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PubMed1980

The modification of the peptidyltransferase activity of 50-S ribosomal subunits, LiCl-split proteins and L16 ribosomal protein by pyridoxal phosphate.

Pyridoxal phosphate photoinactivates the peptidyltransferase activity of 50-S ribosomal subunits, LiCl split proteins and protein L16. Ethyromycin exhibits significant protection. These results, taken together with earlier reports, indicate the involvement of the single histidine of L16 in peptidyltransferase activity. The adjacent association in L16 of histidine and lysine indicates that pyridoxal phosphate should represent a selective inhibitor of peptidyltransferase activity.

Acyltransferases↗
PubMed1985

The mode of action of restrictocin and mitogillin on eukaryotic ribosomes. Inhibition of brain protein synthesis, cleavage and sequence of the ribosomal RNA fragment.

The relationship between the process of rat brain protein synthesis inhibition by restrictocin and mitogillin and the induction of a specific cleavage in 28S rRNA has been examined. Restrictocin or mitogillin at a concentration of 6 nM inhibits protein synthesis to a level of 80%. The inhibition induced by 6 nM alpha-sarcin is of the same order, indicating that those molecules all catalytically inhibit protein synthesis. When restrictocin or mitogillin was reduced and alkylated, a 100-fold higher concentration of these chemically modified molecules was needed in order to obtain the same inhibition as with native molecules, suggesting a close correlation between activity and configuration of the inhibitors. The inhibitory activity of restrictocin or mitogillin was completely lost after oxidation with performic acid. The inhibition of protein synthesis was always correlated with the production of a fragment from the 3'-end of the 28S rRNA. This rRNA fragment had the same electrophoretic mobility as that produced by alpha-sarcin. The 5'-end sequence of the rRNA fragment produced by restrictocin, mitogillin or alpha-sarcin is AGGAA, demonstrating that restrictocin and mitogillin inhibit protein synthesis in the same way as does alpha-sarcin. The conservation of this region of the rRNA from archaebacteria to eukaryotic ribosomes indicates its importance in the elongation process.

Alkylation↗
PubMed1985

Location of the binding region for 23S ribosomal RNA on ribosomal protein L2 from Bacillus stearothermophilus.

Tryptic and chymotryptic digestions of a complex between ribosomal protein L2 and the 23S RNA of Bacillus stearothermophilus produced two protected fragments (designated TF and CF). These protein fragments remained tightly bound to the RNA and were able to rebind specifically to 23S RNA. Amino acid sequence analysis of the isolated fragments revealed that both fragments TF and CF originated from the central half of the protein L2 (positions 60-206 and 58-201) with molecular masses of 15918 Da and 15690 Da respectively. From these results it is concluded that the protected central half is the primary RNA-binding region of the protein L2. A combination of these and other results suggests that the N and/or C-terminal (but not the central) regions may be involved in the peptidyltransferase activity of the 50S subunit.

Amino Acids↗
PubMed1986

Cross-linking between 16S ribosomal RNA and protein S4 in Escherichia coli ribosomal 30S subunits effected by treatment with bisulfite/hydrazine and bromopyruvate.

Cytosine in nucleic acids can be modified by treatment with a mixture of bisulfite and hydrazine. The reaction is specific for single-stranded regions of nucleic acids and the product is N4-aminocytosine. Bromopyruvate has been used for alkylation of protein SH groups and through its 2-oxo group it can form a hydrazone with N4-aminocytosine. Escherichia coli ribosomal 30S subunits were treated with 1 M sodium bisulfite + 2 M hydrazine in the presence of 10 mM MgCl2 at pH 7.0 and 37 degrees C for 30 min. By this treatment, 2.4 cytosine residues/molecule 16S rRNA were derivatized into N4-aminocytosines. 35S-labeled 30S subunits were modified in this way and then treated with 10 mM bromopyruvate at pH 8.0 and 37 degrees C for 5 min. Analysis in sodium dodecyl sulfate/sucrose density gradient centrifugation showed co-sedimentation of a part of the 35S radioactivity with the RNA. The co-sedimentation was dependent on both the bisulfite/hydrazine and the bromopyruvate treatments. The RNA-protein complex was prepared from unlabeled 30S subunits. The protein portion was labeled with 125I, the RNA portion was digested with nucleases, and then the hydrazone linkage between the protein and oligonucleotides was cleaved by treatment with 0.2 M HCl. The oligonucleotides formed were removed by dialysis and the protein was identified as S4 by two-dimensional electrophoresis and by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. The results indicate that the cysteinyl residue of protein S4 at position 31 from the N-terminus is located close to a cytosine residue which is non-base-paired and easily accessible by the externally present bisulfite/hydrazine reagent.

Electrophoresis, Polyacrylamide Gel↗
PubMed2006

Combined use of 16S ribosomal DNA and automated ribosomal intergenic spacer analysis to study the bacterial community in catfish ponds.

AIMS: To apply culture-independent techniques to explore the bacterial community composition in catfish pond water. METHODS AND RESULTS: 16S rDNA libraries were constructed and sequenced from 15 pond water samples. Automated ribosomal intergenic spacer analysis (ARISA) was used to fingerprint each bacterial community. A broad diversity in bacterial species composition was found by 16S rDNA analysis. Alphaproteobacteria was the most represented class in all ponds, followed by Gammaproteobacteria and Gram-positive high G + C content bacteria. Uniqueness of bacterial communities from each individual pond was confirmed by ARISA. Catfish pathogens were detected sporadically. CONCLUSIONS: Bacterial communities in a catfish aquaculture setting can vary from pond to pond at one given point. No correlation could be made between bacteria composition and fish strain or between bacterial profile and the presence of catfish pathogens in a particular pond. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report showing the composition of bacterial communities in catfish ponds. Fish health specialists and catfish aquaculture managers should be aware of the wide differences in bacterial communities between ponds and include this variable in fish husbandry practices.

Animals↗
PubMed1982

Ribosomal DNA of Leishmania brasiliensis: number of ribosomal copies and gene isolation.

The DNA content of the hemoflagellate Leishmania brasiliensis, strain Y, has been determined by colorimetric reactions and found to be nearly 0.226 pg/cell. When this DNA is bound to filters and hybridized with labeled rRNA from the same organism, saturation is reached at 0.47% of the DNA, corresponding to an estimated 160 ribosomal gene copies. When the DNA is sheared and centrifuged to equilibrium in CsCl gradients, two major satellites of the main band (rho = 1.712 g/cm3) are observed: a heavy one (1.720 g/cm3), which hybridizes with labeled rRNA, and a light one (1.699 g/cm3) with the electron microscopic characteristics of the kinetoplast DNA network.

Animals↗
PubMed2001

Bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analyses and 16S ribosomal DNA sequencing.

We investigated the bacterial community structure in an aerated plug-flow lagoon treating pulp and paper mill effluent. For this investigation, we developed a composite method based on analyses of PCR amplicons containing the ribosomal intergenic spacer (RIS) and its flanking partial 16S rRNA gene. Community percent similarity was determined on the basis of RIS length polymorphism. A community succession was evident in the lagoon, indicated by a progressive community transition through seven sample locations. The most abrupt changes in community structure were associated with a temperature change from 39 to 35 degrees C and with increases in dissolved oxygen. The temporal differences in community structure, based on summer and winter samplings, were greater than the spatial differences during either season. Clone libraries of rDNA-RIS amplicons were constructed from each of three summer samples. Among 90 clones analyzed (30 clones from each sample), 56 phylotypes were distinguished by restriction fragment length polymorphism. Indices of phylotype richness, evenness, and diversity all increased in clone libraries from the beginning to the end of the lagoon. A representative clone of each phylotype was phylogenetically analyzed on the basis of its partial 16S rRNA gene sequence (ca. 450 bp). Phylogenetic analysis confirmed the increase in diversity and further indicated increasing richness of bacterial divisions. Pioneers in the community spatial succession appeared to include thermotolerant, microaerophilic methanol-oxidizing bacteria related to the genus Methylobacillus, as well as thermotolerant, microaerophilic nitrogen-fixing bacteria related to the genus Azospirillum.

Bacteria↗
PubMed1984

Two genes for ribosomal protein 51 of Saccharomyces cerevisiae complement and contribute to the ribosomes.

We cloned and sequenced the second gene coding for yeast ribosomal protein 51 (RP51B). When the DNA sequence of this gene was compared with the DNA sequence of RP51A (J.L. Teem and M. Rosbash, Proc. Natl. Acad. Sci. U.S.A. 80:4403--4407, 1983), the following conclusions emerged: both genes code for a protein of 135 amino acids; both open reading frames are interrupted by a single intron which occurs directly after the initiating methionine; the open reading frames are 96% homologous and code for the same protein with the exception of the carboxy-terminal amino acid; DNA sequence homology outside of the coding region is extremely limited. The cloned genes, in combination with the one-step gene disruption techniques of Rothstein (R. J. Rothstein, Methods Enzymol. 101:202-211, 1983), were used to generate haploid strains containing mutations in the RP51A or RP51B genes or in both. Strains missing a normal RP51A gene grew poorly (180-min generation time versus 130 min for the wild type), whereas strains carrying a mutant RP51B were relatively normal. Strains carrying mutations in the two genes grew extremely poorly (6 to 9 h), which led us to conclude that RP51A and RP51B were both expressed. The results of Northern blot and primer extension experiments indicate that strains with a wild-type copy of the RP51B gene and a mutant (or deleted) RP51A gene grow slowly because of an insufficient amount of RP51 mRNA. The growth defect was completely rescued with additional copies of RP51B. The data suggest that RP51A contributes more RP51 mRNA (and more RP51 protein) than does RP51B and that intergenic dosage compensation, sufficient to rescue the growth defect of strains missing a wild-type RP51A gene, does not take place.

Base Sequence↗
PubMed2001

5S ribosomal and U1 small nuclear RNA genes: a new linkage type in the genome of a crustacean that has three different tandemly repeated units containing 5S ribosomal DNA sequences.

We investigated the 5S ribosomal RNA (rRNA) genes of the isopod crustacean Asellus aquaticus. Using PCR amplification, three different tandemly repeated units containing 5S rDNA were identified. Two of the three sequences were cloned and sequenced. One of them was 1842 bp and presented a 5S rRNA gene and a U1 small nuclear RNA (snRNA) gene. This type of linkage had never been observed before. The other repeat consisted of 477 bp and contained only an incomplete 5S rRNA gene lacking the first eight nucleotides and a spacer sequence. The third sequence was 6553 bp long and contained a 5S rRNA gene and the four core histone genes. The PCR products were used as probes in fluorescent in situ hybridization (FISH) experiments to locate them on chromosomes of A. aquaticus. The possible evolutionary origin of the three repeated units is discussed.

Animals↗
PubMedDate not supplied

Ribosomal protein S1 and initiation factor IF3 do not promote the ribosomal binding of approximately 19-nucleotide-long mDNA and mRNA models.

A number of model mDNAs and mRNAs, about 19 nucleotides in length, were obtained by automated synthesis and T7 RNA polymerase directed transcription from synthetic DNA templates, respectively. These mDNAs and mRNAs had Shine-Dalgarno sequences that were four to eight nucleotides long and their sequence was similar to the R17 coat protein initiation site. The effect of S1 or initiation factors (IFs) on the rate and extent of ribosomal binding of these mDNAs and mRNAs was investigated by nitrocellulose filtration. No effect was detected, suggesting that the main function of S1 or IFs included neither the direct recognition or binding of short messengers to the 30S subunits, nor their rejection as "false" for possessing the wrong sugars or an insufficient length. A pulse-chase experiment with one of the mRNAs also showed that S1 or IF3 did not influence the exchange rate of mRNA bound to the 30S subunit.

Bacterial Proteins↗
PubMed2004

The first complete monogenean ribosomal RNA gene operon: sequence and secondary structure of the Gyrodactylus salaris Malmberg, 1957, large subunit ribosomal RNA gene.

The sequence of the Gyrodactylus salaris Malmberg, 1957, large subunit, or 28S, ribosomal RNA (rRNA) gene has been determined. This gene is the final portion of the Gyrodactylus rRNA gene operon to be sequenced and results in the first complete sequence of all rRNA genes and spacers from a monogenean. The nucleotide sequence was used to predict the secondary structure of the large subunit rRNA, and regions of conserved and variable sequence and structure were identified. The site where the 5' terminus of the 5.8S rRNA binds to a region within the large subunit rRNA was predicted and complements the anticipated interaction of the 3' terminus of the 5.8S with the 5' terminus of the large subunit rRNA. The large subunit gene may be useful in phylogenetic analysis of the Monogenea or Platyhelminthes and comparisons with other eukaryotes. The variable domains C and H may be most suitable for this purpose.

Animals↗
PubMed2006

Molecular characterization of the recombinant A-chain of a type II ribosome-inactivating protein (RIP) from Viscum album coloratum and structural basis on its ribosome-inactivating activity and the sugar-binding properties of the B-chain.

Mistletoe (Viscum album) lectins, which are classified as a type II ribosome-inactivating protein (RIP) due to their unique biological function and the potential medical and therapeutic application in cancer cells, receive a rising attention. The heterodimeric glycoproteins contain the Achain with catalytic activity and the B-chain with sugar binding properties. In recent years, studies involving the lectins from the white berry European mistletoe (Viscum album) and the yellow berry Korean mistletoe (Viscum album coloratum) have been described. However, the detailed mechanism in exerting unique cytotoxic effect on cancer cells still remains unclear. Here, we aim to understand and define the molecular basis and biological effects of the type II RIPs, through the studies of the recombinant Korean mistletoe lectin. To this end, we expressed, purified the recombinant Korean mistletoe lectin (rKML), and investigated its molecular characteristics in vitro, its cytotoxicity and ability to induce apoptotic cell death in cancer cells. To gain structural basis for its catalytic activity and sugar binding properties, we performed homology modeling studies based on the high degree of sequence identity and conserved secondary structure prediction between Korean and European, Himalayan mistletoe lectins, and Ricin.

Amino Acid Sequence↗
PubMedDate not supplied

[Interactions of ribosomal protein L1 with ribosomal and messenger RNAs].

Crystal structures of unbound protein L1 and of its complexes with ribosomal an messenger RNAs are analyzed. It is shown that the values of the apparent association rate constant for L1-RNA depend on conformation of unbound protein L1. It is suggested that L1 binds to rRNA with higher affinity than to mRNA because of additional interactions between domain II of L1 and the loop rRNA region, which is absent in mRNA.

Archaeal Proteins↗
PubMed1991

Differential localization of two epitopes of Escherichia coli ribosomal protein L2 on the large ribosomal subunit by immune electron microscopy using monoclonal antibodies.

Two monoclonal antibodies (mAb), directed toward different epitopes of Escherichia coli ribosomal protein L2, have been used as probes in immune electron microscopy. mAb 5-186 recognizes an epitope within residues 5-186 of protein L2; it is seen to bind to 50 S subunits at or near the peptidyl transferase center, beside the subunit head on the L1 shoulder. mAb 187-272 recognizes an epitope within residues 187-272. This antibody binds to the face of the 50 S subunit, below the head and slightly toward the side with the stalk; this site is near the translocation domain. Both antibodies can bind simultaneously to single subunits. This indicates that protein L2 is elongated, reaching from the peptidyl transferase center to below the subunit head and approaching the translocational domain. The different locations of the two epitopes are consistent with previous biochemical results with the two antibodies (Nag, B., Tewari, D. S., Etchison, J. R., Sommer, A., and Traut, R. R. (1986) J. Biol. Chem. 261, 13892-13897).

Antibodies, Monoclonal↗
PubMedDate not supplied

[Changes in the content of ribosomal RNA and the activity of ribosomal RNAase in the brain under natural physiological conditions].

Optimal activity of RNAase from brain ribosomal fraction was observed at pH 5.4 and pH 7.9. After alimentary and conditioned-alimentary stimulation content of rRNA was significantly increased in brain, but the RNAase activity was decreased more than two-fold. After conditioned-alimentary inhibition content of rRNA was slightly decreased as compared to experiments with alimentary and conditioned-alimentary stimulation, but it was distinctly higher than in control. As compared with alimentary stimulation in the conditioned-alimentary stimulation the RNAase activity was increased at pH 5.4 and decreased at pH 7.9.

Animals↗
PubMed1978

[Topography of rRNA in ribosomes. Effect of pancreatic RNAse on small ribosomal subunits].

The treatment of E. coli 30S ribosome subunits with pancreatic RNase under certain conditions resulted in the release of rRNA (about 15%). The subunit retained as a whole structure: sedimentation coefficient was unchanged and no protein release was observed. The released RNA is a set of oligonucleotides from 1 to 9 bases, except hepta- and octanenucleotides. Base composition of this RNA fraction is similar to 16S RNA, a slight increase of purines content being due to the specificity of nuclease. Analysis of isoplit content has revealed that a spliting of long oligonucleotides in stechiometric amount from 30S subunits takes place: one nonanucleotide, one hexanucleotide and two pentanucleotides.

Escherichia coli↗
PubMed1981

The binding site for ribosomal protein L11 within 23 S ribosomal RNA of Escherichia coli.

Ribosomal protein L11 of Escherichia coli was bound to 23 S rRNA and the resultant complex was digested with ribonuclease T1. A single RNA fragment, protected by protein L11, was isolated from such digests and was shown to rebind specifically to protein L11. The nucleotide sequence of this RNA fragment was examined by two-dimensional fingerprinting of ribonuclease digests. It proved to be 61 residues long and the constituent oligonucleotides could be fitted perfectly between residues 1052 and 1112 of the nucleotide sequence of E. coli 23 S rRNA.

Bacterial Proteins↗
PubMed1983

RNA polymerase I-dependent selective transcription of yeast ribosomal DNA. Identification of a new cellular ribosomal RNA precursor.

Selective transcription of hybrid plasmids containing yeast rDNA was achieved with a template-dependent S100 fraction from whole cell extracts of Saccharomyces cerevisiae. A small region of the yeast rDNA which directs selective initiation in vitro was identified by subcloning. An initiation site was mapped within this region on the basis of the molecular weights of transcripts synthesized in vitro from templates which were cleaved with restriction endonucleases at a series of sites downstream from the site of initiation. The initiation site maps to a position 3.0 kilobase pairs upstream from the sequences which encode the 5' terminus of 18 S rRNA. In vitro initiation from this site is not inhibited by 50 micrograms/ml of alpha-amanitin and is completely abolished when the reactions contain 0.2 M (NH4)2SO4. Based on these data, selective transcription of yeast rDNA in vitro is RNA polymerase I-dependent. Several S1 nuclease-resistant hybrids are formed between DNA probes labeled at restriction endonuclease sites downstream from the in vitro initiation site and high molecular weight cellular RNA. The 5' terminus of the most abundant rRNA precursor maps approximately 0.7 kilobase pair upstream from sequences which encode the 5' terminus of 18 S rRNA. This corresponds to the 5' terminus of the 35 S rRNA precursor reported by others. The 5' terminus of the largest detectable precursor synthesized in vivo corresponds closely with the initiation site identified in vitro. Based on the data presented here, RNA polymerase I traverses the interspersed 5 S rRNA gene. Since these two ribosomal genes are transcribed in opposite directions, this arrangement of the RNA polymerase I and III promoters may ensure that equivalent amounts of the two gene products are synthesized in vivo.

Base Sequence↗