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PubMed1978

Non-ribosomal nucleotide sequences in 7-S RNA, the immediate precursor of 5.8-S ribosomal RNA in yeast.

The topography and the length of the non-ribosomal sequences present in 7-S RNA, the immediate precursor of 5.8-S ribosomal RNA, from the yeast Saccharomyces carlsbergensis were determined by analyzing the nucleotide sequences of the products obtained after complete digestion of 7-S RNA with RNase T1. The results show that 7-S RNA contains approximately 150 non-ribosomal nucleotides. The majority (90%) of the 7-S RNA molecules was found to have the same 5'-terminal pentadecanucleotide sequence as mature 5.8-S rRNA. The remaining 10% exhibited 5'-terminal sequences identical to those of 5.9-S RNA, which has the same primary structure as 5.8-S rRNA except for a slight extension at the 5' end [Rubin, G.M. (1974) Eur. J. Biochem. 41, 197--202]. These data show that the non-ribosomal nucleotides present in 7-S RNA are all located 3'-distal to the mature 5.8-S rRNA sequence. Moreover, it can be concluded that 5.9-S RNA is a stable rRNA rather than a precursor of 5.8-S rRNA. The 3'-terminal sequence of 5.8-S rRNA (U-C-A-U-U-UOH) is recovered in a much longer oligonucleotide in the T1 RNase digest of 7-S RNA having the sequence U-C-A-U-U-U-(C-C-U-U-C-U-C)-A-A-A-C-A-(U-U-C-U)-Gp. The sequences enclosed in brackets are likely to be correct but could not be established with absolute certainty. The arrow indicates the bond cleaved during processing. The octanucleotide sequence -A-A-A-C-A-U-U-C- located near the cleavage site shows a remarkable similarity to the 5'-terminal octanucleotide sequence of 7-S RNA (-A-A-A-C-U-U-U-C-). We suggest that these sequences may be involved in determining the specificity of the cleavages resulting in the formation of the two termini of 5.8-S rRNA.

Base Sequence↗
PubMed1978

Stimulation of enzymatic phe-tRNA binding to mammalian ribosomes by thallium ions at concentrations blocking other ribosomal functions.

Thallium acetate (TIOAc) effectively stimulates poly(U)-directed Phe-tRNA binding to mouse ascitic tumour ribosomes under conditions when other ribosomal functions are completely blocked. The TI+ optimum is about 200 mM. The reaction is stimulated by EF-1, but not significantly by GTP. EF-1-dependent ribosomal GTPase is inhibited by T1+. The isolated Phe-tRNA . ribosome complex is relatively stable. The bound Phe-tRNA does not react with puromycin in the presence of 175 mM KCl. The complex formed in the presence of 90-100 mM TlOAc can, after isolation, be directly utilized for polyphenylalanine synthesis. The complex formed at 200 mM TlOAc is less active, apparently because of damage to the 60-S subunits. TlOAc at low concentrations (8 mM) stimulates K+ -containing poly(U)-translating systems, probably by stabilizing the translation complex.

Animals↗
PubMed1978

Binding of labeled initiation factor IF-1 to ribosomal particles and the relationship to the mode of IF-1 action in ribosome dissociation.

The binding of labeled initiation factor IF-1 to ribosomal particles has been studied in relation to the mode of action of this factor in the dissociation of 70-S ribosomes. It is demonstrated that IF-1 interacts specifically with active 70-S tight couples and free 30-S subunits. The binding of IF-1 to both 70-S and 30-S particles is not influenced by the Mg2+ concentration and the affinity of the factor for both particles is about the same. The interaction of IF-1 with these particles is highest at low Tris-HCl concentrations. Under these conditions IF-1 shows a slight dissociating activity. Using 3H-labeled IF-1 and 14C-labeled IF-3 the formation of a 30-S-subunit.IF-1 . IF-3 complex from 70-S ribosomes is demonstrated. Our studies show that IF-3 enhances the binding of IF-1 to the 30-S subunit. In contrast to IF-1, which binds about equally well to 70-S and 30-S particles in the absence of IF-3, 14C-labeled IF-3 binds predominantly to the 30-S subunit. This finding confirms the view that IF-3 acts as an anti-association factor. On the other hand, IF-1 enhances the supply of 30-S subunits in the presence of IF-3 by acting on the 30-S moiety of the 70-S ribosome.

Escherichia coli↗
PubMed1972

Delayed hypersensitivity reactions provoked by ribosomes from acid-fast bacilli. I. Ribosomal isolation, characterization, delayed hypersensitivity, and specificity.

Ribosomes and ribosomal subunits of Mycobacterium bovis (strain BCG) and M. smegmatis have been isolated and employed as skin test antigens in guinea pigs sensitized with homologous or heterologous organisms. Ribosomes and ribosomal subunits were found to be potent antigens for skin test purposes, and the 30S subunits were found to be more specific and active than the 50S subunits.

Animals↗
PubMed1983

A pair of Bacillus subtilis ribosomal protein genes mapping outside the principal ribosomal protein cluster.

Before now, the only ribosomal protein gene loci to be identified in Bacillus subtilis map within the principal ribosomal protein gene cluster at about 10 degrees on the linkage map. Using mutants with alterations in large subunit ribosomal proteins L20 or L24, I mapped the corresponding genes near leuA at approximately 240 degrees. The data were fully consistent with the fact that the genes for the two proteins were close together but not near any other ribosomal protein genes, as is also the case with the genes for the corresponding proteins of Escherichia coli.

Bacillus subtilis↗
PubMed1989

Internal entry of ribosomes and ribosomal scanning involved in hepatitis B virus P gene expression.

The recent demonstration that the synthesis of duck hepatitis B virus (HBV) reverse transcriptase does not require translational frameshifting and the finding that poliovirus mRNA translation occurs in a cap-independent manner by internal binding of ribosomes in the 5' noncoding region led us to design experiments to test the hypothesis of internal entry of ribosomes on C gene mRNA for HBV P gene expression. We show that in human cells, translation can be initiated at the first AUG of the HBV P gene by entry of ribosomes in a region located upstream of the P gene. Moreover, the leaky scanning of ribosomes observed on the first AUG of the HBV P gene could be responsible for the synthesis of the two forms of reverse transcriptase described for HBV particles.

Amino Acid Sequence↗
PubMed1994

Sensitivity of translation by Brevibacterium lactofermentum ribosomes to type 1 and type 2 ribosome-inactivating proteins.

An active cell-free translation system was prepared from Brevibacterium lactofermentum, a Gram-positive bacteria used in molecular cloning and protein expression. The system contained high speed postribosomal supernatant (S 370), purified ribosomes and a tRNA mixture from Escherichia coli, and synthesized polyuridylic acid-directed polyphenylalanine once optimized for mono and divalent ions, time, and temperature. The translation system was evaluated for sensitivity to several translational inhibitors including several N-glycosidase ribosome-inactivating proteins (RIPs) isolated from plants. The pattern of inhibition by RIPs resembled that observed recently for Gram-negative bacteria such as Escherichia coli and Agrobacterium tumefaciens [Girbés et al., J. Bacteriol., 175, 6721-6724 (1993)]. A typical inhibitory type 1 RIP such as crotin 2 promoted depurination of the rRNA, which upon treatment with acid aniline released a fragment of approximately 230 nucleotides. On these grounds, we propose that bacterial ribosome sensitivity to plant RIPs depends on the bacterial ribosome-specific presence of protein recognition domains in the RIP present only in some RIP but not in others.

Base Sequence↗
PubMedDate not supplied

[Ribosomal protein binding with the first intron of the human ribosomal protein S26 pre-mRNA stimulates its interaction with proteins extracted from Hela cells].

As shown by nitrocellulose filtration assays with RNA fragments transcribed from various regions of the human ribosomal protein (rp) S26 gene, proteins of the 40S ribosome subunit bind to the first intron of the rpS26 pre-mRNA. The binding involved mostly S23, S26 and, to a lesser extent, S13/16. Negligible binding was observed for S2/3a, S6, S8, S10, S11, and S20. Small-subunit proteins did not affect the efficiency of in vitro splicing of a pre-mRNA fragment corresponding to the first intron, second exon, second intron, and a part of the third exon of the rpS26 gene. However, ribosomal proteins substantially increased UV-induced adduction of the pre-mRNA fragments with nuclear extract proteins of HeLa cells. The same set of HeLa proteins was observed with each pre-mRNA fragment. Ribosomal proteins formed adducts only in the absence of HeLa proteins.

Cell Extracts↗
PubMed1991

Primary structure of rat ribosomal protein S2. A ribosomal protein with arginine-glycine tandem repeats and RGGF motifs that are associated with nucleolar localization and binding to ribonucleic acids.

The amino acid sequence of the rat 40 S ribosomal subunit protein S2 was deduced from the sequence of nucleotides in two recombinant cDNAs and confirmed from the amino acid sequence of a cyanogen bromide peptide obtained from the protein. Ribosomal protein S2 has 293 amino acids and has a molecular weight of 31,211. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 23-28 copies of the S2 gene. The mRNA for the protein is about 1,000 nucleotides in length. The highly conserved repetitive mammalian gene family designated LLRep3, but not identified before, encodes ribosomal protein S2. Rat S2 is related to Saccharomyces cerevisiae S4, Methanococcus vannielii S5, Escherichia coli S5, and other members of the prokaryotic S5 family. S. cerevisiae S4 and E. coli S5 are involved in the binding of aminoacyl-tRNA to ribosomes and in conditioning the fidelity of translation; it is plausible to assume that rat S2 serves similar functions. The NH2-terminal region of S2 is rich in arginine-glycine repeats including eight that occur in tandem and has two consecutive copies of the motif RGGF; these sequences have been associated with nucleolar localization and binding to RNA.

Amino Acid Sequence↗
PubMed1984

Ribosomal subunit antiassociation activity in rabbit reticulocyte lysates. Evidence for a low molecular weight ribosomal subunit antiassociation protein factor (Mr = 25,000).

A ribosomal subunit antiassociation activity has been purified from both the postribosomal supernatant and ribosomal salt-wash protein fractions of rabbit reticulocyte lysates. A majority (greater than 90%) of the activity is associated with a low molecular weight protein of Mr of approximately 25,000. A small but significant level of antiassociation activity (less than 10%) was found to be associated with higher molecular weight protein fractions. The purified 25,000-dalton antiassociation factor interacts with 60 S ribosomal subunits to prevent them from reassociating with 40 S ribosomal subunits. The factor does not seem to interact directly with 40 S subunits nor does it dissociate 80 S monosomes. The properties of this factor are thus similar to the eukaryotic initiation factor 6 isolated from both wheat germ and calf liver extracts.

Animals↗
PubMed1995

Effects and molecular action of ribosome-inactivating proteins on ribosomes from Streptomyces lividans.

The effects of 29 type 1 and 2 type 2 ribosome-inactivating proteins (RIPs) from plants on polyuridylic acid-directed polyphenylalanine synthesis carried out by purified ribosomes from Streptomyces lividans were studied. Only dianthin 32, saporins R1 and R3, momordin I, trichokirin, Hura crepitans RIP 5 from latex, crotins 2 and 3, and PAPs C, R, and S, inhibited polyphenylalanine synthesis. Both the type 2 RIPs ricin and volkensin were ineffective on translation. The magnesium concentration affected the inhibition of translation to a considerable extent. Upon treatment with inhibitory RIPs, extraction of rRNA and further treatment with acid aniline, S. lividans ribosomes released an RNA fragment of about 130 nucleotides. The 5' terminal sequence of this rRNA fragment was 5'-GAGGACCGGGACGGACGAACCUCUGGUGUGCCAGUUGU-3', similar to the sequence obtained in Escherichia coli. This indicates that the most probable molecular action of these RIPs on S. lividans and E. coli ribosomes is the same: depurination of the rRNA at a site relevant to the translation mechanism and that has been highly conserved throughout evolution.

Base Sequence↗
PubMed1975

The ribosomal proteins of drosophila melanogaster. IV. Characterization by two-dimensional gel electrophoresis of the ribosomal proteins from nine postembryonic developmental stages.

The ribosomal proteins from nine postembryonic developmental stages of Drosophila melanogaster were analyzed by two-dimensional gel electrophoresis. The ribosomal protein patterns thus obtained constitute reliable control patterns against which any potential mutant can be compared. Furthermore, the results provide increased evidence for a qualitative and quantitative change in the protein composition of the total population of ribosomes which occurs mainly during the third larval instar. Two acidic proteins were found, which may be homologous with rat liver ribosomal proteins L40/L41 and E. coli proteins L7/L12.

Animals↗
PubMed1996

Ribosome-initiator tRNA complex as an intermediate in translation initiation in Escherichia coli revealed by use of mutant initiator tRNAs and specialized ribosomes.

For functional studies of mutant Escherichia coli initiator tRNAs in vivo, we previously described a strategy based on the use of tRNA genes carrying an anticodon sequence change from CAU to CUA along with a mutant chloramphenicol acetyltransferase (CAT) gene carrying an initiation codon change from AUG to UAG. Surprisingly, under conditions where the mutant initiator tRNA is optimally active, the CAT gene with the UAG initiation codon produced more CAT protein (3- to 9-fold more depending on the conditions) than the wild-type CAT gene. Here we show that two new mutant CAT genes having GUC and AUC initiation codons also produce more of the CAT protein in the presence of the corresponding mutant initiator tRNAs. These results are most easily understood if assembly of the 30S ribosome-initiator tRNA-mRNA initiation complex in vivo proceeds with the 30S ribosome binding first to the initiator tRNA and then to the mRNA. In cells overproducing the mutant initiator tRNAs, most ribosomes would carry the mutant initiator tRNA and these ribosomes would select the mutant CAT mRNA over the other mRNAs.

Acylation↗
PubMed1988

The binding site for ribosomal protein L2 within 23S ribosomal RNA of Escherichia coli.

Ribosomal protein L2 from Escherichia coli binds to and protects from nuclease digestion a substantial portion of 'domain IV' of 23S rRNA. In particular, oligonucleotides derived from the sequence 1757-1935 were isolated and shown to rebind specifically to protein L2 in vitro. Other L2-protected oligonucleotides, also derived from domain IV (i.e. from residues 1955-2010) did not rebind to protein L2 in vitro nor did others derived from domain I. Given that protein L2 is widely believed to be located in the peptidyl transferase centre of the 50S ribosomal subunit, these data suggest that domain IV of 23S rRNA is also present in that active site of the ribosomal enzyme.

Base Sequence↗
PubMed1984

Interaction of ribosomal proteins S6, S8, S15 and S18 with the central domain of 16 S ribosomal RNA from Escherichia coli.

The co-operative interaction of 30 S ribosomal subunit proteins S6, S8, S15 and S18 with 16 S ribosomal RNA from Escherichia coli was studied by (1) determining how the binding of each protein is influenced by the others and (2) characterizing a series of protein-rRNA fragment complexes. Whereas S8 and S15 are known to associate independently with the 16 S rRNA, binding of S18 depended upon S8 and S15, and binding of S6 was found to require S8, S15 and S18. Ribonucleoprotein (RNP) fragments were derived from the S8-, S8/S15- and S6/S8/S15/S18-16 S rRNA complexes by partial RNase hydrolysis and isolated by electrophoresis through Mg2+-containing polyacrylamide gels or by centrifugation through sucrose gradients. Identification of the proteins associated with each RNP by gel electrophoresis in the presence of sodium dodecyl sulfate demonstrated the presence of S8, S8 + S15 and S6 + S8 + S15 + S18 in the corresponding fragment complexes. Analysis of the rRNA components of the RNP particles confirmed that S8 was bound to nucleotides 583 to 605 and 624 to 653, and that S8 and S15 were associated with nucleotides 583 to 605, 624 to 672 and 733 to 757. Proteins S6, S8, S15 and S18 were shown to protect nucleotides 563 to 605, 624 to 680, 702 to 770, 818 to 839 and 844 to 891, which span the entire central domain of the 16 S rRNA molecule (nucleotides 560 to 890). The binding site for each protein contains helical elements as well as single-stranded internal loops ranging in size from a single bulged nucleotide to 20 bases. Three terminal loops and one stem-loop structure within the central domain of the 16 S rRNA were not protected in the four-protein complex. Interestingly, bases within or very close to these unprotected regions have been shown to be accessible to chemical and enzymatic probes in 30 S subunits but not in 70 S ribosomes. Furthermore, nucleotides adjacent to one of the unprotected loops have been cross-linked to a region near the 3' end of 16 S rRNA. Our observations and those of others suggest that the bases in this domain that are not sequestered by interactions with S6, S8, S15 or S18 play a role involved in subunit association or in tertiary interactions between portions of the rRNA chain that are distant from one-another in the primary structure.(ABSTRACT TRUNCATED AT 400 WORDS)

Base Sequence↗
PubMed1987

Higher-order structure of domain III in Escherichia coli 16S ribosomal RNA, 30S subunit and 70S ribosome.

We have investigated in detail the conformation of domain III of 16S rRNA (nucleotides 913-1408), using a variety of chemical and enzymatic structure probes. The sites of reaction were identified by primer extension with reverse transcriptase using appropriate oligodeoxyribonucleotide primers. This study has been done on 16S rRNA in its naked form, in the 30S subunit and in the 70S ribosome. Data obtained with naked RNA broadly confirm the secondary structure model proposed essentially by comparative sequence analysis, and allow identification of nucleotides involved in tertiary interactions. Our results are in reasonably good agreement with structure probing experiments of Moazed et al. [1]. However, several discrepancies have been observed. Within the 30S subunit, a high number of nucleotides become unreactive whereas other nucleotides show an enhanced reactivity. This probably reflects local conformational changes. Interestingly, they are located in strategic regions of the RNA, e.g. around C1400 (involved in tRNA binding) and C1192 (involved in spectinomycin recognition). Results are also discussed together with the topographical localization of the ribosomal proteins in this area. The study on the 70S particle allows identification of regions at the interface of subunits or exposed at the surface of the ribosome.

Base Sequence↗
PubMed1992

Comparison of electrophoretic distribution patterns of ribosomal RNA gene restriction fragments and of ribosomal subunit proteins of Lactococci, Streptococci, and Pediococci.

Comparison of electrophoretic distribution patterns of ribosomal RNA gene restriction fragments and of ribosomal subunit proteins are equally effective procedures for detecting differences and similarities in the Lactococci, Streptococci and Pediococci examined. Electrophoretic distribution patterns of ribosomal subunit proteins may be a useful tool in taxonomic studies.

DNA, Ribosomal↗