Systematics of the ascomycetous yeasts assessed from ribosomal RNA sequence divergence

Extent of divergence in partial nucleotide sequences from large and small subunit ribosomal RNAs was used to estimate genetic relationships among ascomycetous yeasts and yeastlike fungi. The comparisons showed four phylogenetically distinct groups comprised of the following taxa: Group 1. The budding yeastsSaccharomyces, Saccharomycopsis, Debaryomyces, Metschnikowia, Saturnospora, andLipomyces, and the yeastlike generaAscoidea, Cephaloascus, Dipodascus, Dipodascopsis, andGalactomyces; Group 2.Eremascus, Emericella andCeratocystis; Group 3.Taphrina andProtomyces; Group 4.Schizosaccharomyces. Because of the genetic relationships indicated by sequence analysis, Group 1 taxa are retained in the order Endomycetales, andSchizosaccharomyces is retained in the Schizosaccharomycetales Prillinger et al. ex Kurtzman.     

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.     

Ribosomes in Dormant and Germinating Conidia of Aspergillus oryzae

Ribosomes were isolated from dormant and germinating conidia of Asp. oryzae No. 13. The ribosomes which consisted of 80 S were easily dissociated into 40 S and 60 S in low Mg^{+ +} buffer. Polyribosomes were not found in dormant conidia, but were found in germinating conidia. Ribosomes in Aspergillus fungi consisted of almost equal amount of RNA and protein, and the base compositions of RNA were alike, as compared as ribosomal RNA between dormant and germinating conidia.     

Comparison of amino acid compositions of mitochondrial and cytoplasmic ribosomal proteins of Saccharomyces cerevisiae.

Summary The amino-acid compositions of the mitochondrial ribosomal subunits of Saccharomyces cerevisiae have been determined and compared to those of cytoplasmic ribosomal subunits. For the large subunits, the mitochondrial and cytoplasmic ribosomes showed major differences in the proportions of arginine, alanine and methionine. For the small subunits, arginine, aspartic acid, alanine, valine and methionine showed marked differences.We have compared these amino-acid compositions with those already published of bacterial and eukaryotic ribosomes by a statistical method of data analysis. It appeared clearly that the yeast mitoribosomes are more distant from bacterial ribosomes than from eukaryotic cytoribosomes.Abbreviations r-proteins ribosomal proteins     

Characterization of Ribosomes from Dormant Spores of Bacillus cereus

Characterization of ribosomes from dormant spores and vegetative cells of Bacillus cereus strain T has been carried out. Polyuridylic acid binding activity, ribonuclease activity associated with ribosomes, thermal denaturation profile, and sedimentation coefficients are essentially identical for both ribosomal preparations. However, ribosomal protein content of dormant spore ribosomes is about 70% of that of vegetative ribosomes. Polyacrylamide gel electrophoresis of ribosomal proteins shows that some ribosomal proteins are missing from dormant spore ribosomes. Sucrose density gradient centrifugation of ribosomes shows the existence of defective ribosomal subunits, in addition to 30S and 50S subunits, in dormant spore ribosomes. These results indicate that the ribosomes from dormant spores are distinctively different from those of vegetative cells.     

Adaptive Potential of Wheat Ribosomes toward Heat Depends on the Large Ribosomal Subunit and Ribosomal Protein Phosphorylation

In a study of the translational efficiency of ribosomal subunits as a function of an in vivo temperature pretreatment, ribosomes were isolated from heat-pretreated (36°C) and reference (20°C) wheat seedlings (Triticum aestivum L.). The efficiency of recombined subunits in translating polyuridylic acid was assessed. A threefold increase in the rate of incorporation of phenylalanine by ribosomes from heat-pretreated plants was due to the large ribosomal subunit. This adaptive temperature effect was not correlated with a higher thermal stability of ribosomes or subunits from heat-pretreated seedlings, and two-dimensional gel electrophoresis failed to detect structural alterations of ribosomal proteins. Phosphorylation of ribosomal proteins in vitro showed no differences between ribosomes or subunits from heat-pretreated and reference plants. Incubation with [³²P]orthophosphate in vivo led to twice the amount of phosphate in ribosomal proteins from heat-pretreated wheat seedlings. This result is important with respect to the evaluation of the molecular basis of enhanced translational efficiency of ribosomes isolated from heat-pretreated wheat seedlings.     

The cytoplasmic ribosomes of Chlamydomonas reinhardtii: characterization of antibiotic sensitivity and cycloheximide-resistant mutants

Summary In vitro protein synthesis was used to characterize the antibiotic sensitivity of cytoplasmic ribosomes from wild-type and antibiotic-resistant strains of Chlamydomonas reinhardtii. Cytoplasmic ribosomes from two cycloheximide-resistant mutants, act-1 and act-2, were resistant to the antibiotic in vitro. The alteration effected by the act-1 mutation, which was dominant in diploids, was localized to the large subunit of the cytoplasmic ribosomes, but no ribosomal protein alterations were detected using two-dimensional gel electrophoresis. The act-2 mutation, which was semidominant in diploids, was frequently associated with a charge alteration in the large subunit ribosomal protein (r-protein) cyL38 that segregated independently from the antibiotic-resistant phenotype in crosses.     

Alteration of the structure of theEscherichia coli ribosomes on treatment with Fab fragment of immunoglobulin raised against the ribosomes

Rabbits were immunised againstEscherichia coli ribosomes and the partially purified immunoglobulin G fraction had maximum ability to precipitate the ribosomes as well as the extracted ribosomal proteins. By digestion of immuno-globulin G with papain, monovalent Fab fragments were produced. The 70 S ribosome and its subunits (50 S and 30 S) were separately treated with Fab and then tested in the kinetic assay of degradation of ribosomes by ribonuclease I at various Mg²⁺ concentrations. Treated ribosomes and their subunits were degraded at faster rates than the nontreated ones; the rates in both the control and the treated cases were dependent on the concentration of Mg²⁺. These results indicate the unfolding of the structure of the ribosome on treatment with antibody fragments, which may be due to the weakening of the interaction between rRNAs and ribosomal proteins.     

A comparison of the ribosomal proteins of Drosophila ovary, adult, and embryo

Summary The proteins in the 80S ribosomes of Drosophila melanogaster ovaries and adults have been characterized by two-dimensional polyacrylamide gel electrophoresis. When ribosomal proteins of ovaries and adults were compared with those from embryos, all 3 tissues showed a similar number of proteins. In addition, qualitatively, the electrophoretograms of proteins extracted from the ribosomes of these 3 tissues were found to be indistinguishable. However, apparent quantitative differences in certain acidic proteins were observed between tissues. Using ribosomes from embryos as a standard for comparison, ribosomes from adult flies that were more than 14 days old appeared to have relatively larger amounts of acidic protiens S7 and S9, and relatively smaller amounts of acidic proteins S14 and S25/S27. The transition period occured during the ninth to thirteenth day of adult fly development. Significant differences were not detected between ovarian and embryonic acidic ribosomal proteins. In contrast to the differential ratio of acidic proteins in ovaries, adults, and embryos, a similar distribution of basic proteins was found in these tissues.     

Isolation of active 30S and 50S ribosomal subunits from a psychrotrophic bacterium

Ribosomes from the psychrotroph,Bacillus insolitus, were successfully dissociated into 30S and 50S ribosomal subunits, which were active in carrying out in vitro protein synthesis, measured by the poly U-directed incorporation of¹⁴C-l-phenylalanine into polyphenylalanine. As opposed to the undissociated ribosomes, which are heat sensitive (30°C), the dissociated ribosomes were not thermally sensitive. The heat-sensitive component(s) was found to be removed from the ribosomes during dissociation into 30S and 50S ribosomal subunits; when added back to the ribosomal subunits, heat sensitivity was conferred.     

Protein synthesis in resting and stimulated human lymphocytes

Summary The ribosomal profiles in lysates from resting and phytohemagglutinin stimulated human lymphocytes have been analyzed by sucrose gradient centrifugation. The percentage of polyribosomes increased during lymphocyte transformation reaching a maximal value of 60 to 70% of the total ribosomes after 72 hours of mitogen addition. This time period coincides with maximalin vivo protein synthesis. On the other hand, in nonstimulated lymphocytes, about 25% of the ribosomal particles appeared as aggregates, independently of the incubation period.Experiments performed with homologous cell free systems containing ribosomes and supernatant fluids prepared from unstimulated or activated lymphocytes demonstrate that the mixtures containing both components from stimulated lymphocytes are several fold more active in polypeptide synthesis than the systems which contain ribosomal particles and cell sap from resting cells. Assays carried out with mixtures combining the components from both sources indicate that the increased activity depends on ribosomes as well as on the supernatant fractions.Dedicated to Professor LUIS F. LELOIR on the occasion of his 70^th birthday.     

Phosphorylation of ribosomal proteins from eukaryotes in homologous and heterologous cell-free systems

The phosphorylation of ribosomal proteins from eukaryotes in homologous and heterologous cell-free systems has been studied. The ribosomes and protein kinases from yeast (Saccharomyces cerevisiae, strain Bu), wheat (Triticum vulgare) and rabbit (Orystolagus cuniculus) have been used.It has been found that five ribosomal proteins incorporate γ-³²P from ATP during the incubation of wheat ribosomes with wheat protein kinase. When the phosphorylation of isolated wheat ribosomal proteins was examined more phosphoproteins were detected. These data confirm the suggestion that the ribosomal structure affects the phosphorylation. Probably some ribosomal proteins remain hidden for the action of protein kinase.The results from the crossed experiments show that there is no barrier for phosphorylation of yeast ribosomes with liver protein kinase, of wheat ribosomes with yeast and liver protein kinases and of liver ribosomes with yeast and plant protein kinases. The wheat protein kinase does not phosphorylate the yeast ribosomes under these experimental conditions. Some differences in the set of phosphoproteins obtained with various protein kinases have been detected. These data suggest that the ribosomal protein phosphorylation is not highly species specific although it is not universal.     

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.     

Influence of superinfection on the photoreversible phase of UV induced lysogenic bacteria

Summary Bombyx mori L. ribosomal proteins have been analyzed by four related two-dimensional polyacrylamide gel electrophoretic systems (Madjar et al. 1977a). In the small and large subunits are present 32 and 45 proteins, respectively, whose numbering is proposed. No significant differences in composition or migration could be detected between proteins in membranebound ribosomes and free ribosomes. The molecular weights of the proteins vary from 60,000 to less than 10,000. In vivo phosphorylation was investigated by labeling with ³²P-orthophosphate. Autoradiograms of four two dimensional gels unambiguously show five labeled ribosomal proteins: S1, S7, L6, L29, and L40.     

Protein synthesis by 80S ribosomes during plant development

Protein synthesis by ribosomes from the meristematic region of pea roots (0–0·3 cm) and 2-day-old corn shoots (young tissues) relative to ribosomes from matured regions of pea roots (2·0–2·5 cm) and 10-day-old corn leaves (aged tissues) was compared in the poly U-phenylalanine system. With normal polyribosome preparations, ribosomes from young tissues required approx. 16 mM Mg²⁺ while ribosomes from aged tissues required 20–22 mM Mg²⁺ for optimal activity. With monomeric ribosome preparations induced by anaerobic treatment of the seedlings, the Mg²⁺ optimum was 20–22 mM for ribosomes from both young and aged tissues. A higher level of peptidyl-tRNA in ribosomes from young tissues accounts, at least in part, for the differences in Mg²⁺ optima between ribosomes from young and aged tissues. Monomeric ribosomes were used for assaying the activity of ribosomes per se. Ribosomes from young pea root tips and ribosomes from 2-day-old corn shoots were 25–30% and 100–150% more active, respectively, than the corresponding ribosomes from aged tissues. Differences in ribosomal proteins revealed by gel electrophoresis correlated with the change in ribosomal activity. Reduced activity in the aged ribosomes was not due to RNase activity or inhibitors.     

Fungal plasmocoagulase

Summary The cell extracts isolated from 73 species of fungi belonging to different taxonomic groups were studied to ascertain the presence of plasmocoagulase and protease. Plasmocoagulase was found to be widespread among these microorganisms. They were most constantly found in yeasts and yeastlike fungi. The active substance was not found in culture media. When studying the purified preparation ofCandida albicans plasmocoagulase in comparison with staphylocoagulase the mode of action of both coagulases was found to represent the enzymatical proteolysis of prothrombin with the formation of thrombin or thrombinlike substance.     

Induction of mycelial type of development in Candida albicans by low glucose concentration

A new simple method for synchronous germ tube production in Candida albicans has been described, based on the further incubation of cells released from stationary grown cultures in aerated mineral medium enriched with vitamins and low glucose concentration (5 mmol/l). At higher initial glucose (e.g. 250 mmol/l) the growth proceeded in yeastlike form. At low glucose concentration germ tubes developed at 28°C which is in contradiction with the results of many authors, considering 37°C besides other factors to be an inevitable requirement. On the other hand the cell population from stationary growth phase was the absolute prerequisite for massive germ tube production. Its importance for other inductive techniques is assumed.The report brings comparative results concerning the physiological and biochemical properties as well as the ultrastructure of the yeastlike and mycelial forms. Neither were found any differences in respiration intensity nor in respiration quotients during the development of both growth forms. Slight dissimilarities resulted from the incorporation experiments (using ¹⁴C labeled adenine, leucine and especially glycine). The mycelial cell walls were found to contain twice as much chitin as the yeastlike form.Some suggestion for further biochemical elucidation of dimorphism in Candida albicans and fungal morphogenesis generally are presented.     

Heterogeneity of ribosomal populations in Escherichia coli cells grown in different media

Summary In order to establish whether ribosomes exhibit heterogeneity with respect to their protein pattern in vivo, E. coli cells were grown in rich or minimal medium and labeled with ¹⁴C and ³H amino acid mixture, respectively. After harvesting, the cells from the different media were mixed, the differently labeled ribosomes isolated and the ribosomal proteins separated. For each protein the ratio of ¹⁴C to ³H was determined and used as an indication of whether differences exist in ribosomal populations synthesized under different growth conditions.With respect to their ratio the ribosomal proteins can be classified as follows: Many of the proteins have a ratio of 1, i. e. they are present in the same amount in both preparations. The ratios for about 30% of the proteins differ only slightly from 1 whereas three proteins namely S6, S21 and L12 have ratios of 2.5 and 3.1 respectively. This means that ribosomal populations isolated from cells grown in rich medium contain these three proteins in two to three fold greater amounts compared to those synthesized in minimal medium.The relevance of these results with respect to the occurrence of heterogeneous ribosomal populations in vivo is discussed.Paper Nr. 36 on Ribosomal Proteins. Preceding paper is by H. J. Weber, Mol. Gen. Genetics 119, 233–248 (1972).     

Colocalization of single ribosomes with intermediate filaments in puromycin-treated and serum-starved mouse embryo fibroblasts*

Previous experiments have revealed a relatively weak electrostatic binding capacity of in vitro reconstituted intermediate filaments (IFs) as well as of natural IFs of whole cell mount preparations for purified ribosomal particles of mammalian origin. In order to demonstrate that such associations also occur in vivo, intact cells were subjected to double immunofluorescence microscopy using antibodies directed against vimentin and ribosomal protein S17. Since in proliferating cells the majority of the ribosomal particles are assembled into polyribosomes and these are to a great extent associated with microfilaments, in vitro cultured mouse embryo skin fibroblasts (MSF cells) were treated with puromycin to allow the formation of single ribosomes. Employing confocal laser scanning microscopy, the ribosomes were detected in colocalization with vimentin IFs. Disassembly of polyribosomes was also achieved by serum starvation of cultured cells. In this case, MSF cells of a low passage attained an extended and flattened appearance with the vimentin IFs being directly associated with the cell nuclei, radiating into the peripheral areas of the cells or showing a stress fiber-like distribution. In both cases, considerable quantities of ribosomal material were seen in close neighborhood to vimentin IFs. Frequently, these ribosome-IF associations were coaligned with microtubules and they also surrounded myosin I-decorated stress fibers. Double labeling with the vital, RNA-specific fluorochrome SYTO 14 produced a fluorescence pattern largely super-imposable on that of ribosomal protein S17. Treatment of the starved cells with either demecolcine or cytochalasin D had an only moderately disturbing effect on vimentin IF distribution and the ribosomes stayed in contact with the vimentin IFs. On the basis of these results, it is conceivable that IFs play a role in the storage of ribonucleoprotein particles in general and non-translating ribosomes in particular in the cytoplasm of animal cells. In addition, the often seen coalignment of IFs with microtubules and microfilaments might serve facilitated and directional transport of ribonucleoprotein particles from the nucleus to peripheral areas of the cell.