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PubMed2002

Characterization of Mycobacterium tuberculosis ribosome recycling factor (RRF) and a mutant lacking six amino acids from the C-terminal end reveals that the C-terminal residues are important for its occupancy on the ribosome.

Ribosome recycling factor (RRF), coded for by the frr locus, is involved in the disassembly of post-termination complexes and recycling of the ribosomes for a fresh round of initiation in bacteria and in eukaryotic organelles. In a cross-species-complementation experiment, it was shown that the Thermus thermophilus RRF protein lacking five amino acids from its C-terminal end (deltaC5TthRRF) but not the full-length protein (TthRRF) complemented Escherichia coli for its frr(ts) phenotype. It was also shown that the Mycobacterium tuberculosis RFF protein (MtuRRF) did not complement E. coli LJ14 for frr(ts). However, simultaneous expression of elongation factor G (EFG) and RRF from M. tuberculosis resulted in complementation of E. coli LJ14. Here it is shown that unlike deltaC5TthRRF, an equivalent mutant of MtuRRF lacking six amino acids from its C-terminal end (deltaC6MtuRRF) did not complement E. coli LJ14. Surprisingly, deltaC6MtuRRF failed to complement the strain even in the presence of homologous EFG (MtuEFG). The biochemical and biophysical characterization of these proteins suggested that the mutant RRF folded properly. However, ribosome-binding assays showed that the mutant protein was compromised in its binding to E. coli ribosomes. It is suggested that the conserved amino acids at the C-terminal end of the RRFs contribute to their residency on ribosomes and that the specific interactions between RRF and EFG are crucial in the disassembly of the termination complex.

Amino Acid Sequence↗

PubMed1981

On the immunogenicity of ribosomes and ribosomal proteins isolated from Klebsiella pneumoniae and Streptococcus pneumoniae.

The two pathogenic species Streptococcus pneumoniae and Klebsiella pneumoniae were used to analyze the immunogenic role of proteins in ribosomal preparations. The protective activity of ribosomes prepared from either strain and further purified by washing with high-salt concentrations, followed or not by sucrose gradient separation of the particles, was identical to that of crude unwashed ribosomes. Similarly, no substantial alteration of the level of protection was observed after treatment with the antibiotic puromycin. Therefore, the immunizing efficacy of ribosomes does not appear to be due either to the nonribosomal proteins adsorbed at the surface of organelles or to the growing polypeptide chain. It seems rather to be attributable to the structural ribosomal proteins themselves, which were indeed shown to induce alone a significant level of protection.

Animals↗

PubMed1983

Unbalanced ribosomal protein synthesis in a strain of Escherichia coli containing a cloned, truncated 16-S ribosomal RNA gene.

An Escherichia coli K12 strain, carrying the promotor and proximal portion of the 16-S rRNA gene from rrnB cloned in the high-copy-number plasmid psF2124, has been examined for abnormalities in ribosome biogenesis. Both ribosomal RNA accumulation and ribosome content are depressed in this strain as compared to the control strain carrying the plasmid vector alone. The rate of total protein synthesis, however, appears to be normal. In contrast, the rate of ribosomal protein synthesis, relative to total protein synthesis, is elevated. The rates of synthesis of individual ribosomal proteins were determined and found to vary greatly, ranging from severe under-synthesis (displayed especially by proteins L7/L12) to massive over-synthesis (displayed particularly in the case of protein S7). Analysis of the rates of synthesis of other proteins coded for by the S12 operon revealed that protein S12 was moderately over-produced, but elongation factors EF-G and EF-Tu appear to be synthesized at the same rate as EF-Ts, all three being moderately under-synthesized relative to total soluble proteins.

Bacterial Proteins↗

PubMed1984

Ribosomal RNA-protein cross-links, induced by gamma-irradiation of 40S and 60S ribosomal subunits of L cells.

The 40S and 60S ribosomal subunits of L cells are gamma-irradiated in the absence of oxygen at low radiation doses to keep the integrity of the ribosomal structure. We show that under these experimental conditions, specific cross-links are induced in situ between rRNA and ribosomal proteins due to close contact between their reactive groups. We found that about 15 proteins are cross-linked to the 28S RNA. Most of them belong to the core proteins of the 60S ribosomal subunits. A few high-molecular mass proteins which might be factors are also bound to 28S RNA. Between 8 and 11 proteins are covalently linked to 18S RNA; 8 of these have been previously described as transferable proteins from one subunit to the other. Only 3 are core proteins of the small subunit. The contribution of these results to the study of the three-dimensional ribosomal structure is also discussed.

Animals↗

PubMed1987

Phosphorylation of a 40S ribosomal subunit protein in Tetrahymena. Lack of correlation with cellular growth and ribosome stability.

In Tetrahymena the small ribosomal subunit protein S7, which appears to be the equivalent of S6 of higher eukaryotes, undergoes reversible phosphorylation under a set of defined conditions. In an attempt to understand the physiological role of such reversible phosphorylation, we examined the status of ribosomal protein S7 in growing cells and growth-arrested cells, starving either non-specifically for nutrients or specifically for a single essential amino acid. These experiments allowed us to dissociate S7 phosphorylation from changes in the translational activity and the stability of ribosomes. The results revealed complete lack of correlation between phosphorylation of S7 and both the growth status of the cells and the in vivo stability of ribosomes. Taken together with the observation that phosphorylation of S7 occurs only when the cells are starved in buffers containing sodium chloride or high concentrations of Tris, non-essential ions for normal growth, our data suggest that this protein modification is required to maintain the functional integrity of the ribosomes in an altered electrostatic environment, induced by changes in the extracellular ionic conditions.

Amino Acids, Essential↗

PubMed1992

YmL9, a nucleus-encoded mitochondrial ribosomal protein of yeast, is homologous to L3 ribosomal proteins from all natural kingdoms and photosynthetic organelles.

The nuclear gene for mitochondrial ribosomal protein YmL9 (MRP-L9) of yeast has been cloned and sequenced. The deduced amino acid sequence characterizes YmL9 as a basic (net charge + 30) protein of 27.5 kDa with a putative signal peptide for mitochondrial import of 19 amino acid residues. The intact MRP-L9 gene is essential for mitochondrial function and is located on chromosome XV or VII. YmL9 shows significant sequence similarities to Escherichia coli ribosomal protein L3 and related proteins from various organisms of all three natural kingdoms as well as photosynthetic organelles (cyanelles). The observed structural conservation is located mostly in the C-terminal half and is independent of the intracellular location of the corresponding genes [Graack, H.-R., Grohmann, L. & Kitakawa, M. (1990) Biol. Chem. Hoppe Seyler 371, 787-788]. YmL9 shows the highest degree of sequence similarity to its eubacterial and cyanelle homologues and is less related to the archaebacterial or eukaryotic cytoplasmic ribosomal proteins. Due to their high sequence similarity to the YmL9 protein two mammalian cytoplasmic ribosomal proteins [MRL3 human and rat; Ou, J.-H., Yen, T. S. B., Wang, Y.-F., Kam, W. K. & Rutter, W. J. (1987) Nucleic Acids Res. 15, 8919-8934] are postulated to be true nucleus-encoded mitochondrial ribosomal proteins.

Amino Acid Sequence↗

PubMed1963

RIBOSOMAL RNA ON THE SURFACE OF RIBOSOMES.

Ribonuclease from pancreas releases nucleotide from Escherichiacoli ribosomes while not altering significantly the base composition of the total ribosomal RNA. Ribonuclease hydrolyzes ribsomal RNA without destroying the structure of 70S or 30S and 50S ribosomes. The RNA in 30S and 50S ribosomes appears more sensitive to the action of ribonuclease. The data suggest that RNA may be a surface component of the ribosome.

Centrifugation↗

PubMed1976

Neurospora crassa cytoplasmic ribosomes; ribosomal ribonucleic acid synthesis in the wild type.

The biosynthesis of ribosomal ribonucleic acid (rRNA) In wild-type Neurospora crassa growing at 25 degrees C was investigated by continuous-labeling and pulsechase experiments using [5-3H]uridine. The results of these experiments suggest the following precursor-product relationships: the first RNA molecule to be synthesized in significant quantities is the 2.4 X 10(6)-dalton (2.4-Mdal) ribosomal precursor RNA. This RNA is cleaved to produce two species of RNA with weights of 0.7 and 1.4-Mdal. The former is the mature 17S rRNA of the 37S ribosomal subunit. The 1.4-Mdal RNA is subsequently cleaved to produce the mature 1.27-Mdal (25S) and 61,000-dalton (5.8S) rRNA's of the 60S ribosomal subunit. In the maturation process, approximately 15 to 20% of the 2.4-Mdal ribosomal precursor rRNA molecule is lost. As in other eukaryotes that have been examined, 5S rRNA is not derived from this precursor molecule.

Kinetics↗

PubMed1979

Comparative surfact structure of 16S ribosomal ribonucleic acid of 30S ribosomes of procaryotic cells.

Ribonuclease T(1) treatment of 30S ribosomes of Escherichia coli converts a large region at the 3' OH end of 16S ribosomal ribonucleic acid (rRNA) to low-molecular-weight RNA. The final 25 nucleotides at the 3' terminus of the molecule emerge relatively intact, whereas most of the region "upstream," for about 150 nucleotides, is converted to oligonucleotides. Identical enzyme treatment generates a fragment of about 60 nucleotides from the middle of 16S rRNA (section D'). To determine whether there are similar sequences in other bacteria, which occupy similar accessible surface locations, we treated 30S ribosomes from Azotobacter vinelandii and Bacillus stearothermophilus with RNase T(1). In each case, a fragment of RNA about 25 nucleotides in length containing the 3' OH end of 16S rRNA and a fragment of about 60 nucleotides in length similar, but not identical, in oligonucleotide composition to section D' of E. coli 16S rRNA were obtained from nuclease-treated 30S ribosomes. These data indicate that, although the primary structure at the 3' end and the middle (section D') of the various 16S rRNA's is not completely conserved, their respective conformations are conserved. A number of identical oligonucleotides were found in the low-molecular-weight fraction obtained from RNase T(1)-treated E. coli, A. vinelandii, and B. stearothermophilus 30S ribosomes. These results show that identical RNase T(1)-sensitive sequences are present in all three bacteria. Hydrolysis of these regions leads to the production of the fragments 25 and 60 nucleotides in length.

Azotobacter↗

PubMed1983

Cyclic nucleotide-independent protein kinases from ribosomes and phosphorylation of a single 40S ribosomal subunit protein in zoospores of Blastocladiella emersonii.

Cyclic nucleotide-independent protein kinase (EC 2.7.1.37) activity was found in the nuclear cap organelle, within which ribosomes of zoospores of Blastocladiella emersonii are sequestered. Two protein kinase activities were resolved from the high-salt wash fraction of zoospore ribosomes by selective adsorption to DEAE-cellulose. Both enzymes phosphorylated in vitro a 32,000 Mr protein of the 40S ribosomal subunit. Phosphorylation of this ribosomal protein, which exhibits electrophoretic properties similar to those of mammalian ribosomal protein S6, was also observed in vivo in 32P-labeled zoospores.

Blastocladiella↗

PubMed1975

Cell-free protein synthesis in t,e rabbit liver ribosomal system. II. Large scale preparation of purified 80S ribosomes.

A procedure for the preparation of a large quantity of biologically active, highly purified ribosomes from rabbit liver is described. The method employs polyethylene glycol-dextran sulfate parition and DEAE-cellulose chromatography to overcome the limitations encountered in conventional procedures. The entire process takes only 48 h to obtain 10,000 A(260) units of ribosomes. The ribosomes thus obtained are predominantly 78S particles with a constant protein-RNA ratio of 0.95. The ribosomes are free from RNase, amino-acyl-tRNA synthetase, and amino-acyl-tRNA: protein transferase activity. The protein synthesizing activity is dependent on added mRNA and protein factors. These ribosomes are stable for prolonged periods of storage in a liquid nitrogen refrigerator.

Amino Acyl-tRNA Synthetases↗

PubMed1990

Immunoelectron microscopic studies on the location of ribosomal proteins on the surface of the 40S ribosomal subunit from rat liver.

Seven ribosomal proteins have been localized by means of immunoelectron microscopy on the surface of the 40S ribosomal subunit from rat liver using monospecific antibodies. The location of ribosomal proteins S13/16, S19, and S24 is described for the first time, and that of ribosomal proteins S2, S3, S3a, and S7, which has been published previously on the basis of experiments performed with less well characterized antibody preparations [Lutsch et al., Mol. Gen. Genet. 176, 281-291 (1979) and Biomed. Biochim. Acta 42, 705-723 (1983)], is corrected in this paper. The results are discussed with respect to the involvement of these proteins in functional sites of the 40S ribosomal subunit.

Aniline Compounds↗

PubMedDate not supplied

[Study of the mRNA-binding region of ribosomes at different steps of translation. II. Affinity modification of Escherichia coli ribosomes by benzylidene derivative of AUGU6 in the 70S initiation complex].

2',3'-O-(4-[N-(2-chloroethyl)-N-methylamino]) benzylidene derivative of AUGU6 was used for identification of the proteins in the region of the mRNA-binding centre of E. coli ribosomes. This derivative alkylated ribosomes (preferentially 30S ribosomal) with high efficiency within the 70S initiation complex. In both 30S and 50S ribosomal subunits proteins and rRNA were modified. Specificity of the alkylation of ribosomal proteins and rRNA with the reagent was proved by the inhibitory action of AUGU6. Using the method of two-dimensional electrophoresis in polyacrylamide gel the proteins S4, S12, S13, S14, S15, S18, S19 and S20/L26 which are labelled by the analog of mRNA were identified.

Alkylation↗

PubMed1985

Modification of Escherichia coli ribosomes: in vitro termination is less dependent on histidine residues at the peptidyl transferase centre when ribosomes lack protein L11.

Chemical modification of ribosomes with the histidine specific reagents, 1-fluoro-2,4-dinitrobenzene (FDNB) and diethylpyrocarbonate (DEP), result in a loss of activities in vitro of codon-dependent termination and peptide bond formation. The binding of release factor (RF) to the ribosome is unaffected but the hydrolysis of peptidyl-tRNA is inhibited. On reversal of the modification activity can be restored. Partial protection is provided by chloramphenicol indicating that one or more of the affected residues is at the peptidyl transferase centre. Codon-dependent termination on ribosomes lacking L11, which have a greater affinity for RF-2, is significantly less affected by the modification than on control ribosomes. Peptide bond formation is affected similarly on L11 lacking and normal ribosomes.

Acyltransferases↗

PubMed1994

Ribosomal protein P0, contrary to phosphoproteins P1 and P2, is required for ribosome activity and Saccharomyces cerevisiae viability.

Protein P0 in Saccharomyces cerevisiae is found only in the ribosomes and not free in a cytoplasmic pool like the structurally related acidic P1 and P2 proteins. Analogously, P0 stays bound to the particles in conditions that release the other P proteins. Attempts to obtain yeast strains carrying an interrupted P0 gene by direct gene disruption techniques of different yeast strains always resulted in haploid cells carrying one disrupted and one intact copy of the gene. Disruption of the unique P0 genomic copy seems to induce a duplication and occasionally a chromosomal transposition of the gene. Conditional null mutants of P0 were then constructed carrying the P0 gene under the control of the inducible GAL1 promoter. A 2-3-fold excess of P0 mRNA is found in the conditional mutant when grown in galactose; however, only a small increase of the P0 protein is detected in total cell extracts. No P0 protein is detected in the cell supernatant, indicating that, like the standard ribosomal proteins and opposite to the other P proteins, the protein not bound to the ribosomes is degraded. Transfer of the mutants to the restrictive conditions causes, after some generations, a growth stop that finally leads to cell death. The growth decline is paralleled by a reduction in the polysome number and the appearance of half-mer particles as well as by an accumulation of 60 S particles deficient in P0 and in the acidic proteins P1 and P2. These results indicate that P0 is required for the interaction of the acidic P1 and P2 proteins with the ribosomes, and in its absence, deficient 60 S ribosomes are assembled which are inactive in protein synthesis resulting in cell lethality.

Blotting, Southern↗

PubMed1999

Yeast proteins related to the p40/laminin receptor precursor are required for 20S ribosomal RNA processing and the maturation of 40S ribosomal subunits.

Numerous studies have linked the overexpression of the Mr 37,000 laminin receptor precursor (37-LRP) to tumor cell growth and proliferation. The role of this protein in carcinogenesis is generally considered in the context of its putative role as a precursor for the Mr 67,000 high-affinity laminin receptor. Recent studies have shown that 37-LRP, also termed p40, is a component of the small ribosomal subunit indicating that it may be a multifunctional protein. The p40/37-LRP protein is highly conserved phylogenetically, and closely related proteins have been identified in species as evolutionarily distant as humans and the yeast, Saccharomyces cerevisiae. Yeast homologues of p40/37-LRP are encoded by a duplicated pair of genes, RPS0A and RPS0B. The Rps0 proteins are essential components of the 40S ribosomal subunit. Previous results have shown that cells disrupted in either of the RPS0 genes have a reduction in growth rate and reduced amounts of 40S ribosomal subunits relative to wild-type cells. Here, we show that the Rps0 proteins are required for the processing of the 20S rRNA-precursor to mature 18S rRNA, a late step in the maturation of 40S ribosomal subunits. Immature subunits that are depleted of Rps0 protein that contain the 20S rRNA precursor are preferentially excluded from polysomes, which indicates that their activity in protein synthesis is dramatically reduced relative to mature 40S ribosomal subunits. These data demonstrate that the assembly of Rps0 proteins into immature 40S subunits and the subsequent processing of 20S rRNA represent critical steps in defining the translational capacity of yeast cells. If the function of these yeast proteins is representative of other members of the p40/37-LRP family of proteins, then the role of these proteins as key components of the protein synthetic machinery should also be considered as a basis for the linkage between the their overexpression and tumor cell growth and proliferation.

Fungal Proteins↗

PubMed1992

Variable arrangement of 5S ribosomal genes within the ribosomal DNA repeats of arthropods.

The polymerase chain reaction and hybridization to genomic blots were used to investigate whether the previously observed inclusion of 5S ribosomal RNA genes in the 28S-18S ribosomal DNA intergenic regions of some crustacean species (copepods) could also be detected in other arthropods. Such an arrangement was found not only in other calanoid copepod species but also in a cirriped, an euphausid, and a spider. It is interesting that species from two different calanoid copepod genera do not have this type of arrangement. We conclude that the inclusion of 5S ribosomal RNA genes within the ribosomal DNA repeats has probably occurred repeatedly during the evolution of arthropod species and that the mechanism(s) responsible for these insertions could also be responsible for their loss.

Animals↗

PubMed1989

Localization of the site of cleavage of ribosomal RNA by colicin E3. Placement on the small ribosomal subunit by electron microscopy of antibody--complementary oligodeoxynucleotide complexes.

Colicin E3 is a ribonuclease that inactivates Escherichia coli ribosomes by cleaving the RNA of the small ribosomal subunit after nucleotide 1493. A series of oligodeoxynucleotides that complement 16 S RNA in the region of the colicin cleavage site has been synthesized, and their ability to form complexes with 30 S ribosomal subunits has been measured using a nitrocellulose filter-binding assay. The most efficiently bound probe, complementary to residues 1485-1496, was modified with antibody-recognizable derivatives at the 5'-end, the 3'-end, or both. Antibody-oligonucleotide-subunit complexes were then generated and examined by electron microscopy. Antibody binding was seen at the tip of the platform of the 30 S subunit. The complementary oligonucleotide and thus the site at which colcin E3 cleavage occurs is therefore in the same physical region as the 3'-end of the 16 S ribosomal RNA and its message-positioning "Shine-Dal-garno" sequence.

Antibodies↗