Ribosomes and ribonucleic acids of Coxiella burneti

This report describes the direct isolation and characterization of rickettsial ribosomes. Ribosomes from the rickettsia Coxiella burneti were isolated and partially characterized. The ribosomes had a sedimentation constant of about 70S and could be dissociated into 50 and 30S subunits. Electron microscopy revealed ribosomal particles with dimensions similar to those reported for other procaryotic organisms. Ribonucleic acid (RNA) species (23 and 16S) were isolated from the ribosomal particles. The nucleotide compositions of the ribosomal RNAs were found to be similar to those reported for bacterial ribosomal RNA. In addition to the high-molecular-weight ribosomal RNA, 5S RNA was also extracted from the organism.     

Hybrid 80S monomers formed from subunits of ribosomes from protozoa,fungi, plants,and mammals

Free 80S ribosomes of eukaryotic organisms are dissociated by KCl (0.8–1.0 m) in the presence of 2-mercaptoethanol and magnesium ions (10–15mm); the large and small subunits so formed can be recombined to yield 80S monomers. We have now studied the ability of ribosomal subunits from protozoa (Tetrahymena pyriformis), fungi (Allomyces arbuscula, Saccharomyces cerevisiae), plants (pea, wheat), and mammals (rat, mouse, rabbit) to combine to form hybrid ribosomes. In general, both subunits of the species studied participate in the formation of hybrid particles, with the exception of the 60S subunit of Tetrahymena, which does not combine with the small subunit of fungal, plant, or mammalian ribosomes. The interaction of subunits from rat and Tetrahymena ribosomes has been visualized by an electron microscope study of negatively stained preparations. The base sequences of the ribosomal RNAs of these organisms have been compared to those of Saccharomyces by nucleic acid hybridization-competition.This work was supported by a fellowship #PF-529 from the American Cancer Society and by United States Public Health Service, National Institutes of Health grant GM 12449.     

In vivo and in vitro phosphorylation of ribosomal proteins by protein kinases from Saccharomyces cerevisiae.

From the high salt wash of the ribosomes of the yeast Saccharomyces cerevisiae, three protein kinases have been isolated and separated by DEAE-cellulose chromatography. The three kinases differ in their abilities to phosphorylate substrates such as histones (calf thymus), casein, and S. cerevisiae ribosomes; two of the kinases showed increased activity in the presence of cyclic adenosine 3',5'-monophosphate when histones and 40S ribosomal subunits were used as substrates. The protein kinases catalyzed phosphorylation of certain proteins of the 40S and 60S ribosomal subunits, and 80S ribosomes in vitro. Nine proteins of the 80S ribosome, seven proteins of the 40S subunit, and eleven of the 60S subunit were phosphorylated; different proteins were modified to various extents when different kinases were used. We have identified several proteins of 40S and 60S ribosomal subunits which are not available to the kinases in the 80S particles. Ribosomes isolated from S. cerevisiae cells growing in logarithmic phase of growth were found to contain a number of phosphorylated proteins. Studies by two-dimensional polyacrylamide gel electrophoresis indicated that the ribosomal proteins phosphorylated in vivo correspond with those phosphorylated in vitro. The relationship of in vivo phsophorylation of ribosomes to the growth and physiology of S. cerevisiae is not known.     

Effect of chronic ethanol consumption on hepatic mitochondrial transcription and translation.

Liver mitochondria from ethanol-fed rats display an impaired ability for protein synthesis in vitro. Studies were conducted to explore the possible mechanisms which might account for this impaired capacity of ethanol mitochondria for protein synthesis. The present studies did not demonstrate any significant ethanol-induced lesion in mitochondrial nucleic acid metabolism in organelles isolated from ethanol-fed rats for any of the parameters investigated (mtDNA content, steady-state mtRNA concentration, mtRNA polymerase activity, concentration of specific mRNAs and rRNAs, mtRNA processing). An investigation of ribosome function in isolated mitochondria demonstrated significant decreases in the number of active ribosomes (55% fewer) in mitochondria from ethanol-fed rats. Initiation of protein synthesis was also significantly depressed (46%) in ethanol mitochondria. In addition, the yield of ribosomal particles from ethanol mitochondria was decreased 32% as compared to the yield of ribosomal particles from control mitochondria. However, isolated ribosomes from ethanol mitochondria were determined to be fully functional in a poly(U)-directed phenylalanine polymerization system. Soluble translation factors from ethanol mitochondria were also found to support full activity of control ribosomes in a poly(U)-directed phenylalanine polymerization system. These results suggest strongly that the ethanol-induced depression of mitochondrial protein synthesis is due to a decrease in the number of competent ribosomes in hepatic mitochondria from chronically ethanol-fed rats.     

Isolation and study of the properties of Streptococcus pyogenes ribosomes

Ribosomes from Streptococcus pyogenes, group A, strain 29 were studied. A comparison of different methods of ribosomal isolations has shown that the homogenous ribosomal samples can be obtained by the method of differential ultracentrifugation using tris-HCl buffer. The ribosomes of S. pyogenes had the sedimentation coefficient of 70S and consisted of 65% of protein and 35% of nucleic acids; the ribosomes dissociated into subparticles with the sedimentation coefficients of 50S and 30S under a low magnesium concentration. Thus the S. pyogenes ribosomes do not differ from the ribosomes of procaryotes. It was shown that the ratios of 70S, 50S and 30S ribosomal subparticles in the cells depend on the growth phase of S. pyogenes. The cells of the middle and the late logarithmic phase contained 50S and 30S particles in a stoichiometric ratio. In the cells of the late stationary growth phase there was a deficiency of 30S ribosomal subparticles which does not result from a loss during the isolation procedure, as it was already observed in the initial 30S fraction.     

Ribosome reactivation by replacement of damaged proteins

Ribosomal functions are vital for all organisms. Bacterial ribosomes are stable 2.4 MDa particles composed of three RNAs and over 50 different proteins. Accumulating damage to ribosomal RNA or proteins can disturb ribosome functioning. Organisms could benefit from degrading or possibly repairing inactive or partially active ribosomes. Reactivation of chemically damaged ribosomes by a process of protein replacement was studied in vitro. Ribosomes were inactivated by chemical modification of Cys residues. Incubation of modified ribosomes with total ribosomal proteins led to reactivation of translational activity. Intriguingly, ribosomal proteins extracted by LiCl are equally active in the restoration of ribosome function. Incubation of 70S ribosomes with isotopically labelled r‐proteins followed by separation of ribosomes was used to identify exchangeable proteins. A similar set of proteins was found to be exchanged in vivo under stress conditions in the stationary phase. We propose that repair of damaged ribosomes might be an important mechanism for maintaining protein synthesis activity following chemical damage.     

Immunochemical analysis of the structure of eukaryotic ribosomes

Summary Antibodies were prepared in rabbits and sheep to rat liver ribosomes, ribosomal subunits, and to mixtures of proteins from the particles. The antisera were characterized by quantitative immunoprecipitation, by passive hemagglutination, by immunodiffusion on Ouchterlony plates, and by immunoelectrophoresis. While all the antisera contained antibodies specific for ribosomal proteins, none had precipitating antibodies against ribosomal RNA. Rat liver ribosomal proteins were more immunogenic in sheep than rabbits, and the large ribosomal subunit and its proteins were more immunogenic than those of the 40S subparticle. Antisera specific for one or the other ribosomal subunit could be prepared; thus it is unlikely that there are antigenic determinants common to the proteins of the two subunits. When ribosomes, ribosomal subunits, or mixtures of proteins were used as antigens the sera contained antibodies directed against a large number of the ribosomal proteins.Abbreviations TP total proteins—used to designate mixtures of proteins from ribosomal particles, hence TP80 is a mixtures of all the proteins from 80S ribosomes - TP60 the proteins from 60S subunits - TP40 the proteins from 40S particles     

Heterotrophic Nature of the Cell-Free Protein-Synthesizing System from the Strict Chemolithotroph, Thiobacillus thiooxidans

A cell-free protein-synthesizing system prepared from the strict chemolithotroph, Thiobacillus thiooxidans, was similar to that of heterotrophs. The poly-U directed system had a temperature optimum of 37 C, but in the presence of spermidine (3 mM) the optimum shifted to 45 C. Although growth of the chemolithotroph occurs only in acid conditions, the pH optimum for the cell-free system was pH 7.2. The endogenous-directed activity in the presence or absence of spermidine was maximal at pH 7.8. Spermidine had a stimulatory effect; however, this effect was dependent on the magnesium and tris(hydroxymethyl)aminomethane (Tris) concentrations. At low Tris concentrations (10 mM), spermidine (3 to 5 mM) could completely replace magnesium. When the Tris concentration was increased (50 mM), spermidine could not replace magnesium. Supernatant and ribosomal fractions from T. thiooxidans were exchanged with those of Bacillus thuringiensis and Escherichia coli, and the ribosomal fraction from the chemolithotroph gave good to moderate stimulation when exchanged with the supernatant from the heterotrophs. On the other hand, the supernatant from T. thiooxidans gave good stimulation when mixed with ribosomes from B. thuringiensis but poor activity with ribosomes from E. coli. Both supernatant and ribosomal fractions prepared from stationary phase extracts of T. thiooxidans were inactive in the cell-free system.     

Mobility of ribosomes bound to microsomal membranes. A freeze-etch and thin-section electron microscope study of the structure and fluidity of the rough endoplasmic reticulum

The lateral mobility of ribosomes bound to rough endoplasmic reticulum (RER) membranes was demonstrated under experimental conditions. High- salt-washed rough microsomes were treated with pancreatic ribonuclease (RNase) to cleave the mRNA of bound polyribosomes and allow the movement of individual bound ribosomesmfreeze-etch and thin-section electron microscopy demonstrated that, when rough microsomes were treated with RNase at 4 degrees C and then maintained at this temperature until fixation, the bound ribosomes retained their homogeneous distribution on the microsomal surface. However, when RNase- treated rough microsomes were brought to 24 degrees C, a temperature above the thermotropic phase transition of the microsomal phospholipids, bound ribosomes were no longer distributed homogeneously but, instead, formed large, tightly packed aggregates on the microsomal surface. Bound polyribosomes could also be aggregated by treating rough microsomes with antibodies raised against large ribosomal subunit proteins. In these experiments, extensive cross-linking of ribosomes from adjacent microsomes also occurred, and large ribosome-free membrane areas were produced. Sedimentation analysis in sucrose density gradients demonstrated that the RNase treatment did not release bound ribosomes from the membranes; however, the aggregated ribosomes remain capable of peptide bond synthesis and were released by puromycin. It is proposed that the formation of ribosomal aggregates on the microsomal surface results from the lateral displacement of ribosomes along with their attached binding sites, nascent polypeptide chains, and other associated membrane proteins; The inhibition of ribosome mobility after maintaining rough microsomes at 4 degrees C after RNase, or antibody, treatment suggests that the ribosome binding sites are integral membrane proteins and that their mobility is controlled by the fluidity of the RER membrane. Examination of the hydrophobic interior of microsomal membranes by the freeze-fracture technique revealed the presence of homogeneously distributed 105-A intramembrane particles in control rough microsomes. However, aggregation of ribosomes by RNase, or their removal by treatment with puromycin, led to a redistribution of the particles into large aggregates on the cytoplasmic fracture face, leaving large particle-free regions.     

Biochemical and kinetic characteristics of the interaction of the antitumor antibiotic sparsomycin with prokaryotic and eukaryotic ribosomes

Using 125I-labeled phenol-alanine sparsomycin, an analogue of sparsomycin having higher biological activity than the unmodified antibiotic, we studied the requirements and the characteristics of its interaction with the ribosome. The drug does not bind to either isolated ribosomal subunits or reconstituted whole ribosomes. For sparsomycin binding to 70S and 80S ribosomes, the occupation of the peptidyltransferase P-site by an N-blocked aminoacyl-tRNA is a definitive requirement. The sparsomycin analogue binds to bacterial and yeast ribosomes with Ka values of around 10(6) M-1 and 0.6 x 10(6) M-1, respectively, but its affinity is probably affected by the character of the peptidyl-tRNA bound to the P-site. Chloramphenicol, lincomycin, and 16-atom ring macrolides compete with sparsomycin for binding to bacterial ribosomes, but streptogramins and 14-atom ring macrolides do not. Considering the reported low affinity of puromycin for bacterial ribosomes, this antibiotic is also a surprisingly good competitor of sparsomycin binding to these particles. In the case of yeast ribosomes, blasticidin is a relatively good competitor of sparsomycin interaction, but anisomycin, trichodermin, and narciclasin are not. As expected, puromycin is a poor competitor of the binding in this case. The results from competition studies carried out with different sparsomycin analogues reveal, in some cases, a discrepancy between the drug ribosomal affinity and its biological effects. This suggests that some intermediate step, perhaps a ribosomal conformational change, is required for the inhibition to take place.     

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.     

Acidic ribosomal proteins from eukaryotic cells. Effect on ribosomal functions.

Precipitation of Saccharomyces cerevisiae ribosomes by ethanol under experimental conditions that do not release the ribosomal proteins can affect the activity of the particles. In the presence of 0.4 M NH4Cl and 50% ethanol only the most acidic proteins from yeast and rat liver ribosomes are released. At 1 M NH4Cl two more non-acidic proteins are lost from the ribosomes. The release of the acidic proteins causes a small inactivation of the polymerizing activity of the particles, additional to that caused by the precipitation itself. The elongation-factor-2-dependent GTP hydrolysis of the ribosomes is, however, more affected by the loss of acidic proteins. These proteins can stimulate the GTPase but not the polymerising activity when added back to the treated particles. Eukaryotic proteins cannot be substituted for bacterial acidic proteins L7 and L12. We have not detected immunological cross-reaction between acidic proteins from Escherichia coli and those from yeast, Artemia salina and rat liver or between acidic proteins from these eukaryotic ribosomes among themselves.     

Retention of mRNA on the endoplasmic reticulum membranes after in vivo disassembly of polysomes by an inhibitor of initiation

Membrane-bound ribosomes and messenger RNA remained associated with the microsomal membranes of human fibroblasts after cultures were treated with Verrucarin A, an inhibitor of initiation which led to extensive run-off of ribosomes from polysomal structures. When a membrane fraction from Verrucarin-treated cells containing such inactive ribosomes and mRNA was suspended in a medium of high salt concentration, extensive release of ribosomal subunits occurred without the need for puromycin. The mRNA nevertheless remained associated with the membranes. These results add support to the conclusion that, in human fibroblasts, mRNA is bound directly to ER membranes, independently of the ribosomes and nascent polypeptide chains.     

In vitro exchange of ribosomal subunits between free and membrane-bound ribosomes

Studies on the distribution of isotopieally labeled ribosomal subunits between free and membrane-bound ribosomes from rat liver showed that, upon release of nascent polypeptides in vitro, the small subunits of membrane-bound ribosomes could exchange with small subunits derived from free polysomes. However, under the same conditions, the large subunits of membrane-bound ribosomes did not exchange efficiently with large subunits derived either from free or bound polysomes; instead, the addition of large subunits caused a transfer of microsomal small subunits into a newly formed pool of free monomers.The small subunit exchange required a macromolecular fraction of the cell sap, was stimulated by ATP or GTP, and occurred at low concentrations of magnesium ions.Sodium dodecyl sulfate, polyacrylamide gel electrophoresis revealed close similarities between the protein complement of subunits from free and membrane-bound ribosomes, with the exception of one protein band which was more intense in free large subunits.     

The Mode of Action of Pederin,a Drug Inhibiting Protein Synthesis in Eucaryotic Organisms

Abstract

Pederin, a toxic substance isolated from the insect Paederus fuscipes, inhibits growth of Saccharomyces cerevisiae and EUE cells but not of Bacillus subtilis. Protein synthesis in vitro appears to be inhibited by the drug in preparations obtained from organisms containing 80 S ribosomes (yeast, EUE cells and rat liver) but not in those from organisms endowed with 70 S ribosomes (E. coli and B. subtilis). Pederin inhibits protein synthesis at a stage subsequent to the formation of the ternary complex between ribosomes, aminoacyl-tRNA and messenger RNA. Resistance or susceptibility to the drug appears to be a characteristic of ribosomes.     

The effect of both homologous and heterologous DNA on integration efficiencies in pneumococcal transformation

Summary A mutant of the yeast Saccharomyces cerevisiae has been isolated that is resistant to narciclasine, an inhibitor of peptide bond formation on 80S ribsomes. The mutant shows cross-resistance to a number of inhibitors of peptidyl transferase including anthelmycin, a 4-aminohexosyl cytosine antibiotic, which does not compete with narciclasine for its ribosomal binding site. The mutation is within the gene tcm1 or a closely linked gene on chromosome XV; it is expressed in the 60S ribosomal subunit. The parameters of the binding of (³H)narciclasine to ribosomes and ribosomal subunits from both wild-type and mutant strains have been calculated by ultracentrifugation. One molecule of narciclasine is bound per ribosome or per 60S ribosomal subunit, the values of the dissociation constants being 0.054 and 0.13 m respectively, for 80S and 60S particles from the wild-type cells. Ribosomes of the mutant strain have a lower affinity for narciclasine and trichodermin than ribosomes from wild-type cells. The mutation is semidominant in heterozygous diploid cells.     

Structure and evolution of ribosomes

Ribosomes are the only cell organelles occurring in all organisms. E. coli ribosomes, which are the best characterized particles, consist of three RNAs and 53 proteins. All components have been isolated and characterized by chemical, physical and immunological methods. The primary structures of the RNAs and of all the proteins are known. Information about the secondary structure of the proteins derives from circular dichroism measurements and from secondary structure prediction methods. The tertiary structure is being studied by limited proteolysis, proton magnetic resonance and crystallization followed by X-ray analysis. Various methods are being used to elucidate the architecture of the ribosomal particle: three-dimensional image reconstruction of crystals of bacterial ribosomes and/or their subunits; immune electron microscopy; neutron scattering; protein-protein, protein-RNA and RNA-RNA crosslinking; total reconstitution of ribosomal subunits. The results from these studies yield valuable information on the architecture of the ribosomal particle. Many mutants have been isolated in which one or a few ribosomal proteins are altered or even deleted. The genetic and biochemical characterization of these mutants allows conclusions about the importance of these proteins for the function of the ribosome. Ribosomal proteins from various prokaryotic and eukaryotic species have been compared by two-dimensional gel electrophoresis, immunological methods, reconstitution and amino acid sequence analysis. These studies show a strong homology among prokaryotic ribosomal proteins but only a weak homology between proteins from prokaryotic and eukaryotic ribosomes. Comparison of the primary and secondary structures of the ribosomal RNAs from various organisms shows that the secondary structure of the RNA molecules has been strongly conserved throughout evolution.     

Ribosomal complexes from an extremely halophilic bacterium and the role of cations

Concentrated extracts of Halobacterium cutirubrum were prepared at 0 C by gently disrupting cells with a nonionic detergent in a medium containing 3.0 m KCl, 0.5 m NH(4)Cl, and 0.04 m (or more) magnesium acetate and then treating the gelatinous mass with deoxyribonuclease. On KCl-sucrose gradients containing 0.5 m NH(4)Cl and 0.04 m magnesium acetate, these extracts showed 30S and 50S ribosomal subunits plus a flat profile of faster-sedimenting material up to high S values. Only after frozen storage or brief incubation of the extract were 70S ribosomes and distinct classes of small polyribosomes detected. Digestion with ribonuclease converted faster-sedimenting material to 70S particles. The presence of chloramphenicol during preparation of the extracts did not affect these results. The evidence suggests that ribosomal particles exist in these cells as subunits or as polyribosomes but not as 70S ribosomes. To investigate the function of Mg(++) and NH(4) (+) ions in ribosomal complexes from this halophile, concentrated cell extracts and extracts incubated with (14)C-leucine were examined on KCl-sucrose gradients containing different concentrations of these ions. Polyribosomes and the bulk of 70S ribosomes dissociated reversibly to subunits at about 0.01 m Mg(++), whereas a small fraction of the 70S particles, including those which in vitro incorporated (14)C-leucine into nascent protein, dissociated only below 1 mm Mg(++). Below this concentration of Mg(++), nascent protein remained attached to the 50S subunit even at 0.04 mm Mg(++) in the presence of 0.35 to 0.5 m NH(4)Cl. Nascent protein, presumably as peptidyl-transfer ribonucleic acid, dissociated reversibly from 50S subunits only at 0.04 mm Mg(++) and 0.1 m or less NH(4) (+). Thus, the stability of polyribosomes from H. cutirubrum depends specifically on both Mg(++) and NH(4) (+) ions.     

Conservation of active ribosomes in acetone-treated cells of Tetrahymena pyriformis.

The preparation of an acetone powder of cells of Tetrahymena pyriformis GL is described. A comparison of ribosomal particles isolated from acetone-treated and untreated cells shows that structurally and functionally intact ribosomes can be isolated from acetone-treated cells. Fully active ribosomes have been isolated from acetone powder of Tetrahymena that had been stored for more than 6 months at 4 degrees C. Thus, this procedure allows easy storage of large quantities of cells for the bulk preparation of active ribosomes.     

Ribosome Synthesis in Thermally Shocked Cells of Staphylococcus aureus

Thermally shocked cells of Staphylococcus aureus rapidly synthesized ribonucleic acid (RNA) during the early stages of recovery. During this period, protein synthesis was not observed and occurred only after RNA had reached a maximum level. Even in the absence of coordinated protein synthesis, a large portion of the RNA appeared in newly synthesized ribosomes. Although the 30S subunit was specifically destroyed by the heating process, both ribosomal particles were reassembled during recovery. The addition of chloramphenicol did not inhibit the formation of the ribosomal subunits, nor was the presence of immature chloramphenicol particles detected. Extended recovery with highly prelabeled cells showed that the original ribosomal proteins present before heating are conserved and recycled. Furthermore, the data indicate that the 50S subunit is turned over and used as a source of protein for new ribosome assembly. Kinetic studies of the assembly process by pulse labeling have not revealed the presence of the normally reported precursor particles. Rather, the data suggest that assembly may occur, in this system, in a manner similar to that reported for in vitro assembly of Escherichia coli subunits.