Low buoyant density proteoglycans from saline and dissociative extracts of embryonic chicken retinas

Abstract: Retinas were labeled in culture with [³H]glucosamine or [³H]leucine and [³⁵S]sulfate and extracted sequentially with physiologically balanced saline and 4 M guanidine HCl. They were dialyzed into associative conditions (0.5 M NaCl) and chromatographed on agarose columns. Under these conditions, some of the proteoglycans were associated in massive complexes that showed low buoyant densities when centrifuged in CsCl density gradients under dissociative conditions (4 M guanidine HCl). Much of the label in these complexes was in molecules other than proteoglycans. Most of the proteoglycans, however, were included on the agarose columns, where they appeared to be constitutionally of low buoyant density. They resisted attempts to separate potential low buoyant density contaminants from the major proteoglycans by direct CsCl density gradient centrifugation or by the fractionation of saline or 8 M urea extracts on diethylaminoethyl-Sephacel. The diethylaminoethyl-Sephacel fractions were either subjected to CsCl density gradient centrifugation or were chromatographed on Sephacryl S-300, in both cases before and after alkaline cleavage, to confirm the presence of typical O-linked glycosaminoglycans. The medium and balanced salt extracts were enriched in chondroitin sulfate and other sul-fated macromolecules, possibly highly sulfated oligosaccharides, that resisted digestion by chondroitinase ABC but were electrophoretically less mobile than heparan sulfate. Guanidine HCl or urea extracts of the residues were mixtures of high and low density proteoglycans that were enriched in heparan sulfate.     

Preparation of Synaptic Plasma Membrane and Postsynaptic Density Proteins Using a Discontinuous Sucrose Gradient

Neuronal subcellular fractionation techniques allow the quantification of proteins that are trafficked to and from the synapse. As originally described in the late 1960’s, proteins associated with the synaptic plasma membrane can be isolated by ultracentrifugation on a sucrose density gradient. Once synaptic membranes are isolated, the macromolecular complex known as the post-synaptic density can be subsequently isolated due to its detergent insolubility. The techniques used to isolate synaptic plasma membranes and post-synaptic density proteins remain essentially the same after 40 years, and are widely used in current neuroscience research. This article details the fractionation of proteins associated with the synaptic plasma membrane and post-synaptic density using a discontinuous sucrose gradient. Resulting protein preparations are suitable for western blotting or 2D DIGE analysis.     

Subcellular structure of bovine thyroid gland. A study on bovine thyroid membranes by buoyant-density-gradient centrifugation in a B-XIV zonal rotor.

A combined mitochondrial and light mitochondrial fraction and a microsomal fraction were isolated from bovine thyroid gland and fractionated further in a B-XIV zonal rotor. A density gradient ranging from 20 to 50% (w/w) sucrose was used. The rotor was operated for 3 h at 45 000 rev./min. All manipulations were performed at 4 degrees C and at pH 7.4. 2. Membranous material was recovered in two zones: zone I, containing microsomal material derived from both smooth endoplasmic reticulum and plasma membranes and probably also from other smooth membranes; zone II, containing material from rough endoplasmic reticulum. 3. Increasing the pH of the medium up to 8.6, or the addition of Mg2+ to the medium resulted in the formation of a single zone at intermediate densities (aggregation of membranes?). An analogous effect was obtained after treatment with Pb (NO3) 2. 4. In the presence of heparin (50 i.u./ml) the bulk of the membranes was found in zone I. This was due to the release of ribosomes from the rough endoplasmic reticulum.     

Equilibrium sedimentation of a polyelectrolyte in a density gradient of a low-molecular weight electrolyte. I. DNA in CsCl

Previous work had indicated that the molecular weight calculated from the equilibrium distribution of DNA in a CsCl density gradient appears to be one half the estimated value of the true molecular weight. In the present study, the sedimentation equilibrium of a polyclectrolyte in a density gradient generated by a low molecular weight electrolyte is treated in terms of the representation according to which a constant fraction of the counterions is considered permanently immobilized and the remaining fraction completely free. Equations for the preferential hydration and the molecular weight are obtained. The validity of the treatment is tested by applying it to experimental data on the equilibrium sedimentation of ?X 174 DNA in CsCl, and it is found that the molecular weight calculated in this way is in agreement with the accepted value for this molecule. Also, recalculation of published data on density gradient centrifugation of T2 DNA in CsCl according to the present treatment brings up the molecular weight to within the range of values given by other methods.     

The binding of poly(rA) and poly(rU) to denatured DNA. I. Model studies with homopolymers.

We have compared the properties of the poly(rA).oligo(dT) complex with those of the poly(rU).oligo(dA)n complex. Three main differences were found. First, poly(rA) and oligo(dT)n do not form a complex in concentrations of CsCl exceeding 2 M because the poly(rA) is insoluble in high salt. If the complex is made in low salt, it is destabilized if the CsCl concentration is raised. Complexes between poly(rU) and oligo(dA)n, on the other hand, can be formed in CsCl concentrations up to 6.6 M. Second, complexes between poly(rA) and oligo(dT)n are more rapidly destabilized with decreasing chain length than complexes between poly(rU) and oligo(dA)n. Third, the density of the complex between poly(rA) and poly(dT) in CsCl is slightly lower than that of poly(dT), whereas the density of the complex between poly(rU) and poly(dA) in CsCl is at least 300 g/cm3 higher than that of poly(dA). These results explain why denatured natural DNAs that bind poly(rU) in a CsCl gradient usually do not bind poly(rA).     

Association of Replicative T4 Deoxyribonucleic Acid and Bacterial Membranes

Experiments utilizing CsCl density gradient analysis and radioactive labels specific for bacteriophage T4 deoxyribonucleic acid (DNA) and membranes have shown that replicative T4 DNA is associated with host membranes. The association is inhibited by chloramphenicol and takes place just prior to semi-conservative replication of the phage DNA.     

Characterization, by Size, Density, Osmotic Fragility, and Immunoaffinity, of Acetylcholine- and Vasoactive Intestinal Polypeptide-Containing Storage Particles from Myenteric Neurones of the Guinea-Pig

When cytoplasmic extracts of guinea-pig myenteric neurones are submitted to centrifugal density gradient fractionation in a zonal rotor acetylcholine is bimodally distributed in the gradient, in a peak (I) rich in synaptic vesicles of the classic type and in a denser peak (II/VI) rich in densecored vesicles and vasoactive intestinal polypeptide (VIP). The putative stable synaptic vesicle markers synaptophysin (p38), vesicular proteoglycan, and Mg2+-activated ATPase were also bimodally distributed, with a peak coincident with peak I and another, broader peak embracing peak II/VI, and neighbouring peaks of other neuropeptides resolved from peak II/VI by the density gradient separation procedure used. To establish whether the stable markers, acetylcholine and VIP in peak II/VI were present in one particle or several, attempts were made to separate them by particle-exclusion chromatography and differential osmotic fragility. These were unsuccessful, leading us to conclude that the storage particles in peak II/VI contain both neurotransmitters and all three putative stable synaptic vesicle markers. It is suggested that such particles are the counterparts, in cholinergic neurones of the myenteric plexus, of the dense-cored, enkephalin- and noradrenaline-containing vesicles of certain adrenergic neurones and, like the latter, may exist in a precursor-product relationship with the classic synaptic vesicles containing the small-molecular-mass transmitters and found in the same nerve terminals.     

EVIDENCE FOR A COMMON EVOLUTIONARY ORIGIN OF LIGHT-HARVESTING FUCOXANTHIN CHLOROPHYLL a/c-PROTEIN COMPLEXES OF PAVLOVA GYRANS (PRYMNESIOPHYCEAE) AND PHAEODACTYLUM TRICORNUTUM (BACILLARIOPHYCEAE)1

A fucoxanthin-chlorophyll a/c-protein complex has been isolated from the prymnesiophyte Pavlova gyrans. Thylakoid membranes were treated with the mild anionic detergent sodium taurodeoxycholate followed by sucrose density gradient centrifugation. The brown fraction produced by this procedure was treated with Triton X-100 followed by a second sucrose density gradient centrifugation. A brown fraction isolated from this gradient was shown to be a light-harvesting complex nearly identical to that which is present in the diatom Phaeodactylum tricornutum. The complexes from the two organisms have nearly identical absorption and flourescence spectra, both complexes contain fucoxanthin and two other carotenoids, both contain four polypeptides of similar molecular weights, and polypeptides from both complexes cross react with antibodies raised to polypeptides of the Phaeodactylum tricornutum complex. Results suggest a common evolutionary origin for these light-harvesting complexes, in apparent contrast to the great differences in cell structure between prymnesiophytes and diatoms.     

Unstable association in vitro between donor and recipient DNA in Bacillus subtilis.

In addition to stable donor-recipient DNA complexes, unstable complexes between donor and recipient DNA were formed in vitro with Bacillus subtilis. Whereas the stable complexes survived CsCl gradient centrifugation at pH 11.2 and phenol plus sodium p-aminosalicylate extraction with 0.17 M NaCl, the unstable complexes dissociated during these manipulations. The donor moiety from the unstable complexes remained associated with the recipient DNA during phenol plus sodium p-aminosalicylate treatment at 0.85 M NaCl. The unstable complexes could be stabilized artificially by cross-linking with 4,5',8-trimethylpsoralen. Dissociation of the complexes during CsCl gradient centrifugation could be prevented by centrifuging at pH 10. Heterologous DNA fragments derived from phage H1 DNA appeared to be unable to form complexes with the recipient B. subtilis DNA. Unstable complexes were also formed with Escherichia coli DNA, although under all conditions tested, more complex was detectable by using homologous B. subtilis DNA.     

Incomplete reversion of double stranded DNA cleavage mediated by Drosophila topoisomerase II: formation of single stranded DNA cleavage complex in the presence of an anti-tumor drug VM26.

Anti-tumor drug VM26 greatly stimulates topoisomerase II mediated DNA cleavage by stabilizing the cleavable complex. Addition of a strong detergent such as SDS to the cleavable complex induces the double stranded DNA cleavage. We demonstrate here that heat treatment can reverse the double stranded DNA cleavage; however, topoisomerase II remains bound to DNA even in the presence of SDS. This reversed complex has been shown to contain single strand DNA breaks with topoisomerase II covalently linked to the nicked DNA. Chelation of Mg++ by EDTA and the addition of salt to a high concentration also reverse the double strand DNA cleavage, and like heat reversion, topoisomerase II remains bound to DNA through single strand DNA break. The reversion complex can be analyzed and isolated by CsCl density gradient centrifugation. We have detected multiple discrete bands from such a gradient, corresponding to protein/DNA complexes with 1, 2, 3, ..... topoisomerase II molecules bound per DNA molecule. Analysis of topoisomerase II/DNA complexes isolated from the CsCl gradient indicates that there are single stranded DNA breaks associated with the CsCl stable complexes. Therefore, topoisomerase II/DNA complex formed in the presence of VM26 cannot be completely reversed to yield free DNA and enzyme. We discuss the possible significance of this finding to the mechanism of action of VM26 in the topoisomerase II reactions.     

Involvement of Protein and Ribonucleic Acid in the Association of Deoxyribonucleic Acid with Other Cell Components of Escherichia coli

Cells of Escherichia coli were labeled with precursors of ribonucleic acid (RNA), deoxyribonucleic acid (DNA), and protein, lysed with detergent, and examined by starch-block electrophoresis and CsCl density gradient centrifugation. A large amount of the DNA was seen to remain at positions of low electrophoretic mobility and light density along with tryptophan and arginine-containing proteins and some RNA. Addition of labeled, phenol-extracted DNA to unlabeled cells prior to lysis and electrophoresis showed that only a small amount of the DNA became associated during or after lysis. Sonic treatment of a lysate removed most of the DNA to a position of electrophoretic mobility and density similar to that of free DNA, whereas pronase and ribonuclease released only a part of the DNA. We concluded that binding of DNA to cell membranes or other cell components occurs in the cell prior to lysis and involves protein and probably a specific type of RNA.     

Use of Zonal Ultracentrifuge Systems for Biophysical Studies of Rhinoviruses

This paper reports the use of zonal ultracentrifuge techniques to conduct biophysical studies of rhinoviruses grown with WI-38 cells. Good clean-out of infectivity from rhinovirus harvests was obtained with the continuous-flow B-V and B-IX rotors. Use of the B-V rotor resulted in the successful concentration of rhinovirus infectivity and antigenicity. Additional purification was achieved by the combined use of continuous-flow centrifugation and isopycnic banding procedures. Two particle sizes were found to be associated with the virus-infected cell harvests. The infectious 22-nm particle banded in density ranges of 1.38 to 1.40 g/cm(3) in CsCl and 1.26 to 1.27 g/cm(3) in potassium citrate. The 8.0 nm capsomere was composed of 2.0 nm subunits and banded with a density of protein at 1.28 g/cm(3) in CsCl. Equivalent sedimentation coefficients of 155 or 185, depending on particle density in sucrose, were calculated from rate zonal experiments by use of the B-IV zonal rotor.     

Identification and separation of components of calf thymus DNA using a CsCl-netropsin density gradient

Calf thymus DNA containing satellite components of various densities was used as a model to study the effect of netropsin on the density of DNA in a CsCl gradient. The binding of netropsin resulted in a decrease in density which depended upon the quantity of netropsin added and on the average composition of the DNA. Differences in density of DNA components were higher in CsCl - netropsin gradients than in simple CsCl gradients. By use of netropsin a main band and four satellite bands could be differentiated in calf thymus DNA. Satellite DNA's were isolated using preparative CsCl - netropsin gradient centrifugation and were characterised by density and homogeneity in native and in reassociated state. Two of the satellite components, with densities of 1.722 and 1.714 g/cm³, are probably of homogenous sequence, the other two components of densities 1.709 and 1.705 g/cm³ appear to be heterogeneous.     

Preparative Scale Isolation of Basal-Lateral Plasma Membranes from Rat Intestinal Epithelial Cells

A simple, efficient procedure is described for the preparative scale isolation of basal-lateral membranes from the rat intestinal epithelium. The intestinal mucosa was mildly homogenized and soluble protein and RNA were separated from the homogenate by differential centrifugation. The basal-lateral membranes were then separated from nuclei, mitochondria, and brush border membranes by differential centrifugation in a medium close to the equilibrium density of the basal-lateral membranes. Final purification of the basal-lateral membranes was achieved on a linear density gradient in a high-capacity zonal rotor. The final product (usually at least 40 mg protein) represented a 34% yield of basal-lateral membranes purified 18-fold with respect to protein, 26-fold with respect to brush border membranes, and 53-fold with respect to mitochondria.     

Preparative scale isolation of basal-lateral plasma membranes from rat intestinal epithelial cells.

A simple, efficient procedure is described for the preparative scale isolation of basal-lateral membranes from the rat intestinal epithelium. The intestinal mucosa was mildly homogenized and soluble protein and RNA were separated from the homogenate by differential centrifugation. The basal-lateral membranes were then separated from nuclei, mitochondria, and brush border membranes by differential centrifugation in a medium close to the equilibrium density of the basal-lateral membranes. Final purification of the basal-lateral membranes was achieved on a linear density gradient in a high-capacity zonal rotor. The final product (usually at least 40 mg protein) represented a 34% yield of basal-lateral membranes purified 18-fold with respect to protein, 26-fold with respect to brush border membranes, and 53-fold with respect to mitochondria.     

Hepatitis B core antigen. Detection of antibody by radioimmunoprecipitation.

Radioactive cores were prepared from concentrated Dane particles by DNA polymerase reaction followed by CsCl density gradient centrifugation. Two radioactive peaks were obtained: one peak with an average density of 1.36 g/cm-3 in CsCl contained cores that possessed full serologic reactivity; the other peak, with a density of 1.28 to 1.32 g/cm-3, contained cores associated with globulin. A double antibody immunoprecipitation test was developed, using the radioactive heavy cores as a source of antigen. The test was at least 300 times as sensitive as complement fixation for detecting antibody to core.     

Basal-lateral membranes from rabbit renal cortex prepared on a large scale in a zonal rotor

Basal-lateral membranes from the renal cortex of the rabbit were isolated by sucrose gradient centrifugation in a zonal rotor which allows for a large-scale preparation of these membranes. A heterogeneous population of membranes (P4) which contained 29% of the (Na+ + K+)-ATPase found in the homogenate of renal cortex was prepared by differential centrifugation. When pellet P4 was subjected to centrifugation in a sucrose gradient the activity of (Na+ + K+)-ATPase, a marker for basal-lateral membranes, could be separated from enzymatic markers of other organelles. The specific activity of (Na+ + K+)-ATPase was enriched 12-fold at a density of 1.141 g/cm3. Membranes (P alpha) contained in the (Na+ + K+)-ATPase-rich fractions consisted primarily of closed vesicles which exhibited probenecid inhibitable transport of rho-aminohippurate. These membranes did not exhibit Na+-dependent, phlorizin-inhibitable D-glucose transport. Sodium dodecyl sulfate polyacrylamide gel electrophoresis of proteins from P alpha revealed at least six major protein bands with molecular weights of 91000, 81000, 73000, 65000, 47000 and 38000. A small fraction of total alkaline phosphatase found in the homogenate was found in pellet P4. Membranes containing this alkaline phosphatase activity were distributed widely over the gradient, with peak activity found at a density of 1.141 g/cm3. In contrast, when brush borders were subjected to gradient centrifugation under the same conditions as P4, alkaline phosphatase was found in a narrow distribution, with peak activity at a density of 1.158 g/cm3. The principle subcellular localization of the alkaline phosphatase found in P4 could not be determined unambiguously from the data, but the activity did not seem to be primarily associated with classical brush borders.     

Co-operative binding of the globular domain of histone H5 to DNA.

The globular domain of histone H5 (GH5) was prepared by trypsin digestion of H5 that was extracted from chicken erythrocyte nuclei with NaCl. Electron microscopy, sucrose gradient centrifugation, native agarose gel electrophoresis and equilibrium density gradient ultracentrifugation show that GH5 binds co-operatively to double-stranded DNA. The electron microscopic images suggest that the GH5-DNA complexes are very similar in structure to co-operative complexes of intact histone H1 (or its variants) with double-stranded DNA, studied previously, which have been proposed to consist of two parallel DNA double helices sandwiching a polymer of the protein. For complexes with GH5 or with intact H1, naked DNA co-sediments with the protein-DNA complexes through sucrose gradients, and DNA also appears to protrude from the ends and sides of the complexes; measurements of the protein-DNA stoichiometry in fractionated samples may not reflect the stoichiometry in the complexes. An estimate of the stoichiometry obtained from the buoyant density of fixed GH5-DNA complexes in CsCl suggests that sufficient GH5 is present in the complexes for the GH5s to be in direct contact, as required by a simple molecular mechanism for the co-operative binding. Chemical crosslinking demonstrates that GH5s are in close proximity in the complexes. In the absence of DNA, GH5-GH5 interactions are weak or non-existent.     

The organization of gangliosides and other lipid components in synaptosomal plasma membranes and modifying effects of calcium ion

Synaptosomes were prepared from bovine brain by zonal rotor sucrose density centrifugation. While a major fraction of lipid-bound sialic acid is included uniformly within the synaptosomal distribution profile, the sialoglycoproteins and some gangliosides do not follow this pattern, Exposure to extrasynaptosomal calcium results in alterations in the surface labeling properties of some gangliosides and membrane plasmalogens, suggesting that extrasynaptic Ca²⁺ may influence the conformation of complex lipids in synaptic plasma membranes. The level of intrinsic membrane-associated sialidase activity that liberates sialic acid from these sialoglycoconjugates parallels the synaptosomal buoyant density distribution profile, supporting a view that this enzyme resides in synaptosomal membranes in close association with a sialolipid substrate.