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At least 19 recordsLinked to original sources
PubMed1975

Wheat-embryo ribonucleates. IV. Factors that influence the formation and stability of a complex between 5S rRNA and 18S rRNA.

Under the conditions used in this study, wheat-embryo 5S rRNA complexes with its homologous 18S rRNA from wheat embryos and with heterologous 18S rRNA from other eukaryotic source materials such as yeast, L cells, and HeLa cells, but it does not complex with heterologous 16S rRNA from a prokaryote such as Escherichia coli or with homologous or heterologous 26S (23S) rRNA of either eukaryotic or prokaryotic origin. If a solution of wheat-embryo rRNA is simply made 0.3 M with respect to NaCl and then heated at 60 degress C for 3 min before quick cooling to room temperature (ca. 20 degrees C), there is both preferential and efficient complex formation between 5S and 18S rRNA. The 'laboratory-prepared' complex between wheat-embryo 5S rRNA and its homologous 18S rRNA is more thermostable in 0.1 M NaCl solution than is the 'natural' complexes 'melt' over a narrow range of temperature. The possible physicochemical and physiological importance of both homologous and heterologous rRNA complexes is the subject of a brief discussion.

Binding Sites↗
PubMed1979

DNA sequences of promoter regions for rRNA operons rrnE and rrnA in E. coli.

The nucleotide sequences have been determined for the promoter regions of two ribosomal RNA operons, rrnA and rrnE, in E. coli. The sequences cover the two in vitro transcription start sites identified for each operon (Gilbert, der Boer and Nomura, 1979). The first two start sites are 283 and 291 bp preceding the mature 16S rRNA (m16S rNA) coding regions for rrnE and rrnA, respectively; the second start sites are 174 and 174 +/- 1 bp preceding the m16S rRNA coding regions for rrnE and rrnA, respectively. Each of these start sites has an identifiable "Pribnow box" sequence 6-7 bp upstream from the start site. The nucleotide sequences of the two operons have nearly complete homology from the m16S rRNA coding regions to positions 145 bp upstream from those regions, and at the regions surrounding the Pribnow boxes preceding the first start sites. The DNA sequences indicate that the RNAs transcribed from the first start sites of rrnE and rrnA are quite different in their first 150 nucleotides. These heterogeneous regions, however, precede the RNAse III cleavage sites (deduced previously by Young and Steitz, 1978), and the "precursor 16S rRNA" molecules are largely homogeneous. The nucleotide sequences of the promoter regions of the two rRNA operons are also compared with those or rrnD and rrnX, determined by Young and Steitz (1979), and some common features are discussed.

Base Sequence↗
PubMed1979

Identification of initiation sites for the in vitro transcription of rRNA operons rrnE and rrnA in E. coli.

The transcription initiation sites of E. coli rRNA operons were determined using various DNA fragments derived from transducing phage lambda metA20 carrying rrnE and from hybrid plasmid pLC19-3 carrying rrnA. In vitro transcription products were analyzed for their 5' end sequences and their oligonucleotide compositions. The results are in full agreement with the nuceotide sequences of the DNA templates described in an accompanying paper (de Boer, Gilbert and Nomura, 1979) and allow us to make the following conclusions. First, there are two transcription, start sites on each of the rRNA operons; they are 109 bp apart in the case of rrnE and 117 +/- 1 bp aprart in rrnA. Second, the first start site is 283 bp upstream from the m16S rRNA coding region in the case of rrnE, while is 291 bp upstream in rrnA. Initiation starts with ATP in both cases. Finally, the second start sites are 174 and 174 +/- 1 bp from the m16S rRNA genes in rrnE and rrnA, respectively. Initiation starts with CTP in both cases. We have also shown that in the present in vitro transcription system, guanosine tetraphosphate (ppGpp) inhibits the synthesis of full-sized RNAs from both start sites in each rRNA operon.

Base Sequence↗
PubMed1979

The intervening sequence in the 26S rRNA coding region of T. thermophila is transcribed within the largest stable precursor for rRNA.

We studied the transcription of the intervening sequence in the 26S rRNA coding region of the extrachromosomal rDNA molecules in the macronucleus of T. thermophila by hybridization of purified nuclear rRNA precursors or cytoplasmic 26S rRNA to purified native rDNA or specific rDNA restriction fragments. Examination of R loop hybrids in the electron microscope and analyses of S1-protected rDNA fragments in alkaline agarose gels showed that mature 26S rRNA, nuclear pre-26S rRNA and a fraction of the pre-rRNA molecules containing both the sequences for 17S and 26S rRNA all lack the region corresponding to the intervening sequence. The rest of the pre-rRNA molecules, however, hybridize in a colinear fashion to the whole coding region, and thus must contain the intervening sequence. We can conclude from these results that the intervening sequence is transcribed within the primary transcription product of the rDNA, and that the post-transcriptional removal of the intervening RNA sequence is a very early processing event in the organism.

Animals↗
PubMed1979

Intermolecular base-paired interaction between complementary sequences present near the 3' ends of 5S rRNA and 18S (16S) rRNA might be involved in the reversible association of ribosomal subunits.

Highly conserved sequences present at an identical position near the 3' ends of eukaryotic and prokaryotic 5S rRNAs are complementary to the 5' strand of the m2(6)A hairpin structure near the 3' ends of 18S rRNA and 16S rRNA, respectively. The extent of base-pairing and the calculated stabilities of the hybrids that can be constructed between 5S rRNAs and the small ribosomal subunit RNAs are greater than most, if not all, RNA-RNA interactions that have been implicated in protein synthesis. The existence of complementary sequences in 5S rRNA and small ribosomal subunit RNA, along with the previous observation that there is very efficient and selective hybridization in vitro between 5S and 18S rRNA, suggests that base-pairing between 5S rRNA in the large ribosomal subunit and 18S (16S) rRNA in the small ribosomal subunit might be involved in the reversible association of ribosomal subunits. Structural and functional evidence supporting this hypothesis is discussed.

Base Sequence↗
PubMed2025

Molecular phylogeny of some Carangid species from the Egyptian Red Sea using cytochrome c oxidase subunit I (COI) and small (12S rRNA) mitochondrial rRNA genes.

BACKGROUND: Study of five Carangid species to estimate the degree of genetic divergence and draw phylogenetic relationships by using cytochrome c oxidase subunit I (COI), and small (12S rRNA) mitochondrial rRNA genes. AIM: This investigation was designed to evaluate genetic relationships and association analyses in the taxonomy studies of Carangid fishes using mitochondrial sequences. METHODS: The present study analyzed sequence data using two genes to estimate the relationships among five species of the family Carangidae (ray-finned fish), such as Carangoides bajad (gold-spotted trevally), Carangoides malabaricus (Malabar trevally), Caranx melampygus (Bluefin trevally), Caranx sexfasciatus (Bigeye trevally), and Scomberoides lysan (doublespotted queenfish) and to assess the phylogenetic utility of these markers. RESULTS: The classification analysis of the family Carangidae is controversial. Our study was performed to examine the phylogenetic relationships among five Carangid species using 12S rRNA and COI genes, that illustrated certain Carangidae family genera are not monophyletic that does not include all the descendants of a common ancestor (Paraphyletic) refers to a taxonomic grouping that includes a common ancestor and some, but not all, of its descendants. This means that a paraphyletic group consists of the last common ancestor and excludes certain lineages that are part of the broader group, for example, in traditional taxonomy, the class of fish is considered paraphyletic because it does not include all descendants. The data reported here may be employed in study and analysis of the phylogenetic variety and relationships among species and genera of the family Carangidae. CONCLUSION: Our results confirmed the thermostability and environmental adaptation of the five species of the Carangidae family due to higher A+T content. Our results also confirmed the earlier conclusions of other authors that several genera of the Carangidae family are not monophyletic which does not include all the descendants of a common ancestor (Paraphyletic) and demonstrated the usefulness of the 12S rRNA gene and the COI gene in the phylogenetic analysis of the Carangid species.

RNA, Ribosomal↗
PubMed1976

Transfer RNA genes between 16S and 23S rRNA genes in rRNA transcription units of E. coli.

We have identified genes for tRNAGLU/2 on the transducing phages o80d3ilvsu7+ (see Ohtsubo et al., 1974) and lambdarifd18 (Kirschbaum and Konrad, 1973), and a gene for tRNAlle/1 on the transducing phage o80rifr (Konrad, Kirschbaum, and Austin, 1973). All these phages have previously been shown to carry genes for rRNA (Ohtsubo et al., 1974; Lindahl et al., 1975; Jaskunas et al., 1975a). We have analyzed the position of these tRNA genes by hybridizing purified RNAs to restriction fragments of the phage DNA. The tRNA genes are located inside the rRNA transcription unit in the spacer region between the 16S and 23S rRNA genes.

Chromosome Mapping↗
PubMed1978

Processing of rRNA by RNAase P: spacer tRNAs are linked to 16S rRNA in an RNAase P RNAase III mutant strain of E. coli.

To determine which enzymes are responsible for the processing cleavages of ribosomal RNA transcripts in Escherichia coli, we constructed a mutant strain lacking RNAase III and containing a thermolabile RNAase P. At the nonpermissive temperature, this strain accumulates a novel "19S" RNA species which contains 17S precursor rRNA sequences covalently linked to tRNA sequences transcribed from the ribosomal RNA spacer region between the 16S and the 23S rRNA cistrons. In vitro treatment of 19S RNA with cell extracts releases tRNA2Glu and other tRNA species. These "spacer" tRNA sequences are apparently not contained with the 18S RNA species found in an RNAase III- RNAase P+ cell. RNAase P-deficient extracts are incapable of cleaving space tRNA from 19S RNA, indicating that RNAase P is required for the release of spacer tRNAs from rRNA transcripts of E. coli cells.

Escherichia coli↗
PubMed1979

Homology of the 3' terminal sequences of the 18S rRNA of Bombyx mori and the 16S rRNA of Escherchia coli.

The terminal 220 base pairs (bp) of the gene for 18S rRNA and 18 bp of the adjoining spacer rDNA of the silkworm Bombyx mori have been sequenced. Comparison with the sequence of the 16S rRNA gene of Escherichia coli has shown that a region including 45 bp of the B. mori sequence at the 3' end is remarkably homologous with the 3' terminal E. coli sequence. Other homologies occur in the terminal regions of the 18S and 16S rRNAs, including a perfectly conserved stretch of 13 bp within a longer homology located 150--200 bp from the 3' termini. These homologies are the most extensive so far reported between prokaryotic and eukaryotic genomic DNA.

Animals↗
PubMed1979

Organization of tRNA and rRNA genes in N. crassa mitochondria: intervening sequence in the large rRNA gene and strand distribution of the RNA genes.

Through analysis of cloned fragments of N. crassa mitochondrial DNA, we have derived a physical map for the region of the mitochondrial genome which encodes the ribosomal RNAs and most of the tRNAs. We have located RNA genes on this map by hybridization of purified 32P end-labeled RNA probes, and our findings are as follows. First, the gene for the large ribosomal RNA contains an intervening sequence of approximately 2000 bp. Second, the genes for the small and large ribosomal RNAs are not adjacent, as previously reported, and the region between them contains a number of tRNA genes, including that for the mitochondrial tRNATyr, which is located close to the small rRNA gene on the same strand of the mitochondrial DNA. Third, there is a second cluster of tRNA genes on the mitochondrial DNA following the large ribosomal RNA gene, but there is no evidence for the presence of tRNA genes in the intervening sequence of the large ribosomal RNA. Fourth, hybridization of labeled ribosomal and transfer RNAs to the separated strands of a cloned 16 kbp DNA fragment covering this region indicates that the two ribosomal RNAs and most, if not all, of the mitochondrial tRNAs are encoded on one strand of the mitochondrial DNA.

Base Sequence↗
PubMed1979

Fine structure of ribosomal RNA. II. Distribution of methylated sequences within Xenopus laevis rRNA.

The distribution of methyl groups in rRNA from Xenopus laevis was analyzed by hybridization of rRNA to subfragments of either of two cloned rDNA fragments, X1r11 and X1r12, which together constitute a complete rDNA repeat unit. Using a mixture of 3H-methyl plus 32P-labelled rRNA as probe, the molar yield of methyl groups per rRNA region in hybrid could be calculated. For this calculation the length of the rRNA coding region in each DNA subfragment is needed, which was determined for X1r11 subfragments by the nuclease S1 mapping method of Berk and Sharp. The results show that both in 18S and 28S rRNA the methyl groups are nonrandomly distributed. For 18S rRNA, clustering was found within a 3' terminal fragment of 310 nucleotides. For 28S rRNA, clustering of methyl groups was found within a region of 750 nucleotides in length, which ends 500 nucleotides from the 3' end. In contrast, the 28S rRNA 5' terminal region of 900 nucleotides is clearly undermethylated. The general position of methyl groups in 28S rRNA correlates with the location of evolutionarily conserved sequences in this molecule, as recently determined in our laboratory.

Animals↗
PubMed2024

Diversity of ribosomes at the level of rRNA variation associated with human health and disease.

Ribosomal DNA and RNA (rDNA and rRNA) sequences are usually discarded from sequencing analyses. But with hundreds of copies of rDNA genes it is unknown whether they possess sequence variations that form different types of ribosomes that affect human physiology and disease. Here, we developed an algorithm for variant-calling between paralog genes (termed RGA) and compared rDNA variations found in short- and long-read sequencing data from the 1,000 Genomes Project (1KGP) and Genome In A Bottle (GIAB). We additionally developed a novel protocol for long-read sequencing full-length rRNA (RIBO-RT) from actively translating ribosomes. Our analyses identified hundreds of rDNA variants, most of which, surprisingly, are short insertion-deletions (indels) and dozens of highly abundant rRNA variants that are incorporated into translationally active ribosomes. To visualize variant ribosomes at the single cell level, we developed an in-situ rRNA sequencing method (SWITCH-seq) which revealed that variants are co-expressed within individual cells. Strikingly, by analyzing rDNA, we found that variants assemble into distinct ribosome subtypes. We discovered that these subtypes acquire different rRNA structures by successfully employing dimethyl sulfate (DMS) probing of full length rRNA. With this atlas we investigated rRNA variation changes across human tissues and cancer types. This revealed tissue-specific rRNA subtype expression in endoderm/ectoderm-derived tissues. In cancer, low abundant rRNA variants can become highly expressed, which suggests the presence of cancer-specific ribosomes. Together, this study identifies and comprehensively characterizes the diversity of ribosomes at the level of rRNA variants which is dominated by indel variants, their chromosomal location and unique structure as well as the association of ribosome variation with tissue-specific biology and cancer.

Journal Article↗
PubMed1976

Studies on the amount and location of the tRNA and 5-S rRNA genes in Tetrahymena pyriformis GL.

The amount and location of tRNA and 5-S rRNA genes in the macronucleus of Tetrahymena pyriformis GL was investigated by DNA-RNA hybridization. Hybridization of 32P-labelled tRNA in excess of unlabelled rRNA (25-S + 17-S + 5-S) showed that at saturation 0.021% of the macronuclear DNA was complementary to tRNA. Hybridization of 32P-labelled 5-S rRNA in excess of unlabelled 25-S + 17-S rRNA and tRNA showed a saturation value of 0.017%. In contrast to the 25-S + 17-S rRNA genes, which are found in DNA of high bouyant density, tRNA and 5-S rRNA genes were distributed evenly throughout the main peak observed when bulk macronuclear DNA was fractionated by density centrifugation in CsCl gradients. Sucrose gradient analyses of total macronuclear DNA showed that tRNA and 5-S rRNA genes were found in DNA of all size classes but a significant enrichment in the slowly sedimenting DNA fraction was observed. Saturation hybridization of 5-S rRNA to purified rDNA showed that rDNA did not contain any 5-S rRNA genes.

Animals↗