Comparison of primary and secondary 26S rRNA structures in twoTetrahymena species: Evidence for a strong evolutionary and structural constraint in expansion segments

Engberg, Jan; Nielsen, Henrik; Lenaers, Guy; Murayama, Ohoshi; Fujitani, Hideo; Higashinakagawa, Toru

doi:10.1007/bf02101107

Cited by 31 publications

(28 citation statements)

References 36 publications

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“…The 28S rRNA divergent domains have neither a known evolutionary origin nor any known functions (13), and they have evolved within strict frames for secondary, but not primary, structure (19). The D2, D6, and D8 domains, which were implicated in apoptosis ( Fig.…”

Section: Discussionmentioning

confidence: 99%

Fine Mapping of 28S rRNA Sites Specifically Cleaved in Cells Undergoing Apoptosis

Houge

Robaye

Eikhom

et al. 1995

Molecular and Cellular Biology

115

135

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Bona fide apoptosis in rat and human leukemia cells, rat thymocytes, and bovine endothelial cells was accompanied by limited and specific cleavage of polysome-associated and monosome-associated 28S rRNA, with 18S rRNA being spared. Specific 28S rRNA cleavage was observed in all instances of apoptotic death accompanied by internucleosomal DNA fragmentation, with cleavage of 28S rRNA and of DNA being linked temporally. This indicates that 28S rRNA fragmentation may be as general a feature of apoptosis as internucleosomal DNA fragmentation and that concerted specific cleavage of intra-and extranuclear polynucleotides occurs in apoptosis. Apoptosis-associated cleavage sites were mapped to the 28S rRNA divergent domains D2, D6 (endothelial cells), and D8. The D2 cuts occurred in hairpin loop junctions considered to be buried in the intact ribosome, suggesting that this rRNA region becomes a target for RNase attack in apoptotic cells. D8 was cleaved in two exposed UU(U) sequences in bulge loops. Treatment with agents causing necrotic cell death or aging of cell lysates failed to produce any detectable limited D2 cleavage but did produce a more generalized cleavage in the D8 region. Of potential functional interest was the finding that the primary cuts in D2 exactly flanked a 0.3-kb hypervariable subdomain (D2c), allowing excision of the latter. The implication of hypervariable rRNA domains in apoptosis represents the first association of any functional process with these enigmatic parts of the ribosomes.

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Section: Discussionmentioning

confidence: 99%

Fine Mapping of 28S rRNA Sites Specifically Cleaved in Cells Undergoing Apoptosis

Houge

Robaye

Eikhom

et al. 1995

Molecular and Cellular Biology

115

135

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“…Differenc~s the !TS regions have also been found between strains and species of ciliates. For example, the nucleotide sequence of 4 wild isolates of Cryptocaryon irritans differed by 0.6 to 4.1 % in the ITSl (Diggles & Adlard 1997) while that of 2 species of Tetrahymena differed by 3% in ITSl and 10 % in ITS2 (Engberg et al 1990). …”

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confidence: 99%

“…A. vulgaris (Prince Edward Island, Canada, AF107774) and Pisaster ochraceus (British Columbia, Canada, AF107775 fungi, plants and animals (Torres et al 1990). However, there is also an imbalance in the G C content of the ITSl and ITS2 in the ciliate Tetrahymena therrnophila (ITS1 = 29.8% GC content, ITS2 = 43.3%) (Engberg et al 1990), the dinoflayellate Dictyostelium discoideum (ITS1 = 28%, ITS2 = 43%) (Ozaki et al 1984), the kelp Alaria marginata (ITS1 = 52%, ITS2 = 67 %) and many plants (Saunders & Druehl 1993). As expected, the 5.8s rRNA gene was highly conserved between these scuticociliates.…”

mentioning

confidence: 99%

Conservation of sequence in the internal transcribed spacers and 5.8S ribosomal RNA among geographically separated isolates of parasitic scuticociliates (Ciliophora, Orchitophryidae)

Goggin

Murphy²

2000

Dis. Aquat. Org.

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Nucleotide sequence from the internal transcribed spacers (ITS1 and ITS2) and the 5.8s gene from the r~bosomal RNA gene cluster of isolates of the scuticociliate Orchitophrya stellarum from 4 asteroid hosts were compared. Surprisingly, these data (495 bp) were identical for 0. stellarum isolated from the testes of Astenas amurensis from Japan; Pisaster ochraceus from British Columbia, Canada; Asterias rubens from The Netherlands; and Astenas vulgaris from Prince Edward Island, Canada. These sequence data were compared to those from 3 scuticociliates which parasitise crustaceans: Mesanophrys pugettensis, M. chesapeakensis and Anophryoides haemophila. No difference was found in this region between the nucleotide sequence of M pugettensis and M. chesapeakensis The sequence of Mesanophrys spp. differed by 9 2 % in the ITS1 and 4.7 % in the ITS2 from that of 0. stellarum. The sequence from the ITS1 (135 bp) and ITS2 (233 bp) of A. haenlophila differed by 42 6 and 20.5% respectively from those of 0. stellarum. Therefore, nucleotide sequence of the ITS regions in these scuticociliates is highly conserved.

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“…Some rRNAs are fragmented (2,5,12,13,15,36,39,45,47) (44). Comparison of rRNA sequences from diverse phyla offers support for the secondary structure model of most of the LSU rRNA but is uninformative for variable regions because they are so divergent.…”

mentioning

confidence: 99%

“…Some rRNAs are fragmented (2,5,12,13,15,36,39,45,47), and all breakpoints lie within variable regions (18). Based partially on this fact, one model (39) proposes that rRNA was originally a collection of small RNAs.…”

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confidence: 99%

An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence.

1994

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Regions extremely variable in size and sequence occur at conserved locations in eukaryotic rRNAs. The functional importance of one such region was determined by gene reconstruction and replacement in Tetrahymena thermophila. Deletion of the D8 region of the large-subunit rRNA inactivates T. thermophila rRNA genes (rDNA): transformants containing only this type of rDNA are unable to grow. Replacement with an unrelated sequence of similar size or a variable region from a different position in the rRNA also inactivated the rDNA. Mutant rRNAs resulting from such constructs were present only in precursor forms, suggesting that these rRNAs are deficient in either processing or stabilization of the mature form. Replacement with D8 regions from three other organisms restored function, even though the sequences are very different. Thus, these D8 regions share an essential functional feature that is not reflected in their primary sequences. Similar tertiary structures may be the quality these sequences share that allows them to function interchangeably.Although much of the secondary structure of rRNA is evolutionarily conserved, these portions are interspersed with discrete variable regions at conserved positions within the structure (18). The more prominent ones have been identified as expansion segments (7,46), divergent domains (27), or variable regions (17). The variability of some regions is such that closely related organisms such as mice and rats show many sequence differences (26), and sequence differences are even detected in different copies of the rRNA genes (rDNAs) from a single organism (25). These regions are absent in most eubacteria and archaebacteria and present in most eukaryotes (19,46), although exceptions to this rule have recently been found (4, 10, 43). The functional role of variable regions has not been identified. While their absence from most eubacteria suggests that they are dispensable, their almost universal presence in eukaryotes implies that they may be important in these organisms.Two models for the evolution of rRNA both imply that variable regions initially had no functional role. Some rRNAs are fragmented (2,5,12,13,15,36,39,45,47) (44). Comparison of rRNA sequences from diverse phyla offers support for the secondary structure model of most of the LSU rRNA but is uninformative for variable regions because they are so divergent. Secondary structure models for variable regions have been proposed based on the assumption that, in addition to having a low free energy, a model must be structurally similar for all species (26). Comparing the sequences of closely related species has recently produced more-refined models (12,20).No functional role has been defined for any variable region. However, some pertinent evidence does exist. The D2 and D12 regions of the LSU rRNA in Tetrahymena thennophila tolerate insertion mutations with no apparent diminution of rRNA function in vivo, while insertions in the D8 region totally obliterate rRNA function (40a, 41). In Saccharomyces cerevisiae, rRNAs beari...

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Comparison of primary and secondary 26S rRNA structures in twoTetrahymena species: Evidence for a strong evolutionary and structural constraint in expansion segments

Cited by 31 publications

References 36 publications

Fine Mapping of 28S rRNA Sites Specifically Cleaved in Cells Undergoing Apoptosis

Fine Mapping of 28S rRNA Sites Specifically Cleaved in Cells Undergoing Apoptosis

Conservation of sequence in the internal transcribed spacers and 5.8S ribosomal RNA among geographically separated isolates of parasitic scuticociliates (Ciliophora, Orchitophryidae)

An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence.

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