Secondary methylation of yeast ribosomal precursor RNA.

The timing of methylation of the ribosomal sequences of ribosomal precursor RNA (pre-rRNA) from the yeast Saccharomyces carlsbergensis was investigated by fingerprint analysis of the methylated oligonucleotides derived from the various precursors. From the total of 37 ribose and 6 base-methyl groups found in 26-S rRNA, the two copies of the base-methylated nucleoside m3U as well as the doubly methylated sequence Um-Gm psi are not yet present in 37-S RNA, the predominant common precursor of 26-S and 17-S rRNA. Introduction of these methyl groups into the ribosomal sequences appears to take place at the level of 29-S pre-rRNA, the immediate precursor to 26-S rRNA. From the total of 18 ribose-methylated and 6 base-methylated nucleosides found in 17-S rRNA, the latter group (one copy of m7G, the m62A-m62A- sequence and the hypermodified methylated nucleoside "mX") is completely missing in 37-S pre-rRNA. The methyl group of m7G is introduced into 18-S pre-rRNA, the direct precursor of 17-S rRNA, in the nucleus. The -m62A-m62A- sequence is methylated after transport of the 18-S pre-rRNA to the cytoplasm prior to the final maturation into 17-S rRNA.     

Evidence for extensive methylation of ribosomal RNA genes in a rat XC cell line

The effects of extracellular Na+, K+ and Cl- on neurite outgrowth of PC12 pheochromocytoma cells were studied. Nerve growth factor (NGF)-induced neurite formation was inhibited upon substitution of choline chloride for NaCl under normal culture conditions. It was found that neurite formation increased proportionately with the concentration of Na+ in medium up to 150 mM. When PC12 cells were exposed to NGF in suspension culture followed by transfer to new dishes, they showed neurite extention in response to NGF in an RNA- and protein synthesis-independent manner. Under these conditions, neurite outgrowth occurred normally in 60-150 mM Na+, whereas it decreased significantly at lower concentrations of Na+. Na+ dependency was also observed for cyclic AMP-mediated neurite formation of PC12 cells. In contrast neurite outgrowth was independent of K+ in the range 5-106 mM, suggesting that membrane potential did not play a role in this process. No alterations were observed in neurite outgrowth with Cl- replaced by NO3-, SO2-4, or 2-hydroxyethanesulfonate. Thus, extracellular Na+ plays a role in controlling neurite formation of these cells. An attempt was made to relate this effect to a decrease in cytoplasmic Ca2+ concentration monitored by a fluorescent dye sensitive to Ca2+.     

Characterization of the ribosomal RNA precursor in Ilyanassa

Ilyanassa embryos synthesized a high molecular weight, rapidly-labeled RNA species that, as time progressed, diminished in proportion to increasing amounts of nascent ribosomal RNA. We tentatively identify this rapidly-labeled RNA species as the ribosomal RNA precursor. Its molecular weight, determined by acrylamide gel electrophoresis, was 2.4–2.5 × 10⁶; a molecule of intermediate size (1.8 × 10⁶ Daltons) was also detected.     

The 32 S RNA of Neurospora crassa mitochondria is not a precursor of the mitochondrial ribosomal RNAs.

Studies on the synthesis of Neurospora mitochondrial ribosomal RNAs by Kuriyama &; Luck 1973 have led to the currently accepted idea that the mature 19 S and 25 S rRNA species are synthesized via a common 32 S precursor RNA. The present results provide evidence that the 32 S RNA band analyzed by Kuriyama &; Luck was in fact a mixture of low concentrations of rapidly labeled RNA species, probably including separate precursors of 19 S and 25 S RNA, along with higher concentrations of aggregates of mature 19 S and 25 S RNA. The former account for the pulse-labeling characteristics of the 32 S band, whereas the latter contribute most of the mass-label, resulting in misleading hybridization data.     

Formation of lariats and circles in self-splicing of the precursor to the large ribosomal RNA of yeast mitochondria

Self-splicing of the precursor to large ribosomal RNA of yeast mitochondria leads not only to circles but also to lariats, structures that have not been observed before as products of self-splicing. Lariats were studied by electron microscopy after hybridization with an RNA complementary to the 3' half of the precursor. This leads to differentiation in at least two classes of lariats that vary in the position of the branch point. In all lariats the tail carries the 3' end, which suggests that a 5' end is used for branch formation with an internal nucleotide. The circles are formed from excised introns. They lack only three nucleotides encoded by mitochondrial DNA along with the 5'-terminal G added in the course of self-splicing. The diverse number of self-splicing products arising in vitro testifies to the considerable reactivity of this intron. The formation of lariats in an RNA catalyzed reaction may have implications for views on the mechanism of splicing of nuclear pre-mRNAs.     

Evidence that the decarboxylation reaction occurs before the first methylation in ubiquinone biosynthesis in rat liver mitochondria

Biosynthesis of ubiquinone-9 was studied by incubating rat liver mitochondria with p-hydroxy[U-14C]benzoate, solanesyl diphosphate and S-adenosyl-L-methionine. When methylation reactions were inhibited by replacing S-adenosyl-L-methionine with S-adenosyl-L-homocysteine, nonaprenyl p-hydroxybenzoate and three other labeled peaks, designated as P1, P2 and P3 according to their retention times on HPLC, were observed. No carboxyl group was present in P1, P2 or P3 because the radioactivities disappeared when p-hydroxy[U-14C]benzoate was replaced by p-hydroxy[carboxyl-14C]benzoate. Compound P2 seemed to be hydroxylated but not methylated because its radioactivity markedly diminished under anaerobic conditions and the radioactivity was not incorporated into the compound from S-adenosyl-L-[methyl-3H]methionine, suggesting that P2 is 6-hydroxynonaprenylphenol. The complete correspondence of the retention times of P2 and chemically synthesized 6-hydroxynonaprenylphenol on HPLC further confirmed this possibility. P2 was a precursor of ubiquinone-9 because the radioactivity of the compound was incorporated into ubiquinone when incubated with mitochondria. The results suggest that the decarboxylation may occur prior to the first methylation in the ubiquinone biosynthesis in rat liver mitochondria, though it has been generally considered that in eukaryotes the first methylation precedes the decarboxylation.     

Methylation status of 13S ribosomal RNA from hamster mitochondria: the presence of a novel riboside, N4-methylcytidine.

The ribosomal RNA ("13S" RNA) of the small ribosomal subunit of hamster cell mitochondria has been found to have a distinctive pattern of methylated residues. Each molecule contained, on the average, approximately one residue of m4Cp, m5Cp and m5Up, and two residues of m62Ap. The natural occurrence of m4Cp has not previously been reported; we propose that this nucleotide is homologous to its ribose-methylated congener, m4Cmp, which is characteristic of bacterial 16S ribosomal RNA. We detected neither m4Cp nor m4Cmp in the hamster cell cytoplasmic ribosomal RNA. This is the first documentation of a modified residue present in mitochondrial RNA but absent from the cytoplasmic RNA of the same cells.