Reassociation and dissociation of cytoplasmic membrane-associated DNA

The relationship between nuclear DNA and cytoplasmic membrane-associated DNA, extracted from a human lymphocyte cell line, was examined by DNA-DNA reannealing and by dissociation of renatured molecules. Up to 2% of the total cellular DNA is found in the cytoplasm as cytoplasmic membrane-associated DNA and of this 2%, approximately 70% is comprised of repeated sequences. These sequences are homologous to only about 4% of the repeated sequences of nuclear DNA. The repeat fraction of cytoplasmic membrane-associated DNA consists of sequences which are only moderately repeated. The number of copies in the average “family” could range from about 1500 copies to as few as 25 copies. A small rapidly reannealing portion of cytoplasmic membrane-associated DNA (C₀t < 4 × 10^?3) appears to consist of sequences derived from a single “family”.About 30% of cytoplasmic membrane-associated DNA reassociates slowly with a $\text{C}{}_0\text{t}\text{1}\text{2}$ value of 223 (unique cytoplasmic membrane-associated DNA). This fraction has homology with about 11% of the unique sequences of nuclear DNA. However, unique cytoplasmic membrane-associated DNA comprises only about 0·6% of the total cellular DNA. If it is assumed that each cell has the same amount of cytoplasmic membrane-associated DNA, homology with 11% of the unique sequences of nuclear DNA suggests that different cells may have different unique nucleotide sequences in the cytoplasm.     

A cytoplasmic membrane-associated DNA from rapidly proliferating tissue

A membrane fraction obtained from the post-microsomal supernatant of Novikoff hepatoma and rat tissues has been shown to contain nucleic acid which can stimulate DNA synthesis. Based on the insensitivity to specific RNases and the sensitivity to DNase, the stimulatory nucleic acid is presumed to be DNA. The occurence of this cytoplasmic membrane-associated DNA is related to the proliferative state of the tissue.     

Induction of a cytoplasmic activator of DNA synthesis in lymphocytes is mediated through a membrane-associated protein kinase.

We have shown previously that cytoplasmic extracts from actively dividing lymphoid cells are capable of inducing DNA synthesis in isolated nuclei. One of the factors involved in this activity, ADR, appears to be a greater than 90 kDa heat-labile protease. Cytoplasmic extracts prepared from nonproliferating lymphocytes express little to no ADR activity. However, ADR activity can be generated in these extracts by brief exposure to a membrane-enriched fraction of spontaneously proliferating, leukemic human T lymphoblastoid (MOLT-4) cells. This suggests that ADR activity is present in the resting cytoplasm in an inactive or precursor form. This in vitro generation of ADR activity can be inhibited in a dose-dependent manner by the isoquinolinesulfonamide derivative, H-7 (1-(5-isoquinoline-sulfonyl)-2-methylpiperazine dihydrochloride), an inhibitor of both cyclic adenosine monophosphate (cAMP)-dependent protein kinases and protein kinase C (PKC). However, more specific inhibitors of cAMP-dependent protein kinases, including N-[( 2-methylamino)ethyl]-5-isoquinolinesulfonamide dihydrochloride (H8) and N-(2-gua-nidinoethyl)-5-isoquinolinesulfonamide (HA-1004), had little to no effect on the in vitro generation of ADR activity. Furthermore, membranes from MOLT-4 cells depleted of PKC by long-term exposure (24 h) to phorbol esters and calcium ionophores were unable to induce ADR activity in resting peripheral blood lymphocytes extracts. The results of these studies suggest 1) ADR activity is present in resting cell cytoplasm in an inactive or precursor form; and 2) ADR activity can be induced in this resting cytoplasm through a mechanism involving a membrane-associated protein kinase, possibly PKC. The ability of alkaline phosphatase to deplete the activity of preformed ADR suggests the possibility that ADR itself is phosphoprotein.     

Arginine deiminase of Mycoplasma hominis: cytoplasmic and membrane-associated forms

Membrane and cytoplasmic fractions of Mycoplasma hominis inhibited the multiplication of this mycoplasma. Arginine deiminase (EC 3.5.3.6), isolated from both fractions, reproduced the inhibition. The purified cytoplasmic deiminase had a subunit Mr of 49,000, a specific activity of 53 units (mg protein)-1 and an A280/A260 ratio of 1.76. The membrane-associated enzyme had an identical Mr but lower values for specific activity [39 units (mg protein)-1] and the A280/A260 ratio (1.46). In experiments in vitro, recent clinical isolates of M. hominis produced less arginine deiminase, but grew faster than the laboratory reference strain PG 21. In addition, other growth inhibitory components associated with membrane preparations were detected in recent clinical isolates but were absent from strain PG 21.     

Physical and topological properties of circular DNA

Several types of circular DNA molecules are now known. These are classified as single-stranded rings, covalently closed duplex rings, and weakly bonded duplex rings containing an interruption in one or both strands. Single rings are exemplified by the viral DNA from φX174 bacteriophage. Duplex rings appear to exist in a twisted configuration in neutral salt solutions at room temperature. Examples of such molecules are the DNA''s from the papova group of tumor viruses and certain intracellular forms of φX and λ-DNA. These DNA''s have several common properties which derive from the topological requirement that the winding number in such molecules is invariant. They sediment abnormally rapidly in alkaline (denaturing) solvents because of the topological barrier to unwinding. For the same basic reason these DNA''s are thermodynamically more stable than the strand separable DNA''s in thermal and alkaline melting experiments. The introduction of one single strand scission has a profound effect on the properties of closed circular duplex DNA''s. In neutral solutions a scission appears to generate a swivel in the complementary strand at a site in the helix opposite to the scission. The twists are then released and a slower sedimenting, weakly closed circular duplex is formed. Such circular duplexes exhibit normal melting behavior, and in alkali dissociate to form circular and linear single strands which sediment at different velocities. Weakly closed circular duplexes containing an interruption in each strand are formed by intramolecular cyclization of viral λ-DNA. A third kind of weakly closed circular duplex is formed by reannealing single strands derived from circularly permuted T2 DNA. These reconstituted duplexes again contain an interruption in each strand though not necessarily regularly spaced with respect to each other.     

Physical properties and subunits of DNA dubia erythrocruorin.

The erythrocruorin of the freshwater leech Dina dubia possessed an S20,w of 61 S and exhibited a slightly sigmoid oxygenation curve with n congruent to 1.6 and P50 = 2.4 mm at pH 7.4. A minimum mol. wt of 23 000 +/- 2100 per heme group was determined from the iron and heme contents, 0.22 +/- 0.02 and 2.92 +/- 0.35 weight %. The subunit composition of this erythrocruorin was investigated using polyacrylamide gel electrophoresis and gel filtration in sodium dodecyl sulfate at neutral pH and gel filtration at pH 9. Sodium dodecyl sulfate electrophoresis of Dina erythrocruorin revealed the presence of five subunits (1-5) with mol. wts of about 13 000, 21 000, 23 000, 25 000 and 31 000, respectively. When the erythrocruorin was reduced with mercaptoethanol prior to dodecyl sulfate electrophoresis, three subunits (I-III) were observed, two possessing molecular weights in the range 12 000-14 000 (I and II) and one possessing a molecular weight of about 28 000. One of the subunits I, II, was provided by the dissociation of the 31 000 subunit. Subunit III (28 000) consisted of subunits 2, 3, and 4. It is likely that not all of the polypeptide chains constituting Dina erythrocruorin are associated each with a heme group.     

Physical properties of a plasmid-like DNA from Euglena gracilis

A small circular extrachromosomal DNA of the flagellate protozoan Euglena gracilis has been characterized as having a contour length of 11.3 kb, with a consistent restriction map. The buoyant density (rho = 1.717) and melting temperature (tm = 89 degrees C) both indicate a base content of 59% G + C. The DNA is found in both wild-type cells and those lacking plastids. The copy number is estimated to be about 1000.     

Functional properties of membrane-associated complement receptor CR1

It was previously shown that membrane receptors for C3b (CR1) purified from human erythrocytes were powerful inhibitors of the complement cascade and that they encompass the regulatory functions of the serum proteins beta 1H (H) and C4-binding protein (C4bp). In the present report we study the functional properties of membrane-associated CR1. When tonsil lymphocytes, which contain between 30 and 60% of CR1-bearing B cells, are incubated with the red cell complement intermediate EAC14oxy2lim or EAC14oxy23lim, they inhibit both C42 and C423 in a dose-dependent manner. These effects are mediated by membrane-associated molecules. Indeed, mild trypsinization of the lymphocytes abolishes their activity, and formaldehyde-fixed cells are as effective as viable cells. The inhibitory effects are in part mediated by CR1. The lymphocyte activities are reversed about 60% if monoclonal antibodies to CR1 or fluid phase C3b are present in the incubation medium. Moreover, upon addition of C3b-inactivator (l), lymphocytes release C3c fragments from EAC14oxy23b. The release of C3c was also abolished by antibodies to CR1. These results support the idea that CR1, as well as other molecules from the lymphocyte membrane, can function as inhibitor(s) of complement activation in their vicinity.     

Identification of a cytoplasmic membrane-associated component of the maltose transport system of Escherichia coli

The maltose transport system of Escherichia coli contains at least five components, three of which, i.e. the products of lamB, malE, and malF genes, have so far been identified as constituents of the outer membrane, periplasmic space, and cytoplasmic membrane, respectively. We identified another component, a cytoplasmic membrane protein of an apparent molecular weight of 43,000, as the product of the malK gene on the basis of polyacrylamide gel electrophoretic analysis of various mutants and suppressed strains and by the incorporation of extra tyrosine residue into this proten in malK amber mutants containing the suppressor Su3+ allele. The transport of maltose thus appears to require at least two proteins associated with the cytoplasmic membrane.     

Physical characterization of a kinetoplast DNA fragment with unusual properties

A 414-base pair fragment from a Leishmania tarentolae kinetoplast DNA minicircle has unusual physical properties. We reported previously that in comparison to phi X174 and pBR322 control fragments, the kinetoplast fragment behaves in gel electrophoresis, gel filtration, and electric dichroism experiments as if it has an unusually compact conformation. We accounted for these unusual properties by proposing that the fragment is a systematically bent helix (Marini, J.C., Levene, S.D., Crothers, D.M., and Englund, P.T. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 7664-7668). In this paper, we further explore the properties of the kinetoplast fragment. Because of its compact conformation, the kinetoplast fragment has difficulty in snaking through polyacrylamide gels and therefore migrates unusually slowly in electrophoresis experiments. Warming (53 degrees C) and ethanol (5-20%) partially normalize gel migration; glyoxal treatment results in denatured strands with electrophoretic mobility close to that expected for their size. In vivo modification does not appear to be responsible for the fragment's properties; its anomalous electrophoretic behavior persists after proteinase K treatment, phenol extraction, or after cloning into pBR322 and reisolation. Velocity sedimentation experiments rule out fragment aggregation. Secondary structure, such as a cruciform, is not detectable by S1 or mung bean nuclease digestion. The kinetoplast fragment has circular dichroism spectra characteristic of a B-type helix. With increasing temperature, there is an increase in the 270/280 ellipticity ratio. Circular dichroism spectra taken in the presence of ethanol show a B to A helix transition at unusually low ethanol concentrations (between 44 and 54% (w/w]. Thermal denaturation reveals a triphasic melting curve.     

A lymphoma plasma membrane-associated protein with ankyrin-like properties

In this study we have used several complementary techniques to isolate and characterize a 72-kD polypeptide that is tightly associated with a major mouse T-lymphoma membrane glycoprotein, gp 85 (a wheat germ agglutinin-binding protein), in a 16 S complex. These two proteins do not separate in the presence of high salt but can be dissociated by treatment with 2 M urea. Further analysis indicates that the 72-kD protein has ankyrin-like properties based on the following criteria: (a) it cross-reacts with specific antibodies raised against erythrocyte and brain ankyrin; (b) it displays a peptide mapping pattern and a pI (between 6.5 and 6.8) similar to that of the 72-kD proteolytic fragment of erythrocyte ankyrin; (c) it competes with erythrocyte ghost membranes (spectrin-depleted preparations) for spectrin binding; and (d) it binds to purified spectrin and fodrin molecules. Most importantly, in intact lymphoma cells this ankyrin-like protein is localized directly underneath the plasma membrane and is found to be preferentially accumulated beneath receptor cap structures as well as associated with a membrane-cytoskeleton complex preparation. It is proposed that the ankyrin-like 72-kD protein may play an important role in linking certain surface glycoprotein(s) to fodrin which, in turn, binds to actin filaments required for lymphocyte cap formation.     

Purification and properties of nuclear and cytoplasmic DNA polymerases from JLS-V9 cells.

Four DNA polymerases, two enzymes from the nucleus and two from the cytoplasm, were purified 2000- to 7000-fold from continuous mouse cell-line (JLS-V9), by sequential column chromatography. Each of these polymerases require all the deoxynucleoside-5′-triphosphates in order to synthesize DNA, using activated DNA as a primer-template, and can copy the ribonucleotide strand of hybrid templates, but their rate of efficiency varies. The molecular weights of these DNA polymerases range from 35,000 to 160,000, as estimated by Sephadex column chromatography. Three out of the four DNA polymerases are probably a single polypeptide chain, since they have a single major band in polyacrylamide gel electrophoresis as well as one enzymatically active peak in guanidine hydrochloride gel filtration. The highly purified preparation of the high molecular weight cytoplasmic DNA polymerase contains two major bands in sodium dodecyl sulfate polyacrylamide gel electrophoresis and two enzymatically active peaks in guanidine hydrochloride gel filtration.     

Increased intracellular glycerophosphoinositol is a biochemical marker for transformation by membrane-associated and cytoplasmic oncogenes

Transformation of rodent fibroblasts by cytoplasmic (mos, raf) and membrane-associated (ras, src, met, trk), but not nuclear (myc, fos) oncogenes results specifically in a very significant elevation of intracellular levels of glycerophosphoinositol (GPI). This elevation is specifically associated with the transformed state of the cells and not merely with their active state of proliferation. The basal phospholipase A2 (PLA2) activity of the same cells is also significantly stimulated in vivo. Our results are consistent with the notion that the elevated levels of GPI result from deacylation of lysophosphatidylinositol released by the enhanced PLA2 activity. GPI is a water-soluble, easily detectable metabolite which may constitute a convenient biochemical marker for malignant transformation by this particular group of oncogenes.     

Identification of cytoplasmic and membrane-associated complexes in human embryonic stem cells using blue native PAGE

Human embryonic stem cells (hESCs) have great potential for use in developmental biology studies, functional genomics applications, drug screening, and regenerative medicine. A detailed understanding of the molecular mechanisms that are responsible for maintaining the undifferentiated and pluripotent nature of hESCs is essential for their effective therapeutic application. It has become evident that many complex cellular processes are carried out by assemblies of protein molecules (protein complexes). Blue native polyacrylamide gel electrophoresis (BN-PAGE) has been used to separate protein complexes from whole cell lysates. Using BN-PAGE, we resolved cytoplasmic and membrane-associated complexes from hESCs and characterised their composition, stoichiometry, and dynamics by denaturing SDS-PAGE. The reliability of the fractionation was examined by western blot analysis of membrane and cytosolic markers. MALDI TOF/TOF mass spectrometry identified 119 cytosolic and 69 membrane proteins from the BN-PAGE proteome maps. Potential protein complexes were validated by computational prediction of possible protein-protein interactions using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Based on BN-PAGE gels and validation by databases, 82 heteromultimeric and 47 homomultimeric protein complexes have been found in hESCs. Resolving some of the protein complexes provided insight into the function of previously uncharacterised complexes in hESCs.     

Physical properties of the DNA of bacteriophage SP50

Summary The following properties of the DNA of B. subtilis phage SP50 were established: Molecular weight (in Daltons) 102×10⁶ (sedimentation velocity) 97×10⁶ (viscosity) 97×10⁶ (contour lengths of electron micrographs) Base Composition (in % GC) 41.7 (chemical analysis) 44 (melting point) 44 (buoyant density) No unusual bases were observed. The complementary strands of the DNA can be separated. The phage DNA has genuine single strand breaks. The number and distribution of such breaks appears to be determined by the host on which phages were grown.This investigation was supported in part by a Public Health Service research grant GM 13,666 from the National Institutes of General Medical Sciences, AI 01267 from the National Institutes of Allergy and Infectious Diseases, AM 04763 from the National Institutes of Arthritis and Metabolic Diseases; cancer research funds from the University of California; and a grant from the Hartford Foundation.     

Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Corynebacterium glutamicum

Like many other bacteria, Corynebacterium glutamicum possesses two types of L-malate dehydrogenase, a membrane-associated malate:quinone oxidoreductase (MQO; EC 1.1.99.16) and a cytoplasmic malate dehydrogenase (MDH; EC 1.1.1.37) The regulation of MDH and of the three membrane-associated dehydrogenases MQO, succinate dehydrogenase (SDH), and NADH dehydrogenase was investigated. MQO, MDH, and SDH activities are regulated coordinately in response to the carbon and energy source for growth. Compared to growth on glucose, these activities are increased during growth on lactate, pyruvate, or acetate, substrates which require high citric acid cycle activity to sustain growth. The simultaneous presence of high activities of both malate dehydrogenases is puzzling. MQO is the most important malate dehydrogenase in the physiology of C. glutamicum. A mutant with a site-directed deletion in the mqo gene does not grow on minimal medium. Growth can be partially restored in this mutant by addition of the vitamin nicotinamide. In contrast, a double mutant lacking MQO and MDH does not grow even in the presence of nicotinamide. Apparently, MDH is able to take over the function of MQO in an mqo mutant, but this requires the presence of nicotinamide in the growth medium. It is shown that addition of nicotinamide leads to a higher intracellular pyridine nucleotide concentration, which probably enables MDH to catalyze malate oxidation. Purified MDH from C. glutamicum catalyzes oxaloacetate reduction much more readily than malate oxidation at physiological pH. In a reconstituted system with isolated membranes and purified MDH, MQO and MDH catalyze the cyclic conversion of malate and oxaloacetate, leading to a net oxidation of NADH. Evidence is presented that this cyclic reaction also takes place in vivo. As yet, no phenotype of an mdh deletion alone was observed, which leaves a physiological function for MDH in C. glutamicum obscure.     

Visualization of membrane-associated R-plasmid DNA in fraction ofEscherichia coli minicell lyzate

Minicells ofEscherichia coli P678-54 containing plasmid R1drd19 were submitted to careful controlled lysis. By sedimentation of the resulting lyzate in a sucrose gradient, the material absorbing at 260 nm was separated into three distinct bands. Among the most rapidly sedimenting particles, doublestranded topological circles of DNA attached to patches of membrane were visualized by electron microscopy, while single-stranded molecules (probably RNA) with associated proteins were detected in the medium band. Covalently closed and open circles of the R1drd19 DNA were found at the top of the gradient. Their contour lengths corresponded to the size of the DNA sedimenting together with the membrane in the first peak. This finding implies a direct intracellular interaction between R1drd19 DNA and membrane inE. coli minicells. Preliminary results were presented at the 12th FEBS Meeting in Dresden (July 2–8, 1978).