Sequence of the Small Subunit Ribosomal RNA Gene from the Hypotrichous Ciliate <i>Euplotes aediculatus</i><sup>1</sup>

Sogin, Mitchell L.; Swanton, Marshal T.; Gunderson, John H.; Elwood, Hille J.

doi:10.1111/j.1550-7408.1986.tb05550.x

Cited by 67 publications

(24 citation statements)

References 17 publications

(2 reference statements)

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“…There was also support in all analyses for a relationship between Colpoda injlata, Paramecium tetraurelia, Opisthonecta henneguyi and the hymenostomes. Euplotes aediculatus was recovered on the branch leading to the stichotrichs in the distance and parsimony analyses and this is in agreement with previous work (Sogin et al, 1986;Schlegel et al, 1991). Interestingly, the linear invariants method (Lake, 1987) and its modification (Sidow & Wilson, 1990) placed Euplotes significantly with the outgroup Prorocentrum micans.…”

Section: Resultssupporting

confidence: 80%

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The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont

Roeder

et al. 1992

Journal of General Microbiology

154

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~ ~~The polymerase chain reaction (PCR) was used to amplify small-subunit ribosomal DNA from the anaerobic ciliated protozoon Metopus pdaeformis, 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 pdaeformis 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.

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Section: Resultssupporting

confidence: 80%

“…This is a violation of the assumptions of the linear invariants method (and all other methods to some extent) and thus the results of these analyses should be treated with caution. The Euplotes sequence is also unusual in that it contains a number of insertions which are absent in the other ciliates (Sogin et al, 1986).…”

Section: Resultsmentioning

confidence: 99%

The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont

Roeder

et al. 1992

Journal of General Microbiology

154

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“…If so, then further comparisons of DNA or RNA sequences, along with characterization of termination codon use (i.e., by in vitro translation) should demonstrate a distinct divergence of ciliate lines that use different genetic codes. Although 5S RNA (27) and small subunit ribosomal RNA (28) sequences demonstrate significant divergence of the Euplotids from Tetrahymena and Paramecium (27) or from Oxytricha and Stylonychia (28), the sequence data base for ciliates is much too small to argue for or against the divergence of distinct lines of ciliates.…”

Section: Resultsmentioning

confidence: 99%

Differential use of termination codons in ciliated protozoa.

Harper

Jahn

1989

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

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Sequence analysis of genes in four species of ciliated protozoa and analysis of tRNAs in Tetrahymena has demonstrated that TAG and TAA encode glutamine or glutamic acid in these organisms and TGA is the only stop codon. Thus, it has generally been assumed that all ciliates use a nonuniversal genetic code in which TGA acts as the sole termination codon. We have sequenced the linear DNA molecules that carry an actin gene and a P-tubulin gene from the ciliate Euplotes crassus. These genes are shown to use TAA as a termination codon based on homology to known actin and ,-tubulin gene sequences. In addition, we have sequenced a portion of the 3' terminus of the E. crassus H4 histone gene and show that it also uses TAA as a termination codon. These data indicate that the timing of genetic code changes in the ciliates must be reconsidered.Ciliated protozoa are characterized by the possession of two types of nuclei: a germ-line micronucleus, which is transcriptionally inactive, and a vegetative macronucleus, which is responsible for most, if not all, transcription in the cell. Hypotrichous ciliates such as Euplotes, Stylonychia, and Oxytricha undergo a macronuclear developmental process that involves the degradation of >90% of all micronuclear DNA sequences and amplification of the remaining macronuclear-destined sequences (for review see ref. 1). These macronuclear molecules range in size from 400 base pairs (bp) to 20 kilobase pairs (kb) and are present in thousands of copies. Each molecule is believed to encode a single gene product and to contain all the information necessary for its replication and transcription. Holotrichous ciliates, such as Tetrahymena, undergo a similar, but less drastic, process of macronuclear development, in which 10-20% of all micronuclear sequences are degraded (2), and the resulting macronuclear molecules average 600 kb in size (3). Amplification of macronuclear sequences also occurs in Tetrahymena, resulting in -45 copies of each macronuclear chromosome (3).All ciliate macronuclear genes sequenced to date use TGA as a stop codon (4). A number of these genes appear to use TAA and TAG as glutamine or glutamic acid codons at internal positions in the gene. A comparison of the derived amino acid sequence of Stylonychia lemnae a-tubulin with other known a-tubulins showed that a single TAA codon in the Stylonychia gene corresponded to glutamine (5). In addition, actin and two different H3 histone genes in Tetrahymena thermophila appear to use TAA as a glutamine codon (6-8), and two surface antigen genes in Paramecium contain both TAA and TAG codons that specify either glutamine or glutamic acid (9, 10). Both a TAA and a TAG codon are internal to an open reading frame that shares significant homology with ADP/ATP carrier proteins from other organisms and is found on an alternatively processed family of macronuclear chromosomes in Oxytricha fallax (11). Recent experiments have shown that T. thermophila possesses tRNAs with anticodons specific for TAA and TAG codons that are aminoacylated...

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“…Comparison of the small-subunit rRNAs from Euplotes aediculatus and 0. nova demonstrated considerable divergence in sequence (36). On the basis of this sequence divergence, it appears that the relationship between Euplotes and Oxytricha species is similar to that between Paramecium and Tetrahymena species (35).…”

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confidence: 98%

Telomere structure in Euplotes crassus: characterization of DNA-protein interactions and isolation of a telomere-binding protein.

Price¹

1990

Mol. Cell. Biol.

104

107

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The nucleoprotein structure of telomeres from Euplotes crassus was studied by using nuclease and chemical footprinting. The macronuclear telomeres were found to exist as DNA-protein complexes that are resistant to micrococcal nuclease digestion. Each complex encompassed 85 to 130 base pairs of macronuclear DNA and appeared to consist of two structural domains that are characterized by dissimilar DNA-protein interactions. Dimethyl sulfate footprinting demonstrated that very sequence-specific and salt-stable interactions occur in the most terminal region of each complex. DNase I footprinting indicated that DNA in the region 30 to 120 base-pairs from the 5' end lies on a protein surface; the interactions in this region of the complex are unlikely to be sequence specific. A 50-kilodalton telomere-binding protein was isolated. Binding of this protein protected telomeric DNA from BAL 31 digestion and gave rise to many of the sequence-specific DNA-protein interactions that were observed in vivo. The telomeric complexes from E. crassus were very similar in overall structure to the complexes found at Oxytricha telomeres. However, telomeric complexes from the two ciliates showed significant differences in internal organization. The telomeric DNA, the telomere-binding proteins, and the resultant DNA-protein interactions were all somewhat different. The telomere-binding proteins from the two ciliates were found to be less closely conserved than might have been expected. It appears that the proteins are tailored to match their cognate telomeric DNA.

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Sequence of the Small Subunit Ribosomal RNA Gene from the Hypotrichous Ciliate Euplotes aediculatus¹

Cited by 67 publications

References 17 publications

The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont

The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont

Differential use of termination codons in ciliated protozoa.

Telomere structure in Euplotes crassus: characterization of DNA-protein interactions and isolation of a telomere-binding protein.

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Sequence of the Small Subunit Ribosomal RNA Gene from the Hypotrichous Ciliate Euplotes aediculatus1

Cited by 67 publications

References 17 publications

The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont

The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont

Differential use of termination codons in ciliated protozoa.

Telomere structure in Euplotes crassus: characterization of DNA-protein interactions and isolation of a telomere-binding protein.

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Sequence of the Small Subunit Ribosomal RNA Gene from the Hypotrichous Ciliate Euplotes aediculatus¹