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Does 3'-terminal poly(A) stabilize human fibroblast interferon mRNA in oocytes of Xenopus laevis?

Polynucleotide phosphorylase (polyribonucleotide:orthophosphate nucleotidyltransferase, EC 2.7.7.8) purified from Escherichia coli was used enzymatically to deadenylate polyadenylated human fibroblast interferon mRNA preparations obtained from human diploid fibroblasts (FS-4 strain) induced by poly(I)-poly(C) (20 microgram/ml) in the presence of cycloheximide (50 microgram/ml, 4 hr). Both the polyadenylated and the deadenylated interferon mRNA preparations were translated into biologically active human interferon when injected into oocytes of Xenopus laevis. In the oocytes the functional stability of deadenylated interferon mRNA was indistinguishable from that of polyadenylated interferon mRNA.

Animals↗

Hydroxyl radical-induced strand break formation in single-stranded polynucleotides and single-stranded DNA in aqueous solution as measured by light scattering and by conductivity.

Combining conductivity measurements and molecular weight determination by means of low-angle laser light scattering, we have found for the polyribonucleotides (polyuridylic acid (poly(U], polyadenylic acid (poly(A], polycytidylic acid (poly(C] and polyguanylic acid (poly(G] and for single-stranded DNA (ssDNA) that, on average, 8.5 counterions per single-strand break (ssb) are liberated under salt-free conditions. This relationship allows us to estimate, from conductivity measurements alone, G-values of single-strand break formation (G(ssb] for the polydeoxyribonucleotides (polydeoxyriboadenylic acid (poly(dA], polydeoxyribocytidylic acid (poly(dC], polydeoxyribothymidylic acid (poly(dT], polydeoxyribouridylic acid (poly(dU] and polydeoxyriboguanylic acid (poly(dG]. The following G(ssb) values (units of mumol J-1) have been obtained for anoxic conditions: poly(dA), 0.23; poly(dC), 0.14; poly(dT), 0.06; poly(dU), 0.046 and poly(dG), 0.009. Time-resolved conductivity measurements in pulse radiolysis enable us to measure the rate of strand break formation. The rate has been found to be similar for poly(dA) and ssDNA over a range of pH values. Poly(dC) and poly(dU) exhibit conductivity increase components with half-lives similar to those of poly(dA) and ssDNA at corresponding pH values. The implications of these results are discussed.

DNA Damage↗

Interactions of 4', 6-diamidine-2-phenylindole with synthetic polynucleotides.

4', 6-Diamidine-2-phenylindole forms fluorescent complexes with synthetic DNA duplexes containing AT, AU and IC base pairs; no fluorescent complexes were observed with duplexes containing GC base pairs or with duplexes containing a single AT base pair sandwiched between GC pairs. The binding site size is one molecule of dye per 3 base pairs. The intrinsic binding constants are higher for alternating sequence duplexes than for the corresponding homopolymer pairs. With the exception of the four-stranded helical poly rI which exhibits considerable fluorescence enhancement upon binding of the ligand, none of the single- or multi- stranded polyribonucleotides and ribo-deoxyribonucleotide hybrid structures form fluorescent complexes with the dye. Poly rI is the only RNA which forms a DNA B-like structure (Arnott et al. (1974) Biochem. J. 141, 537). The B conformation of the helix and the absence of guanine appear to be the major determinants of the specificity of the fluorescent binding mode of the dye. Nonfluorescent interactions of the dye with polynucleotides are nonspecific; UV absorption and circular dichroic spectra demonstrate binding to synthetic single- and double-stranded DNA and RNA analogs, including those containing GC base pairs.

Amidines↗

Terminal uridylyl transferase of Vigna unguiculata: purification and characterization of an enzyme catalyzing the addition of a single UMP residue to the 3'-end of an RNA primer.

An enzyme which catalyzes the addition of a single UMP residue from UTP to the 3'-end of an RNA primer and which is referred to as terminal uridylyl transferase (TUT) has been extensively purified from the membrane fraction of vigna unguiculata leaves. The purification procedure involved (i) solubilization by cation depletion (ii) DEAE-Sepharose CL-6B column chromatography (iii) affinity chromatography of poly(U)-Sepharose 4B and (iv) glycerol gradient centrifugation. The molecular weight of the native enzyme was approximately 50,000 as determined by velocity sedimentation. Under conditions that were optimal for UMP-incorporation (5 mM Mg2+, low salt, 30 degrees C) TUT displayed a marked specificity for UTP as substrate, was unable to incorporate deoxyribonucleoside triphosphates and required a single-stranded oligo- or polyribonucleotide as primer. When oligoA20, tRNAasp of E. coli or alfalfa mosaic virus RNA 4 were used as primers at various substrate to primer ratio's, the vast majority of the product appeared to consist of primer molecules elongated with a single UMP residue as shown by polyacrylamide gelelectrophoresis and nearest neighbour analysis. We believe TUT to be a novel enzyme which has not been reported before and which may be a feasible tool in RNA sequencing as it enables the specific 3'-terminal labeling of RNA molecules.

Cell Membrane↗

Effects of polyamines on the degradation of ribonucleic acids by polynucleotide phosphorylase of Micrococcus luteus.

The effects of polyamines on the breakdown of synthetic polynucleotides [poly(A), poly(C), and poly(U)] by polynucleotide phosphorylase [polyribonucleotide: orthophosphate nucleotidyltransferase, EC 2.7.7.8] from Micrococcus luteus have been studied. Although the breakdown of all the synthetic polynucleotides tested was stimulated by polyamines, the degree of stimulation by polyamines was in the order poly(C) greater than poly(A) greater than poly(U) at pH 7.5. However, the difference in degree of stimulation among polynucleotides decreased as the pH or monovalent cation concentration was increased. In the presence of heparin, an inhibitor of polynucleotide phosphorylase hydrolysis of polynucleotides, spermidine clearly stimulated the breakdown of poly(C) and poly(A), while the breakdown of poly(U) was stimulated only slightly by the addition of spermidine. Although binding of [14C]spermine to polynucleotide phosphorylase was observed by gel filtration, the amount of spermine bound to the enzyme was much less than that to RNA.

Binding Sites↗

Purification and properties of polynucleotide phosphorylase from photosynthetic bacterium Rhodospirillum rubrum.

1. Polynucleotide phosphorylase [polyribonucleotide: orthophosphate nucleotidyltransferase, EC 2.7.7.8] was purified to near homogeneity from the photosynthetic bacterium, Rhodospirillum rubrum. The purified enzyme had a molecular weight of approximately 160,000, and consisted of two equivalent subunits of approximately 76,000 daltons. It catalyzed the three reactions described below. 2. In the exchange reaction of the beta-phosphate of nucleoside diphosphates with Pi by the purified enzyme in the presence of 3.3 mM Pi, 6.7 mMCl2, and 0.33 mM or 1.0 mM nucleotide at pH 8.0 and 20 degrees C, ADP, GDP, and CDP, and CDP were better substrates than UDP, while IDP and deoxyribonucleoside diphosphates hardly served as substrates. The ADP-Pi exchange activity was significantly inhibited by high concentrations of either ADP or Pi. 3. In the polymerization reaction of ribonucleoside diphosphates by the purified enzyme in the presence of 6.7 mM nucleotide and 6.7 mM MgCl2 at pH 8.0 and 20 degrees C, ADP was the best substrate; the activities relative to that with ADP were 55% with UD, 51% with CDP, and 48% with IDP, while GDP hardly served as a substrate, 4. In the phosphoryolysis reaction of polynucleoside diphosphates by the purified enzyme in the presence of 1.0 mM polynucleotide, 6.7 mM Pi, and 6.7 mM MgCl2 at pH 8.0 and 20 degrees C, poly[U] was the best substrate; the activities relative to that with poly[U] were 32% with poly[A], 28% with poly[I], 21% with poly[C], and 2% with yeast RNA, while poly[G] and yeast DNA hardly served as substrates. 5. The three kinds of activities of the purified enzyme described above were stimulated by divalent cations such as Mg2+, Mn2+, Cd2+, and Co2+.

Cations, Divalent↗

RNA 3'-tail synthesis in Streptomyces: in vitro and in vivo activities of RNase PH, the SCO3896 gene product and polynucleotide phosphorylase.

As in other bacteria, 3'-tails are added post-transcriptionally to Streptomyces coelicolor RNA. These tails are heteropolymeric, and although there are several candidates, the enzyme responsible for their synthesis has not been definitively identified. This paper reports on three candidates for this role. First, it is confirmed that the product of S. coelicolor gene SCO3896, although it bears significant sequence similarity to Escherichia coli poly(A) polymerase I, is a tRNA nucleotidyltransferase, not a poly(A) polymerase. It is further shown that SCO2904 encodes an RNase PH homologue that possesses the polymerization and phosphorolysis activities expected for enzymes of that family. S. coelicolor RNase PH can add poly(A) tails to a model RNA transcript in vitro. However, disruption of the RNase PH gene has no effect on RNA 3'-tail length or composition in S. coelicolor; thus, RNase PH does not function as the RNA 3'-polyribonucleotide polymerase [poly(A) polymerase] in that organism. These results strongly suggest that the enzyme responsible for RNA 3'-tail synthesis in S. coelicolor and other streptomycetes is polynucleotide phosphorylase (PNPase). Moreover, this study shows that both PNPase and the product of SCO3896 are essential. It is possible that the dual functions of PNPase in the synthesis and degradation of RNA 3'-tails make it indispensable in Streptomyces.

Bacterial Proteins↗

A comparative study on the catalytic properties of guanyl-specific ribonucleases.

The kinetic parameters of reactions catalyzed by four guanyl-specific RNases T1, Pb1, Th1 and Sa were studied comparatively using three types of substrates; guanosine-2',3'-cyclophosphates, GpN dinucleoside phosphates and synthetic polyribonucleotides. The kinetic parameters were shown to be similar in spite of considerable differences in primary structures of these RNases, including amino acid residues of the active sites. Therefore, primary structures of guanyl RNases allow for a considerable number of substitutions (both in the 'recognising' and catalytical parts of the active site) without changes in the catalytical parameters.

Amino Acid Sequence↗

Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaea.

We compared the detection of bacteria and archaea in the coastal North Sea and at Monterey Bay, Calif., after fluorescence in situ hybridization (FISH) either with rRNA-targeted oligonucleotide probes monolabeled with the cyanin dye Cy3 (oligoFISH) or with fluorescein-labeled polyribonucleotide probes (polyFISH). During an annual cycle in German Bight surface waters, the percentages of bacteria visualized by polyFISH (annual mean, 77% of total counts) were significantly higher than those detected by oligoFISH (53%). The fraction of total bacteria visualized by oligoFISH declined during winter, whereas cell numbers determined by polyFISH remained constant throughout the year. Depth profiles from Monterey Bay showed large differences in the fraction of bacterial cells visualized by polyFISH and oligoFISH in the deeper water layers irrespective of the season. Image-analyzed microscopy indicated that the superior detection of cells by polyFISH with fluorescein-labeled probes in bacterioplankton samples was less a consequence of higher absolute fluorescence intensities but was rather related to quasi-linear bleaching dynamics and to a higher signal-to-background ratio. The relative abundances of archaea in North Sea and Monterey Bay spring samples as determined by oligoFISH were on average higher than those determined by polyFISH. However, simultaneous hybridizations with oligonucleotide probes for bacteria and archaea suggested that the oligoFISH probe ARCH915 unspecifically stained a population of bacteria. Using either FISH technique, blooms of archaea were observed in North Sea surface waters during the spring and summer months. Marine group II archaea (Euryarchaeota) reached >30% of total picoplankton abundances, as determined by polyFISH. We suggest that studies of pelagic microbial community structure using oligoFISH with monolabeled probes should focus on environments that yield detections > or =70% of total cell counts, e.g., coastal surface waters during spring and summer.

Archaea↗

Molecular adjuvants and immunomodulators: new approaches to immunization.

Epitopes on microbial antigens responsible for protective immunity have begun to be identified and isolated, and their chemical structures have been determined. Ensuing knowledge of their weak immunizing capacity per se has led to an appreciation of the need for adjuvants to increase the immunogenicity of these low-molecular-weight synthetic structures. As such, a recent surge in adjuvant research has emerged. Accordingly, this review will highlight a number of those adjuvant substances whose activity in animals indicates a potential use in human vaccines. In addition, the potential of several well-defined substances, termed immunomodulators, which nonspecifically stimulate resistance of animals to multiple 50% lethal doses of microbial challenge is described. Among the most extensively characterized adjuvants of microbial origin discussed in detail are (i) the lipopolysaccharides isolated from gram-negative bacteria and their nontoxic analogs, (ii) the synthetic muramyl dipeptides and their multiple analogs, and (iii) the synthetic polyribonucleotide complexes, mimicking the interferon-inducing capacity of viruses. Discussed also are the heat-labile enterotoxin of Escherichia coli, the nonionic block copolymers, the saponins, a quinolamine derivative, and the hormone dihydroepiandrosterone.

Acetylmuramyl-Alanyl-Isoglutamine↗

Comparison between photo-induction and microsomal activation of polycyclic hydrocarbons with different oncogenic potency.

The binding of five polycyclic aromatic hydrocarbons (PAH) (anthracene (A), benzo(a)anthracene (BA), dibenz(a,h)anthracene (DBA), benzo(a)pyrene (BP) and 7,12-dimethylbenz(a)anthracene (DMBA)) to calf thymus DNA and synthetic polyribonucleotides was studied. Binding was mediated by near-ultraviolet (NUV) irradiation and 3-methylcholanthrene-induced microsomes from rat liver, in order to compare the effectiveness of these two activating systems in forming in vitro intermediates capable of binding covalently to nucleic acids. With NUV irradiation, an interaction among PAH and nucleic acids was obtained regardless of the PAH or the nucleic acid employed. The effectiveness of this activating system was higher (between 1 to 2 orders of magnitude) than that shown by induced microsomes. The enzymatic pathway bioactivated all PAH, except A, to interact with DNA. Therefore, a certain degree of correlation between the extent of DNA binding and oncogenic potency of the chemicals seemed to exist. Polynucleotide labeling was always higher than DNA labeling.

Animals↗

Inhibition of immunoglobulin production stimulating activity of glyceraldehyde-3-phosphate dehydrogenase by nucleotides.

We have previously identified glyceraldehyde-3-phosphate dehydrogenase as an immunoglobulin production stimulating factor (IPSF) which facilitated immunoglobulin production by hybridomas and lymphocytes. The IPSF activity of this enzyme was suppressed by the coexistence of some sorts of nucleotides. We now report that the IPSF effect of GAPDH was suppressed by the coexistence of DNA, the inhibiting effect of degraded DNA being inferior to that of long-chain DNA. Both single-stranded and double-stranded synthetic polyribonucleotides also inhibited the IPSF activity of GAPDH. Moreover, nicotinamide adenine dinucleotide (NAD+) repressed the IPSF effect.

Biological Factors↗

Nucleic acid-binding activities of the intermediate filament subunit proteins desmin and glial fibrillary acidic protein.

In analogy to experimental results previously obtained with vimentin and neurofilament triplet proteins, the intermediate filament (IF) proteins desmin and glial fibrillary acidic protein (GFAP) were also found to have high capacities to associate with nucleic acids. Employing a collection of native and heat-denatured pro- and eukaryotic DNAs, a series of naturally occurring single-stranded (ss)RNAs and a variety of synthetic polynucleotides of the RNA and DNA type, both proteins could be shown to bind preferentially to single-stranded polynucleotides. In the case of ssDNA and synthetic polyribonucleotides, a clear dependency of the binding activity on the G-content of the nucleic acids was demonstrated. The interaction of desmin with ssDNA and tRNA was characterized by strong cooperativity. When a mixture of desmin and vimentin was offered to excess ssDNA, the cooperativity effect brought about segregation of both protein species into two distinct populations of deoxyribonucleoprotein particles with substantially different sedimentation rates; this segregation is in sharp contrast to the ability of desmin and vimentin to form heteropolymers in filament assembly. In general, desmin and GFAP were found to be similar to vimentin and neurofilament proteins in their nucleic acid-binding properties. However, there were also striking differences between individual non-epithelial IF proteins at this level.

Animals↗

The effect of prostaglandin E1 on in vitro transcription of sperm chromatin, isolated from patients with azoospermia, teratospermia and chronic prostatitis.

We have investigated the influence of Prostaglandin E1 on the in vitro transcription of chromatin, isolated from spermatozoa of patients suffering from different pathologies, leading to infertility, namely, azoospermia, teratospermia and chronic prostatitis. Our studies indicate that prostaglandin E1 has a stimulatory effect both on in vitro transcription, on the number of RNA polymerase molecules and the polyribonucleotide elongation rates as compared to sperm chromatin from healthy patients. The results on the incorporation of alpha-32P-ATP in to RNA in the presence and absence of Prostaglandin E1 correlate well with the data on the number of actively transcribing RNA polymerase molecules and the rate of RNA elongation, which might be due to low levels of prostaglandin E1 in human semen.

Alprostadil↗

Inhibition of human neutrophil elastase by polyguanylic acid and other synthetic RNA homopolymers.

Human neutrophils contain large amounts of a neutral serine protease, human neutrophil elastase (HNE), which has been implicated as a mediator of acute and chronic lung injury. We found that this enzyme is effectively inhibited, at physiological ionic strength, by several synthetic non-base-paired polyribonucleotides. Among the most active of these is polyguanylic acid (poly G). Inhibitory activity is greatest with high-molecular-weight poly G fractions, but poly G fractions even as low as 60K Mr (app) are effective. Both amidolysis of synthetic elastase substrates, such as succinyl-ala-ala-ala-p-nitroanilide, and proteolysis of elastin are blocked. Poly G inhibits elastin proteolysis even when subsequently added to mixtures of elastin and HNE that have first been preincubated together for 10 min. Under these conditions, polyribosylribitol phosphate, a polyanion derived from Haemophilus influenzae capsular polysaccharide, is not inhibitory. Complex formation between HNE and poly G is dependent on ionic rather than covalent interactions, since it is blocked by 0.6 M NaCl but not by inactivation of the enzyme's catalytic-site serine residue with diisopropylfluorophosphate. However, nonspecific ionic interactions alone cannot explain complex formation, since pancreatic elastase and cathepsin G, an even more basic serine protease from human neutrophils, do not form complexes with poly G, even at low ionic strength. Moreover, in the presence of the amphiphiles taurocholic acid and glycocholic acid, HNE is much less effectively blocked by poly G. Peptide chloromethyl ketone-inactivate HNE (which has its extended substrate-binding pocket occupied by the peptidyl inactivator) also fails to form complexes with poly G. These results indicate that HNE may utilize both hydrophobic and ionic binding sites to couple with poly G, and suggest that these sites may be close to or within the extended substrate-binding pocket of the enzyme.

Amino Acid Chloromethyl Ketones↗

[Dynamic properties of water bound to matrices of natural DNA and model complexes].

From experimental data on the hydration energetics of nucleic acids obtained by differential scanning calorimetry under isothermal conditions, dielectric relaxation time tau d and "free volume" Vf occupied by water molecules in hydration shells of natural DNA and model polyribonucleotides were calculated. In addition, systems consisting of dinucleotides ApA, TpT, UpU, TpU, UpT and water clusters of various sizes (from 20 to 400 water molecules) were studied by Monte Carlo computer simulation. It was shown that, as water content in systems increases, the dynamic characteristics of bound water obtained with both methods approached the values for bulk water.

Algorithms↗

[Ribonucleases of rat liver nuclear membranes].

A comparative study of ribonuclease activity of isolated rat liver nuclei, nuclear membranes with buoyant density rho 1,19 and rho 1,22 and pH 8 nuclear membrane extract showed high nuclear membranes activity with different affinity to RNA and synthetic polyribonucleotides. Chromatographic analysis of poly-U degradation products demonstrates that the nuclear membrane extract contains at least two ribonucleases: a 3'-endonuclease and a 5'-endonuclease.

Animals↗

[Preparatory extraction of 5'-oligoribonucleotides using ribonuclease from cobra venom].

Cobra (Naja oxiana) venom ribonuclease, which catalyses hydrolysis of polyribonucleotides to 5'-oligonucleotides, was used to obtain preparatively isoplit oligonucleotide fractions, containing 2-30 nucleotides. The yield of hydrolysis products varied depending on the degree of hydrolysis. Hydrolysis rates of different polynucleotides were studied. Hydrolysis rate of polyadenylic acid was 20 times as high as that for polyuridylic acid. Quantitative ratios of isoplit fractions did not vary significantly under similar degree of hydrolysis of polyadenylic and polyuridilic acids. Chromatography on QAE-Sepahdex in ammonium bicarbonate concentration gradient containing 15% dioxan was used to separate enzymatic hydrolysates of polynucleotides, which permitted to bring the fraction isolation to simple evaporation.

Animals↗