6-(gamma,gamma-Dimethylallylamino)Purine As A Precursor of Zeatin

A 6-(γ,γ-dimethylallylamino) purine-like compound was found in the culture medium of Rhizopogon roseolus, which had been shown earlier to synthesize zeatin. The role of 6-(γ,γ-dimethylallylamino) purine as a precursor of zeatin was studied. Rhizopogon was furnished with 6-(γ,γ-dimethylallylamino) purine-8-¹⁴C. Cochromatography, oxidation studies with potassium permanganate, and bromination indicated that labeled zeatin ribonucleoside was isolated from the medium. The fungus also incorporated labeled adenine, hypoxanthine, and 4-amino-5-imidazole carboxamide into zeatin ribonucleoside.     

Synthesis of isotopically labeled D-[1'-13C]ribonucleoside phosphoramidites

The preparation of fully protected labeled diisopropylamino-beta-cyanoethyl-[1'-13C]ribonucleoside phosphoramidites with regioisomeric purity is described. We demonstrated in this paper that a regioselective 2'-O-silylation, through a 3',5'-O-di-tert-butylsilanediyl protection, has been applied for the synthesis of [1'-13C]ribonucleoside phosphoramidite units. This method allowed us to obtain only the desired 2'-O-silyl-3'-O-phosphoramidites avoiding the undesired 3'-O-silyl-2'-O-phosphoramidite nucleosides isolated by standard procedures. This is a suitable procedure to RNA precursors with respect to the isotope-containing precursors.     

A novel endoribonuclease from the marine sponge Tethya aurantium specific to 2',5'-phosphodiester bonds

In the marine sponge Tethya aurantium a novel endoribonuclease was found which specifically catalyzed the degradation of 2′,5′-phosphodiester linkages and was therefore named endo-2′,5′-ribonuclease. This enzymatic reaction yielded 2′,3′-cyclic phosphate and 5′-OH products similarly to the 3′–5′ bond cleavage in RNA, catalyzed by metal-independent ribonucleases. The partially purified enzyme preparation was used for its biochemical characterization. The enzyme did not require the presence of metal ions for its activity. The novel nuclease exhibited a preference for 5′-phosphorylated 2′,5′-oligoadenylates, but 2′–5′ linkage in 5′-triphosphorylated hetero-oligomers or homo-dimers comprising guanylate or uridylate residues instead of adenylate was cleaved as well. The enzyme was also able to catalyze the degradation of 5′-unphosphorylated 2′,5′-oligoadenylates, except for 2′,5′-diadenylate, which were weaker substrates for the enzyme than the respective 5′-triphosphorylated forms. The observed substrate specificity may refer to the specific role of the enzyme in the degradation of natural 2′,5′-oligoadenylates (2-5A) that function in the interferon-induced mammalian 2-5A system as allosteric regulators of ribonuclease L. They are produced by 2-5A synthetases (OAS) that are also present in sponges, the most ancient phylum of Metazoa. We suggest that the newly discovered endoribonuclease found in the marine sponge T. aurantium could be a representative of the group of 2′,5′-specific ribonucleases that primarily control the cellular levels of 2′,5′-oligoadenylates.     

Steroidogenesis in isolated adrenal cells of rat. II. Effect of caffeine on ACTH and cyclic nucleotide-induced steroidogenesis and its relation to cyclic nucleotide phosphodiesterase (PDE)

Corticosterone production in isolated adrenal cells (IAC) of rat has been measured in response to ACTH or ribonucleoside 3′,5′-cyclic phosphate of adenosine (c-AMP), guanosine (c-GMP), inosine (c-IMP) and N⁶-2′-0 dibutyryl adenosine monophosphate (dc-AMP) in the presence and absence of caffeine. Caffeine inhibited ACTH-induced steroidogenesis in a manner independent of its effect on PDE. Study of PDE in whole adrenal homogenate showed hydrolysis of c-AMP, c-GMP and c-IMP but not of dc-AMP and other cyclic nucleotides. No PDE activity was demonstrable in IAC. High sensitivity of IAC to minute quantities of ACTH and various cyclic nucleotides may be due in part to lack of PDE activity in these preparations.     

Guanosine-5'-diphosphate at the 5' termini of reovirus RNA: evidence for a segmented genome within the virion

All ten double-stranded RNA fragments isolated from purified reovirus contain ppGp at the 5′ termini. The presence of a unique 5′-terminal nucleotide indicates that the viral genome in situ consists of segments which are synthesized as discrete units in infected cells. The penultimate base is a pyrimidine. This 5′ sequence, ppGpPyp, is identical to that reported previously for the ten reovirus messenger RNA species synthesized in vitro. The results indicate that the double-stranded RNA segments are perfect duplexes which are transcribed end-to-end by the virion-associated RNA polymerase.     

Characterization of human phosphodiesterase 12 and identification of a novel 2'-5' oligoadenylate nuclease - The ectonucleotide pyrophosphatase/phosphodiesterase 1

The vertebrate 2-5A system is part of the innate immune response and central to cellular antiviral activities. Upon activation by viral double-stranded RNA, 5′-triphosphorylated, 2′-5′-linked oligoadenylate polyribonucleotides (2-5As) are synthesized by one of several 2′-5′ oligoadenylate synthetases. The 2-5As bind and activate RNase L, an unspecific endoribonuclease, resulting in viral and cellular RNA decay. Given that most endogenous RNAs are degraded by RNase L, continued enzyme activity will eventually lead to cell growth arrest and cell death. This is averted, when 2-5As and their 5′-dephosphorylated forms, the so-called 2-5A core molecules, are cleaved and thus inactivated by 2′-5′-specific nuclease(s), e.g. phosphodiesterase 12, thereby turning RNase L into its latent form. In this study, we have characterized the human phosphodiesterase 12 in vitro focusing on its ability to degrade 2-5As and 2-5A core molecules. We have found that the enzyme activity is distributive and is influenced by temperature, pH and divalent cations. This allowed us to determine V_max and K_m kinetic parameters for the enzyme. We have also identified a novel 2′-5′-oligoadenylate nuclease; the human plasma membrane-bound ectonucleotide pyrophosphatase/phosphodiesterase 1, suggesting that 2-5A catabolism may be a multienzyme-regulated process.     

A high-pressure liquid chromatographic method for measuring 3', 5'-cyclic AMP in brain.

A method is described for the estimation of adenosine 3′,5′-monophosphate (3′,5′-cyclic AMP) in rat brain by high-pressure liquid chromatography (HPLC). The nucleotide is purified initially by being passed through two columns, alumina and AG-1X2. The peak in HPLC was identified by a number of methods. Optimum parameters for HPLC were obtained by using 1 mm KH₂PO₄ buffer, pH 4.8, at a flow rate of 57 ml/hr at room temperature. Using this technique the concentration of 3′,5′-cyclic AMP in rat brain was found to be 2.53 ± 0.40 nmol/g (mean ± SD, n = 5).     

A new reagent for preparing radioactively labeled nucleoside derivatives.

The identification of benzimidazole incorporated into RNA of Escherichia coli as benzimidazole nucleoside by means of mass spectrometry is reported. Trimethylsilylation of an enzymatic digest of bacterial RNA allowed the separation of the different nucleosides by gas chromatography. The coupled mass spectrometer was used as a mass specific detector and allowed the sensitive detection of single components of the complex mixture. Thus, benzimidazole ribonucleoside could be detected in hydrolysates of RNA from E. coli fed benzimidazole in the culture broth, although this nucleoside could not be completely separated from uridine by the gas chromatographic systems explored. Quantitation of the benzimidazole nucleoside content revealed that benzimidazole is incorporated into RNA amounting to 16% relative to adenosine.     

Enhanced uridine kinase and RNA synthesis in regenerating rat liver after 5-azacytidine administration

The administration of 5-azacytidine to partially hepatectomized rats results in the increase of uridine kinase activity in cell-free liver extracts 24–72 hr after drug administration. At the same time the activity of uridine phosphorylase and of uridine 5′-nucleotidase is decreased, while uridinemonophosphate kinase and uridine 5′-triphosphatase are not affected. The repeated administration of 5-azacytidine leads to a further enhancement of uridine kinase which is 6- to 8-fold higher in 96-hr regenerating livers than in untreated controls. Simultaneously the enhanced incorporation of uridine into liver ribonucleic acids was observed. The metabolic alterations occurring in the liver at later phases after 5-azacytidine in vivo administration are discussed.     

In vitro polyoma DNA synthesis: Involvement of RNA in discontinuous chain growth

Short fragments of DNA (5 S) isolated by denaturation from polyoma replicative intermediates pulse-labeled in vitro were shown to have RNA covalently attached by three criteria: (1) such fragments were slightly denser than bulk viral DNA. (2) They could be labeled directly with α-³²P-labeled ribotriphosphates. (3) Alkaline hydrolysis of fragments labeled with α-³²P-labeled deoxynucleoside triphosphates showed ³²P transfer to 3′ ribonucleoside monophosphates. Except for a preference of transfer from dC, the link showed little sequence specificity. The data are compatible with the notion that all short fragments in replicating viral DNA are initiated by an RNA primer. This RNA is maximally 30 bases long and is rather short-lived.     

Absence of detectable RNA ligase activity in eukaryotic cells.

Reports of the existence of eukaryotic RNA ligases may be incorrect. Evidence for this activity has been based upon the conversion of [5′-32p]-terminated oligoribonucleotides to an alkaline phosphatase resistant form and upon the detection of radioactive ribonucleoside monophosphates after alkaline hydrolysis of the reaction products. Although we have in part confirmed these observations, we find the labeled ribonucleoside monophosphate to be the 5′-isomer, and not the expected 2′ (3′)-isomer. In addition, roughly equivalent amounts of ribonucleoside monophosphate were observed whether or not alkaline hydrolysis was performed. We conclude that the existence of RNA ligase activity in eukaryotic cells is suspect.     

S1 nuclease of Aspergillus oryzae: characterization of the associated phosphomonoesterase activity

S₁ nuclease (EC 3.1.30.1) of Aspergillus oryzae was found to catalyze the hydrolysis of 2′- or 3′-phosphomonoester groups from several mono- and oligonucleotides. The specificity of the enzyme for mononucleotide substrates was determined by steady-state kinetic measurements at pH 4.5. The values of V were similar for all ribonucleoside 3′-phosphates tested, and they were 50–400 times greater than those for the corresponding deoxyribonucleotides or ribonucleoside 2′-phosphates. Purine nucleotides had lower apparent K_m values than pyrimidine nucleotides. Apparent K_m values of mononucleotides were also strongly dependent on the type of sugar and the positions of phosphoryl groups. Substrate specificity, as expressed by $\text{V}\text{K}{}_{\mathrm{m}}$, occurred in the following order: ribonucleoside 3′,5′-bisphosphate > ribonucleoside 3′-phosphate > deoxyribonucleoside 3′,5'-bisphosphate > deoxyribonucleoside 3′-phosphate ≈ ribonucleoside 2′-phosphate. S₁ nuclease also catalyzed the dephosphorylation of the dinucleotide ApAp at a high rate and the release of PP_i from adenosine 3′-diphosphate 5′-phosphate at a low rate. The phosphomonoesterase activity of the enzyme was competitively inhibited by single-stranded DNA and 5′-nucleotides. Apparent K_i values for adenosine compounds occurred in the order ATP < ADP < AMP ? adenosine. Tests of S₁ nuclease for phosphotransferase activity at pH 4.5 and 7.0 were negative.     

Short, synthetic and selectively 13C-labeled RNA sequences for the NMR structure determination of protein–RNA complexes

We report an optimized synthesis of all canonical 2′-O-TOM protected ribonucleoside phosphoramidites and solid supports containing [¹³C₅]-labeled ribose moieties, their sequence-specific introduction into very short RNA sequences and their use for the structure determination of two protein–RNA complexes. These specifically labeled sequences facilitate RNA resonance assignments and are essential to assign a high number of sugar–sugar and intermolecular NOEs, which ultimately improve the precision and accuracy of the resulting structures. This labeling strategy is particularly useful for the study of protein–RNA complexes with single-stranded RNA in solution, which is rapidly an increasingly relevant research area in biology.     

Rotational correlation time of spin-labeled alpha-chymotrypsin

α-Chymotrypsin has been spin labeled with (I), 3-carboxy 2,2,5,5-tetramethyl pyrrolidine-N-oxyl-p-nitrophenyl ester, and (II), the N-oxyl-4′,4′-dimethyl oxazolidine of 5-α-androstan-3-one-17-β-methyl phosphono-fluoridate. The positions of the high field hyperfine components in the paramagnetic resonance spectra of the spin-labeled enzymes have been measured as a function of solvent viscosity and have been used to determine a rotational correlation time of 12 nanoseconds for α-chymotrypsin in water at 20° C.     

The hybrid recombinational repair pathway operates in a χ activity deficient recC1004 mutant of Escherichia coli

Homologous recombination is a crucial process for the maintenance of genome integrity. The two main recombination pathways in Escherichia coli (RecBCD and RecF) differ in the initiation of recombination. The RecBCD enzyme is the only component of the RecBCD pathway which acts in the initiation of recombination, and possesses all biochemical activities (helicase, 5′-3′ exonuclease, χ cutting and loading of the RecA protein onto single-stranded (ss) DNA) needed for the processing of double stranded (ds) DNA breaks (DSB). When the nuclease and RecA loading activities of the RecBCD enzyme are inactivated, the proteins of the RecF recombination machinery, i.e., RecJ and RecFOR substitute for the missing 5′-3′ exonuclease and RecA loading activity respectively. The above mentioned activities of the RecBCD enzyme are regulated by an octameric sequence known as the χ site (5′-GCTGGTGG-3′). One class of recC mutations, designated recC*, leads to reduced χ cutting in vitro. The recC1004 strain (a member of the recC* mutant class) is recombination proficient and resistant to UV radiation. In this paper, we studied the effects of mutations in RecF pathway genes on DNA repair (after UV and γ radiation) and on conjugational recombination in recC1004 and recC1004 recD backgrounds. We found that DNA repair after UV and γ radiation in the recC1004 and recC1004 recD backgrounds depends on recFOR and recJ gene products. We also showed that the recC1004 mutant has reduced survival after γ radiation. This phenotype is suppressed by the recD mutation which abolishes the RecBCD dependent nuclease activity. Finally, the genetic requirements for conjugational recombination differ from those for DNA repair. Conjugational recombination in recC1004 recD mutants is dependent on the recJ gene product. Our results emphasize the importance of the canonical χ recognition activity in DSB repair and the significance of interchange between the components of two recombination machineries in achieving efficient DNA repair.     

Affinity chromatography of transaminases

It is shown that glutamic-oxaloacetic transaminase from pig heart can be selectively and reversibly bound to a Sepharose column substituted with N′-alkyl derivatives of pyridoxamine 5′-phosphate. A simple procedure is described which includes formation of apotransaminase, its binding to the substituted Sepharose, and its elution under the same conditions that were used to prepare the apoenzyme. There is no binding of the transaminase to Sepharose substituted with unmodified pyridoxamine 5′-phosphate, indicating the importance of a certain “length” of the substituent for binding.     

Radioactive labeling of alpha1-antitrypsin, trypsin, and chymotrypsin by reductive methylation: properties of the labeled derivatives.

Human plasma α₁-antitrypsin (α₁-AT), bovine trypsin, and α-chymotrypsin were labeled with either ¹⁴C or ³H by reductive methylation. The labeled inhibitor retained the capacity to inactivate and to form 1:1 molar complexes with either the unlabeled or labeled trypsin and α-chymotrypsin. After intravenous injection of reductively methylated α₁-AT into rats, the labeled glycoprotein showed a circulating half-life of 12 h. When the N-acetylneuraminic acid residues were removed from the labeled α₁-AT by neuraminidase in vitro, injection into rats of this product resulted in a rapid (half-life of about 5 min) and almost complete disappearance of the label from the circulation in 30 min. There was a concomitant accumulation of radioactivity in the liver of over 75% of the injected dose. The reductively methylated radioactively labeled trypsin and chymotrypsin experienced no loss of enzymatic activities. They showed the ability to form complexes in vivo with the two major plasma inhibitors, namely, α₁-AT and α₂-macroglobulin. High-voltage paper electrophoretic separation of acid hydrolysates of the labeled proteins revealed that ?-N-monomethyllysine and ?N,N-dimethyllysine are the only residues found to be radioactive.     

Fluorimetric studies of actin labeled with dansyl aziridine.

F-actin has been specifically labeled with a fluorescent probe, dansyl aziridine, at cysteine-373 of the protein. The fluorescence property of the conjugated probe serves as a spectroscopic indicator of several processes in which actin participates. The sulfhydryl modification does not impair the G-F transformation of actin, nor does it affect the complex formation of actin and myosin or the dissociation of the complex by ATP as judged by viscosity measurements. However, both labeled actin and actin modified by N-ethylmaleimide, which also reacts at cysteine-373, stimulate the Mg²⁺-ATPase of myosin only about 75% as well as unmodified actin. The probe attached to actin exhibits a 65-nm blue shift of its emission maximum from 560 to 495 nm and a sixfold fluorescence enhancement indicating that it is located in a hydrophobic environment. The excitation spectrum of labeled actin indicates that a tryptophan and a tyrosine residue are close to the probe and transfer excitation energy to the dansyl fluorophore. Upon depolymerization of F-actin, the fluorescence intensity of labeled actin increases about 20%. The fluorescence of labeled actin is also enhanced by the addition of EDTA, ATP, and pyrophosphate, but Mg²⁺ antagonizes this effect reversibly. However, in the presence of 10 mm orthophosphate buffer (pH 7.4) these effects disappear. When labeled F-actin binds with myosin subfragment-1 (SF-1) or heavy meromyosin (HMM), the fluorescence of the actin adduct is enhanced. The fluorescence properties of labeled acto-SF-1 and acto-HMM become insensitive to EDTA and polyphosphates even in the absence of orthophosphate. These results suggest that the two-stranded helical structure of the F-actin filament is stabilized by the presence of phosphate and/or the binding of the myosin “head”.     

Synthesis of deuterium labeled 17-methyl-testosterone

The synthesis of two forms of selectively deuterated 17-methyl-testosterone is described. 17-Methy1-d₃-testosterone was prepared by the Grignard reaction of dehydroepiandrosterone with deuterium labeled methyl magnesium iodide followed by an Oppenauer oxidation. 17-Methyl-d₃-testosterone-19, 19, 19-d₃ was prepared by treating 3, 3-ethylenedioxy-5, 10-epoxy-5α, 10α-estran-17-one with deuterium labeled methyl magnesium bromide followed by hydrolysis and dehydration of the 5α-hydroxyandrostane derivative.