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PubMed1978

DNA-dependent RNA polymerase III from cauliflower. Characterization and template specificity.

Class III DNA-dependent RNA polymerase (EC 2.7.7.6) was highly purified from cauliflower (Brassica oleracea, var. bortytis) by using polyethyleneimine precipitation. The specific activity of the enzyme was comparable to that reported for mammalian enzymes. Glycerol gradient sedimentation analysis indicated that the sedimantation coefficient (23 S) was slightly higher than that of enzyme II from cauliflower. The class III enzyme was inhibited by alpha-amanitin at high concentrations (50% inhibition at 200 microgram/ml). The Km value for nucleoside triphosphate was determined. Template specificities for single synthetic polymers showed that the enzyme read pyrimidine homopolymers as templates and preferred poly(dT) to poly(dC). The enzyme transcribed both strands of homopolymer pairs of poly(dI). poly(dC) and poly(dA).poly(dT). The synthetic polyribonucleotides were not effectively read. Competition experiments with these synthetic polymers indicated that the enzyme had different binding specificities which were not the same as their template specificities. The different binding affinities and template specificites for synthetic templates of the three classes of enzyme suggest that the enzyme can discriminate among different template sequences.

Amanitins↗

PubMed1978

Composition and properties of messenger ribonucleoprotein fragments containing and lacking polyadenylate.

Ribonucleoprotein fragments were isolated from Ehrlich ascites cell messenger ribonucleoprotein (mRNP), immobilized on oligo(dT)-cellulose, by successive RNAase and formamide treatments and their RNA and protein moieties were characterized. A 8--10 S formamide-eluted (F) RNP primarily contained the poly(A) segment as an RNA moiety, as evidenced by its characteristic electrophoretic mobility, resistance to RNAase digestion, affinity for nitrocellulose filters and poly(U), and base composition. In contrast, the RNAase-eluted (R) fraction was composed of a 2--3 S RNP carrying a much shorter polyribonucleotide fragment of heterogeneous base composition and properties unlike poly(A). Sodium dodecyl sulfate-polyacrylamide electrophoresis indicated that the protein moieties of the R fraction were composed primarily of 56 000, 67 000, and 71 000 molecular weight polypeptides whereas those of the F fraction contained the latter three polypeptides as well as a major species exhibiting a molecular weight of 81 000. The data demonstrate that RNA sequences other than poly(A) interact with protein in mRNP, that three major mRNP polypeptides are associated with both poly(A) and non-poly(A) RNA binding sites, and that one major polypeptide is specifically bound to the poly-(A) region of mRNP.

Animals↗

PubMed1979

Dissociation of double-stranded poly(I) . poly(C) by cis-diammine-dichloro-Pt(II).

The covalent binding of cis-Pt(NH3)2Cl2 on the double stranded poly(I) . poly(C) induced an irreversible dissociation of the two strands. This dissociation was evidenced mainly by poly(I)-Agarose affinity chromatography which allowed to recover free strands of cis-Pt(NH3)2Cl2-poly(I) from a cis-Pt(NH3)2Cl2-poly(I) . poly(C) complex, by density equilibrium centrifugation where free poly(C) could be isolated, and by acid titrations of the metal-poly(I) . poly(C) complexes. The separation of the two strands of the polyribonucleotide upon cis-Pt(NH3)2Cl2 fixation was shown not to exceed 90--95%. A dissociation curve of the polynucleotide double helix as a function of the amount of bound cis-Pt(NH3)2Cl2 was determined and was shown to be of a characteristic cooperative effect. The fixation of the paltinum compound to poly(I) . poly(C) seemed also to be cooperative.

Chemical Phenomena↗

PubMed1980

Oligo(U)- and poly(U)-containing RNA of wheat embryo.

A UMP-rich RNA fraction was separated from the bulk cellular RNA by affinity chromatography of wheat embryo total RNA. The obtained preparation was heterogeneous and contained polyribonucleotide chain segments which were resistant to RNAase T1 and consisted mainly of UMP residues (87 mol%). The UMP-rich segments were of various sizes, including large oligonucleotides and polynucleotides (up to approx. 150 nucleotides in length). The oligo(U)- and poly(U)-containing RNA fraction occurred in a low amount (approx. 1% of total RNA) both in dry and germinating wheat embryos. However, at the onset of germination, labelled precursors were preferentially incorporated into the UMP-rich RNA species. The early-synthesized RNA appeared and underwent a considerable degradation within the cell nuclei. It is assumed that both delayed maturation of structural gene transcripts and rapid transcription of regulatory gene units during initial germination stages contribute to the transient abundance of newly made UMP-rich RNA in the early wheat embryos.

Base Sequence↗

PubMed1980

Thermal perturbation differential spectra of ribonucleic acids. III. Chain length effect.

Thermal perturbation differential spectra of several adenylic acid oligomers, two single-strand polyribonucleotides, poly(A) and poly(C), and five trinucleoside diphosphates, U-A-A, U-A-G, U-G-A, C-U-C and C-U-A, were obtained and analysed. It is shown that these differential spectra cannot be entirely described by the nearest-neighbour approximation devised from the appropriate mononucleotides and dinucleoside monophosphates. In an attempt to determine the origin of this discrepancy, we have examined the possible optical changes arising from increased electronic interactions, changes in conformation, solvent accessibility or thermodynamic properties. This study indicates that dinucleoside monophosphates on one the hand and trinucleoside diphosphates on the other hand, are separate classes from the conformational point of view. The capacity to assume stacks, absent or negligible in higher oligomers or polymers, makes them poor models for the stacking interaction in longer nucleic acids. It is also shown that in trinucleoside diphosphates, interaction between the two terminal bases arising from bulging out of the middle base is very likely to occur. This type of interaction has to be taken into account in the description of the temperature perturbation differential spectra of trimers.

Macromolecular Substances↗

PubMed1980

Ionic control of enzymic degradation of double-stranded RNA.

The pattern of the degradation of various double-stranded polyribonucleotides by several ribonucleases (bovine RNAase A and its cross-linked dimer, bovine seminal RNAase, and pike-whale pancreatic RNAase) has been studied as a function of ionic strength and pH. It appears that (1) there is no direct correlation between the secondary structure of double-stranded RNA and its resistance against enzymatic breakdown, i.e., the stability of the secondary structure of double-helical RNA is not the main variable in the process. (2) The acstivity responses of the enzymes examined to changes of ionic strength and pH suggest that enzymic degradation of double-stranded RNA is mainly controlled by ion concentration, and that the process may fall within the phenomena interpreted by the theory of the ionic control of biochemical reactions advanced by Douzou and Maurel (Douzou, P. and Maurel, P. (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 1013--1015). (3) The activity curves of the enzyme studied show, at a given pH, a shift toward higher ionic strengths as a function of the basicity of the enzyme protein. This finding explains the already observed correlation between number and/or density of positive charges of a ribonuclease molecule and its ability to attack double-stranded RNA in 0.15 M sodium chloride/0.015 M sodium citrate (SSC). (4) A careful analysis of the influence of ionic strength and pH on the reaction appears to be necessary in order to characterize a ribonuclease which shows activity towards double-stranded RNAs, and to allow a meaningful comparison between different enzymes capable of attacking these substrates.

Endonucleases↗

PubMed1983

DNA and ribonucleotide binding characteristics of two forms of the androgen receptor from rat prostates.

Androgen receptors (sedimentation value approximately 4S and Stokes radius 2.8 nm) present in the cytoplasmic fraction obtained from prostates of castrated rats bind to DNA-Sepharose and double stranded DNA. A receptor fragment (sedimentation value approximately 3S and Stokes radius 2.3 nm) obtained from rat prostates in the course of a purification procedure showed greatly diminished binding affinity for both DNA-Sepharose and soluble DNA. In contrast, both the 4S cytosol receptor and the 3S receptor form interacted with equal affinity with prostate RNA or poly(UG). These observations provide evidence that for DNA binding a different or additional part of the receptor molecule is required than for RNA and polyribonucleotide binding.

Animals↗

PubMed1981

Some properties of the irreversible complexes of nitracrine (ledakrin, C-283) with polynucleotides.

In the presence of sulfhydryl compounds an anticancer drug nitracrine (NA), 1-nitro-9-aminoalkylacridine derivative forms strong, probably covalent complexes with DNA. It has been found that it binds with similar efficiency to RNA and DNA exhibiting a certain preference for single-stranded structure. At NA/polynucleotide ratio of 0.15 and nucleic acids concentration 100 microgram/ml the numbers of drug molecules bound per 10(3) nucleotides were about 10--13 for native calf thymus DNA, 19--28 for denatured DNA and 23--36 for RNA. Some base specificity to guanine is observed both in polydeoxyribo- and polyribonucleotides. The complexes of NA with DNA and double-stranded synthetic polynucleotides exhibit decreased transcriptional template activity in bacterial RNA synthesis in vitro system except poly(A) synthesis on poly(dA) x poly(dT) which is insensitive to the drug. The drug binding in vitro leads to cross-link formation in DNA as shown by means of ultraviolet spectrophotometry and hydroxylapatite chromatography of heat-denatured NA-DNA complexes. The amount of the double bonds introduced by the drug is however relatively low as compared with cross-linking of irradiated 8-methoxy-psoralen-DNA (MOP-DNA) complexes.

Aminoacridines↗

PubMed1983

NMR analyses on the molecular mechanism of the conformational rigidity of 2-thioribothymidine, a modified nucleoside in extreme thermophile tRNAs.

1H-NMR analyses have been made on the conformations of 2-thioribothymidine (s2T), 2-thiodeoxyribothymidine (s2dT), as well as ribothymidine (T) and deoxyribothymidine (dT). s2T and s2dT exclusively take the anti form rather than the syn form. The C3'-endo-gg form of the sugar moiety is remarkably stabilized on modification of T to s2T, but not on modification of dT to s2dT. The steric effects of the 2-thiocarbonyl group and the 2'-hydroxyl group cause the rigidity of the C3'-endo-gg form of s2T. Such rigidity of s2T probably contributes to the thermostability of 2-thiopyrimidine polyribonucleotides and extreme thermophile tRNAs.

Eubacterium↗

PubMed1984

Chromatin-bound and free RNA polymerase A activities in rat thymus cells following glucocorticoid treatment.

Treatment of rat thymus cell suspensions with dexamethasone resulted in inhibition of engaged RNA polymerase A, without significant change in free pool activity. Studies with the re-initiation inhibitor, rifamycin AF/0-13, and measurements of numbers of RNA polymerase A molecules and of elongation rates showed that the inhibition of pre-rRNA synthesis resulted from a decrease in elongation rate. This effect was selectively abolished by mild proteolysis of nuclei. It is concluded that glucocorticoid treatment of rat thymus cells suppresses 45 S rRNA synthesis primarily by decreasing the polyribonucleotide elongation rate, rather than by effecting a change in enzyme redistribution or concentration.

Animals↗

PubMed1986

Novel specificity of an endoribonuclease of yeast.

Investigations of the cleavage specificity of a cyclizing endoribonuclease of yeast show that it hydrolyzes Y-A bonds of single-stranded regions of RNA and that oligonucleotides are hydrolyzed poorly. The stringent specificity of the enzyme suggests that it may be useful for generating specific fragments of polyribonucleotides. An isolation technique employing ethanol extraction has now been used to isolate the enzyme free of other RNases, and the studies show that it is a small protein, 10 kDa or less in molecular mass.

Endoribonucleases↗

PubMed1995

Mutations in the hydrophobic domain of poliovirus protein 3AB abrogate its permeabilizing activity.

Poliovirus protein 3AB contains a predicted amphipathic helix that could lead to pore formation in membranes. We have introduced various mutations in the hydrophobic domain of the protein and the membrane-modifying properties of the resulting mutants have been analyzed. Expression of wild type 3AB protein in E. coli increases the influx and efflux of different molecules such as nucleosides, lactose analogues and antibiotics. Thus, 3AB expression makes E. coli cells two orders of magnitude more sensitive to hygromycin B, a non-permeant inhibitor of translation, and causes a 15-20-fold enhancement in the efflux of uridine. Changes in membrane permeability take place under conditions where no cellular lysis is detected and when other molecules such as beta-galactosidase or polyribonucleotides are kept inside the cell. These membrane modifications can be blocked to different extents by amino acid substitutions in the membrane-spanning region of the protein. These results suggest that poliovirus protein 3AB could possess an intrinsic ability to form pores in natural membranes, thus allowing the flux of small hydrophylic molecules through them.

Amino Acid Sequence↗

PubMed1988

Interactions of Escherichia coli transcription termination factor rho with RNA. I. Binding stoichiometries and free energies.

In this paper we examine the binding of Escherichia coli transcription termination factor rho to single-stranded RNA. Random polyribonucleotide copolymers containing low ratios of the fluorescent base 1,N6-ethenoadenosine have been synthesized using polynucleotide phosphorylase. Binding of rho to these polynucleotides elicits a significant increase in fluorescence, thus allowing either the direct monitoring of the titration of these polynucleotides with rho or measurement of the competitive displacement of the protein from these probes with other nucleic acids, even in the presence of biologically significant concentrations of ATP. By these techniques, it is shown that the binding site size (n) of rho protein to polynucleotides is 13(+/- 1) nucleotide residues per rho monomer (or 78(+/- 6) nucleotide residues per rho hexamer). Binding constants (K) and co-operativity parameters (omega) for the binding of rho to these polynucleotides have been measured as a function of nucleotide composition and of salt concentration. The results show that the affinity of rho for cytosine residues is quite strong and salt concentration independent, whilst binding to uridine residues is somewhat weaker and very salt concentration dependent. Poly(rC) and poly(dC) bind to rho competitively and with equal affinity and site size, although poly(rC) is the strongest cofactor for activating rho-dependent ATPase and poly(dC) has no ATPase cofactor activity at all. It is also shown that ATP (or ADP or ATP-gamma-S) binding does not change the binding site size of rho on RNA nor decrease its affinity for RNA binding. Circular dichroism measurements of rho binding to phage R17 RNA suggest that the affinity (K omega) of rho for RNA may be increased by ATP. The possible significance of these results for models of rho-dependent transcription termination is discussed in the companion paper.

Adenosine Diphosphate↗

PubMed1984

Glucocorticoids modify the rate of ribosomal RNA synthesis in rat thymus cells by regulating the polymerase elongation rate.

The mechanism by which glucocorticoids inhibit RNA polymerase A activity, and hence rRNA synthesis, in rat thymus cells has been investigated. Studies of the intranuclear distribution of RNA polymerase A between chromatin bound ("engaged") and unbound ("free") forms revealed that the steroid-mediated inhibition of the activity of the "engaged" form of the enzyme was not accompanied by significant changes in "free" pool activity. In the presence of rifamycin AF/0-13, an inhibitor of re-initiation of RNA polymerase A, the rate of [3H]UMP incorporation into RNA was slower in nuclei from steroid-treated cells than in those from control cells, although in both conditions similar plateau levels of UMP incorporation were attained. Direct measurements of the numbers of transcribing RNA polymerase A molecules and of elongation rates showed that the inhibition of pre-rRNA synthesis was the result of a decrease in enzyme elongation rate; no significant change was observed in the number of transcribing enzymes. The steroid-induced inhibition of pre-rRNA synthesis was selectively abolished by mild proteolysis of nuclei, suggesting the involvement of a labile, regulatory glucocorticoid-induced protein. It is concluded that glucocorticoid treatment of rat thymus cells decreases 45S rRNA synthesis primarily by decreasing the polyribonucleotide elongation rate of RNA polymerase A, possibly by modification of the enzyme.

Animals↗

PubMed1991

Evidence for spontaneous circle formation in the replication of the satellite RNA of tobacco ringspot virus.

Replication of the satellite RNA of tobacco ringspot virus (sTobRV RNA) has been postulated to require rolling circle transcription. The expected product of rolling circle transcription, multimeric sTobRV RNA, is known to undergo self-cleavage in vitro to release unit-length sTobRV RNA. A spontaneous, efficient, not enzymically-catalyzed in vitro circularization reaction is characteristic of unit-length sTobRV RNA of the less abundant, (-) polarity. We mutated sTobRV RNA at two sites that are distant from each other in the polyribonucleotide chain. A third form of the sTobRV RNA was mutated at both sites. Multimeric forms of the one-site mutants of sTobRV(+)RNA and sTobRV(-)RNA showed, respectively, undiminished and slightly diminished self-cleavage, whereas the spontaneous circularization of each one-site-mutated, unit-length sTobRV(-)RNA was greatly reduced, compared to the reactions of wild-type sTobRV RNA and the two-site mutant. The two-site mutant and the wild-type sTobRV RNAs replicated with similar efficiency. They reduced the titer of, and severity of, symptoms induced by coinoculated tobacco ringspot virus (TobRV). When coinoculated with TobRV, neither one-site mutant increased or provided protection against TobRV. Rather, each induced a substantial accumulation of what is apparently an endogenous form of sTobRV RNA. Our results are consistent with the formation of circular sTobRV(-)RNA as an essential step in sTobRV RNA replication.

Base Sequence↗

PubMedDate not supplied

Results of space experiment program "Interferon".

The results of the biological space experiment "Interferon" performed by two international cosmonaut teams (26 May 1980, and 16 May 1981) aboard space laboratory Solyut-6 are reported: (1) Human lymphocytes separated from blood of healthy donors and placed into "Interferon I" equipment could be kept for 7 days in suspension culture under spaceflight conditions. Interferon production could be induced in human lymphocytes by preparations of different origin: virus, synthetic polyribonucleotides, bacterial protein and plant pigment. An increased lymphocyte interferon production in space laboratory compared to ground control was observed. (2) Human interferon preparations and interferon inducers placed in space laboratory at room temperature for 7 days maintained their biological activity. (3) A decrease of induced interferon production and natural killer activity of lymphocytes isolated from peripheral blood of cosmonauts was observed on the 1st day on Earth after 7-days spaceflight.

Animals↗

PubMed1984

Generation of hybridoma antibodies to double-stranded DNA from non-autoimmune BALB/c strain: studies on anti-idiotype.

A hybridoma obtained between normal spleen cells from BALB/c mice (a non-autoimmune strain) and SP2-O-Ag 14 myeloma cell line was designated as HB2. These hybrid cells produced an IgM kappa-anti-ds-DNA antibody, but their specificity was limited to some polydeoxyribonucleotides such as natural ds-DNA from calf thymus, poly dG-poly dC, poly d(GC) and poly d(GC)-poly d(GC). In contrast, poly dA-poly dT, poly d(AT) were not recognized. The configuration of the nucleic acid helix plays a small role if any, in the building of the epitopes recognized by the hybridoma HB2 antibodies, while the presence of G and C appeared to be essential. These epitopes could not be found on ss- and ds-polyribonucleotides. B cells able to produce anti-ds-DNA antibodies are therefore present in non-autoimmune BALB/c mice, but not enough to produce the corresponding antibodies at a detectable level in the serum. Following immunization of BALB/c mice with hybridoma HB2 monoclonal antibodies, anti-idiotype antibodies were obtained which also recognized idiotopes present in the serum from both murine MRL/1 and human systemic lupus erythematosus (SLE).

Animals↗

PubMed1992

Hidden high-avidity anti-DNA antibodies occur in normal human gammaglobulin preparations.

An ability to detect hidden high-avidity DNA-binding protein in human gammaglobulin samples was investigated. Using ion exchange chromatography on QAE-Sephadex A-50 a highly positive Farr assay DNA-binding fraction was reproducibly isolated from several commercial normal human gammaglobulin preparations. The estimated dissociation constant had a value of 1.04 x 10(-11) M thus confirming high avidity protein-DNA complex formation. Anti-DNA antibodies (Ab) ELISA data revealed that immunoglobulin (Ig) G, IgM and IgA participated in the protein-DNA interaction. Inhibitory experiments involving a number of polynucleotides, synthetic and natural polyanions demonstrated that both double-stranded DNA (dsDNA) and heat-denatured DNA but not RNA inhibited the protein-3H-DNA binding. Generally, the inhibiting effect was more pronounced when purine base-containing polynucleotides and polydeoxy- rather than polyribonucleotides were used. Synthetic polyanions and normal human sera (NHS) also markedly reduced the binding. The presence of hidden high-avidity DNA-binding antibodies in normal gammaglobulin preparations was suggested.

Antibodies, Antinuclear↗