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At least 19 recordsLinked to original sources
PubMed2000

Comparative sequence analyses reveal frequent occurrence of short segments containing an abnormally high number of non-random base variations in bacterial rRNA genes.

rRNA genes are thought unlikely to be laterally transferred, because rRNA must coevolve with a large number of cellular components to form the highly sophisticated translation apparatus and perform protein synthesis. In this paper, the authors first hypothesized that lateral gene transfer (LGT) might occur to rRNA genes via replacement of gene segments encoding individual domains of rRNA: the 'simplified complexity hypothesis'. Comparative sequence analyses of the 16S and 23S rRNA genes from a large number of actinomycete species frequently identified rRNA genes containing short segments with an abnormally high number of non-random base variations. These variations were nearly always characterized by complementing covariations of several paired bases within the stem of a hairpin. The nature of these base variations is not consistent with random mutations but satisfies well the predictions of the 'simplified complexity hypothesis'. The most parsimonious explanation for this phenomenon is the lateral transfer of rRNA gene segments between different bacterial species. This mode of LGT may create mosaic rRNA genes and occur repeatedly in different regions of a gene, gradually destroying the evolutionary history recorded in the nucleotide sequence.

Actinomycetales↗
PubMed1982

Transposition of a chromosomal segment bounded by redundant rRNA genes into other rRNA genes in Escherichia coli.

We have constructed several mutants of Escherichia coli which have the chromosomal segment between the directly repeated rrnB and rrnE genes deleted from the normal position and transposed into another one of the seven redundant rRNA genes. We have examples where the transposition has been into rrnC, rrnD, rrnG, and rrnH. Included in the evidence for each of these transpositions was the finding that each transposition specifically affected a different one of the seven BamHI-PstI restriction nuclease fragments known to correspond to the seven rrn genes. The transposition mutants were generally healthy, but sensitive mixed-growth experiments revealed that most of them grew somewhat more slowly than the parental control in rich medium. The maximal detrimental effect was a 4 to 5% reduction in growth rate when the transposition of the rrnB-rrnE segment was into rrnG. We have found that a rrnF gene, reported by others to be linked to malA, does not exist in our standard strain, a derivative of Cavalli Hfr. Instead of rrnF, we identified a new rrn gene, rrnH, which mapped near min 5.

Chromosome Mapping↗
PubMed1994

Comparison of PCR-based restriction length polymorphism analysis of urease genes with rRNA gene profiling for monitoring Helicobacter pylori infections in patients on triple therapy.

Multiple isolates of Helicobacter pylori from antral biopsies of nine patients were examined by DNA fingerprinting. Analysis of rRNA gene patterns and HaeIII restriction fragment length polymorphism of PCR-amplified urease genes were compared and used to study colonization before and after failed triple therapy. H. pylori isolates from a single biopsy shared the same HaeIII DNA fingerprint regardless of the isolation method (plate or broth). DNA pattern types of paired strains of H. pylori were distinct between patients and were not grossly affected by treatment except for one patient with an altered strain type. H. pylori infections were generally associated with several subpopulations of strains, evident from the subtypic variation before and after treatment, detectable by both DNA fingerprinting methods. The urease gene patterns also provided evidence that some cultures of H. pylori probably contained a mixture of genomic subtypes. The study suggests that triple therapy has the effect either of inducing minor genomic variations or of changing the proportions of different subtypes of H. pylori. It was concluded that urease gene profiling provides a simple yet reliable method of establishing whether treatment failures are attributable to incomplete eradication of H. pylori.

Anti-Bacterial Agents↗
PubMed2000

Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny.

Almost complete 23S rRNA gene sequences were obtained from 13 planctomycete strains, the fimbriated, prosthecate bacterium Verrucomicrobium spinosum and two strains of the genus Prosthecobacter. The 23S rRNA genes were amplified by the PCR, using modified primers. The majority of the planctomycete strains investigated were shown to have 23S rRNA genes that were not linked to the 16S rRNA genes. Amplification of the 5'-termini of these genes was achieved using a novel primer-design strategy. Comparative phylogenetic analyses were performed using the 23S rRNA gene sequences determined in this study and previously determined 16S rRNA gene sequences. The phylogenetic dendrograms constructed from both datasets showed that the planctomycetes form a coherent group and distinct lineage within the domain Bacteria. Analysis of 23S rRNA gene sequences of Verrucomicrobium spinosum, Prosthecobacter fusiformis and Prosthecobacter sp. strain FC-2 showed that these organisms cluster together, as was also shown here and previously by analysis of 16S rRNA gene sequences. The distinct phylogenetic position of the division Verrucomicrobia was also supported by analysis of the 23S rRNA gene sequences, and no statistically significant phylogenetic relationship between the division Verrucomicrobia and the planctomycetes was found. The analyses presented in this study also provide further evidence that the chlamydiae are no more related to members of the order Planctomycetales and the division Verrucomicrobia than they are to members of other bacterial lineages.

Bacteria↗
PubMed1986

Organization of the ribosomal RNA genes in Mycoplasma hyopneumoniae: the 5S rRNA gene is separated from the 16S and 23S rRNA genes.

In order to study the organization of the ribosomal RNA genes of Mycoplasma hyopneumoniae the rRNA genes were cloned in phage vectors lambda EMBL3 and lambda EMBL4. By subcloning the restriction fragments into various plasmids and analysing the resulting clones by Southern and Northern blot hybridization, a restriction map of the rRNA genes was generated and the organization of the rRNA genes was determined. The results show that the genes for the 16S and 23S rRNAs are closely spaced and occur only once in the genome, whereas the 5S rRNA gene is separated from the other two genes by more than 4 kb.

Base Sequence↗
PubMed2002

Sequence diversity of Neisseria meningitidis 16S rRNA genes and use of 16S rRNA gene sequencing as a molecular subtyping tool.

We investigated the diversity of the primary sequences of 16S rRNA genes among Neisseria meningitidis strains (Men) and evaluated the use of this approach as a molecular subtyping tool. We aligned and compared a 1,417-bp fragment of the 16S rRNA gene from 264 Men strains of serogroups A, B, C, and Y (MenA, MenB, MenC, and MenY, respectively) isolated throughout the world over a 30-year period. Thirty-one positions of difference were found among 49 16S types: differences between types ranged from 1 to 14 positions (0.07 to 0.95%). 16S types and serogroups were highly associated; only 3 out 49 16S types were shared by two or more serogroups. We have identified 16S types that are exclusively associated with strains of certain hypervirulent clones: 16S type 5 with MenA subgroup III, 16S type 4 with the MenB electrophoretic type 5 (ET-5) complex, and 16S types 12 and 13 with MenC of the ET-37 complex. For MenC strains, 16S sequencing provided the highest sensitivity and specificity and the best overall association with the outbreak-related versus sporadic isolates when compared with pulsed-field gel electrophoresis, multilocus enzyme electrophoresis, and multilocus sequence typing. We demonstrated for the first time an unexpected diversity among 16S rRNA genes of Men strains, identified 16S types associated with well-defined hypervirulent clones, and showed the potential of this approach to rapidly identify virulent strains associated with outbreaks and/or an increased incidence of sporadic disease.

Bacterial Typing Techniques↗
PubMed2006

Development of a 9600-clone procedure for oligonucleotide fingerprinting of rRNA genes: utilization to identify soil bacterial rRNA genes that correlate in abundance with the development of avocado root rot.

Oligonucleotide fingerprinting of rRNA genes (OFRG) is an array-based method that generates microbial community profiles through analysis of rRNA gene clone libraries. The original OFRG method allowed 1536 clones to be analyzed per experiment. This report describes a procedure for analyzing 9600 clones per experiment, including a new probe set for bacterial analysis, and improved data processing and statistical analysis tools. The software tools are available at the OFRG website (). Use of the 9600-clone procedure was demonstrated by examining the bacterial rRNA gene compositions of soils subjected to various temperature treatments. These treatments produced a series of soils with a range of abilities to suppress avocado root rot, enabling the identification of bacterial rRNA genes that correlate in abundance with root rot suppressiveness. OFRG analysis of these soils produced 8876 bacterial rRNA gene fingerprints grouped into 5123 clusters, or operational taxonomic units (OTUs). Eleven OTUs exhibited a positive correlation between the number of clones and the percentage of healthy roots. An in silico analysis was performed to examine the relationship between the number of rRNA genes analyzed and the number of correlates (rRNA gene-avocado root rot symptoms) identified. As the number of clones decreased, fewer correlates were identified. To further increase the throughput of the OFRG method, use of a glass slide-fluorescent probe microarray format was also explored.

DNA Fingerprinting↗
PubMed1980

The distal end of the ribosomal RNA operon rrnD of Escherichia coli contains a tRNA1thr gene, two 5s rRNA genes and a transcription terminator.

The distal region of the Escherichia coli ribosomal RNA operon rrnD has been sequenced to identify transfer RNA genes which might be contained within this transcriptional unit, and to define a possible transcription termination site. A nucleotide sequence corresponding to the gene for tRNA1thr is located between two genes for 5S rRNA. The spacer region between the proximal 5S rRNA gene and the tRNA1thr gene is 12 base pairs long, whereas the spacer region between the distal 5S rRNA gene and the tRNA1thr gene is 37 base pairs. Possible sites for RNA processing are discussed, and the sequence of the tRNA1thr gene is found to possess the same anticodon as the tRNA3thr gene. A putative transcription termination site for rrnD was located about 25 base pairs distal to the 3' end of the second 5S rRNA gene. The rrnD and rrnC terminators are compared with each other and with other prokaryotic terminators. Located at exactly the same site on the complementary strand is another putative transcription termination site for a gene being transcribed towards rrnD. The possibility of overlapping terminators is discussed.

Base Composition↗
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↗
PubMed1997

Localization of the 18S, 5.8S and 28S rRNA genes and the 5S rRNA genes in the babirusa and the white-lipped peccary.

The locations of the genes encoding 18S, 5.8S and 28S rRNA and 5S rRNA were studied in two relatives of the domestic pig, the babirusa (Babyrousa babyrussa) and the white-lipped peccary (Tayassu pecari). In the babirusa, the 18S, 5.8S and 28S rDNA is located on chromosomes 6, 8 and 10. The genes on chromosomes 8 and 10 are actively transcribed, in contrast to those on chromosomes 6. In the white-lipped peccary, this rDNA was found to be located on chromosomes 4 and 8. The genes on both of these pairs of chromosomes are actively transcribed. The 5S rDNA was physically mapped to chromosome 16 in the babirusa, and to chromosome 11 in the white-lipped peccary. These data are compared to similar data obtained for the domestic pig, and confirm previously recognized chromosome homologies.

Animals↗
PubMed2003

Phylogenetic relationship in the genus Panax: inferred from chloroplast trnK gene and nuclear 18S rRNA gene sequences.

Chloroplast trnK gene and nuclear 18S rRNA gene sequences of 13 Panax taxa, collected mainly from Sino-Japanese floristic region, were investigated in order to construct phylogenetic relationship and to assist taxonomic delimitation within this genus. The length of trnK gene sequence varied from 2537 bp to 2573 bp according to the taxa, whereas matK gene sequences, embedded in the intron of trnK gene, were of 1512 bp in all taxa. Species-specific trnK/ matK sequence provided much insight into phylogeny and taxonomy of this genus. 18S rRNA gene sequences were of 1808 or 1809 bps in length, only 9 types of 18S rRNA sequences were observed among 13 taxa. Parsimony and neighbor-joining analyses of the combined data sets of trnK-18S rRNA gene sequences yielded a well-resolved phylogeny within genus Panax, where three main clades were indicated. P. pseudoginseng and P. stipuleanatus formed a sister group located at a basal position in the phylogenetic tree, which suggested the relatively primitive position of these two species. Monophyly of P. ginseng, P. japonicus (Japan) and P. quinquefolius, which are distributed in northern parts of Asia or America, was well supported (Northern Clade). The remaining taxa distributed in southern parts of Asia formed a relatively large clade (Southern Clade). The taxonomic debated taxa traditionally treated as subspecies or varieties of P. japonicus or P. pseudoginseng showed various nucleotide sequences, but all fell into one cluster. It might suggest these taxa are differentiated from a common ancestor and are in a period of high variation, which is revealed not only on morphological appearance, but also on molecular divergence. By comparing trnK and 18S rRNA gene sequences among 13 Panax taxa, a set of valuable molecular evidences for identification of Ginseng drugs was obtained.

Cell Nucleus↗
PubMed2006

Intrageneric structure of the genus Gluconobacter analyzed by the 16S rRNA gene and 16S-23S rRNA gene internal transcribed spacer sequences.

Forty-nine strains belonging to the genus Gluconobacter were re-examined with respect to their species identification based on the sequences of the 16S rDNA and 16S-23S rDNA internal transcribed spacer regions (ITS). A phylogenetic tree constructed from the 16S rDNA sequences indicated the presence of five clusters corresponding, respectively, to the major five species of the genus Gluconobacter, namely G. albidus, G. cerinus, G. frateurii, G. oxydans (type species), and G. thailandicus. The type strain of G. asaii, NBRC 3276T (T=type strain) was included in the G. cerinus cluster, which is consistent with the report that G. asaii is a junior subjective synonym of G. cerinus. Existence of the G. albidus, G. cerinus, G. frateurii, G. oxydans, and G. thailandicus clusters was also recognized by the ITS sequence analysis. Both sequence analyses revealed that the G. cerinus and G. frateurii clusters were heterogeneous. The G. cerinus cluster comprised three strains of G. cerinus and one strain of G. frateurii, while the G. frateurii cluster included ten strains of G. frateurii, three of G. cerinus, and eleven of G. oxydans. These results suggest that phenotypic differences among Gluconobacter species are ambiguous and the species definition must be re-evaluated. The 16S rDNA and ITS sequences determined in this study are valuable for the identification and phylogenetic analysis of Gluconobacter species.

Base Sequence↗
PubMed1997

A novel algorithm for the search of 5S rRNA genes in DNA databases: comparison with other methods and identification of new potential 5S rRNA genes.

We report here a new algorithm for the identification of 5S rRNA genes in DNA databases. Based on an improved version of the general weight matrix method, this search procedure relies on the recognition of three informative regions within 5S rRNA genes, and on the weighted evaluation of the distance between them. As an additional step, the algorithm extends the weight matrix analysis to the full-length 5S rRNA sequence. This combined strategy, which includes a fast, but poorly selective, preliminary search procedure and an auxiliary step, that is slow but highly selective, strongly reduces the number of false positive instances, yielding a total false positive rate of 0.00076%. On the other hand, 97.5% of the 1045 known 5S rRNA genes were correctly recognized by this algorithm, and 29 previously unidentified potential 5S rRNA sequences were uncovered. A detailed analysis of these candidate sequences, including prediction of 5S rRNA secondary structure and checking for the presence of transcriptional termination signals, showed that eight of them correspond to authentic 5S rRNA genes. The performance of this specialized algorithm for the detection of 5S rRNA genes was compared with that of the general hidden Markov model search procedure. Due to their utilization of different filtering rules, the two approaches proved to be highly complementary. Their combined use will thus provide a very effective tool for the detection of dispersed 5S rRNA genes, either active or inactive, in the vertebrate genome.

Algorithms↗
PubMed1993

Coordinated decreases in rRNA gene transcription factors and rRNA synthesis during muscle cell differentiation.

rRNA synthesis decreases significantly during the differentiation of rat L6 myoblasts to myotubes. Nuclear run-on assays demonstrated that the decrease was attributable to decreased rates of rRNA gene transcription. Immunoblot analysis indicated a marked reduction in amounts of the RNA polymerase I transcription factors UBF1 and UBF2 (upstream binding factors 1 and 2, respectively). The levels of these factors dropped in parallel with the down-shift in rRNA gene transcription. The amount of UBF does not fall due to a general decrease in cellular protein, as myosin heavy-chain protein accumulates markedly during this same time. RNA blots of total RNA isolated from myoblasts and differentiating myotubes showed a decrease in the mRNA for UBF, at the same time the mRNA for myogenin was accumulating. The down-shift in UBF mRNA levels preceded the decrease in the protein levels for UBF. There have been reports that the acute response of the rRNA gene transcription system to physiological signals in many systems involves an RNA polymerase I-associated factor. However, our results imply that the regulation of rRNA gene DNA transcription in response to physiological processes, such as differentiation, may involve multiple regulatory pathways.

Adenosine Triphosphate↗
PubMed1995

[Study on the characteristics of molecular epidemiology for Salmonella typhi isolated in China. II. Analysis of 16S rRNA gene restriction patterns (16S rRNA GRP) of S. typhi isolated in China].

16S rRNA gene, a highly conservative gene in molecular evolution, was labeled with digoxigenin-11-dUTP by PCR. Using it as a probe, we investigated the 16S rRNA gene restriction patterns (16S rRNA GRP) of S. typhi after their chromosomes were digested with Pst I. Results show that the Pst I 16S rRNA GRP appears obvious polymorphism in strains of distinctive sources. The fragments containing 16S rRNA gene are sized 7.0-26.5kb in 16S rRNA GRP of Pst I. 119 strains can be divided into 38 ribotypes. Most of the strains causing outbreaks from Dalian in 1990 and strains isolated during the pandemic from Yili, Xinjiang in 1991 have the same ribotype; some ribotypes contain epidemic strains which are from different geographic areas; some strains from sporadic cases have their unique ribotypes. We also find the 16S rRNA GRP with Pst I of S. typhimurium rather different from that of S. typhi. Data from further analysis of Pst I ribotypes by mean-linkage clustering method show that pandemic strains, outbreak strains and epidemic strains cluster at 0.55 in genetic distance; nonepidemic strains and strains from sporadic cases gather to form another cluster at 0.70 in genetic distance. Ribotype of strain 251, which was isolated forman asymptomatic carrier is different from the two clusters. The ribotype of S. typhimurium is apparently far distant, comparing with that of S. typhi.

China↗
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↗
PubMed1987

An intron in the 23S rRNA gene of the Chlorella chloroplasts: complete nucleotide sequence of the 23S rRNA gene.

A 243 bp intron was found within the 23S rRNA gene of the unicellular green alga Chlorella ellipsoidea. This intron is A+T-rich (63.7%) compared with the 23S rRNA (50.5%) and is located in domain II of the 23S rRNA. In contrast to rRNA introns so far known, this intron is considerably small and does not possess features of group I introns in spite of its possible folded secondary structure; this is a new type rRNA intron. The complete nucleotide sequence of the 23S rRNA gene (2,965 bp) was also compared with that of tobacco chloroplasts and E. coli.

Base Sequence↗
PubMed2000

Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes.

The nearly universal colonization of surfaces in marine waters by bacteria and the formation of biofilms and biofouling communities have important implications for ecological function and industrial processes. However, the dynamics of surface attachment and colonization in situ, particularly during the early stages of biofilm establishment, are not well understood. Experimental surfaces that differed in their degrees of hydrophilicity or hydrophobicity were incubated in a salt marsh estuary tidal creek for 24 or 72 h. The organisms colonizing these surfaces were examined by using a cultivation-independent approach, amplified ribosomal DNA restriction analysis. The goals of this study were to assess the diversity of bacterial colonists involved in early succession on a variety of surfaces and to determine the phylogenetic affiliations of the most common early colonists. Substantial differences in the representation of different cloned ribosomal DNA sequences were found when the 24- and 72-h incubations were compared, indicating that some new organisms were recruited and some other organisms were lost. Phylogenetic analyses of the most common sequences recovered showed that the colonists were related to organisms known to inhabit surfaces or particles in marine systems. A total of 22 of the 26 clones sequenced were affiliated with the Roseobacter subgroup of the alpha subdivision of the division Proteobacteria (alpha-Proteobacteria), and most of these clones were recovered at a high frequency from all surfaces after 24 or 72 h of incubation. Two clones were affiliated with the Alteromonas group of the gamma-Proteobacteria and appeared to be involved only in the very early stages of colonization (within the first 24 h). A comparison of the colonization patterns on the test surfaces indicated that the early bacterial community succession rate and/or direction may be influenced by surface physicochemical properties. However, organisms belonging to the Roseobacter subgroup are ubiquitous and rapid colonizers of surfaces in coastal environments.

Alphaproteobacteria↗