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At least 955 records · Page 53Linked to original sources
PubMed1984

Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs.

The primary structure of the gene for 18 S rRNA of the crustacean Artemia salina was determined. The sequence has been aligned with 13 other small ribosomal subunit RNA sequences of eukaryotic, archaebacterial, eubacterial, chloroplastic and plant mitochondrial origin. Secondary structure models for these RNAs were derived on the basis of previously proposed models and additional comparative evidence found in the alignment. Although there is a general similarity in the secondary structure models for eukaryotes and prokaryotes, the evidence seems to indicate a different topology in a central area of the structures.

Animals↗
PubMed1975

Studies on ribosomal ribonucleic acid from yeast. III. Secondary structure of 18 and 26S yeast ribosomal RNA's and their complex: circular dichroism and infrared analyses.

Circular dichroism (CD) and infrared (IR) spectroscopic analyses were performed of 26 and 18S yeast ribosomal RNA's (rRNA) and their specific complex, 30S RNA. The molecular ellipticity coefficients [thota] of 18, 26, and 30S rRNA's were 2.72, 2.63, and 2.65X10(4) degree-cm2/decimole at 264 nm, respectively. The base-pairing contents of 18, 26, and 30S rna's determined by iC), and 70% (32% AU, 38% GC), respectively. These results suggest that 18 and 26S rRNA have very similar secondary structures, and that 30S rna may have a slightly higher base-pairing content than the estimated sum of those of 18 and 26S rRNA's. The biological significance of this phenomenon is discussed in this report.

Binding Sites↗
PubMed1991

Xenopus borealis and Xenopus laevis 28S ribosomal DNA and the complete 40S ribosomal precursor RNA coding units of both species.

We have determined the nucleotide sequence of Xenopus borealis 28S ribosomal DNA (rDNA) and have revised the sequence of Xenopus laevis 28S rDNA (Ware et al., Nucl. Acids Res. 11, 7795-7817 (1983)). In the regions encoding the conserved structural core of 28S rRNA (2490 nucleotides) there are only four differences between the two species, each difference being a base substitution. In the variable regions, also called eukaryotic expansion segments (ca. 1630 nucleotides) there are some 61 differences, due to substitutions, mini-insertions and mini-deletions. Thus, evolutionary divergence in the variable regions has been at least 20-fold more rapid than in the conserved core. A search for intraspecies sequence variation has revealed minimal heterogeneity in X. laevis and none in X. borealis. At three out of four sites where heterogeneity was found in X. laevis (all in variable regions) the minority variant corresponded to the standard form in X. borealis. Intraspecies heterogeneity and interspecies divergence in the 28S variable regions are much less extensive than in the transcribed spacers. The 28S sequences are from the same clones that were used previously for sequencing the 18S genes and transcribed spacers. The complete sequences of the 40S precursor regions of the two reference clones are given.

Animals↗
PubMed1994

Ribosomal protein methylation in Escherichia coli: the gene prmA, encoding the ribosomal protein L11 methyltransferase, is dispensable.

The prmA gene, located at 72 min on the Escherichia coli chromosome, is the genetic determinant of ribosomal protein L11-methyltransferase activity. Mutations at this locus, prmA1 and prmA3, result in a severely undermethylated form of L11. No effect, other than the lack of methyl groups on L11, has been ascribed to these mutations. DNA sequence analysis of the mutant alleles prmA1 and prmA3 detected point mutations near the C-terminus of the protein and plasmids overproducing the wild-type and the two mutant proteins have been constructed. The wild-type PrmA protein could be crosslinked to its radiolabelled substrate, S-adenosyl-L-methionine (SAM), by u.v. irradiation indicating that it is the gene for the methyltransferase rather than a regulatory protein. One of the mutant proteins, PrmA3, was also weakly crosslinked to SAM. Both mutant enzymes when expressed from the overproducing plasmids were capable of catalysing the incorporation of 3H-labelled methyl groups from SAM to L11 in vitro. This confirmed the observation that the mutant proteins possess significant residual activity which could account for their lack of growth phenotype. However, a strain carrying an in vitro-constructed null mutation of the prmA gene, transferred to the E. coli chromosome by homologous recombination, was perfectly viable.

Alleles↗
PubMed2004

RNA-guided nucleotide modification of ribosomal and non-ribosomal RNAs in Archaea.

Archaea use ribonucleoprotein (RNP) machines similar to those found in the eukaryotic nucleolus to methylate ribose residues in nascent ribosomal RNA. The archaeal complex required for this 2'-O-ribose-methylation consists of the C/D box sRNA guide and three proteins, the core RNA-binding aL7a protein, the aNop56 protein and the methyltransferase aFib protein. These RNP machines were reconstituted in vitro from purified recombinant components, and shown to have methylation activity when provided with a simple target oligonucleotide, complementary to the sRNA guide sequence. To obtain a better understanding of the versatility and specificity of this reaction, the activity of reconstituted particles on more complex target substrates, including 5S RNA, tRNA(Gln) and 'double target' oligonucleotides that exhibit either direct or reverse complementarity to both the D' and D box guides, has been examined. The natural 5S and tRNA(Gln) substrates were efficiently methylated in vitro, as long as the complementarity between guide and target was about 10 base pairs in length, and lacked mismatches. Maximal activity of double guide sRNAs required that both methylation sites be present in cis on the target RNA.

Archaeal Proteins↗
PubMed1976

Conservation of the 5'-terminal nucleotide sequences of ribosomal 18-S RNA in eukaryotes. Differential evolution of large and small ribosomal RNA.

The 5'-terminal nucleotide sequences of ribosomal 18-S and 28-S RNA of seven species of eukaryotes including three mammals, one bird, one amphibian, one echinoderm and one slime mold, were analyzed either by means of terminal phosphorylation of RNA with polynucleotide kinase of by fingerprint analysis of uniformly labeled RNA. The following conclusions were obtained. 1. The 5'-terminal sequences of the 18-S RNA of the mouse, chicken and Dictyostelium discoideum were pUpApCp(Cp,Up)Gp---, suggesting strongly that all the eukaryotes had this same sequence at the 5'-terminus. Preliminary analysis of the 5'-termini of the 18-S RNA from human, rat, Xenopus and sea urchin cells revealed the same pUp(Np)Gp--- type 5'-terminal structure, supporting the above hypothesis. 2. The 5'-terminal sequences of the 28-S RNA of the human, rat, mouse and chicken cells were all pCpGp---, whereas those of the lower animals such as Xenopus, sea urchin and Dictyostelium were different.

Alkaline Phosphatase↗
PubMed1978

The mechanism of codon-anticodon interaction in ribosomes. Quantitative study of codon-dependent binding of tRNA to the 30-S ribosomal subunits of Escherichia coli.

The formation of a ternary complex 30-S-subunit . poly(U) . tRNAPhe is discussed and the conditions for its correct description by Langmuir's isotherm are deduced. The affinity constant of the binary complex 30-S-subunit . poly(U) is measured. The reversibility of binding of tRNAPhe to the complex 30-S-subunit . poly(U) is proved in a direct way. The main reason for the heterogeneity of ternary complexes was found to be due to the ability of high-molecular-weight poly(U) to form complicated aggregates with 30-S subunits. If a fraction of poly(U) of moderate molecular weight (30 000) is used, then the ternary complexes are homogeneous in stability and yield the same affinity constants for deacylated, aminoacylated and peptidyl-tRNAPhe (1 X 10(8) M-1 at 20 mM Mg2+, 200 mM NH+4 and 0 degrees C). Ribosomal protein S1 increases the binding constant of poly(U) with 30-S subunits but does not change the binding constant of tRNAPhe with the 30-S-subunit . poly(U) complex. All 30-S subunits, even partially stripped of S1 protein, are active in the binding of both poly(U) and tRNAPhe.

Anticodon↗
PubMed1982

Ribosomal protein S1 associates with Escherichia coli ribosomal 30-S subunit by means of protein-protein interactions.

Ribosomal proteins S1 when associated with the 30-S subunit does not interact with 16-S RNA but its binding is determined mostly by protein-protein interactions. These conclusions are based on the following data. 1. Ultraviolet irradiation (lambda = 254 nm) of the 30-S subunit does not result in the covalent cross-linking of S1 with 16-S RNA at irradiation doses up to 150 quanta/nucleotide, whereas the irradiation under the same conditions of S1 . polynucleotide complexes [S1 . poly(U), S1 . poly(A) and S1 . Q beta phage RNA] induces effective formation of polynucleotide-protein cross-links. 2. Mild treatment of 30-S subunits lacking S-1 with RNase A or with cobra venom endonuclease results in removal of 10--20% of the total nucleotide material but does not affect their sedimentation characteristics of their S1 binding capacity. 3. The association of S1 with S1-depleted 30-S subunits is insensitive to aurintricarboxylic acid, which is known as a strong inhibitor of complex formation between S1 and polynucleotides. 4. Mild trypsin treatment of S1-depleted 30-S subunits greatly reduces their S1 binding capacity.

Bacterial Proteins↗
PubMed1983

500-MHz 1H-NMR studies of ribosomal proteins isolated from 70-S ribosomes of Escherichia coli.

A method for the large-scale isolation of ribosomal proteins is described avoiding pre-separation of 30-S and 50-S subunits. Five proteins isolated in this way were studied with high-resolution 1H NMR at 500 MHz. These are S21, L18, L25, L30 and L33. The results show that L18, L25 and L30 exhibit tertiary structure in solution and indications for secondary structure in S21 are found. Protein L33 appears to be a random coil. Several resonances in the 1H NMR spectra are assigned to particular protons of amino acid residues, e.g. the aromatic ring protons of tyrosines and histidines, and epsilon-protons of lysines.

Aniline Compounds↗
PubMed1986

Control of ribosome biosynthesis in plant cell cultures under heat-shock conditions. Ribosomal RNA.

The immediate block of ribosome biosynthesis in heat-shocked tomato cell cultures is primarily caused by the complete inhibition of pre-rRNP processing. Depending on the heat-shock conditions synthesis of pre-rRNP goes on, though at a reduced level. Synthesis and/or preservation of pre-rRNP during heat shock as well as its efficient processing in the recovery period are thoroughly improved by preconditioning of cells to the hyperthermic treatment. Such preinduced cultures are characterized by their content of preformed heat-shock proteins, whose dominant representative (hsp 70) becomes highly enriched in the characteristic granular rRNP material observed in nucleoli of heat-shocked cells. This is shown by immune fluorescence staining and microautoradiography.

Autoradiography↗
PubMed1974

Delayed hypersensitivity reactions provoked by ribosomes from acid-fast bacilli: physical characteristics and immunological aspects of core ribosomal proteins from Mycobacterium smegmatis.

Ribosomal subunits from Mycobacterium smegmatis were analyzed by using sedimentation velocity, sedimentation equilibrium, and acrylamide gel electrophoresis experiments. These s(20.w) values for the subunits are 48.7S and 28.1S. The molecular weight of the 49S subunit is about 1.65 x 10(6), and that of the 28S subunit is 7.8 x 10(5). Both subunits contain about 37% protein and 63% ribonucleic acid. A protein-deficient particle having an s(20.w) value of 15.7S contains about 11% protein and 89% ribonucleic acid. Skin tests showed all subunits and proteins to be active as agents in provoking delayed hypersensitivity, but the 16S protein-deficient particle, as well as the proteins derived from it, was more specific than the subunits themselves.

Animals↗
PubMed1976

Characterization of the hybridization between purified 16S and 23S ribosomal ribonucleic acid and ribosomal deoxyribonucleic acid from Escherichia coli.

An assay to distinguish specifically between 16S and 23S ribosomal ribonucleic acid (rRNA) has been developed. The assay involves hybridization of radioactive rRNA to deoxyribonucleic acid (DNA) from lambdailv5 transducing phage, which carries an rRNA transcription unit. Radioactive 16S or 23S rRNA can be specifically and completely competed from hybrids by using highly purified nonradioactive 16S or 23S competitor RNA, respectively. The preparation and purification of 16S rRNA and 23S rRNA are described in detail. The hybridization assay is extremely sensitive and efficient; 65 to 70% or more of the input radioactivity hybridizes to specific DNA in the absence of homologous competitor RNA, and at saturation virtually all of the specific DNA sequences are hybridized to rRNA. The results indicate that: (i) the 16S rRNA and 23S rRNA prepared as described are greater than 99% pure, (ii) 16S RRNA and 23S rRNA hybridize with equal efficiency and in equal molar amounts of lambdailv5 DNA; (iii) at saturation, about one molecule of 16S and one molecule of 23S rRNA are hybridized per genome equivalent of lambda ilv 5 DNA; (iv) essentially no cross-hybridization occurs between 16S and 23S rRNA; and (v) the sequence homology between 16S and 23S rRNA is negligible.

Coliphages↗
PubMed2005

A cross-kingdom internal ribosome entry site reveals a simplified mode of internal ribosome entry.

Rhopalosiphum padi virus (RhPV) is an insect virus of the Dicistroviridae family. Recently, the 579-nucleotide-long 5' untranslated region (UTR) of RhPV has been shown to contain an internal ribosome entry site (IRES) that functions efficiently in mammalian, plant, and insect in vitro translation systems. Here, the mechanism of action of the RhPV IRES has been characterized by reconstitution of mammalian 48S initiation complexes on the IRES from purified components combined with the toeprint assay. There is an absolute requirement for the initiation factors eIF2 and eIF3 and the scanning factor eIF1 to form 48S complexes on the IRES. In addition, eIF1A, eIF4F (or the C-terminal fragment of eIF4G), and eIF4A strongly stimulated the assembly of this complex, whereas eIF4B had no effect. Although the eIF4-dependent pathway is dominant in the RhPV IRES-directed cell-free translation, omission of either eIF4G or eIF4A or both still allowed the assembly of 48S complexes from purified components with approximately 23% of maximum efficiency. Deletions of up to 100 nucleotides throughout the 5'-UTR sequence produced at most a marginal effect on the IRES activity, suggesting the absence of specific binding sites for initiation factors. Only deletion of the U-rich unstructured 380-nucleotide region proximal to the initiation codon resulted in a complete loss of the IRES activity. We suggest that the single-stranded nature of the RhPV IRES accounts for its strong but less selective potential to bind key mRNA recruiting components of the translation initiation apparatus from diverse origins.

5' Untranslated Regions↗
PubMedDate not supplied

Regulation of the Escherichia coli S10 ribosomal protein operon by heterologous L4 ribosomal proteins.

We have cloned the L4 ribosomal protein genes from Morganella morganii and Haemophilus influenza. The sequences of these genes were compared with published sequences for Escherichia coli, Yersinia pseudotuberculosis, and Bacillus stearothermophilus. All five of these L4 genes were expressed in E. coli and shown to function as repressors of both transcription and translation of the E. coli S10 operon. Possible implications for regulation of r-protein synthesis in species other E. coli are discussed.

Amino Acid Sequence↗
PubMed2005

The p53 protein is a novel substrate of ribosomal S6 kinase 2 and a critical intermediary for ribosomal S6 kinase 2 and histone H3 interaction.

The tumor suppressor p53 protein is one of the most highly connected nodes in cellular signal transduction pathways and acts as a central regulatory switch in networks controlling cell proliferation and apoptosis. It is involved in the activation of genes that maintain control over cellular responses to DNA errors such as DNA repair, chromosomal recombination, and chromosome segregation. Here we show that ribosomal S6 kinase 2 (RSK2) activates and phosphorylates p53 (Ser15) in vitro and in vivo and colocalizes with p53 in the nucleus. Deficiency of p53 diminishes RSK2-mediated phosphorylation of histone H3 (Ser10) and adding back p53 to p53-/- embryonic fibroblasts restored phosphorylation of histone H3 at Ser10. These results show that the p53 protein is an important substrate of RSK2 and a critical intermediary in the RSK2 and histone H3 interaction. The RSK2-p53-histone H3 complex may likely contribute to chromatin remodeling and cell cycle regulation.

Animals↗
PubMed1976

Isolation of eukaryotic ribosomal proteins. Purification and characterization of the 60 S ribosomal subunit proteins L4, L5, L7, L9, L11, L12, L13, L21, L22, L23, L26, L27, L30, L33, L35', L37, and L39.

The proteins of the large subunit of rat liver ribosomes were separated into seven groups by stepwise elution from carboxymethylcellulose with LiCl at pH 6.5. Seventeen proteins (L4, L5, L7, L9, L11, L12, L13, L21, L22, L23, L26, L27, L30, L33, L35', L37, and L39) were isolated from three of the groups (B60, D60, G60) by ion exchange chromatography on carboxymethylcellulose and by filtration through Sephadex. The amount of protein obtained varied from 0.5 to 15 mg. Eight of the proteins (L9, L11, L13, L21, L22, L35', L37 and L39) had no detectable contamination; the impurities in the others were no greater than 9%. The molecular weight of the proteins was estimated by polyacrylamide gel electrophoresis in sodium dodecyl sulfate; the amino acid composition was determined.

Amino Acids↗
PubMed1975

Structural analyses of mammalian ribosomal ribonucleic acid and its precursors. Nucleotide sequence of ribosomal 5.8 S ribonucleic acid.

The nucleotide sequence of ribosomal 5.8 S RNA (also known as 7 S or 5.5 S rRNA) from Novikoff hepatoma ascites cells has been determined to be (see article). Estimations of the secondary structure based upon maximized base pairing and the fragments of partial ribonuclease digestion indicate that there may be five base-paired regions in the molecule, three forming a folding of the termini and two forming secondary hairpin loops. The sequence of Novikoff hepatoma 5.8 S rRNA is about 75% homologous with that of yeast 5.8 S rRNA (Rubin, G.M. (1973) J. Biol. Chem. 248, 3860-3875) and similar models for secondary structure are proposed. Both models contain a very stable G-C rich hairpin loop (residues 116 to 138), a less stable A-U-rich hairpin loop (residues 64 to 91) and two symmetrical bulges (residues 15 to 25 and 40 to 44).

Animals↗