Modification of specific lysine residues in E. coli methionyl-tRNA synthetase by crosslinking to E. coli formylmethionine tRNA

A protein affinity labeling derivative of E. coli tRNAfMet has been prepared which carries an average of one reactive side chain per molecule, distributed over four structural regions. Each side chain contains a disulfide bond capable of reaction with cysteine residues and an N-hydroxysuccinimide ester group capable of coupling to lysine epsilon-amino groups in proteins. Reaction of the modified tRNA with E. coli methionyl-tRNA synthetase leads to crosslinking only by reaction with lysine residues in the protein. Examination of the tRNA present in the crosslinked complex reveals that the enzyme is coupled to side chains attached to the 5' terminal nucleotide, the dihydrouridine loop, the anticodon and the CCA sequence. Digestion of the crosslinked enzyme with trypsin followed by peptide mapping reveals that the major crosslinking reactions occur at four specific lysine residues, with minor reaction at two additional sites. Native methionyl-tRNA synthetase contains 90 lysine residues, 45 in unique sequences of the dimeric alpha 2 enzyme. Crosslinking of the protein to different regions in tRNAfMet thus occurs with the high degree of selectivity necessary for use in determining the peptide sequences which are near specific nucleotide sequences of tRNA bound to the protein.     

The primary structure of ribosomal protein S7 from E. coli strains K and B.

Ribosomal proteins S7 from 30S subunits of Escherichia coli strains K and B differ extensively in their aminoacid compositions. The experimental details which led to the determination of the complete primary structures of proteins S7K and S7B are presented. Protein S7K consists of a single polypeptide chain of 177 aminoacids giving a calculated molecular weight of 19, 732, whereas protein S7B has 153 residues which amount to a molecular weight of 17,131. Aminoacid sequences were determined by a combination of automated Edman degradation of the intact proteins in a modified Beckman sequenator and sequencing of peptides obtained by digestion with trypsin. Staphylococcus aureus protease, thermolysin and pepsin, either by solid-phase Edman degradation or by dansyl-Edman degradation. Additional information about the primary structure was derived from peptides resulting from chemical cleavages of the protein by 2-(2-nitrophenyl-sulphenyl)-3-methyl 3' bromoindolenine at its tryptophanyl bonds and by cyanogen bromide at its methionyl bonds leading to large fragments. The mutational event occurring between S7B and S7K was characterized. Protein S7K contains an additional sequence of 24 aminoacids at its C-terminal end. The aminoacid sequence of both proteins S7K and S7B was compared to the published sequences of the other ribosomal proteins of Escherichia coli and predictions for the secondary structure of these proteins were made.     

1,25-Dihydroxyvitamin D3 metabolism. The effect of dietary calcium and phosphorus

Rats maintained on tritiated 1,25-dihydroxyvitamin D₃ as their sole source of vitamin D and placed on diets differing in calcium content had similar intestinal levels of tritiated 1,25-dihydroxyvitamin D₃. Since 1,25-dihydroxyvitamin D₃ administration eliminated adaptation of intestinal calcium transport, it appears that increased production of 1,25-dihydroxyritamin D₃ is responsible for the stimulation of calcium transport by low dietary calcium. When maintained on tritiated 1,25-dihydroxyvitamin D₃, rats fed a low-phosphorus diet had somewhat higher levels of tritiated 1,25-dihydroxyvitamin D₃ in the duodenum and plasma than rats on a normal-phosphorus diet. In addition to stimulating 1,25-dihydroxyvitamin D₃ synthesis, low dietary phosphorus may increase the accumulation of 1,25-dihydroxyvitamin D₃ in both intestine and plasma.     

Inactivation of Salmonella phosphoribosylpyrophosphate synthetase by specific chemical modification of a lysine residue.

Phosphoribosylpyrophosphate synthetase from Salmonella typhimurium contains nine lysine residues per subunit and can be inactivated by reagents specific for this amino acid. Pyridoxal-P reversibly inhibited the enzyme by about 70% by forming a Schiff base derivative with lysine. Reduction with NaBH₄ made this inactivation irreversible. Kinetic experiments indicated that the failure to inactivate the enzyme completely in a single treatment with pyridoxal-P reflects a reversible equilibrium between inactive Schiff base and a noncovalent complex. Modification of one lysine residue per subunit correlated with apparently total loss of activity. The rate of inactivation of the enzyme was decreased fourfold by saturating concentrations of ATP and was decreased at least 20-fold by formation of a quaternary complex of the enzyme with Mg²⁺, α,β-methylene ATP, and ribose-5-P. Trinitrobenzenesulfonate also irreversibly inactivated the enzyme, but this reagent was less specific in that the loss of activity corresponded to the modification of four to five lysine residues. These results suggest that an essential lysine is near the active site of Phosphoribosylpyrophosphate synthetase.     

The pathway of lectin-mediated lymphocytotoxicity by Con A-coupled Sepharose beads

Soluble concanavalin A (Con A) can effectively mediate nonspecific target cell lysis by cytolytic T lymphocytes (LDCC). Because Con A bound to Sepharose beads (Con A-Seph) is also effective, it has been concluded by Z. K. Ballas, W. R. Green, and C. S. Henney. (Cell. Immunol.59, 411, 1981) that Con A-mediated “activation” of the cytolytic cell to kill in LDCC can occur without intracellular penetration of the lectin. No preincubation of either effector or target cells with Con A-Seph has been performed. Exploiting the previous finding of G. Berke (Immunol. Rev. 72, 5, 1983) that in LDCC Con A exerts its effect(s) strictly by affecting the target rather than by bridging effector and target cells and activating the effector, identical results with Con A-Seph are shown. Preincubation of Con A-Seph with the target but not with the effector cells results in substantial killing. Moreover it is shown that the ability of Con A-Seph to mediate LDCC can be attributed to free Con A dissociating from the beads (about 1%) during the assay. Evidence is presented to indicate that the dissociated Con A, not unlike free Con A, reacts with the target cells, thereby rendering them recognizable by the effector cells. It is concluded that the activity of Con A-Seph may not be taken as evidence for Con A-mediated activation of the cytolytic cell, as suggested by Ballas et al., and that the putative Con A-mediated lymphocyte activation relevant to killing still remains to be demonstrated. Evidence contradicting Con A-mediated activation of the effector and supporting the target cell modification theory has been discussed by G. Berke, V. Hu, E. McVey, and W. R. Clark (J. Immunol.127, 776, 1981).     

Monomeric structure of glutamyl-tRNA synthetase in Escherichia coli.

An investigation of the subunit structure of glutamyl-tRNA synthetase (EC 6.1.1.17) from Escherichia coli indicates that this enzyme is a monomer. The enzyme purified to apparent homogeneity is a single polypeptide chain with a molecular weight of 62,000 ± 3,000 and K^Glu_m ? 50 μM in the aminoacylation reaction. Analytical gel electrophoretic procedures were used to determine the molecular weight of species exhibiting glutamyl-tRNA synthetase activity in freshly prepared extracts of several strains of E. coli, which had been grown under various nutritional conditions and harvested at different stages of growth. In all cases, glutamyl-tRNA synthetase activity was associated with a protein having about the same molecular weight and K^Glu_m as the purified enzyme. Thus, no evidence of an oligomeric form of glutamyl-tRNA synthetase with a greater affinity for l-glutamate was obtained, in contrast to a previous report of J. Lapointe and D. Söll (J. Biol. Chem.247, 4966–4974, 1972).     

The effect of vitamin D3 metabolites on membrane proteins of chick duodenal brush borders.

Chick intestinal brush border proteins were examined by polyacrylamide-gel electrophoresis in the presence of sodium dodecyl sulfate. Following injection of 25-hydroxyvitamin D₃ and 1,25-dihydroxyvitamin D₃, a large molecular weight protein present in the vitamin D-deficient brush borders diminishes and a larger protein appears. This change occurs before calcium binding protein can be detected by Chelex assay and prior to the increase in total alkaline phosphatase but correlates closely with increased intestinal calcium absorption in response to the metabolites. The two brush border proteins have been solubilized with n-butanol and partially characterized. The vitamin D-deficient protein has a molecular weight of about 200,000 and has alkaline phosphatase activity but no detectable calcium binding activity. The protein which appears in response to metabolites has a molecular weight of 230,000, binds calcium, and also has alkaline phosphatase activity.     

Effect of the overproduction of phenylalanyl- and threonyl-tRNA synthetases on tRNAPhe and tRNAThr concentrations in E. coli cells

Transformation of an E. coli strain with a recombinant plasmid DNA (pB1) encoding the genes for phenylalanyl- and threonyl-tRNA synthetases causes overproduction of these enzymes by about 100- and 5-fold, respectively. A possible effect of the overproduction of the two aminoacyl-tRNA synthetases on intracellular cognate tRNA levels has been searched for by comparing tRNAThr and tRNAPhe aminoacylation capacities in the RNA extracts from strains carrying pB1 or pBR322 plasmid DNA. The answer is that the levels of these tRNAs are not changed by selective increase of the cognate synthetases.     

Kinetics of the inactivation of Escherichia coli glutamate apodecarboxylase by phenylglyoxal.

The possible interaction of the phosphate moiety of pyridoxal phosphate with a guanidinium group in glutamate apodecarboxylase was investigated. The holoenzyme is not inactivated significantly by incubation with butanedione, glyoxal, methylglyoxal, or phenylglyoxal. However, the apoenzyme is inactivated by these arginine reagents in time-dependent processes. Phenylgloxal inactivates the apoenzyme most rapidly. The inactivation follows pseudo-first-order kinetics at high phenylglyoxal to apoenzyme ratios. The rate of inactivation is proportional to phenylglyoxal concentration, increases with increasing pH, and is also dependent on the type of buffer present. The rate of inactivation of the apoenzyme by phenylglyoxal is fastest in bicarbonate — carbonate buffer and increases with increasing bicarbonate — carbonate concentration. Phosphate, which inhibits the binding of pyridoxal phosphate to the apoenzyme, protects the apodecarboxylase against inactivation by phenylglyoxal. When the apodecarboxylase is inactivated with [¹⁴C]phenylglyoxal, approximately 1.6 mol of [¹⁴C]phenylglyoxal is incorporated per mol subunit. The phenylglyoxal is thought to modify an arginyl residue at or near the pyridoxal phosphate binding site of glutamate apodecarboxylase.     

Metal ion requirement by glutamine synthetase of Escherichia coli in catalysis of gamma-glutamyl transfer.

The requirement for metal ions by glutamine synthetase of Escherichia coli in catalyzing the γ-glutamyl transfer reaction has been investigated. In order of decreasing V at pH 7.0, Cd²⁺, Mn²⁺, Mg²⁺, Ca²⁺, Co²⁺, or Zn²⁺ will support the activity of the unadenylylated enzyme in the presence of ADP. With AMP substituted for ADP to satisfy the nucleotide requirement, only Mn²⁺ or Cd²⁺ will support the activity of the unadenylylated enzyme. Kinetic and equilibrium binding measurements show a 1:1 interaction between the nonconsumable substrate ADP and each enzyme subunit of the dodecamer. (To obtain this result, each enzyme subunit must be active in catalyzing γ-glutamyl transfer.) The stability constant of the unadenylylated subunit for ADP-Mn is 3.5 × 10⁵m^?1, or ～2.86 × 10⁷m^?1 under assay conditions, with arsenate, Mn²⁺, and glutamine being responsible for this large affinity increase. Saturation of two Mn²⁺ ion-binding sites per enzyme subunit is absolutely required for activity expression. While apparently not affecting the affinity of the first Mn²⁺ bound (K′ = 1.89 × 10⁶ M^?1), glutamine increases the stability constant for the second Mn²⁺ bound from 2 × 10⁴ to 5.9 × 10⁵m^?1. Reciprocally, increasing Mn²⁺ concentrations decreases the apparent K_m′ value for glutamine. Glutamine (by producing a net uptake of protons in binding to the enzyme) is responsible for changing the proton release from 3 to about 1 for 2 Mn²⁺ bound per enzyme subunit, with ～0.5 H⁺ displaced in both fast and slow processes. The uv spectral change induced by the binding of the first Mn²⁺ to each enzyme subunit remains unchanged by the presence of glutamine. However, glutamine reduces the half-time of the spectral change or slow proton release from ～30 to ～20 sec at 37 °C. Binding and kinetic results indicate a mechanism involving a random addition of Mn²⁺ to two subunit sites. Saturation of the high-affinity site with Mn²⁺ induces a conformational change to an active configuration, while activity expression depends also on the saturation of a second Mn²⁺ binding site (at or near the catalytic site). Once the first Mn²⁺ binding site of the subunit is saturated, an active enzyme complex can be formed either by the sequential binding of Mn²⁺ and ADP at the second site or by the binding of ADP-Mn complex directly to this site if the concentration of ADP-Mn is greater than 10^?8m in the assay. Some additional observations on the binding of Mg²⁺, Ba²⁺, Ca²⁺, and Zn²⁺ to the enzyme are presented.     

Human granulocyte 6 phosphogluconate dehydrogenase. Purification by elective elution with NADP+, immunological and kinetic properties.

Human granulocyte 6 phosphogluconate dehydrogenase has been totally purified from a single patient with chronic granulocytic leukaemia. 48 mg of protein, of specific activity 20 IU per mg of protein, have been obtained in the course of three different steps only. The overall yield was 30 p. cent and the purification was 100 folds. Purified 6 phosphogluconate dehydrogenase was homogeneous when tested in acrylamide and acrylamide SDS gel electrophoresis or in immunodiffusion. The enzyme was immunologically identical in red blood cells, blood platelets and normal leukocytes. The fixation of both substrates, NADP-+ and 6 phosphogluconate, seemed to proceed through a non ordered mechanism. NADPH was an inhibitor strictly competitive with respect to NADP-+ and non competitive with respect to 6 phosphogluconate. 2-3 Diphosphoglycerate seemed to be able to bind on both the fixation sites of NADP-+ and 6 phosphogluconate. The inhibition by ATP was competitive with 6 phosphogluconate and non competitive with NADP-+. 6 phosphogluconate dehydrogenase was inactivated by SH reagents and was partially protected against this inactivation by both substrates. Both substrates protected the enzyme against thermal inactivation. The influence of ionic strength, pH and ions have been studied, and the results have been compared to those reported by other authors for erythrocyte enzyme.     

Study of the internal structure of Escherichia coli ribosomes by neutron and x-ray scattering.

Neutron scattering curves of the small and large subparticles of Escherichia coli ribosomes are presented over a wide range of scattering angles and for several contrasts. It was verified that the native ribosome structure was not affected by ²H₂O in the buffer. The reliability of the neutron scattering curves, obtained in H₂O buffer, was established by X-ray scattering experiments on the same material.The non-homogeneous distribution of RNA and protein in the subparticles of E. coli ribosomes is confirmed, with RNA predominantly within the particle and protein predominantly on its periphery. The distances between the centres of gravity of the RNA and protein components do not exceed 25 Å and 30 Å, in the large and small subparticles, respectively.The volume occupied by the RNA within the large and small subparticles is determined. The ratio of the “dry” volume of the RNA to the occupied volume is found to be 0.56; it is the same in both subparticles. Such packing of RNA is characteristic of single helices of ribosomal RNA at their crystallization and of the helices in transfer RNA crystals. A conclusion is drawn that RNA in ribosomes is in a similar state.Experimental scattering curves for the small subparticle depend significantly on the contrast in the angular region in which the scattering is mainly determined by the particle shape. The scattering curve, as infinite contrast is approached, is similar to that calculated for the particle as observed by electron microscopy. Thus, the long-existing contradiction between electron microscopy data (an elonggated particle with an axial ratio 2:1) and X-ray data (an oblate particle with an axial ratio 1:3.5), concerning the overall shape of the 30 S subparticle, is settled in favour of electron microscopy. The experimental neutron scattering curve of RNA within the small subparticle is well-described by the V-like RNA model proposed recently by Vasiliev et al. (1978).Experimental data are given to support the hypothesis that the maxima in the X-ray scattering curves, in the region of scattering angles corresponding to Bragg distances of 90 to 20 Å, arise from the ribosomal RNA component alone. It is shown that the prominence of the peaks in this region of the scattering curve depends only on the scattering fraction of the RNA component. The scattering fraction can be changed both by using the “native contrast” (ribosomal particles containing different amounts of protein) and by varying the solvent composition. The maxima are most pronounced where the RNA scattering fraction is highest or in solvents where the protein density is matched by the solvent. The scattering vectors of the maxima in the X-ray and neutron scattering curves, however, remain unchanged. This allows us to propose the tight packing of RNA as a common principle for the structural arrangement of RNA in ribosomes.     

Chicken fumarase. II. Kinetic studies.

The catalysis of the hydration of fumarate and deshydration of L - malate by chicken fumarase was measured spectrophotometrically over a range of substrate concentrations from 4 times 10(-3) M to 8 times 10(-5) M for fumarate and from 8 times 10(-2) M to 10(-3) M for L - malate. For the forward and reverse reactions, linear Lineweaver and Burk plots were obtained. The Michaelis constants and the maximum initial velocities for both substrates were determined and the Haldane relation was found to be obeyed. The effect of pH on activity was investigated over a pH range from 5.5 to 9.0 and the data indicate the presence, in the active site, of two ionizable groups, one in the acidic form and one in the basic form. The values of the ionization constants, determined for the enzyme - substrate complexes, agree closely with the ones obtained for the porcine enzyme. The mode of action of twenty-four structural analogs on the initial velocity of the dehydration of L-malate, by chicken fumarase was examined. From these studies, two regions positively charged appear necessary for the effective binding of the carboxylates of the substrates and competitive inhibitors to the active center. Moreover, the data suggest the presence of an additional group, in the catalytic site of chicken fumarase, that stabilizes the carbon-carbon double bond common to fumarate and its structural analogs. Finally, from the comparison of the kinetic properties of the chicken and pig fumarases, it may be concluded that the catalytic mechanism of the homologous enzymes are very similar, if not identical.     

Oxygen-18 studies of the mechanism of pyrophosphoryl group transfer catalyzed by phosphoribosylpyrophosphate synthetase.

The formation of phosphoribosylpyrophosphate (PRPP) and adenosine 5′-monophosphate (AMP) from ribose 5-phosphate and adenosine 5′-triphosphate, catalyzed by purified PRPP synthetase from Salmonella typhimurium, was conducted in ¹⁸O-enriched water. The products were isolated, and inorganic phosphate was isolated from AMP and the pyrophosphoryl moiety of PRPP. Oxygen-18 was incorporated into PRPP but not into AMP. These results indicate that PRPP synthesis proceeds with scission of a βPO bond of adenosine 5′-triphosphate. Oxygen-18 enters PRPP by prior exchange of H₂¹⁸O into ribose 5-phosphate; the rate of this exchange was measured by combined gas chromatography-mass spectrometry of the trimethylsilyl derivative of ribose 5-phosphate.     

On the control of septation in Escherichia coli.

Mutants of E. coli defective in cell septation (ftsA to ftsG, conditional thermosensitive mutants isolated by Ricard and Hirota) were studied with respect to their membrane protein composition, murein hydrolase activities and rates of synthesis of murein and phospholipids. Three classes of mutants have been distinguished: 1) those affected in both murein and phospholipid synthesis; 2) those affected in either murein or phospholipid synthesis and 3) those affected in neither of these parameters. Overall murein hydrolase activities, after activation, is of the same order in all the mutants screened. In addition to soluble products of murein splitting, we have found insoluble products that appear to be in dynamic equilibrium with the murein of the sacculus. Endogenous levels of cyclic adenosine 3',5'-monophosphate measured after blocking septation showed no variation. This suggests that the cyclic nucleotide is not involved in the metabolic control of septation.     

Rotational diffusion of Escherichia coli ribosomes. II. - Ribosome attachment to polyurydilic acid.

Ribosome attachment to poly(U) has been studied by following the rotational diffusion of polyribosomes in solution. On the average, 13-17 and 50 nucleotides are found to be associated with 30S and 70S ribosome respectively. For an equal length of poly(U), the number of particles in a 30S polysome is four times that in a 70S polysome. The results are consistent with a structure of the polysome in which individual ribosomes are in close contact.