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Results for “RNA, Ribosomal, 16S”

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At least 19 recordsLinked to original sources
PubMed1992

The 23S/5S ribosomal RNA genes (rrl/rrf) are separate from the 16S ribosomal RNA gene (rrs) in Borrelia burgdorferi, the aetiological agent of Lyme disease.

DNA fragments containing the rRNA genes for Borrelia burgdorferi strain B31 were cloned in bacteriophage lambda EMBL3. A restriction map of the fragments was constructed and the organization of the rRNA genes was determined by Southern hybridization. One genomic DNA fragment contained a single copy of the rrs sequence and another cloned fragment contained both rrl and rrf sequences. The results revealed that the rrs gene is located separately from the set of rrl/rrf genes, suggesting that these rRNA genes are expressed independently in B. burgdorferi.

Blotting, Southern↗
PubMed1994

Oligonucleotide probes for Bordetella bronchiseptica based on 16S ribosomal RNA sequences.

Bordetella bronchiseptica 16S ribosomal RNA (rRNA) gene was cloned and identified. On the basis of information from computer-assisted sequence comparison of the B. bronchiseptica 16S RRNA sequences with that of other bacterial species, we constructed B. bronchiseptica-specific oligonucleotide probes complementary to variable regions in the 16S rRNA molecule. Specificity of these 32P-labeled oligo-nucleotide probes was tested in a RNA/DNA hybridization with B. bronchiseptica strains and other bacterial strains. Probe BB4 was more specific than three other oligonucleotide probes. This probe BB4 was sensitive enough to be able to detect 10(4) bacterial cells.

Base Sequence↗
PubMed1996

The 16S ribosomal RNA mutation database (16SMDB).

The 16S ribosomal RNA mutation database (16SMDB) provides a list of mutated positions in 16S ribosomal RNA from Escherichia coli and the identity of each alteration. Information provided for each mutation includes: (i) a brief description of the phenotype(s) associated with each mutation; (ii) whether a mutant phenotype has been detected by in vivo or in vitro methods; (iii) relevant literature citations. The database is available via ftp and on the World Wide Web.

Computer Communication Networks↗
PubMed1994

The 16S ribosomal RNA mutation database (16SMDB)

The 16S ribosomal RNA mutation database (16SMDB), provides a list of mutated positions in 16S ribosomal RNA from Escherichia coli and the identity of each alteration. Information provided for each mutation includes: (1) a brief description of the phenotype(s) associated with each mutation, (2) whether a mutant phenotype has been detected by in vivo or in vitro methods, and (3) relevant literature citations. The database is available via ftp.

Databases, Factual↗
PubMed1997

A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA.

Direct evidence is presented for a conformational switch in 16S ribosomal RNA (rRNA) that affects tRNA binding to the ribosome and decoding of messenger RNA (mRNA). These data support the hypothesis that dynamic changes in rRNA structure occur during translation. The switch involves two alternating base-paired arrangements apparently facilitated by ribosomal proteins S5 and S12, and produces significant changes in the rRNA structure. Chemical probing shows reciprocal enhancements or protections at sites in 16S rRNA that are at or very near sites that were previously crosslinked to mRNA. These data indicate that the switch affects codon-anticodon arrangement and proper selection of tRNA at the ribosomal A site, and that the switch is a fundamental mechanism in all ribosomes.

Anticodon↗
PubMedDate not supplied

[Determination of the phylogenetic position of Sulfobacillus thermosulfidooxidans on the basis of analysis of the 5S and 16S ribosomal RNA].

The nucleotide sequence of the 16S rRNA gene of the type strain Sulfobacillus thermosulfidooxidans VKM-1269 was determined. This microorganism belongs to the group of thermophilic acidophilic chemolithotrophic bacteria capable of utilizing elemental sulfur and iron ions as the sole energy sources. The phylogenetic position of the bacterium studied among Gram-positive bacteria was estimated by a comparative analysis of 16S rRNA nucleotide sequences. It was shown that Sulfobacillus forms a coherent group with species of a new genus Alicyclobacillus. The Sulfobacillus-Alicyclobacillus group is suggested to represent a separate evolutionary branch within the clostridial subdivision of Gram-positive bacteria.

Base Sequence↗
PubMed1976

Extensions of the known sequences at the 3' and 5' ends of 23S ribosomal RNA from Escherichia coli, possible base pairing between these 23S RNA regions and 16S ribosomal RNA.

Extensions of the known sequences at both 3' and 5' ends of 23S ribosomal RNA are presented: The 5' terminal is pG-G-U-U-A-A-G-Cp or pG-G-U... G-U-U-A-A-G-Cp, with a very short sequence between Up and Gp and the 3'terminal is G-A-A-C-C-G-A-(G)-G-C-U-U-A-A-C-C-U-UOH. These two terminal regions exhibit a high degree of complementarity. In addition, extensive complementarities are also found between the 5'terminal sequence of 23S RNA and a sequence contained in section A of the 16S ribosomal RNA, and between the 3'terminal sequence of 23S RNA and sequences in sections O and J in the 16S RNA. The degree of complementarity between the two extremities of 23S RNA, and between these extremities and regions of the 16S RNA, is far greater than would be expected on a random basis suggesting a possible involvement of this base-pairing in the functioning of ribosomes. This possibility is discussed.

Base Sequence↗
PubMed1989

Rapid identification of Campylobacter species using oligonucleotide probes to 16S ribosomal RNA.

A comparison of the 16S ribosomal RNA sequences from various Campylobacter species was used to identify unique sequences which distinguish pathogenically significant campylobacters from other members of the genus. Oligonucleotides complementary to these sequences were synthesized, and under stringent conditions hybridization reactions using these probes and total RNA as the target nucleic acid displayed the desired species specificity. A simple, rapid lysis procedure was developed that allowed the specific detection of C. jejuni or C. coli from as few as 10(6) bacterial cells in less than eight hours. This method provides immediate advantages for the unequivocal identification of Campylobacter species in the microbiology laboratory, and demonstrates the potential for the use of these probes in a rapid diagnostic test of clinical samples for Campylobacter infection.

Campylobacter↗
PubMed1998

Regions of 16S ribosomal RNA proximal to transfer RNA bound at the P-site of Escherichia coli ribosomes.

Unmodified uridines have been randomly replaced by 4-thiouridines in transfer RNAPhe (tRNAPhe) transcribed in a T7 RNA polymerase system. These 4-thiouridines serve as conjugation sites for attachment of the cleavage reagent 5-iodoacetamido-1,10-o-phenanthroline (IoP). In a reducing environment, when complexed with Cu2+, 1,10-o-phenanthroline causes cleavage of nearby nucleic acids. We show here that tRNA-phenanthroline (tRNA-oP) conjugates, when bound at the P-site of 70S ribosomes and 30S ribosomal subunits, caused cleavage of ribosomal RNA (rRNA) mainly in domains I and II of 16S rRNA. Some positions were cleaved only when tRNA-oP was bound to 70S ribosomes or to 30S ribosomal subunits. In domain I, most cleavage sites occurred in or near the 530 pseudoknot region. In domain II, most nucleotides cleaved were near the 690 region and the 790 region. The only positions cleaved in domain III were near the 1050 region. There were no discernible nucleotides cleaved near the 1400 (decoding) region. Our results corroborated results of others, which have shown these sites to be protected from chemical modification by tRNA binding or to be cross-linked to P-site-bound tRNA. Use of cleavage reagents tethered to tRNA provides evidence for additional regions of rRNA that may be proximal to bound tRNA.

Base Sequence↗
PubMed1998

Directed hydroxyl radical probing of 16S ribosomal RNA in ribosomes containing Fe(II) tethered to ribosomal protein S20.

The 16S ribosomal RNA neighborhood of ribosomal protein S20 has been mapped, in both 30S subunits and 70S ribosomes, using directed hydroxyl radical probing. Cysteine residues were introduced at amino acid positions 14, 23, 49, and 57 of S20, and used for tethering 1-(p-bromoacetamidobenzyl)-Fe(II)-EDTA. In vitro reconstitution using Fe(II)-derivatized S20, together with the remaining small subunit ribosomal proteins and 16S ribosomal RNA (rRNA), yielded functional 30S subunits. Both 30S subunits and 70S ribosomes containing Fe(II)-S20 were purified and hydroxyl radicals were generated from the tethered Fe(II). Hydroxyl radical cleavage of the 16S rRNA backbone was monitored by primer extension. Different cleavage patterns in 16S rRNA were observed from Fe(II) tethered to each of the four positions, and these patterns were not significantly different in 30S and 70S ribosomes. Cleavage sites were mapped to positions 160-200, 320, and 340-350 in the 5' domain, and to positions 1427-1430 and 1439-1458 in the distal end of the penultimate stem of 16S rRNA, placing these regions near each other in three dimensions. These results are consistent with previous footprinting data that localized S20 near these 16S rRNA elements, providing evidence that S20, like S17, is located near the bottom of the 30S subunit.

Base Sequence↗
PubMed1993

The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences.

Partial sequences of the 16S ribosomal RNA genes of eleven autotrophic ammonia-oxidizing bacteria were determined by PCR amplification from small amounts of heat-lysed biomass followed by direct sequencing of PCR products. The sequences were aligned with those of representative Proteobacteria and phylogenetic trees inferred using both parsimony and distance matrix methods. This confirmed that the autotrophic ammonia-oxidizers comprise two major lines of descent within the Proteobacteria. Nitrosomonas spp., Nitrosococcus mobilis, and strains of Nitrosovibrio, Nitrosospira and Nitrosolobus were located in the beta-subdivision. The recovery of Nitrosococcus oceanus strains as a deep branch in the gamma-subdivision supported the RNA catalogue data which had indicated that the genus Nitrosococcus is polyphyletic. The autotrophic ammonia-oxidizing bacteria of the beta-Proteobacteria formed a coherent group which is interpreted as representing a single family. Within this clade, the genera Nitrosovibrio, Nitrosospira and Nitrosolobus exhibited very high levels of homology in their 16S ribosomal RNA gene sequences and can be accommodated within a single genus. Separation of these genera is currently based entirely on gross morphological differences and these can now be considered more appropriate for the identification of species within this group. It is therefore proposed that Nitrosolobus, Nitrosovibrio and Nitrosospira strains be reclassified in a single genus for which the name Nitrosospira has priority.

Ammonia↗
PubMed1991

Scanning tunnelling microscopy of 16S ribosomal RNA in water.

The scanning tunnelling microscope has been used to image 16S ribosomal RNA molecules in water electrophoretically deposited on graphite surface. Two kinds of images have been obtained: images showing aggregates of 16S ribosomal RNA molecules similar to those obtained from DNA solutions and others showing individual 16S ribosomal RNA molecules. An interesting characteristic of these images, recorded in constant current mode, is that the 16S ribosomal RNA molecules appear to be located below the graphite surface. The morphology and several structural parameters of the molecules were consistent with the data obtained from electron microscopy.

Centrifugation, Zonal↗
PubMed1994

Methylation of the conserved A1518-A1519 in Escherichia coli 16S ribosomal RNA by the ksgA methyltransferase is influenced by methylations around the similarly conserved U1512.G1523 base pair in the 3' terminal hairpin.

An in vitro system developed for the site-specific mutagenesis of 16S rRNA of Escherichia coli ribosomes was used to make five mutations around the highly conserved U1512.G1523 base pair in the 3' terminal hairpin. Each of the mutant RNAs was reconstituted with a complete mixture of 30S proteins to yield 30S ribosomal particles, which were tested for the ability of the ksgA methylase to form m6(2)A1518 and m6(2)A1519. Dimethylation of A1518 and A1519 in the hairpin loop was inhibited 20-80% by the mutations. The results indicate that G1523 and C1524 in the stem are important determinants for the dimethylation of A1518 and A1519 in the loop. Either the enzyme recognition region extends that far or the effect of mutations in the stem are propagated in some manner to the loop. The conserved U.G base pair does not of itself appear to play a major role in ksgA methylase recognition.

Base Composition↗
PubMed1996

A phylogenetic study of Rubrobacter radiotolerans by sequence analysis of the 16S ribosomal RNA gene.

Partial sequence of the 16S ribosomal RNA gene of an extremely high radiotolerant bacterium, Rubrobacter radiotolerans (reclassified from Arthrobacter radiotolerans by chemical characteristics) was determined by PCR-amplification from a small amount of heat-lysed biomass, followed by direct sequencing of the PCR product. The sequence was aligned with seven species of Arthrobacter and also with representatives of various other bacterial groups. R. radiotolerans was confirmed to be out of the Arthrobacter group justifying the reclassification. Moreover, it has an individual position among the selected representatives being closer to the eubacterial groups.

Arthrobacter↗
PubMed1997

Exact determination of UV-induced crosslinks in 16S ribosomal RNA in 30S ribosomal subunits.

Escherichia coli 30S ribosomal subunits were UV-irradiated to induce intramolecular crosslinks in the 16S rRNA. Intact 16S rRNA was purified and subjected to gel electrophoresis, under denaturing conditions, to separate molecules on the basis of the crosslinked loop size. Molecules separated this way were enriched for specific crosslinks and could be analyzed by the reverse transcription arrest assay to determine exact crosslinking sites. Thirteen crosslinking sites have been identified at single nucleotide resolution. Of these, eight are within or adjacent to secondary structure elements: one of these (C582 x G760) involves an interaction between nucleotides within an interior loop, one (C1402 x X1501) involves an interaction between nucleosides in adjacent base pairs, and the others involve interactions between nucleotides that are within junction regions (A441 x G494, U562 x U884, C934 x U1345, and U991 x U1212) or are interactions between nucleotides (C54 x A353 and U1052 x C1200) that somehow cross known base pairs. Five other crosslinks connect sites distant in the secondary structure and provide global constraints for the arrangement of RNA regions within RNA domains I and II (U244 x G894, G894 x A1468, C967 x C1400) and within domain III (U1126 x C1281 and A1093 x G1182). These crosslinks, known at single-nucleotide resolution, are useful in the prediction of local RNA regions, as well as the global structure.

Base Sequence↗
PubMed2001

Characterization of culture-derived spiral bacteria by 16S ribosomal RNA gene sequence analysis.

Broad range amplification and sequence analysis of the 16S ribosomal RNA gene was used to identify three spiral-form organisms. The agents were identified as Campylobacter fetus, "Flexispira rappini", and Borrelia burgdorferi, respectively, using either proprietary or public sequence databases. In each case, the rDNA sequence showed 99-100% homology with known sequence data. Sequence-based analysis for each isolate required only 2-3 days, whereas traditional means of identification took 8-12 days to complete. The identification of spirochetes and vibrio-like agents from human clinical samples is often time consuming and results may be difficult to interpret, sometimes due to atypical phenotypic characteristics. Analysis of 16S rDNA or other molecular targets may provide a way to accurately and rapidly characterize isolates that are recalcitrant to speciation.

Adult↗
PubMed1980

[Secondary and topographic structure of ribosomal RNA 16S of Escherichia coli].

We present a model for the secondary structure of 16S ribosomal RNA from E. coli. This model has been deduced by restricting the total number of theoretical base pairings using the following criteria: (1) susceptibility of residues towards enzymatic probes that are specific for either paired or single stranded regions; (2) reactivity of certain residues to chemical modification; (3) evidence for medium and long range interactions; (4) comparative analysis of ribosomal RNA sequences from other organisms.

Base Sequence↗
PubMed2004

Molecular phylogeny of songbirds (Passeriformes) inferred from mitochondrial 16S ribosomal RNA gene sequences.

Phylogenetic relationships among the families of passerine birds have been the subject of many debates. These relationships have been investigated by using a number of different character sets, including morphology, proteins, DNA-DNA hybridization, and mitochondrial DNA gene sequences. Our objective was to examine the phylogenetic relationships of a set of passerine songbirds (Oscines) and to test the taxonomic relationships proposed by. We sequenced 1403 aligned bases encompassing the mitochondrial transfer-RNA-Valine and 16S ribosomal RNA genes in 27 species from 14 families (including a Suboscine outgroup). Our results differ in significant ways from the superfamily designations of Sibley and Ahlquist by questioning the monophyly of the Sylvioidea and by placing the Regulidae in the Corvoidea.

Animals↗