Ribonucleoside 3'-di- and -triphosphates. Synthesis of guanosine tetraphosphate (ppGpp).

A procedure has been outlined for the synthesis of ribonucleoside 3'-di- and -triphosphates. The synthetic scheme involves the conversion of a ribonucleoside 3'-monophosphate to its 2'-(5'-di)-O-(1-methoxyethyl) derivative, followed by successive treatments of the blocked ribonucleotide with 1,1'-carbonyldiimidazole and mono(tri-n-butylammonium) phosphate or pyrophosphate. The resulting ribonucleoside 3'-di- and -triphosphate derivatives are then deblocked by treatment with dilute aqueous acetic acid, pH 3.0. The use of this procedure is illustrated for adenosine 3'-monophosphate, which has been converted to its corresponding 3'-di- and -triphosphates in 61% overall yield. The decomposition of adenosine 3'-di- and -triphosphates to adenosine 2'-monophosphate, adenosine 3'-monophosphate, and adenosine cyclic 2',3'-monophosphate as a function of pH at 100 degrees has been studied as has the attempted polymerization of adenosine 3'-diphosphate with polynucleotide phosphorylase. Also prepared was guanosine 5'-diphosphate 3'-diphosphate (guanosine tetraphosphate; ppGpp), which was accessible via treatment of 2'-O-(1-methoxyethyl)guanosine 5'-monophosphate 3'-monophosphate with the phosphorimidazolidate of mono(tri-n-butyl ammonium) phosphate. The resulting blocked tetraphosphate was deblocked in dilute aqueous acetic acid to afford ppGpp in an overall yield of 18%.     

Oxidation of thymidylate synthase by inorganic compounds

Thymidylate synthase from methotrexate-resistant Lactobacillus casei was rapidly and completely inactivated by low concentrations of permanganate, periodate, or potassium triiodide at 0 degree C. The enzyme was not inactivated to any appreciable extent by iodate, iodide, ferricyanate, iodosobenzoate, or hydrogen peroxide. The inactivation by permanganate was retarded by the substrate 2'-deoxyuridylate and, to a lesser extent, by phosphate. Titration of enzyme activity with permanganate showed that two moles of permanganate were required to completely inactivate one mole of thymidylate synthase.     

A configurational interpretation of the axial phosphate spacing in polynucleotide helices and random coils

The structural implications arising from the observation (set forth in the preceding paper) that the charge density of a single-stranded randomly coiling polynucleotide chain is approximately equal to that of one strand of the familiar double helix are here examined. A computational scheme is described to obtain (using bond lengths, valence bond angles, and internal rotation angles) the mean phosphate–phosphate spacing parameter b along the chain axes of any single-stranded polynucleotide molecule. Attention is then focused upon the computed interphosphate spacing associated with both the theoretical randomly coiling polynucleotide that reproduces the observed experimental unperturbed dimensions and the familiar single-stranded helix. The calculations clearly demonstrate that the parameter b only weakly reflects the spatial configuration of the chain. The approximate equivalence of the b values associated with the single-stranded helix and the unperturbed randomly coiling polynucleotide is not indicative of strong configurational similarities between the two forms. The familiar helix is composed of a sequence of identically conformed compact structural residues while the random coil is characterized by a variety of chain-repeating residues of which a large proportion are extended units.     

A spectrophotometric study of the secondary structure of ribonucleic acid based on a method for diminishing single-stranded base-`stacking'' without affecting multihelical structures

1. On the basis of studies with model compounds it was concluded that in 8m-urea-m-potassium chloride (or 4m-guanidinium chloride) in 0.01m-potassium phosphate buffer, pH7.0, multi-helical structures have about the same stability as in 0.1m-potassium phosphate buffer, pH7.0, whereas the tendency of base residues to ;stack' along a single polynucleotide chain is much decreased. 2. Base-pairing was eliminated whereas base-;stacking' persisted after RNA in 1% formaldehyde-0.1m-potassium phosphate buffer, pH7.0, was heated to 95 degrees . 3. From a study of the thermal denaturation of unfractionated transfer RNA from Escherichia coli and of RNA from the fractionated sub-units of rabbit reticulocyte ribosomes in 8m-urea-m-potassium chloride (or 4m-guanidinium chloride) in 0.01m-potassium phosphate buffer, pH7.0, it was inferred that ;stacked' residues may account for up to 25% of the increase in E(260) found on heating RNA in solvents such as 0.1m-potassium phosphate buffer, pH7.0. 4. Changes in the spectrum with temperature were analysed on the basis of the assumptions that (a) the polynucleotide chain is amorphous on denaturation (which is probable in 8m-urea-m-potassium chloride-0.01m-potassium phosphate buffer, pH7.0) and that (b) the polynucleotide chain adopts a single-stranded ;stacked' conformation on denaturation (which is probable when ordinary solvents such as 0.1m-potassium phosphate buffer, pH7.0, are used).     

Biopterin

An enzyme that catalyzes the conversion of 2-amino-6-(5'-triphosphoribosyl)amino-5- or 6-formamido-6-hydroxypyrimidine, but not of guanosine triphosphate, to quinonoid 6-(D-erythro-1'-2'-3'-trihydroxypropyl)dihydropterin triphosphate and formic acid has been purified to homogeneity from some mammalian brain and liver. The enzyme of a single strand is a basic protein of 9177 daltons consisting of 68 amino acid residues--except the enzyme from rat brain, which has one additional aspartic acid as residue 7. The enzyme possesses three free SH groups and, in its most active form, 1 mol of phosphate per mole of enzyme. Peptides isolated after hydrolysis with trypsin, chymotrypsin, or weak acid were separated by thin-layer chromatography and sequenced manually by Edman degradation. The complete sequence of the molecule was established as follows: (formula: see text)     

Calorimetric investigations of crystalline 3′,5′-cyclic nucleotides

Differential enthalpic analysis of a series of 3′,5′-cyclic nucleotides indicates that homolytic cleavage of the six-membered phosphate ring occurs either immediately prior to or concurrent with decomposition of the crystal lattice. Homolysis is followed by a rapid polymerization to yield oligonucleotides. The enthalpies of these reactions have, with the exception of guanosine 3′,5′-cyclic phosphate, almost identical values of 25 kcal/mole. The anomalous case is attributed to a more stabilized phosphate ring as a result of hydrogen bonding through the two position of the purine ring. The pair of overlapping exothermic peaks observed in each of the thermograms for cAMP and cIMP is related to the presence of two conformational arrangements within the unit cell of each compound.     

Guanosine 5′‐diphosphate 3′‐diphosphate (ppGpp) as a negative modulator of polynucleotide phosphorylase activity in a ‘rare’ actinomycete

With the beginning of the idiophase the highly phosphorylated guanylic nucleotides guanosine 5′‐diphosphate 3′‐diphosphate (ppGpp) and guanosine 5′‐triphosphate 3′‐diphosphate (pppGpp), collectively referred to as (p)ppGpp, activate stress survival adaptation programmes and trigger secondary metabolism in actinomycetes. The major target of (p)ppGpp is the RNA polymerase, where it binds altering the enzyme activity. In this study analysis of the polynucleotide phosphorylase (PNPase)‐encoding gene pnp mRNA, in Nonomuraea sp. ATCC 39727 wild‐type, constitutively stringent and relaxed strains, led us to hypothesize that in actinomycetes (p)ppGpp may modulate gene expression at the level of RNA decay also. This hypothesis was supported by: (i) in vitro evidence that ppGpp, at physiological levels, inhibited both polynucleotide polymerase and phosphorolytic activities of PNPase in Nonomuraea sp., but not in Escherichia coli, (ii) in vivo data showing that the pnp mRNA and the A40926 antibiotic cluster‐specific dpgA mRNA were stabilized during the idiophase in the wild‐type strain but not in a relaxed mutant and (iii) measurement of chemical decay of pulse‐labelled bulk mRNA. The results of biochemical tests suggest competitive inhibition of ppGpp with respect to nucleoside diphosphates in polynucleotide polymerase assays and mixed inhibition with respect to inorganic phosphate when the RNA phosphorolytic activity was determined.     

"Single Addition" substrates for the synthesis of specific oligoribonucleotides with polynucleotide phosphorylase. Synthesis of 2'-(alpha-methoxyethy) nucleoside 5'-diphosphates.

A number of synthetic methods for the preparation of the 2-O-(alpha-methoxyethyl) derivatives of the 5-diphosphates of adenosine, cytidine, guanosine, and uridine have been studied in order to provide nucleotide substrates that can be applied to the synthesis of specific oligoribonucleotides using polynucleotide phosphorylase. The reaction of nucleoside 5-diphosphates with methyl vinyl ether for a limited time produces low yields of the corresponding 2-O-(alpha-methoxyethyl) derivatives because the rate of methoxyethylation of the 3-hydroxyl groups. A study of the rates of acidic hydrolysis of alpha-methoxyethyl groups in the 2 and 3 positions of nucleosides and nucleotides has been made, and the results obtained form the basis of a more efficient method for the synthesis of the blocked nucleoside diphosphates. The method involves the reaction of nucleoside 5-diphosphates with methyl vinyl ether to give the corresponding 2,3-di-O-(alpha-methoxyethyl)nucleoside 5-diphosphates, and exploits the fact that, in the acidic hydrolysis of these derivatives, the rate of removal of the 3-methoxyethyl group is about twice that of the group in the 2 position. Alternative syntheses were based on the phosphorylation of methoxyethylated nucleosides and nucleotides. The derivatives, 2-O- and 2,3-di-O-(alpha-methoxyethyl)uridine, were prepared by the methoxyethylation of 3,5-di-O-acetyluridine and 5-O-acetyluridine followed by removal of the acetyl groups. The corresponding guanosine derivatives were made by the synthetic routes: (i) guanosine leads to O-2,O-3,O-5,N-2-tetrabenzoylguanosine leads to 2-N-benzoylguanosine leads to O3-acetyl-N-2,O5-dibenzoylguanosine leads to 2-O-(alpha-methoxyethyl)guanosine, and (ii) 2,3-O-isopropylideneguanosine leads to N-2,O5-diacetyl-2,3-O-isopropylideneguanosine leads to N-2,O-5-diacetylguanosine leads to 2,3-di-O-(alpha-methoxyethyl)guanosine. These methoxyethylated nucleosides were converted to the corresponding 5-phosphates by reaction with cyanoethyl phosphate and dicyclohexylcarbodiimide, and then to the corresponding 5-diphosphates by subsequent reaction with 1,1-carbonyldiimidazole and inorganic phosphate.     

Polynucleotide phosphorylase-based photometric assay for inorganic phosphate

Polynucleotide phosphorylase is a prokaryotic enzyme that catalyzes phosphorolysis of polynucleotides with release of nucleotide diphosphates. By taking advantage of this property, we developed a photometric assay for inorganic phosphate. In the presence of polyadenylic acid, phosphate is converted into adenosine 5'-diphosphate (ADP) by this enzyme. ADP then reacts with phosphoenolpyruvate in a pyruvate kinase-catalyzed reaction, thus giving rise to adenosine 5'-triphosphate and pyruvate. Finally, pyruvate oxidizes reduced nicotinamide adenine dinucleotide (NADH) through the action of L-lactate dehydrogenase, with concomitant decrease in absorbance at 340 nm. As expected, in this detection system 1 mol of NADH was oxidized per mole of phosphate. The assay showed an excellent reproducibility, as the standard deviations never exceeded 5%. It also was shown to be unaffected by several compounds that are regarded as major interferents of the traditional colorimetric assays. Absence of interference was also demonstrated when determining phosphate content in different biological samples, such as human serum and perchloric acid extracts from Escherichia coli, yeast, and bovine liver. An E. coli strain overexpressing His-tagged polynucleotide phosphorylase developed in our laboratories allowed quick and straightforward purification of enzyme, making the assay feasible and convenient. Since all other reagents required are inexpensive, the assay represents a cheaper alternative to commercially available phosphate assay kits.     

Scanning molecular sieve chromatography of interacting protein systems. IV. The difference profile method as applied to the Gibbs-Duhem expression in the analysis of the dimer-tetramer equilibria of oxyhemoglobin A

The recently-developed large zone difference profile method in scanning molecular sieve chromatography is applied to the analysis of the Gibbs-Duhem expression in the tetramer-dimer equilibrium of human oxyhemoglobin A. The preferential binding term and solvation parameters of the Hofmeister anion phosphate are examined. Results indicate that as the concentration of phosphate ions increase, a hydrated phosphate is formed which enhances the association by perturbing the solvation layer of the hemoglobin molecules. The standard free energy change at a given Hofmeister anion activity of InA(x) = -3.2476 is 9.4 +/- 0.2 kcal mole . DeltaG degrees at InA(x) = -1.2711 is 10.90 +/- 0.05 kcal mole , suggesting that approximately 11 kcal are required to dissociate one mole of tetramer into dimer.     

Scanning molecular sieve chromatography of interacting protein systems. IV. The difference profile method as applied to the Gibbs-Duhem expression in the analysis of the dimer-tetramer equilibria of oxyhemoglobin A.

The recently-developed large zone difference profile method in scanning molecular sieve chromatography is applied to the analysis of the Gibbs-Duhem expression in the tetramer-dimer equilibrium of human oxyhemoglobin A. The preferential binding term and solvation parameters of the Hofmeister anion phosphate are examined. Results indicate that as the concentration of phosphate ions increase, a hydrated phosphate is formed which enhances the association by perturbing the solvation layer of the hemoglobin molecules. The standard free energy change at a given Hofmeister anion activity of ln Ax = -3.2476 is 9.4 +/- 0.2 kcal/mole. delta G0 at ln Ax = -1.2711 is 10.90 +/- 0.05 kcal/mole, suggesting that approximately 11 kcal are required to dissociate one mole of tetramer into dimer.     

p-Aminobenzoate-p-aminobenzoate.

p-Aminobenzoate (PABA) synthase from Bacillus subtilis is an aggregate composed of two nonidentical subunits and has the following properties. (i) In crude extracts this enzyme catalyzes the formation of PABA in the presence of chorismate and either glutamine (amidotransferase) or ammonia (aminase). The amidotransferase activity is about 5- to 10-fold higher than the aminase activity and is stable for at least 1 week when frozen at -70 C. (II) Although no divalent cation requirement could be demonstrated with crude extracts, 2 mM ethylene-diaminetetraacetic acid completely inhibits both activities. (iii) After ammonium sulfate fractionation both the aminase and amidotransferase activities require Mg2+ and guanosine in addition to the substrates indicated above for optimal activity. The guanosine requirement can be replaced by guanosine 5'-monophosphate, guanosine 5'-diphosphate, and guanosine 5'-triphosphate but not by guanine, adenosine 5'-triphosphate, uridine 5'-triphosphate, cytidine 5'-triphosphate, thymidine 5'-triphosphate, inorganic phosphate, and phosphoribosylpyrophosphate. Furthermore, at a pH above 7.4 or below 6.4 activity is rapidly lost a 4 C, or -60 C. (IV) The enzyme is composed of two non-identical subunits, designated subunit A and subunit X. Subunit A has an estimated molecular weight of 31,000, whereas subunit X has an estimated molecular weight of 19,000. Subunit A has aminase activity but no amidotransferase activity; a mutation at the pabA locus results in the loss of PABA synthase activity. Subunit X, which is also a component of the anthranilate synthase complex, has no PABA synthase activity itself but complexes with subunit A to give an AX aggregate that can use glutamine as a substrate. (v) The molecular weight of the AX complex has been estimated at 50,000, suggesting a 1:1 ratio of subunits. (vi) The enzyme is readily associated and dissociated.     

cGAS-STING信号通路：免疫监视的重要机制

免疫系统识别病原微生物的主要机制之一是识别其核酸。环磷酸鸟苷-腺苷合成酶(cGAS)是一种胞质DNA感受器,感知病原DNA后激活cGAS-STING通路。该通路不仅介导天然免疫应答以抵抗多种含DNA的病原微生物感染,还能感知肿瘤来源的DNA而产生抗肿瘤免疫应答。然而,自体DNA对cGAS-STING通路的异常激活也会导致自身免疫性和炎症性疾病。本文综述了cGAS-STING信号通路及其在抗病毒天然免疫中的调控作用与功能,阐述了cGAS-STING通路在抗病毒感染和疾病中发挥的作用。     

Beta-cyanoalanine synthase: Its purification and basic physico-chemical properties]

A method has been developed for the purification of beta-cyano-L-alanine synthase from etiolated 10-day-old seedlings of blue lupine. High purity preparations of the enzyme were obtained with specific activity exceeding 4000-fold that of the seedling homogenate. Preparations were homogeneous on electrophoresis in polyacrylamide gel. The yield of total activity after purification was approximately 20%. Glutamic acid is the enzyme's only N-terminal amino acid; the molecular weight of the enzyme (both native and treated with 6 M urea) is 52000. The synthase containes one mole of pyridoxal-P per mole of protein; its isoelectric point is situated at pH 4,8. The enzyme's absorption spectrum has a maximum at 410 nm i.e., in the characteristic range of many pyridoxal-U-containing enzymes. Data on the amino acid composition of the enzyme are presented.     

Phosphorylation of rabbit skeletal muscle glycogen synthase by casein kinase 1: Evidence of phosphorylation sites specific for casein kinase 1

Casein kinase 1 phosphorylated rabbit skeletal muscle glycogen synthase at both seryl and threonyl residues. With glycogen synthase phosphorylated up to 7.5 mol phosphate/mol subunit, about 26% of the phosphate was present in the N-terminal cyanogen bromide fragment (CB1) and 74% in the C-terminal fragment (CB2). Both fragments contained phosphothreonine (11 to 14%) in addition to phosphoserine. When ³²P-labeled glycogen synthase was totally digested with trypsin and chromatographed on reversephase high-performance liquid chromatography, seven phosphopeptides were observed. Peptide I eluted in the vicinity of the peptide containing site 1a, peptide II coincided with sites 4 + 5, peptides III and IV eluted in the region corresponding to sites 3a + 3b + 3c, peptide V appeared slightly after the peptide containing site 1b and peptide VII behaved as the peptide containing site 2, whereas peptide VI did not coincide with any of the known phosphopeptides. Limited trypsinization prior to analysis by HPLC led to the disappearance of peaks V and VI without altering peaks I to IV and VII. Only peaks I and VII remained when limited chymotrypsinization was performed prior to HPLC analysis. Chromatography on HPLC of the fragments derived from complete trypsinization of CB2 showed the presence of peaks II to VI. Phosphoamino acid analysis of the different peptides demonstrated the presence of quantitative amounts of phosphothreonine in peptides V, VI, and VII. These results indicate that multiple phosphorylation sites for casein kinase 1 must exist in both the N-terminal and C-terminal regions of glycogen synthase, some of which would only be labeled by casein kinase 1.     

Neurotransmitter release regulated by nitric oxide in PC-12 cells and brain synaptosomes

BACKGROUND: Nitric oxide is a messenger molecule of the nervous system, which is produced by the enzyme nitric oxide synthase, which may regulate cyclic guanosine monophosphate levels and which has been implicated in the control of neurotransmitter release. PC-12 pheochromocytoma cells differentiate to form neuronal cells in culture when they are exposed to nerve growth factor. The levels of cyclic guanosine monophosphate in the cells and their ability to release acetylcholine in response to K(+)-depolarization are both maximal after eight days of treatment with nerve growth factor. We set out to assess a possible role for nitric oxide in the processes that occur in differentiating PC-12 cells. RESULTS: Nitric oxide synthase is first evident in differentiating PC-12 cells eight days after beginning treatment with nerve growth factor, coinciding with the marked increase in K(+)-depolarization-induced release of acetylcholine. The release of both acetylcholine and dopamine in response to K(+)-depolarization is blocked by inhibitors of nitric oxide synthase and by hemoglobin, which binds nitric oxide. Providing l-arginine, a precursor required for nitric oxide synthesis, reverses the effects of the inhibitors. In synaptosomal preparations from the corpus striatum, inhibitors of nitric oxide synthase prevent the release of glutamate in response to the glutamate derivative N-methyl-d-aspartate but not in response to K(+)-depolarization. CONCLUSION: Nitric oxide may mediate the release of acetylcholine and dopamine in response to K(+)-depolarization in PC-12 cells and the release of glutamate in response to N-methyl-d-aspartate in striatal synaptosomes. Nitric oxide synthase expression is induced after eight days of treating PC-12 cells with nerve growth factor, coinciding with a marked enhancement of the release of neurotransmitters in response to K(+)-depolarization.     

Some acyclic analogues of nucleotides and their template-directed reactions

Summary Bismonophosphoimidazolides of acyclic analogues of guanosine IV and adenosine V were synthesized. They undergo oligomerization in the presence of complementary polynucleotide templates. Details of their synthesis and their subsequent template-and nontemplate-directed reactions are described, and their possible relevance to the origin of life is discussed.     

Template-directed synthesis of acyclic oligonucleotide analogues

Bis-phosphoimidazolides of an analogue of adenosine (in which ribose is replaced by an acyclic chain) and of two related analogues of guanosine undergo oligomerization in the presence of complementary polynucleotide templates. Data on the template- and nontemplate-directed reactions are presented, and the possible relevance to origins of life is discussed.     

Role of sucrose phosphate synthase in sucrose biosynthesis in ripening bananas and its relationship to the respiratory climacteric

During ripening of bananas (Musa spp. [AAA group, Cavendish subgroup]), there is a massive conversion of starch to sucrose. Also during ripening there is a rise in respiration known as the respiratory climacteric. In this study changes in carbohydrate content, activities of starch and sucrose metabolizing enzymes, and respiration were measured to assess their potential interrelationships. Sucrose phosphate synthase activity increased dramatically during the first 4 days after initiation of ripening by ethylene treatment. Starch concentration decreased and sucrose concentration increased during this time period. Developmental changes in sucrose phosphate synthase activity were measured with limiting substrate (plus Pi) and saturating substrate concentrations. Activities were not parallel under the two assay conditions, providing tentative evidence that kinetically different forms of the enzyme may exist at different stages of ripening. Sucrose accumulation rate was most highly correlated with sucrose phosphate synthase activity assayed with limiting substrate concentrations (plus Pi). The cumulative amount of CO₂ respired during ripening was positively correlated with sugar accumulation (R² = 0.97). From this linear regression it was calculated that a constant 0.605 millimoles of CO₂ was evolved per mole of sucrose formed throughout ripening. Using this quantity, the percentage of the total respiratory ATP produced which was required for the conversion of starch to sucrose was calculated assuming different models for carbon export from the amyloplast. The results suggest that sucrose biosynthesis during ripening constitutes a significant sink for respiratory ATP.     

Increased binding of ethidium bromide to polynucleotide duplexes containing mismatched bases.

The binding of the intercalating dye ethidium bromide to a series of synthetic polynucleotide duplexes containing varying concentrations of mismatched bases has been measured by fluorescence titration. The dye binds more strongly to duplexes with mismatches, the estimated increase in affinity being twenty-fold for the series of molecules poly (I).poly (C,Ax) with x denoting the mole fraction of mismatched A residues in the C strand. The results are consistent with one requirement of the Streisinger model for frameshift mutagenesis, namely that frameshifting agents can function by stablizing mismatched transient intermediates in DNA.