Compartmentation of uridine 5′-triphosphate occurs during synthesis of cytoplasmic and mitochondrial ribosomal RNAs of cultured tomato cells but not during synthesis of cytoplasmic ribosomal and transfer RNAs

Compartmentation of uridine 5-triphosphate (UTP) was studied during the nucleolar synthesis of cytoplasmic ribosomal RNA (cyt-rRNA) and the synthesis of cytoplasmic transfer RNA (cyt-tRNA) in the nuclear matrix as well as the synthesis of mitochondrial ribosomal RNA (mt-rRNA) in tomato (Lycopersicon esculentum Mill. cv. Lukullus) cell-suspension culture using the approach of Wiegers et al. (Eur. J. Biochem. 64, 535–540, 1976). Before measurements were made, it was ensured that: (i) there was steady-state labeling of all RNAs studied as well as UTP; (ii) there was stability of cyt-tRNA and cyt-rRNA; (iii) there was no label randomization through degradation of [³H]uridine; (iv) there were significant differences in the specific radioactivity of UTP, the final immediate precursor of RNA, after supplying the cells with two different exogenous [³H]uridine concentrations.By comparing the steady-state specific radioactivity of UTP with that of cyt-tRNA and cyt-18S rRNA during constant [³H]uridine supply, we found that the three molecules had equal specific radioactivities which, however, differed significantly from that of the mt-rRNA. With a 20-fold higher uridine concentration, i.e. a 20-fold lower specific radioactivity of exogenous [³H]uridine, the specific radioactivity of cyt-rRNA, cyt-tRNA and UTP decreased proportionally whereas that of mt-RNA increased. These results argue against different UTP pools during synthesis of cyt-rRNA and cyt-tRNA, but indicate compartmentation of UTP during rRNA synthesis in the nucleus and the mitochondria of tomato cells.Abbreviations CMP cytidine 5-monophosphate - cyt-rRNA cytoplasmic ribosomal RNA - cyt-tRNA cytoplasmic transfer RNA - mt-rRNA mitochondrial rRNA - NC nitrocellulose - PAGE polyacrylamide gel electrophoresis - TLC thin-layer chromatography - Tris 2-amino-2-(hydroxymethyl)-1,3-propanediol - UDP uridine 5-diphosphate - UMP uridine 5-monophosphate - UTP uridine 5-triphosphate     

Studies on compartmentation of uridine 5'-triphosphate during synthesis of cytoplasmic and plastid ribosomal RNA's in Euglena gracilis

• 1.1. Compartmentation of uridine 5'-triphosphate (UTP) was studied during synthesis of cytoplasmic ribosomal RNA (cyt-rRNA) and plastid ribosomal RNA (pl-rRNA) in photoorganotrophically grown cells of Euglena gracilis Z.
• 2.2. Using the approach of Wiegers et al. (1976) the steady state specific radioactivity of UTP was compared with that ofcyt-20S rRNA, cyt-25S rRNA, pl-16S rRNA and pl-23S rRNA under low and at 100-fold higher specific radioactivity of exogenously fed pHl-uracil.
• 3.3. The equal steady state specific radioactivities of all rRNAs at both feeding conditions argue against compartmentation of UTP during their synthesis.
• 4.4. At high specific radioactivity of exogenous [³H]-uracil the salvage-derived labelled UMP was shown to be diluted 15,000-fold by unlabelled UMP formed de novo, whereas this dilution factor was 100-fold lower at low specific radioactivity of [³H]-uracil indicating inhibition of the de novo synthesis of UMP.
• 5.5. Transport is suggested of uridine nucleotides into chloroplasts by the 15-fold higher specific radioactivity of intracellular [³H]-uracil than that of UTP as well as UMP residues in pl-rRNA.

     

Synthetic rates of chloroplast and cytoplasmic ribosomal ribonucleic acids during the cell cycle of Chlorella

By feeding radioisotopic precursors of RNA ([5-³H]uracil and[5-³H]uridine) to cells of Chlorella ellipsoidea at variousstages in the cell cycle effected by autotrophic synchronousculture, we examined synthetic rates of the chloroplast andthe cytoplasmic ribosomal ribonucleic acids (chl-rRNA and cyt-rRNA,respectively). The net incorporation of the precursors intochl-rRNA was higher than that into cyt-rRNA in the early stagesof the cell cycle, and vice versa in the late stages. The specificactivity of chl-rRNA was extremely high, and this phenomenonwas likely to be intrinsic to small cells at the start of thecell cycle under autotrophic conditions, namely, cell-cyclestagespecific. We conclude that algal cells grown autotrophicallysynthesize chl-rRNA at a distinctly higher rate than cyt-rRNAin the early stages of the cell cycle. (Received July 21, 1978; )     

Regulation of chloroplast and cytoplasmic rRNA accumulation by light energy and its relation to reproductive events during the cell cycle of the alga Scenedesmus quadricauda

Synchronous cultures of the green alga Scenedesmus quadricauda were grown at different mean irradiances (ranging from 20 W/m² to 150 W/m²). At these irradiances, the algae were exposed to illumination regimes which differed in the ratio between light and dark intervals (from 02.22 to 24.00 h). The patterns of accumulation of chloroplast and cytoplasmic ribosomal RNA (chl- and cyt-rRNA) and variations in their ratio were followed under the above mentioned growth conditions. The chl-rRNA accumulated at a high specific rate even in the dark while the synthesis of cyt-rRNA was depressed. Consequently, the ratio of chl-/cyt-rRNA increased during the dark period to the high value of 0.4. After the start of the light period, this ration decreased gradually to the low value of 0.2. In continuously illuminated cells, the chl-rRNA and cyt-rRNA were accumulated at the same specific rate of that their ratio remained constant (0.2) during entire cell cycle. However, the absolute amount of cyt-rRNA accumulated in light was about 10 times higher than that of chl-rRNA. In an experiment with 5-fluorodeoxyuridine treated cells, the evidence was provided that DNA replications, nuclear divisions and chloroplast nucleoid fissions interferred with the course of neither chl-rRNA nor cyt-rRNA during the cell cycle. Chloroplastkinesis and cytokinesis were the only reproductive events that prevented the accumulation of both chl- and cyt-rRNA.     

Competition between the Rex1 exonuclease and the La protein affects both Trf4p-mediated RNA quality control and pre-tRNA maturation

Although nascent noncoding RNAs can undergo maturation to functional RNAs or degradation by quality control pathways, the events that influence the choice of pathway are not understood. We report that the targeting of pre-tRNAs and certain other noncoding RNAs for decay by the TRAMP pathway is strongly influenced by competition between the La protein and the Rex1 exonuclease for access to their 3' ends. The La protein binds the 3' ends of many nascent noncoding RNAs, protecting them from exonucleases. We demonstrate that unspliced, end-matured, partially aminoacylated pre-tRNAs accumulate in yeast lacking the TRAMP subunit Trf4p, indicating that these pre-tRNAs normally undergo decay. By comparing RNA extracted from wild-type and mutant yeast strains, we show that Rex1p is the major exonuclease involved in pre-tRNA trailer trimming and may also function in nuclear CCA turnover. As the accumulation of end-matured pre-tRNAs in trf4Delta cells requires Rex1p, these pre-tRNAs are formed by exonucleolytic trimming. Accumulation of truncated forms of 5S rRNA and SRP RNA in trf4Delta cells also requires Rex1p. Overexpression of the La protein Lhp1p reduces both exonucleolytic pre-tRNA trimming in wild-type cells and the accumulation of defective RNAs in trf4Delta cells. Our experiments reveal that one consequence of Rex1p-dependent 3' trimming is the generation of aberrant RNAs that are targeted for decay by TRAMP.     

Half-lives of messenger RNA species during growth and differentiation of Dictyostelium discoideum

The half-lives of functional messenger RNAs were determined by a method employing the drugs actinomycin D and daunomycin for the inhibition of mRNA synthesis; the activity of extracted mRNAs was determined by an in vitro translation assay. Several controls indicated that this method yielded reliable values for mRNA half-lives; in particular, the declining rate of protein synthesis in the presence of the drugs is due predominantly to the decay of translatable mRNA. This method was used to determine the half-lives of two specific mRNAs—encoding actin and a protein of MW 51,000—as well as that of total cytoplasmic mRNA activity during growth and at several times in differentiation. The half-lives of at least these two mRNAs were shown to be distinctly different from that of the total mRNA population—about 4 hr. However, no significant change in any of these half-lives was observed between growing and developing cells. Therefore wholesale alterations in the degradation rates of total and at least specific messages do not appear to play a role in the regulation of gene expression during Dictyostelium development.     

A microcomputer-based image analysis system and applications to chlorophyll fluorescence studies

An IBM-PC based software system to quantify images of biological sytems is presented. To illustrate the potential of the imaging system described, UV light-induced chlorophyll fluorescence of Chlorella vulgaris cells was monitored using a video camera interfaced to a microscope. The photoinhibitor, DCMU (30 μM) inhibited the UV-induced fluorescence decay in heterotrophically grown cells but not in autotrophically grown cells. Algal cells were also incubated in various concentrations of ascorbic acid (500, 250, 100, 50, 10 and 0 mM) prior to UV light exposure. In the presence of 500, 250 and 100 mM ascorbic acid, the decay of chlorophyll fluorescence was significantly delayed in both heterotrophically and autotrophically grown cells. Heterotrophically grown cells were more sensitive to ascorbic acid than autotrophically grown cells since 10 nM ascorbic acid delayed fluorescence decay in heterotrophic cultures.     

The degradation of ribonucleic acids injected into Xenopus laevis oocytes

Different radioactive RNAs were injected into Xenopus laevis oocytes, and their degradation followed with time. Deproteinized ribosomal RNAs and synthetic polynucleotides, with the exception of polyadenylic acid, were degraded rapidly with apparent first order kinetics and half-lives ranging from 1–6 hr. Transfer RNA, poly(A), and ribosomal RNA injected as whole ribosomal particles were quite stable during the period studied (20 hr). Messenger RNAs from Dictyostelium discoideum and Vesicular Stomatitis Virus, which have poly(A) sequences at their 3′ terminus, presented biphasic degradation kinetics. Approximately 60% of these RNAs was degraded in the first 6 hr, whereas the remaining 30–40% was stable for at least 22 hr. Analysis of the stable material by sucrose gradients showed that it had the same sedimentation pattern as the original material, except that it contained, in addition, free poly(A) sequences sedimenting somewhat smaller than 4S. Puromycin treatment of the cells injected with Dictyostelium mRNAs reduced the percentage of stable RNA to 10%, approximately the poly(A) content of these RNAs. Similar treatment with emetine, which also inhibited cellular protein synthesis, did not affect the stable mRNA fraction.     

Isolation and characterization of nonhistone chromosomal protein C-14 which stimulates RNA synthesis.

The nonhistone chromatin protein, C-14, was extracted from chromatin of Novikoff hepatoma ascites cells and isolated in high purity as shown by its migration as a single dense spot on two-dimensional polyacrylamide gels. Its mobility on sodium dodecyl sulfate gels is consistent with a molecular weight of approximately 70 000. The amino acid composition shows that protein C-14 has an acidic:basic amino acid ratio of 1.8. Its amino terminal amino acid is lysine. Protein C-14 stimulated the incorporation of [3H]UMP into RNA by approximately 30% when added to naked DNA and homologous RNA polymerase I. A 30% stimulation of [3H]UMP incorporation into RNA was also found when protein C-14 was added to an E. coli RNA polymerase system containing either E. coli or Novikoff hepatoma DNA.     

Demonstration of rRNA Synthesis in Pre-Gastrular Embryos of Xenopus Laevis

Isolated cells from Xenopus laevis embryos at various developmental stages were incubated with (methyl-³H) methionine to label newly synthesized RNAs. Methylation of RNAs was studied by analyzing nuclease-digests of high-molecular-weight RNAs by DEAE-Sephadex column chromatography. Labeled rRNA, mRNA and 4s RNA were distinguished by their characteristic patterns of 2'-0-methylation and base-methylation. It was concluded that rRNA synthesis starts during the mid- to late-blastula stage. This is about 4 hr, or at least 3 cell cycles earlier than the initiation of gastrulation, which was previously considered to be the stage when rRNA synthesis begins.     

In vitro replication of mouse hepatitis virus strain A59.

An in vitro replication system for mouse hepatitis virus (MHV) strain A59 was developed using lysolecithin to produce cell extracts. In extracts of MHV-infected cells, radiolabeled UMP was incorporated at a linear rate for up to 1 h into RNA, which hybridized to MHV-specific cDNA probes and migrated in denaturing formaldehyde-agarose gels to the same position as MHV genomic RNA. The incorporation of [32P]UMP into genome-sized RNA in vitro correlated with the observed increase of [3H]uridine incorporation in MHV-infected cells labeled in vivo. Incorporation of [32P]UMP into genome-sized RNA was inhibited when extracts were incubated with puromycin. The addition to the assay of antiserum to the MHV-A59 nucleocapsid protein N inhibited synthesis of genome-sized RNA by 90% compared with the addition of preimmune serum. In contrast, antiserum to the E1 or E2 glycoproteins did not significantly inhibit RNA replication. In vitro-synthesized RNA banded in cesium chloride gradients as a ribonucleoprotein complex with the characteristic density of MHV nucleocapsids isolated from virions. These experiments suggest that ongoing protein synthesis is necessary for replication of MHV genomic RNA and indicate that the N protein plays an important role in MHV replication.     

Autotrophic and heterotrophic metabolism inHydrogenomonas facilis

The rate of entry of glucose (and -methyl glucoside) into autotrophically (A) and heterotrophically (H) grown cells ofHydrogenomonas facilis was found to be approximately equal even though H cells utilize glucose at a higher rate. Various enzymatic activities of A and H cells were examined and significant differences were found in 1) glucose-6-phosphate dehydrogenase activity and 2) the activity of the enzymes of the Entner-Doudoroff system, both of which were much higher in H cells. Both systems were found to be inducible. It is suggested that this accounts for the different ability of A and H forms to utilize glucose.     

Effects of cordycepin on the synthesis of nuclear and cytoplasmic RNAs in embryonic cells of Xenopus laevis

Effects of cordycepin on the incorporation of [3H] guanosine into embryonic Xenopus cells were examined. Cordycepin inhibited the labeling not only of poly(A) + RNA, but of all the other major classes of RNAs. Cellular fractionation showed that this inhibition was much stronger in the labeling of cytoplasmic RNAs than of nuclear RNAs. [3H]Cordycepin was incorporated into both poly(A) + RNA and other RNA species.     

Cellular RNA and influenza-virion RNA are synthesized from different pyrimidine-nucleoside-triphosphate pools in chick-embryo cells.

Chick embryo cells infected with an influenza A (fowl plague) virus have been labelled with (3H)-uridine for different lengths of time. Virion RNA and cellular RNA have been separated by specific hybridization with a surplus of unlabelled viral complementary RNA and RNase digestion. The ratio of the specific radioacticity in the UMP and CMP moieties of both types of RNA has been determined. Since the rate of approach to equilibrium of CMP to UMP labelling of both types of RNA is completely different it is concluded that cellular and virion RNA are synthesized using different pyrimidine nucleoside triphosphate pools.     

4.5S RNA is encoded by hundreds of tandemly linked genes, has a short half-life, and is hydrogen bonded in vivo to poly(A)-terminated RNAs in the cytoplasm of cultured mouse cells.

4.5S RNA is a group of RNAs 90 to 94 nucleotides long (length polymorphism due to a varying number of UMP residues at the 3' end) that form hydrogen bonds with poly(A)-terminated RNAs isolated from mouse, hamster, or rat cells (W. R. Jelinek and L. Leinwand, Cell 15:205-214, 1978; F. Harada, N. Kato, and H.-O. Hoshino, Nucleic Acids Res. 7:909-917, 1979). We have cloned a gene that encodes the 4.5S RNA. It is repeated 850 (sigma = 54) times per haploid mouse genome and 690 (sigma = 59) times per haploid rat genome. Most, if not all, of the repeats in both species are arrayed in tandem. The repeat unit is 4,245 base pairs long in mouse DNA (the complete base sequence of one repeat unit is presented) and approximately 5,300 base pairs in rat DNA. This accounts for approximately 3 X 10(6) base pairs of genomic DNA in each species, or 0.1% of the genome. Cultured murine erythroleukemia cells contain 13,000 molecules per cell of the 4.5S RNA, which can be labeled to equilibrium in 90 min by [3H]uridine added to the culture medium. The 4.5S RNA, therefore, has a short half-life. The 4.5S RNA can be cross-linked in vivo by 4'-aminomethyl-4,5',8-trimethylpsoralen to murine erythroleukemia cell poly(A)-terminated cytoplasmic RNA contained in ribonucleoprotein particles.