Isolation of ribosomal RNA precursors from Physarum polycephalum

Ribosomal RNA synthesis in Physarum polycephalum was studied by labeling intact microplasmodia with [³H]uridine. Labeled, high-molecular-weight RNA species were found in a 30,000 S structure released by phenol extraction at room temperature. RNA was released from the structure by further phenol extraction at 65–70 °C. If the labeling period was 15 min or longer, the labeled RNA was seen by polyacrylamide gel electrophoresis to be of two major types, a heterodisperse collection of 45-35 S molecules and a 26 S species. If the labeling was carried out for 30 min in the presence of cycloheximide, the major labeled species had an electrophoretic mobility corresponding to 40 S. Studies of the labeling kinetics, methylation, and base composition of these RNA molecules indicate that they are precursors to ribosomal RNA. The molecular weights of the homogeneous 40 and 26 S precursors are 3.0 × 10⁶ and 1.45 × 10⁶ daltons, respectively, in comparison with molecular weights of 1.29 × 10⁶ and 0.68 × 10⁶ daltons for the completed ribosomal RNA's.     

RNA metabolsim during vegetative growth and morphogenesis of the cellular slime mold Dictyostelium discoideum

During vegetative growth of the cellular slime mold Dictyostelium discoideum, RNA is rapidly labeled by radioactive precursor and both the 25 S and the 17 S ribosomal RNA species appear in the cytoplasm 6–7 min after the onset of labeling. Thirty minutes after further incorporation of radioactive RNA precursors has been blocked, less than 10% of the label in RNA is associated with the nuclear fraction. After aggregation of the slime mold amoebae, RNA appears in the cytoplasm at a reduced rate, the small ribosomal subunit appearing in the cytoplasmic fraction more slowly than the larger ribosomal subunit. Some labeled RNA remains in the nuclei of developing cells long after the incorporation of ³H-uridine is blocked.     

Demonstration of the "5-8 S" ribosomal sequence in HeLa cell ribosomal precursor RNA

HeLa cell “5.8 S” ribosomal RNA was digested with T₁ ribonuclease and the digestion products were characterized. In particular several hexa-, or larger, oligonucleotides were well fractionated by T₁ ribonuclease plus alkaline phosphatase fingerprints. The sequences of these large products were determined. The same large products were identified in fingerprints of “native” 28 S RNA, that is, 28 S RNA to which 5.8 S RNA is attached. The products were demonstrably absent in fingerprints of heat-denatured 28 S RNA, which lacks the 5.8 S fragment. The oligonucleotides were present in fingerprints of 32 S RNA, whether previously heated or not. One of the largest 5.8 S oligonucleotides contains an alkali-stable (2′-O-methylated) dinucleotide, Gm-C. This product was identified in fingerprints of methyl-labelled 45 S RNA. These findings prove that the 5.8 S ribosomal sequence is present within HeLa cell ribosomal precursor RNA. In addition to the methylated nucleotide, two pseudouridylate residues were discovered in HeLa cell 5.8 S RNA.     

RNA metabolism during light-induced chloroplast development in euglena

Methods are described which provide good recoveries of non-degraded chloroplast and non-chloroplast RNAs from Euglena gracilis var. bacillaris. These have been characterized by comparing the RNA from W₃BUL (an aplastidic mutant of Euglena), with that of wild-type cells which have been resolved into chloroplast and non-chloroplast fractions. Using E. coli RNA as a standard, the RNAs from W₃BUL and from the non-chloroplast fraction of green cells exhibit optical density peaks, upon sucrose gradient centrifugation, at 4S, 10S, and 19S. The chloroplast fraction exhibits optical density peaks at 19S and 14S with the 19S component predominating. Application of various techniques for the separation of RNAs to the problem of separating the chloroplast and non-chloroplast RNAs, without prior separation of the organelle, have not proven successful.

³²P_i is readily incorporated into RNA by cells undergoing light-induced chloroplast development, and fractionation at the end of development reveals that although chloroplast RNAs have a higher specific activity, the other RNAs of the cells are significantly labeled as well. The succession of labeling patterns of total cellular RNA as light-induced chloroplast development proceeds are displayed and reveal that all RNA species mentioned above eventually become labeled. In contrast, cells kept in darkness during this period incorporate little ³²P_i into any RNA fraction. In addition, a heavy RNA component, designated as 28S, while representing a negligible fraction of the total RNA, becomes significantly labeled during the first 24 hours of illumination. While there is light stimulated uptake of ³²P_i into the cells, this uptake is never limiting in the light or dark, for RNA labeling.

On the basis of these findings, we suggest that extensive activation of non-chloroplast RNA labeling during chloroplast development is the result of the activation of the cellular synthetic machinery external to the chloroplast necessary to provide metabolic precursors for plastid development. Thus the plastid is viewed as an auxotrophic resident within the cell during development. Other possibilities for interaction at this and other levels are also discussed.

     

Neutron scattering study of the 13 S fragment of 16 S RNA and its complex with ribosomal protein S4

A fragment with a molecular weight of 170,000 and a sedimentation coefficient of 13 S which is capable of specifically binding ribosomal protein S4 has been obtained by digestion of Escherichia coli 16 S RNA with ribonuclease A. The 13 S fragment of 16 S RNA and its complex with protein S4 have been studied by different physical methods; in the first place, by neutron scattering. It has been shown that this fragment is very compact in solution. The radii of gyration of this fragment (50 ± 3 Å) and of protein S4 within the complex (17 ± 3 Å) coincide, within the limits of experimental error, with the radii of gyration for the free RNA fragment (47 ± 2 Å) and the free ribosomal protein S4 in solution (18 ± 2 Å). Hence the conclusion is drawn that the compactness of the RNA fragment and the ribosomal protein does not change on complex formation. The compact 13 S fragment of 16 S RNA is shown to be contrast-matched in solvent containing 70% ²H₂O which corresponds to a value for the partial specific volume of RNA of 0.537 cm³/g.     

Small stable RNA of Neurospora crassa.

Summary Small stable RNAs in wild-type Neurospora crassa were investigated by analyzing the cell contents of long term ³²P_i labeled cultures in thin slab polyacrylamide gels. Because of the rigid fungal cell wall and the potency of nucleases the degradation of RNA in opening the cells was rather extensive. Some of these degradation problems were circumvented by using a slime strain of N. crassa which lacks a rigid cell wall. Our findings show that N. crassa. like many other eukaryotes, contains a number of small stable RNA molecules. We also found that the ribosomal RNA, the so called 5.8S, migrates slower on polyacrylamide gels than the 6S RNA of E. coli, which contains 184 nucleotides. The relative migration of the molecules was not changed when the samples were denatured prior to electrophoresis. The mobility of the Neurospora rRNA molecule suggested a chain length of 220 nucleotides. Fingerprinting of a T₁ ribonuclease digest indicated a chain length of 212 nucleotides. Because of the unusually large size of the so-called 5.8S rRNA we found it more appropriate to refer to this molecule as a 7S rRNA. It seems that the N. crassa 7S rRNA is the largest low molecular weight ribosomal RNA studied thus far.     

Accumulation and turnover of 23S ribosomal RNA in azithromycin-inhibited ribonuclease mutant strains of <Emphasis Type="Italic">Escherichia coli</Emphasis>

Ribosomal RNA is normally a stable molecule in bacterial cells with negligible turnover. Antibiotics which impair ribosomal subunit assembly promote the accumulation of subunit intermediates in cells which are then degraded by ribonucleases. It is predicted that cells expressing one or more mutated ribonucleases will degrade the antibiotic-bound particle less efficiently, resulting in increased sensitivity to the antibiotic. To test this, eight ribonuclease-deficient strains of Escherichia coli were grown in the presence or absence of azithromycin. Cell viability and protein synthesis rates were decreased in these strains compared with wild type cells. Degradation of 23S rRNA and recovery from azithromycin inhibition were examined by ³H-uridine labeling and by hybridization with a 23S rRNA specific probe. Mutants defective in ribonuclease II and polynucleotide phosphorylase demonstrated hypersensitivity to the antibiotic and showed a greater extent of 23S rRNA accumulation and a slower recovery rate. The results suggest that these two ribonucleases are important in 23S rRNA turnover in antibiotic-inhibited E. coli cells.     

Labeling of non poly(A) associated RNA in the rabbit cerebral cortex 24 hours after a single electroconvulsive shock

The labeling pattern of non poly(A) associated (poly(A)^–) RNA of rabbit cerebral cortex was studied 24 hr after a single electroconvulsive shock (ECS). The animals were injected subarachnoidally with [³H]uridine and sacrificed 1 hr later. The fractionation pattern of labeled nuclear poly(A)^– RNA in the cerebral cortex of ECS treated animals was identical to that of the controls. However, microsomal poly(A)^– RNA from the treated animals showed an increased labeling of 18S ribosomal RNA. Also 28S RNA displayed a higher labeling but the effect was not statistically significant. These results indicate a more efficient production of ribosomal RNA in the late post-ECS period which might be in relationship with an increased activity of brain protein synthesis machinery.     

Ribosomal RNA synthesis in mitochondria of Neurospora crassa

Ribosomal RNA synthesis in Neurospora crassa mitochondria has been investigated by continuous labeling with [5-³H]uracil and pulse-chase experiments. A short-lived 32 S mitochondrial RNA was detected, along with two other short-lived components; one slightly larger than large subunit ribosomal RNA, and the other slightly larger than small subunit ribosomal RNA. The experiments give support to the possibility that 32 S RNA is the precursor of large and small subunit ribosomal RNA's. Both mature ribosomal RNA's compete with 32 S RNA in hybridization to mitochondrial DNA. Quantitative results from such hybridization-competition experiments along with measurements of electrophoretic mobility have been used to construct a molecular size model for synthesis of mitochondrial ribosomal RNA's. The large molecular weight precursor (32 S) of both ribosomal RNA's appears to be 2.4 × 10⁶ daltons in size. Maturation to large subunit RNA (1.28 × 10⁶ daltons) is assumed to involve an intermediate ~1.6 × 10⁶ daltons in size, while cleavage to form small subunit RNA (0.72 × 10⁶ daltons) presumably involves a 0.9 × 10⁶ dalton intermediate. In the maturation process ~22% of the precursor molecule is lost. As is the case for ribosomal RNA's, the mitochondrial precursor RNA has a strikingly low G + C content.     

The use of ribonuclease U2 in RNA sequence determination

The catalog of oligomers produced by ribonuclease T₁ digestion ofEscherichi coli 16S ribosomal RNA has been determined by a new method that involves the use of ribonuclease U₂ fromUstilago sphaerogena. The sequences for the larger T₁ oligomers (8 or more bases) determined in this way differ in more than 50 % of the cases from those reported previously (determined by other methods).     

Recognition of template RNA by Q polymerase: sequence at the 3'-terminus of Q 6S RNA

The major 3′-terminal sequences of Qβ 6S RNA have been determined by a combination of 3′-terminal labeling with ³H via the periodate-borohydride procedure, labeling of specific bases using ¹⁴C-labeled triphosphates and by ribonuclease T₁ digestion. The predominant sequence was GpCpCpA_OH with lesser amounts of GpCpC_OH and GpCpCpG_OH. Since the sole 5′-terminal base of 6S RNA is G, these results provide another example of the ability of Qβ polymerase to add a noncomplementary adenosine to the 3′-end and the first example of an ability to add a guanosine. Thus, all major sequences found may be considered derivatives of the sequence GpCpC_OH. This sequence differs significantly from those of other Qβ polymerase templates studied thus far, and thus reaffirms the requirement for additional internal structural features by which Qβ polymerase recognizes its templates.     

Occurrence of heat-dissociable ribosomal RNA in insects: the presence of three polynucleotide chains in 26 S RNA from cultured Aedes aegypti cells

When RNA extracted from a mixture of cultured mosquito (Aedes aegypti) and hamster (BHK) cells is heated at 60 °C for five minutes the 26 S mosquito RNA but not the 28 S BHK RNA is converted to 18 S products. These products are not separable from each other or from pre-existent 18 S RNA on 2.4% acrylamide gels and have molecular weights near 0.7 × 10⁶. The large ribosomal RNA from insects belonging to ten different orders shows a similar conversion, although this property is absent in two species of aphid.A. aegypti 26 S RNA dissociates over a narrow temperature range. The reaction equilibrium favours dissociation and is dependent on ionic strength, showing a 6 deg. C change in T_m′ (the temperature of 50% dissociation) with tenfold change in salt concentration. Although the T_m of 26 S RNA from Drosophila melanogaster and A. aegypti is markedly different, reflecting the difference in base composition, the T_m′ of the two RNA species was virtually the same.High molecular weight ribosomal RNA from Escherichia coli, BHK cells and A. aegypti cells was terminally labelled with [³H]isonicotinic acid hydrazide. The specific activities of the large RNA species show the presence of one, two and three polynucleotide chains in 23 S, 28 S and 26 S RNA, respectively. A. aegypti 26 S RNA contains a small, heat-dissociable “IRNA” similar in relative amount and mobility to that found in BHK cells.     

Effect of 5-fluoroorotic acid administration of the 32 P base composition, DNA-RNA hybridization properties, and labeling of polyadenylate-rich RNA in the cytoplasm of rat liver cells

5-Fluoroorotic acid treatment lowered the (Guanine + Cytosine)/(Adenine + Uracil) base ratio of ³²P-labeled microsomal RNA from a control value of 1.36 to 1.00. Low doses of actinomycin D, which are effective in inhibiting ribosomal RNA synthesis without significantly affecting messenger RNA synthesis, caused a similar decrease in the base ratio. Microsomal RNA labeled by [³H]orotate in the presence of 5-fluoroorotic acid had approximately $\text{1}\text{2}$ the specific radioactivity but twice the hybridization efficiency of RNA labeled in its absence. Evidence is presented that this RNA (1) has a different structure from that of ribosomal RNA, (2) hybridizes to DNA with an efficiency consistent with that of other published studies of polysome-associated messenger RNA, and (3) possesses sequences which are present in other samples of liver microsomal RNA but not in kidney microsomal RNA. These properties differ from those known to be exhibited by 18 S and 28 S ribosomal RNA. Electrophoretic analysis of this [³H]orotate-labeled microsomal RNA indicated that the analogue greatly inhibited precursor incorporation into ribosomal RNA but had little or no effect on incorporation into messenger RNA. Ribosomal RNA and polyadenylate-rich nonribosomal RNA were prepared from total polyribosomes by phenol extraction at pH 7.6 and pH 9.0, respectively. 5-Fluoroorotic acid inhibited [³H]orotate or ³²P_i incorporation into the pH 7.6 fraction much more effectively than incorporation into the pH 9.0 fraction. A subfraction of the pH 9.0 RNA which was retained by a polythymidylate-cellulose column had a greatly increased adenylate content.     

The polyadenylated RNA of zoospores and growth phase cells of the aquatic fungus,Blastocladiella

The stored poly(A) + RNA from zoospores of the aquatic fungus Blastocladiella emersonii represents 2.5% of the total RNA and has a model MW of 425,000 daltons and an average poly(A) isostich of 32 bases. The poly(A) + RNA also represents 2.5% of the total RNA from early growth phase cells and has a modal MW of 360,000 daltons and an average poly(A) isostich of 38 bases. The poly(A) + RNA from spores and 2-hr plants contains a structure resistant to RNases T₁, T₂, and A, which can be labeled with ³²PO₄ and which will bind to DBAE-cellulose. These characteristics strongly suggest that both the zoospore poly(A) + RNA and the 2-hr cell poly(A) + RNA are capped at the 5′ end; and, hence, it is unlikely that capping is involved in the control of protein synthesis during germination.Approximately 80% of the poly(A) + RNA of the spore is located in the membrane-enclosed ribosomal nuclear cap, and more than 90% of the poly(A) + RNA within the cap is found in the 80S monoribosome and heavier fractions.Synthesis of new poly(A) + RNA occurs very early during zoospore germination, and the labeled poly(A) + RNA rapidly enters the newly organized polysomes. The labeling data for early germination also suggest that cytoplasmic polyadenylation occurs.     

Characterization and mutational analysis of yeast Dbp8p, a putative RNA helicase involved in ribosome biogenesis

RNA helicases of the DEAD box family are involved in almost all cellular processes involving RNA molecules. Here we describe functional characterization of the yeast RNA helicase Dbp8p (YHR169w). Our results show that Dbp8p is an essential nucleolar protein required for biogenesis of the small ribosomal subunit. In vivo depletion of Dbp8p resulted in a ribosomal subunit imbalance due to a deficit in 40S ribosomal subunits. Subsequent analyses of pre-rRNA processing by pulse–chase labeling, northern hybridization and primer extension revealed that the early steps of cleavage of the 35S precursor at sites A₁ and A₂ are inhibited and delayed at site A₀. Synthesis of 18S rRNA, the RNA moiety of the 40S subunit, is thereby blocked in the absence of Dbp8p. The involvement of Dbp8p as a bona fide RNA helicase in ribosome biogenesis is strongly supported by the loss of Dbp8p in vivo function obtained by site-directed mutagenesis of some conserved motifs carrying the enzymatic properties of the protein family.     

Analysis of the coding activity and stability of messenger RNA in Drosophila oocytes.

The coding activity of the messenger RNA in the ooplasm of late stage 14 (S14) oocytes of Drosophila melanogaster was analyzed by labeling the oocytes in vitro with [³⁵S]methionine and examining the labeled products by two-dimensional gel electrophoresis and fluorography. This analysis was done both with newly formed S14 oocytes from rapidly laying females and with S14 oocytes stored for about 10 days in females that were prevented from laying. Comparison of the fluorographs showed that the proteins labeled in the newly formed oocytes were also labeled in the stored oocytes. Thus, the coding activity of S14 oocyte messenger RNA appears to remain stable during prolonged storage in utero. The oocyte proteins synthesized during oogenesis and incorporated into S14 oocytes were labeled in vivo by injecting [³⁵S]methionine into newly eclosed females, and the S14 oocytes were removed 2 days later for gel electrophoresis and fluorography. Comparison of the fluorographs produced by the in vivo and in vitro labeling procedures showed that most of the oocyte proteins labeled in vivo were also labeled in vitro. The S14 oocytes, therefore, appear to contain messenger RNA for most of the oocyte proteins synthesized during oogenesis. There were also several additional proteins detected only in the fluorographs of the in vivo labeled oocytes; the most prominent of these were identified by immunoprecipitation tests as vitellogenin proteins of yolk granules, which are known to be synthesized outside the oocyte, in fat bodies. The occurrence of stable S14 oocyte messenger RNA for most of the oocyte proteins suggests that the synthesis of those proteins during oogenesis occurs in the developing oocytes, specified by a stable population of oocyte messenger RNA.     

The Kinetics of the Synthesis of Ribosomal RNA in E. coli

The kinetics of the synthesis of ribosomal RNA in E. coli has been studied using C¹⁴-uracil as tracer. Two fractions of RNA having sedimentation constants between 4 and 8S have kinetic behavior consistent with roles of precursors. The first consists of a very small proportion of the RNA found in the 100,000 g supernatant after ribosomes have been removed. It has been separated from the soluble RNA present in much larger quantities by chromatography on DEAE-cellulose columns. The size and magnitude of flow through this fraction are consistent with it being precursor to a large part of the ribosomal RNA.

A fraction of ribosomal RNA of similar size is also found in the ribosomes. This fraction is 5 to 10 per cent of the total ribosomal RNA and a much higher proportion of the RNA of the 20S and 30S ribosomes present in the cell extract. The rate of incorporation of label into this fraction and into the main fractions of ribosomal RNA of 18S and 28S suggests that the small molecules are the precursors of the large molecules. Measurements of the rate of labeling of the 20, 30, and 50S ribosomes made at corresponding times indicate that ribosome synthesis occurs by concurrent conversion of small to large molecules of RNA and small to large ribosomes.