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Biomedical subjects

D Job

Publications and source records attributed to D Job.

At least 109 records · Page 6Linked to original sources
PubMed1987

Biochemical assay of microtubule mean length.

We present a method for the rapid determination of microtubule mean length in vitro. This method rests on mathematical analysis of the rate of polymer disassembly induced by the introduction of calcium at a known concentration. The rate of disassembly is monitored in our assay by filter trapping of residual microtubule polymers, which contain a radioactive tracer, [3H]GTP. We show that the assay is accurate and reproducible, by comparison with physical measurement of lengths from electron micrographs. Furthermore, we show that the assay can be used to determine rapid shifts in polymer length induced in polymer populations that exhibit "dynamic instability".

Animals↗
PubMed1987

Model of anaphase chromosome movement based on polymer-guided diffusion.

We propose a motility mechanism that may result in the displacement of objects within the cell. The mechanism, which we call polymer-guided diffusion, involves a microscopic cycle of polymer association and dissociation from a lateral binding site. Reassociation occurs at the polymer subunit adjacent to that which has just dissociated, thus generating an apparent sliding movement. The displacement involves only free diffusion and the spontaneous fluctuations of the polymer; the movement thus requires no other energy sources than thermal energy and the energy originally required for the formation of the polymer. In this manner polymer-associated organelles can be guided (inevitably) by diffusional processes toward a final destination. The specific example of the anaphase movement of chromosomes poleward is detailed.

Anaphase↗
PubMed1986

Effect of salts on abortive and productive elongation catalysed by wheat germ RNA polymerase II.

Modification of the ionic conditions in reaction assays containing wheat germ RNA polymerase II and poly(dAT) as template markedly alters the catalytic properties of the transcription complexes. These effects have been studied by measuring the rate of abortive initiation and the extent of productive RNA synthesis. Using combinations of metal ions or various salts, a marked inhibition of abortive initiation was always associated with an increased length of RNA chains. These results are discussed in terms of modulation of the stability of transcription complexes induced by salts or divalent cations. The behavior exhibited by wheat germ RNA polymerase II is also discussed in comparison with previously reported results for procaryotic and eucaryotic RNA polymerases.

Escherichia coli↗
PubMed1986

Purification and assay of a 145-kDa protein (STOP145) with microtubule-stabilizing and motility behavior.

The capacity of microtubules to disassemble in vitro is profoundly affected by a protein factor designated STOP (stable tubule only polypeptide). Here we report the isolation of STOP protein and confirm that its activity is, as predicted, highly substoichiometric to the tubulin in microtubules. The isolation of the 145-kDa STOP (STOP145) protein has been effected from isolated cold-stable microtubules by two column steps: DEAE ion-exchange and a calmodulin affinity column. To confirm the protein's activity we have produced an antibody against STOP145 and have used the antibody to specifically remove the protein and the activity using an antibody-linked affinity column. We conclude that the STOP145 protein accounts for the observed in vitro stabilization of microtubules.

Animals↗
PubMed1986

Sliding of STOP proteins on microtubules: a model system for diffusion-dependent microtubule motility.

STOP proteins, of 145 kD, act substoichiometrically to block end-wise disassembly of microtubules. STOPs bind to microtubules either during microtubule assembly or when added at steady state, and when binding to the polymers is apparently irreversible. They are not measurably lost from polymers under competition conditions, and there is no measurable exchange between polymers. Nonetheless, STOP proteins exhibit an extraordinary behavior: they "slide" laterally on the surface of the microtubule. Displacement is assayed by forming hybrid microtubules in which cold stable or cold labile region subunits are labeled. Displacement of STOPs on the polymer with time will cause labeled subunits of cold-stable regions to become increasingly cold labile in a manner reciprocal to cold stabilization of previously cold-labile subunits. Because equilibrium exchange of STOP proteins onto and off the polymers can be ruled out, the displacement of STOPs relative to subunits can only be explained by lateral diffusion or "sliding." Axonal transport and mitotic mechanisms were discussed as implications of such a lateral translocation mechanism for microtubule-dependent motility.

Animals↗
PubMed1985

Poly(dAT) dependent trinucleotide synthesis catalysed by wheat germ RNA polymerase II. Effects of nucleotide substrates and cordycepin triphosphate.

Kinetics of condensation of ribonucleotides to dinucleotides, leading to trinucleotide products formation, have been studied using wheat germ RNA polymerase II and poly(dAT). Assay conditions can be selected under which both ApUpA and UpApU are formed in catalytic amounts. The kinetic parameters associated with these reactions indicate that the rate of trinucleotide formation might be affected by DNA sequence, as reported for E.coli RNA polymerase. Kinetics of disappearance of ApUpA and UpApU were studied under experimental conditions allowing poly(rAU) synthesis. The results can be interpreted as if after formation of a phosphodiester bond, a slow isomerisation step of the ternary transcription complex could occur. During this step, transcription complexes could dissociate with a finite probability, releasing trinucleotides in an abortive pathway. The above results are discussed in the view that, under these experimental conditions, wheat germ RNA polymerase II catalyses poly(rAU) synthesis, as if it is a non-processive enzyme. Cordycepin triphosphate can be condensed to a dinucleotide primer, yielding ApUpA. However the ATP analogue cannot be incorporated into longer products than a trinucleotide. On the other hand 3'-dATP behaves as a very potent inhibitor of translocation, with an inhibition constant of 0.15 microM, a value which is two orders of magnitude smaller than the Km value corresponding to ATP utilization in poly(rAU) synthesis. Simple models are proposed which allow a comparison with E.coli RNA polymerase, for which the results are well documented.

Deoxyadenine Nucleotides↗
PubMed1985

Generation of microtubule stability subclasses by microtubule-associated proteins: implications for the microtubule "dynamic instability" model.

We have developed a method to distinguish microtubule associated protein (MAP)-containing regions from MAP-free regions within a microtubule, or within microtubule sub-populations. In this method, we measure the MAP-dependent stabilization of microtubule regions to dilution-induced disassembly of the polymer. The appropriate microtubule regions are identified by assembly in the presence of [3H]GTP, and assayed by filter trapping and quantitation of microtubule regions that contain label. We find that MAPs bind very rapidly to polymer binding sites and that they do not exchange from these sites measurably once bound. Also, very low concentrations of MAPs yield measurable stabilization of local microtubule regions. Unlike the stable tubule only polypeptide (STOP) proteins, MAPs do not exhibit any sliding behavior under our assay conditions. These results predict the presence of different stability subclasses of microtubules when MAPs are present in less than saturating amounts. The data can readily account for the observed "dynamic instability" of microtubules through unequal MAP distributions. Further, we report that MAP dependent stabilization is quantitatively reversed by MAP phosphorylation, but that calmodulin, in large excess, has no specific influence on MAP protein activity when MAPs are on microtubules.

Animals↗
PubMed1984

Sliding of STOP proteins on microtubules.

Microtubules are stabilized against cold temperature disassembly by 145-kilodalton proteins [stable tubule only polypeptides (STOPs)] that block the end-wise dissociation of subunits from the polymers. We describe here several kinetic parameters of the interaction of STOPs with microtubules. STOPs will bind to microtubules either during assembly of the polymer or at steady state. The addition appears random on the polymers and does not require the mediation of tubulin subunits. Tubulin subunits compete with microtubules for STOP binding, but binding to the polymers is apparently irreversible. We demonstrate that STOPs do not exchange measurably between polymers at steady state. Nonetheless, a displacement of STOPs within a single polymer is readily demonstrable. We have determined that the displacement is apparently due to a surface translocation, or "sliding", of STOPs on microtubules.

Animals↗
PubMed1984

Isolation from bovine brain of a superstable microtubule subpopulation with microtubule seeding activity.

Cold-stable microtubule protein isolated from beef brain is capable of seeding microtubule assembly under conditions that prevent the initiation of self-assembly of cold-labile microtubules. We have developed a quantitative assay for the determination of seeding activity. Using this assay, we find that seeding activity is apparently due to microtubule fragments that resist -80 degrees C, a condition that causes the depolymerization of cold-stable microtubules ("cold stability" is defined as resistance to 0 degree C disassembly), but rapidly depolymerize when exposed to 3.0 mM free calcium, to micromolar Ca2+-calmodulin, or to 0.2 M NaCl at 4 degrees C. After salt treatment, seeding activity is permanently lost although microtubule cold stability is retained through further assembly cycles. Similarly, after sedimentation of microtubule seeds the supernatant protein assembles into cold-stable microtubules, which are permanently devoid of seeding activity. By contrast, seeding activity can be recovered by recycling of supernatant protein from preparations exposed to 3.0 mM calcium or to Ca2+-calmodulin prior to centrifugation, indicating the solubilization of an active component (designated "preseeds") under these conditions. Polyacrylamide gels show some differences in polypeptides between seeding and non-seeding cold-stable microtubule preparations. Approximately 35% of the microtubule population assembled from beef brain crude extract is cold stable, while approximately 2% constitutes -80 degrees C resistant seeds. The formation of seeds from seed-forming subunits (preseeds) occurs rapidly, is apparently a cooperative phenomenon, and occurs on preexisting microtubules under either assembly initiating or steady-state conditions.

Animals↗
PubMed1984

Complex RNA chain elongation kinetics by wheat germ RNA polymerase II.

Kinetics of RNA chain elongation catalyzed by wheat germ RNA polymerase II have been studied using various synthetic DNA templates in the presence of excess dinucleotide monophosphate primers. With single- or double-stranded homopolymer templates, the double reciprocal plots 1/(velocity) as a function of 1/(nucleotide substrate) exhibit positive, negative or no curvature. With poly(dAT) as template, the mechanism of nucleoside monophosphate incorporation into RNA is not the ping-pong kinetic mechanism which was derived for E. coli RNA polymerase (6). Noncomplementary nucleoside triphosphates inhibit RNA transcription allosterically. Cordycepin triphosphate behaves as ATP, and not only inhibits AMP incorporation but also that of UMP and GMP on appropriate templates. The reason for this complex kinetic behavior is not yet understood. Possibilities are raised that there are several nucleoside triphosphate binding sites on wheat germ RNA polymerase II, that additional nucleoside triphosphate dependent enzymatic activities are required for reaction to occur or that the Km value for incorporation of a given nucleoside monophosphate into RNA is dependent on the length of the RNA chain and/or the nucleotide sequence surrounding the complementary base on the DNA template.

Kinetics↗
PubMed1983

Comparative transcription of right- and left-handed poly[d(G-C)] by wheat germ RNA polymerase II.

The template properties of left-handed synthetic polymers, the Z* form of poly[d(G-C)] and the Z form of poly[d(G-m5C)], have been investigated using an eucaryotic RNA polymerase, the class II enzyme from wheat germ. Results from a comparative kinetic study of transcription using the polynucleotide substrates in the B and Z conformations are reported. Optimal conditions for enzyme activity compatible with the preservation of the desired template conformation were determined. On the basis of several criteria, both physical (c.d. spectra of the polymers, sedimentability of the Z* form) and biochemical, it was demonstrated that the left-handed conformations of poly[d(G-C)] and poly[d(G-m5C)] serve as templates for wheat germ RNA polymerase II. The level of incorporation was less than that exhibited by the B form of poly[d(G-C)], the relative activity being a function of the precise experimental conditions. Activity ratios (Z*/B or Z/B) ranged from 0.1 to 0.5. The effect of various incubation parameters, including pH, salt concentration, temperature, and the presence of dinucleoside monophosphate primers were investigated. The Km values for nucleoside triphosphate substrates were slightly smaller for the Z* form of poly[d(G-C)] than for the B conformation. Titration of DNA (Z* or B) with enzyme and reciprocal experiments suggested that the reduced activity of left-handed templates might derive from the availability of fewer and/or lower affinity sites for initiation and/or translocation on these templates. Specific antibodies raised against left-handed DNA strongly inhibited the observed transcription of Z* and Z DNAs by wheat germ RNA polymerase II.

Ammonium Sulfate↗
PubMed1983

Regulation of microtubule cold stability by calmodulin-dependent and -independent phosphorylation.

Cold-labile microtubule protein can be rendered cold-stable by addition of a fraction containing a small number of polypeptides that are derived from cold-stable microtubules. These polypeptides can be obtained from purified cold-stable microtubules by passage through a DEAE-cellulose (DE-52) ion exchange column from which they emerge in the first eluate fraction. The stabilizing activity of these proteins is abolished by phosphorylation catalyzed by two types of protein kinases, one dependent on calmodulin and the other independent of that regulatory protein. The calmodulin-dependent reaction appears to phosphorylate mainly two polypeptides, 56 and 72 kilodaltons; the reaction is blocked by trifluoperazine. The calmodulin-independent reaction appears to phosphorylate different cold-stable microtubule-associated proteins. That reaction is observed only in purified material obtained from vigorously homogenized brain tissue. Gently homogenization yields cold-stable microtubules that are responsive only to the calmodulin-dependent protein kinase. A distinguishing feature of the calmodulin-independent reaction is that it does not occur on polypeptides while they are bound to the microtubules.

Animals↗
PubMed1983

Purification and characterization of sheep brain cold-stable microtubules.

The isolation of cold-stable microtubules in high yields, described previously only from rodents, was extended to the brain of higher animals. Under optimal conditions, yields of 30 mg of cold-stable microtubles per 100 g of sheep brain could be obtained routinely. Material purified by two polymerization cycles displayed the same stability to cold temperature or to millimolar concentrations of calcium and the same lability to calmodulin and to ATP as did the purified material obtained from the rat [Job, D., Rauch, C.T., Fischer, E.H. & Margolis, R.L. (1982) Biochemistry 21, 509]. Furthermore, DE-52 chromatography of this material yielded a fraction that restored cold stability when added to cold-labile microtubules. Known to bind to calmodulin and to enhance microtubule assembly, tau proteins had no cold-stabilizing activity. Protein profiles of the cold-stabilizing fraction from sheep and rat brain were similar to one another but showed no protein bands corresponding to the tau proteins.

Animals↗
PubMed1982

Non-processive transcription of poly[d(A-T)] by wheat germ RNA polymerase II.

RNA product distribution obtained during the transcription of poly[d(A-T)] by wheat germ RNA polymerase IIA under various experimental conditions was analyzed by high resolution polyacrylamide gel electrophoresis. Poly[r(A-U)] synthesis proceeded as if wheat germ RNA polymerase II was a non-processive enzyme: a ladder of RNA products of increasing lengths was obtained, which apparently, terminated at every other nucleotide. RNA release was not dependent upon nucleoside triphosphate substrate concentrations. A likely explanation would be that ternary complexes enzyme: DNA: RNA were very much unstable; moreover, oligonucleotides released were not re-used for further elongation by the enzyme.

DNA-Directed RNA Polymerases↗