5S Ribosomal RNA data bank

Szymański, Maciej; Barciszewska, Mirosława Z.; Barciszewski, Jan; Erdmann, Volker A.

doi:10.1093/nar/27.1.158

Cited by 22 publications

(19 citation statements)

References 22 publications

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“…Results of 16S rRNA phylogeny were consistent with those of a previous analysis (15). Both 23S rRNA-and 5S rRNA-based phylogenies consistently placed T. whippelii within the Actinobacteria, while a more detailed resolution of relationships between this organism and the actinomycetes with group B peptidoglycan and the cellulomonads was not possible, due to a lack of a sufficient number of related sequences in both 23S rRNA (2) and 5S rRNA (27) databases.…”

supporting

confidence: 81%

Organization, Structure, and Variability of the rRNA Operon of the Whipple's Disease Bacterium ( Tropheryma whippelii )

et al. 2000

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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.Whipple's disease was described in 1907 (as intestinal lipodystrophy) and is a multisystem disorder of humans involving the intestinal tract as well as various other organs (3). A constant feature of the disease is the presence in affected tissues of uniform bacteria that are approximately 0.2 by 1.5 to 2.5 m. These bacteria have a characteristic morphology when viewed with electron microscopy (25). However, numerous attempts to cultivate this bacterium have failed (3). In 1997, propagation in human macrophage cell cultures was reported (24), and recently, propagation in human fibroblasts (20), but these findings have not yet been confirmed by other groups. Thus, this organism remains poorly characterized.Molecular data from the Whipple's disease bacterium became available through broad-range 16S ribosomal DNA (rDNA) PCR and sequence analysis (21, 31). A phylogenetic assessment based on 1,321 bp of 16S rDNA established the bacterium (Tropheryma whippelii) as an actinomycete (21). Taxon-specific 16S rDNA primers have since been used to detected the bacterium in additional patients with Whipple's disease (19,21,28,29), as well as in sewage effluent (16). The determination of a nearly complete 16S rDNA sequence and the 16S-23S ribosomal RNA intergenic spacer sequence has provided additional information (16). A reassessment of its phylogeny revealed a position between the actinomycetes with group B peptidoglycan and the family Cellulomonadaceae.The 16S-23S rDNA spacer has been used for strain differentiation in a variety of bacterial species (4). Two recent studies, both from the same group in Switzerland, addressed the potential variability of the 16S-23S ribosomal intergenic spacer of T. whippelii (5, 6). In the first study, the spacer region was found to be homogenous in specimens from 9 Swiss individuals; in the second study, three types of intergenic spacers were detected in specimens from 28 individuals. In contrast to the 16S-23S rDNA spacer, little information has been published on the intraspecies variability of the 23S-5S rDNA spacer and of regions immediately upstream and downstream of the rRNA operon.

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supporting

confidence: 81%

Organization, Structure, and Variability of the rRNA Operon of the Whipple's Disease Bacterium ( Tropheryma whippelii )

et al. 2000

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“…454 datasets. Duplicate reads (100% identity) were removed and FASTA files divided into rRNA and non-rRNA reads by using BLASTn (top hit, e-values <0.0001, bit scores >50) to compare with a reference database comprised of combined SILVA release 106 SSU and LSU databases and a 5S database (80). Using BLASTx or LAST (79), non-rRNA reads were compared with a reference database (SI Appendix) and their taxonomic affiliation determined in MEGAN (81).…”

Section: Methodsmentioning

confidence: 99%

Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean

Lincoln

Wai

Eppley

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

134

106

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Archaea are ubiquitous in marine plankton, and fossil forms of archaeal tetraether membrane lipids in sedimentary rocks document their participation in marine biogeochemical cycles for >100 million years. Ribosomal RNA surveys have identified four major clades of planktonic archaea but, to date, tetraether lipids have been characterized in only one, the Marine Group I Thaumarchaeota. The membrane lipid composition of the other planktonic archaeal groups-all uncultured Euryarchaeota-is currently unknown. Using integrated nucleic acid and lipid analyses, we found that Marine Group II Euryarchaeota (MG-II) contributed significantly to the tetraether lipid pool in the North Pacific Subtropical Gyre at shallow to intermediate depths. Our data strongly suggested that MG-II also synthesize crenarchaeol, a tetraether lipid previously considered to be a unique biomarker for Thaumarchaeota. Metagenomic datasets spanning 5 y indicated that depth stratification of planktonic archaeal groups was a stable feature in the North Pacific Subtropical Gyre. The consistent prevalence of MG-II at depths where the bulk of exported organic matter originates, together with their ubiquitous distribution over diverse oceanic provinces, suggests that this clade is a significant source of tetraether lipids to marine sediments. Our results are relevant to archaeal lipid biomarker applications in the modern oceans and the interpretation of these compounds in the geologic record.euryarchaea | glycerol dialkyl glycerol tetraether | oceanography | environmental genomics | TEX 86 index

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“…Encoded RNAs and RNA genes were identified by systematic sequence comparison to orthologous RNAs from different prokaryotic and eukaryotic species and to GenBank and to available RNA databases for specific RNA types (21)(22)(23)(24)(25). We did not consider other completely novel or non-consensus RNA variants (26,27).…”

Section: Identification Of Genes and Reading Frame Lengthmentioning

confidence: 99%

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames

Dandekar

Huynen²,

Regula

et al. 2000

Nucleic Acids Research

237

192

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5S Ribosomal RNA data bank

Cited by 22 publications

References 22 publications

Organization, Structure, and Variability of the rRNA Operon of the Whipple's Disease Bacterium ( Tropheryma whippelii )

Organization, Structure, and Variability of the rRNA Operon of the Whipple's Disease Bacterium ( Tropheryma whippelii )

Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames

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