Phylogenetic measurement in procaryotes by primary structural characterization

Sogin, S. J.; Sogin, Mitchell L.; Woese, Carl R.

doi:10.1007/bf01659163

Cited by 76 publications

(28 citation statements)

References 18 publications

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“…Moreover, this approach is limited by its reliance on pure-culture techniques, which detect only a fraction of extant microorganisms (1). In the 1970s, Woese and colleagues described the use of comparative rRNA analysis for phylogenetic studies (13,24,31,32). This work not only provided an evolutionary basis for prokaryotic taxonomy but also led to the three-domain organization of the living world (Archaea, Bacteria, and Eucarya) (31,33).…”

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Analysis of Bacterial Community Composition by Oligonucleotide Fingerprinting of rRNA Genes

Valinsky¹,

Vedova

Scupham³

et al. 2002

Appl Environ Microbiol

120

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One of the first steps in characterizing an ecosystem is to describe the organisms inhabiting it. For microbial studies, experimental limitations have hindered the ability to depict diverse communities. Here we describe oligonucleotide fingerprinting of rRNA genes (OFRG), a method that permits identification of arrayed rRNA genes (rDNA) through a series of hybridization experiments using small DNA probes. To demonstrate this strategy, we examined the bacteria inhabiting two different soils. Analysis of 1,536 rDNA clones revealed 766 clusters grouped into five major taxa: Bacillus, Actinobacteria, Proteobacteria, and two undefined assemblages. Soil-specific taxa were identified and then independently confirmed through cluster-specific PCR of the original soil DNA. Near-species-level resolution was obtained by this analysis as clones with average sequence identities of 97% were grouped in the same cluster. A comparison of these OFRG results with the results obtained in a denaturing gradient gel electrophoresis analysis of the same two soils demonstrated the significance of this methodological advance. OFRG provides a cost-effective means to extensively analyze microbial communities and should have applications in medicine, biotechnology, and ecosystem studies.

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confidence: 99%

Analysis of Bacterial Community Composition by Oligonucleotide Fingerprinting of rRNA Genes

Valinsky¹,

Vedova

Scupham³

et al. 2002

Appl Environ Microbiol

120

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“…Kid, described by Ryan and Morowitz (9)], M. gallisepticum strain A5969 [described by Tourtellotte and Jacobs (10)], A. laidlawii strains JA1 [described by Liss and Maniloff (11)] and B [described by Tourtellotte and Jacobs (10) Media were depleted of phosphate by the general protocol of Kimball et al (14). Mycoplasma and Acholeplasma were grown in tryptose broth medium prepared as follows: 10 g of phosphate-depleted tryptose (described below), 5 g of NaCl, 3.75 g of Tris, 20 mg of adenosine, 20 mg of guanosine, 20 mg of cytidine, 20 mg of uridine, and 10 mg of thymidine were dissolved in 1 liter of water, adjusted to pH 8.0, and autoclaved. To this were added 20 ml of phosphate-depleted PPLO serum fraction (Difco) prepared as described below and 10 g of sterile glucose (in 50 ml of water).…”

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Phylogenetic analysis of the mycoplasmas.

Woese¹,

Maniloff²,

Zablen³

1980

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

323

198

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The phylogenetic relationships between the mycoplasmas and bacteria have been established from a comparative analysis of their 16S rRNA oligonucleotide citalogs. The genera Mycoplasma, Spiroplasma, and Atholeplasma arose b degenerative evolution, as a deep branch of the subline of costridial ancestry that led to Bacillus and Lactobacillus.Thermoplasma has no specific relationship to the other mycoplasmas; it belongs with the archaebacteria.Mycoplasma is the general name for a group of prokaryotes that do not have cell walls; each cell is bounded by a single lipoprotein membrane (for reviews, see refs. 1 and 2). The various isolates have been placed in the class Mollicutes, order Mycoplasmatales and classified into the genera Mycoplasma (containing about 50 currently recognized species), Acholeplasma (6 species), Ureaplasma (1 species), and Spiroplasma (1 species). In addition, the class Mollicutes contains two genera of uncertain taxonomic position: Anaeroplasma (two species) are obligate anaerobes and Thermoplasma (one species) is an acidophilic thermophile. The taxonomy and characteristics of these genera have been reviewed recently by Tully (3). All mycoplasmas, except Acholeplasma and some Anaeroplasma isolates, require sterol for growth. The genome size of the Mycoplasma and Ureaplasma is about 0.5 X 109 daltons, that of the Acholeplasma, Spiroplasma, and Thermoplasma about 1.0 X 109 daltons. The G.C content of the cell DNA is: Mycoplasma, 23-41%; Acholeplasma, 29-35%; Ureaplasma, 28%; Spiroplasma, 26%; Anaeroplasma, 29-34%; and Thermoplasma, 46% (2).A review of the biochemical and biophysical studies of the mycoplasmas concluded that, in general, their biology is qualitatively similar to that of other prokaryotes, the only differences being quantitative ones due to the limited size of the mycoplasma cell and genome (1). In particular, mycoplasma ribosomal and transfer RNAs contain many kinds of modified bases, but in smaller amounts than reported for other prokaryotes (1, 4, 5).The origin of and relationships among mycoplasmas have been controversial for many years. Their small genome sizes and general simplicity led some workers to suggest that they might be descendants of a primitive type of organism that preceded the typical bacteria in the evolutionary progression (6). However, mycoplasmas may merely be degenerate forms. If so, there is still the question of whether mycoplasmas constitute a separate and major branch of the bacteria, as the name Mollicutes connotes, or whether they represent a diverse collection of wall-less forms derived from many different branches of bacteria.In the studies presented here, we have examined the question of mycoplasma genealogy through comparative analyses of their 16S rRNA sequences. This technique, rRNA cataloging, has been used successfully in determining the phylogenetic structure of a variety of bacterial groups (7,8). We find that the mycoplasmas are not a phylogenetically coherent group in the sense that all derive from a common ancestor, itself a mycopl...

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“…The primary structures of these rRNA molecules are sufficiently constrained that on the whole they have not changed rapidly in time. Moreover, they contain regions of both extreme conservation (4, 19) and hypervariablity (16,19) so that both distant and close relationships can be examined. Since three distinct rRNA molecules exist, one can ultimately examine the extent to which a particular classification is dependent on the choice of RNA molecule.…”

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confidence: 99%