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PubMed1991

Assembly of 60S ribosomal subunits is perturbed in temperature-sensitive yeast mutants defective in ribosomal protein L16.

Temperature-sensitive mutants defective in 60S ribosomal subunit protein L16 of Saccharomyces cerevisiae were isolated through hydroxylamine mutagenesis of the RPL16B gene and plasmid shuffling. Two heat-sensitive and two cold-sensitive isolates were characterized. The growth of the four mutants is inhibited at their restrictive temperatures. However, many of the cells remain viable if returned to their permissive temperatures. All of the mutants are deficient in 60S ribosomal subunits and therefore accumulate translational preinitiation complexes. Three of the mutants exhibit a shortage of mature 25S rRNA, and one accumulates rRNA precursors. The accumulation of rRNA precursors suggests that ribosome assembly may be slowed in this mutant. These phenotypes lead us to propose that mutants containing the rpl16b alleles are defective for 60S subunit assembly rather than function. In the mutant carrying the rpl16b-1 allele, ribosomes initiate translation at the noncanonical codon AUA, at least on the rpl16b-1 mRNA, bringing to light a possible connection between the rate and the fidelity of translation initiation.

Amino Acid Sequence↗
PubMed1976

Ribosomal RNA: the message or matrix for ribosomal proteins.

The known nucleotide sequence of Escherichia coli 16S ribosomal RNA has been converted to amino acid sequences in all possible ways, and compared to known ribosomal protein sequences. The degree of similarity is precisely what one would expect by chance alone, providing additional evidence that ribosomal proteins cannot be coded for by ribosomal RNA.

Amino Acid Sequence↗
PubMedDate not supplied

[Peptidyltransferase center of ribosomes. Structure and relationship to other ribosomal functions].

Structural analysis of the ribosomal peptidyl transferase center using model substrates "minimal" peptide acceptors and donors is reported in the present work. Recent data on the ribosomal proteins and rRNA organizing the peptidyl transferase center and other functional centers of the large ribosomal subunits are given and the know facts about the catalytic mechanism of the peptide bond formation are considered. An analysis of the interaction of the peptidyl transferase center and the centers binding the cytoplasmic translocation factors and stringent-factor (for E. coli ribosome) is presented; a possible contribution of the peptidyl transferase center ot the translocation is discussed.

Acyltransferases↗
PubMed1978

Identification by affinity chromatography of the eukaryotic ribosomal proteins that bind to 5 S ribosomal ribonucleic acid.

Rat liver 5 S ribosomal RNA was oxidized with periodate and coupled by its 3' terminus to Sepharose 4B through an adipic acid dihydrazide spacer. The ribosomal proteins that bind to that nucleic acid were isolated by affinity chromatography and identified by electrophoresis in polyacrylamide gels. The eukaryotic 5 S rRNA binding proteins were L6 and L19: small amounts of L7, L23', L27/L27', L35', and L39 also were bound to the affinity column, but whether they associate directly and specifically with 5 S rRNA is not known. The proteins of the 40 S subunit of rat liver ribosomes did not bind to the 5 S rRNA affintiy column, nor did the proteins of either the large or small subparticle of Escherichia coli ribosomes.

Animals↗
PubMed1993

Changes in ribosomal protein and ribosomal RNA synthesis during rat intestinal differentiation.

Subtraction hybridization studies, used to identify genes involved in the control of enterocyte proliferation and/or differentiation, allowed detection of a clone shown to have homologies with rat, chicken, and human acidic ribosomal phosphoprotein P1. Since increases in P1 transcript have been associated with intestinal malignancy, we explored the relationship of P1 and other ribosomal proteins to normal intestinal proliferation and differentiation. Male rats were used to prepare enterocytes as isolated cell fractions representative of the crypt to villus axis of differentiation. Total RNA was extracted from pooled cell fractions and evaluated for mRNA and rRNA steady-state levels. Nuclei were prepared from isolated enterocytes, and nuclear runoff studies were performed to estimate rates of nascent transcription. The P1 complementary DNA from the crypt cell library detected a mRNA of 650 base pairs which showed approximately 8-fold greater steady-state levels in crypt than in villus cells. Similar crypt specificity was also noted for mRNAs coding for elongation factor EF-12 and for ribosomal proteins P0, P1, and S6 (using clones from Y-L. Chan and I. G. Wool). In contrast, 28S rRNA steady-state levels did not differ between villus and crypt, indicating that ribosomal content had remained constant. In situ hybridization studies confirmed the predominant crypt localization of P1 mRNA. Nascent transcription rate studies showed that the proportion of newly synthesized P1 mRNA to total RNA was the same for the villus and crypt, suggesting that the lower content of villus P1 mRNA may be due to increased degradation.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1995

The interaction between "R/S domain" of rat 28S ribosomal RNA and ribosome-inactivating proteins investigated by fusidic acid.

The interaction between "R/S domain" of rat 28S rRNA and ribosome-inactivating proteins (RIPs) has been studied by blocking the action site of RIPs on "R/S domain" of 28S rRNA with fusidic acid or S100. Fusidic acid alone could form stable complexes with rat ribosomes and block the action site of RNA N-glycosidases. incubation of fusidic acid and S100 or GDP with ribosomes could also protect ribosomes from the action of ricin A-chain. However, different effect of fusidic acid, S100 an dGDP was observed when alpha-sarcin was used. Fusidic acid alone could not block the action site of alpha-sarcin. Fusidic acid together with the elongation factors in S100 could block the action site of alpha-sarcin. These results are consistent with the previous report that ricin A-chain and alpha-sarcin recognized different conformation of "R/S domain" in rat 28S rRNA.

Animals↗
PubMed1996

Sensitivity of ribosomes from Agrobacterium tumefaciens to the ribosome-inactivating protein crotin 2 depending on the translocational state.

The GTP analog guanylylmethylene diphosphonate (GppCH2p) strongly inhibited polyuridylic acid-directed polypeptide synthesis in a cell-free translation system prepared from Agrobacterium tumefaciens. Fusidic acid increased even further the inhibitory action. The pre-translocational ribosomal complexes formed with the GppCH2p and the elongation factor G protected the ribosome against the depurinating action of crotin 2 assayed as the acid-dependent release of the RNA fragment whose terminal sequence is 5'-GAGGACCGGGAUGGAC-3'. The results allowed to conclude that the interaction of both crotin 2 and the elongation factor G with the A. tumefaciens ribosomes in the pre-translocational state must take place at overlapping, either sterically or allosterically, ribosomal sites which are equally accessible to the RIP.

Agrobacterium tumefaciens↗
PubMed1971

Drastic alteration of ribosomal RNA and ribosomal proteins in showdomycin-resistant Escherichia coli.

In a mutant of Escherichia coli resistant to showdomycin, both the 50S and 30S ribosomal subunits contain RNA species in which the purine concentration greatly exceeds that of pyrimidines. The same is true for total rapidly-labeled RNA. The modified ribosomal RNA hybridizes poorly with homologous DNA, which is apparently unchanged in base composition. Acrylamide gel electrophoresis of mutant ribosomal proteins shows a highly altered protein pattern for both ribosomal subunits, although the activity of these ribosomes is not decreased.

Antibiotics, Antineoplastic↗
PubMed1974

The chloroplast and cytoplasmic ribosomes of euglena: I. Stability of chloroplast ribosomes prepared by an improved procedure.

A new isolation procedure has resulted in an improved yield of stable 68S chloroplast ribosomes from Euglena gracilis var. bacillaris. Chloroplasts are isolated by suspending the cells in buffer I (sorbitol, 250 mm; sucrose, 250 mm; Ficoll, 2.5% [w/v]; magnesium acetate, 1 mm; bovine serum albumin, 0.01% [w/v]; mercaptoethanol, 14 mm; N-2-hydroxyethyl-piperazine-N'-2-ethanesulfonic acid, pH 7.6, 5 mm) and passing through a French press at less than 1500 pounds per square inch. The crude chloroplasts are purified by three washings with buffer II (sorbitol, 150 mm; sucrose, 150 mm; Ficoll, 2.5% [w/v]; magnesium acetate, 1 mm; bovine serum albumin, 0.01% [w/v]; mercaptoethanol, 14 mm; N-2-hydroxyethyl-piperazine-N'-2-ethanesulfonic acid, pH 7.6, 5 mm). Stable 68S chloroplast ribosomes are obtained when the isolated chloroplasts are resuspended in ribosome buffer (tris-HCI, pH 7.6, 10 mm; magnesium acetate, 12 mm; KCI, 60 mm) containing spermidine, 0.5 mm; mercaptoethanol, 14 mm; sucrose, 8% (w/w), passed through a French press at 4000 pounds per square inch and extracted with either 0.1% (w/v) sodium deoxycholate or 1.0% (v/v) Triton X-100. At 0 to 4 C in ribosome buffer, the purified 68S chloroplast monosome forms a 53S particle while the 35S particle, an expected product of monosome dissociation, cannot be detected. Spermidine and mercaptoethanol prevent the formation of 53S particles from 68S monosomes. The purified 53S particles derived from 68S monosomes contain 23S RNA as well as a significant amount of 16S RNA, suggesting that this particle may not be a true ribosomal subunit.

Journal Article↗
PubMed1983

Patterns of major divergence between the internal transcribed spacers of ribosomal DNA in Xenopus borealis and Xenopus laevis, and of minimal divergence within ribosomal coding regions.

We have determined the nucleotide sequences of the two internal transcribed spacers, the adjacent ribosomal coding sequences and the boundary between the external transcribed spacer and the 18S coding sequence in a cloned ribosomal transcription unit from Xenopus borealis. The transcribed spacers differ very extensively from those of X. laevis. Nevertheless, embedded in the internal transcribed spacers are several short sequence elements which are identical between the two species. These conserved elements are laterally displaced by substantial distances in the X. borealis sequence with respect to that of X. laevis. These relative displacements imply that insertions and deletions have played a major role in transcribed spacer divergence in Xenopus. This in turn implies that large regions of the transcribed spacers do not play a sequence-specific role in ribosome maturation. In contrast, the sequenced parts of the ribosomal coding regions, which encompass 670 nucleotides, differ at only three points from the corresponding sequences in X. laevis, each by a single substitution. These substitutions are readily accommodated by current models for rRNA higher order structure.

Animals↗
PubMed1999

A gene coding for a ribosomal protein L41 in cycloheximide-resistant ribosomes has a promoter which is upregulated under the growth-inhibitory conditions in yeast, Candida maltosa.

We previously found by using yeast, Candida maltosa, that cycloheximide (CYH) sensitivity of ribosomes is dependent on the 56th amino acid residues of a ribosomal protein, L413 (proline in sensitive and glutamine in resistant ribosomes). We also revealed that in this yeast, which has both L41-P type and L41-Q type genes, the expression of the latter type genes is induced by the addition of CYH in the medium to make the cells inducibly resistant to CYH. In this paper, we analyzed the promoter region of L41-Q2a, one of the CYH-inducible L41-Q type genes and found two elements required for the induction of expression: one was a GCRE (Gcn4p-responsive element of Saccharomyces cerevisiae)-like element and the other was a GT-rich element. This promoter region was also required for its expression under some other growth inhibitory conditions. Furthermore, it was suggested that Q-type ribosomes synthesized under these conditions are more resistant to these inhibitory conditions.

Base Sequence↗
PubMed1994

Mutations in helix 34 of Escherichia coli 16 S ribosomal RNA have multiple effects on ribosome function and synthesis.

Helix 34 of E. coli 16 S rRNA (1046 to 1067 and 1189 to 1211) has been proposed to participate directly in the termination of translation at UGA stop codons. We have constructed mutations in this helix in plasmid-encoded rDNA to explore the specific functional roles of the sequence UCAUCA (1199 to 1204) and a secondary structure also involving positions 1054 and 1057-1058. The rRNA mutations were analyzed for their effects on in vivo translational accuracy (stop codon readthrough and frameshifting) as well as growth rate, ribosome synthesis and incorporation into polysomes. Mutations at positions 1054, 1057, 1058, 1199 and 1200 had significant effects on translational accuracy, causing non-specific readthrough of all three stop codons as well as enhanced +1 and -1 frameshifting. Mutations at 1202 and 1203, however, had no effect. The incorporation of deleterious mutant subunits into 70 S ribosomes and polysomes was severely reduced and was associated with a slower growth rate and increased synthesis of host-encoded ribosomes. These data support the proposal that helix 34 is an essential component of the decoding center of the 30 S ribosomal subunit and is not restricted in function to UGA-codon specific termination.

Base Sequence↗
PubMed1995

Incorporation of the yeast mitochondrial ribosomal protein Mrp2 into ribosomal subunits requires the mitochondrially encoded Var1 protein.

Mrp2 is a protein component of the small subunit of mitochondrial ribosomes in the yeast Saccharomyces cerevisiae. We have examined the expression of Mrp2 in yeast mutants lacking mitochondrial DNA and found that the steady-state level of Mrp2 is dramatically decreased relative to wild type. These data suggest that the accumulation of Mrp2 depends on the expression of one or more mitochondrial gene products. The mitochondrial genome of S. cerevisiae encodes two components of the small ribosomal subunit, 15S rRNA and the Var1 protein, both of which are necessary for the formation of mature 37S subunits. Several studies have shown that in the absence of Var1 incomplete subunits accumulate, which lack a limited number of ribosomal proteins. Here, we show that Mrp2 is one of the proteins absent from subunits lacking Var1, indicating that Var1 plays an important role in the incorporation of Mrp2 into mitochondrial ribosomal subunits.

DNA, Mitochondrial↗
PubMed1982

Interaction of the intermediate filament protein vimentin with ribosomal subunits and ribosomal RNA in vitro.

If in a low ionic strength extract of Triton X-100-resistant residual cell structures derived from Ehrlich ascites tumour (EAT) cells Mg2+ was chelated by EDTA, vimentin became associated with unfolded ribosomal subunits. The first molecular characterization of this association has shown that (1) vimentin binds to the RNA moiety of the ribosomes, (2) vimentin has a higher affinity for unfolded small ribosomal subunits or 18S rRNA than for unfolded large ribosomal subunits or 28S rRNA, (3) the limited degradation of vimentin by the vimentin-specific, Ca2+-activated proteinase, with the formation of a 48 Kd breakdown product, abolishes its affinity for rRNA, (4) the association products are rather sensitive to moderate concentrations of KCl and Mg2+, and (5) reductive alkylation of vimentin with pyridoxal-5'-phosphate and NaBH4 has no effect on the affinity of vimentin for rRNA. Actin and tubulin do not interact with EAT cell rRNA under the above ionic conditions.

Animals↗
PubMedDate not supplied

Probing surface structure of sarcin domain on ribosomes of Escherichia coli by complementary oligo DNAs and ribosome-inactivating protein.

The regional structure of the sarcin domain of 23S rRNA of Escherichia coli ribosomes was determined by a combinatory approach of oligo DNA probes and the action of alpha-sarcin. The sarcin domain is protected by a reactive complementary oligo DNA probe against the hydrolytic action of alpha-sarcin. This protective effect is dependent upon the length and the complementary sequence of oligo DNA probes that react to ribosomes. Under UV irradiation and using of the primer extension, nucleotides that contacted by reactive oligo DNA probes were determined. Nucleotides at the 3' side of the domain (positions from G2659 to C2676) were targeted by oligo DNA probes that have their sequences to complement the domain, indicating that the 3' side region was exposed on the surface of ribosomes, whereas nucleotides at the 5' side of stem and extented to two bases at the loop (positions from C2646 to A2654) were not accessible to any oligo DNA probes, implying that the region could be buried in ribosomes. This study also provided evidence that the conformation of the sarcin domain is subjected to alteration if the exposed 3' side of domain is targeted by the reactive DNA probe. The importance of the topological arrangement of the sarcin domain that engages in the translocation event during translation is discussed.

Base Sequence↗
PubMed1977

Messenger RNA binding of a ribosome-associated protein kinase and a ribosomal phosphoprotein(s) in mouse plasmacytoma.

A specific ribosome-associated protein kinase (protein kinase II) and phosphoprotein(s) from the ribosomal KCl wash fraction termed "PPx" have been isolated from plasmacytoma, and tested for their ability to bind to poly(A) and to different plasmacytoma polynucleotides. The nitrocellulose filter binding technique was used to measure RNA-protein interaction. Protein kinase II and PPx preferentially bound mRNA compared to poly(A). They did not bind ribosomal RNA, soluble RNA or DNA. The optimal conditions (temperature, time, protein concentration, ionic strength) for mRNA-protein interaction were determined. Ribosomal protein kinase (protein kinase II) phosphorylated PPx proteins which bound to mRNA represented at least two bands as determined by sodium dodecyl sulphate polyacrylamide gel electrophoresis (Mr = 90 000 and 80 000). The high affinity of protein kinase II and PPx for mRNA suggests that they may function in regulating protein synthesis.

Adenosine Triphosphate↗
PubMed1993

Ribosomal proteins, TL4 and TL5, from Thermus thermophilus form hybrid complexes with 5 S ribosomal RNA from different microorganisms.

Hybrid complexes of the ribosomal proteins, TL4 and TL5, from Thermus thermophilus with 5 S ribosomal RNA from Escherichia coli and Bacillus stearothermophilus have been prepared. There was no competition between the two proteins for the binding sites. Stoichiometry of 5 S RNA binding for both proteins was 1:1 (protein/RNA). The TL4 protein competed with the E. coli ribosomal L5 protein, and the TL5 protein competed with the E. coli ribosomal proteins, L18 and L25, for binding with 5 S RNA.

Escherichia coli↗