Nucleotide sequence of the 18S–26S rRNA intergene region of the sea urchin

Abstract

The DNA sequence which spans the internal transcribed spacers of a cloned ribosomal transcription unit from the sea urchin, Lyteehinus variegatus, has been determined. The region extends from the conserved Eco RI site near the 3' end of the 18S rDNA to a Bam HI site in the 26S rDNA and includes 232 nucleotides coding for 18S rRNA, 367 nucleotides of internal transcribed spacer, 159 nucleotides coding for 5.8S rRNA, 338 nucleotides of internal transcribed spacer, and 505 nucleotides coding for 26S rRNA. The rRNA coding regions were identified by direct analysis of 3'-labeled 18S and 5.8S rRNA and 5'-labeled 5. . INTBODUCTLIQNEukaryotic ribosomal RNA is synthesized as a large precursor containing 17/18S, 5.8S, and 26/28S rRNAs plus spacer sequences. The RNA is posttranscriptionally modified and cleaved at specific sites to produce a set of intermediate precursors and finally the mature rRNAs (1,2). Interest in the nature of these processing sites has led investigators to sequence gene/spacer junctions, as well as the entire internal transcribed spacer regions in the cases of yeast, Xenopus, rat, and mouse (3-7). In yeast, the 3' termini of precursor and mature rRNAs share a sequence homology which suggests a recognition signal for processing; the same is true for the 5' terminus/spacer junctions (3,4). However, equivalent features are not apparent in Xenopus, rat, or mouse rDNA (5-7). Comparison of mature RNA-internal transcribed spacer junctions among species revealed no consensus sequences outside of the conserved termini of the rRNA (viz., 3 '-18S, 5'-5.8S, and 5'-26/28S), although some homologies were found between Xenopus and rat spacer regions (6).In this paper, we present the nucleotide sequence of a portion of

Secondary structural modeling of the second internal transcribed spacer (ITS2) from Pfiesteria-like dinoflagellates (Dinophyceae)

“…S1) in the same region of all the predicted ITS2 secondary structures. This 18 nt conserved motif, located between 78 and 95 nt or 169 and 186 nt from the 5 0 start of ITS2, is consistent with a ribosomal processing site previously identified in yeast (Veldman et al, 1981) and rats (Reddy et al, 1983) and implicated to have a similar function in Xenopus (Hall and Maden, 1980), sea urchin (Hidenach and Stafford, 1984), flies (Tautz et al, 1988;Wesson, 1992), and parasitic flatworms (Morgan and Blair, 1998). Thus, this conserved region likely serves as a processing site in the PLDs as well.…”

Evolution of nuclear rDNA its sequences in the Cladophora albida/sericea clade (Chlorophyta)

“…Secondary-structural features of this model include the formation within both ITS regions of long hairpin structures and complementarity between the 18S rRNA 3'-region and the ITS1 Y-region, as well as between the 5.8S rRNA 3'-region and the 28S rRNA 5'-region. The latter features have also been demonstrated in green algae (Aimi et al 1992), fungi (Hansner et al 1993), higher plants (Venkateswarlu and Nazar 1991;Sub et al 1992;Ritland and Straus 1993), echinoderms (Hindenach and Stafford 1983), and several vertebrates (Subrahmanyam et al 1982;Furlong and Maden 1983), indicating their broad conservation. Most conserved domains within the Cladophora ITS sequences (Fig.…”

Secondary structure of mouse 28S rRNA and general model for the folding of the large rRNA in eukaryotes

“…In some cases, the presence of common structural features at equivalent positions in all species provided a means to extend the boundaries of the common structural core, and consequently to better delimitate the domains of variable size. Partial sequence data available for other eukaryotes (14)(15)(16)(17)(18) were also considered for testing several secondary structure features, as indicated in Figures and Table 1.…”