Loosening and unfolding of E. coli 50 S ribosomal subunits: Dependence on magnesium content and temperature

Reversible change of 50 S ribosomal subunits to 40 S particles takes place in cold buffered 0.5 M NH₄Cl solutions either containing Mg⁺⁺ (up to 0.1 M), or free from Mg⁺⁺ and even supplemented with EDTA (1 mM). The 40 S particles were stable only within a definite temperature range. Heating of the samples caused completely irreversible unflding of the 40 S particles. This melting appeared to be co-operative and took place within a very narrow range of temperature, which for samples containing Mg⁺⁺ was a linear function of the log of Mg⁺⁺ concentration.The results suggest that two types of bonds maintained the compact structure of the ribosomal subunits: ionic bonds involving Mg⁺⁺ and heat-labile weak interactions between ribosomal components.     

Requirement of DNA topoisomerases for in vitro chromatin assembly by 3T6 mouse cell extracts

Nuclear extracts of 3T6 mouse cells were able to assemble in vitro minichromosomes which displayed a 150-bp periodicity. Activities of both DNA topoisomerases I and II were detected in these extracts. When a supercoiled pUC DNA was added, it was first relaxed in less than 3 min, then slowly supercoiled again in 1-4 h. Both reactions occurred either in the absence or the presence of added Mg2+ and/or ATP, they were not blocked by DNA topoisomerase II inhibitors and they were inhibited by an antiserum against DNA topoisomerase I and by camptothecin. These findings led us to propose that, under our in vitro assay conditions, chromatin assembly is mainly carried out by a DNA topoisomerase I.     

Effect of oligomycin on NADH oxidation and its coupled phosphorylation with the particulate fraction from dark aerobically grown Rhodospirillum rubrum

Summary NADH oxidation with the particulate fraction from dark aerobically grown Rhodospirillum rubrum is significantly stimulated by the addition of phosphate (Pi) and Mg⁺⁺, or Pi, Mg⁺⁺, ATP and the hexokinase-glucose system. K _m values for Pi in NADH oxidation and phosphorylation are 10^–3 m and 8×10^–4 m, respectively. These K _m values are almost the same as in corresponding photophosphorylation and oxidative phosphorylation catalyzed with chromatophores. As in the case of NADH oxidation with chromatophores, NADH oxidation with the particulate fraction has an optimal pH at 7.5 without additions, which is shifted to 6.9 by the addition of Pi and Mg⁺⁺, or Pi, Mg⁺⁺, ATP and the hexokinase-glucose system. The optimal pH for coupled phosphorylation is 6.9. 10 g per ml of oligomycin can suppress stimulation of NADH oxidation by Pi, or by the energy trapping system, and prevent the shift of optimal pH. The particulate fraction can catalyze Pi-incorporation into glucose-6-phosphate without externally added ATP, so that Pi-incorporation is inhibited by oligomycin. From these findings, it is concluded that NADH oxidation in the particulate fraction is tightly coupled to phosphorylation.     

Studies on streaming. I. Inhibition of protoplasmic streaming and cytokinesis of Chaos chaos by adenosine triphosphate and reversal by magnesium and calcium ions

In Chaos chaos streaming, motility, and cytokinesis were inhibited nearly 100% for several hours by 2.5–5 mM sodium adenosine triphosphate (ATP)¹ added to culture fluid. All three effects were completely prevented by the addition of equimolar Mg⁺⁺ or Ca⁺⁺ ions but not Na⁺ to the ATP/culture fluid solution. The effects of ATP were not reproduced by EDTA, EGTA, colchicine, or AMP. Sodium pyrophosphate produced about 50% inhibition at 5 mM. Studies with ¹⁴C-ATP showed that 5 x 10^-5 to 5 x 10^-4 mmole of ATP was firmly associated with each milliliter of packed cells after an hour''s incubation at 24°C. Labeling studies also showed that prevention of the ATP effects by Mg⁺⁺ ions was not due to a decrease in the amount of ATP associated with the cells.     

Conformational changes of membrane-bound (Na+−K+)-ATPase as revealed by antibody inhibition

Summary As different structural states of the (Na⁺–K⁺)-ATPase (EC 3.6.1.3) may lead to a changed reactivity to antibodies, the influence of Na⁺, K⁺, Mg⁺⁺, P_i and ATP on the reaction between highly purified (Na⁺–K⁺)-ATPase and antibodies directed against the membrane-bound enzyme was measured. The antigen antibody reaction was registered by measuring the antibody inhibition of (Na⁺–K⁺)-ATPase activity.In themembrane-bound but not in thesolubilized enzyme four different degrees of antibody inhibition were obtained at equilibrium of the antigen antibody reaction if different combinations of Na⁺, K⁺, Mg⁺⁺ and ATP were present during the incubation with the antibodies. Corresponding to the different degrees of inhibition, different rates of enzyme inhibition were measured. (a) The smallest degree of enzyme inhibition was obtained when (i) only Mg⁺⁺, (ii) Mg⁺⁺ and Na⁺ or (iii) Mg⁺⁺ and K⁺ were present during the antigen antibody reaction. (b) The enzyme activity was inhibited more strongly if Na⁺, Mg⁺⁺ and ATP were present together. (c) It was inhibited even more if only (i) Na⁺, (ii) K⁺, (iii) ATP or both (iv) ATP and Na⁺, (v) ATP and K⁺, (vi) ATP and Mg⁺⁺, or if (vii) no ATP and activating ions were present. (d) The highest degree of antibody inhibition was obtained if Mg⁺⁺, ATP and K⁺ were present together.In the presence of Mg⁺⁺ plus ADP and in the presence of Mg⁺⁺ plus the ATP analog adenylyl (--methylene) diphosphonate, Na⁺ and K⁺ did not influence the degree of antibody inhibition as they did in the presence of Mg⁺⁺ plus ATP. It was further found that the degree of antibody inhibition in the presence of Mg⁺⁺, ATP and K⁺ was affected by the sequence in which K⁺ and ATP were added to the enzyme prior to the addition of the antibodies.It is suggested that by antibody inhibition different conformations of the (Na⁺–K⁺)-ATPase could be detected. These conformations may possibly not occur in the solubilized enzyme and therefore do not seem to be necessarily linked to the intermediary steps of the ATP hydrolysis of the enzyme. The structural changes which are induced by Na⁺ and K⁺ in the presence of Mg⁺⁺ plus ATP are proposed to occur during the Na⁺–K⁺ transport.     

Studies on the ultrastructural localization of adenosine triphosphatase activity in fracture callus

Summary The fine structural localization of Mg⁺⁺-activated and Mg⁺⁺-independent neutral adenosine triphosphatase (ATPase) was studied in fracture callus of the rat using EDTA-decalcified DMSO-treated tissues incubated in Wachstein-Meisel type lead-containing media, and N-ethylmaleimide, NaF, EDTA and histidine as inhibitors to test the specificity of the reaction. Final product was found to be deposited on the plasma membranes and associated structures (subplasmalemmal vesicles and vacuoles) of phagocytic monocytoid cells, fibroblasts, osteoblasts and ruffled border regions of osteoclasts when Mg⁺⁺ was present in the incubation medium; the most abundant precipitate was noted on the plasma membranes of osteoblasts. When Mg⁺⁺ was omitted from the medium, the ruffled borders of osteoclasts were the only plasmalemmal sites showing conspicuous activity. This apparently Mg⁺⁺-independent ATPase was also demonstrated in the lysosomes of all the different cell types in the callus and in the vacuoles and specific granules located beneath the ruffled border of osteoclasts; lack of inhibition with NaF suggested that the enzyme was not a conventional nonspecific acid phosphatase. Neither the Mg⁺⁺-activated nor the Mg⁺⁺-resistant ATPase were inhibited by EDTA or histidine, indicating that they were unrelated to non-specific alkaline phosphatase. Deposition of final product did not occur on the plasma membranes of chondroblasts, chondrocytes of osteocytes.     

Effect of exogenous ATP on the volume of TA3 ascites tumor cells

When exogenous ATP is added to suspensions of TA₃ ascites tumor cells suspended in Ca⁺⁺ and Mg⁺⁺ free media, a significant increase in cell volume can be measured. This increase is reversible upon addition of Ca⁺⁺ and/or Mg⁺⁺ back to the media. The enlargement of these cells is temperature sensitive and specific for ATP; no other nucleotides, EDTA or ouabain were effective. The evidence suggest that this phenomena may be due to an alteration in membrane permeability and that the regulation of membrane permeability is an energy dependent process.     

A thermodynamic analysis of the correlation between active Na+ transport and the rate of oxygen consumption in epithelia

Summary Insulin decreased markedly the adenylyl cyclase activity associated with fat cell membranes purified by centrifugation in sucrose gradients. The hormone effect was not readily evident in crude membrane preparations.The kinetics of this effect indicate that some time was required for the onset of the insulin-induced inactivation. This lag period decreased when the insulin concentration was increased. The hormone dose dependence for adenylyl cyclase inactivation measured at a fixed time (3 min) showed a 10 to 15% decrease in activity at 1 to 30 U per ml insulin; 30 to 40% at 100 to 1000 U per ml; and 75% at 0.1 U per ml.The insulin effect was completely abolished by 0.1mm GMP-P(NH)P, 10mm fluoride, or 50 ng per ml glucagon, or by increasing the Mn⁺⁺ concentration to 4mm. In addition, it was partially reversed by the addition of a fraction from the sucrose gradient, which contained soluble factors.The kinetics of the adenylyl cyclase-catalyzed reaction were studied using ATP or AMP-P(NH)P as adenylyl donor, and Mn⁺⁺ or Mg⁺⁺ as divalent cation, in the absence or presence of insulin. With ATP and Mg⁺⁺ there was a striking reduction of the transient reaction rates after 1.5 min of incubation. Under these conditions the insulin effect was not evident. On the contrary, with ATP and Mn⁺⁺ this spontaneous reduction of activity was less evident; however, in the presence of insulin there was a clear and marked reduction of the transient reaction rate measured after 1.5 min of incubation. With AMP-P(NH)P the kinetic data were qualitatively similar to those observed with ATP.It is concluded that under certain assay conditions adenylyl cyclase may be converted to an inactive enzyme form, and that such a conversion is more evident in the presence of Mg⁺⁺ than with Mn⁺⁺. In the latter case, insulin appears to enhance the rate of this conversion.     

Studies on Isomerization of Sugars by Bacteria

An enzyme, which catalyzes the isomerization of d-glucose to d-fructose, has been found in a newly isolated bacterium which tentatively identified as Pacacolobacterum aerogenoides. The enzyme converts not only d-glucose but also d-mannose to d-fructose, and NAD and Mg⁺⁺ are required as cofactor for this isomerization. The properties of this enzyme were summarized as follows: (1) As a cofactor for the isomerization by this enzyme, NAD was absolutely necessary, whereas NADP, FMN and FAD were not. (2) The optimum pH was found to be at 7.5 and optinum temperature was at about 40°C. (3) The enzyme activity was markedly reduced by EDTA treatment and the reduced activity by EDTA was restored by the addition of Mg⁺⁺, Mn⁺⁺ or Co⁺⁺. (4) The enzyme activity was strongly inhibited by monoiodoacetate, p-chloromercuribenzoate, and Cu⁺⁺, however, the activity was recovered by adding cysteine or glutathione.     

Preparation of metaphase chromatin of Physarumpolycephalum without the loss of repressed RNA synthesis

A novel method for the preparation of intact chromatin from the slime mold $\text{Physarum}\text{polycephalum>}$ which retains the $\text{in}\text{vivo}$ property of RNA synthesis is described. Preparations from G₂-cells were highly active, while those from metaphase-cells were inactive. The plasmodial cells were disrupted by gentle homogenization on a polyethylene sieve in a neutral isotonic sucrose medium containing Mg⁺⁺, deoxycholate and EGTA, a Ca⁺⁺-chelating agent. The nuclei were lysed in a hypotonic buffer without use of EDTA and chromatin was precipitated by centrifugation after addition of Mg⁺⁺.     

Characterization of fructose-1,6-diphosphate-insensitive catabolic glycerol kinase ofPseudomonas aeruginosa

Glycerol kinase is induced in cells ofPseudomonas aeruginosa strain PAO when grown in the presence of glycerol or glycerol-3-phosphate. The enzyme was isolated from the soluble cytoplasmic fraction of cell extracts and purified 500-fold by ammonium sulfate precipitation and chromatography on columns of Sephadex G-25, DEAE-Sephadex, hydroxyapatite, and Sephadex G-200. A molecular weight of 120,000 was estimated by gel filtration of the catalytically active enzyme. In polyacrylamide gel electrophoresis the purified product contained one major band of Coomassie Blue staining material. The enzyme exhibited an apparent Km of 40 M for glycerol and 23 M for ATP. Of the nucleotide triphosphates tested, only ATP served as a phosphoryl group donor. Mg⁺⁺ or Mn⁺⁺ was required for activity, although a threefold greater concentration of Mn⁺⁺ was required when Mn⁺⁺ substituted for Mg⁺⁺. In contrast to most other catabolic glycerol kinases in bacteria, the enzyme was not inhibited by fructose-1,6-diphosphate nor by other tested metabolites.     

Biologically active recombinant formed through DNA pairing by purified recA protein in vitro

Summary We have detected in vitro homologous recombination mediated by purified recA protein of Escherichia coli as a recombinant phage produced by using the DNA packaging system of phage . When double-stranded DNA of phage carrying amber mutations is incubated with double-stranded DNA carrying the wild-type genes in the presence of recA protein, Mg⁺⁺ and ATP, and the DNA packaged, amber ⁺ recombinant phage is produced at a high frequency. This reaction depends completely upon the function of the wild-type recA protein. After incubation of ³²P-labeled linear DNA (Form III) with bromouracil-labeled circular DNA (Form I-Form II mixture) in the presence of recA protein, Mg⁺⁺ and ATP, about 10% of the ³²P-counts band at an intermediate density in CsCl equilibrium gradient. This fraction yields a high percentage of the recombinant phage after DNA packaging and shows the -shaped and -shaped joint molecules of linear and circular DNA under the electron microscope. Furthermore, we demonstrate that a non-homologous region inhibits the recombination reaction when it is between the marker concerned and the closer cos end. Our results indicate thatrecA protein acts directly in the initial step of recombination to join the homologous double-stranded DNA and that the resulting molecule can be matured into the recombinant DNA.Abbreviations kb kilobase pairs - PFU plaque forming units - Form I superhelical closed circular DNA - Form II open circular DNA - Form III linear DNA     

Cloning,expression and characterization of a gene which encodes a topoisomerase I with positive supercoiling activity in pea

We have isolated and sequenced the full length cDNA for topoisomerase I. Using degenerate primers, based on the conserved amino acid sequences of five eukaryotic topoisomerase I, a 386 bp fragment was PCR amplified using pea cDNA as template. This fragment was used as a probe to screen a pea cDNA library. Two partial cDNA clones were isolated which were truncated at the 5 end. RACE-PCR was employed to isolate the remaining portion of the gene. The total size of the gene was 3055 bp with an open reading frame of 2676 bp. The deduced structure of pea topoisomerase I contain 892 amino acids with a calculated molecular weight of 100 kDa and an estimated pI of 9.3. A comparison of the deduced amino acid sequences of the pea topo I with the other eukaryotic topoisomerases clearly suggested that they are all related. Pea topoisomerase I has been overexpressed in E. coli system and the recombinant topoisomerase purified to homogeneity. The purified protein relaxes both positive and negative supercoiled DNA in the absence of divalent cation Mg²⁺. In the presence of Mg²⁺ ions the purified enzyme introduces positive supercoils a unique property not reported in any other organism except in archaebacterial topoisomerase I. Polyclonal antibodies were raised against recombinant topoisomerase I and western blotting with sub-cellular fractions indicated the localization of this topoisomerase in pea nuclei.     

TSH-treatment of thyroid slices increases the amount of DNA released from nuclei by mild DNase-I digestion

Nuclei from TSH-treated and control thyroid slices were subjected to very limited digestion by DNase I, and then centrifuged at 1200×g. The amount of DNA released into supernatants was increased significantly by TSH when <0.1% to 3% of total DNA was rendered acid-soluble. This effect could be detected in buffers containing 2mM Mg⁺⁺ (with chromatin condensed) or <0.05mM Mg⁺⁺ (chromatin decondensed). Gel electrophoresis showed that the length of the majority of the DNA fragments in the supernatants (<0.1% of DNA acid-soluble) was greater than 4 kilobases; no TSH-dependent shift in size distribution was observed. We speculate that TSH may affect specific DNase I-hypersensitive sites in chromatin.     

13S condensin actively reconfigures DNA by introducing global positive writhe: implications for chromosome condensation.

Xenopus 13S condensin converts interphase chromatin into mitotic-like chromosomes, and, in the presence of ATP and a type I topoisomerase, introduces (+) supercoils into DNA. The specific production of (+) trefoil knots in the presence of condensin and a type II topoisomerase shows that condensin reconfigures DNA by introducing an ordered, global, (+) writhe. Knotting required ATP hydrolysis and cell cycle-specific phosphorylation of condensin. Condensin bound preferentially to (+) supercoiled DNA in the presence of ATP but not in its absence. Our results suggest a mechanism for the compaction of chromatin by condensin during mitosis.     

A Cytochemical Study on the Pancreas of the Guinea Pig : VI. Release of Enzymes and Ribonucleic Acid from Ribonucleoprotein Particles

Ribonucleoprotein (RNP)¹ particles isolated by DOC treatment from pancreatic microsomes have a RNA content of 35 to 45 per cent of their dry weight. In the analytical ultracentrifuge about 85 per cent of the material has a sedimentation coefficient of ∼85 S. These particles contain amylase, RNase, and trypsin-activatable proteolytic activities which cannot be washed off or detached by incubation in 0.44 M sucrose. The enzymes are released, however, by incubation in the presence of low concentrations of ATP, PP, or EDTA, and high concentrations of IP and AMP. At the same time, and at the same concentrations, ∼80 per cent of the RNA and ∼25 per cent of the protein of the particles becomes also non-sedimentable. The simultaneous addition of Mg⁺⁺ to the incubation medium prevents these losses. This finding, together with the observation that all the Mg⁺⁺ of the particles is released by the same agents, makes it likely that Mg⁺⁺ holds the particles together, and that its removal by the chelators used causes the particles to disintegrate. These findings are discussed in relation to the molecular structure of the RNP particles.