Comparisons of large subunit rRNAs reveal some eukaryote-specific elements of secondary structure

Michot, Bernard; Bachellerie, Jean‐Pierre

doi:10.1016/0300-9084(87)90267-7

Cited by 103 publications

(90 citation statements)

References 35 publications

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“…The fact that D2 can be differentially cleaved depending upon (primary) cleavage in D8 makes a direct structural interaction between D2 and D8 more likely. This supports the hypothesis that the coevolution of the D2 and D8 domains with respect to both size and GC content reflects a functional link between these two major ribosomal variable regions (35). In all cases the fragmentation patterns obtained were reproduced when the same cells were exposed to okadaic acid (data not shown), an inducer of apoptosis in several experimental systems (2).…”

Section: Discussionsupporting

confidence: 79%

“…The fragments formed after cleavage in the D8 domain corresponded to those found in the other cell systems studied, but cleavage of the D6 domain was unique to the bovine endothelial cells. Since bovine 28S rRNA has not been sequenced, an accurate probing of cleavage sites could not be performed, but it is of interest that the D2, D6, and D8 domains all have particularly variable nucleotide sequences (16,35).…”

Section: Resultsmentioning

confidence: 99%

“…The small arrow between the CC and GG in cleavage site 1 marks the cleavage position suggested by the S1 nuclease protection analysis. The proposed secondary structure of the complete D2 domain is shown in the box (35). Arrows orient the sequence in the 5Ј-to-3Ј direction.…”

Section: Discussionmentioning

confidence: 99%

“…(C) Schematic drawing of the D8b subdomain showing the apoptotic cleavage sites (numbered 3 and 4). The proposed secondary structure of the complete D8 domain is in the box (35). Arrows orient the sequence in the 5Ј-to-3Ј direction.…”

Section: Discussionmentioning

confidence: 99%

“…Arrows orient the sequence in the 5Ј-to-3Ј direction. The circled U was not included in the published genomic rat 28S rRNA sequence (3), but a U in this position was found in human 28S rRNA (30,35). The two bases in lowercase letters indicate nucleotides in the genomic rat sequence that were not found in IPC-81 rRNA.…”

Section: Discussionmentioning

confidence: 99%

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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: Discussionsupporting

confidence: 79%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 3 more Smart Citations

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

Houge

Robaye

Eikhom

et al. 1995

Molecular and Cellular Biology

115

135

View full text Add to dashboard Cite

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Functional analysis of transcribed spacers of yeast ribosomal DNA.

et al. 1990

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Making use of an rDNA unit, containing oligonucleotide tags in both the 17S and 26S rRNA gene, we have analyzed the effect of various deletions in the External Transcribed Spacer (ETS) and in one of the Internal Transcribed Spacers 1 (ITS1) on the process of ribosome formation in yeast. By following the fate of the tagged transcripts of this rDNA unit in vivo by Northern hybridization we found that deleting various parts of the ETS prevents the accumulation of tagged 17S rRNA and its assembly into 40S subunits, but not the formation of 60S subunits. Deleting the central region of ITS1, including a processing site that is used in an early stage of the maturation process, was also found to prevent the accumulation of functional 49 S subunits, whereas no effect on the formation of 60S subunits was detected. The implications of these findings for yeast pre‐rRNA processing are discussed.

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Ribosomal DMA sequences discriminate among toxic and non‐toxic Pseudonitzschia species

et al. 1994

Natural Toxins

103

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Cultured isolates of Pseudonitzschia australis Frenguelli, P. delicatissima (Cleve) Heiden, P. americana (Hasle) Fryxell, P. pungens (Grunow) Hasle, and P. pungens f. multiseries (Hasle) Hasle from Monterey Bay, California, were compared on the basis of their large-subunit ribosomal RNA gene (LsrDNA). Pseudonitzschia australis, P. pungens f. multiseries, and P. delicatissima were previously shown to produce the neurotoxin domoic acid; the remaining isolates are considered non-toxic. For each isolate approximately 800 base pairs of LsrDNA, encompassing both evolutionarily conserved and evolutionarily variable regions of the molecule, were amplified using the polymerase chain reaction (PCR) and sequenced. Phylogenetic trees generated by parsimony analysis of aligned sequences afford a preliminary view of the organisms genetic relationships. Species defined by morphological criteria are also distinguishable by LsrDNA sequence. Organisms known or suspected to produce domoic acid cluster at different termini on the phylogenetic tree. Two genetically distinct strains of P. australis and P. pungens were identified. Development of a restriction fragment length polymorphism (RFLP) assay of the LsrDNA is described. The RFLP assay discriminates each species, including distinguished strains of P. australis and P. pungens. The restriction test provides a rapid and convenient method for screening isolates' LsrDNA, facilitating further tests of the apparent positive correlation between Pseudonitzschia species' ribosomal gene signatures, morphology, and capacity to produce domoic acid.

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Comparisons of large subunit rRNAs reveal some eukaryote-specific elements of secondary structure

Cited by 103 publications

References 35 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

Functional analysis of transcribed spacers of yeast ribosomal DNA.

Ribosomal DMA sequences discriminate among toxic and non‐toxic Pseudonitzschia species

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