Ara-ATP impairs 3''-end processing of pre-mRNAs by inhibiting both cleavage and polyadenylation.

Previous studies have demonstrated that Ara-ATP can inhibit poly(A) polymerase activity by competing with ATP. To elucidate the mechanism of action of this compound, its effect on the cleavage and polyadenylation of two specific substrates, SV40L and adenovirus L3 pre-mRNAs, was studied in HeLa nuclear extracts. Unlike cordycepin 5' triphosphate, Ara-ATP inhibited both cleavage and poly(A) addition. Addition of poly(A) polymerase fraction devoid of any other factors required for the processing reactions overcame the inhibitory effect on cleavage as well as polyadenylation of pre-mRNAs. These data suggest that Ara-ATP inhibits both cleavage and polyadenylation reactions by interacting with the ATP-binding site on poly(A) polymerase, the activity of which is essential for the cleavage reaction. Ara-ATP also blocked formation of the post-cleavage and polyadenylation-specific complexes, which further confirmed the inhibitory effect of the ATP analog on the two tightly coupled 3'-end processing reactions.     

Inhibition of the polyadenylation reaction in vitro by polyamines

The effect of polyamines on the polyadenylation reaction in vitro was investigated. Varying concentrations of spermine were added to the reaction catalyzed by purified poly(A) polymerase using rat liver nuclear RNA, poly(A), Escherichia coli tRNA or (Ap)₃A as exogenous primers. The enzyme activity decreased progressively with increasing concentrations of polyamines; complete inhibition was obtained at 0.4 and 1.2 mm spermine for the nuclear RNA- and poly(A)-primed reactions, respectively. No inhibition was observed for the (Ap)₃A-primed reaction. Spermidine and putrescine also inhibited polyadenylation but to a lesser extent than spermine. The degree of inhibition by spermine was related to the polynucleotide primer concentrations. Spermine prevented polyadenylation by binding to the primer but not to the poly(A) polymerase molecule as shown by the migration of [¹⁴C]spermine through glycerol gradients after preincubation with enzyme or tRNA. At concentrations inhibitory to polyadenylation in vitro, spermine could stimulate the DNA-dependent RNA synthesis catalyzed by RNA polymerase II. The present study suggests that low levels of polyamines could be used as specific inhibitors of the poly(A) synthesis in vitro.     

Differential effects of cordycepin triphosphate and 9 beta-D-arabinofuranosyladenine triphosphate on tRNA and 5 S RNA synthesis in isolated nuclei.

Although cordycepin 5'-triphosphate (3'-dATP), at low concentrations, preferentially inhibits chromatin-associated poly(A) synthesis in isolated nuclei, higher levels of the inhibitor prevent both rRNA (RNA polymerase I activity) and hnRNA (RNA polymerase II activity) synthesis in vitro (Rose, K.M., Bell, L.E. and Jacob, S.T. (1977) Nature 267, 178-180). The present studies demonstrate that this nucleotide can also inhibit tRNA and 5 S RNA synthesis (RNA polymerase III activity). At 50-200 microgram/ml, 3'-dATP inhibits incorporation of [3H]UTP into tRNA and 5 S RNA by approximately 65%, whereas the syntheses of these RNAs were completely blocked when [3H]GTP was used as the substrate. These data suggest the formation of poly(U) in the tRNA and 5 S RNA regions, which is resistant to 3'-dATP. In contrast, another ATP analog, Ara-ATP, which selectively inhibits poly(A) synthesis, does not block tRNA and 5 S RNA synthesis in isolated nuclei. The production of these RNA species in isolated nuclei is also insensitive to Ara-CTP and 2'-dATP. These data suggest that 3'-dATP exerts general inhibitory effects on RNA synthesis and further substantiate the conclusion that Ara-ATP is a selective inhibitor of the polyadenylation reaction in vitro.     

Effects of 3′-deoxyadenosine triphosphate on in vitro RNA synthesis of plant RNA-dependent RNA polymerases

3′-deoxyadenosine triphosphate inhibited $\text{in}\text{vitro}$ [³H]UMP incorporation by RNA-dependent RNA polymerases from tobacco and cowpea plants. The inhibition of [³H]UMP incorporation could be reversed by simultaneous addition of higher ATP concentrations but not with increasing concentrations of UTP or when excess ATP was added 10 min after the inhibitor. These results suggest 3′-deoxyadenosine triphosphate competes specifically with ATP in reaction mixtures and results in premature termination of RNA synthesis $\text{in}\text{vitro}$ by RNA-dependent RNA polymerase.     

Spin coupling between electron carriers in the dehydrogenase segments of the respiratory chain.

The $\text{in vitro}$ RNA synthesis and poly(A) synthesis catalyzed by cauliflower RNA polymerase are stimulated by an addition of polyethylenimine (PEI) at a low concentration to the reaction medium. Evidence is presented that PEI exerts its stimulative effect on a reaction coexisting of enzyme, template, and substrate, and not on the template or enzyme alone.     

Selective inhibition of initial polyadenylation in isolated nuclei by low levels of cordycepin 5"-triphosphate.

The effect of cordycepin 5'-triphosphate on poly(A) synthesis was investigated in isolated rat hepatic nuclei. Nuclei were incubated in the absence and presence of exogenous primer in order to distinguish the chromatin-associated poly(A) polymerase from the "free" enzyme (Jacob, S.T., Roe, F.J. and Rose, K.M. (1976) Biochem. J. 153, 733--735). The chromatin-bound enzyme, which adds adenylate residues onto the endogenous RNA, was selectively inhibited at low concentrations of cordycepin 5'-triphosphate, 50% inhibition being achieved at 2microng/ml. At least 80 times more inhibitor was required for 50% reduction in the "free" nuclear poly(A) polymerase activity. Inhibition of DNA-dependent RNA synthesis also required higher concentrations of the nucleotide analogue. These data not only offer a mechanism for the selective inhibition of initial polyadenylation of heterogeneous nuclear RNA in vivo by cordycepin, but also provide a satisfactory explanation for the indiscriminate effect of the inhibitor on partially purified or "free" poly(A) and RNA polymerases.     

Effects of nuclear proteins on the activity of soybean DNA polymerase

The effects of nuclear proteins on DNA synthesis were investigated before and after incubation with radioactive ATP and a crude preparation of nuclear protein kinase. After partial purification by DEAE-cellulose chromatography, the major protein fractions were added separately to DNA polymerase assays. One of the seven protein fractions inhibited DNA synthesis by 50%, whereas three other fractions stimulated DNA polymerase activity 3 to 4-fold. After incubation with ATP, one fraction became inhibitory, and the three stimulatory fractions, which had high levels of radioactivity, were more effective. This stimulation of DNA polymerase activity was proportional to added nuclear protein and was maximum at $\text{6 μ}\text{g}\text{20 μ}\text{g}$ DNA.     

A template independent, rifampicin sensitive poly (A).poly (U) synthesizing activity present in Bacillus subtilis.

A template independent poly (A)·poly (U) synthesizing activity has been isolated from $\text{Bacillus subtilis}$. This activity is eluted from a DNA-cellulose column along with DNA-dependent RNA polymerase. The column fractions which exhibit this activity contain RNA polymerase holoenzyme plus a polypeptide which is slightly larger than sigma factor; pure RNA polymerase holoenzyme did not synthesize poly (A)·poly (U). The activity was dependent on the presence of ATP, UTP, and Mn⁺⁺ (Mg⁺⁺ could not substitute), and was inhibited by rifampicin, streptolydigin, and Cibacron Blue. The incorporation of nucleotides was not linear with time, but appeared after a lag period. The results suggest that a modified form of DNA-dependent RNA polymerase analogous to $\text{Escherichia coli}$ holoenzyme II is catalyzing the synthesis of poly (A)·poly (U).     

Stimulation of poly(dT) transcription by Bacillussubtilis RNA polymerase in the presence of adenosine monophosphate

The rate of synthesis of poly(A) on a ply(dT) template by $\text{Bacillus}\text{subtilis}$ RNA polymerase is a function of ATP concentration and is expressed as a sigmoidal curve. The addition of millimolar concentration of AMP to low concentrations of ATP stimulates synthesis of poly(A) twenty fold and raises the rate of synthesis to the levels obtained at high ATP concentrations. The reaction is completely dependent upon the presence of poly(dT) and requires the complementary mononucleotide. Stimulation of poly(A) synthesis by AMP is more evident with the holoenzyme. Analysis of poly(A) products by acrylamide gels showed that the poly(A) synthesized in the presence of AMP has an higher molecular weight than poly(A) synthesized in the absence of AMP.     

Isolation of an androgen acceptor from salt extract of rat prostatic chromatin

The soluble androgen acceptor has been isolated from 0.35 M NaCl extract of rat prostatic chromatin by affinity chromatography on DNA-cellulose. The acceptor activity was assayed by interaction with 5α-dihydrotestosterone-receptor. Native DNA enhances this interaction. Polyacrylamide gel electrophoresis of the acceptor under denaturing conditions reveals a single polypeptide of molecular weight of 14,000. Amino acid analysis shows that the acceptor protein contains a higher content of acidic amino acid residues than basic amino acid residues. In an $\text{in}\text{vitro}$ RNA synthesizing system catalyzed by rat RNA polymerase II, addition of the acceptor stimulates RNA synthesis. Based on incorporation of [γ-³²P]ATP and [γ-³²P]GTP, the stimulation by the acceptor is mainly on the initiation of RNA chains.     

Inhibition of reverse transcriptase activity of RNA-tumor viruses by fagaronine+.

Fagaronine, a benzophenanthridine alkaloid from roots of $\text{Fagara zanthoxyloides}$ (Rutaceae), has been reported to possess anti-leukemic activity. It inhibited RNA-directed DNA polymerase activity from avian myeloblastosis virus, Rauscher leukemia virus and simian sarcoma virus. With poly rA·oligo dT, the alkaloid concentration for 50% inhibition of the enzyme activity from these viruses was in the range of 6–12 μg (15 – 31 nmoles) per ml of reaction mixture. The enzyme reaction was also inhibited with activated DNA and 70S RNA as templates; however, with poly rC·oligo dG no inhibition of enzyme activity was obtained. These results suggest that fagaronine inhibits enzyme activity by interaction with the A:T templateprimer.     

Effect of aphidicolin on viral and human DNA polymerases.

DNA polymerases induced by Herpes simplex and Vaccinia viruses are inhibited by aphidicolin and this inhibition is probably the basis of its antiviral activity $\text{in vivo}$. Its possible clinical use is however hampered by the concomitant effect on human replicative DNA polymerase α. The inhibition of human α-polymerase is reversible both $\text{in}$$\text{vitro}$ and $\text{in vivo}$ and the changes in the rate of incorporation of thymidine into DNA, following treatment with aphidicolin for a generation time, indicate the likely synchronization of the cells due to this agent. DNA polymerase β, which has recently been shown to carry out repair synthesis of damaged nuclear DNA, is not inhibited by aphidicolin either $\text{in vitro}$ on $\text{in vivo}$ suggesting that the drug could allow a rapid and simple evaluation of DNA repair synthesis due to DNA polymerase β.     

RNA polymerase activity in double-stranded ribonucleic acid virus particles from Aspergillus foetidus.

RNA polymerase activities have been detected in purified particles of $\text{Aspergillus foetidus}$ viruses S and F. Incorporation of [³H]-UTP into acid insoluble RNA was dependent on ATP, GTP, CTP and magnesium ions. No pretreatment of the particles was required and the rate of reaction was proportional to the amount of virus added. In the conditions used RNA synthesis by $\text{A. foetidus}$ virus S was complete in 4 h. The reaction could be stimulated by Triton X-100, but was unaffected by heat shock, dithiothreitol, potassium chloride or ammonium chloride; it was inhibited by ethidium bromide but not by actinomycin D. The major reaction product was single-stranded RNA, as indicated by its sensitivity to degradation by ribonuclease A. This is the first report of synthesis of single-stranded RNA by a double-stranded RNA mycovirus.     

Differential effects of cycloheximide on protein and RNA synthesis as a function of dose

The $\text{in}$$\text{vivo}$ dose response of rat liver protein and DNA synthesis to cycloheximide have been determined. Protein synthesis was quite sensitive to relatively low doses of cycloheximide being inhibited by more than 90% with 1.5 mg/kg. Maximal inhibition of 98% was achieved with 5 mg/kg. There was no inhibition of RNA synthesis with this dose of cycloheximide. Larger doses of cycloheximide did lead to quite marked inhibition of RNA synthesis without any change in the already maximally inhibited rate of protein synthesis. This differential effect of cycloheximide on protein and RNA synthesis as a function of dose indicates that the inhibition of RNA synthesis caused by the antibiotic is not a consequence of the inhibition of protein synthesis but related otherwise to the effects of large doses of cycloheximide.     

Mutational alteration of Bacillus subtilis DNA polymerase 3 to hydroxyphenylazopyrimidine resistance: polymerase 3 is necessary for DNA replication

A spontaneous mutant of $\text{Bacillus}\text{subtilis}$ resistant to killing by two hydroxyphenylazopyrimidines has been isolated. The DNA polymerase III of this mutant is resistant to inhibition by these drugs. The K_i for 6-(p-hydroxyphenylazo)-uracil (HPUra) is 20 μM, about 40 times higher than the K_i of the wild-type enzyme. The mutant and wild-type polymerases behave similarly during purification, are sensitive to N-ethylmaleimide and to 0.1 M KCl, and have the same K_m for dGTP (0.5 μM). The HPUra inhibition of both enzymes is attenuated competitively by dGTP. We conclude that polymerase III is the target for hydroxyphenylazopyrimidines $\text{in}\text{vivo}$, and since the drugs specifically inhibit replicative DNA synthesis, polymerase III is necessary for DNA replication.     

Evidence for the regulation of pyridoxal 5′-phosphate formation in liver by pyridoxamine (pyridoxine) 5′-phosphate oxidase

Pyridoxamine (pyridoxine) 5′-phosphate oxidase (EC 1.4.3.5) purified from rabbit liver is competitively inhibited by the reaction product, pyridoxal 5′-phosphate. The K_i, 3 μM, is considerably lower than the K_m for either natural substrate (18 and 24 μM for pyridoxamine 5′-phosphate and 25 and 16 μM for pyridoxine 5′-phosphate in 0.2 M potassium phosphate at pH 8 and 7, respectively). The K_i determined using a 10% rabbit liver homogenate is the same as that for the pure enzyme; hence, product inhibition $\text{in}\text{vivo}$ is probably not diminished significantly by other cellular components. Similar determinations for a 10% rat liver homogenate also show strong inhibition by pyridoxal 5′-phosphate. Since the reported liver content of free or loosely bound pyridoxal 5′-phosphate is greater than K_i, the oxidase in liver is probably associated with pyridoxal 5′-phosphate. These results also suggest that product inhibition of pyridoxamine-P oxidase may regulate the $\text{in}\text{vivo}$ rate of pyridoxal 5′-phosphate formation.     

Translational control of the expression of the β subunit gene of E., coli RNA polymerase

Using the plasmid pNF1337 as template, a mRNA preparation has been obtained that directs the $\text{in}\text{,}\text{vitro}$ synthesis of fMet-Val, the N-terminal dipeptide of the β subunit of RNA polymerase. RNA polymerase holoenzyme specifically inhibits the mRNA-directed synthesis of fMet-Val showing that the autoregulation by RNA polymerase of β,β′ synthesis is at the level of translation. L factor ($\text{nusA}$ gene product) stimulates the synthesis of fMet-Val from a DNA template but not from mRNA. Rifampicin has no effect on the mRNA-directed synthesis of fMet-Val or the ability of RNA polymerase to inhibit fMet-Val synthesis.     

Nδ-(phosphonacetyl)-L-ornithine,a potent transition state analogue inhibitor of ornithine carbamoyltransferase

$\text{N}$^δ-(Phosphonacetyl)-L-ornithine, a transition state analogue for the reaction catalyzed by ornithine carbamoyltransferase (EC 2.1.3.3), was synthesized. It strongly inhibited bovine liver ornithine carbamoyltransferase. The inhibition was competitive with respect to carbamoyl-phosphate; the apparent $\text{K}$_m values for carbamoyl-phosphate were 15 μM in 0.05 M $\text{N}$-2-hydroxyethylpiperazine-$\text{N′}$-2-ethanesulfonate (pH 7.2) and 33 μM in 0.1 M Tris-HCl (pH 8.5), and the inhibition constants at pH 7.2 and 8.5 were 7.1 and 4.7 nM, respectively. The inhibition was non-competitive with L-ornithine, the other substrate of the enzyme. This analogue may provide an effective reagent for the elucidation of carbamoyl-phosphate metabolism and its regulation in the liver of ureotelic animals.