Partial Purification of a Membrane-Associated Deoxyribonucleic Acid Complex from Mycoplasma gallisepticum

A Mycoplasma gallisepticum subcellular fraction (P2), which contains the deoxyribonucleic acid replication complex, can be isolated by differential centrifugation of freeze-thaw-lysed cells. The nascent deoxyribonucleic acid is released from P2 by Lubrol-WX, sodium dodecyl sulfate, Pronase, and deoxyribonuclease, but not by saponin, ribonuclease, phospholipase C, or high-frequency sonic treatment. Sonic treatment further fractionates the cell ghost and allows partial purification, on sucrose density gradients, of a deoxyribonucleic acid replication complex attached to the cells' polar membrane-bleb-infrableb structures.     

The Nissl substance of living and fixed spinal ganglion cells. II. An ultraviolet absorption study

Living chick spinal ganglion neurons grown for 19 to 25 days in vitro were photographed with a color-translating ultraviolet microscope (UV-91) at 265, 287, and 310 mmicro. This instrument was unique in permitting rapid accumulation of ultraviolet information with minimal damage to the cell. In the photographs taken at 265 mmicro of the living neurons, discrete ultraviolet-absorbing cytoplasmic masses were observed which were found to be virtually unchanged in appearance after formalin fixation. These were identical with the Nissl bodies of the same cells seen after staining with basic dyes. The correlation of ultraviolet absorption, ribonuclease extraction, and staining experiments with acid and basic dyes confirmed the ribonucleoprotein nature of these Nissl bodies in the living and fixed cells. No change in distribution or concentration of ultraviolet-absorbing substance was observed in the first 12 ultraviolet photographs of a neuron, and it is concluded that the cells had not been subjected to significant ultraviolet damage during the period of photography. On the basis of these observations, as well as previous findings with phase contrast microscopy, it is concluded that Nissl bodies preexist in the living neuron as discrete aggregates containing high concentrations of nucleoprotein.     

THE NISSL SUBSTANCE OF LIVING AND FIXED SPINAL GANGLION CELLS : II. AN ULTRAVIOLET ABSORPTION STUDY

Living chick spinal ganglion neurons grown for 19 to 25 days in vitro were photographed with a color-translating ultraviolet microscope (UV-91) at 265, 287, and 310 mµ. This instrument was unique in permitting rapid accumulation of ultraviolet information with minimal damage to the cell. In the photographs taken at 265 mµ of the living neurons, discrete ultraviolet-absorbing cytoplasmic masses were observed which were found to be virtually unchanged in appearance after formalin fixation. These were identical with the Nissl bodies of the same cells seen after staining with basic dyes. The correlation of ultraviolet absorption, ribonuclease extraction, and staining experiments with acid and basic dyes confirmed the ribonucleoprotein nature of these Nissl bodies in the living and fixed cells. No change in distribution or concentration of ultraviolet-absorbing substance was observed in the first 12 ultraviolet photographs of a neuron, and it is concluded that the cells had not been subjected to significant ultraviolet damage during the period of photography. On the basis of these observations, as well as previous findings with phase contrast microscopy, it is concluded that Nissl bodies preexist in the living neuron as discrete aggregates containing high concentrations of nucleoprotein.     

Penetration of various mononuclear ribonucleases into rat experimental granulation-tissue fibroblasts and their intracellular effects

The penetration of five different mononuclear ribonucleases into the subcellular particles of rat experimental granulation-tissue fibroblasts was compared, along with the effects of the enzymes on the fibroblast RNA fractions. Ribonucleases from normal and silica-treated rat peritoneal macrophages have been shown before to regulate the nucleic acid and protein metabolism of rat experimental granulation-tissue fibroblasts. These biologically active enzymes were taken into the fibroblasts in a greater amount than the corresponding human monocyte enzymes and the biologically inactive rat macrophage ribonuclease. The biologically active macrophage enzymes were incorporated mainly into the nuclear fraction. The other three mononuclear ribonucleases were not found particularly in any subcellular compartment. Both biologically active macrophage enzymes degraded the nuclear RNA of fibroblasts and released it to the soluble fraction in contrast to the biologically inactive macrophage enzyme and ribonuclease from normal human monocytes. Instead the ribonuclease from normal human monocytes seemed to degrade RNA in the soluble fraction. There were no marked differences in the subcellular effects of ribonucleases from normal and silica-treated macrophages. However, the treatment of human monocytes with silica changed their ribonuclease so that it split the nuclear RNA of fibroblast and released it to the soluble fraction in the same way as the biologically active macrophage enzymes did.     

Lethal action of ribonuclease for thermophilic bacilli

Thompson, T. L. (University of Nebraska, Lincoln), and J. M. Shively. Lethal action of ribonuclease for thermophilic bacilli. J. Bacteriol 91:673-676. 1966.-Exposure of a thermophilic bacillus, NU 47, to 0.2 mug/ml of pancreatic ribonuclease resulted in a drastic reduction of viable cells. The observed lethality is thought to be associated specifically with the ribonuclease, since heat treatment did not diminish activity and the addition of ribonucleic acid to the cells completely eliminated the action of the enzyme. Cells from 2-hr cultures, buffered between pH 6.0 and 7.0, were most sensitive. The lethal action was most pronounced when cells were exposed to the enzyme at temperatures between 25 and 45 C. A greater proportion of cells survived at higher temperatures. The release of ultraviolet-absorbing materials into the medium after exposure to enzyme could not be detected.     

Cationic proteins of polymorphonuclear leukocyte lysosomes. II. Composition, properties, and mechanism of antibacterial action

Zeya, H. I. (University of North Carolina, Chapel Hill), and J. K. Spitznagel. Cationic proteins of polymorphonuclear leukocyte lysosomes. II. Composition, properties, and mechanism of antibacterial action. J. Bacteriol. 91:755-762. 1966.-A basic proteins fraction from guinea pig polymorphonuclear (PMN) granules was obtained by acid extraction and precipitation with 20% (v/v) ethyl alcohol. The fraction accounted for most of the antibacterial activity of the PMN granules and corresponded to the antibacterial cationic components of intact granules (bands I, II, and III) resolved by zone electrophoresis. Absence from the fraction of components identical to the enzymatic components of intact lysosomes showed that the fraction was essentially free from lysosomal enzymes. The amino acid analysis of proteins in the fraction gave a preponderance of basic amino acids (25%), especially of arginine (16%). The comparative amino acid analysis showed that the lysosomal cationic proteins (LCP) fraction was markedly different from nuclear histones. The LCP fraction manifested antibacterial activity against certain gram-positive and gram-positive microorganisms, including Candida albicans, and exhibited stoichiometric relationship in its activity. Microorganisms treated with LCP fraction were agglutinated. Anionic substances such as nucleic acids, heparin, and endotoxin effectively blocked the antibacterial activity of the fraction. The LCP fraction caused suppression of oxygen uptake by bacterial cells and damaged the permeability barriers of cells as manifested by rapid release of P(32) as well as ultraviolet-absorbing material at 260 mmu, in the supernatant fluid.     

Characterization of the mycoplasma membrane proteins: V. Release and localization of membrane-bound enzymes in Acholeplasma laidlawii

The peripheral membrane protein fraction released by washing Acholeplasma laidlawii membranes with low-ionic strength buffers contained about 50 % of the total membrane-bound ribonuclease and deoxyribonuclease activities. The ATPase, NADH oxidase and p-nitrophenylphosphatase activities remained bound to the membrane even when EDTA was added to the wash fluids, and thus appear to belong to the integral membrane protein group.Serving as a marker for peripheral membrane proteins, the membrane-bound ribonuclease activity was solubilized by bile salts much more effectively than the integral membrane-bound enzymes. On the other hand, the solubilized ribonuclease showed a much lower capacity to reaggregate with other solubilized membrane components to membranous structures. Yet, most of the ribonuclease molecules which were bound to the reaggregated membranes could not be released by low-ionic strength buffer. The reaggregated membranes differed from the native membranes in the absence of particles on their fracture faces obtained by freeze cleaving, and by their much higher labeling by the [¹²⁵I]lactoperoxidase iodination system. These results suggest that most of the proteins are exposed on the reaggregated membrane surfaces, with very little, if any, protein embedded in its lipid bilayer core.Enzyme disposition in the A. laidlawii membrane was studied by comparing the activity of isolated membranes with that of membranes of intact cells after treatment with pronase or with an antiserum to membranes. The data indicate the asymmetrical disposition of these activities, the ATPase and NADH oxidase being localized on the inner membrane surface, while the nucleases are exposed on the external membrane surface.     

Characterization of the mycoplasma membrane proteins. V. Release and localization of membrane-bound enzymes in Acholeplasma laidlawii.

The peripheral membrane protein fraction released by washing Acholeplasma laidlawii membranes with low-ionic strength buffers contained about 50% of the total membrane-bound ribonuclease and deoxyribonuclease activities. The ATPase, NADH oxidase and p-nitrophenylphosphatase activities remained bound to the membrane even when EDTA was added to the wash fluids, and thus appear to belong to the integral membrane protein group. Serving as a marker for peripheral membrane proteins, the membrane-bound ribonuclease activity was solubilized by bile salts much more effectively than the integral membrane-bound enzymes. On the other hand, the solubilized ribonuclease showed a much lower capacity to reaggregate with other solubilized membrane components to membranous structures. Yet, most of the ribonuclease molecules which were bound to the reaggregated membranes could not be released by low-ionic strength buffer. The reaggregated membranes differed from the native membranes in the absence of particles on their fracture faces obtained by freeze cleaving, and by their much higher labeling by the [125-I]lactoperoxidase iodination system. These results suggest that most of the proteins are exposed on the reaggregated membrane surfaces, with very little, if any, protein embedded in its lipid bilayer core. Enzyme disposition in the A. laidlawii membrane was studied by comparing the activity of isolated membranes with that of membranes of intact cells after treatment with pronase or with an antiserum to membranes. The data indicate the asymmetrical disposition of these activities, the ATPase and NADH oxidase being localized on the inner membrane surface, while the nucleases are exposed on the external membrane surface.     

Intracellular distribution of ribonuclease activity during erythroid cell development.

Five ribonuclease activities, separable by polyacrylamide gel electrophoresis, have been detected in erythroid bone marrow cells from anaemic rabbits. Their intracellular distribution has been investigated and compared with that of the ribonucleases in reticulocytes. Both the acid and alkaline ribonuclease activities of reticulocytes are much lower (30--50 fold) than those of bone marrow erythroid cells. The most marked decrease in enzyme activity occurs in the fractions containing ribosomes and mitochondria plus lysosomes. In these subcellular organelles there was also a qualitative change in the ribonuclease electrophoretic pattern, whereas the cytosol enzymes of marrow erythroid cells and reticulocytes remained largely unchanged. Several ribonucleases released from reticulocyte membranes with urea were similar to those present in the lysosomal plus mitochondrial fraction, as shown by detection of enzyme activity after polyacrylamide gel electrophoresis. The decline in ribonuclease activity was found to begin in the orthochromatic cells, which have a highly condensed nucleus and are no longer active in DNA and RNA synthesis, and to coincide with a decrease in acid phosphatase activity and loss of lysosomes.     

The carbohydrate moieties of human urinary ribonuclease UL

Ribonuclease UL purified from pooled human urine contains approximately 20.7% of neutral sugar and 7.8% of aminosugar. All sugars were quantitatively released as oligosaccharides on hydrazinolysis. The oligosaccharides were converted to tritium-labeled oligosaccharides on reduction with NaB3H4. The radioactive oligosaccharide fraction was separated into a neutral and an acidic fraction on paper electrophoresis. All oligosaccharides in the acidic fraction could be converted to neutral oligosaccharides with the release of one sialic acid residue by sialidase digestion. Both fractions were shown to be mixtures of more than fourteen oligosaccharides by gel permeation chromatography. Structural studies on these oligosaccharides involving sequential exoglycosidase digestion in combination with methylation analysis revealed that ribonuclease UL contains sialylated and non-sialylated mono, bi-, tri-, and tetraantennary complex type sugar chains with N-acetyllactosamine outer chains, and tri- and tetraantennary complex type sugar chains with various numbers of Gal beta 1----4GlcNAc beta 1----3Gal beta 1----4GlcNAc beta 1----outer chains. An important finding was that all sialic acid residues in the acidic oligosaccharides only occur as the Sia alpha 2----6Gal beta 1----4GlcNAc beta 1----2Man alpha 1----3 group. Both fucosylated and non-fucosylated trimannosyl cores were found among the asparagine-linked sugar chains of ribonuclease UL.     

Preribosomal ribonucleoprotein particles are a major component of a nucleolar matrix fraction

Biochemical and morphological studies were performed on Novikoff hepatoma ascites cell nucleolar matrix fractions prepared by deoxyribonuclease I digestion and high-molarity salt extractions essentially according to a published method [Berezney, R., & Buchholz, L. A. (1981) Exp. Cell Res. 20, 4995-5002]. The nucleolar matrix fraction was enriched in polypeptides of molecular mass of 28, 37.5, 40, 70, 72, 110 (protein C23), and 160 kDa, compared to the nuclear fraction in which polypeptides of molecular mass of 31, 33.5, 43.5, 46, 50, 56, and 59 kDa were predominant. About one-fourth of the protein, half of the RNA, and less than 4% of the DNA originally present in the nucleoli remained in the matrix fraction. Addition of single agents such as ethylenediaminetetraacetic acid, ribonuclease A, or mercaptoethanol during preparation had no significant effect on the polypeptide composition of the nucleolar matrix fraction. However, the combination of mercaptoethanol and ribonuclease A caused most of the RNA and protein to be removed, including protein C23 and the 160-kDa polypeptide, with polypeptides in the range of Mr 30 000-50 000 remaining. Electron microscopy of nucleolar matrix fractions revealed the presence of particles similar in size to the granular elements of nucleoli. However, when ribonuclease A and mercaptoethanol were included in the procedure, only amorphous material remained. Many proteins of nucleolar preribosomal RNP particles were also associated with the nucleolar matrix fraction. RNA from the nucleolar matrix fraction was enriched in sequences from 18S and 28S ribosomal RNA. These results indicate that preribosomal RNP particles are major constituents of a nucleolar matrix fraction prepared by the deoxyribonuclease I-high-molarity salt method.     

Hepatic nucleases. Extrahepatic origin and association of neutral liver ribonuclease with lysosomes.

In the large granule fraction of rat liver, the density distribution of inhibitor-sensitive neutral ribonuclease is similar to that for acid hydrolases and its density distribution is similarly modified by Triton WR-1339 accumulation in lysosomes. Particulate neutral ribonuclease is latent; the enzyme is unmasked by very low digitonin concentrations or hypoosmotic shock. These observations demonstrate that the bulk of liver neutral ribonuclease is associated with the lysosomal system. In view of the neutral pH optimum of the enzyme and of some particularities of its distribution in fractionation experiments, the possiblilty of an extrahepatic origin of neutral ribonuclease has been investigated. After partial pancreatectomy, a significant decrease is observed in both plasma and liver neutral ribonuclease. The effect is specific, for it does not occur for other lysosomal enzymes. Also, labelled bovine pancreatic ribonuclease, when injected intravenously, is taken up by the liver. The sedimentable labelled enzyme has a density distribution similar to the distribution of other foreign proteins, horseradish peroxidase or yeast invertase. These results are explained by the uptake of plasmatic neutral ribonuclease from pancreatic origin by the liver.     

Secretion of intact proteins and peptide fragments by lysosomal pathways of protein degradation

We report that degradation of proteins microinjected into human fibroblasts is accompanied by release into the culture medium of peptide fragments and intact proteins as well as single amino acids. For the nine proteins and polypeptides microinjected, acid-precipitable radioactivity, i.e. peptide fragments and/or intact proteins, ranged from 10 to 67% of the total released radioactivity. Peptide fragments and/or intact protein accounted for 60% of the radioactivity released into the medium by cells microinjected with ribonuclease A. Two major radiolabeled peptide fragments were found, and one was of an appropriate size to function as an antigen in antigen-presenting cells. The peptides released from microinjected ribonuclease A were derived from lysosomal pathways of proteolysis based on several lines of evidence. Previous studies have shown that microinjected ribonuclease A is degraded to single amino acids entirely within lysosomes (McElligott, M. A., Miao, P., and Dice, J. F. (1985) J. Biol. Chem. 260, 11986-11993). We show that release of free amino acids and peptide fragments and/or intact protein was equivalently stimulated by serum deprivation and equivalently inhibited by NH4Cl. We also show that lysosomal degradation of endocytosed [3H]ribonuclease A was accompanied by the release of two peptide fragments similar in size and charge to those from microinjected [3H]ribonuclease A. These findings demonstrate that degradation within lysosomes occurs in a manner that spares specific peptides; they also suggest a previously unsuspected pathway by which cells can secrete cytosol-derived polypeptides.     

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.     

Properties of Yeast Cell Ghosts Obtained by Ribonuclease Action

Cell ghosts were obtained from Candida utilis and Saccharomyces cerevisiae by the action of some conformational isomers of pancreatic ribonuclease which passed through the cell wall and penetrated the cell membrane. In the interior, the enzyme caused extensive disorganization of the cellular structure as evidenced by the results of vital staining and electron microscopy. Ribonucleic acid was degraded to fragments that leaked out into the suspending medium. Other cytoplasmic constituents, including the amino acid pool, were released, but most of the cellular protein and deoxyribonucleic acid remained in the ghosts. The lesions in the cytoplasmic membrane were too small to be seen by conventional electron microscopy. The membrane clung to the cell wall even after obliteration of most of the intracellular structure.     

Radioiodination of L 1210 cells.

The lymphoid leukaemia L 1210 cells of mice were labelled with 125I. The cell homogenates were fractionated and from the microsomal fraction 90 per cent of the radioactive material could be precipitated with perchloric acid, whereas only 4 per cent was precipitated from the soluble fraction. Papain bound with Enzacryl AH released 31 per cent of radioactivity. It was concluded therefrom that the surface proteins of the cells were labelled. Electrophoretic separation of these proteins in polyacrylamide gel with sodium dodecyl sulphate was performed and 6--8 radioactive fractions of surface peptides were found.     

Characterization of ribonucleases and ribonuclease inhibitor in subcellular fractions from rat adrenals

1. The presence of two RNA-degrading enzymes, one with optimum activity at pH5.6 (acid ribonuclease) and the other with optimum activity at pH7.8 (alkaline ribonuclease), in rat adrenals has been demonstrated. The acid ribonuclease was localized in the mitochondrial fraction whereas the alkaline ribonuclease was present in mitochondria as well as in the supernatant fraction. Freezing and thawing of mitochondria and treatment with Triton X-100 gave a three- to four-fold increase in acid-ribonuclease activity, whereas the mitochondrial alkaline-ribonuclease activity was practically unaffected. 2. The amount of free ribonuclease in the adrenal supernatant was small. Treatment of the supernatant fraction with N-ethylmaleimide resulted in release of large amounts of ribonuclease activity, indicating the presence of a ribonuclease inhibitor having reactive thiol groups. 3. Considerable amounts of free ribonuclease inhibitor in excess over the bound alkaline ribonuclease are present in the rat-adrenal supernatant fraction. The inhibitor is heat-labile and non-diffusible. A 400-500-fold purification of the ribonuclease inhibitor was achieved by ammonium sulphate fractionation, treatment with calcium phosphate gel and DEAE-cellulose chromatography. It is concluded that the adrenal inhibitor is protein in nature, similar to the inhibitor present in rat liver.     

Endocytosis and breakdown of ribonuclease oligomers by sinusoidal rat liver cells in vivo. I. Effect of size.

Aspects of protein structure determining endocytosis of proteins by sinusoidal rat liver cells in vivo have been studied, using cross-linked or aggregated derivatives of bovine pancreatic ribonuclease A (labelled with 125I) as probes. Ribonuclease was cross-linked by reaction with dimethylsuberimidate, a way of modification that does not change the charge of the protein. Monomer, dimer and polymer fractions were isolated by gel filtration and characterized in respect of size and number of amino groups modified. Maintenance of enzyme activity, stability of disulfide bonds, and lack of susceptibility to endoproteases showed that the cross-linking procedure did not result in gross conformational changes of the ribonuclease molecules. Monomer, dimer and polymer fractions were injected into nephrectomized rats and plasma clearance and uptake in liver and spleen were determined. About 30% of the injected polymer fraction was found in liver 15 min after injection; for dimer and monomer fractions values of 6% and 2% of the dose were found. Similar differences were found in spleen. Autoradiography, cell isolation, and subcellular fractionation showed that in liver the radioactive proteins were taken up in lysosomes of sinusoidal cells. Similar results were obtained with fractions of aggregated ribonuclease prepared by freeze-drying the protein from 50% acetic acid. Our results demonstrate that the rate of uptake of the ribonuclease derivatives is positively correlated with the size of the molecules. Similarity of the results obtained with cross-linked and aggregated fractions suggests that the number of ribonuclease 'subunits'/molecule, rather than the procedures used to prepare the polymers, determine the rate of uptake by liver and spleen.     

hnRNA and its attachment to a nuclear protein matrix

In this study, DNA-depleted nuclear protein matrices are isolated from HeLa S3 cells. These nuclear matrices consist of peripheral laminae, residual nucleoli, and internal fibrillar structures. High molecular weight, heterogeneous nuclear RNA (hnRNA) is quantitatively associated with these structures and can be released intact only by affecting the integrity of the matrices. It is, therefore, concluded that hnRNA is part of a highly organized nuclear structure. By irradiation of intact cells or isolated nuclear matrices with ultraviolet light, proteins tightly associated with hnRNA can be induced to cross-link with the RNA. Performing the cross-linking in vivo is an extra guarantee that only hnRNA-protein (hnRNP) complexes existing in the intact cell are covalently linked. Such hnRNP complexes were isolated and purified under conditions that completely dissociate nonspecific RNA-protein complexes. By comparison of the hnRNP found in nuclear matrices and the published data on the composition of hnRNP particles, it was found that the so-called hnRNP "packaging" proteins (32,000-38,000 mol wt) were not efficiently cross-linked to hnRNA by UV irradiation. They were, however, present in the matrix preparations, bound to hnRNA, because they were released from nuclear matrices after ribonuclease treatment of these structures. On the other hand, two major hnRNPs (41,500 and 43,000 mol wt) were efficiently cross-linked to hnRNA. These proteins were not released by ribonuclease treatment, which suggests that they are involved in the binding of hnRNA to the nuclear matrix.     

Selective Release of Proteins from Spirillum itersonii by Tris(hydroxymethyl)aminomethane and Ethylenediaminetetraacetate

Treatment of Spirillum itersonii with tris(hydroxymethyl)aminomethane (Tris)-ethylenediaminetetraacetate (EDTA) results in the quantitative release of alkaline phosphatase and ribonuclease into the surrounding medium. At the same time, about 90% of the total cellular soluble cytochrome c is liberated. This process occurs within 1 min of treatment at both 24 and 4 C. Release of these proteins by Tris-EDTA treatment is highly selective, since only 9% of the total cell protein is liberated, concomitantly with less than 5% ribonucleic acid, deoxyribonucleic acid, and malate dehydrogenase. Different sigmoidal curves are obtained for release of proteins as a function of EDTA concentration. The order of liberation with increasing EDTA is as follows: alkaline phosphatase, protein, soluble cytochrome c, and ribonuclease. Treatment of cells with Tris-EDTA under conditions which cause extensive loss of alkaline phosphatase, soluble cytochrome c, and ribonuclease results in cell death, with cessation of protein and ribonucleic acid synthesis. Cells treated with EDTA in phosphate buffer (in the absence of Tris) liberate a large portion of their soluble cytochrome c, but negligible amounts of alkaline phosphatase and ribonuclease. Addition of Tris to cells pretreated with phosphate-buffered EDTA releases high levels of alkaline phosphatase, but not ribonuclease. These results suggest that a common surface alteration is not solely responsible for release of periplasmic proteins. More likely, each protein of the periplasm is bound in an independent and specific manner.