Adenylyl-(5′, 2′)-adenosine 5′-Phosphate ((2′-5′) pA-A) in Crude Crystals of 5′-Adenylic Acid Isolated from Nuclease P1 (Penicillium Nuclease) Digest of Technical Grade Yeast RNA

Adenylyl (5′,2′)-adenosine 5′-phosphate ((2′-5′)pA-A) was detected in crude crystals of 5′-AMP prepared from Penicillium nuclease (nuclease P₁) digest of a technical grade yeast RNA. While (3′–5′)A-A was split by nuclease P₁, spleen phosphodiesterase, snake venom phosphodiesterase or alkali, (2′–5′)A-A was not split by a usual level of nuclease P₁ or spleen phosphodiesterase. Nuclease P₁ digests of 12 preparations of technical grade yeast RNA tested were confirmed to contain (2′–5′)pA-A. Its content was about 1 to 2% of the AMP component of each RNA preparation. As poly(A) was degraded completely by the Penicillium enzyme into 5′-AMP without formation of any appreciable amount of (2′–5′)pA-A, the technical grade RNA is supposed to contain 2–5′ phosphodiester linkages in addition to 3′–5′ major linkages.     

Purification of spermidine synthase from rat ventral prostate by affinity chromatography on immobilized S-adenosyl(5′)-3-thiopropylamine

A novel affinity chromatographic adsorbent was developed for purification of spermidine synthase from rat prostate. The adsorbent (S-adenosyl(5′)-3-thiopropylamine-Sepharose) possesses a ligand structurally similar to S-adenosyl(5′)-3-methylthiopropylamine (decarboxy AdoMet), a substrate of spermidine synthase. The S-adenosyl(5′)-3-thiopropylamine-Sepharose was prepared by an alkylation on sulfur of S-adenosyl-3-thiopropylamine by bromoacetamidohexyl-Sepharose under mild acidic conditions. The enzyme has been purified to homogeneity in 40% yield by using DEAE-cellulose, affinity chromatography employing S-adenosyl(5′)-3-thiopropylamine-Sepharose, and gel filtration. The enzyme had a molecular weight of approximately 73,000 and was composed of two subunits of equal size. The specificity of the reaction was rather strict, but cadaverine could replace putrescine as the aminopropyl acceptor, and the rate was 1/20th of the rate for spermidine formation. Apparent K_m values for putrescine and decarboxy AdoMet were 0.1 mm and 1.1 μm, respectively. Inhibition by decarboxy AdoMet and 5′-deoxy-5′-methylthioadenosine was observed. The inhibition by 5′-deoxy-5′-methylthioadenosine was partially noncompetitive with respect to decarboxy AdoMet.     

Probing mechanism of metal catalyzed hydrolysis of Thymidylyl (3′-O, 5′-S) thymidine phosphodiester derivatives

Hydrolysis of nucleic acids is of fundamental importance in biological sciences. Kinetic and theoretical studies on different substrates wherein the phosphodiester bond combined with alkyl or aryl groups and sugar moiety have been the focus of attention in recent literature. The present work focuses on understanding the mechanism and energetics of alkali metal (Li, Na, and K) catalyzed hydrolysis of phosphodiester bond in modeled substrates including Thymidylyl (3′-O, 5′-S) thymidine phosphodiester (Tp-ST) (1), 3′-Thymidylyl (1-trifluoroethyl) phosphodiester (Tp-OCH₂CF₃) (2), 3′-Thymidylyl (o-cholorophenyl) phosphodiester (Tp-OPh(o-Cl)) (3) and 3′-Thymidylyl(p-nitrophenyl) phosphodiester (Tp-OPh(p-NO₂)) (4) employing density functional theory. Theoretical calculations reveal that the reaction follows a single-step (A_ND_N) mechanism where nucleophile attack and leaving group departure take place simultaneously. Activation barrier for potassium catalyzed Tp-ST hydrolysis (12.0 kcal mol^?1) has been nearly twice as large compared to that for hydrolysis incorporating lithium or sodium. Effect of solvent (water) on activation energies has further been analyzed by adding a water molecule to each metal ion of the substrate. It has been shown that activation barrier of phosphodiester hydrolysis correlates well with basicity of leaving group.

Ribonuclease activities in bean roots

Vicia faba meristematic and elongating root cells (zones 0–4 and 10–20 mm) contained one nuclease (A₁) and four ribonucleases (A₂, A₃, C₁, C₂). When the overall activity of each enzyme was expressed per cell, the elongating cells contained 4-, 4-, 4-, 10- and 17-fold more activity than meristematic cells for A₁, C₁, C₂, A₂ and A₃, respectively.     

Occurrence and some properties of carbonic anhydrases from legume root nodules

Carbonic anhydrase activity (hydration of CO₂ was found in homogenates of leaves (116–500 units.mg^?1 protein) and root nodules (27–255 units.mg^?1 protein) from 8 legume genera inoculated in each case with a host specific Rhizobium. No enzyme, or only trace amounts (2–7 units.mg^?1 protein), were detected in root extracts, The enzymatic activity was inhibited in all cases by azide and acetazolamide. The sizes of nodule and leaf carbonic anhydrases, estimated by gel filtration of partially purified preparations from Phaseolus vulgaris, were around 45 000 and 205 000 respectively. These enzymes also differed in sensitivity to inhibitors. More than 99% of the activity present in Vicia faba nodules was recovered as a soluble enzyme and only a trace was located in the isolated bacteroids.     

Complex of cis-(NH3)2PtCl2 with guanylyl(3′-5′)-cytidine

The predominant complex formed by the reaction of cis-(NH₃)₂PtCl₂ and guanylyl(3′-5′)cytidine has been isolated. The molar ratio of the binding of cis-(NH₃)₂PtCl₂ to guanylyl(3′-5′)-cytidine is 1:2. The values of proton dissociation constant due to guanine and cytosine bases provide useful information for determining the binding site of the isolated complex. In addition, nmr and ir spectral data were used to determine the binding site. cis-(NH₃)₂PtCl₂ coordinates to guanylyl(3′-5′)cytidine through N(7) position of the guanine base, but cytosine base does not participate in the binding to cis-(NH₃)₂Pt²⁺. Interbase crosslink has not been detected. The binding specificity of cis-(NH₃)₂PtCl₂ to guanine base is discussed.     

Amino acid substrate specificity of asparaginyl-,aspartyl- and glutaminyl-tRNA synthetase isolated from higher plants

AspNH₂-, Asp- and GluNH₂-tRNA synthetases were purified from Phaseolus aureus; their optimum assay conditions, substrate specificities and salt sensitivities were investigated. AspNH₂-tRNA synthetase from β-cyanoalanine-producing (Vicia sativa), and non-producing (P. aureus and V. faba) species was able to utilize the analogue as a substrate irrespective of the source of the enzyme. Asp-tRNA synthetase from P. aureus was able to utilize α-aminomalonate and threo-β-hydroxy Asp as a substrate. The transfer of ¹⁴C-GluNH₂ to tRNA, catalyzed by GluNH₂-tRNA synthetase, was only inhibited by high concentrations of those analogues tested; albizziine was the most efficient, but no difference could be demonstrated between the substrate specificities of the enzyme isolated from an albizziine-producer (A. julibrissin and a non-producer (P. aureus) species.     

Purification and properties of bacteriophage T4-induced RNA ligase

RNA ligase has been extensively purified by a new procedure in high yield from T4-infected Escherichia coli. The enzyme consists of a single polypeptide chain of molecular weight 47,000. It catalyzes the formation of a phosphodiester bond between a 5′-PO₄-terminated oligonucleotide and a 3′-OH terminated oligonucleotide. The purified enzyme catalyzes both the intramolecular formation of single-stranded circles with longer oligonucleotides of the type pAp(Ap)_nA_?OH, where n is about 15 or greater and the intermolecular joining of pAp(Ap)₃A_OH (where the 5′-PO₄-terminated oligonucleotide is short enough to prevent apposition of its 3′ and 5′ ends) to UpUpU_OH when high concentrations of the 3′-OH-terminated acceptor oligonucleotide are present. Preparations of RNA ligase at all stages of purification show an unusual dependence of specific activity of the enzyme on the concentration of enzyme present in the assay. However, when care is taken to determine meaningful specific activities at each step, the ligase is found to be very stable during chromatography on various ion-exchange columns and may be purified by conventional techniques.     

6-Azauridine, a nucleoside with unusual ribose conformation. The molecular and crystal structure

The cytostatic analogue ribo-6-azauridine crystallizes in the orthorhombic space group P2₁2₁2₁ with eight molecules per unit cell of dimensions $\text{a = 20.230, b = 7.709, c = 12.863}\text{A}\text{?}$. A trial structure was obtained by direct methods. Least-squares refinement of co-ordinates and anisotropic thermal parameters based on 1998 reflections measured on a four-circle diffractometer led to a discrepancy index R = 4.0%. Like uridine, 6-azauridine has the anti conformation about the glycosidic bond and a C(3′)-endo sugar pucker. Unlike uridine, it exhibits a close approach of N(6) to C(2′) at only 2.814 and 2.844 Å in the two independent molecules, and a C(5′)(5′) bond that is gauche to C(4′)O(1′) but trans to C(4′)C(3′); this conformation about a C(4′)C(5′) bond has never been observed before for C(3′)-endo puckered riboses in the crystalline state. The crystal structure displays a pseudo-A face centering and very similar conformational parameters for the two independent molecules. Every OH and NH group in the structure serves as a proton donor in a hydrogen bond, including an unusual N(3)—H(3) … O(1′) link. Molecular orbital calculations by the extended Hückel method indicate that from uridine to 6-azauridine the net charge changes sign at ring positions 5 and 6 and disappears at 1.     

Polyphenol Oxidation by Vicia faba Chloroplast Membranes: STUDIES ON THE LATENT MEMBRANE-BOUND POLYPHENOL OXIDASE AND ON THE MECHANISM OF PHOTOCHEMICAL POLYPHENOL OXIDATION

The mechanism whereby light effects polyphenol oxidation was examined with Vicia faba chloroplast membranes known to contain a bound latent polyphenol oxidase. Results obtained with the inhibitors 3-(3′,4′-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-idopropyl-p-benzoquinone (DBMIB) indicated an involvement of the non-cyclic electron transport pathway in the light-dependent oxidation of polyphenols, such as dihydroxyphenylalanine (DOPA). Further evidence was provided by experiments in which (a) DOPA replaced H₂O as electron donor for the photoreduction of NADP, (b) NADP replaced O₂ as electron acceptor in the photochemical oxidation of DOPA, and (c) the variable fluorescence associated with photosystem II was increased by DOPA. The photochemical oxidation of DOPA by V. faba chloroplast membranes was insensitive to KCN and to antibodies against purified latent polyphenol oxidase. The results are consistent with the conclusion that the light-dependent oxidation of polyphenols by V. faba chloroplast membranes is achieved independently of the latent membrane-bound polyphenol oxidase. Electrons derived from polyphenols seem to enter the noncyclic electron transport chain on the oxidizing side of photosystem II and to react with O₂ at an unidentified site on the photosystem I side of the DCMU/DBMIB blocks.     

Isoenzymes of lactate dehydrogenase in the root growth zones ofVicia faba L.

The present studies of the LDH isoenzymes have been made as a part of our studies on the respiration systems of the roots ofVicia faba. All the root zones had 5 LDH isoenzymes and 2 antibands, but there were differences in their relative quantity. Cathodic isoenzymes (LDH₅, LDH₄) prevailed in the meristematic zone, whereas the anodic ones (LDH₁) prevailed in the others. The different enzyme activity in individual zones is probably connected with the transition of the anaerobic metabolism in the meristem to the aerobic one in the differentiating parts of the root.     

Nuclear magnetic resonance study of the impact of ribose 2′-O-methylation on the aqueous solution conformation of cytidylyl-(3′ → 5′)-cytidine

In order to obtain information about the conformational characteristics at the nearestneighbor level in the 2′-O-methylated region of t-RNA, as well as in the bizarre 5′-terminus of eucaryotic mRNA, a detailed nuclear magnetic resonance study of 2′-O-methyl-cytidylyl-(3′ → 5′)-cytidine (CmpC) was conducted. Proton spectra were recorded at 270 MHz in the Fourier mode in D₂O solutions, 0.01M, pD 7.3 in the temperature range 5–80°C. Complete accurate sets of nmr parameters were derived for each of the nucleotidyl units by a combination of homo-nuclear decouplings and simulation iteration methods. The data were translated into conformational parameters using procedures developed in earlier studies from these laboratories. It is shown that the ribofuranose ring exists at a ²E ? ³E equilibrium with clear preference [(75–80)%] for the ³E mode. The C(4′)-C(5′) and C(5′)-O(5′) bonds form a stable conformational network with outspoken preference for conformers in which Ψ₁, Ψ₂ ? 60° and ?₂ ? 180°. The orientation of the 3′-phosphate and 2′-O-methyl groups is such that ?₁′ ? 210° and ?″ ? 60°. The phosphodiester bonds are flexible and shift trends for base, H(1′), and H(5″) suggest the existence of a conformational blend of right-handed stack (g^?g^?), left-handed stack (g⁺g⁺), and unstacked arrays (tg^? and tg⁺). Elevation of temperature perturbs the ²E ? ³E equilibrium accompanied with modest depopulation of ψ₁, ψ₂ ? 60° and ?₂ ? 180° conformers. The major effect of elevation of temperature is in the increase of unstacked arrays at the expense of g^?g^? and g⁺g⁺ conformers. The shift trend of Cmp-H(3′) with temperature shows that torsional variation about O(3′)-P is facilitated by increase in temperature and the preferred rotamer about O(3′)-P in the unstacked form is t (ω₁′ = 180°). A detailed comparison of the aqueous solution conformations of CpC and CmpC reveals that 2′-O-methylation causes: (i) a reduction in the magnitude of _χ1; (ii) an increase in the population of ³E pucker at the 3′-nucleotidyl unit; and (iii) modest perturbations in the O(3′)-P and P-O(5′) bond conformations. Comparison of the aqueous solution conformations of AmpA and CmpC makes clear that the conformational properties of pyrimidine-pyrimidine and purine-purine dimers which carry a 2′-O-methylated 3′-nucleotidyl unit are significantly different.     

紫茎泽兰叶片水浸液对蚕豆的化感效应

外来入侵植物可以通过淋溶、自然挥发、根系分泌和植株凋落物分解等途径向周围环境释放化感物质,抑制伴生植物的生长、发育。该研究以不同浓度紫茎泽兰(Eupatorium adenophorum)叶片水浸液处理蚕豆(Vicia faba)种子,研究紫茎泽兰叶片水浸液对蚕豆根尖细胞微核、染色体畸变、细胞凋亡、蚕豆幼苗叶片叶绿素和N含量、光合生理特性、生物量的影响。结果表明:(1)紫茎泽兰叶片水浸液处理显著抑制蚕豆根尖的伸长和细胞的有丝分裂,并诱导蚕豆根尖细胞染色体畸变和细胞微核的产生,有丝分裂指数随着叶片水浸液浓度增加而减小,根尖细胞微核率随叶片水浸液浓度增加而增大,高浓度叶片水浸液处理对蚕豆根尖细胞的凋亡及坏死有明显影响。(2)紫茎泽兰叶片水浸液处理引起蚕豆幼苗叶片的叶绿素和N含量显著降低,并导致蚕豆幼苗最大净光合速率和生物量的显著下降。总之,紫茎泽兰叶片水浸液可能引起蚕豆根尖的氧化损伤和抑制根尖的伸长,且叶片水浸液的抑制作用呈现一定的剂量效应。紫茎泽兰叶片水浸液对蚕豆根尖的损伤和抑制作用可能影响了植株对氮素的吸收,进而对蚕豆幼苗光合生理表现以及生物量积累产生显著负面效应。     

Activity of myrosinase from Sinapis alba seeds immobilized into Ca-polygalacturonate as a simplified model of soil-root interface mucigel

Ca-polygalacturonate is a demethoxylated component of pectins which are constitutive of plant root mucigel. In order to define the role of root mucigel in myrosinase immobilization and activity at root level, a myrosinase enzyme which had been isolated from Sinapis alba seeds was immobilized into Ca-polygalacturonate. The activity profile for the immobilized and free enzyme was evaluated using the pH-Stat method as a function of time, temperature, and pH. The Michaelis-Menten kinetic parameters change between the immobilized (V _max ?=?127?±?13 U mg^?1 protein; K _M ?=?6.28?±?0.09?mM) and free (V _max ?=?17?±?1 U mg^?1 protein; K _M ?=?0.96?±?0.01?mM) forms of myrosinase, probably due to conformational changes involving the active site as a consequence of enzyme immobilization. Immobilized enzyme activity evaluated as a function of different substrates gave the highest value with nasturtin, the glucosinolate that is typical of several brassicaceae plant roots containing the glucosinolate-myrosinase defensive system. No feedback regulation mechanism was found in the presence of an excess of enzymatic reaction products (i.e. allyl isothiocyanate or sulphate). The high enzyme immobilization yield into Ca-polygalacturonate and its activity preservation under different conditions suggest that the enzyme released by plants at root level could be entrapped in root mucigel in order to preserve its activity.     

A novel ferromagnetic coupling one-dimensional complex {Cu(II)(NIT3Py)2[N(CN)2]2(H2O)2}

The novel ferromagnetic coupling one-dimensional complex {Cu(NIT3Py)₂[N(CN)₂]₂(H₂O)₂} (NIT3Py=2-(3^′-pyridyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide) was synthesized and characterized structurally and magnetically. It crystallizes in the monoclinic space group C2/c. The Cu(II) ion is in a distorted octahedral environment. The units of {Cu(NIT3Py)₂[N(CN)₂]₂(H₂O)₂} were connected as one-dimensional structure by the intermolecular hydrogen bonds. Magnetic measurements show that there are intramolecular ferromagnetic interactions and intermolecular antiferromagnetic interactions within the chain.     

Fabacyl acetate, a germination stimulant for root parasitic plants from Pisum sativum

A germination stimulant, fabacyl acetate, was purified from root exudates of pea (Pisum sativum L.) and its structure was determined as ent-2′-epi-4a,8a-epoxyorobanchyl acetate [(3aR,4R,4aR,8bS,E)-4a,8a-epoxy-8,8-dimethyl-3-(((R)-4-methyl-5-oxo-2,5-dihydrofuran-2-yloxy)methylene)-2-oxo-3,3a,4,5,6,7,8,8b-decahydro-2H-indeno[1,2-b]furan-4-yl acetate], by 1D and 2D NMR spectroscopic, ESI- and EI-MS spectrometric, X-ray crystallographic analyses, and by comparing the ¹H NMR spectroscopic data and relative retention times (RR_t) in LC-MS and GC-MS with those of synthetic standards prepared from (+)-orobanchol and (+)-2′-epiorobanchol. The ¹H NMR spectroscopic data and RR_t of fabacyl acetate were identical with those of an isomer prepared from (+)-2′-epiorobanchol except for the opposite sign in CD spectra. This is the first natural ent-strigolactone containing an epoxide group. Fabacyl acetate was previously detected in root exudates of other Fabaceae plants including faba bean (Vicia faba L.) and alfalfa (Medicago sativa L.).     

Heterozygosity for phosphodiester glycosidase deficiency: a novel human mutation of lysosomal enzyme processing

Summary We have carried out studies on the fibroblasts of III-3, a clinically normal Lebanese individual previously reported to have abnormally high plasma lysosomal enzyme levels. Mannose-6-phosphate (man-6-P) receptors in III-3 fibroblasts were found to be functioning normally, but the cells had only half normal levels of phosphodiester glycosidase activity. Pinocytosis of III-3 fibroblast secreted -hexosaminidase B (hex B) into Sandhoff disease fibroblasts was 18% of control, and the apparent K_D for binding of III-3 hex B to man-6-P receptors was 3.7x10^-9 M compared to 1.25x10^-9 M for control enzyme. Hex B secreted by III-3 fibroblasts included an enzyme pool less electro-negative than controi enzyme which had a very low affinity for man-6-P receptors and which did not bind to DEAE-Sephadex. Treatment of this abnormal hex B with exogenous placental phosphodiester glycosidase increased its binding to man-6-P receptors three-fold. Secretion rates of seven lysosomal enzymes from III-3 fibroblasts were, on average, twice as great as rates measured for two I-cell disease heterozygote fibroblast lines. The results suggest that III-3 fibroblasts are heterozygous for phosphodiester glycosidase deficiency. The possibility that an individual homozygous for this enzyme deficiency would develop I-cell disease is discussed.     

Discrimination of three Scrophularia plants utilizing ‘Scrophularia Radix’ by DNA markers based on internal transcribed spacer (ITS) sequences

One of the medicinal materials produced by plants belonging to the genus Scrophularia, ‘Scrophularia Radix’ (SR), has been prescribed for many centuries to treat diseases such as inflammation, abscesses of carbuncles and constipation. In China, the dried root of S. ningoensis Hemsley is the source of SR. In contrast, the root of S. buergeriana is generally prescribed as SR in Korea. Studies conducted to identify the bioactive compounds in these two Scrophularia plants have revealed marked differences in the contents and concentration of the compounds they contain. However, S. ningpoensis has been indiscriminately prescribed in Korea along with S. buergeriana as SR. Furthermore, S. koraiensis has long been used in lieu of S. buergeriana as SR in Korea. Therefore, a standard or method to reliably distinguish these three species of Scrophularia is needed. Recently, we found that the differences in the nucleotide sequences of the internal transcribed spacer (ITS) of Scrophularia plants could be applied to develop DNA markers to discriminate each plant. In this study, ITS sequences of 22 samples including three types of Scrophularia plants were amplified, determined and analyzed. Based on the results of these analyses, we designed the following primer sets: Ni F (5′-TTAACCATATAGGGGCCTCG-3′) / Ni R (5′-C CCCTCTCTGTATCCCAA-3′) to amplify a 379 bp DNA marker for the identification of S. ningpoensis; Bu F (5′-TTAACC ATATCGGGGCCAAG-3′) / Bu R (5′-ATCACGACAGCAC GCGA-3′) to amplify a 491 bp DNA marker for S. buergeriana; and Ko F (5′-ATAACCATATCGGGGCCTC-3′) / Ko R (5′-TCAAGAAACGCACTATCCC-3′) to amplify a 167 bp DNA marker of S. koraiensis. Using these primer sets, we were able to efficiently identify Scrophularia plants sold as SR in the herbal market in dried and sliced states after processing as medicinal materials.     

Synthesis and in vitro activities of new anticancer duplex drugs linking 2′-deoxy-5-fluorouridine (5-FdU) with 3′-C-ethynylcytidine (ECyd) via a phosphodiester bonding

Two isomeric cytostatic duplex drugs 2′-deoxy-5-fluorouridylyl-(3′→5′)-3′-C-ethynylcytidine [5-FdU(3′→5′)ECyd] and 2′-deoxy-5-fluorouridylyl-(5′→5′)-3′-C-ethynylcytidine [5-FdU(5′→5′)ECyd] were designed and synthesized at gram scale according to the hydrogenphosphonate method in an overall yield of about 40%. The in vitro evaluation of the anticancer effects indicated highly varying sensibilities of the panel of 60 tested tumor cell lines against the duplex drugs. 5-FdU(3′→5′)ECyd had a 50% growth inhibition (IC₅₀ ? 10^?8 M) in 44/58 cell lines. However, only 25/53 of those cell lines showed corresponding IC₅₀ values when the isomeric 5-FdU(5′→5′)ECyd was tested. Total growth inhibition was achieved using micromolar concentrations of the duplex drugs. The 5-FdU residue of the duplex drug can cause very different effects like additive, synergistic, antagonistic as well as sequence-depending activities, which drastically changed efficiency as well as specificity of the anticancer activities of the duplex drugs, in comparison to those of the monomeric drugs.     

Glucofructosan metabolism in Cichorium intybus roots

A 10-fold purification of sucrose sucrose fructosyl transferase from Cichorium intybus roots was achieved by ammonium sulphate fractionation and DEAE-cellulose column chromatography. The energy of activation for this enzyme was ca 48 kJ/mol sucrose. Sucrose sucrose fructosyl transferase and invertase were prominent during early months of growth. Evidence obtained from: (1) the changes in carbohydrate composition at monthly intervals; (2) comparative studies on fructosyl transferase and invertase at different stages of root growth; and (3) incubation studies with [¹⁴C]glucose, [¹⁴C]fructose and [¹⁴C]sucrose revealed that, during the later stages of root growth, fructosan hydrolase is responsible for fructosan hydrolysis. No evidence for the direct transfer of fructose from sucrose to high M_r glucofructosans was obtained.