Characterization of the ribosomal ribonucleic acids of blue-green algae

Summary The ribosomal RNA components of 12 species of blue-green algae have been characterized. The 23S RNA of most species is labile and discrete cleavage products were detected by polyacrylamide gel electrophoresis. In contrast, the 23S and 16S RNA's of three species, Anacystis nidulans, Nostoc sp. and Oscillatoria tenuis were essentially undegraded (apart from a hidden break in some of the 23S RNA molecules) and these are the most suitable species for further study. The undegraded 23S and 16S RNA's have similar molecular weights (1.07×10⁶ and 0.53–0.54×10⁶ respectively) to the corresponding molecules from bacteria and eukaryote chloroplasts. The nucleotide base compositions of separated, intact, 23S and 16S RNA's from blue-green algae are also of the prokaryotic type. For instance, the (G+C) content of each RNA is approximately 52 moles % and the (G-C)+(A-U) values are high (16–24 moles %). Blue-green algae, like other organisms, contain a 5S ribosomal RNA. Its electrophoretic mobility in polyacrylamide gels and its behaviour on methylated-albumen-kieselguhr-columns relative to E. coli, plant cytoplasmic and plant chloroplast 5S RNA's, are described.     

Identification and partial characterization of multiple discrete polyadenylic acid containing RNA components coded for by HeLa cell mitochondrial DNA

Poly(A)-containing RNA isolated from the components of a HeLa cell mitochondrial lysate which sediment in the polysome region of a sucrose gradient have been analyzed for the presence of discrete species. Eight distinct components have been identified by polyacrylamide gel electrophoresis after formaldehyde treatment. These components, which are highly reproducible in their occurrence and relative amounts under widely varying conditions of isolation, have been characterized as to their sedimentation behavior under denaturing conditions, poly(A) content and homology to separated strands of mitochondrial DNA.One of the discrete components was previously shown to have a sedimentation coefficient of about 7 S in the native state and a molecular weight of about 9.0 × 10⁴, as estimated from its sedimentation rate in formaldehyde. The molecular weights of the other seven components, as derived from sedimentation data, range between 2.6 and 5.3 × 10⁵.The 7 S RNA is complementary to the light mitochondrial DNA strand, while the other seven components are complementary to the heavy strand. Together with the two mitochondrial rRNA species and with mitochondrial 4 S RNA, the eight poly(A)-containing RNA components, if distinct in sequence, would account for about 70% of the single-strand informational content of HeLa mitochondrial DNA.     

Expression of the mitochondrial genome in HeLa cells : XIV. The relative positions of the 4 s RNA genes and of the ribosomal RNA genes in mitochondrial DNA

HeLa mitochondrial 4 s RNA has been covalently coupled to the electron opaque label, ferritin, which is visible in the electron microscope. Mixtures of HeLa mitochondrial 12 s ribosomal RNA, 16 s rRNA and/or the 4 s RNA-ferritin conjugate have been hybridized to separated heavy (H) and light (L) strands of HeLa mitochondrial DNA, or to a mixture of H and L strands. The relative positions of the duplex regions corresponding to the 12 s and 16 s rRNA—DNA hybrids and of the ferritin-labeled 4 s RNA's have been mapped in the electron microscope after spreading the DNA strands by the formamide modification of the basic protein film technique. The 12 s and 16 s duplex regions have lengths of 0·-26 ± 0.04 μm and 0.46 ± 0.07 μm, respectively. They are separated by a single-strand region of length 0.047 ± 0.017 μm, corresponding to 160 ± 60 nucleotides. There are nine reproducible binding sites for 4 s RNA on the H strand. One such site lies within the spacer region between the 12 s and 16 s coding sequences, one site is immediately adjacent to the other side of the 12 s sequence and one is adjacent to the other side of the 16 s sequence. The other 4 s sites are rather evenly spaced along the DNA strand of total length 15,600 nucleotides, except that two of them are clustered with a spacing of 120 ± 30 nucleotides between them. There are three 4 s RNA coding sequences on the L strand, separated from one another by 2280 and 3900 nucleotides, respectively.     

Fine mapping of the ribosomal RNA genes of HeLa cell mitochondrial DNA

A fine mapping study of the ribosomal RNA region of HeLa cell mitochondrial DNA has been carried out by using as an approach the protection by hybridized 12 S and 16 S rRNA of the complementary sequences in DNA against digestion with the single strand-specific Aspergillus nuclease S₁ or Escherichia coli exonuclease VII. No inserts have been detected in the main body of the 12 S and 16 S rRNA cistrons, in contrast to the situation described in the large mitochondrial ribosomal RNA gene of some strains of yeast and of Neurospora crassa. Furthermore, it has been possible to assign more precisely than previously the positions of the 5′ and 3′-ends of the 12 S rRNA and 16 S rRNA genes in the HpaII restriction map of HeLa cell mitochondrial DNA.     

The chromosome of bacteriophage T5 : II. Arrangement of the single-stranded DNA fragments in the T5 and T5st(O) chromosomes

Denatured bacteriophage T5 DNA contains a large number of single-stranded DNA fragments which have been separated by agarose gel electrophoresis and classified as “major” or “minor” species on the basis of their relative abundances (Hayward & Smith, 1972). For further study of these fragments we have centrifuged denatured T5 DNA in CsCl density-gradients in the presence of poly(G). Gel electrophoretic analysis of fractions from these gradients shows that the 37.0 and 13.9 million major fragments of T5⁺ DNA and the 35.3 and 17.2 million of T5st(O) DNA are found in the high buoyant density regions. The other fragments vary in the extent of their interactions with poly(G) and a minor fragment, which has anomalous electrophoretic properties, exhibits the strongest poly(G) interaction.     

Mutational analysis of S12 protein and implications for the accuracy of decoding by the ribosome

The fidelity of aminoacyl-tRNA selection by the ribosome depends on a conformational switch in the decoding center of the small ribosomal subunit induced by cognate but not by near-cognate aminoacyl-tRNA. The aminoglycosides paromomycin and streptomycin bind to the decoding center and induce related structural rearrangements that explain their observed effects on miscoding. Structural and biochemical studies have identified ribosomal protein S12 (as well as specific nucleotides in 16S ribosomal RNA) as a critical molecular contributor in distinguishing between cognate and near-cognate tRNA species as well as in promoting more global rearrangements in the small subunit, referred to as “closure.” Here we use a mutational approach to define contributions made by two highly conserved loops in S12 to the process of tRNA selection. Most S12 variant ribosomes tested display increased levels of fidelity (a “restrictive” phenotype). Interestingly, several variants, K42A and R53A, were substantially resistant to the miscoding effects of paromomycin. Further characterization of the compromised paromomycin response identified a probable second, fidelity-modulating binding site for paromomycin in the 16S ribosomal RNA that facilitates closure of the small subunit and compensates for defects associated with the S12 mutations.     

Genome wide sequence analysis grants unbiased definition of species boundaries in “Candidatus Phytoplasma”

The phytoplasmas are currently named using the Candidatus category, as the inability to grow them in vitro prevented (i) the performance of tests, such as DNA-DNA hybridization, that are regarded as necessary to establish species boundaries, and (ii) the deposition of type strains in culture collections. The recent accession to complete or nearly complete genome sequence information disclosed the opportunity to apply to the uncultivable phytoplasmas the same taxonomic approaches used for other bacteria. In this work, the genomes of 14 strains, belonging to the 16SrI, 16SrIII, 16SrV and 16SrX groups, including the species “Ca. P. asteris”, “Ca. P. mali”, “Ca. P. pyri”, “Ca. P. pruni”, and “Ca. P. australiense” were analyzed along with Acholeplasma laidlawi, to determine their taxonomic relatedness. Average nucleotide index (ANIm), tetranucleotide signature frequency correlation index (Tetra), and multilocus sequence analysis of 107 shared genes using both phylogenetic inference of concatenated (DNA and amino acid) sequences and consensus networks, were carried out. The results were in large agreement with the previously established 16S rDNA based classification schemes. Moreover, the taxonomic relationships within the 16SrI, 16SrIII and 16SrX groups, that represent clusters of strains whose relatedness could not be determined by 16SrDNA analysis, could be comparatively evaluated with non-subjective criteria. “Ca. P. mali” and “Ca. P. pyri” were found to meet the genome characteristics for the retention into two different, yet strictly related species; representatives of subgroups 16SrI-A and 16SrI-B were also found to meet the standards used in other bacteria to distinguish separate species; the genomes of the strains belonging to 16SrIII were found more closely related, suggesting that their subdivision into Candidatus species should be approached with caution.     

Characteristics of ribonucleic acids isolated from Botryodiplodia theobromae pycnidiospores

Nucleic acids isolated from dormant and germinated Botryodiplodia theobromae pycnidiospores contain five distinct species of RNA. They include two ribosomal species, two ribosomal-associated species and transfer RNAs. Sedimentation coefficients of 25.1S and 18S were obtained for the two ribosomal RNA species and 5.8S and 5S for the two ribosomal-associated RNA components. Molecular weights of 1.20, 0.67, 0.054 and 0.035x10⁶ daltons were obtained after formaldehyde treatment and electrophoresis on polyacrylamide gels for these same four RNAs. Methylated nucleotides were present in the transfer RNAs and large and small ribosomal RNAs; in contrast 5.8S and 5S RNAs contained few methylated nucleotides. In addition to the 5 distinct RNA species, polyadenylate-containing RNA was isolated from both dormant and germinated spores.Published with the approval of the Director as paper no. 5006, Journal Series, Nebraska Agricultural Experiment Station. The work was conducted under Nebraska Agricultural Experiment Station Project no. 21-17.     

Identification of polydisperse RNA in the cytoplasm of neurons isolated from the immature brain cortex

The cytoplasmic RNA of 10-day-old rats was studied in bulk-isolated, cortical neurons, obtained under conditions which minimize nuclear contamination. Two RNA fractions, one enriched in rRNA and the other in polydisperse RNA, were obtained by differential extraction with phenol. Gel electrophoresis and pulse labelling with 5-[³H]uridine were used to confirm the delayed appearance of newly synthesized rRNA in the cytoplasm and to demonstrate its stability. Polydisperse RNA appeared in the cytoplasm earlier and had a shorter half-life than rRNA. A wide range of molecular weights for this RNA was found with no predominant individual species. A set of cytoplasmic RNA components of molecular size between 28S and 18S was also present probably reflecting the in vivo degradation of rRNA. The significance of the unexpectedly high amounts of neuronal polydisperse RNA is discussed.     

Further evidence that the ribosomal 30S proteins S3, S5, S9, S11, S12, and S18 possess specific 16S RNA binding sites

Summary E. coli ribosomal 16S RNA preparted by an acetic acid-urea extraction technique individually binds, in addition to the seven established proteins, 6 new 30S ribosomal proteins (S3, S5, S9, S12, S18 and S11) (Hochkeppel et al., 1976). In this communication we demonstrate the site specificity of these proteins. Binding curves of the individual proteins with acetic acid-urea 16S RNA show that the binding of all six proteins to the RNA reaches a plateau at 0.3–0.97 copies per 16S RNA molecule. No significant binding of these proteins to classical phenol extracted 16S RNA is observed, with the exception of S13 which binds 0.2 copies of protein per molecule of 16S RNA. Specificity of binding of these proteins is also demonstrated in chase experiments. The site specificity of individual [³H]-labeled 30S proteins bound to 16S RNA is tested by the addition of non-radioactive 30S total protein to the reaction mixture.     

Molecular weights of the ribosomal ribonucleic acid of fungi

Summary The molecular weights of the 18s and 25s ribosomal RNA components of fungi from all major classes were determined by electrophoresis in polyacrylamide gels. The molecular weight of the 18s RNA was found to be very similar for all fungi (range 0.71–0.75 million) and about 4–5% larger than the 18s RNA of HeLa cells and soybean. The molecular weight of the 25s RNA ranged between 1.45 million in the Myxomycetes and 1.30–1.31 million in the Ascomycetes and Basidiomycetes. The differences in the 25s RNA molecular weights between various classes of fungi were interpreted as being in agreement with a monophyletic origin of the Chytridiomycetes, Zygomycetes, Ascomycetes and Basidiomycetes, and independent origins for the Myxomycetes and the Oomycetes. The Hyphochytridiomycete examined could not be placed unequivocally in any group on the basis of its 25s RNA. Fungal RNA extracted with a p-aminosalicylate-triisopropylnaphthalene sulfonate-phenol mixture at 40–60°C contained a high molecular weight aggregate of the 18s and 25s ribosomal RNA; this suggested significant base sequence homology between the two ribosomal RNA species in fungi.     

FRACTIONATION OF RNA FROM BRAIN SYNAPTOSOMES AND CYTOPLASMIC SUBCELLULAR FRACTIONS

—RNA from rat brain synaptosomes, mitochondria and microsomes was analysed by gel electrophoresis under conditions allowing good resolution in three different molecular weight ranges: 4s-16s, 16s-28s and >28s. Two synaptosome specific RNA bands were found, one with comparatively low molecular weight (8-9 × 10⁴ Daltons) and another very large (s_E > 60s). RNA species with electrophoretic characteristics similar to those reported for liver mitochondrial RNA were found in brain mitochondria. From the electrophoretic data their mean geometric radii were determined.     

Optimal conditions for the interaction of ribosomal protein S8 and 16S RNA and studies on the reaction mechanism

Summary Protein S8 occurred in two conformations. A minor component, constituting up to about 30% of the total protein, which bound to 16S RNA at 0°, and a major component which did not bind to the 16S RNA at 0°. The latter could be converted to a binding conformation by heating (E12 kcal/mole). The RNA binding site, for most of the RNA population, was stable at 0°, but a minimum Mg⁺⁺ concentration of 5×10^-3 M, and an optimum concentration of 3×10^-2 M or higher, was necessary for this stability. Specific binding of protein S8 to 16S RNA occurred over a wide range of K⁺ concentrations, but below 0.25 M KCl there was some additional non-specific binding, and above 0.35 M KCl there was a gradual decrease in the binding affinity of S8 for 16S RNA. A maximum in the pH dependence binding curve was at pH 7.4 to 8.0.Paper No. 41 on Ribosomal Proteins. Preceding paper is in press in Mol. Gen. Genetics (1972).     

hESC derived neuro-epithelial rosettes recapitulate early mammalian neurulation events; an in vitro model

The in vitro neuralization of hESCs has been widely used to generate central and peripheral nervous system components from neural precursors (Bajpai et al., 2009; Curchoe et al., 2010), most often through an intermediate “rosette” stage. Here we confirm that hESC derived neuro-epithelial rosettes express many characteristics of the developing embryonic neural plate (Aaku-Saraste et al., 1996), characterized by expression of the tight junction proteins ZO-1 and N-Cadherin. Moreover, neuro-epithelial rosettes display a characteristic acetylated alpha tubulin cytoskeletal arrangement (similar to that observed in the developing embryonic neural plate) (Bhattacharyya et al., 1994).Demonstrated here for the first time MKLP was observed in a hESC model system. We found MKLP expression in small particles in between mitotic spindles, large particles aggregating in the lumen of neuroepithelial rosettes, and we did not observe MKLP in the nucleus of hESC derived neural precursors as previously described in the HeLa cell line. We observed MKLP + particles in aggregations in the lumen of “early” rosette structures. Furthermore, we observed that MKLP⁺ particle aggregations can also be lost from the lumens of hESC derived neuro-epithelial rosettes, similar to a phenomenon observed in the developing neural tube in vivo (Marzesco et al., 2005). We determined that this loss of MKLP⁺ particles occurs from “late” as opposed to “early” stage neuro-epithelial rosettes (characterized by junction type).Disrupting the apical-basal polarization of “early” stage rosettes with a 1% Matrigel overlay (Krtolica et al., 2007) nearly ablates MKLP particle aggregation in the lumen of rosettes, demonstrating that the apical-basal polarity of early NE cells is necessary for lumenal MKLP particle aggregation.We conclude that early hESC derived neuro-epithelial rosettes can model early neurulation events, such as the transition from neural plate like cells to neural tube like cells (i.e. symmetric to asymmetric NE cell division) demonstrated by polarized MKLP particle inheritance and distribution using junction type as a measure of stage.     

Characterisation of physiological and immunological differences between Pacific oysters (Crassostrea gigas) genetically selected for high or low survival to summer mortalities and fed different rations under controlled conditions

Within the framework of a national scientific program named “MORtalités ESTivales de l'huître creuse Crassostrea gigas” (MOREST), a family-based experiment was developed to study the genetic basis of resistance to summer mortality in the Pacific oyster, Crassostrea gigas. As part of the MOREST project, the second generation of three resistant families and two susceptible families were chosen and pooled into two respective groups: “R” and “S”. These two groups of oysters were conditioned for 6 months on two food levels (4% and 12% of oyster soft-tissue dry weight in algal dry weight per day) with a temperature gradient that mimicked the Marennes-Oléron natural cycle during the oyster reproductive period. Oyster mortality remained low for the first two months, but then rapidly increased in July when seawater temperature reached 19 °C and above. Mortality was higher in “S” oysters than in “R” oysters, and also higher in oysters fed the 12% diet than those fed 4%, resulting in a decreasing, relative order in cumulative mortality as follows; 12% “S” > 12% “R” > 4% “S” > 4% “R”. Although the observed mortality rates were lower than those previously observed in the field, the mortality differential between “R” and “S” oysters was similar. Gonadal development, estimated by tissue lipid content, followed a relative order yielding a direct, positive relationship between reproductive effort and mortality as we reported precedently by quantitative histology. Regarding hemocyte parameters, one of the most striking observations was that reactive oxygen species (ROS) production was significantly higher in “S” oysters than in “R” oysters in May and June, regardless of food level. The absence of known environmental stress under these experimental conditions suggests that the ROS increase in “S” oyster could be related to their higher reproductive activity. Finally, a higher increase in hyalinocyte counts was observed for”S” oysters, compared to “R” oysters, in July, just before mortality. Taken together, our results suggest an association of genetically based resistance to summer mortality, reproductive strategy and hemocyte parameters.     

PATTERN OF RNA SYNTHESIS IN THE SCIATIC NERVE OF THE HEN DURING WALLERIAN DEGENERATION

The pattern of synthesis of rapidly-labelled RNA of hen sciatic nerve was studied during Wallerian degeneration. At 2,4,8, 16 and 30 days of degeneration the proximal and distal stumps of the severed nerve as well as the intact contralateral sciatic nerve (functional control) were excised and incubated with either [5-³H]uridine or [2-¹⁴C]uridine for 0.5 h. The electrophoretic pattern of RNA from the normal adult sciatic nerve showed that most of the radioactivity was incorporated into RNA species migrating between the 18 S and 4 S components of the bulk RNA. The synthesis of RNA was sensitive to actinomycin-D, an indication that it was directed by a DNA template. The electrophoretic patterns of the rapidly-labelled RNA in the proximal and distal nerve stumps demonstrated a change following nerve section. After 2–4 days of Wallerian degeneration the degenerating distal nerves incorporated more radioactivity in the 4 S region than the corresponding controls, but at 8 and 16-days after degeneration relatively more label appeared in higher molecular weight RNA species. In the intact sciatic nerve of the operated hens progressively more radioactivity was detected in the 4 S region with increasing time after the contralateral nerve section. At each stage of Wallerian degeneration the specific radioactivities of RNA in the control nerves from experimental hens were higher than those of the normal adult sciatic nerve. These results indicated a change of RNA metabolism in increased functional activity and during Wallerian degeneration.     

Identification of discrete electrophoretic components among the products of mitochondrial protein synthesis in HeLa cells.

Proteins synthesized in vivo by HeLa cell mitochondria in the presence of emetine, an inhibitor of cytoplasmic protein synthesis, have been characterized as to their electrophoretic mobility, solubility properties in organic solvents, and kinetics of labeling with [³H]isoleucine.Ten distinct electrophoretic components in the molecular weight range from about 11,000 to 42,000 have been identified with high reproducibility among the products of mitochondrial protein synthesis. Control experiments involving direct sodium dodecyl sulfate lysis of whole cells, or the use of the protease inhibitor phenylmethylsulfonylfluoride during cell homogenization and fractionation, have excluded a significant role of enzymic degradation during extraction in producing the observed electrophoretic pattern of mitochondrial protein products.A selective solubilization of mitochondrial protein products, representing a 20 to 30-fold purification with respect to the cytoplasmically synthesized proteins, has been obtained by using a neutral chloroform/methanol mixture. At least six of the electrophoretic components with a molecular weight greater than 20,000 were found to be extracted to an appreciable extent with neutral chloroform/methanol.A fairly co-ordinate labeling of the discrete electrophoretic components has been observed during a one-hour exposure period of the cells to [³H]isoleucine in the presence of emetine, without any clear evidence of intorconversion.