A group I intron in the small subunit ribosomal RNA gene from Naegleria andersoni ssp. andersoni strain PPMFB-6.
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Animals↗
Biomedical subjects
T M Embley
Publications and source records attributed to T M Embley.
RNA sequence analysis shows that the symbionts in the ciliate Metopus contortus are polymorphs of a single methanogen species.
The polymerase chain reaction was used to amplify and partially sequence the 16S ribosomal RNA genes of symbiotic bacteria within the anaerobic ciliate Metopus contortus. In situ probing with fluorescent oligonucleotides showed that the amplified sequences originated from a single species of archaebacterium which is closely related to Methanocorpusculum parvum. The probed symbionts exhibited a variety of shapes and sizes. These data support the hypothesis, first proposed on the basis of electron microscopy, that the symbionts undergo a morphological transformation as part of the symbiotic process.
Animals↗
The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont.
The polymerase chain reaction (PCR) was used to amplify small-subunit ribosomal DNA from the anaerobic ciliated protozoon Metopus palaeformis, and from its uncultured endosymbiotic bacteria. This was accomplished directly from total DNA extracted from protozoa without prior isolation or enrichment for symbiont cells. The double-stranded amplification products were precipitated and directly sequenced using the linear PCR reaction. Fluorescent oligonucleotide probes were designed and used in whole-cell hybridizations to provide direct visual evidence that the sequences originated from the host ciliate and from the endosymbiont. Phylogenetic analysis of the Metopus palaeformis sequence consistently placed it as a deep-branching lineage near the root of the ciliate tree. However, the present data were insufficient to resolve the detailed relationship between Blepharisma and Metopus and thus to determine if the heterotrichs are mono- or paraphyletic. Phylogenetic analysis of the symbiont partial sequence clearly demonstrated that it is an archaeobacterium and that it is closely related to, but distinct from, Methanobacterium formicicum.
Animals↗
Direct amplification and sequencing of the 16S ribosomal DNA of an intracellular Legionella species recovered by amoebal enrichment from the sputum of a patient with pneumonia.
DNA coding for the 16S rRNA of an intracellular bacterium was directly amplified from lysed cells of a host amoebae using the polymerase chain reaction and primers specific for eubacteria. The amoebae had been used to recover an uncultured bacterium observed in the sputum of a patient with pneumonia. The amplified DNA was sequenced directly and compared with published 16S rRNA sequences. The analysis revealed that the intracellular bacterium is a member of the genus Legionella and that it is different from species, including L. pneumophila, for which 16S ribosomal RNA sequence data are available.
Acanthamoeba↗
The use of 16S ribosomal RNA analyses to investigate the phylogeny of the family Legionellaceae.
The 16S ribosomal RNA sequences of Legionella pneumophila, L. erythra, L. hackeliae, L. spiritensis, L. longbeachae, L. bozemanii (Fluoribacter bozemanae) and L. micdadei (Tatlockia micdadei) were determined using reverse transcriptase. The sequences were compared with published sequences for Gram-negative bacteria and phylogenetic trees were constructed. The data confirm previous work which showed that the family Legionellaceae forms a monophyletic subgroup within the gamma subdivision of the Proteobacteria. The data show that all of the legionellae studied are highly related (greater than 95%) on the basis of 16S rRNA sequences and do not support the division of the family Legionellaceae into three genera.
Base Sequence↗
The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes.
The linear polymerase chain reaction was used to sequence amplified RNA genes from strains of Bacillus, Thermus and Legionella. The technique described is simple and reproducible and it works well with double standard product which has been PEG precipitated directly from PCR reactions.
Bacillus↗
Reverse transcriptase sequencing of 16S ribosomal RNA from Faenia rectivirgula, Pseudonocardia thermophila and Saccharopolyspora hirsuta, three wall type IV actinomycetes which lack mycolic acids.
The phylogenetic relationships of three mycolateless wall type IV actinomycetes, Faenia rectivirgula, Pseudonocardia thermophila and Saccharopolyspora hirsuta, were examined using reverse transcriptase sequencing of 16S ribosomal RNA. The sequences generated were aligned and the level of sequence homology calculated. The homology values were then use to produce a phylogenetic tree and to estimate S(AB) values for the construction of a dendrogram. Both analyses show the three taxa to be closely related genera which form a distinct subdivision within the broader phylogenetic grouping defined by Mycobacterium, Dactylosporangium and their relatives.
Actinomycetales↗
Lipid and wall amino acid composition in the classification of Rothia dentocariosa.
Seven strains of Rothia dentocariosa were degraded by acid methanolysis and the nonhydroxylated fatty acid methyl esters released were examined by thin-layer and gas chromatography. The fatty acid profiles were composed of iso-, anteiso- and straight chain saturated fatty acids with 12-methyltetradecanoic (anteiso-C15), 14-methylpentadecanoic (iso-C16), 14-methylhexadecanoic (anteiso-C17) and hexadecanoic acid (C16) as major components. A small scale integrated procedure was used for the sequential extraction of isoprenoid quinones and polar lipids. The latter were examined by two-dimensional thin-layer chromatography and all of the test strains contained diphosphatidylglycerol, phosphatidylglycerol and two uncharacterised glycolipids. In all cases the major isoprenoid quinones were unsaturated menaquinones with seven isoprene units. Analyses of the cell wall amino acid composition using gas chromatography showed that the strains contained 2.5 to 5 moles of alanine and 1 mole each of glutamic acid and lysine. The chemical data support the integrity of Rothia dentocariosa and can be used to separate it from all other actinomycetes especially those which contain lysine in the wall peptidoglycan.
Actinomycetaceae↗
Systematic and morphological diversity of endosymbiotic methanogens in anaerobic ciliates.
The identities and taxonomic diversity of the endosymbiotic methanogens from the anaerobic protozoa Metopus contortus, Metopus striatus, Metopus palaeformis, Trimyema sp. and Pelomyxa palustris were determined by comparative analysis of their 16S ribosomal RNA sequences. Fluorescent oligonucleotide probes were designed to bind to the symbiont rRNA sequences and to provide direct visual evidence of their origins from methanogenic archaea contained within the host cells. Confocal microscopy was used to analyze the morphology of the endosymbionts in whole cells of Metopus palaeformis, Metopus contortus, Trimyema sp, and Cyclidium porcatum. The endosymbionts are taxonomically diverse and are drawn from three different genera; Methanobacterium, Methanocorpusculum and Methanoplanus. In every case the symbionts are closely related to, but different from, free-living methanogens for which sequences are available. It is thus apparent that symbioses have been formed repeatedly and independently. Ciliates which are unrelated to each other (Trimyema sp. and Metopus contortus) may contain symbionts which are closely related, and congeneric ciliates (Metopus palaeformis and M. contortus) may contain symbionts which are distantly related to each other. This suggests that some of the symbiotic associations must be relatively recent. For example, at least one of the symbioses in Metopus must postdate the speciation of M. palaeformis and M. contortus. Despite this, Metopus contortus, Trimyema sp., Cyclidium porcatum and their respective endosymbionts show sophisticated morphological interactions which probably facilitate the exchange of materials between the partners.
Anaerobiosis↗