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At least 19 recordsLinked to original sources
PubMed1992

Distribution of split 5.8S ribosomal RNA in Diptera.

Although the 5.8S ribosomal RNA (rRNA) of most eucaryotes consists of 155-170 nucleotides, in two dipterous species the 5.8S rRNA consists of two pieces, 123 and 30 nucleotides in length. The distribution of split 5.8S rRNA was studied in other Diptera and the most closely related order Siphonaptera to learn the origin of split 5.8S rRNA. Four species of mosquitoes, Culex tritaeniorhynchus, Culex pipiens molestus, Aedes albopictus, Anopheles sp. (Culicidae) had a single 5.8S rRNA consisting of approximately 154 nucleotides. A flea Ctenocephalides felis (Siphonaptera: Pulicidae) also had a single RNA of approximately 158 nucleotides. A crane fly (Tipulidae). a midge Orthocladius akamusi (Chironomidae), a robber fly (Asilidae), and a house fly Musca domestica (Muscidae), on the other hand, had divided 5.8S rRNA as did a fruit fly Drosophila melanogaster (Drosophilidae) and a dark-winged fungus gnat Sciara coprophila (Sciaridae). Three hypotheses are proposed on the relationship between the evolution of the 5.8S rRNA and the phylogeny of Diptera.

Animals↗
PubMed2006

Identification and typing of miso and soy sauce fermentation yeasts, Candida etchellsii and C. versatilis, based on sequence analyses of the D1D2 domain of the 26S ribosomal RNA gene, and the region of internal transcribed spacer 1, 5.8S ribosomal RNA gene and internal transcribed spacer 2.

We analyzed sequences of the D1D2 domain of the 26S ribosomal RNA gene (26S rDNA sequence), and the region of internal transcribed spacer 1, 5.8S ribosomal RNA gene and internal transcribed spacer 2 (ITS sequence) of the miso and soy sauce fermentation yeasts, Candida etchellsii and Candida versatilis, in order to evaluate the usefulness of this sequence analysis for identification and typing of these two species. In the 26S rDNA sequence method, the numbers of base substitutions among C. etchellsii strains were up to 2 in 482 bp (99.6% similarity), and they were divided into three types (types A, B, and C). Those of C. versatilis strains were also up to 2 in 521 bp (99.6% similarity) and they were divided into three types (types 1, 2, and 3). In the ITS sequence method, those of C. etchellsii strains were zero in 433 bp (type a, 100% similarity). Those of C. versatilis were 5 in 409 bp (98.8% similarity), divided into 4 types (types I, II, III and IV). It was found that molecular methods based on the sequences of the 26S rDNA D1D2 domain and the ITS region were rapid and precise compared with the physiological method for the identification and typing of these two species.

Base Sequence↗
PubMed1978

Non-ribosomal nucleotide sequences in 7-S RNA, the immediate precursor of 5.8-S ribosomal RNA in yeast.

The topography and the length of the non-ribosomal sequences present in 7-S RNA, the immediate precursor of 5.8-S ribosomal RNA, from the yeast Saccharomyces carlsbergensis were determined by analyzing the nucleotide sequences of the products obtained after complete digestion of 7-S RNA with RNase T1. The results show that 7-S RNA contains approximately 150 non-ribosomal nucleotides. The majority (90%) of the 7-S RNA molecules was found to have the same 5'-terminal pentadecanucleotide sequence as mature 5.8-S rRNA. The remaining 10% exhibited 5'-terminal sequences identical to those of 5.9-S RNA, which has the same primary structure as 5.8-S rRNA except for a slight extension at the 5' end [Rubin, G.M. (1974) Eur. J. Biochem. 41, 197--202]. These data show that the non-ribosomal nucleotides present in 7-S RNA are all located 3'-distal to the mature 5.8-S rRNA sequence. Moreover, it can be concluded that 5.9-S RNA is a stable rRNA rather than a precursor of 5.8-S rRNA. The 3'-terminal sequence of 5.8-S rRNA (U-C-A-U-U-UOH) is recovered in a much longer oligonucleotide in the T1 RNase digest of 7-S RNA having the sequence U-C-A-U-U-U-(C-C-U-U-C-U-C)-A-A-A-C-A-(U-U-C-U)-Gp. The sequences enclosed in brackets are likely to be correct but could not be established with absolute certainty. The arrow indicates the bond cleaved during processing. The octanucleotide sequence -A-A-A-C-A-U-U-C- located near the cleavage site shows a remarkable similarity to the 5'-terminal octanucleotide sequence of 7-S RNA (-A-A-A-C-U-U-U-C-). We suggest that these sequences may be involved in determining the specificity of the cleavages resulting in the formation of the two termini of 5.8-S rRNA.

Base Sequence↗
PubMed1976

Nucleotide sequence study of mouse 5.8S ribosomal RNA.

The primary structure of 5.8S mouse ribosomal RNA has been studied and compared to the structures previously established for other animal species. The results obtained show that mouse 5.8S ribosomal RNA yields pancreatic oligonucleotides with the same nucleotide sequence as the homologous oligonucleotides from rat cells. Furthermore T1 oligonucleotides of 5.8S ribosomal RNA from rat, mouse and human cells behave identically on fingerprinting fractionation and have the same composition as judged by pancreatic digestion. These results strongly suggest that the primary structures of 5.8S ribosomal RNA from rat, mouse and human cells are identical. This identity of structure is also found when the presence of several modified bases (psi and methylated bases) is considered. The findings emphasize the remarkable evolutionary stability of ribosomal gene structure. Comparison of the terminal regional of 5.8S RNA with those of 18S RNA reveals differences which imply a more complex mechanism underlying the maturation of 45S precursor RNA than the finding of identical structure would have suggested.

Animals↗
PubMed1999

Discrimination between two Perkinsus spp. isolated from the softshell clam, Mya arenaria, by sequence analysis of two internal transcribed spacer regions and the 5.8S ribosomal RNA gene.

The internal transcribed spacer (ITS-1 and ITS-2) regions and the 5.8S ribosomal RNA gene of 2 Perkinsus spp. (G117 and H49) originating from the softshell clam, Mya arenaria, of the Chesapeake Bay were cloned and sequenced to obtain evidence for their genetic divergence. A high level of heterogeneity in both regions, probably resulting from deletions, insertions, and base substitutions, was evident from alignments of the sequences of the 2 isolates with published sequences of other Perkinsus spp. The isolate G117 and other Perkinsus spp. were highly divergent (13-26% and 19-20% sequence divergence in ITS-1 and ITS-2, respectively). These regions in the isolate H49 and Perkinsus marinus were similar (99.07% and 99% for ITS-1 and ITS-2, respectively). Evidence obtained from a phylogenetic analysis using the aligned sequences suggests that G117 and H49 belong to 2 distinct species of Perkinsus. The isolate G117 possibly belongs to an as yet undescribed species of Perkinsus, and H49 belongs to the species P. marinus. The conclusions drawn from the genetic analysis of H49 and G117 are supported by previously reported morphological characteristics (McLaughlin & Faisal, 1998b). Isolates H49 and G117 originated from the same molluscan species demonstrating that at least 2 different species of Perkinsus can co-exist in 1 host.

Animals↗
PubMed1998

Comparison of the nucleotide sequence and secondary structure of the 5.8S ribosomal RNA gene of Chlamydomonas tetragama with those of green algae.

We have determined the nucleotide sequence of a PCR product corresponding to the 5.8S ribosomal RNA gene in Chlamydomonas tetragama and compared the obtained sequence with those of one red and eleven green algae. A phylogenetic tree based on the 5.8S rDNAs and comparison of their predicted secondary RNA structure, with attention to a region which has been proposed to base-pair with an internal guide sequence of an intron in the large subunit chloroplast rRNA, suggested that C. tetragama was not closely related with Chlamydomonas reinhardtii. These results support the previous idea that the genus Chlamydomonas is heterogenous.

Animals↗
PubMed1994

Inhibition of protein synthesis by an efficiently expressed mutation in the yeast 5.8S ribosomal RNA.

Recent studies on the inhibition of protein synthesis by specific anti 5.8S rRNA oligonucleotides strongly suggested that this RNA plays an important role in eukaryotic ribosome function. To evaluate this possibility further, a ribosomal DNA transcription unit from Schizosaccharomyces pombe was cloned into yeast shuttle vectors with copy numbers ranging from 2 to approximately 90 per cell; to allow direct detection of expressed RNA and to disrupt the function of the 5.8S rRNA molecule, a five base insertion was made in a universally conserved GAAC sequence. The altered mobility of the mutant RNA was readily detected by gel electrophoresis and analyses indicated that mutant RNA transcription reflected the ratio of plasmid to endogenous rDNA. The highest copy number plasmid resulted in about 40-50% mutant RNA. This mutant RNA was readily integrated into the ribosome structure resulting in an in vivo ribosome population which was also about 40-50% mutant; the rates of growth and protein synthesis were equally reduced by approximately 40%. A comparable level of inhibition in protein synthesis was demonstrated in vitro and polyribosomal profiles revealed a consistent increase in size. Subsequent RNA analyses indicated a normal distribution of mutant RNA in both monoribosomes and polyribosomes, but elevated tRNA levels in mutant polyribosomes. Additional mutations in alternate GAAC sequences revealed similar but cumulative effects on both protein synthesis and polyribosome profiles. Taken together, these results suggest little or no effect on initiation but provide in vivo evidence of a functional role for the 5.8S rRNA in protein elongation.

Base Sequence↗
PubMed1983

Structure of the ribosome-associated 5.8 S ribosomal RNA.

The structure of the 5.8 S ribosomal RNA in rat liver ribosomes was probed by comparing dimethyl sulfate-reactive sites in whole ribosomes, 60 S subunits, the 5.8 S-28 S rRNA complex and the free 5.8 S rRNA under conditions of salt and temperature that permit protein synthesis in vitro. Differences in reactive sites between the free and both the 28 S rRNA and 60 S subunit-associated 5.8 S rRNA show that significant conformational changes occur when the molecule interacts with its cognate 28 S rRNA and as the complex is further integrated into the ribosomal structure. These results indicate that, as previously suggested by phylogenetic comparisons of the secondary structure, only the "G + C-rich" stem may remain unaltered and a universal structure is probably present only in the whole ribosome or 60 S subunit. Further comparisons with the ribosome-associated molecule indicate that while the 5.8 S rRNA may be partly localized in the ribosomal interface, four cytidylic acid residues, C56, C100, C127 and C128, remain reactive even in whole ribosomes. In contrast, the cytidylic acid residues in the 5 S rRNA are not accessible in either the 60 S subunit or the intact ribosome. The nature of the structural rearrangements and potential sites of interaction with the 28 S rRNA and ribosomal proteins are discussed.

Animals↗
PubMed1982

The sequence of the 5.8 S ribosomal RNA of the crustacean Artemia salina. With a proposal for a general secondary structure model for 5.8 S ribosomal RNA.

We report the primary structure of 5.8 S rRNA from the crustacean Artemia salina. The preparation shows length heterogeneity at the 5'-terminus, but consists of uninterrupted RNA chains, in contrast to some insect 5.8 S rRNAs, which consist of two chains of unequal length separated in the gene by a short spacer. The sequence was aligned with those of 11 other 5.8 S rRNAs and a general secondary structure model derived. It has four helical regions in common with the model of Nazar et al. (J. Biol. Chem. 250, 8591-8597 (1975)), but for a fifth helix a different base pairing scheme was found preferable, and the terminal sequences are presumed to bind to 28 S rRNA instead of binding to each other. In the case of yeast, where both the 5.8 S and 26 S rRNA sequences are known, the existence of five helices in 5.8 S rRNA is shown to be compatible with a 5.8 S - 26 S rRNA interaction model.

Animals↗
PubMed1990

The primary structure of lupin seed 5.8 S ribosomal RNA.

The lack of colinearity between nucleotide sequence of the lupin 5.8 S rDNA gene (Rafalski, A.J., Wiewiórowski, M. and Soll, D. (1983) FEBS Lett. 152, 241-246) and 5.8 S rRNA of other plants (Erdmann, V.A. and Wolters, J. (1986) Nucleic Acids Res. 14, r1-r59.) prompted us to clarify this point by sequencing the native lupin 5.8 S rRNA. The sequence analysis was carried out using enzymatic and chemical methods. Lupin seed 5.8 S rRNA contains 164 nucleotides, including four modified ones: two residues of 2'-O-methylguanosine, one pseudouridine and one 2'-O-methyladenosine. The nucleotide sequence homology with the other plant 5.8 S rRNAs is approx. 88-96%.

Base Sequence↗
PubMed2000

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

Nucleotide sequence from the internal transcribed spacers (ITS1 and ITS2) and the 5.8S gene from the ribosomal RNA gene cluster of isolates of the scuticociliate Orchitophrya stellarum from 4 asteroid hosts were compared. Surprisingly, these data (495 bp) were identical for O. stellarum isolated from the testes of Asterias amurensis from Japan; Pisaster ochraceus from British Columbia, Canada; Asterias rubens from The Netherlands; and Asterias 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 O. stellarum. The sequence from the ITS1 (135 bp) and ITS2 (233 bp) of A. haemophila differed by 42.6 and 20.5% respectively from those of O. stellarum. Therefore, nucleotide sequence of the ITS regions in these scuticociliates is highly conserved.

Animals↗
PubMed1998

[Molecular phylogeny of the nuclear 5.8S ribosomal RNA genes in 37 species of Nicotiana genus].

The primary structure of the 5.8S rRNA gene was established in 37 species of the genus Nicotiana representing four different sections of the subgenus Petuniodes: Acuminatae, Alatae, Noctiflorae, and Suaveolentes. On the basis of these data, phylogenetic analysis was performed. The obtained results are in good agreement with the modern systematics of the genus. However, the bootstrap analysis gives only poor statistical support for the branches of the phylogenetic tree owing to a small number of phylogenetically informative positions.

Base Sequence↗
PubMed1990

Heterogeneity and expression of the Plasmodium falciparum 5.8S ribosomal RNA genes.

The number and expression of some of the large ribosomal RNA (rRNA) gene classes present in the human malaria parasite Plasmodium falciparum was determined. Southern blot analyses, using the 5.8S rRNA coding region as a marker, indicate that the P. falciparum genome contains at least 5 distinct subclasses of large rRNA genes. Dideoxy sequencing of the 5.8S rRNA domain and Northern blot analyses demonstrate that only one subclass is transcribed during the parasite's asexual erythrocytic life cycle.

Animals↗
PubMed2000

Inter- and intra-strain variation in the 5.8S ribosomal RNA and internal transcribed spacer sequences of Entamoeba histolytica and comparison with Entamoeba dispar, Entamoeba moshkovskii and Entamoeba invadens.

The ribosomal RNA genes in Entamoeba histolytica are located on circular DNA molecules in about 200 copies per genome equivalent. Nucleotide sequence analysis of the 5.8S rRNA gene and the flanking internal transcribed spacers was carried out to determine the degree of sequence divergence in the multiple rRNA gene copies of a given strain; amongst three different E. histolytica strains (HM-1:IMSS, Rahman and HK-9); and amongst four species of Entamoeba (Entamoeba histolytica, Entamoeba dispar, Entamoeba moshkovskii and Entamoeba invadens). The results show that all rRNA gene copies of a given strain are identical. Few nucleotide positions varied between strains of a species but the differences were very pronounced amongst species. In general, the internal transcribed spacer 2 sequence was more variable and may be useful for strain- and species-identification. The 5.8S rRNA gene and the internal transcribed spacer 2 of E. invadens were unusually small in size.

Animals↗
PubMed1986

Demonstration of the GC-rich common arm in yeast ribosomal 5.8S RNA via 500-MHz proton nuclear magnetic resonance and Overhauser enhancements.

In this paper we report the first 1H NMR study of the base-paired secondary structure of yeast 5.8S RNA. On the basis of a combination of homonuclear Overhauser enhancements and temperature dependence of the proton 500-MHz NMR spectrum, we are able to identify and assign eight of the nine base pairs in the most thermally stable helical arm: G116.C137-C117.G136-C118.G135- C119.G134-C120.G133-U121.G132- U122.A131-G123.C130. This arm contains an unusually temperature-stable (to 71 degrees C) segment of four consecutive G.C base pairs. This work constitutes the most direct evidence to date for the existence and base-pair sequence of the GC-rich helix, which is common to most currently popular secondary structural models for eukaryotic 5.8S ribosomal RNA.

Base Composition↗