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At least 379 records · Page 21Linked to original sources
PubMed1995

Synthesis of non-translating or translating specialized ribosomes causes feedback regulation of ribosomal RNA synthesis in Escherichia coli.

Specialized ribosomes carry a mutant anti-Shine-Dalgarno region that disrupts the complementary base pairing that stabilizes the translation initiation complex with E. coli mRNAs. It has been reported that production of specialized ribosomes does not cause the inhibition of chromosomal rRNA synthesis that follows production of wild-type ribosomes. We proposed that enabling translation on specialized ribosomes by providing mRNA with a complementary mutation in the Shine-Dalgarno region would restore feedback regulation and inhibit chromosomal rRNA synthesis. With both our system and the system studied previously, we saw feedback regulation regardless of whether the specialized ribosomes were translating. As reported previously, transcription from plasmid-borne promoters decreased as chromosomal rRNA synthesis was repressed, suggesting that the lambda PL and tac promoters may be sensitive to the effector(s) of feedback regulation.

Base Sequence↗
PubMed1997

Solution scattering structural analysis of the 70 S Escherichia coli ribosome by contrast variation. II. A model of the ribosome and its RNA at 3.5 nm resolution.

Selectively deuterated 70 S E. coli ribosomes and isolated 30 S and 50 S subunits were analyzed by X-ray and neutron solution scattering. The resulting contrast variation data set (42 curves in total) was proven to be consistent in describing the ribosome as a four-phase system composed of the protein and rRNA moieties of both subunits. This data set thus provides ten times more information than a single scattering curve. A solid body four-phase model of the 70 S ribosome at low resolution was built from the envelope functions of the 30 S and 50 S subunits and of those of the corresponding RNA moieties. The four envelopes were parameterized at a resolution of 3.5 nm using spherical harmonics and taking into account interface layers between the phases. The initial approximation for the envelopes of the subunits was taken from electron microscopic data presented recently by J. Frank and co-workers (Albany); the rRNA envelopes were initially approximated by spheres. The optimization and the refinement of the model proceeded by non-linear least squares minimization fitting the available experimental data. The refined envelopes of the subunits differ by about 10% from the starting approximation and the shape of the final 70 S model lies between the outer envelopes of the models by Frank and by M. von Heel & R. Brimacombe (Berlin). The rRNA moiety in the 30 S subunit is more anisometric than the subunit itself, whereas the rRNA of the 50 S subunit forms a compact core. The rRNAs protrude to the surfaces of the subunits and occupy approximately 30 to 40% of the corresponding surface areas. X-ray scattering curves of the two main functional elongation 70 S complexes (pre- and post-translocational) differ only marginally from those of the non-programmed ribosomes, suggesting that the low resolution four-phase model is also valid for the elongating 70 S ribosome.

Escherichia coli↗
PubMed1999

Erythromycin resistance mutations in ribosomal proteins L22 and L4 perturb the higher order structure of 23 S ribosomal RNA.

We have used chemical modification to examine the conformation of 23 S rRNA in Escherichia coli ribosomes bearing erythromycin resistance mutations in ribosomal proteins L22 and L4. Changes in reactivity to chemical probes were observed at several nucleotide positions scattered throughout 23 S rRNA. The L4 mutation affects the reactivity of G799 and U1255 in domain II and that of A2572 in domain V. The L22 mutation influences modification in domain II at positions m5U747, G748, and A1268, as well as at A1614 in domain III and G2351 in domain V. The reactivity of A789 is weakly enhanced by both the L22 and L4 mutations. None of these nucleotide positions has previously been associated with macrolide antibiotic resistance. Interestingly, neither of the ribosomal protein mutations produces any detectable effects at or within the vicinity of A2058 in domain V, the site most frequently shown to confer macrolide resistance when altered by methylation or mutation. Thus, while L22 and L4 bind primarily to domain I of 23 S rRNA, erythromycin resistance mutations in these ribosomal proteins perturb the conformation of residues in domains II, III and V and affect the action of antibiotics known to interact with nucleotide residues in the peptidyl transferase center of domain V. These results support the hypothesis that ribosomal proteins interact with rRNA at multiple sites to establish its functionally active three-dimensional structure, and suggest that these antibiotic resistance mutations act by perturbing the conformation of rRNA.

Drug Resistance, Microbial↗
PubMed1979

Assembly of ribosomal subunits affected in a ribosomal mutant of E. coli having an altered L22 protein.

In this article we describe some in vivo properties of a coldsensitive ribosomal mutant from Escherichia coli. The mutation affects the rplV gene which is the structural gene of ribosomal protein L22. Our work shows that at 22 degrees C, the biosynthesis of both ribosomal subunits and the maturation processing of 15S and 23S ribosomal RNA are impaired. Integration of our results in a general model of in vivo ribosomal assembly in E. coli is presented.

Cold Temperature↗
PubMed1977

Exchange of individual ribosomal proteins between ribosomes as studied by heavy isotope-transfer experiments.

Whether the individual ribosomal proteins undergo exchange between robosomes in vivo during cell growth was examined using heavy isotope transfer methodology. E. coli was grown first in a heavy isotope medium in the presence of [3H] leucine and then transferred to normal medium and allowed to grow for one generation in the presence of [14C] leucine. The "heavy" and "light" ribosomes that were present in such cells were separated by sedimentation and the ribosomal proteins resolved by two-dimensional gel electrophoresis. The individual proteins were burnt in O2 and their contents of [3H] and [14C] labels determined. From the analysis of the data we find that the great majority of the ribosomal proteins of E. coli does not undergo exchange during cell growth. Proteins which were found to exchange to varying levels in different transfer experiments were S1, S2, L7/L12, L9, L10 and L33. All of them except L9 exchanged to the same levels in control experiments in which separately grown heavy and light cells were mixed and processed. These proteins therefore undergo exchange during cell breakage and ribosome isolation. Protein L9 consistently showed appreciably greater exchange in transfer experiments as compared to the controls suggesting that it may exchange in vivo.

Bacterial Proteins↗
PubMed1986

The role of magnesium and potassium ions in the molecular mechanism of ribosome assembly: hydrodynamic, conformational, and thermal stability studies of 16 S RNA from Escherichia coli ribosomes.

In an attempt to understand the role of magnesium ion in ribosome assembly in vitro, the hydrodynamic shape, conformation, and thermal stability of ribosomal 16 S RNA were studied systematically as a function of Mg2+ concentration by sedimentation velocity, intrinsic viscosity, circular dichroism, and difference ultraviolet absorption spectroscopy. These results were then compared with the corresponding parameters obtained for 16 S RNA under the optimal conditions of reconstitution, i.e., at 37 degrees C, 20 mM Mg2+, an ionic strength equal to 0.37, and pH 7.8 [S. H. Allen, and K.-P. Wong (1978) J. Biol. Chem. 253, 8759-8766]. When the 360 mM KCl required for reconstitution of 30 S ribosomes is added to the medium, only subtle conformational changes are observed, consistent with the destabilization of the conformation, thus making the RNA molecule more "open" and accessible to protein binding. However, when the concentration of Mg2+ is lowered from 20 to 1 mM, the hydrodynamic parameters indicate that the 16 S RNA is partially unfolded, while thermal denaturation studies suggest that the amount of base-stacking and base-pairing is not concomitantly altered. Further removal of the Mg2+ by dialysis against a pH 7.8 buffer containing no Mg2+ results in a drastic decrease of secondary structure and indicates that the Mg2+ is required for maintenance of the pairing, stacking, and stability of the nucleotide bases, in addition to the long range interactions which result in a compact structure. The results suggest that the 20 mM Mg2+ is required for the 16 S RNA molecules to assume the proper secondary and tertiary structure containing the protein-binding sites, while the high K+ concentration (360 mM KCl) is needed for "loosening up" the RNA, making the protein binding sites more accessible to the ribosomal proteins for molecular recognition and binding as well as for the conformational changes that occur during ribosome assembly.

Circular Dichroism↗
PubMed1976

Free and membrane-bound ribosomes. VI. Distribution of free sulphydryl groups in rabbit reticulocyte ribosomes.

When free and membrane-bound ribosomes were titrated with N-ethyl[14C]-maleimide or 5,5'-dithio-bis(2-nitrobenzoic acid), 25 free SH groups were detected in polysomes, 10 in the 60 S subunit and 14 in the 40 S subunits. When individual ribosomal proteins were analysed, one large subunit protein L14 was found to be strongly labelled compared to the other ribosomal proteins, in polysomes, monosomes and subunits. However, two additional protein spots from the small subunit were more radioactive in monosomes and subunits than inpolysomes. In all these studies, it was found that the distribution of free SH groups in free and membrane-bound ribosomes was identical except for the few proteins which were reported before to be specific for free or membrane-bound ribosomes (Fehlmann, ., Bellemare, G. and Godin, C. (1975) Biochim. Biophys. Acta 378, 119-124 and Fehlmann, M., Bellemare, G. and Godin, C. (1975) FEBS Lett. 59, 8-12).

Animals↗
PubMed1979

The effect of magnesium starvation on the dissociation of ribosomal proteins from Escherichia coli K-12 ribosomes.

The effect of magnesium starvation upon the fate of individual ribosomal proteins was studied in Escherichia coli. During a 21 h incubation in the absence of Mg2+ the 30 S subunit was more susceptible to degradation, retaining an average 31.9% of its ribosomal proteins as compared to 40.0% for the 50 S subunit. An examination of those 50-S proteins dissociated to a lesser extent than the average value (L1, L2, L3, L7, L10, L13, L16, L17, L19, L21, L22, L23, and L29) revealed that, with the exception of L16, all were classified by Dohme and Nierhaus [5] as tightly bound. Of the ribosomal proteins dissocated during magnesium starvation only five were reincorporated (and these to a minimal degree) during recovery of cells in a medium containing Mg2+. These studies suggest that ribosomal proteins once released from the ribosome particles during magnesium starvation are not reutilized in the assembly of new subunits.

Bacterial Proteins↗
PubMed1984

Differences in physical and biological properties of 50S ribosomes and 23S RNAs derived from tight and loose couple 70S ribosomes.

Tight couple (TC) 50S ribosomes on treatment with kethoxal lose their capacity to associate with 30S ribosomes whereas loose couple (LC) 50S ribosomes on such treatment fully retain their association capacity. The same is true for 23S RNAs isolated from treated 50S ribosomes or isolated 23S RNAs directly treated with kethoxal, so far as their capacity to associate with 16S RNA is concerned. At certain Mg++ concentrations TC 23S RNA is highly susceptible to the nucleolytic action of single-strand specific enzyme RNase I; LC 23S RNA is quite resistant. The Mg++-dependencies of the two species of 23S RNAs for association with 16S RNA are also quite different. The fluorescence enhancement of ethidium bromide due to binding to TC 23S RNA is slightly less than LC 23S RNA. The hyperchromicity of LC 23S RNA due to thermal denaturation is somewhat more than TC 23S RNA. LC 23S RNA has slightly more elliptic CD spectrum than TC 23S RNA. These results clearly show that 23S RNAs present in TC and LC 50S ribosomes are distinct from each other. It has been recently demonstrated in this laboratory that they can be interconverted by the agents involved in translocation and thus appear to be conformomers.

Aldehydes↗
PubMed1991

Bilateral hydrophobic zipper as a hypothetical structure which binds acidic ribosomal protein family together on ribosomes in yeast Saccharomyces cerevisiae.

Acidic ribosomal protein family of yeast Saccharomyces cerevisiae consists of four species of 13-kDa proteins and one species of 38-kDa protein. These proteins are thought to form a complex on ribosomes functioning in the translational elongation reaction, but the structural basis how to associate with one another is not known. In this communication, we show for the first time the presence of a structure equivalent to the leucine zipper on a putative alpha-helix in the 38-kDa acidic ribosomal protein, A0. Then, all the 13-kDa acidic ribosomal proteins are shown to have two periodic arrays of hydrophobic amino acid residues arranged on the opposite sides of a putative alpha-helix, which is referred to as the "bilateral hydrophobic zipper". Therefore, it is proposed that one of the 13-kDa acidic ribosomal proteins associates with 38-kDa protein A0 via the hydrophobic zipper and then the other 13-kDa proteins associate side by side via the bilateral hydrophobic zippers.

Amino Acid Sequence↗
PubMed1992

Pseudouridine in the large-subunit (23 S-like) ribosomal RNA. The site of peptidyl transfer in the ribosome?

On evolutionary grounds, it has been advocated for more than 40 years that RNA generally, and more recently rRNA in particular, may participate, catalytically, in protein biosynthesis. A specific molecular mechanism has never been proposed. We suggest here that the N-1 position(s) in one or more of the approximately 4 pseudouridine (omega) residues in E. coli 23 S rRNA catalyzes transfer of the aminoacyl moiety from teh 3'-terminus of peptidyl tRNA in the P site to aminoacyl tRNA in the A site of the ribosome. Evidence that supports the proposal in the case of E. coli ribosomes, and relevant information pertaining to eukaryotic ribosomes, is summarized. Essential features of the evidence are that (i) the N-1 position in 1-acetylthymine (a direct analogue of 1-acetylpseudouridine) has an especially high potential for acyl-group transfer, comparable to that found for N-acetylimidazole (Spector, L.B. and Keller, E.B. (1958) J. Biol. Chem. 232, 185-192), (ii) most of the omega residues in prokaryotic 23 S rRNA are confined to the peptidyl transferase center in E. coli ribosomes, and (iii) Um-Gm-omega, the most densely modified sequence in eukaryotic 26 S rRNA, is universally conserved at a fixed site in the putative peptidyl transferase center of all eukaryotic ribosomes.

Animals↗
PubMed1992

Mechanism and site of action of a ribosome-inactivating protein type 1 from Dianthus barbatus which inactivates Escherichia coli ribosomes.

A single chain ribosome-inactivating protein with RNA N-glycosidase activity, here named Dianthin 29, was isolated from leaves of Dianthus barbatus L. Incubation of intact Escherichia coli ribosomes with Dianthin 29 and subsequent aniline treatment of the isolated rRNA releases a rRNA fragment of 243 nucleotides from 23 S rRNA. Nucleotide sequence studies showed that the site of N-glycosidic bond cleavage is at A-2660 within the universally conserved sequence 5'-AGUACGAGAGGA-3' near the 3'-end of 23/28 S rRNAs. To our knowledge, Dianthin 29 is the first ribosome-inactivating protein which is shown to inactivate intact prokaryotic ribosomes in the same manner as eukaryotic ribosomes.

Base Sequence↗
PubMed1985

Phosphorylation of ribosomal and ribosome-associated proteins in isoproterenol-induced cardiac hypertrophy.

Cardiac hypertrophy in adult rabbits was induced by subcutaneous injection of isoproterenol. The rate of [3H]leucine incorporation into acid insoluble material was increased and the extent of [32P]phosphate incorporation into several ribosomal proteins was altered. Specifically, a ribosomal protein with a molecular weight of 32,000 from the 40S ribosomal subunit showed a five-fold increase in phosphate incorporation in the hypertrophic heart whereas a protein with a molecular weight of 28,000 from the 60S subunit showed a four-fold decrease. Phosphorylation of ribosome-associated proteins, which could be removed from ribosomes with 0.72 M KCl, was also changed in the hypertrophic hearts. Six major phosphoproteins (with molecular weights 62,000, 49,000, 36,000, 30,000, 20,000 and 12,000) were detected in both the normal and the hypertrophic hearts. Phosphorylation of the 62 K and the 49 K protein was increased by two- and three-fold, respectively, in the hypertrophic hearts, whereas phosphorylation of the 36 K and the 30 K protein decreased by two-fold. The level of phosphorylation of the 20 K and the 12 K protein was not significantly changed in hypertrophic hearts.

Animals↗
PubMed1984

Crosslinking of phenylalanyl-tRNA to the ribosomal A site via a photoaffinity probe attached to the 4-thiouridine residue is exclusively to ribosomal protein S19.

Phe-tRNA of Escherichia coli, specifically derivatized at the S4U8 position with the 9 A long p-azidophenacyl photoaffinity probe, can be crosslinked to 30 S ribosomal protein when the tRNA is placed at the ribosomal A site. This protein has now been identified by immunological methods. The protein-[3H]Phe-tRNA covalent complex, obtained by extraction with 6 M-urea, was reacted separately with each of the 21 purified antisera to 30 S ribosomal proteins. The double antibody technique was used. Anti-S19 was the only antiserum able to precipitate the radioactivity, and 66 to 81% of the added radioactivity could be precipitated. The same result was obtained with three different ribosome preparations, at low as well as high crosslinking yield, with dipeptidyl-tRNA in the A site as well as aminoacyl-tRNA, and when binding and crosslinking were performed at 20 mM-Mg2+ instead of at 5 mM. Therefore, when aminoacyl-tRNA or peptidyl-tRNA is in the ribosomal A site, position 8, which is always uridine or 4-thiouridine, must be within 9 A of protein S19.

Affinity Labels↗
PubMed1991

Recognition of the highly conserved GTPase center of 23 S ribosomal RNA by ribosomal protein L11 and the antibiotic thiostrepton.

The antibiotic thiostrepton, a thiazole-containing peptide, inhibits translation and ribosomal GTPase activity by binding directly to a limited and highly conserved region of the large subunit ribosomal RNA termed the GTPase center. We have previously used a filter binding assay to examine the binding of ribosomal protein L11 to a set of ribosomal RNA fragments encompassing the Escherichia coli GTPase center sequence. We show here that thiostrepton binding to the same RNA fragments can also be detected in a filter binding assay. Binding is relatively independent of monovalent salt concentration and temperature but requires a minimum Mg2+ concentration of about 0.5 mM. To help determine the RNA features recognized by L11 and thiostrepton, a set of over 40 RNA sequence variants was prepared which, taken together, change every nucleotide within the 1051 to 1108 recognition domain while preserving the known secondary structure of the RNA. Binding constants for L11 and thiostrepton interaction with these RNAs were measured. Only a small number of sequence variants had more than fivefold effects on L11 binding affinities, and most of these were clustered around a junction of helical segments. These same mutants had similar effects on thiostrepton binding, but more than half of the other sequence changes substantially reduced thiostrepton binding. On the basis of these data and chemical modification studies of this RNA domain in the literature, we propose that L11 makes few, if any, contacts with RNA bases, but recognizes the three-dimensional conformation of the RNA backbone. We also argue from the data that thiostrepton is probably sensitive to small changes in RNA conformation. The results are discussed in terms of a model in which conformational flexibility of the GTPase center RNA is functionally important during the ribosome elongation cycle.

Base Composition↗
PubMed1983

The spatial arrangement of the complex between eukaryotic initiation factor eIF-3 and 40 S ribosomal subunit. Cross-linking between factor and ribosomal proteins.

The binding site for eIF-3 on the small ribosomal subunit was studied (a) by use of a complex of eIF-3 and derived 40 S ribosomal subunit from rat liver, and (b) by use of native small ribosomal subunits from rabbit reticulocytes. After treatment of both complexes with dimethyl 4,7-dioxo-5,6-dihydroxy-3,8-diazadecanbisimidate ribosomal proteins S3a, S4, S6, S7, S8, S9, S10, S23/24 and S27 became covalently linked to eIF-3 and were isolated together with the factor by gradient centrifugation. The ribosomal proteins were identified by two-dimensional polyacrylamide gel electrophoresis after periodate cleavage of the link(s).

Animals↗
PubMed1983

The lasting ribosome alteration produced by virginiamycin M disappears upon removal of certain ribosomal proteins.

Transient incubation of bacterial ribosomes with virginiamycin M produces a lasting damage of 50 S ribosomal subunits, whereby the elongation of peptide chains is still blocked after removal of the antibiotic. To elucidate the mechanism of this inactivation, ribosomal proteins were stepwise removed from 50 S subunits previously incubated with virginiamycin M, and cores were submitted to three functional tests. Total removal of proteins L7, L8, L12 and L16, and partial removal of L6, L9, L10 and L11, resulted in a loss of the virginiamycin M-induced alteration. When the split protein fractions were added back to these cores, unaltered functional particles were obtained. The reconstituted subunits, on the other hand, proved fully sensitive to virginiamycin M in vitro as they underwent, upon transient contact with the antibiotic, an alteration comparable to that of native particles. It is concluded that the virginiamycin M-induced ribosome damage is due to the production of a stable conformational change of the 50 S subunit. These data parallel those of an accompanying paper (Cocito, C., Vanlinden, F. and Branlant, C. (1983) Biochim. Biophys. Acta 739, 158-163) showing the intactness of all rRNA species from ribosomes treated in vivo and in vitro with virginiamycin M.

Cell-Free System↗
PubMed1994

Direct shape determination of ribosomal proteins in solution and within the ribosome by means of neutron scattering.

Following the 'strategy of the glassy ribosome' single protonated ribosomal proteins (r-proteins) were reconstituted into deuterated 50S subunits of Escherichia coli. The deuteration of both rRNA and r-proteins were individually adjusted to such a degree that the ribosomal matrix appeared nearly homogeneous with respect to coherent neutron scattering and had a scattering density equivalent to a D2O solution of about 90%. Neutron scattering of ribosomal subunits was recorded in reconstitution buffer containing three different concentrations of D2O around 90% D2O (contrast variation). The signal-to-noise ratio achieved allowed us to make a direct determination of the radii of gyration of r-proteins within the 50S subunit and thus provides the first information relating to the shape of these proteins in situ. We present the radii of gyration of 11 r-proteins incorporated into 50S subunits and of 9 isolated r-proteins in solution. In addition, the data concerning the overall dimensions of the r-proteins we report on indicate that conformational changes of at least two individual r-proteins occur during the assembly process of the ribosome.

Escherichia coli↗