Characterization of rRNAs from the chrysophyte alga Ochromonas danica

Electrophoretic analysis of intact rRNAs extracted from the Chrysophyte alga Ochromonas danica reveals 5 peaks of high molecular weight rRNA. The subcellular origin of the rRNA species in each peak was deduced from ultrastructural evidence, comparison of RNA from light- and dark-grown cells (the chloroplast in dark-grown cells exists as a small proplastid containing relatively few ribosomes) and experiments with ethidium bromide. The molecular weights of the cytoplasmic heavy and light rRNAs in non-denaturing gels are 1.18 × 10⁶ and 0.66 × 10⁶ respectively. The molecular weights of the chloroplast heavy rRNA and mitochondrial heavy rRNA are both 0.94 × 10⁶, while the chloroplast light rRNA and mitochondrial light rRNA have values of 0.50 × 10⁶ and 0.55 × 10⁶ respectively.Chloroplast heavy rRNA from Ochromonas is thermolabile and dissociates in a specific pattern when heated. From the size and stoichiometry of the dissociates in products, we suggest that at least three nicks are present in Ochromonas chloroplast heavy rRNA.     

Specific fluorescent antiglobulins for the detection and identification of blastomyces dermatitidis yeast-phase cells

Summary Two lots of rabbit anti-Blastomyces dermatitidis globulins were conjugated with fluorescein isothiocyanate. These reagents stained brightly elements of the yeast and mycelial phases of 10 strains ofB. dermatitidis. In addition, the labeled antibodies cross-reacted with elements of the yeast and mycelial phases of 7 strains ofHistoplasma capsulatum and cells of numerous other heterologous fungi. Adsorption of one lot of labeled antibodies twice with yeast cells ofH. capsulatum and once with elements ofGeotrichum candidum rendered the conjugate specific for the yeast phase ofB. dermatitidis. Three adsorptions with yeast cells ofH. capsulatum followed by a single adsorption with elements ofG. candidum rendered the second conjugate specific for yeast-phase cells ofB. dermatitidis. The specific reagents did not react with the mycelial phase of this fungus.     

Transcription and processing of rRNA in higher plant cells (Daucus carota,Petroselinum crispum,Acer pseudoplatanus)

Actively dividing cells from parsley (Petroselinum crispum) and carrot (Daucus carota) (bothApiaceae) andAcer pseudoplatanus (Aceraceae) were used to detect the primary gene product of the rDNA in plant cells. Parsley and carrot cells were labelled with [³²P] orthophosphate. In both cases only one high molecular weight rRNA precursor was present on polyacrylamide gels under non-denaturing conditions. Its molecular weight did not exceed 2.5 × 10⁶ daltons. The component emerged from the heterogenous material after a labelling period of 5–10 min. In parsley cells 45 min after onset of incubation labelled mature rRNA (25S and 18S) arrived in the cytoplasm. InAcer pseudoplatanus (incubation period 60 min) two rapidly labelled components did emerge from polyacrylamide gels; their molecular weights were 2.3 and 3.2^? 3.4 × 10⁶ daltons. After electrophoresis under denaturing conditions the larger component was no longer present, thus indicating that it was an aggregate of different RNA molecules. The molecular weights of the rRNA precursors ofD. carota andP. crispum determined after electrophoresis in formamide gels were about 2.1 × 10⁶ daltons. From these results we have no evidence for the existence of rRNA precursors exceeding the molecular weight of 2.5 × 10⁶ daltons.     

Ribosomes and ribosomal proteins of dry and germinating conifer seeds

The electrophoretic properties of ribosomes and ribosomal proteins of coniferous seeds were determined on polyacrylamide gels. Dry seeds of jack pine (Pinus banksiana Lamb.) contained 80S monoribosomes; polysomes were absent. After 48 hr of imbibition the seeds contained monoribosomes and polysomes. The MWs of the ribosomal proteins of the cytoplasm and chloroplasts were 10 to 82 × 10³ and 9 to 65 × 10³ respectively. Ribosormal proteins from Pinus, Abies, and Pseudotsuga were electrophoretically similar.     

A rapid procedure to determine the content of 2'-O-methylation in RNA by homochromatography

The content of 2′-O-methylated dinucleotides from 17 S rRNA of yeast and 18 S rRNAs of chicken cells and Novikoff rat cells was determined by a new procedure using homochromatography. The procedure is simple and can be used to compare the extent of 2′-O-methylation simultaneously in various RNAs. It was of interest that 18 S rRNAs of chicken and rat have two times more 2′-O-methylated dinucleotides as compared to yeast 17 S rRNA.     

Factors affecting mycelial to yeast phase conversion and growth of the yeast phase ofHistoplasma capsulatum

A procedure for rapid induction of mycelial to yeast phase (M→Y) conversion ofHistoplasma capsulatum has been devised. Exposure of mycelial fragments to low oxidation-reduction (O/R) potentials (+5 to+65 mv) either aerobically (ascorbic acid treatment) or anaerobically (nitrogen atmosphere) for 18 to 24 hours at 37° C resulted in induction of the M→Y conversion process whether or not an organic sulfur source was available. However, aerobic conditions and a suitable organic sulfur source, such as cysteine, cystine or lanthionine were found essential for outgrowth and maintenance in the yeastlike phase.     

Removal of pectins from methylated rRNA and precursors by LiCl

The methyl group of radioactive methylmethionine is incorporated preferentially into pectin, a methylated polysaccharide, which massively contaminates RNA preparations. This makes it difficult to discern the methylated RNA species of growing tissues of higher plants. A method for the extraction of pectic substances from RNA preparations of plants is described. Ethanol precipitates containing RNA are suspended in 2m lithium chloride (LiCl) and the pectin is removed with the supernatant after centrifugation. LiCl purification of RNA from Vicia faba root meristems allows the direct identification on polyacrylamide gels of methylated RNA species labeled with [³H]methyl methionine. Presumpive precursors of rRNA which fall into the range of apparent molecular weights of 2.7–2.9, 2.2–2.4, 1.4–1.5, and 0.72–0.75 × 10⁶ are shown to be methylated, in addition to the methylation of the fully processed rRNAs of MW 1.3 and 0.7 × 10⁶.     

Temperature of acrylamide polymerization and electrophoretic mobilities of nucleic acids.

The electrophoretic mobilities of DNA, ribosomal RNAs, and pulse-labeled RNAs were compared on polyacrylamide gels polymerized at temperatures from 4 to 35°C and subjected to electrophoresis at a fixed temperature. DNA migrated the same distance irrespective of polymerization temperature, the ribosomal RNAs, and the major pulse-labeled species (a putative rRNA precursor) migrated more rapidly in gels polymerized at higher temperatures. The linearity of the migration versus the log of the molecular weight remained for the five rRNA species used, but the extrapolated molecular weight of the putative precursor ranged from 1.8 × 10⁶ to 2.5 × 10⁶ depending on polymerization temperatures. By varying polymerization temperatures, the optimal resolution of various groups of RNA species can be obtained. The results are explained in terms of polymerization temperature effects on gel structure as well as nucleic acid conformation.     

Secondary structure maps of ribosomal RNA and DNA: I. Processing of Xenopus laevis ribosomal RNA and structure of single-stranded ribosomal DNA

Precursor and mature ribosomal RNA molecules from Xenopus laevis were examined by electron microscopy. A reproducible arrangement of hairpin loops was observed in these molecules. Maps based on this secondary structure were used to determine the arrangement of sequences in precursor RNA molecules and to identify the position of mature rRNAs within the precursors. A processing scheme was derived in which the 40 S rRNA is cleaved to 38 S RNA, which then yields 34 S plus 18 S RNA. The 34 S RNA is processed to 30 S, and finally to 28 S rRNA. The pathway is analogous to that of L-cell rRNA but differs from HeLa rRNA in that no 20 S rRNA intermediate was found. X. laevis 40 S rRNA (M_r = 2.7 × 10⁶) is much smaller than HeLa or L-cell 45 8 rRNA (M_r = 4.7 × 10⁶), but the arrangement of mature rRNA sequences in all precursors is very similar. Experiments with ascites cell 3′-exonuclease show that the 28 S region is located at or close to the 5′-end of the 40 S rRNA.Secondary structure maps were obtained also for single-stranded molecules of ribosomal DNA. The region in the DNA coding for the 40 S rRNA could be identified by its regular structure, which closely resembles that of the RNA. Regions corresponding to the 40 S RNA gene alternate with non-transcribed spacer regions along strands of rDNA. The latter have a large amount of irregular secondary structure and vary in length between different repeating units. A detailed map of the rDNA repeating unit was derived from these experiments.Optical melting studies are presented, showing that rRNAs with a high (G + C) content exhibit significant hypochromicity in the formamide/urea-containing solution that was used for spreading.     

Peptidases of yeast and filamentous forms ofCandida albicans

A study of the peptidases of the yeast and filamentous forms ofCandida albicans H-317 was carried out. At least three distinct peptidase activities in cell extracts of the yeast and filamentous phases were separated by gel filtration column chromatography or native polyacrylamide gel electrophoresis and measured by an enzyme-coupled colorimetric assay. The first peak of hydrolyzing activity to elute from a Sephadex G-200 column was designated as peak I, an aminopeptidase(s) with broad substrate specificity, and was characterized as follows: It had a molecular weight of 550,000, pH optima 7.5 to 8.0, andK_m of 1 × 10⁻⁴M with trimethionine as substrate, and it was inhibited by EDTA. The activity of peak I showed stereospecificity since it hydrolyzedd-methionyl-l-methionyl-l-methionine andl-methionyl-l-methionyl-d-methionine but notl-methionyl-d-methionyl-l-methionine. The second peak to elute from the gel filtration column was designated peak II. Its molecular weight was estimated to be 120,000, it had a pH optimum of 7.0, and it was inhibited by EDTA. TheK_m with trimethionine as substrate for the yeast and filamentous phase peak II was 3.2 × 10⁻⁴ and 7.5 × 10⁻⁵M, respectively. In addition to peak I and peak II peptidase(s), a dipeptidase activity with a molecular weight of 150,000 was detected in both the yeast and filamentous phases. Thus, a multiplicity of peptidases was present in cell extracts ofC. albicans and no major differences were noted in the partially purified peptidases from either the yeast or filamentous phase.     

Unique arrangement of coding sequences for 5 S, 5.8 S, 18 S and 25 S ribosomal RNA in Saccharomyces cerevisiae as determined by R-loop and hybridization analysis.

The arrangement of the coding sequences for the 5 S, 5.8 S, 18 S and 25 S ribosomal RNA from Saccharomyces cerevisiae was analyzed in λ-yeast hybrids containing repeating units of the ribosomal DNA. After mapping of restriction sites, the positions of the coding sequences were determined by hybridization of purified rRNAs to restriction fragments, by R-loop analysis in the electron microscope, and by electrophoresis of S₁ nuclease-treated rRNA/rDNA hybrids in alkaline agarose gels. The R-loop method was improved with respect to the length calibration of RNA/DNA duplexes and to the spreading conditions resulting in fully extended 18 S and 25 S rRNA R-loops. The qualitative results are: (1) the 5 S rRNA genes, unlike those in higher eukaryotes, alternate with the genes of the precursor for the 5.8 S, 18 S and 25 S rRNA; (2) the coding sequence for 5.8 S rRNA maps, as in higher eukaryotes, between the 18 S and 25 S rRNA coding sequences. The quantitative results are: (1) the tandemly repeating rDNA units have a constant length of 9060 ± 100 nucleotide pairs with one SstI, two HindIII and, dependent on the strain, six or seven EcoRI sites; (2) the 18 S and 25 S rRNA coding regions consist of 1710 ± 80 and 3360 ± 80 nucleotide pairs, respectively; (3) an 18 S rRNA coding region is separated by a 780 ± 70 nucleotide pairs transcribed spacer from a 25 S rRNA coding region. This is then followed by a 3210 ± 100 nucleotide pairs mainly non-transcribed spacer which contains a 5 S rRNA gene.     

Occurrence in vivo of "hidden breaks" at specific sites of 26 S ribosomal RNA of Musca carnaria.

A fragmentation process occurs in 26 S ribosomal RNA of mature cytoplasmic ribosomes of Musca carnaria. It consists of the sequential appearance of three “hidden breaks” that fragment 26 S rRNA (M_r = 1.42 × 10⁶) into four pieces with approximate molecular weights of 0.68 × 10⁶, 0.35 × 10⁶, 0.29 × 10⁶ and 0.096 × 10⁶, respectively. This fragmentation was not observed in 17 S rRNA (M_r = 0.74 × 10⁶).Extremely mild treatment of newly assembled ribosomes with pancreatic RNAase reproduces the 26 S rRNA fragmentation phenomenon in vitro in the same way as it occurs in vivo.This evidence is discussed in relation to the secondary structure of 26 S rRNA and its binding with specific ribosomal proteins.     

Protoplasts of systemic dimorphic fungal pathogens: Histoplasma capsulatum and blastomyces dermatitidis

Summary Protoplasts have been released fromH. capsulatum in the mycelial and yeast phases and from the mycelial and incompletly converted yeast phase ofB. dermatitidis by the enzymatic action of snail digestive juice. There is great variation in the mode of protoplast formation not only between species but between the two morphological forms, particularly inH. capsulatum These studies were supported in part by grants from the American Thoracic Socicty and the United States Public Health Service National Institute of Allergy and Infectious Diseases (1-R1-AI-7520-01).     

Mobilization of newly synthesized RNAs into polysomes inXenopus laevis embryos

Summary The mobilization of newly synthesized 18S and 28S rRNAs, 4S RNA and poly(A)⁺ RNA into polysomes was studied in isolated cells ofXenopus laevis embryos between cleavage and neurula stages. Throughout these stages, 4S RNA and poly(A)⁺ RNA were mobilized immediately following their appearance in the cytoplasm. 18S rRNA however, stayed in the ribosomal subunit fraction for about 30 min until the 28S rRNA appeared, when the two rRNAs were mobilized together at an equimolar ratio. This mobilization, at a 1:1 molar ratio, appeared to be realized at initiation monome formation. Thus, the efficiency of the mobilization of two newly synthesized rRNAs, shortly after their arrival at the cytoplasm, differed considerably but difference disappeared once steady state was reached.The contribution of newly synthesized 18S and 28S rRNAs to polysomes remains small throughout early development. around 3% of newly synthesized 4S RNA is polysomal which is the same distribution observed for unlabeled 4S RNA. Less than 10% of the newly synthesized cytoplasmic poly(A)⁺ RNA was mobilized into polysomes during cleavage, but in later stages the proportion increased to around 20%–25%. These results show that newly synthesized RNAs are utilized for protein synthesis at characteristic rates soon after they are synthesized during early embryonic development. On the basis of the data presented here and elsewhere we discuss quantitative aspects of the utilization of newly synthesized and maternal RNAs during early embryogenesis.     

Ribosomal RNA sequence conservation and gene number in the larval brine shrimp

The haploid genome size of Artemia is determined to be about 0.9·10¹², as evidenced both by Feulgen microspectrophotometry of individual diploid class nuclei, which are but one of five polyploid classes present within the larvae, and by analysis of the reassociation kinetics of the isolated single copy DNA component. Polysomes isolated from 24-h incubation stage larvae contain an average of 10 ribosomes per messenger RNA molecule. Their rRNAs are found to have sedimentation coefficients of 18 S and 26 S, corresponding to molecular weights of 0.70·10⁶ and 1.40·10⁶, respectively, as determined by polyacrylamide electrophoresis and also by sucrose density centrifugation. Denaturation in glyoxal followed by agarose gel electrophoresis shows that unlike deuterostome rRNAs, Artemia 26 S rRNA contains a cryptic nick about midway in the molecule, which is not found in the 18 S molecule. Isolated rRNAs were labelled in vitro with ¹²⁵I and hybridized with filter-immobilized DNA to saturation, which occurred at 0.051% for Xenopus, and at 0.074% for Artemia. From these results, it is calculated that in the haploid Artemia genome there are about 320 copies of the (18 S + 26 S) ribosomal RNA genes. Reciprocal heterologous hybridizations between these two species show that they share about 30% homology between their rDNA coding sequences.     

Identification of a novel calcium binding protein from bovine brain

A novel Ca²⁺ binding protein, named caligulin, was extracted from the heat-treated 100 000 × g supernatant of bovine brain and purified to electrophoretic homogeneity. The apparent M_r of caligulin determined on sodium dodecyl sulfate polyacrylamide gels was 24 000. Analysis by gel filtration chromatography indicated an apparent M_r of 33 000, suggesting a monomeric protein. Amino acid composition data demonstrated the presence of 25% acidic residues, 12% basic residues and 10% leucine. In the presence of 1 mM MgCl₂ and 0.15 M KCl, caligulin bound 1 mol Ca²⁺/mol protein with half-maximal binding at about 0.2 μM Ca²⁺.     

Contitions for optimal growth of a PSTV-infected potato cell suspension and detection of viroid-complementary longer-than-unit-length RNA in these cells

A suspension culture from potato spindle tuber viroid (PSTV)-infected cells of the wild type potato (Solanum demissum) has been established, which is a suitable model system for studying PSTV replicationin vivo. The conditions for rapid growth of these cells and for permanent extensive viroid biosynthesis within them are described. Biosynthesis of PSTV in the potato cells was demonstrated by³²P-incorporation into nucleic acids and their subsequent electrophoretic analysis on polyacrylamide gels. Under optimum culture conditions the amount of³²P-orthophosphate incorporation into PSTV reached 10% of that incorporated into the 2 M LiCl-soluble cellular RNA. (+)PSTV and its complementary form, i.e. (?)PSTV were identified after their electrophoretic separation on polyacrylamide and agarose gels by molecular hybridization. This analysis revealed the presence of six high molecular weight(?)PSTV species, which are possibly multimers of the unit length(+)PSTV molecule consisting of 359 nucleotides.     

Occurrence and location of 7-methylguanine residues in small-subunit ribosomal RNAs from eubacteria,archaebacteria and eukaryotes

Specific cleavage with aniline provides a rapid and convenient method for establishing the presence and approximate location of 7-methyl-guanine (m⁷G) residues in ribosomal RNA (rRNA) molecules. Using this approach, we have shown that a single m⁷G occurs roughly 465 bases from the 5'-end of 16 S rRNA from the archaebacterium. Thermoplasma acidophilum, but that this modified base is absent from several other archaebacterial 16 S rRNAs. We have also demonstrated that a unique m⁷G is found some 220–230 bases from the 3'-terminus of a number of eukaryotic 18 S rRNAs. In both cases, m⁷G is present within evolutionarily conserved structural features, suggesting that this base may optimize the activity of functionally important regions of rRNAs in a kingdom-specific fashion.