HeLa cell DNA polymerase alpha is tightly associated with tryptophanyl-tRNA synthetase and diadenosine 5',5"'-P1,P4-tetraphosphate binding activities

The purified high molecular weight form of HeLa cell DNA polymerase alpha (deoxynucleosidetriphosphate: DNA deoxynucleotidyltransferase, EC 2.7.7.7) was shown to associate tightly with several aminoacyl-tRNA synthetase activities. Fractionation of the high molecular weight enzyme on hexylagarose followed by gel filtration, chromatography on phosphocellulose, or polyacrylamide gel electrophoresis under nondenaturing conditions demonstrated copurification of only tryptophanyl-tRNA synthetase [L-tryptophan:tRNATrp ligase (AMP-forming), EC 6.1.1.2] along with DNA polymerase alpha. The high molecular weight (660,000) and low molecular weight (145,000) forms of DNA polymerase alpha were shown to possess a highly specific, noncovalent, diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A) binding activity. The dissociation constants were determined to be 16 and 22 microM, respectively, by utilization of a charcoal adsorption procedure. No high-affinity binding of ATP could be detected. These findings suggest a link between the amino acid activation process and DNA replication in mammalian cells.

[Comparison of ATP-pyrophosphate exchange reactions, catalyzed by two different "one-site" forms of tryptophanyl-tRNA-synthetase and by native enzyme]

Kinetic parameters of the reaction of ATP-PPi exchange, catalysed by "one-site" form of beef pancreas tryptophanyl-tRNA-synthetase are determined. The one-site form was obtained by affinity labelling of one active centre of the enzyme with alkylated analog of tryptophan. The comparison of kinetic parameters of this one-site form with the other one produced earlier by affinity labelling with analog of tryptophanyl-tRNA and the native enzyme was carried out. It was shown that the presence of tRNA improves the discrimination properties of the enzyme and diminishes the concentrations of "dead-end" complexes. Negative cooperativity in binding of two molecules of tryptophan is observed, which disappears in the presence of ATP, leading to an apparent synergistic effect. The molecule of tryptophan, which is present in the active centre, diminishes affinity of pyrophosphate.

Tryptophanyl-tRNA synthetase from beef pancreas. Spectroscopic analysis of the stoichiometry of formation of the enzyme-tryptophanyl-adenylate complex

The dimeric enzyme tryptophanyl-tRNA synthetase from beef pancreas catalyses the stoichiometric formation of one mole of tryptophanyl-adenylate per subunit. This formation is associated with optical changes (absorbance, fluorescence, optical rotation) and is confirmed by analytical ultracentrifugation. An equal amplitude of the change is observed for each adenylation site at pH 8.0, 25 degrees C, regardless of the optical method used. The formation of two tryptophanyl adenylates per dimer corresponds to a molar absorbance change delta epsilon 291 = 12000 +/- 500 cm-1 M-1, to a fluorescence quenching of 24 per cent at 340 nm and to a variation in optical rotation of 6 per cent at 313 nm. The circular dichroic band of the adenosine moiety of ATP is strongly increased. The addition of sodium pyrophosphate to the tryptophanyl-adenylate-enzyme complex restores the absorbance and fluorescence amplitude observed prior to the addition of ATP to the enzyme. Magnesium ions are necessary to the reaction. A pertubation of the environment of both the protein and the substrates (tryptophan and ATP) have to be taken into account to explain the magnitude of the observed changes.

[Tryptophanyl-tRNA-synthetase: limited proteolysis by elastase and isolation of "one-site" enzyme]

Each subunit of the dimeric tryptophanyl-tRNA-synthetase from beef pancreas is subjected to limited hydrolysis by elastase in two stages, according to scheme: 60 00 +/- 2000 leads to 51 000 +/- 2000 leads to 40 000 +/- 1500 daltons. In the course of the second step tryptophanyl-tRNA-synthetase looses its enzymatic activity. In the presence of substrates the pattern of fragments does not change. Formation of tryptophanyladenylate enzyme complex decreases the rate of proteolysis. Using the ability of synthetase to form one mole of stable aminoacyladenylate per mole of synthetase, the "one-site" enzyme was obtained by action of elastase on aminoacyladenylate-enzyme complex. This "one-site" enzyme consists of two subunits, one of which has a molecular weight of 51 000 daltons and is active and the other has a molecular weight of 40 000 daltons and is inactive. The "one-site" enzyme had Km values for all substrates for both aminoacylation and ATP--[32P]PP exchange reactions which are similar to values of Km for the native enzyme.

Transfer RNA control of the activation of isomeric tRNATrp's

Previous studies of the homologous aminoacylations of Escherichia coli and yeast tRNATrp's terminating in 2'- and 3'-deoxyadenosine established that E. coli tryptophanyl-tRNA synthetase activates its cognate tRNA preferentially on the 2' position, while the corresponding yeast enzyme utilizes the 3' position on its homologous substrate tRNA. As this seemed to be the only change in positional specificity during evolution, the heterologous activations were investigated in an effort to determine the basis for this change. Remarkably, E. coli tRNATrp terminating in 3'-deoxyadenosine was found to be the preferred substrate for both the E. coli and yeast activating enzymes, while the same tryptophanyl-tRNA synthetase preparations both activated the isomeric yeast tRNATrp's preferentially on the 3' position. Thus, the preferred position of activation was found to be specified by the tRNA rather than the activating enzyme and, additionally, to be due to some process not reflected in initial velocity measurements. The variable utilization of individual modified aminoacyl-tRNA's as substrates in an enzyme-catalyzed deacylation process appears to provide the most likely explanation for the experimental observations.

Anticooperative binding of L-tryptophan to tryptophanyl-tRNA synthetase from beef pancreas. Study at equilibrium by dialysis and changes in spectroscopic properties

Equilibrium dialysis and gel filtration studies show that tryptophanyl-tRNA synthetase from beef pancreas binds two molecules of L-tryptophan per dimer in an anticooperative way. The binding of tryptophan ellicits a series of spectroscopic changes in the protein as seen by absorbance, fluorescence and circular dichroism. The molar absorption change of the protein-tryptophan system upon formation of the complex is delta epsilon292 = 10 400 +/- 1000 M(-1) cm(-1) per dimer. Taking an initial symmetrical dimeric protein the two dissociation constants for tryptophan at pH 8, 25 degrees C are respectively K1 = 2.0 +/- 0.5 muM and K2 = 10 +/- 4 muM. They are respectively K1 = 1 +/- 0.25 muM and K2 = 20 +/- 8 muM if one considers a sequenced binding of the two tryptophan molecules. The dichroic band at 290 nm of the free protein disappears when tryptophan is bound. All observed changes are characteristic of tryptophan perturbation and none of tyrosine perturbation. They all exceed the effect that can be expected from the change in environment of the bound tryptophan molecules and modifications of the tertiary structure of the protein have to be taken into account to explain the observed spectroscopic data.

[Immunochemical properties of tryptophanyl-tRNA synthetase and its fragments]

The interaction between beef pancreas tryptophanyl-tRNA synthetase and its fragments produced after limited proteolysis, with IgG fraction of antiserum and with Fab fragment of IgG has been studied. Both the intact antibodies and Fab fragments inhibit the enzyme activity in tRNA aminoacylation and tryptophan dependent ATP-32P pyrophosphate exchange reactions. However, the enzyme inhibited by antibodies is still able to form a complex with tryptophanyl-tRNA. The enzymatically active fragment obtained after endogenous proteolysis interacts only with 1/3 of the antibodies against native enzyme. The fragment produced by trypsinolysis possess similar immunochemical properties. This fragment has almost the same molecular weight but is enzymatically inactive. Pure antibodies against tryptic fragment isolated by means of specific immunoabsorbent inhibit the enzymatic activity. The antibodies which do not interact with this fragment (2/3 of the total amount of antibodies) have no influence on the enzymatic activity. The immunochemical identity of the two synthetase fragments differing in their enzymatic activity supports the assumption that the loss of enzymatic activity of the tryptis fragment is caused by lack of a small peptide which is retained in case of endogenous proteolysis. Probably the amino acid residues of this peptide participate in formation of the active centre of tryptophanyl-tRNA synthetase. A new procedure for determination of the number of antigenic determinants in proteins is developed. It is shown by this method that beef pancreas tryptophanyl-tRNA synthetase contains 9 +/- 1 antigenic determinants.

Inhibition of aminoacyl-transfer ribonucleic acid synthetases and the regulation of amino acid biosynthetic enzymes in Neurospora crassa

Growth conditions that result in the accumulation of the tryptophan intermediate indoleglycerol phosphate or of the histidine intermediate imidazoleglycerol phosphate cause mycelia of Neurospora crassa to exhibit an immediate and sustained increase in the differential rate at which the biosynthetic enzymes of the tryptophan, histidine, and arginine pathways are synthesized. These accumulated intermediates are shown to be inhibitors of the activity of aminoacyltransfer ribonucleic acid (tRNA) synthetases, as judged by an in vitro esterification assay. The tryptophan intermediate is shown to inhibit the charging of tryptophan, and the histidine intermediate is shown to inhibit charging of histidine. The inhibitions noted are consistent with the finding that the level of charged tRNATrp is decreased significantly in cells that have accumulated indoleglycerol phosphate and that of tRNAHis is decreased significantly in cells that have accumulated imidazoleglycerol phosphate. These results are interpreted as support for the involvement of aminoacyl-tRNA species in mediating cross-pathway regulation of the tryptophan, histidine, and arginine biosynthetic pathways as proposed in Lester's polyrepressor hypothesis (G. Lester, 1971). the correlations noted lead to the conclusion that Neurospora utilizes regulatory mechanisms that have the ability to react to changes in the level of charging of tRNA species.

Aminoacylation of tRNA Trp from beef liver, yeast and E. coli by beef pancrease tryptophan-tRNA ligase. Stoichiometry of tRNATrp binding

The Michaelis constants and the maximum velocities in the aminoacylation reaction of tRNATrp from beef liver, yeast and E. coli by pure beef pancreas tryptophan-tRNA ligase show that this mammalian enzyme recognizes and charges the two eucaryotic tRNAs with the same efficiency. The rate of aminoacylation of the procaryotic tRNATrp by the enzyme is three orders of magnitude lower. The pH optimum of aminoacylation is 8 for both eucaryotic tRNAs. The optimum magnesium concentration is different. The rate is maximum when magnesium concentration is stoichiometric to ATP concentration for tRNATrp from beef liver and 10 mM above ATP concentration for tRNATrp from yeast. The number of binding sites on the enzyme for the two eucaryotic tRNAs has been measured by equilibrium filtration on Sephadex G-100 and found equal to two.

Two substrate binding sites on tryptophanyl transfer ribonucleic acid synthetase of Escherichia coli

Tryptophanyl-tRNA synthetase of Escherichia coli has 1.8 binding sites for L-tryptophan with Kdiss of 12 x 10(-5) M as shown by equilibrium dialysis. The results are in accord with the known structure of the enzyme, and alpha2 dimer of 74,000 molecular weight, and with 2 binding sites for tryptophanyl-ATP ester. Ordinary sucrose density gradient centrifugation reveals a complex composed of one tRNATrp bound per enzyme dimer. When tRNATrp is mixed throughout the gradient at concentrations from 5.4 x 10(-6) M to 2.0 x 10(-5) M, a new peak appears in the position expected for a complex with two tRNATrp molecules bound per enzyme dimer. Sedimentation through gradients lacking tRNATrp favors dissociation of the 1:2 complex but not the 1:1 complex. The data indicate 2 binding sites for tRNATrp on tryptophanyl-tRNA synthetase.

[Kinetic model describing the action of tryptophanyl-tRNA-synthetase]

Reaction rates for ATP-PPi isotope exchange (vex) and tryptophanyl-tRNA formation (vaa) catalysed concomitantly in one incubation mixture by beef pancreas tryptophanyl-tRNA synthetase (trsase) have been examined as a function of substrate concentrations. Comparison of the vex/vaa ratio found experimentally with the ratio predicted theoretically conforms the mechanism suggested earlier and permits to describe it in more detail. I. At least two reaction routes exist in which an ATP-PP: exchange is allowed. These routes are interconnected with each other via the stage at which tRNA binds to the enzyme. 2. In both these routes the low molecular weight substrates bind with enzyme in the order ATP first, tryptophan second. 3. Enzyme-aminoacyladenylate complex is an intermediate in the reaction of aminoacyl-tRNA formation. Pyrophosphate is detached from the enzyme prior to tRNA. 4. The enzyme releases AMP and tryptophanyl-tRNA in a random fashion. All the aformentioned properties are common both for trigger mechanism and Yarus-Berg mechanism which up to now were considered in literature independently.

Human tryptophan transfer ribonucleic acid synthetase. Composition, function of thiol groups, and structure of thiol peptides

Human tryptophanyl-tRNA synthetase resembles its counterpart in Escherichia coli in quaternary structure (alpha2), but differs in molecular weight, amino acid composition, the number of thiol groups, and the relationship of the thiol groups to enzyme activity. Nevertheless, one of the thiol groups resides in a heptapeptide sequence homologous to a heptapeptide sequence containing a thiol group in the E. coli enzyme. Each subunit of the enzyme has 6 half-cystine residues, and four thiol groups are readily titrated with 5,5'-dithiobis(2-nitrobenzoic acid). Titration of these four thiol groups inactivates the enzyme, and the inactivation is partially reversible by reduction with dithiothreitol. One thiol group reacts rapidly unless L-tryptophan, ATP, and Mg2+ are present together.

Tryptophanyl transfer ribonucleic acid synthetase of Escherichia coli. Character of required thiol group and structure of thiol peptides

Native tryptophanyl-tRNA synthetase purified from Escherichia coli B has on each identical subunit a single thiol group which rapidly forms a mixed disulfide with a thionitrobenzoate moiety of 5,5'-dithiobis(2-nitrobenzoic acid). The reaction and the concomitant inactivation of the enzyme are both reversible by reductive removal of the thionitrobenzoate with dithiothreitol. Iodoacetamide and N-ethylmaleimide also react with the thiol group required for enzyme activity, but iodoacetic acid inactivates the enzyme through another mechanism. Three or 4 half-cystine residues/subunit were detected by amino acid analysis and by titration of the denatured enzyme with 5,5'-dithiobis(2-nitrobenzoic acid); no disulfide bonds were detected by borohydride reduction. Cleavage of the subunit (molecular weight 37,000) with 2-nitro-5-thiocyanobenzoic acid gave fragments of molecular weights 32,000, 27,000, and 9,500. Five carboxymethylated peptides were isolated from the trypsin products of the denatured enzyme after treatment with iodo[14C]lacetate. Three of these peptides represented unique sequences surrounding thiol groups in the enzyme. One cysteine-containing nonapeptide has a heptapeptide sequence homologous to a heptapeptide sequence in a cysteine containing decapeptide from the tryptophanyl-tRNA synthetase of human placenta. The nonapeptide appears to bear the thiol group required for enzyme activity.

Initiation of DNA synthesis by the avian oncornavirus RNA-directed DNA polymerase: tryptophan tRNA as the major species of primer RNA

The major species of primer RNA required for the initiation of DNA synthesis by the Rous sarcoma virus RNA-directed DNA polymerase can be aminoacylated by tryptophan. Furthermore, an intact 3' terminus is required for the primer to function in the initiation of DNA synthesis.