The physical association between rat liver mitochondria and rough endoplasmic reticulum : I. Isolation, electron microscopic examination and sedimentation equilibrium centrifugation analyses of rough endoplasmic reticulum-mitochondrial complexes

Rough endoplasmic reticulum-mitochondrial (RER-MT) complexes have been isolated from rat liver homogenates by rate zonal Centrifugation using a reorienting zonal rotor. Electron microscopic examination of the isolated complexes reveals a close association between rough endoplasmic reticulum (RER) and mitochondria. The associated RER appears as bilamellar sheets as it does in intact liver tissue, not as microsomal vesicles. When the complexes are subjected to sedimentation equilibrium Centrifugation, the marker enzymes for mitochondria and RER coband at an equilibrium density of 1.190. Electron microscopic analysis of the complexes after sedimentation equilibrium Centrifugation again reveals a close association between RER and mitochondria. Treatment of the complexes with 500 mM KCl or 500 mM KCl plus 20 mM EDTA resulted in a shift in the equilibrium density of the complexes to 1.180 and 1.176, respectively. Concomitant with the density shift was a release of A₂₆₀ units to the top of the gradient. After incubating KCl-EDTA stripped complexes with cytoplasmic ribosomes and ribosomal subunits, the complexes band at the same equilibrium density, 1,190, as do untreated complexes. In order to completely remove the associated RER it is necessary to treat the complexes with digitonin at a concentration of 0.13 mg digitonin/mg protein. Our data suggest that a fraction of the total cellular RER is physically associated with rat liver mitochondria.     

Separation of plant cell organelles by zonal centrifugation in reorienting density gradients

Preparative separations of plant cell organelles (glyoxysomes, proplastids, mitochondria, and endoplasmic reticulum) in an ordinary refrigerated centrifuge were obtained by sucrose density gradient centrifugation in a zonal rotor loaded and unloaded in the static manner. The quality of the separation which was monitored by marker enzymes and electron microscopy compares to analytical separations in swinging-bucket rotors. Membrane alterations observed in glyoxysomes and mitochondria are traced back to sucrose as a major component of the homogenization and density gradient medium.     

Isolation of peroxisomes from the dog kidney cortex.

The present study was undertaken to separate peroxisomes of the dog kidney cortex by the methods of discontinuous sucrose density gradient and zonal centrifugation. The separation of subcellular particles was evaluated by measuring the activities of reference enzymes, beta-glycerophosphatase for lysosomes, succinate dehydrogenase for mitochondria, glucose-6-phosphatase for microsomes, and catalase and D-amino acid oxidase for peroxisomes. The activities of D-amino acid oxidase and catalase were mainly observed in fractions 1 and 2 (1.6 and 1.7 M sucrose) obtained by discontinuous sucrose density-gradient centrifugation. Small amounts of acid phosphatase and succinate dehydrogenase contaminated these fractions. Considerably higher activity of catalase was determined in the supernatant, while D-amino acid oxidase showed a lower activity. By the method of zonal centrifugation, the highest specific activities of catalase and D-amino acid oxidase were found in fraction 50 (1.73 M sucrose) with no succinate dehydrogenase, acid phosphatase or glucose-6-phosphatase activity. These results suggested that peroxisomes of dog kidney cortex were clearly separated in 1.73 M sucrose from mitochondria, lysosomes and microsomes by zonal centrifugation.     

Fractionation by differential and zonal centrifugation of spheroplasts prepared from a glucose-repressed fission yeast Schizosaccharomyces pombe 972h-.

A method is described for the preparation of spheroplasts in high yield from Schizosaccharomyces pombe, by treating cells grown in the presence of glucose and deoxyglucose with snail digestive enzymes. Gentle disruption of such spheroplasts yielded homogenates, from which marker enzymes for nuclei (NAD pyrophosphorylase) and mitochondria (cytochrome c oxidase activity and spectroscopically-detectable cytochromes a + a3) could be quantitatively sedimented by low-speed centrifugation. In contrast to previous findings with Saccharomyces carlsbergensis, cytochrome c oxidase and another mitochondrial enzyme, succinate dehydrogenase, were completely sedimentable by zonal centrifugation in sucrose gradients in the presence of either 2 mM-MgCl2 or 0-4 mM-EDTA. Mitochondria were apparently smaller and of lower buoyant density in gradients containing EDTA. The bulk of the total units of malate dehydrogenase and NADH; cytochrome c oxidoreductase sedimented with mitochondria, whereas NADPH: cytochrome c oxidoreductase was located in fractions containing no mitochondria. The distributions of mitochondrial enzymes were heterogeneous in populations of mitochondria separated on the basis of size or density. The possible origins of mitochondrial heterogeneity in extracts of S. pombe are discussed with special reference to changes in the enzyme activities of cells during the cell cycle.     

Changes in enzyme activities and distributions during glucose de-repression and respiratory adaptation of anaerobically grown Saccharomyces carlsbergensis

1. During anaerobic glucose de-repression the respiration rate of whole cells of Saccharomyces carlsbergensis remained constant and was insensitive to antimycin A but was inhibited by 30% by KCN. Aeration of cells for 1 h led to increased respiration rate which was inhibited by 80% by antimycin A or KCN. 2. Homogenates were prepared from sphaeroplasts of anaerobically grown, glucose de-repressed cells and the distribution of marker enzymes was investigated after zonal centrifugation on sucrose gradients containing MgCl(2). These homogenates contained no detectable cytochrome c oxidase or catalase activity. The complex density distributions of NADH- and NADPH-cytochrome c oxidoreductases and adenosine triphosphatase(s) [ATPase(s)] were very different from those of anaerobically grown, glucose-repressed cells. 3. The specific activity of total ATPase was lowered and sensitivity to oligomycin decreased from 58 to 7% during de-repression. 4. Cytochrome c oxidase and catalase activities were detectable in homogenates of cells after 10min aeration. Zonal centrifugation indicated complex, broad sedimentable distributions of all enzyme activities assayed; the peaks of activity were at 1.27g/ml. 5. Centrifugation of homogenates of cells adapted for 30min and 3 h indicated a shift of density of the major sedimentable peak from 1.25g/ml (30min) to 1.235g/ml (3 h). After 30min adaptation a minor zone of oligomycin-sensitive ATPase and 15% of the total cytochrome c oxidase activities were detected at rho=1.12g/l; these particles together with those of higher density containing cytochrome c oxidase, ATPase and NADH-cytochrome c oxidoreductase activities were all sedimented at 10(5)g-min. 6. Electron microscopy indicated that the mitochondria-like structures of anaerobically grown, glucose-de-repressed cells were similar to those of repressed cells. After 10min of respiratory adaptation highly organized mitochondria were evident which resembled the condensed forms of mitochondria of aerobically grown, glucose-de-repressed cells. High-density zonal fractions of homogenates of cells after adaptation also contained numerous electron-dense vesicles 0.05-0.2mum in diameter. 7. The possibility that the ;promitochondria' of anaerobically grown cells may not be the direct structural precursors of fully functional mitochondria is discussed.     

A specific micromethod for determination of acetyl residues in proteins

A method is described for the separation and concentration of rat liver lysosomes from mitochondria in a one-step procedure by zonal centrifugation. Some of the practical problems associated with the use of the B-XX1X rotor are discussed.     

Progesterone synthesis by luteal mitochondria in vitro.

Mitochondria were prepared from bovine corpora lutea by differential centrifugation and were purified by isopycnic zonal centrifugation. A marked increase in specific cytochrome oxidase activity and a marked decrease in specific DNA and RNA content indicate that the procedure resulted in a highly purified preparation of mitochondria. These organelles had a higher rate of conversion of [4-14C] cholesterol to [4-14C] progesterone than did mitochondria separated only by differential centrifugation, suggesting that luteal mitochondria contain the enzyme systems required for progesterone synthesis.     

Characteristics of potassium ion transport in pea cotyledon mitochondria isolated by a zonal technique.

Methodology was developed for measurement of K+ transport in pea cotyledon mitochondria isolated by zonal centrifugation. The valinomycin-mediated transport process required respiratory energy from Krebs cycle intermediates and was completely reversible in the absence of oxygen. The rate and extent of uptake were dependent on the presence of proton-conducting anions (with acetate plus phosphate being most effective), well-coupled mitochondria, and on the K+ concentration.     

Characterization of the Tumorlike (T) Antigen Induced by Type 12 Adenovirus : II. Physical and Chemical Properties

T antigen, purified from KB cells infected with type 12 adenovirus, was characterized by chemical and physical methods. The immunologically active molecule had an ultraviolet-absorption spectrum characteristic of a protein, and was partially inactivated (i.e., approximately 85%) by trypsin (final concentration of 150 mug/ml). Centrifugation analyses indicated that the purified antigen was a single molecular species with an average sedimentation coefficient of 2.40S (measured by zonal centrifugation in sucrose gradients) and an S(20,w) of 2.58 determined by analytical centrifugation. The antigen was inactivated at temperatures above 40 C, it was stable between pH 5.7 and 8.8, and it had an isoelectric point of approximately 5.0, as determined by electrophoresis on cellulose polyacetate membranes.     

Separation of Subclasses of Human Serum High Density Lipoproteins by Zonal Ultracentrifugation

An improved one-step method for the preparative separation of three subfraotions of high-density lipoproteins from normal human serum has been developed. It employs the method of rate zonal ultracentrifugation in a Z-60 rotor using a discontinuous NaBr gradient in the density range of 1.0 - 1.4. The density gradients were monitored directly by a flow-through density meter allowing the direct read-out of the actual densities in the process of filling and emptying the rotor. The separation of the three density fractions from 5 to 15 ml serum was achieved during a single 12 hours run at 59.000 rpm. The three fractions showed characteristically different patterns on polyacrylamide gel electrophoresis and differences in their lipid and protein composition.     

Separation of subclasses of human serum high density lipoproteins by zonal ultracentrifugation.

An improved one-step method for the preparative separation of three subfractions of high-density lipoproteins from normal human serum has been developed. It employs the method of rate zonal ultracentrifugation in a z-60 rotor using a discontinuous NaBr gradient in the density range of 1.0-1.4. The density gradients were monitored directly by a flow-through density meter allowing the direct read-out of the actual densities in the process of filling and emptying the rotor. The separation of the three density fractions from 5 to 15 ml serum was achieved during a single 12 hours run at 59.000 rpm. The three fractions showed characteristically different patterns on polyacrylamide gel electrophoresis and differences in their lipid and protein composition.     

Spectrum of Physical Properties Among the Virions of a Whole Population of Vaccinia Virus Particles

Populations of virions released from cultures of L cells infected with vaccinia virus are composed of particles which differ substantially from each other in sedimentation rate and buoyant density. Clumps of two and three virions sediment enough faster than single particles so that fractions containing only singles and others with predominantly pairs can be isolated. The observed velocity range for single particles is much greater than that attributable to diffusion and convection in the centrifuge. Plaquing efficiency is three times higher in a small fraction of the slowest-moving virions than in the major part of the population, even though no size difference can be seen in the electron microscope. Isopycnic densities in potassium tartrate range from 1.15 to 1.23, enough to account for the observed range in velocities. Centrifugation was done in the BXIV zonal rotor at very low virion concentration (less than 10⁸ per ml at any point in the spectrum). Virus count and state of aggregation were determined by electron microscopy.     

Unmasking of membrane enzyme activities and the problem of subcellular localization of adenylate cyclase in pig lymph node lymphocytes

A large-scale purification of plasma membranes from pig lymph node lymphocytes is described. Centrifugation on a discontinuous sucrose density gradient was performed in a zonal rotor. Adenylate cyclase activity of untreated fractions displayed a profile different from that of plasma membrane enzymatic markers and was maximal at higher density. However, when latent adenylate cyclase was unmasked by Lubrol PX treatment, its maximum was shifted to lower density and was no longer significantly different from that of plasma membrane markers. These results are discussed in terms of cell surface topography.     

Poly (ADP-ribose) synthetase activity in rat testis mitochondria

A quite active poly (ADP-ribose) synthetase was found in isolated rat testis mitochondria. Similar levels of activity were found in mitochondria isolated from bull and hamster testis. In contrast, mitochondria isolated from rat brain or liver, and demembraned sperm, showed negligible activity. Centrifugation of testis mitochondria through a linear sucrose gradient, showed that, poly (ADP-ribose) synthetase cosediment together with succinatecytochrome c reductase and mitochondrial proteins. Furthermore, treatment with digitonin indicated that, the enzyme is localized in the inner membrane-matrix complex. Finally, kinetic studies demonstrated that, the apparent Km for NAD⁺ of the mitochondrial enzyme, was 22 μM compared with 210 μM for the nuclear enzyme.     

Quantitative isolation of liver mitochondria by zonal centrifugation

A method was developed using zonal centrifugation to recover liver mitochondria quantiatively and free of other cellular components from a sample of whole homogenate. The fractions containing mitochondria were identified by the distribution of cytochrome oxidase and these fractions contained over 90% of the total cytochrome oxidase recovered. The mitochondrial fractions were found to be only slightly contaminated by 5′-nucleotidase (plasma membranes), acid phosphatase (lysosomes), glucose-6-phosphatase (microsomes), and catalase (peroxisomes). There was no detectable contamination by nuclear DNA (nuclei). This method was used to quantitate total liver mitochondrial protein. The development of this procedure provides a means for following total changes in mitochondrial components during mitochondrial biogenesis.     

Qualitative determination of superoxide release at both sides of the mitochondrial inner membrane by capillary electrophoretic analysis of the oxidation products of triphenylphosphonium hydroethidine

Superoxide is released asymmetrically to both sides of the mitochondrial inner membrane. Because this membrane is impermeable to superoxide, two separate pools are formed at either side of the membrane, each with its own characteristics and potential biological effects. Here, we report an attomole-sensitive fast capillary electrophoretic method that can analyze superoxide in a single pool, either the matrix pool or that outside the mitochondria. The method uses triphenylphosphonium hydroethidine, which reacts with the superoxide in both pools. Centrifugation is used to separate the mitochondria (i.e., matrix contents) from the supernatant (i.e., products released outside the mitochondria). Each fraction is then analyzed by capillary electrophoresis with laser-induced fluorescence detection that separates and detects hydroxytriphenylphosphonium ethidium (OH-TPP-E⁺), the fluorescent superoxide-specific product. The separation takes < 3 min and the detection level is down to 3 amol OH-TPP-E⁺. The method has proved to be effective at detecting superoxide release qualitatively in the mitochondria of 143B cells, mouse liver, and rat skeletal muscle, in both the presence and the absence of inhibitors. In addition, this study confirmed that complex I releases superoxide only toward the matrix, whereas complex III releases superoxide toward both sides of the mitochondrial inner membrane. Furthermore, treatment with menadione induces superoxide release toward both sides of the mitochondrial inner membrane.     

Large-scale purification of Qbeta-virus by differential centrifugation

Bacterial RNA virus, Qβ, has been purified in gram amounts by differential centrifugation. Final separation of the virus from host E. coli rRNA was based on the density differential in the pellet. The method provided a simplified alternative to the more conventional rate zonal or isopycnic zonal centrifugation techniques.     

Differential analysis of Saccharomyces cerevisiae mitochondria by free flow electrophoresis

One major problem concerning the electrophoresis of mitochondria is the heterogeneity of mitochondrial appearance especially under pathological conditions. We show here the use of zone electrophoresis in a free flow electrophoresis device (ZE-FFE) as an analytical sensor to discriminate between different yeast mitochondrial populations. Impairment of the structural properties of the organelles by hyperosmotic stress resulted in broad separation profiles. Conversely untreated mitochondria gave rise to homogeneous populations reflected by sharp separation profiles. Yeast mitochondria with altered respiratory activity accompanied by a different outer membrane proteome composition could be discriminated based on electrophoretic deflection. Proteolysis of the mitochondrial surface proteome and the deletion of a single major protein species of the mitochondrial outer membrane altered the ZE-FFE deflection of these organelles. To demonstrate the usefulness of ZE-FFE for the analysis of mitochondria associated with pathological processes, we analyzed mitochondrial fractions from an apoptotic yeast strain. The cdc48(S565G) strain carries a mutation in the CDC48 gene that is an essential participant in the endoplasmic reticulum-associated protein degradation pathway. Mutant cells accumulate polyubiquitinated proteins in microsomal and mitochondrial extracts. Subsequent ZE-FFE characterization could distinguish a mitochondrial subfraction specifically enriched with polyubiquitinated proteins from the majority of non-affected mitochondria. This result demonstrates that ZE-FFE may give important information on the specific properties of subpopulations of a mitochondrial preparation allowing a further detailed functional analysis.     

Identification and characterization of tyrosine kinase activity associated with mitochondrial outer membrane in sarcoma 180 cells

Tyrosine protein kinase activity has been detected in the mitochondrial fraction purified from sarcoma 180 tumor cells. Following hypotonic disruption of mitochondria, tyrosine kinase activity appeared to cosediment with monamine oxidase, marker enzyme of mitochondrial outer membrane; meanwhile, serine and threonine kinases were found to be associated with the inner membrane and matrix of mitochondria. Mitochondrial tyrosine kinase(s) showed thermosensitivity and Mn2+ dependence, useful properties for its characterization and separation from tyrosine kinases associated with other particulate fraction and from serine and threonine kinases associated with mitochondria. Following in vitro incubation of mitochondria with labelled ATP as substrate and analysis by PAGE, a complex pattern of phosphotyrosine containing proteins with a major band of 50-55 kilodaltons resulted.     

Isolation of large amounts of highly pure mitochondria for “omics” studies

Ultracentrifugation on a density gradient remains the only reliable way to obtain highly pure mitochondria preparations. However, it is not readily available for any laboratory and has a serious disadvantage of providing low mitochondria yield, which can be critical when working with limited starting material. Here we describe a combined method for isolation of mitochondria for proteomic studies that includes cell disruption by sonication, differential centrifugation, and magnetic separation. Our method provides remarkable enrichment of mitochondrial proteins as compared to differential centrifugation, magnetic separation, or their combination, and it enables the strongest depletion of cytoplasmic components, as assessed by two-dimensional electrophoresis, mass spectrometry, and Western blot. It also doubles the yield of mitochondria. However, our method should not be used for functional studies as most of the isolated organelles demonstrate disturbed structure in electron microphotographs.