Separation and partial characterization of chloroplast and cytoplasmic ribosomes from Euglena gracilis

Chloroplast and cytoplasmic ribosomes from Euglena graciliswere separated by centrifugation in zonal rotors. The particleswere characterized by their sedimentation rates as well as bytheir RNA components. Total extracts from green cells contained30S, 55S and 89S particles or their aggregates, depending uponthe Mg⁺⁺ concentration. Extracts from fractions enriched forchloroplasts contained essentially 30S and 55S particles, whilethe supernatant (obtained after sedimentation of the chloroplasts)contained predominantly 89S particles or aggregates of cytoplasmicribosomes. The 30S and 55S ribosomes contained RNA componentswhich were unique and distinct from those of the cytoplasmicribosomes. We were unable to detect 70S particles from the chloroplastpreparations. Under our conditions, chloroplast extracts yielded30S and 55S subunits or a series of rapidly sedimenting particles,possibly polysomes. Despite a variety of extraction techniques,we were unable to detect 70S particles from the chloroplasts. ¹This study was supported in part by grant No. HD 01787 fromthe U. S. Public Health Service. Journal paper of the New JerseyAgricultural Experiment Station (Received December 3, 1969; )     

MICROSOMAL NUCLEOPROTEIN PARTICLES FROM PEA SEEDLINGS

Ultracentrifugal analysis of an extract of pea epicotyls, previously freed of debris and larger particles by centrifugation at 40,000 g for 10 minutes, has revealed the presence of a major component which possesses a sedimentation coefficient of 74 S. This component constitutes about 25 per cent of the TCA-precipitable material in the clarified epicotyl extract and is estimated to make up 1 to 2 per cent of the dry weight of the original tissue. In size, chemical composition, and morphology, the 74 S component resembles the nucleoproteins of the microsomes from animal tissues. The 74 S component of pea epicotyl extracts has been purified by repeated cycles of differential centrifugation to yield a preparation which is 80 per cent homogeneous in the analytical ultracentrifuge. It has been found to contain 30 to 37 per cent RNA as judged by a variety of analytical techniques. Approximately 55 per cent of the weight of the material is protein and a further 4.5 per cent phospholipide. Electron micrographs of air-dried specimens of the purified preparation show the 74 S constituent to be flattened spheres with an average height of 180 A and an average diameter of approximately 280 A. The molecular weight of the 74 S particles is computed from sedimentation, viscosity, and partial specific volume data to be 4.5 million ± 10 per cent in agreement with the value estimated from electron micrographs. The 74 S or microsomal component of pea epicotyls is rapidly aggregated in the presence of low concentrations of Mg ions or by somewhat higher concentrations of Ca or K salts. ATP on the contrary causes resolution of electrolyte-induced microsomal aggregates with simultaneous degradation of the particles to an ultracentrifugally inhomogeneous mixture of lower molecular weight materials.     

ISOLATION OF CYTOPLASMIC AND CHLOROPLAST RIBOSOMES AND THEIR DISSOCIATION INTO ACTIVE SUBUNITS FROM CHLAMYDOMONAS REINHARDTII

A mixture of cytoplasmic (80S) and chloroplast (70S) ribosomes from Chlamydomonas reinhardtii was freed of contaminating membranes by sedimentation of the postmitochondrial supernatant through a layer of 1.87 M sucrose. The purified ribosomes were separated into 80S and 70S fractions by centrifugation at a relatively low speed on a 10–40% sucrose gradient containing 25 mM KCl and 5 mM MgCl₂. Both the 80S and 70S ribosomes were dissociated into compact subunits by centrifugations in 5–20% high-salt sucrose gradients. The dissociations of both ribosomal species under these conditions were not affected by the addition of puromycin, indicating that the ribosomes as isolated were devoid of nascent chains. Subunits derived from the 80S ribosomes had apparent sedimentation coefficients of 57S and 37S whereas those from the 70S ribosomes had apparent sedimentation coefficients of 50S and 33S. In the presence of polyuridylic acid and cofactors, the 80S and 70S ribosomes incorporated [¹⁴C]phenylalanine into material insoluble in hot TCA. The requirements for incorporation were found to be similar to those described for eukaryotic and prokaryotic ribosomes. Experiments with antibiotics showed that the activity of the 80S ribosomes was sensitive to cycloheximide, whereas that of the 70S ribosomes was inhibited by streptomycin. The isolated subunits, when mixed together in an incorporation medium, were also active in the polymerization of phenylalanine in vitro.     

A Comparison of the Native and Derived 30S and 50S Ribosomes of Escherichia coli

Four types of ribosomes occurring in E. coli have been separated by sucrose gradient centrifugation. These are the 30S and 50S particles occurring in E. coli extracts (native particles), and the 30S and 50S particles which are the subunits of 70S ribosomes (derived particles). Two criteria were used in comparing these particles: (1) The type of RNA contained in each, as determined by sedimentation velocity in the analytical ultracentrifuge. (2) The ability of mixtures of 30S and 50S ribosomes (derived 30S + derived 50S, native 30S + native 50S) to undergo the reaction: [Formula: see text] Native and derived 30S particles were found to contain 16S RNA. Derived 50S particles contained 23S RNA and a small amount of 15 to 20S RNA, whereas native 50S ribosomes contained only 16S RNA. Derived 30S and 50S particles combined to form 70S particles. However, under identical conditions, native 30S and 50S particles did not form 70S ribosomes.     

Study of the interaction of soluble and particle-bound nicotinamide adenine dinucleotide pyrophosphorylase with cytoplasmic ribosomes

The cytoplasm of cells infected with EMC virus contains new structures which possess activity of the nuclear enzyme NAD pyrophosphorylase [14]. An attempt was made to understand the mode of formation of these structures in the infected cell. It was found that soluble NAD pyrophosphorylase manifests a strong affinity for cytoplasmic ribosomes, sedimenting at 90S. When cytoplasmic ribosomes were dissociated to the 60S and 40S subunits, the enzyme was found to be adsorbed only to the 60S unit. In extracts of rat liver nuclei, NAD pyrophosphorylase is associated with 35S particles, composed mainly of protein and DNA. The bond between enzyme and particle is of a loose nature. When ribosomes are mixed with 35S nuclear particles, most of the enzyme activity is transferred from the nuclear particles to the ribosomes, thus forming particles with an average sedimentation coefficient of 90S. Similar structures are obtained when either soluble NAD pyrophosphorylase or 35S nuclear particles are mixed with preparations of cytoplasm isolated from non-infected cells. The results of these experiments suggest that the 90S cytoplasmic structures found in virus-infected cells could result from an association between either free or particle-bound NAD pyrophosphorylase with cytoplasmic ribosomes.     

Characterization of Ribosomes from Neurospora crassa

Ribosomes isolated from growing hyphae of Neurospora crassa contain 53 per cent protein and 47 per cent RNA and have a sedimentation coefficient of 81S at 20°C and infinite dilution. These ribosomes are stable at pH 7.4 in the presence of 0.01 M and 0.002 M MgCl₂ but undergo a dissociation into smaller particles if the MgCl₂ concentration is lowered to 0.0001 M. Two types of RNA with sedimentation coefficients of 19S₂₀⁵⁰ and 13S₂₀⁵⁰ have been extracted from the 81S particles.     

Nuclear genome codes for chloroplast ribosomal proteins in Acetabularia. I. Isolation and characterization of chloroplast ribosomal particles

A method is described for the isolation of chloroplast ribosomes from Acetabularia cells in yields sufficient for the characterization of these particles. Ribosomal particles sedimenting with 70S, 56S, 44S, and 30S have been obtained. The monoribosome sediments with 70S and dissociates into a larger 44S and a smaller 30S subunit. The sedimentation behaviour of the particles as well as the equilibrium between monoribosomes and their subunits is not influenced by the centrifugation step as could be revealed by formaldehyde fixation.     

Poliovirus morphogenesis. I. Identification of 80S dissociable particles and evidence for the artifactual production of procapsids.

The current model of poliovirus morphogenesis postulates a fundamental role for procapsid, 80S shells that, upon interaction with viral RNA and subsequent proteolytic cleavage, give rise to complete virus particles. Although 80S sedimenting particles can, indeed, be isolated from cytoplasmic extracts of infected cells, their physical properties differ from those reported for procapsids. Far from being stable structures, they can be dissociated by pH 8.5 and 0.1% sodium dodecyl sulfate into slower-sedimenting subunits. The reasons for this discrepancy were investigated, and two main modalities leading to the appearance of procapsids in vitro were identified. The first involves a temperature-mediated conversion of dissociable 80S particles into stable 80S procapsids, and the second involves the self-assembly of endogenous 14S subunits, also primed by an increase in the temperature of cytoplasmic extracts.     

Reassociation of cytoplasmic ribosomal subunits of barley and its virescens mutant to form active hybrids

Polyphenylalamine synthesis by cytoplasmic ribosomes of Gateway barley (Hordeum vulgare) and its virescens single gene nuclear mutant was compared. The cytoplasmic 80S ribosomes were isolated from unimbibed embryo material and the ribosomes were dissociated into their component 60S and 40S subunits by centrifugation through sucrose gradients containing high KCl-to-MgCl₂ buffer. These separated subunits could be reassociated by resuspension in buffer having about equimolar concentrations of MgCl₂ and KCl. Both homologous and heterologous combinations of the subunits reassociated to give monomeric 80S ribosomes, and the derived monomers as well as various combinations of the individual subunits showed equivalent activity in an in vitro system for poly (U)-directed polyphenylalanine synthesis.     

Partial reassembly of active 60S ribosomal subunits from rat liver following treatment with dimethylmaleic anhydride

Rat liver 60S ribosomal subunits were treated with dimethylmaleic anhydride, a reagent for protein amino groups, at a 1/15,000 mol/mol ratio. This caused the dissociation of specific proteins, which were separated from the 56S residual core particles by centrifugation and identified by two-dimensional gel electrophoresis. The core particles lacking 30% of the total proteins retained most of the initial activity measured by the puromycin reaction but only small percentages of activities measured by polyphenylalanine synthesis, elongation-factor-2(EF-2)-dependent GTP hydrolysis and EF-2-mediated GDP binding. Upon reconstitution, the complementary amount of split proteins was incorporated into ribosomal particles, which had almost the same catalytic activities and biophysical properties (density, sedimentation coefficient and capability to reassociate to 40S subunits) as the original subunits.     

Purification and partial characterization of virus-like particles from Schneider line 2 Drosophila cells

A procedure has been developed for the purification of virus-like particles (VLPs) from Schneider line 2 Drosophila cells. The VLPs were precipitated with polyethylene glycol from the cytoplasmic fraction of lysed cells and further purified by equilibrium centrifugation in CsCl density gradients, in which they band at a density of 1.366 g/ml. Electron micrographs of these preparations revealed polyhedral particles with a diameter of 310–330 Å. We have also found particles of this size in thin sections of the intact cells. Sedimentation of the VLPs through 10–70% sucrose gradients yields a sedimentation coefficient of 235 S. Preliminary studies show that the VLPs contain double-stranded RNA species of 10 S, 14.5 S, 16 S, and 18 S.     

Isolation and some properties of components of nuclear polyhedra from the cabbage looper, Trichoplusia ni

Nuclear polyhedra obtained from diseased cabbage looper, Trichoplusia ni, were digested with sodium carbonate-saline buffer, pH 11.0. The dissolved polyhedra formed 3 general zones when subjected to density gradient centrifugation. The slowest sedimenting component (Zone 1) had an ultraviolet absorption curve typical of protein and a sedimentation coefficient of 11 S. Capsids, 310 × 40 nm, were located in Zone 2. Virus particles were found in 1–3 bands (Zone 3); those with envelopes measured 300 × 72 nm, and those without envelopes measured 300 × 33 nm. Virus preparations stained with phosphotungstic acid at pH 7.0 exhibited extensive disruption whereas preparations stained at pH 3.0 did not. Virus particles in the sodium carbonate-saline-digested polyhedra had a sedimentation coefficient of 1228 S. Virus particles isolated by high speed centrifugation had a sedimentation coefficient of 1530 S.     

A STRUCTURAL STUDY OF RAT LIVER RIBOSOMES

Polyribosomes, ribosomes, and ribosomal subunits were prepared from rat liver using sodium deoxycholate and a variety of ionic media. They were examined in the electron microscope, mainly as negatively or positively stained preparations, and in the analytical ultracentrifuge. The polyribosomes consist of up to twelve or more ribosomes linked by a fine strand, 10 to 15 A in diameter, probably of RNA. The ribosomes are approximately spherical with diameters of 250 to 300 A, and are estimated to be about 50 per cent porous. Possibly because of their high protein content, whole ribosomes show no cleavage furrows. Ribosomes were dissociated in phosphate buffer and the subunits separated on sucrose density gradients containing 10 per cent formalin. Three classes of subunit were obtained with sedimentation coefficients of 71S, 50S, and 31S respectively. The smallest, 31S subunit is about 250 A long by 100 A wide. The largest subunits appear to be clusters of smaller particles. It is estimated from their linear dimensions in electron micrographs that the whole 83S ribosome could contain up to six 31S subunits, or their equivalent.     

Characterization of mesosomes of Micrococcus luteus: isolation and properties of mesosomal ribosomes, and localization of penicillin-binding proteins in mesosomal membranes

Mesosomes were isolated and purified from Micrococcus luteus under hypertonic conditions throughout preparation processes. The purified mesosomal preparation was composed of closed tubules and vesicles. Electron-dense ribosome-like particles were observed within the isolated mesosomal vesicles by electron microscopy. The ribosome-like particles were isolated from the purified mesosomes by a procedure involving solubilization of the membranes with detergents followed by centrifugation on a linear density gradient of sucrose. The isolated particles have a sedimentation coefficient of 70S in the presence of 10 mM Mg2+, when Mg2+ concentration was lowered to 0.1 mM, the particles were dissociated into two sub-particles of 30S and 50S. The 70S particles had the same appearance as cytoplasmic 70S ribosome particles upon observations of negatively stained preparations. These findings indicate that mesosomal tubules contain ribosomes. The isolated mesosomal ribosomes had the ability for protein synthesis when polyuridylic acid-directed polyphenylalanine synthesis was assayed. The sensitivity of mesosomal ribosomes to inhibitors, chloramphenicol and streptomycin, for protein synthesis was significantly lower than that of both cytoplasmic and cytoplasmic membrane-bound ribosomes. In addition, three penicillin-binding proteins were detected in the mesosomal membranes. One of these was localized predominantly in the mesosomal membranes and the other two were distributed almost equally in both mesosomal and cytoplasmic membranes.     

Dissociation of ribosomes and seed germination

Ribosomes from rice embryos (Oryza sativa) were dissociated into ribosomal subunits in vitro by systematic reduction of the Mg²⁺ concentration. Ribosomes from imbibed (28 C) embryos were more easily dissociated than those from nonimbibed embryos. This was not observed with ribosomes from either imbibed, nonviable embryos, or from embryos imbibed at 0 C. Ribosomes from embryos which had been imbided and subsequently dehydrated resembled ribosomes from nonimbibed embryos in their resistance to dissociation. The change in the resistance to dissociation was essentially complete after the first 20 minutes of imbibition at 28 C, and accompanied activation in vivo of protein synthesis as determined by amino acid incorporation in vitro. Ribosomes from either imbibed or nonimbibed embryos could be dissociated into subunits by 0.5 m KCl. These subunits were separated by density gradient centrifugation, and, if recombined, were active for polyphenylalanine synthesis in vitro. The individual subunits prepared from nonimbibed embryos could be replaced by the corresponding subunit fraction from imbibed embryos without loss of capacity to support polyphenylalanine synthesis. The change in the ease of dissociation of ribosomes appears to be a physiological process, and its possible relationship to the initiation of protein synthesis during seed germination is discussed.     

Structural dynamics of bacterial ribosomes: IV. Classification of ribosomes by subunit interaction

Previous studies in this series (M. Noll et al., 1973a,b; Noll & Noll, 1974) have established that in Escherichia coli the ability of subunits to form vacant 70 S ribosome couples at 10 mm-Mg²⁺ is a stringent condition for activity in the translation of natural messenger (R17 RNA). The present study examines the structural basis of subunit interaction. It is found that vacant ribosome couples prepared by various methods fall into two classes, “tight” couples and “loose” couples, that differ in the affinity of their subunits for each other. Detection and separation of the two particle species is possible by ultracentrifugation. When analyzed on sucrose gradients at 6 mm-Mg²⁺ and moderate speed (30,000 revs/min), tight couples sediment as undissociated 70 S ribosomes, whereas loose couples are completely dissociated and sediment as 30 S and 50 S subunits. At 15 mm-Mg²⁺ in the gradient, both species sediment as a 70S peak. At 10 mm-Mg²⁺ and 60,000 revs/min, two peaks (63 S and 55 S) are seen because the high hydrostatic pressure causes more pronounced dissociation of the loose than of the tight couples.Association is dependent on the state of each subunit. Removal of Mg²⁺ produces 30 S b-particles that are unable to associate with 50 S subunits unless reconverted to the 30 S a-form by thermal activation according to Zamir et al. (1971). In the dissociated state, 50 S subunits tend to change irreversibly to a 50 S b-modification that produces loose couples upon association with 30 S a-subunits. The 50 S a → 50 S b transition could not be related to breaks in 23 S RNA detectable by sedimentation analysis. However, mild treatment of 50 S a-subunits with RNase produces particles that associate with 30 S a-subunits to couples that are less stable than the loose couples resulting from a dissociation/association step.Fresh S-30 extracts contain only tight couples (approx. 80%) and subunits (approx. 20%). Our results suggest that loose couples are artefacts derived from tight couples by a structural or conformational modification.Interaction-free subunits that previously were found to form a primitive initiation complex with poly(U) and tRNA_Phe (Schreier & Noll, 1970,1971), and to be active in phenylalanine polymerization, are shown to consist of the b-form of each subunit.It is likely that conflicting results obtained in the study of the mechanism of initiation and other aspects of ribosome function are due to the lack of structural criteria required for standardizing the ribosome preparation used by different investigators. This study provides simple methods and criteria to classify and separate physically all ribosome and ribosome subunits that have been observed into well-defined classes of predictable activity.     

Reconstitution of active 50 S ribosomal subunits from Bacillus licheniformis and Bacillus subtilis.

Active 50 S ribosomal subunits from Bacillus licheniformis and Bacillus subtilis can be reconstituted in vitro from dissociated RNA and proteins. The reconstituted 50 S sub-units are indistinguishable from native 50 S subunits in sedimentation on sucrose gradients and in protein composition. The procedure used is similar to that developed for reconstitution of Bacillus stearothermophilus 50 S subunits, though the optimal conditions are somewhat different. Hybrid ribosomes can be reconstituted with 23 S RNA and proteins from different sources (B. stearothermophilus and B. licheniformis or B. subtilis). The thermal stability of these ribosomes depends on the source of the proteins, and not on the source of 23 S RNA.     

The effect of sodium chloride on the structure of ribonucleoprotein particles from rat liver nuclei.

38S (monoparticles) and greater than 50--200S ribonucleoprotein particles (polyparticles) from rat liver nuclei were treated with increasing concentrations of sodium chloride. Treatment of 38S or greater than 50--200S particles, with 0.14, 0.25, 0.5, 1.0, and 2.0M NaCl resulted in a decrease of protein to RNA ratios from 8 to 3.1 for 38S particles and from 4.0 to 1.5 for greater than 20--200S particles. Correspondingly the densities in CsCl increased. Whereas the maximum of the sedimentation profile of polyparticles decreased from 90S to 50S after treatment with increasing NaCl concentrations, a discontinuous change was found in the case of monoparticles. It was shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis that the proteins which were dissociated by NaCl were in the molecular weight range of 30--45 000. Four of the 5 small molecular weight RNAs in the range of 4.5 to 8S remained tightly associated even after treatment of polyparticles with 2.0M NaCl. When 38S or 70--200S nRNP particles were exposed to increasing concentrations of NaCl (0.25, 0.5, 1.0, 2.0M), the molar ellipticity at 264 nm increased progressively to about 40%. Upon NaCl treatment of polyparticles and successive removal of the dissociated proteins by centrifugation the increase in the positive CD band at 264 nm was only 15%.     

Isolation of ribosome particles from meningopneumonitis organisms

In ribonucleic acid (RNA) extracted by phenol and sodium dodecyl sulfate from purified reticulate bodies of meningopneumonitis (MP) organisms, 21S, 16S, and 4S RNA were found by sucrose density gradient sedimentation analysis. When purified reticulate bodies were homogenized by sonic treatment or by treatment with sodium deoxycholate and were fractionated by differential centrifugation, more than 50% of the RNA was recovered in the fraction which was sedimented by centrifugation at 105,000 x g for 2 hr, but not at 13,000 x g for 20 min. From homogenates prepared in this manner, 50S and 30S particles containing RNA were isolated by sucrose density gradient centrifugation. These 50S and 30S particles were also found in lysates of cytoplasmic fractions of infected cells which were labeled by (32)P during 17 to 17.5 hr or 15 to 18 hr after infection. The synthesis of 50S and 30S particles was not inhibited by actinomycin D. When infected cells were homogenized in the presence of 0.01 or 0.02 m MgCl(2), 70S particles were isolated instead of 50S and 30S particles. When dialyzed against low concentrations of MgCl(2), the 70S particles dissociated to 50S and 30S particles. The base ratio of the 70S particles is very similar to that of 16S plus 21S RNA. The characteristics of the 70S, 50S, and 30S particles suggest that these are ribosome particles, similar to bacterial ribosomes.     

Effects of detergents on ribosomal precursor subunits of Bacillus megaterium.

Cell extracts prepared by osmotic lysis of protoplasts were analyzed by sucrose gradient sedimentation. In the absence of detergents, ribosomal precursor particles were found in a gradient fraction which sedimented faster than mature 50S subunits and in two other fractions coincident with mature 50S and 30S ribosomal subunits. Phospholipid, an indicator of membrane, was shown to be associated with only the fastest-sedimenting ribosomal precursor particle fraction. After the extracts were treated with detergents, all phospholipid was found at the top of the gradients. Brij 58, Triton X-100, and Nonidet P-40 did not cause a change in the sedimentation values of precursors; however, the detergents deoxycholate or LOC (Amway Corp.) disrupted the fastest-sedimenting precursor and converted the ribosomal precursor subunits which sedimented at the 50S and 30S positions to five different classes of more slowly sedimenting particles. Earlier reports on the in vivo assembly of ribosomal subunits have shown that several stages of ribosomal precursor subunits exist, and, in the presence of the detergents deoxycholate and LOC, which had been used to prepare cell extracts, the precursors sedimented more slowly. Our data are consistent with the hypothesis that those detergents selectively modify the structure of ribosomal precursors and lend further support to the hypothesis that the in vivo ribosomal precursor subunits have 50S and 30S sedimentation values. In addition, these data support the idea that the ribosomal precursor particles found in the fast-sedimenting fraction may constitute a unique precursor fraction.