Two nucleoside uptake systems in Lactococcus lactis: competition between purine nucleosides and cytidine allows for modulation of intracellular nucleotide pools

A method for measuring internal nucleoside triphosphate pools of lactococci was optimized and validated. This method is based on extraction of (33)P-labeled nucleotides with formic acid and evaluation by two-dimensional chromatography with a phosphate buffer system for the first dimension and with an H(3)BO(3)-LiOH buffer for separation in the second dimension. We report here the sizes of the ribo- and deoxyribonucleotide pools in laboratory strain MG1363 during growth in a defined medium. We found that purine- and pyrimidine-requiring strains may be used to establish physiological conditions in batch fermentations with altered nucleotide pools and growth rates by addition of nucleosides in different combinations. Addition of cytidine together with inosine to a purine-requiring strain leads to a reduction in the internal purine nucleotide pools and a decreased growth rate. This effect was not seen if cytidine was replaced by uridine. A similar effect was observed if cytidine and inosine were added to a pyrimidine-requiring strain; the UTP pool size was significantly decreased, and the growth rate was reduced. To explain the observed inhibition, the nucleoside transport systems in Lactococcus lactis were investigated by measuring the uptake of radioactively labeled nucleosides. The K(m) for for inosine, cytidine, and uridine was determined to be in the micromolar range. Furthermore, it was found that cytidine and inosine are competitive inhibitors of each other, whereas no competition was found between uridine and either cytidine or inosine. These findings suggest that there are two different high-affinity nucleoside transporters, one system responsible for uridine uptake and another system responsible for the uptake of all purine nucleosides and cytidine.     

Crystal structure of a Z-DNA hexamer d(CGCICG) at 1.7 A resolution: inosine.cytidine base-pairing, and comparison with other Z-DNA structures.

The crystal structure of the deoxyhexamer, d(CGCICG), has been determined and refined to a resolution of 1.7A. The DNA hexamer crystallises in space group P2(1)2(1)2(1) with unit cell dimensions of a = 18.412 +/- .017 A, b = 30.485 +/- .036A, and c = 43.318 +/- .024 A. The structure has been solved by rotation and translation searches and refined to an R-factor of 0.148 using 2678 unique reflections greater than 1.0 sigma (F) between 10.0-1.7 A resolution. Although the crystal parameters are similar to several previously reported Z-DNA hexamers, this inosine containing Z-DNA differs in the relative orientation, position, and crystal packing interactions compared to d(CGCGCG) DNA. Many of these differences in the inosine form of Z-DNA can be explained by crystal packing interactions, which are responsible for distortions of the duplex at different locations. The most noteworthy features of the inosine form of Z-DNA as a result of such distortions are: (1) sugar puckers for the inosines are of C4'-exo type, (2) all phosphates have the Zl conformation, and (3) narrower minor grove and compression along the helical axis compared to d(CGCGCG) DNA. In addition, the substitution of guanosine by inosine appears to have resulted in Watson-Crick type base-pairing between inosine and cytidine with a potential bifurcated hydrogen bond between inosine N1 and cytidine N3 (2.9 A) and O2 (3.3-3.A).     

Unusual sensitivity of Escherichia coli to adenine or adenine plus histidine.

The W3110 strain of Escherichia coli K-12 is unusually sensitive to adenine. Inhibition of growth is relieved by a combination of thiamine and uridine (or cytidine). In the presence of histidine, inhibition is more severe and is relieved by a combination of thiamine, glycine, uridine (or cytidine), and inosine (or guanosine).     

Sugar-free growth of mammalian cells on some ribonucleosides but not on others

It was shown earlier that a variety of vertebrate cells could grow indefinitely in sugar-free medium supplemented with either uridine or cytidine at greater than or equal to 1 mM. In contrast, most purine nucleosides do not support sugar-free growth for one of the following reasons. The generation of ribose-1-P from nucleoside phosphorylase activity is necessary to provide all essential functions of sugar metabolism. Some nucleosides, e.g. xanthosine, did not support growth because they are poor substrates for this enzyme. De novo pyrimidine synthesis was inhibited greater than 80% by adenosine or high concentrations of inosine, e.g. 10 mM, which prevented growth on these nucleosides; in contrast, pyrimidine synthesis was inhibited only marginally on 1 mM inosine or guanosine, but normal growth was only seen on 1 mM inosine, not on guanosine. The inhibition of de novo adenine nucleotide synthesis prevented growth on guanosine, since guanine nucleotides could not be converted to adenine nucleotides. Guanine nucleotides were necessary for this inhibition of purine synthesis, since a mutant blocked in their synthesis grew normally on guanosine. De novo purine synthesis was severely inhibited by adenosine, inosine, or guanosine, but in contrast to guanosine, adenosine and inosine could provide all purine requirements by direct nucleotide conversions.     

Sodium-dependent nucleoside transport in choroid plexus from rabbit. Evidence for a single transporter for purine and pyrimidine nucleosides.

The overall goal of this study was to determine the mechanisms by which nucleosides are transported in choroid plexus. Choroid plexus tissue slices obtained from rabbit brain were depleted of ATP with 2,4-dinitrophenol. Uridine and thymidine accumulated in the slices against a concentration gradient in the presence of an inwardly directed Na+ gradient. The Na(+)-driven uptake of uridine and thymidine was saturable with Km values of 18.1 +/- 2.0 and 13.0 +/- 2.3 microM and Vmax values of 5.5 +/- 0.3 and 1.0 +/- 0.2 nmol/g/s, respectively. Na(+)-driven uridine uptake was inhibited by naturally occurring ribo- and deoxyribonucleosides (adenosine, cytidine, and thymidine) but not by synthetic nucleoside analogs (dideoxyadenosine, dideoxycytidine, cytidine arabinoside, and 3'-azidothymidine). Both purine (guanosine, inosine, formycin B) and pyrimidine nucleosides (uridine and cytidine) were potent inhibitors of Na(+)-thymidine transport with IC50 values ranging between 5 and 23 microM. Formycin B competitively inhibited Na(+)-thymidine uptake and thymidine trans-stimulated formycin B uptake. These data suggest that both purine and pyrimidine nucleosides are substrates of the same system. The stoichiometric coupling ratios between Na+ and the nucleosides, guanosine, uridine, and thymidine, were 1.87 +/- 0.10, 1.99 +/- 0.35, and 2.07 +/- 0.09, respectively. The system differs from Na(+)-nucleoside co-transport systems in other tissues which are generally selective for either purine or pyrimidine nucleosides and which have stoichiometric ratios of 1. This study represents the first direct demonstration of a unique Na(+)-nucleoside co-transport system in choroid plexus.     

Some kinetic studies on ribonucleosides degradation by extracts of penicillium citrinum

Cell-free extracts of 3–4 days old mats of nitrate-grown Penicillium citrinum catalyze the hydrolytic cleavage of the N-glycosidic bonds of inosine, guanosine and adenosine optimally at pH 4, 0.1 M citrate buffer. The same extracts catalyze the hydrolytic deamination of cytidine at a maximum rate in 0.08 M Tris-acetate buffer pH 6.5, 40°C and 50°C were the most suitable degrees for purine nucleoside hydrolysis and cytidine deamination, respectively. The incubation of the extracts at 60°C, in the absence of cytidine caused a loss in the deaminating activity, while freezing and thawing had no effect on both activities. The deaminating activity seems to be cytidine specific as neither cytosine, adenine, adenosine nor guanosine could be deaminated. Uridine competively inhibited this activity, while ammonia had no effect. The apparent K_m value of this enzyme for cytidine was 1.57×10^?3M and its K_i value for uridine was 7.8×10^?3M. The apparent K_m values of the N-glycosidic bond cleaving enzyme for inosine, guanosine and adenosine were 13.3, 14.2 and 20×10^?3 M, respectively.     

APOBEC-2, a cardiac- and skeletal muscle-specific member of the cytidine deaminase supergene family.

APOBEC-1, which mediates the editing of apolipoprotein (apo) B mRNA, is the only known member of the C (cytidine)-->U (uridine) editing enzyme subfamily of the cytidine deaminase supergene family. Here we report the cloning of APOBEC-2, another member of the subfamily. Human and mouse APOBEC-2 both contain 224 amino acid residues, and their genes are mapped to syntenic regions of human chromosome 6 (6p21) and mouse chromosome 17. By phylogenetic analysis, APOBEC-2 is shown to be evolutionarily related to APOBEC-1, and analysis of substitution rates indicates that APOBEC-2 is a much better conserved gene than APOBEC-1. APOBEC-2 mRNA and protein are expressed exclusively in heart and skeletal muscle. APOBEC-2 does not display detectable apoB mRNA editing activity. Like other editing enzymes of the cytidine deaminase superfamily, APOBEC-2 has low, but definite, intrinsic cytidine deaminase activity. The identification of APOBEC-2 indicates that APOBEC-1 is not the only member of the C-->U editing enzyme subfamily, which, like the A (adenosine)-->I (inosine) subfamily of editing enzymes, must encompass at least two and possibly more different deaminase enzymes. It suggests that the C-->U editing affecting apoB mRNA and other RNAs is not an isolated event mediated by a single enzyme but involves multiple related proteins that have evolved from a primordial gene closely related to the housekeeping enzyme cytidine deaminase.     

Determination of the activation energy for pseudorotation of the furanose ring in nucleosides by 13-C nuclear-magnetic-resonance relaxation.

The activation energies for the pseudorotation of the furanose ring in adenosine, guanosine, inosine and xanthosine dissolved in liquid deuteroammonia have been determined by analysis of the longitudinal relaxation rates of the single tertiary carbons between +40 degrees C and minus 60 degrees C. For the purine ribosides the average activation energy was found to be 4.7 plus or minus 0.5 kcal x mol-1 (20 plus or minus 2 kJ x mol-1). For the pyrimidine nucleosides cytidine and uridine the respective activation energy should be higher since it could not be determined by 13-C relaxation measurements. This result can be explained by the formation of a hydrogen bond between the 5'-hydroxymethyl group and the base. In adenosine, guanosine, inosine and xanthosine the relaxation rates of C(5') are smaller than all others thus excluding the formation of a hydrogen bond between the purine base and the 5'-hydroxymethyl group of a strength comparable to the one suggested for cytidine and uridine.     

Leishmania donovani: characteristics of adenosine and inosine transporters in promastigotes of two different strains

The nucleoside transport characteristics of two strains of Leishmania donovani promastigotes were studied. Strain S1, growing in fully defined medium, and strain S2 (MHOM/ET/67/HA3) both transported adenosine and inosine, but only strain S1 transported uridine and thymidine. Competition studies in the presence of 100 microM of unlabeled adenosine, inosine, guanosine, 2'-deoxyadenosine, tubercidin, formycin B, 3'-deoxyinosine as well as uridine, thymidine and cytidine, with either 1 microM [3H]adenosine or [3H]inosine as permeant, were carried out. The inhibition profile with [3H]inosine as permeant was essentially identical in S1 and S2 promastigotes, indicating that the same inosine transporter was present in both strains. However, with [3H] adenosine as permeant, significant differences were noted between the two strains. Thus, only adenosine, 2'-deoxyadenosine, tubercidin, uridine, and thymidine were strongly inhibitory in S1 promastigotes, while essentially all nucleosides tested were effective in S2 promastigotes. This indicates that adenosine transport in S2 promastigotes seems to involve a transporter differing from that described for S1 promastigotes.     

Pathways of Nucleotide Biosynthesis in Mycoplasma mycoides subsp. mycoides

By measuring the specific activity of nucleotides isolated from ribonucleic acid after the incorporation of (14)C-labeled precursors under various conditions of growth, we have defined the major pathways of ribonucleotide synthesis in Mycoplasma mycoides subsp. mycoides. M. mycoides did not possess pathways for the de novo synthesis of nucleotides but was capable of interconversion of nucleotides. Thus, uracil provided the requirement for both pyrimidine ribonucleotides. Thymine is also required, suggesting that the methylation step is unavailable. No use was made of cytosine. Uridine was rapidly degraded to uracil. Cytidine competed effectively with uracil to provide most of the cytidine nucleotide and also provided an appreciable proportion of uridine nucleotide. In keeping with these results, there was a slow deamination of cytidine to uridine with further degradation to uracil in cultures of M. mycoides. Guanine was capable of meeting the full requirement of the organism for purine nucleotide, presumably by conversion of guanosine 5'-monophosphate to adenosine 5'-monophosphate via the intermediate inosine 5'-monophosphate. When available with guanine, adenine effectively gave a complete provision of adenine nucleotide, whereas hypoxanthine gave a partial provision. Neither adenine nor hypoxanthine was able to act as a precursor for the synthesis of guanine nucleotide. Exogenous guanosine, inosine, and adenosine underwent rapid cleavage to the corresponding bases and so show a pattern of utilization similar to that of the latter.     

NUCLEOSIDE PHOSPHATASE ACTIVITIES IN RAT CARDIAC MUSCLE

Localizations of aldehyde-resistant nucleoside phosphatase activities in frozen sections of rat cardiac muscle have been studied by electron microscopy. Activities are higher after fixation with formaldehyde than with glutaraldehyde. After incubation with adenosine triphosphate or inosine diphosphate at pH 7.2, reaction product is found in the "terminal cisternae" or "transverse sacs" of the sarcoplasmic reticulum, which, together with the "intermediary vesicles" (T system), constitute the "dyads" or "triads". Reaction product is also present at the membranes of micropinocytotic vacuoles which apparently form from the plasma membrane of capillary endothelial cells and from the sarcolemma. In certain regions of the intercalated discs, reaction product is found within the narrow spaces between sarcolemmas of adjacent cells and within micropinocytotic vacuoles that seem to form from the sarcolemma. With inosine diphosphate, reaction product is also found in other parts of the sarcoplasmic reticulum. After incubation with cytidine monophosphate at pH 5, reaction product is present in the transverse sacs of sarcoplasmic reticulum, in micropinocytotic vacuoles in capillary endothelium, and in lysosomes of muscle fibers and capillaries. The possible significance of the sarcoplasmic reticulum phosphatases is discussed in relation to the role the reticulum probably plays in moving calcium ions and thereby controlling contraction and relaxation of the muscle fiber.     

Characterization of inosine–uridine nucleoside hydrolase (RihC) from Escherichia coli

A non-specific nucleoside hydrolase from Escherichia coli (RihC) has been cloned, overexpressed, and purified to greater than 95% homogeneity. Size exclusion chromatography and sodium dodecyl sulfate polyacrylamide gel electrophoresis show that the protein exists as a homodimer. The enzyme showed significant activity against the standard ribonucleosides with uridine, xanthosine, and inosine having the greatest activity. The Michaelis constants were relatively constant for uridine, cytidine, inosine, adenosine, xanthosine, and ribothymidine at approximately 480 μM. No activity was exhibited against 2′-OH and 3′-OH deoxynucleosides. Nucleosides in which additional groups have been added to the exocyclic N6 amino group also exhibited no activity. Nucleosides lacking the 5′-OH group or with the 2′-OH group in the arabino configuration exhibited greatly reduced activity. Purine nucleosides and pyrimidine nucleosides in which the N7 or N3 nitrogens respectively were replaced with carbon also had no activity.     

Interaction of membrane phospholipids with some DNA substructures studied by means of differential scanning calorimetry.

The interaction of dipalmitoylphosphatidylcholine, dipalmitoylphosphatidic acid and dipalmitoylphosphatidylethanolamine with some DNA substructures such as cytidine, uridine, adenosine 5'di- and triphosphate, guanosine 5'mono- and diphosphate, cytidine 5'mono- and triphosphate, uridine 5'mono- and triphosphate and inosine 5'monophosphate was studied with differential scanning calorimetry. The dependence of pretransition and main transition temperatures and the enthalpy of main transition on the molecular characteristics of the interacting molecular species was calculated by stepwise regression analysis. Nucleosides and nucleotides increased the main transition temperature and peak half width of phospholipids and they decreased the enthalpy of main transition proving the existence of interaction between phospholipids and DNA substructures. Calculation proved that the interaction is mainly of hydrophilic character but the involvement of hydrophobic forces or steric conditions cannot be ruled out.     

Stacking self-association of pyrimidine nucleosides and of cytosines: effects of methylation and thiolation.

Stacking self-association equilibria in aqueous solutions of m3uridine, m34,2',3',5'uridine, 2'-deoxyuridine, m13,4,4cytosine, m14,4,4,5cytosine, s2cytidine and s4thymidine were studied at various temperatures by vapour-pressure osmometry. Equilibrium constants Kst's were computed on the assumption of the isodesmic model of self-association. Enthalpies of association were also obtained from the temperature dependence of Kst according to the van't Hoff equation. Analysis of the equilibrium and thermodynamic parameters demonstrated involvement of hydrophobic interactions in the stabilization of complexes of tetramethyluridine. Dipole-induced dipole interactions seem to predominate in the formation of s2C, s4T and of both dimethylaminocytosine complexes.     

Taxonomic distribution and quantitative analysis of free purine and pyrimidine nucleosides in snake venoms

The nucleoside content of 32 elapid and viperid venoms was examined. Free purines, principally adenosine (ADO), inosine (INO), and guanosine (GUA), comprised as much as 8.7% of the solid components of some venoms. Thus, purines are far more abundant in some venoms than many proteinaceous toxins. Hypoxanthine (HYP) was found in about half of elapid and viperine venoms, in which it is a relatively minor constituent (<60 microg/g). Adenosine monophosphate (AMP) was tentatively identified in only three elapid and two viperid venoms. The pyrimidines, uridine (URI) and cytidine (CYT), were also found in most elapid and viperine venoms. In most of these, the amount of uridine was substantially greater than that of cytidine. Thymidine (THY) was not found in any venom, indicating that DNA from disintegration of glandular cells is not the source of venom nucleosides. In contrast to elapid and viperine venoms, most crotaline venoms are devoid of free nucleosides. Elapid and viperine venoms also contained other minor, low molecular weight constituents that could not be positively identified. Some had spectra identical to those of adenosine, nicotinamide adenine dinucleotide (NAD), inosine, xanthosine (XAN), and guanosine, while others had unique spectra. There is no apparent correlation between quantities of venom nucleosides and literature values for the three dominant venom enzymes that release endogenous nucleosides, 5'-nucleotidase (5NUC), phosphodiesterase (PDE), and alkaline phosphomonoesterase (PME).     

Biochemistry and metabolism of Giardia

Giardia lamblia, an aerotolerant anaerobe, respires in the presence of oxygen by a flavin, iron-sulfur protein-mediated electron transport system. Glucose appears to be the only sugar catabolized by the Embden-Meyerhof-Parnas and hexose monophosphate pathways, and energy is produced by substrate level phosphorylation. Substrates are incompletely oxidized to CO2, ethanol and acetate by nonsedimentable enzymes. The lack of incorporation of inosine, hypoxanthine, xanthine, formate or glycine into nucleotides indicates an absence of de novo purine synthesis. Only adenine, adenosine, guanine and guanosine are salvaged, and no interconversion of these purines was detected. Salvage of these purines and their nucleosides is accomplished by adenine phosphoribosyltransferase, adenosine hydrolase, guanosine phosphoribosyltransferase and guanine hydrolase. The absence of de novo pyrimidine synthesis was confirmed by the lack of incorporation of bicarbonate, orotate and aspartate into nucleotides, and by the lack of detectable levels of the enzymes of de novo pyrimidine synthesis. Salvage appears to be accomplished by the action of uracil phosphoribosyltransferase, uridine hydrolase, uridine phosphotransferase, cytidine deaminase, cytidine hydrolase, cytosine phosphoribosyltransferase and thymidine phosphotransferase. Nucleotides of uracil may be converted to nucleotides of cytosine by cytidine triphosphate synthetase, but thymidylate synthetase and dihydrofolate reductase activities were not detected. Uptake of pyrmidine nucleosides, and perhaps pyrimidines, appears to be accomplished by carrier-mediated transport, and the common site for uptake of uridine and cytidine is distinct from the site for thymidine. Thymine does not appear to be incorporated into nucleotide pools. Giardia trophozoites appear to rely on preformed lipids rather than synthesizing them de novo.(ABSTRACT TRUNCATED AT 250 WORDS)     

Self-association phenomenon specific to the copper complexes with ADP,dADP, and IDP

Circular dichroism spectra between 200 and 800 nm are presented for solutions of nucleotides with pyrophosphate group derived from adenine and inosine in the presence of the Cu₂₊ cation. A study as a function of the pH, temperature, and concentration has shown the existence of a self-association, which implies a strong interaction between the bases of the two nucleotides. The interpretation of the dichroic spectra allows us to show that two oligomer species are formed successively in low concentrations in the presence of the Cu²⁺ cation. The first, constituted by Cu(ADP)^? molecules, appears at pH 5.3 and gives rise to a nonconservative excitonic term. The second, responsible for a conservative excitonic term, is a heterooligomer formed at pH 7.3 by the assembling of a Cu(ADP)^? and a Cu(ADP)(OH)^2? molecule. Furthermore, this self-association is destabilized if the nucleotide derived from adenine is replaced by the corresponding deoxyribonucleotide or by IDP.     

Interaction of metal ions with polynucleotides and related compounds. X. Studies on the reaction of silver (I) with the nucleosides and polynucleotides, and the effect of silver(I) on the zinc(II) degradation of polynucleotides

Potentiometric titration curves of the silver(I) complexes of cytidine, adenosine, and uridine show little uptake of base below pH 7, unlike the curve for silver(I)-guanosine, which shows extensive base uptake at neutral pH. This observation is correlated with spectrophotometric data showing little difference between the silver complex spectra of adenosine, cytidine, and uridine and the spectra of uncomplexed nucleosides, except at high pH, but showing a great difference between the silver complex spectra of guanosine and inosine and the corresponding uncomplexed nucleosides even at pH 6. Similar comparisons of the silver complexes of poly A, poly C, poly I, and poly U, both by potentiometric titration and by spectrophotometry, show that poly I behaves like guanosine and inosine as expected, differing from poly A and poly C. However, poly U behaves like poly I and thus does not resemble uridine in its complexing behavior. There is thus a dichotomy between poly A and poly C on the one hand in silver complexing phenomena, compared with poly U and poly I on the other. When silver(I) is added to systems containing zinc(II) and various polynucleotides, the same dichotomy is noted. Silver(I) inhibits the degradation by zinc(II) of all four polynucleotides, but the degradation of poly I and poly U is prevented virtually completely. Silver(I) alone has no degradative effect on RNA and inhibits, the zinc(II) degradation of RNA. Polynucleotide complexes in which silver(I) and zinc(II) are simultaneously bound to different positions on the macromolecules are postulated as intermediates in the inhibited degradation reactions.     

DNG cytidine: synthesis and binding properties of octameric guanidinium-linked deoxycytidine oligomer

The synthesis of guanidinium-linked cytidyl oligomer (DNG-C(8)), a cationic DNA analog, and the corresponding cytidine monomers is described. The DNG monomer synthesis was streamlined to produce a shorter route to the final monomer than previously reported for thymidine and subsequent solid-phase synthesis produced an octameric cytidyl DNG strand. Because octameric deoxyguanosine would be used as the complementary strand in our studies, it was necessary to investigate guanosine self-association. Singular value decomposition was used to mathematically deconvolve the spectral data and confirm the presence of transitions due to DNA-G(8) self-association. Job plots show the binding stoichiometry of DNG-C(8) with DNA-G(8) to be 1:1. Thermal denaturation studies of the DNG-C(8).DNA-G(8) duplex established a T(m) > or = 90 degrees and a DeltaG degree = -13.3 kcal mol(-1), indicating the DNG-C(8).DNA-G(8) duplex is over 1000 times more stable than that of DNA-C(8).DNA-G(8).