The improbability of prebiotic nucleic acid synthesis

Many accounts of the origin of life assume that the spontaneous synthesis of a self-replicating nucleic acid could take place readily. Serious chemical obstacles exist, however, which make such an event extremely improbable. Prebiotic syntheses of adenine from HCN, of D,L-ribose from adenosine, and of adenosine from adenine and D-ribose have in fact been demonstrated. However these procedures use pure starting materials, afford poor yields, and are run under conditions which are not compatible with one another. Any nucleic acid components which were formed on the primitive earth would tend to hydrolyze by a number of pathways. Their polymerization would be inhibited by the presence of vast numbers of related substances which would react preferentially with them. It appears likely that nucleic acids were not formed by prebiotic routes, but are later products of evolution.     

Purine metabolism in mesophyll protoplasts of tobacco (Nicotiana tabacum) leaves.

The overall metabolism of purines was studied in tobacco (Nicotiana tabacum) mesophyll protoplasts. Metabolic pathways were studied by measuring the conversion of radioactive adenine, adenosine, hypoxanthine and guanine into purine ribonucleotides, ribonucleosides, bases and nucleic acid constituents. Adenine was extensively deaminated to hypoxanthine, whereupon it was also converted into AMP and incorporated into nucleic acids. Adenosine was mainly hydrolysed to adenine. Inosinate formed from hypoxanthine was converted into AMP and GMP, which were then catabolized to adenine and guanosine respectively. Guanine was mainly deaminated to xanthine and also incorporated into nucleic acids via GTP. Increased RNA synthesis in the protoplasts resulted in enhanced incorporation of adenine and guanine, but not of hypoxanthine and adenosine, into the nucleic acid fraction. The overall pattern of purine-nucleotide metabolic pathways in protoplasts of tobacco leaf mesophyll is proposed.     

Purine metabolism by intracellular Chlamydia psittaci.

Purine metabolism was studied in the obligate intracellular bacterium Chlamydia psittaci AA Mp in the wild type and a variety of mutant host cell lines with well-defined deficiencies in purine metabolism. C. psittaci AA Mp cannot synthesize purines de novo, as assessed by its inability to incorporate exogenous glycine into nucleic acid purines. C. psittaci AA Mp can take ATP and GTP, but not dATP or dGTP, directly from the host cell. Exogenous hypoxanthine and inosine were not utilized by the parasite. In contrast, exogenous adenine, adenosine, and guanine were directly salvaged by C. psittaci AA Mp. Crude extract prepared from highly purified C. psittaci AA Mp reticulate bodies contained adenine and guanine but no hypoxanthine phosphoribosyltransferase activity. Adenosine kinase activity was detected, but guanosine kinase activity was not. There was no competition for incorporation into nucleic acid between adenine and guanine, and high-performance liquid chromatography profiles of radiolabelled nucleic acid nucleobases indicated that adenine, adenosine, and deoxyadenosine were incorporated only into adenine and that guanine, guanosine, and deoxyguanosine were incorporated only into guanine. Thus, there is no interconversion of nucleotides. Deoxyadenosine and deoxyguanosine were cleaved to adenine and guanine before being utilized, and purine (deoxy)nucleoside phosphorylase activity was present in reticulate body extract.     

Nitrogen Metabolism in Paramecium aurelia

Nitrogen in cell fractions of Paramecium aurelia varied according to the growth medium. Trichloroacetic acid-soluble fractions of cells were chromatographer. Adenine, adenosine, guanine, guanosine, hypoxanthine, aspartic acid, glutamic acid, histidine, lysine, proline, and phenylalanine were identified. Fyrimidines and xanthine, or their respective ribosides and ribotides, were not detected. Ammonia was released into the medium by both actively growing and "resting" cells. Culture fluids of "resting"cells also contained hypoxanthine and lesser amounts of adenine and guanine. Urea, uric acid, creatine, cretonne, and ailantoin were absent.
Pyrimidine nitrogen seems excreted as dihydrouracil. The following enzymes were detected in homogenates and cell-free preparations: nucleotidases, nucleoside hydrolases, and cytidine deaminase. Urease, uricase, adenase, guanase, xanthine oxidase, adenosine deaminase, and 5'-adenylic acid deaminase were not present in this organism.
Purine and pyrimidine incorporation into nucleic acids was investigated by the use of radioactive tracers. Guanosine gives rise to nucleic-acid guanine and adenine; adenosine was precursor to nucleic acid adenine only. Formate was incorporated into purines; glycine was not. P. aurelia can interconvert cytidine and uridine; both give rise to nucleic acid thymine. The methyl group of thymine may be derived from formate.     

Toxoplasma gondii: Purine synthesis and salvage in mutant host cells and parasites

Toxoplasma gondii, growing exponentially in heavily infected mutant Chinese hamster ovary cells that had a defined defect in purine biosynthesis, did not incorporate [U-¹⁴C]glucose or [¹⁴C]formate into the guanine or adenine of nucleic acids. Intracellular parasites therefore must be incapable of synthesizing purines and depend on their host cells for them. Extracellular parasites, which are capable of limited DNA and RNA synthesis, efficiently incorporated adenosine nucleotides, adenosine, inosine, and hypoxanthine into their nucleic acids; adenosine 5′-monophosphate was the best utilized precursor. Extracellular parasites incubated with ATP labeled with ³H in the purine base and ³²P in the α-phosphate incorporated the purine ring 50-fold more efficiently than they did the α-phosphate. Thus, ATP is largely degraded to adenosine before it can be used by T. gondii for nucleic acid synthesis. Two pathways for the conversion of adenosine to nucleotides appear to exist, one involving adenosine kinase, the other hypoxanthine—guanine phosphoribosyl transferase. In adenosine kinase-less mutant parasites, the efficiency of incorporation of ATP or adenosine was reduced by 75%, which indicates the adenosine kinase pathway was predominant. Extracellular parasites incorporated ATP into both the adenine and the guanine of their nucleic acids, so ATP from the host cell could supply the entire purine requirement of T. gondii. However, ATP generated by oxidative phosphorylation in the host cell is not essential for parasites because they grew normally in a cell mutant that was deficient in aerobic respiration and almost completely dependent upon glycolysis.     

Stimulation of Cu2+-catalyzed Oxidation of Norepinephrine by Nucleic Acid Components

Oxidation of norepinephrine catalyzed by Cu²⁺ was variously regulated with nucleic acid components. The reaction proceeded by a mechanism of sequential random ordered reaction via formation of the mixed complex of nucleic acid component, Cu²⁺ and aromatic reductone. Using norepinephrine as an aromatic reductone, the promoting activities of nucleic acid components on the oxidation of norepinephrine were compared and the effect of these components to the specific stage of the oxidation process was kinetically investigated. The results indicated that velocity of the oxidation was most remarkably stimulated in the presence of adenine. The velocity was followed by guanine, guanosine monophosphate, cytosine, cytidine, NAD⁺, adenosine, cytidine monophosphate, uridine monophosphate, then adenosine monophosphate in that order. It was also discussed that adenine was the most plausible nucleic acid component which could participate in the in vivo oxidation of norepinephrine, taking into account the concentration of Cu²⁺ and nucleic acid components in living tissues.     

Luminescence of stable stacking aggregates of adenine and uracil in water

Luminescence and excitation spectra of the highly luminescent stacking dimers of adenine and uracil in water solutions are studied. By the luminescence excitation spectra method it is shown that the stacking aggregates of adenine and uracil are formed with participation of rare forms of monomer molecules: N7H tautomers of adenine and the uracil molecules in rare forms of hydratation, for example molecules without H-bonds with water. The study of temperature dependence of luminescence intensity of monomers and stacking dimers of uracil has shown that stacking dimers do not dissociate even at 85 degrees C similarly as described earlier for adenine and adenosine. Stable stacking aggregates of nucleic bases are most likely to be the precursors of RNA molecules in chemical evolution. This hypothesis is supported by new data on their stability.     

Luminescence of stable stacking aggregates of adenine and uracil in water

Luminescence and excitation spectra of the highly luminescent stacking dimers of adenine and uracil in water solutions are studied. By the luminescence excitation spectra, it is shown that the stacking aggregates of adenine and uracil are formed with participation of rare forms of monomers: adenine N7H tautomers, and uracil in uncommon hydration states, e.g. lacking H-bonds with water. The temperature dependence of luminescence intensity of monomers and stacking dimers of uracil shows that stacking dimers do not dissociate even at 85°C, just as described earlier for adenine and adenosine. Stable stacking aggregates of nucleic bases are the likely precursors of RNA molecules in chemical evolution. This hypothesis is supported by new data on their heat stability.     

Topography of the interaction of recA protein with single-stranded deoxyoligonucleotides

recA protein, in the presence of adenosine 5'-(gamma-thio)triphosphate, formed stable complexes with single-stranded deoxyoligonucleotides between 9 and 20 residues in length but not with those 8-residues long. The binding of recA protein to a 15-mer and 20-mer completely protected the sugar-phosphate backbone of the nucleic acid from digestion by pancreatic deoxyribonuclease I and protected the 5'-terminal phosphate from cleavage by calf intestinal alkaline phosphatase. Ethylation of the phosphate backbone at any position by ethylnitrosourea blocked the binding of recA protein to the 15-mer but not to the 20-mer. Ethylation of phosphates near the ends of the 15-mer interfered less, suggesting a minimum binding site requirement. In contrast to the protection of the nucleic acid backbone, recA protein did not protect the N-7 position of guanine or the N-3 position of adenine from methylation by dimethyl sulfate, but rather enhanced the methylation of guanine. These results indicate that recA protein binds primarily to the phosphate backbone of single-stranded DNA, leaving the bases free for homologous pairing. We present a model for the organization of the presynaptic filament.     

Effect of long-term phosphate starvation on the levels and metabolism of purine nucleotides in suspension-cultured Catharanthus roseus cells

The effect of long-term phosphate (Pi) starvation of up to 3 weeks on the levels of purine nucleotides and related compounds was examined using suspension-cultured Catharanthus roseus cells. Levels of adenine and guanine nucleotides, especially ATP and GTP, were markedly reduced during Pi-starvation. There was an increase in the activity of RNase, DNase, 5'- and 3'-nucleotidases and acid phosphatase, which may participate in the hydrolysis of nucleic acids and nucleotides. Accumulation of adenosine, adenine, guanosine and guanine was observed during the long-term Pi starvation. Long-term Pi starvation markedly depressed the flux of transport of exogenously supplied [8-(14)C]adenosine and [8-(14)C]adenine, but these labelled compounds which were taken up by the cells were readily converted to adenine nucleotides even in Pi-starved cells, in which RNA synthesis from these precursors was significantly reduced. The activities of adenosine kinase, adenine phosphoribosyltransferase and adenosine nucleosidase were maintained at a high level in long-term Pi starved cells.     

SPONTANEOUS AND INDUCED CHROMOSOME BREAKAGE IN CLAYTONIA VIRGINICA

Meiocytes in three morphologically similar but cytologically different wild populations of Claytonia virginica L. were examined. Over a three-year period levels of spontaneous chromosome breakage were consistent for each population but differed between populations. Random samples of inflorescences from two of the populations were treated with 0.005 % aqueous solutions of nucleic acid precursors: adenine, adenosine, thymine, thymidine, guanosine 5'-monophosphate (GMP), and cytosine 5'-monophosphate (CMP). Statistically significant increases in chromosome breakage were observed in the population with little background breakage when inflorescences were treated with adenosine, thymine, thymidine, GMP, and CMP. In the population with moderate spontaneous breakage, a significant increase was observed only in plants treated with adenosine. Breakage induced with nucleic acid precursors was similar to that which occurred spontaneously; the predominant aberration was the single bridge.     

Adenine nucleotide metabolism in isolated chicken hepatocytes.

The turnover of the adenine nucleotide pool, the pathway of the degradation of AMP and the occurrence of recycling of adenosine were investigated in isolated chicken hepatocytes, in which the adenylates had been labelled by prior incubation with [14C]adenine. Under physiological conditions, 85% of the IMP synthesized by the 'de novo' pathway (approx. 37 nmol/min per g of cells) was catabolized directly via inosine into uric acid, and 14% was converted into adenine nucleotides. The latter were found to turn over at the rate of approx. 5 nmol/min per g of tissue. Inhibition of adenosine deaminase by 1 microM-coformycin had no effect on the formation of labelled uric acid, indicating that the initial degradation of AMP proceeds by way of deamination rather than dephosphorylation. Inhibition of adenosine kinase by 100 microM-5-iodotubercidin resulted in a loss of labelled ATP, demonstrating that adenosine is normally formed from AMP but is recycled. Unexpectedly, 5-iodotubercidin did not decrease the total concentration of ATP, indicating that the loss of adenylates caused by inhibition of adenosine kinase was nearly completely compensated by formation of AMP de novo. Anoxia induced a greatly increased catabolism of the adenine nucleotide pool, which proceeded in part by dephosphorylation of AMP. On reoxygenation, the formation of AMP de novo was increased 8-fold as compared with normoxic conditions. The latter results indicate the existence of adaptive mechanisms in chick liver allowing, when required, channelling of the metabolic flux through the 'de novo' pathway, away from the uricotelic catabolic route, into the synthesis of adenine nucleotides.     

Inhibition of Growth of Lactobacillus bulgaricus by Purine Deoxyribonucleotides.

Morris, George K. (University of Georgia, Athens), and William L. Williams. Inhibition of growth of Lactobacillus bulgaricus by purine deoxyribonucleotides. J. Bacteriol. 90:715-719. 1965.-An inhibition of growth of Lactobacillus bulgaricus GS was observed with deoxyadenylic acid and deoxyguanylic acid. Deoxynucleotides of cytosine, thymine, and uracil, and the deoxynucleosides of adenine, guanine, cytosine, and thymine were inactive as inhibitors. The inhibition was reversed by liver extract (a crude source of two unidentified growth factors for this organism). With suboptimal concentrations of liver extract, the inhibition was reversed by nucleotides of adenine, guanine, uracil, cytosine, and thymine. When the medium contained partially purified sources of the two growth factors rather than crude liver extract, fewer compounds reversed the inhibition. Adenylic acid and guanylic acid reversed the action of either inhibitor. Inosinic acid reversed inhibition caused by deoxyguanylic acid, but not that caused by deoxyadenylic acid. Thymidylic acid reversed inhibition caused by deoxyadenylic acid better than that caused by deoxyguanylic acid. Uridylic acid and cytidylic acid were no longer effective in reversing the inhibitions. This organism preferentially responded to monophosphorylated compounds as inhibitors and as reversers of inhibitions. Studies on the acid-soluble nucleotide pool revealed an accumulation of adenosine triphosphate, guanosine triphosphate, and an unidentified compound which resembled a nucleotide in its physical properties. These data cannot be explained by known metabolic pathways of nucleic acid biosynthesis. This organism responds differently from other related organisms to nucleic acid derivatives; therefore, it may be a new useful tool for studying nucleic acid metabolism and biosynthesis.     

Purine and pyrimidine metabolism in cultured white spruce (Picea glauca) cells: Metabolic fate of 14C-labeled precursors and activity of key enzymes

In order to examine the biosynthesis, interconversion, and degradation of purine and pyrimidine nucleotides in white spruce cells, radiolabeled adenine, adenosine, inosine, uracil, uridine, and orotic acid were supplied exogenously to the cells and the overall metabolism of these compounds was monitored. [8‐¹⁴C]adenine and [8‐¹⁴C]adenosine were metabolized to adenylates and part of the adenylates were converted to guanylates and incorporated into both adenine and guanine bases of nucleic acids. A small amount of [8‐¹⁴C]inosine was converted into nucleotides and incorporated into both adenine and guanine bases of nucleic acids. High adenosine kinase and adenine phosphoribosyltransferase activities in the extract suggested that adenosine and adenine were converted to AMP by these enzymes. No adenosine nucleosidase activity was detected. Inosine was apparently converted to AMP by inosine kinase and/or a non‐specific nucleoside phosphotransferase. The radioactivity of [8‐¹⁴C]adenosine, [8‐¹⁴C]adenine, and [8‐¹⁴C]inosine was also detected in ureide, especially allantoic acid, and CO₂. Among these 3 precursors, the radioactivity from [8‐¹⁴C]inosine was predominantly incorporated into CO₂. These results suggest the operation of a conventional degradation pathway. Both [2‐¹⁴C]uracil and [2‐¹⁴C]uridine were converted to uridine nucleotides and incorporated into uracil and cytosine bases of nucleic acids. The salvage enzymes, uridine kinase and uracil phosphoribosyltransferase, were detected in white spruce extracts. [6‐¹⁴C]orotic acid, an intermediate of the de novo pyrimidine biosynthesis, was efficiently converted into uridine nucleotides and also incorporated into uracil and cytosine bases of nucleic acids. High activity of orotate phosphoribosyltransferase was observed in the extracts. A large proportion of radioactivity from [2‐¹⁴C]uracil was recovered as CO₂ and β‐ureidopropionate. Thus, a reductive pathway of uracil degradation is functional in these cells. Therefore, white spruce cells in culture demonstrate both the de novo and salvage pathways of purine and pyrimidine metabolism, as well as some degradation of the substrates into CO₂.     

Purine metabolism in Saccharomyces cerevisiae.

The synthesis, interconversion, and catabolism of purine bases, ribonucleosides, and ribonucleotides in wild-type Saccharomyces cerevisiae were studied by measuring the conversion of radioactive adenine, hypoxanthine, guanine, and glycine into acid-soluble purine bases, ribonucleosides, and ribonucleotides, and into nucleic acid adenine and guanine. The pathway(s) by which adenine is converted to inosinate is (are) uncertain. Guanine is extensively deaminated to xanthine. In addition, some guanine is converted to inosinate and adenine nucleotides. Inosinate formed either from hypoxanthine or de novo is readily converted to adenine and guanine nucleotides.     

Dependence of Diaminopurine Utilization on the Mutational Site of Purine Auxotrophy in Bacillus subtilis II. Tracer Experiments

Tracer experiments were carried out in an attempt to explain why guanineless auxotrophs can use diaminopurine as a guanine replacement but nonexacting purine auxotrophs cannot do so. Cell suspensions of the nonexacting purineless Bacillus subtilis MB-1356 incorporated more radioactivity from diaminopurine-2-¹⁴C into nucleic acid than did guanineless B. subtilis MB-1517. The radioactivity in MB-1356 ribonucleic acid (RNA) was distributed in both adenine and guanine nucleotides, thus eliminating the possibility that the deamination of diaminopurine to guanine occurred predominantly on the level of nucleoside di- or triphosphates. Strain MB-1517 incorporated adenine-8-¹⁴C into nucleic acids extremely poorly. This correlated with results obtained with cell-free extracts; strain MB-1517 showed much less adenosine monophosphate (AMP) pyrophosphorylase activity than did MB-1356. Likewise, guanineless MB-1517 converted diaminopurine to its nucleotide much more slowly than did the nonexacting purine auxotroph. The results indicated that the lack of growth of nonexacting auxotrophs on diaminopurine alone is due not to an inability to convert the analogue to nucleic acid adenine but to the greater capacity of the nonexacting auxotrophs to convert diaminopurine to its 5′-ribonucleotide. Presumably, this compound, or a coenzyme analogue produced from it, inhibits growth of mutants which cannot make AMP de novo and only when the medium is devoid of adenine.     

The thermodynamic effects of exposing nucleic acid bases to water: solubility measurements in water and organic solvents

In order to examine the thermodynamic effects of exposing nucleic acid bases to water, we have measured the solubility of adenine, cytosine, and uracil in water and in organic solvents as a function of temperature. Transfer of a nucleic acid base from an organic environment into water is characterized by positive values for ΔH and for ΔS. We conclude from this result that the overall interaction between nucleic acid bases and water cannot be hydrophobic. If the effect we observe represents structure breaking in water by nucleic acid bases, this process would account for a major portion of the large, positive melting entropy of DNA, and would also contribute substantially to the melting enthalpy.     

Adenosine deaminase from Streptomyces coelicolor: recombinant expression, purification and characterization

The sequencing of the genome of Streptomyces coelicolor A3(2) identified seven putative adenine/adenosine deaminases and adenosine deaminase-like proteins, none of which have been biochemically characterized. This report describes recombinant expression, purification and characterization of SCO4901 which had been annotated in data bases as a putative adenosine deaminase. The purified putative adenosine deaminase gives a subunit Mr=48,400 on denaturing gel electrophoresis and an oligomer molecular weight of approximately 182,000 by comparative gel filtration. These values are consistent with the active enzyme being composed of four subunits with identical molecular weights. The turnover rate of adenosine is 11.5 s?1 at 30 °C. Since adenine is deaminated ～103 slower by the enzyme when compared to that of adenosine, these data strongly show that the purified enzyme is an adenosine deaminase (ADA) and not an adenine deaminase (ADE). Other adenine nucleosides/nucleotides, including 9-β-D-arabinofuranosyl-adenine (ara-A), 5'-AMP, 5'-ADP and 5'-ATP, are not substrates for the enzyme. Coformycin and 2'-deoxycoformycin are potent competitive inhibitors of the enzyme with inhibition constants of 0.25 and 3.4 nM, respectively. Amino acid sequence alignment of ScADA with ADAs from other organisms reveals that eight of the nine highly conserved catalytic site residues in other ADAs are also conserved in ScADA. The only non-conserved residue is Asn317, which replaces Asp296 in the murine enzyme. Based on these data, it is suggested here that ADA and ADE proteins are divergently related enzymes that have evolved from a common α/β barrel scaffold to catalyze the deamination of different substrates, using a similar catalytic mechanism.     

Stimulus- and cell-type-specific release of purines in cultured rat forebrain astrocytes and neurons

Adenosine is formed during conditions that deplete ATP, such as ischemia. Adenosine deaminase converts adenosine into inosine, and both adenosine and inosine can be beneficial for postischemic recovery. This study investigated adenosine and inosine release from astrocytes and neurons during chemical hypoxia or oxygen-glucose deprivation. In both cell types, 2-deoxyglucose was the most effective stimulus for depleting cellular ATP and for evoking inosine release; in contrast, oxygen-glucose deprivation evoked the greatest adenosine release. alpha,beta-Methylene ADP, an inhibitor of ecto-5'nucleotidase, significantly reduced adenosine release from astrocytes but not neurons. Dipyridamole, an inhibitor of equilibrative nucleoside transporters, inhibited both adenosine and inosine release from neurons. Erythro-9-(2-hydroxy-3-nonyl)adenine, an inhibitor of adenosine deaminase, reduced neuronal inosine release evoked by oxygen-glucose deprivation but not by 2-deoxyglucose treatment. These data indicate that (1). astrocytes release adenine nucleotides that are hydrolyzed extracellularly to adenosine, whereas neurons release adenosine per se, (2). inosine is formed intracellularly and released via nucleoside transporters, and (3). inosine is formed by an adenosine deaminase-dependent pathway during oxygen-glucose deprivation but not during 2-deoxyglucose treatment. In summary, the metabolic pathways for adenosine formation and release were cell-type dependent whereas the pathways for inosine formation were stimulus dependent.     

Purine reutilization in phytohemagglutinin-stimulated human T-lymphocytes.

Incubation of human peripheral blood T-lymphocytes with phytohemagglutinin (PHA) resulted in increased rates of metabolism of the purine bases adenine, hypoxanthine, and guanine. The respective rates decreased to unmeasurable levels in cells incubated without PHA. [¹⁴C]Adenine was converted predominantly into adenine nucleotides, with slight catabolism to hypoxanthine and very low conversion into guanine nucleotides. [¹⁴C]Guanine labeled predominantly the guanine nucleotide pool, but some adenine nucleotide formation also took place. From [¹⁴C]hypoxanthine, adenine nucleotides in the soluble pool were more heavily labeled than the guanine nucleotides, whereas in the nucleic acid fraction the latter contained more radioactivity. Adenosine at low concentrations was mainly phosphorylated to adenine nucleotides, but at higher concentrations this process leveled off, while deamination continued to increase linearly. PHA-stimulation resulted in an increased rate of adenosine metabolism but no qualitative differences in comparison to unstimulated cells were observed. Enzyme assays indicated that after PHA-stimulation the activities of adenine and hypoxanthine phosphoribosyltransferases, and those of adenosine deaminase and kinase, increased with a peak at 48 h, when expressed on a per cell basis, but not at all when expressed per mg of protein. We conclude that stimulation of human T-lymphocytes with PHA increases the capacity of the cells for purine nucleotide synthesis from all the directly re-utilizable catabolic products, namely the purine bases and adenosine.