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At least 73 records · Page 4Linked to original sources
PubMed1994

Transcription analysis of the Streptomyces coelicolor A3(2) rrnA operon.

Transcription start sites and processing sites of the Streptomyces coelicolor A3(2) rrnA operon have been investigated by a combination of in vivo and in vitro transcription analyses. The data from these approaches are consistent with the existence of four in vivo transcription sites, corresponding to the promoters P1-P4. The transcription start sites are located at -597, -416, -334 and -254 relative to the start of the 16S rRNA gene. Two putative processing sites were identified, one of which is similar to a sequence reported earlier in S. coelicolor and other eubacteria. The P1 promoter is likely to be recognized by the RNA polymerase holoenzyme containing sigma hrdB, the principal sigma factor in S. coelicolor. P2 also shares homology with the consensus for vegetative promoters, but has a sequence overlapping the consensus -35 region that is also present in the -35 regions of P3 and P4. The -35 sequence common to P2, P3 and P4 is not similar to any other known consensus promoter sequence. In fast-growing mycelium, P2 appears to be the most frequently used promoter. Transcription from all of the rrnA promoters decreased during the transition from exponential to stationary phase, although transcription from P1 and P2 ceased several hours before that from P3 and P4.

Base Sequence↗
PubMed2000

Characterization of the three ribosomal RNA operons rrnA, rrnB, and rrnC, from Brucella melitensis.

The three Brucella melitensis ribosomal RNA operons rrnA, rrnB, and rrnC were characterized individually. Each locus consisted of the 16S rRNA gene (rrs), followed by an intergenic spacer containing the tRNA-Ile and tRNA-Ala genes, the 23S rRNA gene (rrl), an intergenic spacer devoid of tRNA genes, the 5S rRNA gene (rrf), and an f-Met tRNA gene. The DNA sequences were identical over a 6271bp region, diverging 594bp upstream of rrs and immediately downstream of the f-Met tRNA gene. The previously uncharacterized 23S rRNA genes each contained a 178bp insertion 130bp from the 5' end. The location of the insertion matched intervening sequences (IVSs) found in other Rhizobiaceae. However, the size and sequence of the Brucella IVS differed from all previously reported IVS sequences from bacteria. The IVS region was PCR-amplified from 20 Brucella isolates representing all known Brucella species and biovars. All isolates contained only the complete IVS fragment. We compared the IVS DNA sequences of rrlC from representative strains of each of the six known Brucella species. The data revealed that the sequences were identical and differed from the B. melitensis IVS sequences by a single base pair. In other bacterial species, the IVSs are associated with post-transcriptional processing of the 23S rRNA by RNase III. We found that the Brucella 23S rRNA was slightly smaller than the 23S rRNA of Escherichia coli, known to be devoid of IVS sequences.

Base Sequence↗
PubMed2004

Single-nucleotide polymorphisms in the rRNA operon and variable numbers of tandem repeats in the lipoprotein gene among Mycoplasma genitalium strains from clinical specimens.

We characterized the single-nucleotide polymorphisms in the rRNA operon and variable numbers of tandem repeats in the lipoprotein gene MG309 among Mycoplasma genitalium strains from clinical specimens by PCR and sequencing. Analysis of 31 M. genitalium-infected patient specimens and 7 American Type Culture Collection strains identified six types of rRNA sequences and 11 different numbers of MG309 repeats. Examination of sequential specimens from 10 patients showed that these genotypes were stable for at least 5 weeks. These data suggest the potential usefulness of the rRNA genotypes and the MG309 repeats for genotyping of M. genitalium.

Base Sequence↗
PubMed1984

The in vivo and in vitro initiation site for transcription of the rRNA operon of Saccharomyces carlsbergensis.

We have performed a detailed analysis of the transcription initiation of the rRNA operon in the yeast Saccharomyces carlsbergensis. Electron microscopic analysis of R-looped pre-rRNA molecules together with a very sensitive S1-nuclease mapping showed the use of only a single transcription start at about 700 bp upstream of the 17S rRNA gene and not of the minor start sites proposed for the very closely related species S. cerevisiae by others [Bayev et al. (5), Swanson and Holland (6)]. The sequence of 730 bp of the initiating region is presented. In vitro transcription in concentrated lysates of yeast spheroplasts in the presence of (gamma-SH)ATP or (gamma-SH)GTP, followed by purification of the in vitro initiated RNA via Hg-agarose, revealed that on the endogenous template exactly the same site is used for transcription initiation as in vivo.

Base Sequence↗
PubMed1989

Multiple termination sites in an unlinked 5S rRNA operon in the archaebacterium, Thermococcus celer.

The termini of transcripts from an unlinked 5S rRNA operon were analyzed in the archaebacterium, Thermococcus celer. While the sequences of the 5' termini were completely consistent with the presently accepted consensus promoter sequences, putative multiple termination sites were identified which differed significantly from those identified in other organisms, including archaebacteria. Although termination appears to be dependent on a stem/loop structure this structure does not immediately precede a uridylic acid residue cluster. Rather, an adenylic acid residue cluster follows the termination site. The relationship of this termination site structure to those of other archaebacteria is considered.

Archaea↗
PubMed1983

Spectinomycin resistance due to a mutation in an rRNA operon of Escherichia coli.

A spectinomycin resistance mutation was isolated in an Escherichia coli rRNA operon (rrnH) located on a multicopy plasmid. Cell-free protein-synthesizing extracts made from cells containing the plasmid were partially resistant to spectinomycin. Although spectinomycin is an aminoglycoside antibiotic, the mutation did not confer resistance to any other aminoglycoside antibiotic tested.

Aminoglycosides↗
PubMed1993

Fine mapping of the three rRNA operons on the updated genomic map of Campylobacter jejuni TGH9011 (ATCC 43431).

The three rRNA gene loci of Campylobacter jejuni TGH9011 (ATCC 43431) were cloned. All three rRNA operons were shown to possess a contiguous 16S-23S structure and contain intercistronic tRNA(Ala) and tRNA(Ile). The three RNA operons and additional 14 genetic markers were mapped in the updated genomic map of C. jejuni TGH9011, which now has a total of 24 genetic markers.

Campylobacter jejuni↗
PubMed2005

Gene replacement in Haloarcula marismortui: construction of a strain with two of its three chromosomal rRNA operons deleted.

Site-directed mutagenesis were done in Haloarcula marismortui using the strategy that Khorana and coworkers devised for deleting the bacteriorhodopsin gene from Halobacterium halobium [Krebs et al. Proc Natl Acad Sci USA 90:1987-1991 (1993)]. Strains have been prepared from H. marsimortui, which normally has three rRNA operons, that are missing either its rrnB operon or both its rrnB and rrnC operons. In rich media, both strains grow at about the same rate as wild type. The G2099 in the 23S rRNA gene of the single operon strain was changed to A, and a three amino acid deletion was introduced into the gene for ribosomal protein L22 of the wild-type organism. The structural consequences of these and other such mutations can be determined with unusual accuracy because crystals of the large ribosomal subunit of H. marismortui diffract to atomic resolution.

Base Sequence↗
PubMed1984

Putative promoter region of rRNA operon from archaebacterium Halobacterium halobium.

The 100 bp sequence from the beginning of the 16S rRNA gene of archaebacterium Halobacterium halobium and the adjacent 800 bp upstream sequence were determined. Four long (80 bp) direct repeats were found in the region preceeding the structural gene of the 16S rRNA. These repeats are proposed to constitute the promoter region of the rRNA operon of H. halobium.

Base Composition↗
PubMed2003

Rates and consequences of recombination between rRNA operons.

A mutant strain of Escherichia coli was created by inserting a cassette encoding sucrose sensitivity and neomycin resistance (sacB-neo) into the small-subunit rRNA-encoding gene rrs in the rrnB operon. During growth in a complex medium, the cassette was lost from the population, and a complete rrs gene was restored at a rate of 5 x 10(-9) per cell division. Repair of this lesion required flanking regions of DNA that were similar to the six remaining intact rRNA operons and reestablished the full complement of seven rRNA operons. The relative fitness of strains with restored rrnB operons was 1 to 2% higher than that of the mutant strain. The rrnB operon normally contains a spacer region between the 16S and 23S rRNA-encoding genes that is similar in length and tRNA gene content to the spacer in rrnC, -E, and -G. In 2 of the 14 strains in which rrnB was restored, the spacer region had the same length as the spacer region in rrnA, -D, and -H. The requirement for flanking regions of nearly identical DNA and the replication of the spacer region from other rRNA operons during the repair of rrnB suggest that the restoration was accomplished via gene conversion. The rate of gene conversion was 10-fold less than the fixation of point mutations in the same region of the chromosome but was apparently sufficient to homogenize the sequences of rRNA genes in E. coli. These findings are discussed in the context of a conceptual model describing the presence of sequence heterogeneity in coevolving rRNA genes.

Escherichia coli↗
PubMed1992

Acholeplasma laidlawii has tRNA genes in the 16S-23S spacer of the rRNA operon.

We amplified the 16S-23S rRNA intergenic spacer region of Acholeplasma laidlawii PG8 by polymerase chain reaction (PCR) and obtained two specific PCR products in different sizes. We have sequenced both PCR products and found that one of them has sequence homologous to the spacer tRNA genes in Bacillus subtilis. This is the first evidence of tRNA genes between the 16S-23S rRNA intergenic spacer regions in members of the class Mollicutes.

Acholeplasma laidlawii↗
PubMed1996

Genetic diversity at the internal transcribed spacer regions of the rRNA operon among isolates of Pneumocystis carinii from AIDS patients with recurrent pneumonia.

The opportunistic fungal pathogen Pneumocystis carinii sp. f. hominis is a frequent cause of pneumonia in the immunocompromised host. Analysis of genetic variation among isolates of P. carinii sp. f. hominis from 12 human immunodeficiency virus (HIV)-infected persons with single and multiple episodes of P. carinii pneumonia was undertaken at the internal transcribed spacer (ITS) regions of the nuclear rRNA operon. In samples from 24 episodes of pneumonia, 10 different types of P. carinii sp. f. hominis were identified. More than 1 sequence type was observed in 8 samples, indicating that mixed infection with different types of P. carinii sp. f. hominis is not uncommon. In 4 of 7 patients with recurrent episodes of pneumonia, the sequence types observed at the second episode were different from those of the first, suggesting the occurrence of both reactivation of a previously acquired infection and reinfection from an exogenous source.

AIDS-Related Opportunistic Infections↗
PubMed1987

Characterization of Vibrio fischeri rRNA operons and subcloning of a ribosomal DNA promoter.

Analysis of rRNA genes in Vibrio fischeri indicates the presence of eight rRNA gene sets in this organism. It was found that the genes for 5S rRNA, 16S rRNA, and 23S rRNA are organized in operons in the following order: 5' end 16S rRNA 23S RNA 5S rRNA 3' end. Although the operons are homologous, they are not identical with regard to cleavage sites for various restriction endonucleases. A DNA library was constructed, and three ribosomal DNA clones were obtained. One of these clones contained an entire rRNA operon and was used as a source for subcloning. The promoter region which leads to plasmid instability was successfully subcloned into pHG165. The terminator region was subcloned into pBR322.

Chromosome Mapping↗
PubMed2000

Organization, structure, and variability of the rRNA operon of the Whipple's disease bacterium (Tropheryma whippelii).

Whipple's disease is a systemic disorder associated with a cultivation-resistant, poorly characterized actinomycete, Tropheryma whippelii. We determined a nearly complete rRNA operon sequence of T. whippelii from specimens from 3 patients with Whipple's disease, as well as partial operon sequences from 43 patients. Variability was observed in the 16S-23S rRNA spacer sequences, leading to the description of five distinct sequence types. One specimen contained two spacer sequence types, raising the possibility of a double infection. Secondary structure models for the primary rRNA transcript and mature rRNAs revealed rare or unique features.

Actinomycetales↗
PubMed1995

rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation.

Here we present evidence that only five of the seven rRNA operons present in Escherichia coli are necessary to support near-optimal growth on complex media. Seven rrn operons are necessary, however, for rapid adaptation to nutrient and temperature changes, suggesting it is the ability to adapt quickly to changing environmental conditions that has provided the selective pressure for the persistence of seven rrn operons in E. coli. We have also found that one consequence of rrn operon inactivation is a miscoordination of the concentrations of initiation factor IF3 and ribosomes.

Adaptation, Physiological↗
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↗