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At least 127 records · Page 7Linked to original sources
PubMed1983

Primary sequence of the 5'-terminal region of mouse 18 S rRNA and adjacent spacer. Implications for rRNA processing.

Among the stepwise cleavage reactions involved in the processing of rRNA precursors in mammalian cells, an early event corresponds to the removal of the so-called 'external transcribed regions' which are located upstream 18 S rRNA sequence within the primary transcript. We have determined the primary sequence of the domain of mouse pre-rRNA which encompasses this early processing site and analyzed its structural features with reference to the other eukaryotic homologs available. The potential involvement of secondary structure features of rRNA precursors in the recognition process for cleavage is discussed.

Animals↗
PubMed1992

Half-life of cytoplasmic rRNA and tRNA, of plastid rRNA and of uridine nucleotides in heterotrophically and photoorganotrophically grown cells of Euglena gracilis and its apoplastic mutant W3BUL.

1. For Euglena gracilis half-life data were calculated according to Greenberg's equation (Nature 240, 102-104, 1972) using steady-state specific radioactivities determined for cyt-rRNA, cyt-tRNA and pl-rRNA. 2. For all RNAs equal half-lives were found of 45 and 38 hr, respectively, in heterotrophically and photoorganotrophically grown cells. 3. Using the decay analysis equal half-lives were found for cyt-rRNA, cyt-tRNA and pl-rRNA being 79, 43 and 60 hr, respectively, in heterotrophically and photoorganotrophically grown wild-type cells and the mutant W3BUL. 4. As suggested by the specific radioactivity of intracellular [3H]UMP compared to that of [3H]uracil fed, the remarkable differences between RNA half-lives determined for heterotrophically and photoorganotrophically grown wild-type cells, seem to be caused by a different extent of the de novo synthesis of UMP. 5. Reutilization of RNA breakdown products suggested by increased half-lives of RNAs in the decay analysis compared to those determined by Greenberg's equation seems to occur mainly in heterotrophically grown cells.

Animals↗
PubMed1990

Single base alterations upstream of the E. coli 16S rRNA coding region result in temperature-sensitive 16S rRNA expression.

We have isolated three new temperature-sensitive mutants of 16S rRNA, using the U1192 spectinomycin resistance as a selectable marker. These differ from our previously characterized ts mutants in that they map in the upstream leader region of the rRNA precursor (at positions -13, -30 and -59). The relative distribution of plasmid and chromosome-derived 16S rRNA is similar between 30S subunits, 70S ribosomes and polysomes at the permissive and restrictive temperatures. Processing of the 5' end of the RNA does not appear to be affected by the mutations. Second-site suppressors were found, and all of these except one (which is within 16S rRNA) were also due to point mutations in the upstream leader.

Base Sequence↗
PubMed1998

Destabilizing effect of an rRNA stem-loop on an attenuator hairpin in the 5' exon of the Tetrahymena pre-rRNA.

Self-splicing of the Tetrahymena group I intron is attenuated by an rRNA stem-loop in the 5' exon, which competes with formation of the P1 splice site helix. The equilibrium between the P1 and P(-1) stem-loops is influenced by rRNA sequences upstream and downstream of the intron. To investigate the mechanism of this conformational switch, internal deletions and point mutations were introduced in the second rRNA stem-loop upstream of the 5' splice site. Nuclease protection, native gel electrophoresis, and self-splicing results show that this helix is important for maintaining self-splicing activity. Co-axial base stacking of adjacent helices in the 5' exon is proposed to enable exchange between inactive and active conformations of the pre-rRNA.

Animals↗
PubMed2003

Phylogeny of Astragalus in China: molecular evidence from the DNA sequences of 5S rRNA spacer, ITS, and 18S rRNA.

Radix Astragali (root of Astragalus; Huangqi) is a traditional Chinese medicine commonly used as an immunostimulant, hepatoprotective, diuretic, antidiabetic, analgesic, expectorant, and sedative drug. Although the species of Radix Astragali have been defined as Astragalus membranaceus and A. membranaceus var. mongholicus in Pharmacopoeia of China, their taxonomy remains controversial. The phylogenetic relationships among 10 Astragalus taxa, which are commonly found in China including A. membranaceus, A. membranaceus var. mongholicus, Astragalus propinquus, Astragalus lepsensis, Astragalus aksuensis, Astragalus hoantchy, Astragalus hoantchy subsp. dshimensis,Astragalus lehmannianus, Astragalus sieversianus, and Astragalus austrosibiricus, were determined using the DNA sequences of the 5S ribosomal RNA (5S rRNA) spacer, internal transcribed spacer region (ITS), and 18S rRNA coding region. The 5S rRNA spacer, ITS, and 18S rRNA, amplified by polymerase chain reaction from the isolated genomic DNAs, were sequenced. By using neighbor-joining and maximum parsimony analyses, phylogenetic trees were mapped by their sequence diversity. A. membranaceus and A. membranaceus var. mongholicus shared the greatest sequence homology. In addition, A. propinquus shared a closer relationship with A. membranaceus and A. membranaceus var. mongholicus, while other Astragalus species were less closely related. This is the first paper to show the phylogenetic relationship of Astragalus species related to Radix Astragali in China by the molecular genetic approach.

Astragalus Plant↗
PubMed1995

Angiotensin II-induced hypertrophy of rat vascular smooth muscle is associated with increased 18 S rRNA synthesis and phosphorylation of the rRNA transcription factor, upstream binding factor.

Hypertrophy of vascular smooth muscle cells (VSMC) is an important adaptive response of hypertension. Drug intervention studies have implicated a role for angiotensin II (A-II) in the mediation of VSMC hypertrophy in vivo, and A-II is a potent hypertrophic agent for VSMC in culture. Our laboratory has previously shown that A-II-induced hypertrophy of cultured VSMC is due in part to generalized increases in protein synthesis and increased content of rRNA. The aim of the present study was to determine if A-II stimulates rRNA gene synthesis and whether the rRNA transcription factor, upstream binding factor (UBF), is involved. Nuclear run-on analysis demonstrated that A-II induced a greater than 5-fold increase in rRNA gene synthesis within 6 h of stimulation. A-II also stimulated a rapid increase in UBF phosphorylation as well as nucleolar localization, but no changes in the content of UBF. Phosphoamino acid analysis showed that phosphorylation occurred only on serine residue(s). Results demonstrate that increased transcription of ribosomal DNA contributes to the A-II-induced increase in protein synthesis and VSMC hypertrophy, and suggest that an important regulatory event in this pathway may be the phosphorylation and/or nucleolar localization of UBF.

Angiotensin II↗
PubMed1991

Compilation of 5S rRNA and 5S rRNA gene sequences.

This is an update for the 5S rRNA sequences of the BERLIN RNA DATABANK last published in 1990 (1). The new entry consists of 25 eubacterial and 2 eukaryotic 5S rRNA sequences and 10 plant 5S rRNA pseudogenes (Table 1). Thus the BERLIN RNA DATABANK contains as of February 1, 1991 the 5S rRNA sequences of 44 archaebacteria, 292 eubacteria, 20 plastids, 6 mitochondria, 321 eukaryotes and 21 eukaryotic pseudogenes. The BERLIN RNA DATABANK uses the format of the EMBL Nucleotide Sequence Data Library complemented by a Sequence Alignment (SA) field including secondary structure information.

Bacteria↗
PubMed1981

Sequence homologies between eukaryotic 5.8S rRNA and the 5' end of prokaryotic 23S rRNa: evidences for a common evolutionary origin.

The question of the evolutionary origin of eukaryotic 5.8S rRNA was re-examined after the recent publication of the E. coli 23S rRNA sequence (26,40). A region of the 23S RNA located at its 5' end was found to be approximately 50% homologous to four different eukaryotic 5.8S rRNAs. A computer comparison analysis indicates that no other region of the E. coli ribosomal transcription unit (greater than 5 000 nucleotides in length) shares a comparable homology with 5.8S rRNA. Homology between the 5' end of e. coli 23S and four different eukaryotic 5.8S rRNAs falls within the same range as that between E. coli 5S RNA from the same four eukaryotic species. All these data strongly suggest that the 5' end of prokaryotic 23S rRNA and eukaryotic 5.8S RNA have a common evolutionary origin. Secondary structure models are proposed for the 5' region of E. coli 23S RNA.

Animals↗
PubMed1994

Sequence determination of rRNA genes of pathogenic Vibrio species and whole-cell identification of Vibrio vulnificus with rRNA-targeted oligonucleotide probes.

A comparative analysis of seven new 16S rRNA gene sequences of pathogenic Vibrio species with previously published vibrio sequences confirmed that Vibrio vulnificus represents a group that is not closely related to the core organisms of the genus Vibrio. In addition, we found that V. vulnificus, Listonella (Vibrio) anguillarum and Vibrio diazotrophicus branch off separately from the core group. A comparison of the 16S rRNA gene sequences of V. vulnificus strains belonging to biotypes 1 and 2 revealed that the sequences of all but four biotype 1 strains were identical to each other but slightly different (17 bases) from the sequences of the rest of the V. vulnificus strains investigated. In addition, the sequences of variable regions of the 23S rRNA genes of Vibrio fluvialis, Vibrio furnissii, Vibrio harveyi, Vibrio cholerae, and V. vulnificus C7184 and TW1 were determined, aligned, and compared with all available bacterial 23S rRNA sequences in order to search for specific target sites. As a result, four oligonucleotide probes specific for V. vulnificus were synthesized, and the specificities of these probes were evaluated by dot blot hybridization to membrane-bound RNAs from 21 V. vulnificus strains, 13 strains belonging to other Vibrio species, 61 strains belonging to species that are members of the alpha, beta, and gamma subclasses of the Proteobacteria, and 3 eucaryotic microorganisms. Two probes hybridized with all of the V. vulnificus strains tested, and the other two probes distinguished V. vulnificus biotype 1 strains from all other organisms. In situ identification of V. vulnificus by using tetramethylrhodamine- or fluorescein-labelled oligonucleotides is now possible.

Bacterial Typing Techniques↗
PubMed2004

Taxonomy of the canine Mollicutes by 16S rRNA gene and 16S/23S rRNA intergenic spacer region sequence comparison.

The taxonomy of canine Mollicutes is described, based on phylogenetic analysis of 16S rRNA gene and 16S/23S rRNA intergenic spacer (IGS) region sequences. The nucleotide sequences of the 16S rRNA gene of two untyped mycoplasmas and the IGS region of 11 Mycoplasma species were determined and used for phylogenetic analysis. The two untyped Mycoplasma strains, HRC 689 and VJC 358, were found to be distinct from all known canine mycoplasmas and all published mycoplasma 16S rRNA gene sequences.

Animals↗
PubMed2005

Heterologous rRNA gene expression: internal fragmentation of Sciara coprophila 28S rRNA within microinjected Xenopus laevis oocytes.

Species-specific pre-rRNA processing variations may result in fragmented 18S, 5.8S and 28S rRNAs. Some insect 5.8S and 28S rRNAs are further cleaved, creating within a 'hidden break' or 'gap'. We investigated the specificity of the processing mechanism by microinjecting Sciara coprophila (fungus fly) rDNA into Xenopus laevis oocytes to examine insect rRNA maturation within a cell where endogenous rRNAs are not cleaved at homologous sites. Results confirm insect rDNA transcription and pre-28S rRNA fragmentation, demonstrating that fly-specific processing machinery is not required. Instead, oocytes may provide required accessory factors, suggesting that the insect gap processing mechanism is served by an evolutionarily conserved apparatus. Alternatively, these results may suggest that processing in some lineages is an autocatalytic property of the rRNA.

Animals↗
PubMed1982

Ribonuclease E is involved in the processing of 5-S rRNA from a number of rRNA transcription units.

Strains of Escherichia coli having a thermosensitive RNase E produce a number of 5-S ribosomal RNA precursors at a non-permissive temperature. One of these precursors, 9-S RNA, was reported earlier [Ghora, B.K. and Apirion, D. (1978) Cell, 15, 1055-1066]. Here we show the existence of additional precursors to 5-S rRNA, originating from a number of rRNA genes. All the precursors are very similar in the first 200 nucleotides and the last part of this sequence contains the mature 5-S rRNA. Precursors that contain only these nucleotides (8-S RNA) accumulate. They probably originate from the rrn genes C, D and F which contain trailer tRNAs. The 9-S RNA precursors contain in addition a termination stem and loop structure and are derived from genes which do not contain trailer tRNA (Singh and Apirion, unpublished results). In addition, a 10-S precursor was identified. It contains distal to the 5-S rRNA a trailer tRNA, tRNAAsp, and a transcription termination signal. It is derived from the rrnF gene. The accumulation of an RNA precursor containing an RNase P site in an rne mutant suggests that the efficiency of one RNA processing enzyme depends on the activity of other RNA processing enzymes.

Base Composition↗
PubMed1995

Characterization of the 23S and 5S rRNA genes of Coxiella burnetii and identification of an intervening sequence within the 23S rRNA gene.

Characterization of the rRNA operon from the obligate intracellular bacterium Coxiella burnetii has determined the order of the rRNA genes to be 16S-23S-5S. A 444-bp intervening sequence (IVS) was identified to interrupt the 23S rRNA gene beginning at position 1176. The IVS is predicted to form a stem-loop structure formed by flanking inverted repeats, and the absence of intact 23S rRNA molecules suggests that the loop is removed. An open reading frame in the IVS has been identified that shows 70% similarity at the amino acid level to IVS open reading frames characterized from four species of Leptospira.

Amino Acid Sequence↗
PubMedDate not supplied

[The Thermus thermophilus 5S rRNA-protein complex: Identifications of specific binding sites for proteins L5 and L18 in 5S rRNA].

Three 5S rRNA-binding ribosomal proteins (L5, L18, TL5) of extremely thermophilic bacterium Thermus thermophilus have earlier been isolated. Structural analysis of their complexes with rRNA requires identification of their binding sites in the 5S rRNA. Previously, a TL5-binding site has been identified, a TL5-RNA complex crystallized, and its structure determined to 2.3 A. The sites for L5 and L18 were characterized, and two corresponding 5S rRNA fragments constructed. Of these, a 34-nt fragment specifically interacted with L5, and a 55-nt fragment interacted with L5, L18, and with both proteins. The 34-nt fragment-L5 complex was crystallized; the crystals are suitable for high-resolution X-ray analysis.

Binding Sites↗
PubMed2001

[Sequence analysis of mtDNA 12S rRNA, tRNA(Leu(UUR)),tRNA(Ser(UCN))and 16S rRNA gene of 12 nonsyndromic inherited deafness pedigrees].

OBJECTIVE: To detect the relationship of mtDNA mutation with inherited deafness and the reason for pedigree's hypersensitivity to ototoxicity of aminoglycoside antibiotics(AmAn). METHODS: Pedigree investigations were conducted. The blood samples were obtained from 12 pedigrees, and DNA was extracted from the isolated leukocytes. After that, mtDNA fragments were amplified by PCR. The 1555(G), 3243(G) and 7445(G) mutations were detected by Alw 26 I, Apa I and Xba I restriction endonuclease digestion respectively, and then sequencing of 12S rRNA, tRNA(Leu(UUR)), tRNA(Ser(UCN))and 16S rRNA gene was performed. RESULTS: Restriction endonuclease digestion and sequence analysis showed that all the pedigrees carried mtDNA mutation, among them, 10 pedigrees carried 1555(G) mutation; 2 pedigrees, 7445(G) mutation; no pedigree was found to harbor the 3243(G) mutation. Sequence analysis of 16S rRNA gene showed that the mutations are 2230(G), 2230(AG), 2243(AG), 2230(AA). CONCLUSION: The pedigrees that carried 1555(G) or 7445(G) mutation showed hereditary or congenital hearing loss. The 1555(G) or 7445(G) mutation in association with 16S rRNA gene mutation led to pedigree's hypersensitivity to AmAn ototoxicity.

Base Sequence↗
PubMed2004

Linezolid resistance in sequential Staphylococcus aureus isolates associated with a T2500A mutation in the 23S rRNA gene and loss of a single copy of rRNA.

Linezolid is an important therapeutic option for infections caused by resistant gram-positive bacteria. We report the characterization of sequential methicillin-resistant Staphylococcus aureus (MRSA) bloodstream isolates that developed resistance in a patient treated with a prolonged course of linezolid. Analysis of this series of clinical MRSA isolates detected, in the resistant isolates, the presence of a T2500A mutation in the domain V region of the 23S rRNA gene. In addition, the loss of a single copy of the 23S rRNA gene was found in 2 of the resistant isolates. As a result of these 2 factors, the proportion of mutant : wild-type 23S rRNA genes increased in association with an increase in the minimum inhibitory concentration of linezolid. The most recent isolate of this series was recovered 7 months after the patient discontinued linezolid and demonstrated reversion to a susceptible phenotype associated with a loss of the T2500A mutation.

Acetamides↗
PubMed2006

The mosaic nature of intergenic 16S-23S rRNA spacer regions suggests rRNA operon copy number variation in Clostridium difficile strains.

Clostridium difficile is a major spore-forming environmental pathogen that causes serious health problems in patients undergoing antibiotic therapy. Consequently, reliable and sensitive methods for typing individual strains are required for epidemiological and environmental studies. Ribotyping is generally considered the best method, but it fails to account for sequence diversity which might exist in intergenic 16S-23S rRNA spacer regions (ISRs) within and among strains of this organism. Therefore, this study was undertaken to compare the sequence of each individual ISR in five strains of C. difficile to explore the extent of this diversity and see whether such information might provide the basis for more sensitive and discriminatory strain typing methods. After targeted PCR amplification, cloning, and sequencing, the diversity of the ISRs was used as a measure of rRNA operon copy number. In C. difficile strains 630, ATCC 43593, A, and B, 11, 11, 7, and 8 ISR length variants, respectively, were found (containing different combinations of sequence groups [i to xiii]), suggesting 11, 11, 7, and 8 rrn copies in the respective strains. Many ISRs of the same length differed markedly in their sequences, and some of these were restricted in occurrence to a single strain. Most of these ISRs did not contain any tRNA genes, and only single copies of the tRNA(Ala) gene were found in those that did. The presence of ISR sequence groups (i to xiii) varied between strains, with some found in one, two, three, four, or all five strains. We conclude that the intergenic 16S-23S rRNA spacer regions showed a high degree of diversity, not only among the rrn operons in different strains and different rrn copies in a single strain but also among ISRs of the same length. It appears that C. difficile ISRs vary more at the inter- and intragenic levels than those of other species as determined by empirical comparison of sequences. The precise characterization of these sequences has demonstrated a high level of mosaic sequence block rearrangements that are present or absent in multiple strain-variable rrn copies within and between five different strains of C. difficile.

Bacterial Typing Techniques↗