Collection of published 5S, 5.8S and 4.5S ribosomal RNA sequences

Erdmann, V. A.; Wolters, Jörn; Huysmans, Erik; Wächter, Rupert De

doi:10.1093/nar/13.suppl.r105

Cited by 57 publications

(33 citation statements)

References 7 publications

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“…are usually not included in the coryneform bacteria in bacterial taxonomy because of their morphological differences. This seems to be a good example of the hypothesis that differences in phenotypic (including morphological) characteristics are sometimes superficial and do not always represent the phylo- (3,13 Our previous tree (1) essentially agrees with that in Fig. 4; both the trees show that Streptomyces and Micrococcus spp., the low-G+C gram-positive bacteria, and the gramnegative bacteria separated from one another at early times of bacterial evolution, although in the previous tree, Streptomyces and Micrococcus spp.…”

Section: Methodssupporting

confidence: 74%

Phylogenetic analysis of the coryneform bacteria by 5S rRNA sequences

Park¹,

Hori²,

Suzuki³

et al. 1987

J Bacteriol

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Nucleotide sequences of 5S rRNAs from 11 coryneform bacteria were determined. These were the type strains of Corynebacterium glutamicum, Corynebacterium xerosis, Brevibacterium linens, Arthrobacter globiformis, Cellulomonas biazotea, Aureobacterium testaceum, Curtobacterium citreum, Pimelobacter simplex, and Caseobacter polymorphus and representative strains of "Corynebacterium aquaticum" and Corynebacterium xerosis. A phylogenetic tree constructed from the sequences of these bacteria and published sequences indicated that the coryneform bacteria consist of a distinct eubacterial branch together with Streptomyces and Micrococcus spp. These bacteria could be further divided into four subgroups. ml of buffer containing 10 mM Tris hydrochloride (pH 7.5), 10 mM MgCl2, 0.1 M KCI, and 10 ,ug of DNase I per ml for 10 min at 4°C. The homogenate was centrifuged at 5,000 x g for 15 min at 4°C. Crude RNA was prepared by the phenol method. It was redissolved in 15 ml of 20 mM Tris hydrochloride (pH 7.7-10 mM MgCl2 containing 0.02 M NaCl. DE52 (2 g) was added, and the mixture was stirred for 1 h at 4°C. RNA was then eluted from the DE52 cake with 15 ml of 20 mM Tris hydrochloride (pH 7.7-10 mM MgCl2 containing 1 M NaCl. The RNA preparation obtained was subjected to electrophoresis on a 12% polyacrylamide gel containing 7 M urea, 0.1 M Tris-borate (pH 8.3), and 1 mM EDTA. After the preparation had been stained with ethidium bromide, the 5S rRNA band was eluted with 0.5 M ammonium acetate-0.1 mM EDTA-0.1% sodium dodecyl sulfate at 37°C.The nucleotide sequence of SS rRNA was determined by both chemical and enzymatic methods (2,11). Ambiguous parts of the sequences were confirmed by electrophoresis on a hot plate at 70°C. Identification of 3'-or 5'-labeled termini was done by thin-layer chromatography with nuclease P1 and RNase T2 digests of 5'-or 3'-32P-labeled RNA on cellulose plates as described previously (1).Phylogenetic analysis. The evolutionary distance, Knuc, and the standard error of Knuc, Uk, between two sequences to be compared can be calculated by the following equation described by Kimura (6):"2] where P and Q are the fractions of nucleotide sites showing transition-and transversion-type differences, respectively.However, the G+C content of 5S rRNA differs considerably from one bacterium to another depending on the G+C content of their genomic DNA. To remove any possible influences of the G+C content on the evolutionary distance in 5S rRNA, the following equation was proposed (5): Dnuc = (ci/c)Knuc, where ci and cj (ci 2 cj) are the G+C contents of sequences i andj, respectively. Assuming that the evolutionary distance, Dnuc, is proportional to the number of years that have elapsed since the evolutionary divergence of two molecules from their common ancestor, the value of (112)Dnuc was taken as the relative timescale in the tree.A phylogenetic tree was constructed by the weighted pair group average clustering method (16) with the Dnuc values

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Section: Methodssupporting

confidence: 74%

Phylogenetic analysis of the coryneform bacteria by 5S rRNA sequences

Park¹,

Hori²,

Suzuki³

et al. 1987

J Bacteriol

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“…The boundaries of individual stems were defined by keeping only those positions establishing base-pairing interactions in more than 80% of the taxa. Both A-U and G-C as well as G-U matches (Erdman et al 1985) were considered as belonging to stems. This conservative selection resulted in 35 stems representing 433 positions (44.7% of the aligned positions), a model which appears suitable for all the 43 mammals investigated, marsupials included.…”

Section: Methodsmentioning

confidence: 99%

Molecular evolution of the mitochondrial 12S rRNA in Ungulata (mammalia)

Douzery

Catzeflis

1995

J Mol Evol

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The complete 12S rRNA gene has been sequenced in 4 Ungulata (hoofed eutherians) and 1 marsupial and compared to 38 available mammalian sequences in order to investigate the molecular evolution of the mitochondrial small-subunit ribosomal RNA molecule. Ungulata were represented by one artiodactyl (the collared peccary, Tayassu tajacu, suborder Suiformes), two perissodactyls (the Grevy's zebra, Equus grevyi, suborder Hippomorpha; the white rhinoceros, Ceratotherium simum, suborder Ceratomorpha), and one hyracoid (the tree hyrax, Dendrohyrax dorsalis). The fifth species was a marsupial, the eastern gray kangaroo (Macropus giganteus). Several transition/transversion biases characterized the pattern of changes between mammalian 12S rRNA molecules. A bias toward transitions was found among 12S rRNA sequences of Ungulata, illustrating the general bias exhibited by ribosomal and protein-encoding genes of the mitochondrial genome. The derivation of a mammalian 12S rRNA secondary structure model from the comparison of 43 eutherian and marsupial sequences evidenced a pronounced bias against transversions in stems. Moreover, transversional compensatory changes were rare events within double-stranded regions of the ribosomal RNA. Evolutionary characteristics of the 12S rRNA were compared with those of the nuclear 18S and 28S rRNAs. From a phylogenetic point of view, transitions, transversions and indels in stems as well as transversional and indels events in loops gave congruent results for comparisons within orders. Some compensatory changes in double-stranded regions and some indels in single-stranded regions also constituted diagnostic events. The 12S rRNA molecule confirmed the monophyly of infraorder Pecora and order Cetacea and demonstrated the monophyly of the suborder Ruminantia was not supported and the branching pattern between Cetacea and the artiodacytyl suborders Ruminantia and Suiformes was not established. The monophyly of the order Perissodactyla was evidenced, but the relationships between Artiodactyla, Cetacea, and Perissodactyla remained unresolved. Nevertheless, we found no support for a Perissodactyla + Hyracoidea clade, neither with distance approach, nor with parsimony reconstruction. The 12S rRNA was useful to solve intraordinal relationships among Ungulata, but it seemed to harbor too few informative positions to decipher the bushlike radiation of some Ungulata orders, an event which has most probably occurred in a short span of time between 55 and 70 MYA.

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“…Sequencing of 16s rRNA and of 23s rRNA have great sensitivity. In addition, 5s rRNA sequence determination can be useful (Erdman et al, 1985), however there are limitations due to the small size of the macromolecule and the amount of information gained. Genes encoding 16s rRNA genes (16s rDNA) are amplified in vitro by using PCR.…”

Section: Rrna Oligonucleotide Sequencingmentioning

confidence: 99%

Recommended minimal standards for description of new staphylococcal species

Freney¹,

Kloos

Hájek

et al. 1999

International Journal of Systematic and Evolutionary Microbiology

119

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Assignment of a strain to the genus Staphylococcus requires that it is a Grampositive coccus that forms clusters, produces catalase, has an appropriate cell wall structure (including peptidoglycan type and teichoic acid presence) and G+C content of DNA in a range of 3 0 4 0 mol%. The recommended minimal standards for describing a new Staphylococcus species are based on the results of phenotypic and genomic studies of a t least five independently isolated strains. They include colony morphology and the results of the following conventional tests : pigment production, growth requirements, fermentative and oxidative activity on carbohydrates, novobiocin susceptibility, enzymic activities (nitrate reductase, alkaline phosphatase, arginine dihydrolase, ornithine decarboxylase, urease, cytochrome oxidase, staphylocoagulase in rabbit plasma, heat-stable nuclease, amidases, oxidases, clumping factor, and haemolytic activity on sheep or bovine blood agar). DNA-DNA hybridization experiments may distinguish species when the difference between the binding in the homologous reaction and the binding in the heterologous reaction expressed as a percentage is less than 70%. In addition, rRNA signature sequence criteria, ribotyping characterization of the nomenclature type strain and other strains of the species, and reference strains of other species is recommended to describe the strains of the new species with sets of genetic attributes and reveal possible grouping errors. This proposal has been endorsed by the members of the Subcommittee on the taxonomy of staphylococci and streptococci of the International Committee on Systematic Bacteriology.

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Collection of published 5S, 5.8S and 4.5S ribosomal RNA sequences

Cited by 57 publications

References 7 publications

Phylogenetic analysis of the coryneform bacteria by 5S rRNA sequences

Phylogenetic analysis of the coryneform bacteria by 5S rRNA sequences

Molecular evolution of the mitochondrial 12S rRNA in Ungulata (mammalia)

Recommended minimal standards for description of new staphylococcal species

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