Affinity labeling of Escherichia coli B deoxyribonucleic acid dependent ribonucleic acid polymerase

Effect of the dialdehyde derivative of 5'-deoxyinosine on pyrimidine deoxyribonucleoside metabolism in L1210 cells

The effects of the dialdehyde derivatives of inosine (Inox) and 5'-deoxyinosine (5'-dInox) on L1210 cells were compared. The growth of L1210 cells was inhibited to a greater extent by 5'-dInox than by Inox. The increased inhibition of L1210 cell growth by 5'-dInox was also reflected by the increased inhibition of the incorporation of precursors into RNA, DNA and proteins. Even though 5'-dInox was a more potent inhibitor, Inox accumulated in the L1210 cells to levels 4- to 5-fold greater than 5'-dInox. The metabolism of [5-3H]deoxycytidine and [5-3H]deoxyuridine by L1210 cells in culture, in the presence of Inox or 5'-dInox, indicated that dCMP deaminase was an intracellular site of action for 5'-dInox. The dCMP deaminase activity in cell-free extracts prepared from 5'-dInox-treated cells was reduced markedly. This decrease in activity was not reversed by increased substrate concentrations nor was the activity subject to allosteric activation by dCTP. Deoxyuridine and deoxycytidine were able to reverse the effects of 5'-dInox on the inhibition of L1210 cell growth.

Probes of eukaryotic DNA-dependent RNA polymerase II-II. Covalent binding of two purine nucleoside dialdehydes to the initiation subsite

The catalytic center of wheat germ DNA-dependent RNA polymerase II (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) as a model eukaryotic enzyme system was probed with two purine nucleoside dialdehydes, 6-methylthioinosinedicarboxaldehyde (MMPR-OP) and a derivative 6-[(acetylaminoethyl)-1-naphthylamine-5-sulfonyl]thioinosinedicarboxaldehyde (AMPR-OP). Both drugs gave noncompetitive inhibition with respect to [3H]UMP incorporations into RNA, and inhibitor bindings were reversed with initiation substrates. The Ki values for MMPR-OP and AMPR-OP were determined to be 0.64 mM and 1.0 muM respectively. The drugs were covalently bound to the catalytic center by NaBH4 reduction. Both were found bound to the largest enzyme subunit, IIa. It is tentatively concluded that MMPR-OP and AMPR-OP inhibit RNA polymerase II by binding to an essential lysine in the initiation subsite of the catalytic center located on the IIa subunit.

Probes of eukaryotic DNA-dependent RNA polymerase II-I. Binding of 9-beta-D-arabinofuranosyl-6-mercaptopurine to the elongation subsite

9-beta-D-Arabinofuranosyl-6-mercaptopurine (ara-6-MP) was used to affinity-label wheat germ DNA-dependent RNA polymerase II (or B) (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6). This nucleoside analogue was found to be a competitive inhibitor with respect to [3H]UMP incorporation. Natural substrates protected the enzyme from inactivation by ara-6-MP when the enzyme was preincubated with excess concentrations of substrates, suggesting that the inhibitor binds at the elongation subsite. The inhibitor bound the catalytic center of the enzyme with a stoichiometry of 0.6:1. The sulfhydryl reagent, dithiothreitol, reversed the inhibition by ara-6-MP, suggesting that the 6-thiol group of the inhibitor was interacting closely with an essential cysteine residue in the catalytic center of the enzyme. Chromatographic analysis of the pronase-digestion products of the RNA polymerase II-ara-6-MP complex also showed that ara-6-MP had bound a cysteine residue. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the denatured [6-35S]ara-6-MP-labeled RNA polymerase II revealed that over 80% of the radioactivity was associated with the IIb subunit of the enzyme.

The reaction of bovine glutamate dehydrogenase with periodate-oxidised ADP

1. The reactive analogue oADP produced by periodate oxidation of ADP has been studied as a potential affinity label for the enzyme bovine glutamate dehydrogenase, using circular dichroism (CD) difference spectroscopy to monitor specific binding. 2. The analogue binds stoichiometrically, rapidly and reversibly to the adenine nucleotide binding site with Kd approximately equal to 12 microM (20 degrees C, pH 7) with characteristic intensification of the adenine nucleotide CD at 260 nm. 3. This complex is unstable and decays with a half-life of about 1.5 h; the analogue then becomes attached as a Schiff base to a number of subsidiary sites, including the enzyme active site, with partial inactivation of the enzyme. 4. Depending upon initial concentration of oADP, the enzyme activity is progressively lost during the slow reaction; following borohydride reduction, up to four molecules of analogue are bound/subunit. 5. Protection against loss of enzyme activity is afforded by the coenzyme NAD+ plus glutarate or L-hydroxyglutarate (an effective inhibitor), or by glutarate alone, but not by NAD+ alone. 6. Spectroscopic and protection studies indicate that after the decay of the specific CD signal, the enzyme retains the capacity to bind ADP, but that this is progressively lost in parallel with decay of enzymic activity. 7. The results are consistent with proximity or functional interaction between the adenine nucleotide site and the coenzyme binding portion of the active site. 8. Thus oADP does not act as a true affinity label for the adenine nucleotide binding site, but the reaction subsequent to binding at that site shows some specificity directed towards the active site.

DNA strand specificity in promoter recognition by RNA polymerase

DNA strand and enzyme subunit specificities involved in the interaction between E. coli RNA polymerase and T7 DNA were studied by photo-crosslinking techniques. In non-specific enzyme-DNA complexes, subunits, sigma, beta, and beta' were crosslinked to both strands of the DNA. Under conditions leading to specific enzyme-promoter complexes, however, only sigma and beta subunits were crosslinked. The sigma subunit was crosslinked preferentially to the non-sense strand at promoter sites. No such strand specificity was observed for the beta subunit. These results provide insight into the molecular mechanism of promoter recognition and indicate that the interaction between RNA polymerase and DNA template is different at promoters and at non-specific sites.

Detection of nucleoside triphosphate binding sites of two types in Escherichia coli RNA-polymerase by affinity labeling

The affinity labeling of E. coli RNA polymerase by periodate-oxidized uridin triphosphate (o-UTP) has been carried out under the conditions of poly(dA) and poly(dT) transcription. The extent of RNA polymerase labeling proved to be 2.5 times higher under the transcription of poly(dA) as compared to poly(dT). The amount of o-UTP attached to beta beta'-subunits has been found to decrease if RNA polymerase is labeled in the transcribed complex with poly(dT). These results as well as those obtained in our previous study (1), suggest that there are two types of binding sites for nucleoside triphosphates and their analogs in E. coli RNA polymerase.

Affinity labeling of a cysteine at or near the catalytic center of Escherichia coli B DNA-dependent RNA polymerase

9-beta-D-Arabinofuranosyl-6-thiopurine was used to affinity label DNA-dependent RNA polymerase isolated from Escherichia coli B. This substrate analogue displayed competitive type inhibition which could be reversed by addition of a thiol reagent, such as dithiothreitol, while exposure to hydrogen peroxide, a mild oxidizing agent, caused an increase in both the inhibitory and enzyme binding capability of arabinofuranosyl thiopurine. Chromatographic analysis of the products obtained by pronase digestion of the 9-beta-D-arabinofuranosyl-6-[35S]thiopurine-enzyme complex suggests that disulfide bond formation occurs between the inhibitor and a cysteine residue located in or near the active center of the enzyme. In addition, polyacrylamide gel electrophoresis indicated that the arabinofuranosyl thiopurine moeity was bound to the beta' subunit of the enzyme.

Subunit localizations of zinc(II) in DNA-dependent RNA polymerase from Escherichia coli B

RNA Polymerase holoenzyme and core enzyme from Escherichia coli B have been shown to contain two zinc ions. Flameless atomic absorption spectroscopy of the isolated core subunits indicated that one zinc ion is localized on the beta subunit and the other is bound on the beta' subunit. Atomic fluorescence spectroscopy showed that prolonged dialysis of the metalloenzyme against 0.01 M o-phenanthroline resulted in the removal of both zinc(II) ions with accompanying loss of enzymatic activity. The activity of the apoenzyme was observed to be completely restored by readdition of zinc(II) and partially restored by cobalt(II).

Dialdehydes derived from adenine nucleosides as substrates and inhibitors of adenosine aminohydrolase

A series of nucleoside dialdehydes have been obtained as powders after treatment of various adenine nucleosides with paraperiodic acid. Thus, oxidation gave dialdehydes derived from adenosine (1), 9-alpha-D-mannopyranosyladenine (2), 9-(5-deoxy-alpha-D-arabinofuranosyl)adenine (3), 9-alpha-L-rhamnopyranosyladenine (4), 9-beta-L-fucopyranosyladenine (5), 9-beta-D-fucopyranosyladenine (6), 9-alpha-D-arabinopyranosyladenine (7), 9-beta-D-ribopyranosyladenine (8), and 9-(5-deoxy-beta-D-erythro-pent-4-enofuranosyl)adenine (9). Nucleoside dialdehydes 1-3 and 6-8 were weak substrates for adenosine aminohydrolase from calf intestinal mucosa. Dialdehyde 8 had the strongest affinity, but 1 had the highest Vmax. All of the dialdehydes except 5 were inhibitors of the enzyme. The best inhibitors were 9 (Ki = 4 microM) and 4 (ki = 28 microM), and neither were substrates. The inhibitors did not exhibit time-dependent inhibition and did not appear to form covalent bonds with the protein. The data strongly suggest that the active form of the dialdehydes is as the open-chain dihydrates. The alcohol obtained by reduction of 9 (compound 10) was the strongest inhibitor (Ki = 0.9 microM among the related alcohols and the nucleoside dialdehydes.

Studies on the mechanism of action of histone kinase dependent on adenosine 3':5'-monophosphate. Evidence for involvement of histidine and lysine residues in the phosphotransferase reaction

The reaction of the phosphate residue transfer catalysed by histone kinase dependent on adenosine 3':5'-monophosphate (cyclic AMP) was studied. The phosphotransferase reaction was shown to obey the mechanism of ping-pong bi-bi type. After incubation of the catalytic subunit of histone kinase with [gamma-32P]ATP the incorporation of one mole of [32P]phosphage per mole of protein was observed. The tryptic [32P]phosphohistidine-containing peptide was isolated and its N-terminus and amino acid composition were determined. The 2',3'-dialdehyde derivative of ATP (oATP) was used as the affinity label for the catalytic subunit of cyclic-AMP-dependent histone kinase. The inhibitor formed an alidmine bond with epsilon-amino group of the lysine residue of the active site and was irreversibly bound to the enzyme after reduction by sodium borohydride with concurrent irreversible inactivation of the enzyme. After inactivation, about one mole of 14C-labelled inhibitor was incorporated per mole of the enzyme. ATP effectively protected the catalytic subunit of histone kinase against inactivation by oATP. Tryptic digestion of the enzyme-inhibitor complex led to the isolation of the 14C-labelled peptide of the active site of histone kinase. Basing on these results, the role of histidine and lysine residues in the active site of the catalytic subunit of histone kinase was suggested.

Affinity labeling of Escherichia coli DNA-dependent RNA polymerase with 5-formyl-l-(alpha-D-ribofuranosyl)uracil 5'-triphosphate

5-Formyl-1-(alpha-D-ribofuranosyl)uracil 5'=triphosphate has been used to affinity label E. coli DNA-dependent RNA polymerase. It is a noncompetitive inhibitor of the enzyme with Ki=0.54 mM. A short preincubation of the enzyme and alpha-fo5UTP is required to achieve maximum inhibition, and the entent of the inhibition is dependent upon the alpha-fo5UTP concentration. When a preincubation mixture of alpha-fo5UTP/enzyme is diluted, the enzyme regains activity with time showing that the inhibition is reversible, presumably occurring by Schiff base formation between an amino group on the enzyme and the formyl group. Upon sodium borohydride reduction of an enzyme/alpha-fo5UTP preincubation mixture the enzyme is irreversibly inhibited. alpha-fo5UTP is more effective in inhibiting the enzyme than alpha-fo5U, and the inhibition is decreased by the presence of ATP, UTP, or GTP in the preincubation mixture, suggesting that inhibition is occurring at a triphosphate binding site. The stoichiometry of binding of alpha-fo5UTP to the enzyme was determined using the gamma-32P-labeled derivative. After a 20-s preincubation of enzyme/alpha-fo5UTP followed by NaBH4 reduction the stoichiometry of binding was 1.1:1 (alpha-fo5UTP bound: inactivated enzyme), and this rose to 2.42:1 after a 10-min preincubation. After a 20-s preincubation the [gamma-32P]-alpha-fo5UTP was shown to be located on the beta subunit of RNA polymerase by cellulose acetate electrophoresis in 6 M urea.

Pyruvate carboxylase: affinity labelling of the magnesium adenosine triphosphate binding site

The 2' , 3'-dialdehyde derivative of ATP (oATP) was prepared by periodate oxidation and on the following criteria was considered to be an effective affinity label. The magnesium complex of this derivative (Mg-oATP2) was shown to ba linear competitive inhibitor with respect to MgATP2-in both the acetyl-CoA-dependent and -independent activities of the enzyme but was a non-competitive inhibitor with respect to bicarbonate, and an uncompetitive inhibitor with respect to pyruvate. Mg-oATP was covalently bound to pyruvate carboxylase by reduction using sodium borohydride with concurrent irreversible inactivation of the enzyme...

RNA polymerase mutants of Escherichia coli. III. A temperature-sensitive rifampicin-resistant mutant

Temperature-sensitive mutants of Escherichia coli that are unable to grow at high temperature can be obtained among those selected for resistance to streptovaricin or rifampicin at low temperature (Yura et al., 1973). One of these mutants (KY5323) that was supposed to carry a single mutation affecting both rifampicin resistance and temperature sensitivity was further investigated. Using purified RNA polymerase preparations obtained from the mutant and the wild type, it was found that the activity for RNA chain elongation is more sensitive to heat treatment than that for RNA chain initiation or DNA binding, and that the mutant enzyme is significantly more labile than the wild-type enzyme with respect to RNA chain elongation, when heat treatment is carried out at high salt concentration. These results, taken together with those of the enzyme reconstitution experiments, strongly suggest that the beta subunit of the polymerase is directly involved in both RNA chain initiation and elongation reactions. Enzyme reconstitution experiments using isolated subunits derived from the mutant and the wild-type polymerases demonstrate that the alteration of beta subunit is primarily responsible for both rifampicin resistance and thermolability of the mutant enzyme. In addition, the results suggested the apparent alteration of both beta and alpha subunits in this mutant. Extensive transduction experiments provided genetic evidence that are consistent with the view that the strain KY5323 carries a second mutation affecting the beta subunit, beside the primary mutation affecting the beta subunit. The hypothetical beta subunit mutation seems to modify quantitatively the rifampicin resistance caused by the beta subunit mutation.