP3. Hydrolysis was asymmetric, involving the alpha,beta-pyrophosphate bond. ApnA hydrolysis had a very alkaline pH optimum and was inhibited by EDTA. Michaelis constant (Km) values for Ap3A were 5.1 micro m, 8.0 micro m, and 49.5 micro m for NPP1, NPP2, and NPP3, respectively. Our results suggest that NPP1, NPP2, and NPP3 are major enzyme candidates for the hydrolysis of extracellular diadenosine polyphosphates in vertebrate tissues.     

T4 RNA ligase catalyzes the synthesis of dinucleoside polyphosphates.

T4 RNA ligase has been shown to synthesize nucleoside and dinucleoside 5'-polyphosphates by displacement of the AMP from the E-AMP complex with polyphosphates and nucleoside diphosphates and triphosphates. Displacement of the AMP by tripolyphosphate (P3) was concentration dependent, as measured by SDS/PAGE. When the enzyme was incubated in the presence of 0.02 mm [alpha-32P] ATP, synthesis of labeled Ap4A was observed: ATP was acting as both donor (Km, microm) and acceptor (Km, mm) of AMP from the enzyme. Whereas, as previously known, ATP or dATP (but not other nucleotides) were able to form the E-AMP complex, the specificity of a compound to be acceptor of AMP from the E-AMP complex was very broad, and with Km values between 1 and 2 mm. In the presence of a low concentration (0.02 mm) of [alpha-32P] ATP (enough to form the E-AMP complex, but only marginally enough to form Ap4A) and 4 mm of the indicated nucleotides or P3, the relative rate of synthesis of the following radioactive (di)nucleotides was observed: Ap4X (from XTP, 100); Ap4dG (from dGTP, 74); Ap4G (from GTP, 49); Ap4dC (from dCTP, 23); Ap4C (from CTP, 9); Ap3A (from ADP, 5); Ap4ddA, (from ddATP, 1); p4A (from P3, 200). The enzyme also synthesized efficiently Ap3A in the presence of 1 mm ATP and 2 mm ADP. The following T4 RNA ligase donors were inhibitors of the synthesis of Ap4G: pCp > pAp > pA2'p.     

Hydrolysis of polyphosphates by corn roots

Summary The hydrolysis of seven linear oligomers (P₂, P₃, P₅, P₁₅, P₂₅, P₃₅ and P₆₅) and one cyclic polyphosphate, trimetaphosphate (TMP), by corn (Zea mays) roots was investigated. In these experiments, corn-root homogenate or intact roots were incubated in a polyphosphate solution containing 1 mM polyphosphate or 50 mg P/L, respectively, and the amount of orthophosphate produced was determined. Results showed that the optimal pH value for hydrolysis of P₃, P₅, and TMP by corn-root homogenate was 5.0, whereas for the hydrolysis of P₂, P₁₅, P₂₅, P₃₅ and P₆₅, it was 6.0. The rate of polyphosphate hydrolysis by cornroot homogenate was temperature dependent up to the point of enzyme inactivation (>50°C). Nonsterile intact roots showed higher rates of hydrolysis than sterile roots, especially with P₂. The hydrolysis of all oligomers by sterile and nonsterile intact roots was very slow during the first 18h at 30°C, but increased rapidly after 18h with the oligomers P≦25. The oligomers P₃₅ and P₆₅ were quite resistant to hydrolysis by sterile and nonsterile roots after 48h incubation at 30°C. An experiment with sterile intact roots in pyrophosphate solution suggested that pyrophosphatase was induced in corn roots in the presence of its substrate. The order of hydrolysis rates of the oligomers by intact sterile corn roots was: P₂>P₃>P₅> TMP>P₁₅>P₂₅>P₃₅>P₆₅.     

Factors affecting sensitivity of Staphylococcus aureus 196E to polyphosphates.

The effect of polyphosphates (eight compounds) on growth of Staphylococcus aureus 196E in brain heart infusion broth was studied. The organism was sensitive (in decreasing order) to chain polyphosphates with 21, 3, 13, and 15 PO4 groups, and bactericidal effects were observed with 0.5% of these compounds. No inhibition was effected by PPi or a metaphosphate. The inhibitory effects were pH dependent, and bacterial sensitivity was highest at pH greater than 7.4. Initial populations affected the number of survivors. No growth was observed after 24 h at 35 degrees C when the initial cell population was less than 10(4) CFU/ml, and a 100- to 1,000-fold decline in cell numbers occurred when initial populations were higher than 10(4) CFU/ml. Sodium tripolyphosphate produced less inhibition after heat sterilization (15 min, 121 degrees C) than after filter sterilization, whereas sodium hexametaphosphate (n = 21) retained most of its antimicrobial activity after heat sterilization. Supplementation of broth with Mg2+ was effective in overcoming inhibition by 0.5% sodium tripolyphosphate, and an addition of 0.25 to 1.0 mM cation restored most of the growth. Inhibition was partially eliminated by Ca2+ and Fe2+, but not by Zn2+ or Mn2+.     

Synthesis of novel fluorescent-labelled dinucleoside polyphosphates

A novel tandem synthetic-biosynthetic procedure is described for the synthesis of four new fluorescent dinucleoside polyphosphates: mant-Ap4A, mant-AppCH2ppA, TNP-Ap4A and TNP-AppCH2ppA. These compounds are expected to supplement the existing etheno (epsilon) and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) labelled derivatives, being the fluorescent probes of choice to investigate polyphosphate/enzyme binding behaviour.     

Isolation and assay of red-cell inositol polyphosphates

An inositol pentaphosphate has been found to be present in high concentration in red cells of a number of species of birds examined and is thought to be a major control of the oxygen affinity of hemoglobin. to facilitate further studies on the distribution, function, and metabolism of inositol polyphosphates in red cells of birds and other vertebrates, improved methods were developed for their isolation by ion-exchange column chromatography, for their hydrolysis to free inositol from the isolated phosphates, and for colorimetric analysis of the free inositol. Examples are given of the inositol phosphates found in red cells of a duck, an ostrich, the Pseudemys turtle, a fish (Arapaima gigas), commercial inositol hexaphosphate, corn seeds, and corn seedlings.     

Soil inorganic polyphosphates of microbial origin

Summary Extraction of eight soils with cold 0.5 M perchloric acid yielded acid-labile phosphates in four of them which were shown to be naturally occurring inorganic polyphosphates of microbial origin. The amounts estimated were in the range of 5.0 to 11.1 μg P/g soil. Gel filtration through Sephadex G-25 indicated variation with respect to chain lengths and molecular weights of these polyphosphates. Addition of excess amounts of orthophosphate to 14-day incubated glucose-amended soils resulted in accumulation of larger quantities (up to 22.0 μg P/g soil) of acid-labile polyphosphates in some soils. re]19720407 Department of Agronomy, Ohio State University and Ohio Agricultural Research and Development Center