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At least 451 records · Page 25Linked to original sources
PubMed1983

Ribosomal protein L7/L12 cross-links to proteins in separate regions of the 50 S ribosomal subunit of Escherichia coli.

The 50 S ribosomal subunits from Escherichia coli were modified by reaction with 2-iminothiolane under conditions in which 65 sulfhydryl groups, about 2/protein, were added per subunit. Earlier work showed that protein L7/L12 was modified more extensively than the average but that nearly all 50 S proteins contained sulfhydryl groups. Mild oxidation led to the formation of disulfide protein-protein cross-links. These were fractionated by urea gel electrophoresis and then analyzed by diagonal gel electrophoresis. Cross-linked complexes containing two, three, and possibly four copies of L7/L12 were evident. Cross-links between L7/L12 and other ribosomal proteins were also formed. These proteins were identified as L5, L6, L10, L11, and, in lower yield, L9, L14, and L17. The yields of cross-links to L5, L6, L10, and L11 were comparable to the most abundant cross-links formed. Similar experiments were performed with 70 S ribosomes. Protein L7/L12 in 70 S ribosomes was cross-linked to proteins L6, L10, and L11. The strong L7/L12-L5 cross-link found in 50 S subunits was absent in 70 S ribosomes. No cross-links between 30 S proteins and L7/L12 were observed.

Bacterial Proteins↗
PubMed1983

[Role of the ribosomes in controlling cell differentiation and secondary metabolism in sporulating bacteria. II. The suppression of the phenotypic expression of ribosomal mutations (strA) as affected by RNA-polymerase mutations (rfm) in Bacillus subtilis].

Ribosomal mutants of Bacillus subtilis IG2 and IG7 resistant to 100 mkg/ml of streptomycin have been isolated. The strA80 and strA88 mutations reduce the level of sporulation as well as antibiotic and proteolytic activity of bacteria. RNA polymerase mutations rfm20 and rfm146 transferred by transformation into ribosomal mutants suppress strA80 and strA88 mutations. As a result, sporulation was restored. Both mutations were cotransformed with cysA gene and mapped within the cluster of ribosomal and RNA polymerase genes. It is proposed that the ribosomal strA80 and strA88 mutations influence transcription of gene (s) which regulate initiation of sporulation and that the RNA polymerase rfm20 and rfm146 mutations can restore sporulation. The results suggest that ribosomes are most likely to be not able to play a specific role in sporulation and secondary metabolism of Bac. subtilis.

Anti-Bacterial Agents↗
PubMed1982

Analysis of the Escherichia coli ribosome-ribosomal subunit equilibrium using pressure-induced dissociation.

Hydrostatic pressure can be used to perturb the ribosome-ribosomal subunit equilibrium. We have used glutaraldehyde fixation and subsequent sucrose gradient analysis to determine the equilibrium concentrations of Escherichia coli 70 S, 50 S, and 30 S particles at pressures from 1 to 1400 atm. This method is shown to be sufficiently rapid and free of interfering ribosomal aggregation artifacts when performed at Mg2+ concentrations below 8 mM. We show directly that the E. coli ribosome is in equilibrium with its subunits and that the pressure-sensitive reaction is appropriately described by the expression: In Kp = ln K0 + (P delta V/RT), where Kp and K0 are the equilibrium constants at pressure P and 1 atm, respectively, and delta V is the change in molecular volume that occurs during the reaction. The method provides values for K0 under different conditions, and the effects of Mg2+ ion can be readily ascertained. K0 and delta V were also estimated by a method of fitting computer-generated sucrose gradient profiles to experimental profiles. Determination of delta H0, delta S0, and delta V0 at 5 mM Mg2+ are presented. The results are discussed in the context of previous thermodynamic studies of the E. coli ribosome.

Escherichia coli↗
PubMedDate not supplied

[Studies on the mechanism of translocation in ribosomes. V. Comparison of the effect of antibiotic inhibitors of ribosomes on "enzymatic" and "non-enzymatic" translation].

A comparison of the effect of 11 antibiotic inhibitors of protein synthesis on "enzymatic" and para-chloromercuribenzoateactivated "non-enzymatic" translation was made. It was found that fusidic acid which inhibits protein synthesis by blocking the action of one of the elongation factors (EF-G) did not suppress functioning of the "non-enzymatic" system. On the contrary, all the antibiotics blocking different functional sites of the ribosome itself such as tetracycline, chloramphenicol, erythromycin, edeine, thiostreptone, viridogrisein, spectinomycin, streptomycin, kanamycin and neomycin, were shown to inhibit the "non-enzymatic" translation. The data obtained corroborate the idea that the molecular mechanism which the ribosome utilized during "non-enzymatic" translation are similar or identical to the mechanism of normal "enzymatic" translation. It was found that the "non-enzymatic" working ribosome is more sensitive to all the antibiotics as compared to the ribosome synthesizing peptide with the participation of elongation factors (EF-T and EF-G). This suggests that the elongation factors increase the level of general resistance of the working ribosome against very different hindrances.

Anti-Bacterial Agents↗
PubMed1993

A small novel chloroplast ribosomal protein (S31) that has no apparent counterpart in the E. coli ribosome.

Higher plant chloroplast ribosomes contain several novel protein components whose homologues are not present in the eubacterial E. coli ribosome, indicating a complex evolution of the chloroplast translational apparatus following the endosymbiotic event. Here we describe the isolation and characterization of a new small protein from spinach chloroplast ribosome which has, based on the amino acid sequence and immunological data, no counterpart in the E. coli ribosome. We suggest a nomenclature suitable for this protein and other novel proteins in the chloroplast ribosome.

Amino Acid Sequence↗
PubMed1996

Nucleotide-sugar binding to ribosomes. Comparison of affinity and capacity of gastric mucosa and liver ribosomes to sugar-nucleotides.

Highly purified ribosomes from gastric mucosa and liver were isolated and tested for their affinity and capacity toward UDP- monosaccharide binding. Ribosomes from both tissues bind UDP-N-acetylglucosamine nearly at the same level with similar affinity, but binding capacity of gastric ribosomes to UDP-N-acetylgalactosamine was twice higher than in case of liver ribosomes, and with higher affinity than in case of UDP-N-acetylglucosamine. The binding of UDP-N-acetylgalactosamine to mucosa ribosomes requires the whole sugar-nucleotide structure.

Acetylgalactosamine↗
PubMed1995

Contributions of multiple basic amino acids in the C-terminal region of yeast ribosomal protein L1 to 5 S rRNA binding and 60 S ribosome stability.

Previous studies suggest that the C-terminal region of ribosomal protein L1 from Saccharomyces cerevisiae is important for its interaction with the 5 S rRNA molecule. Within this region are several highly conserved basic amino acids including Lys276, Lys279, Lys289, Arg282, Arg285. To examine potential contributions of these amino acids to RNA-protein interaction and ribosomal assembly, effects of substitutions of these residues by methionine either individually or in combinations were examined. A methionine substitution of any one of the lysine residues did not significantly affect RNA binding in vitro. The mutant RNPs were as stable as the wild-type RNP. Yeast transformants expressing these mutant proteins grew at the same rate as the wild-type. However, mutant proteins containing substitutions of any two of these basic amino acids bound RNA weakly. The resultant RNPs were significantly less stable than the wild-type. Whereas cells expressing mutant L1 with a single substitution at 289 was not lethal, cells expressing mutant L1 with any double substitutions involving Lys289 as one of the substituted amino acids were lethal. These data suggest that Lys289 plays a key role in the binding of ribosomal protein L1 to 5 S rRNA. The other basic residues, particularly Arg282, and Arg285, in this region also contribute to RNA binding. These residues are predicted to locate on the same side of an alpha helix. We would like to propose a structural model for the yeast RNP that involves multiple contact sites located on one side of the helix in the C terminus of the protein and the 5 S rRNA. These basic amino acids also participate, directly or indirectly, in the interaction of the RNP complex with other components of the 60 S ribosomal subunit.

Amino Acid Sequence↗
PubMed1988

Alpha-sarcin cleaves ribosomal RNA at the alpha-sarcin site in the absence of ribosomal proteins.

alpha-Sarcin is capable of specifically cleaving the single phosphodiester bond in the "alpha-sarcin site" of both Escherichia coli and Saccharomyces cerevisiae large rRNAs in the absence of ribosomal proteins. With both sources of rRNA, the rate of cleavage was comparable with and without ribosomal proteins but more complete cleavage was observed in the absence of ribosomal proteins. These observations contrast with earlier findings and indicate that ribosomal proteins are not essential to the unique specificity of the cleavage of rRNA by alpha-sarcin.

Endoribonucleases↗
PubMed1987

Heat-shock-induced changes in the phosphorylation of ribosomal and ribosome-associated proteins in the filamentous fungus Achlya ambisexualis.

In the filamentous fungus Achlya ambisexualis, heat shock resulted in a rapid reduction in the rate of protein synthesis. This was accompanied by dephosphorylation of a prominent basic 30 kD protein associated with the small subunit of Achlya ribosomes and which may be analogous to ribosomal protein S6 of vertebrates. A large ribosomal subunit protein with a relative molecular weight (MW) of 24,500 exhibited increased phosphorylation during heat shock, while a second large subunit protein having a relative MW of 22,000 was dephosphorylated. Several proteins which could be dissociated from Achlya ribosomes by 0.5 M KCl also exhibited altered patterns of phosphorylation during heat shock. These KCl-soluble proteins included proteins at 50, 21, 20 and 19 kD, which exhibited decreased phosphorylation with heat shock and proteins at 32 and 23.5 kD, which exhibited increased phosphorylation with heat shock. Such alterations in the phosphorylation of components of the Achlya translational apparatus may be involved in the qualitative and quantitative changes in protein synthesis which are observed with heat shock in Achlya.

Fungi↗
PubMed1991

Single-chain ribosome inactivating proteins from plants depurinate Escherichia coli 23S ribosomal RNA.

The rRNA N-glycosidase activities of the catalytically active A chains of the heterodimeric ribosome inactivating proteins (RIPs) ricin and abrin, the single-chain RIPs dianthin 30, dianthin 32, and the leaf and seed forms of pokeweed antiviral protein (PAP) were assayed on E. coli ribosomes. All of the single-chain RIPs were active on E. coli ribosomes as judged by the release of a 243 nucleotide fragment from the 3' end of 23S rRNA following aniline treatment of the RNA. In contrast, E. coli ribosomes were refractory to the A chains of ricin and abrin. The position of the modification of 23S rRNA by dianthin 32 was determined by primer extension and found to be A2660, which lies in a sequence that is highly conserved in all species.

Abrin↗
PubMed2005

Ribosomal protein L10a, a bridge between trichosanthin and the ribosome.

Trichosanthin is a type I ribosome-inactivating protein with many pharmacological activities. The trichosanthin-coupled Sepharose affinity purification revealed a protein, which was identified by mass spectrometry as the ribosomal protein L10a. The interaction between trichosanthin and recombinant L10a was further confirmed by in vitro binding assay. Kinetic analysis by surface plasmon resonance technology revealed that L10a had a high affinity to trichosanthin with a K(D) of 7.78nM. The study with mutated forms of trichosanthin demonstrated that this specific association correlates with the ribosome-inactivating activity of trichosanthin. This finding might provide insight into the mechanisms by which trichosanthin inactivates ribosome and that underlies its pharmacological effect.

Chromatography, Affinity↗
PubMed2004

The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit.

The structures of ribosomal proteins and their interactions with RNA have been examined in the refined crystal structure of the Haloarcula marismortui large ribosomal subunit. The protein structures fall into six groups based on their topology. The 50S subunit proteins function primarily to stabilize inter-domain interactions that are necessary to maintain the subunit's structural integrity. An extraordinary variety of protein-RNA interactions is observed. Electrostatic interactions between numerous arginine and lysine residues, particularly those in tail extensions, and the phosphate groups of the RNA backbone mediate many protein-RNA contacts. Base recognition occurs via both the minor groove and widened major groove of RNA helices, as well as through hydrophobic binding pockets that capture bulged nucleotides and through insertion of amino acid residues into hydrophobic crevices in the RNA. Primary binding sites on contiguous RNA are identified for 20 of the 50S ribosomal proteins, which along with few large protein-protein interfaces, suggest the order of assembly for some proteins and that the protein extensions fold cooperatively with RNA. The structure supports the hypothesis of co-transcriptional assembly, centered around L24 in domain I. Finally, comparing the structures and locations of the 50S ribosomal proteins from H.marismortui and D.radiodurans revealed striking examples of molecular mimicry. These comparisons illustrate that identical RNA structures can be stabilized by unrelated proteins.

Animals↗
PubMed1997

Acetylation of ribosomal protein S5 affected by defects in the central pseudoknot in 16S ribosomal RNA?

We have analyzed the ribosomal protein profile of Escherichia coli 30S subunits with the mutation C18A in the central pseudoknot of their 16S ribosomal RNA. This mutation was shown to inhibit translational activity in vivo and to affect ribosome stability in vitro. The majority of the mutant 30S particles were present as free subunits in which a reproducible decrease in amount of proteins S1, S2, S18 and S21 was observed. The protein gels also showed the appearance of a satellite band next to S5. This band reacted with anti-S5 antibodies and had a slightly increased positive charge. The simplest interpretation of these findings, also considering published data, is that the satellite band is S5 with a non-acetylated N-terminal alanine. Underacetylation of S5 due to mutations in the 16S rRNA implies that the modification is performed on the ribosome.

Acetylation↗
PubMed1982

Preparation and characterization of fluorescent 50S ribosomes. Specific labeling of ribosomal proteins L7/L12 and L10 of Escherichia coli.

So that the topographic and dynamic properties of the L7/L12--L10 complex in the 50S ribosome of Escherichia coli could be studied, methods and reagents were developed in order to introduce fluorescent groups at specific positions of these proteins. In the case of L7/L12, this was done by attaching an aldehyde group to Lys-51 of the protein by using 4-(4-formylphenoxy)butyrimidate or by converting the amino terminus of L12 into an aldehyde group by periodate oxidation. Subsequent reaction of the aldehyde groups with newly developed hydrazine derivatives of fluorescein and coumarin resulted in specifically labeled L7/L12 derivatives. L10 was modified at the single cysteine residue with N-[7-(dimethylamino)-4-methylcoumarinyl]maleimide. The fluorescent proteins L10 and L7/L12 could be reconstituted into 50S ribosomes. The resulting specifically labeled 50S ribosomes show 25--100% activity in elongation factor G dependent GTPase as well as in polyphenylalanine synthesis. The fluorescent properties of the labeled 50S ribosomes show that these fluorescent derivatives are suitable for energy transfer studies.

Escherichia coli↗
PubMed1989

Labeling the peptidyltransferase center of the Escherichia coli ribosome with photoreactive tRNA(Phe) derivatives containing azidoadenosine at the 3' end of the acceptor arm: a model of the tRNA-ribosome complex.

Photoreactive derivatives of yeast tRNA(Phe) containing 2-azidoadenosine (2N3A) at position 73 or 76 have been crosslinked to the peptidyl site of Escherichia coli ribosomes. Covalent tRNA-ribosome attachment was dependent upon the replacement of adenosine by 2N3A in the tRNA, irradiation with 300-nm light, and the presence of poly(U). In all cases, the modified tRNAs became crosslinked exclusively to 50S ribosomal subunits. While the tRNA derivative containing 2N3A at position 73 labeled only protein L27, that containing 2N3A at position 76 labeled proteins L15, L16, and L27 as well as a segment of the 23S rRNA. The site of crosslinking in the rRNA was identified as guanosine-1945, which lies within a highly conserved sequence adjacent to a number of modified bases and has not until now been identified at the peptidyltransferase center. On the basis of these results, and previously reported crosslinks from tRNA containing 8-azidoadenosine in the 3'-terminal -A-C-C-A sequence [Wower, J., Hixson, S. S. & Zimmermann, R. A. (1988) Biochemistry 27, 8114-8121], we propose a model for the arrangement of tRNA molecules at the peptidyl and aminoacyl sites that is consistent with most of the information available about the location of the peptidyltransferase center and the decoding domain of the E. coli ribosome.

Acyltransferases↗
PubMed2001

Structural compensation for the deficit of rRNA with proteins in the mammalian mitochondrial ribosome. Systematic analysis of protein components of the large ribosomal subunit from mammalian mitochondria.

The mammalian mitochondrial ribosome (mitoribosome) is a highly protein-rich particle in which almost half of the rRNA contained in the bacterial ribosome is replaced with proteins. It is known that mitochondrial translation factors can function on both mitochondrial and Escherichia coli ribosomes, indicating that protein components in the mitoribosome compensate the reduced rRNA chain to make a bacteria-type ribosome. To elucidate the molecular basis of this compensation, we analyzed bovine mitoribosomal large subunit proteins; 31 proteins were identified including 15 newly identified proteins with their cDNA sequences from human and mouse. The results showed that the proteins with binding sites on rRNA shortened or lost in the mitoribosome were enlarged when compared with the E. coli counterparts; this suggests the structural compensation of the rRNA deficit by the enlarged proteins in the mitoribosome.

Amino Acid Sequence↗
PubMed1984

Basepairing of oligonucleotides to the 3' end of 16S ribosomal RNA is not stabilized by ribosomal proteins.

We have studied the binding of the octanucleotide (5'-3')d(AAGGAGGT) which is fully complementary to the 3' end of 16S ribosomal RNA, to ribosomes and to the isolated target sequence (5'-3') (ACCUCCUUA). The binding constant for 30S or 70S ribosomes is (5 +/- 2) X 10(7) mol-1, whereas the duplex containing the octa- and the nonanucleotide has an association constant of (6 +/- 3) X 10(7) mol-1. The two values are the same within the experimental error. This result suggests that basepairing at the 3' end of 16S rRNA is not stabilized by ribosomal proteins.

Base Composition↗
PubMed1988

Depletion of Saccharomyces cerevisiae ribosomal protein L16 causes a decrease in 60S ribosomal subunits and formation of half-mer polyribosomes.

We constructed yeast strains containing deletion-insertion null alleles of the RPL16A or RPL16B genes encoding the 60S ribosomal subunit protein L16 to determine the role of L16 in the synthesis and function of ribosomes. Strains lacking a functional RPL16A gene grow as rapidly as wild type, whereas those containing a null allele of RPL16B grow more slowly than wild type. RNA analysis using RPL16 probes revealed that both RPL16 genes are transcribed and that RPL16B transcripts accumulate to twice the level of RPL16A transcripts. No evidence was obtained for the occurrence of dosage compensation at the level of RPL16 mRNA accumulation in either mutant. Strains lacking both RPL16 genes are apparently inviable, demonstrating that L16 is an essential yeast ribosomal protein. Introduction of an extra copy of either RPL16 gene into rpl16b mutants restored wild-type growth rates, indicating that the two forms of the L16 protein are interchangeable. rpl16 mutants are deficient in 60S ribosomal subunits relative to 40S subunits. 43S preinitiation complexes accumulate in half-mer polyribosomes in the absence of sufficient 60S subunits. We postulate that the slow-growth phenotype of rpl16 mutants results from the perturbation of initiation of protein synthesis.

Fungal Proteins↗