Complete nucleotide sequence of mouse 18 S rRNA gene: comparison with other available homologs

We present the complete sequence of mouse 18 S rRNA. As indicated by comparison with yeast, Xenopus and rat, the conservation of eukaryotic 18 S rRNA sequences is extensive. However, this conservation is far from being uniform along the molecule: most of the base changes and the size differences between species are concentrated at specific locations. Two distinct classes of divergent traces can be detected which differ markedly in their rates of nucleotide substitution during evolution, and should prove valuable in additional comparative analyses, both for eukaryotic taxonomy and for rRNA higher order organization. Mouse and rat 18 S rRNA sequences differ by only 14 point changes over the 1869 nucleotides of the molecule.     

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

We present a secondary structure model for the entire sequence of mouse 28S rRNA (1) which is based on an extensive comparative analysis of the available eukaryotic sequences, i.e. yeast (2, 3), Physarum polycephalum (4), Xenopus laevis (5) and rat (6). It has been derived with close reference to the models previously proposed for yeast 26S rRNA (2) and for prokaryotic 23S rRNA (7-9). Examination of the recently published eukaryotic sequences confirms that all pro- and eukaryotic large rRNAs share a largely conserved secondary structure core, as already apparent from the previous analysis of yeast 26S rRNA (2). These new comparative data confirm most features of the yeast model (2). They also provide the basis for a few modifications and for new proposals which extend the boundaries of the common structural core (now representing about 85% of E. coli 23S rRNA length) and bring new insights for tracing the structural evolution, in higher eukaryotes, of the domains which have no prokaryotic equivalent and are inserted at specific locations within the common structural core of the large subunit rRNA.     

'boxA'-like sequence between the 16 S/23 S spacer in rRNA operon of mycoplasmas.

We have found that a boxA-like sequence is conserved in the 16 S and 23 S rRNA intergenic spacer regions of mycoplasmas, and that it always locates on loop regions of the hypothetical secondary stem-loop structures. A nucleotide sequence similar to the '-10' box of prokaryotic promoters was identified at upstream sites of the boxA-like sequence in the 16 S/23 S spacer regions. These structures may represent an internal promoter between the 16 S and 23 S rRNA genes in mycoplasmas.     

Intraspecific divergence of Saccharomyces kluyveri as revealed by the nucleotide sequences of 18S-28S rRNA spacer regions and alpha-galactosidase MEL genes

In the five strains classified as the yeast Saccharomyces kluyveri, several substitutions were observed in the two internal transcribed spacer regions between 18S and 28S rRNA. A PCR reaction with primers targeted to the MEL1 gene of Saccharomyces cerevisiae amplified fragments of the expected size, and those sequences showed significant divergence in the strains of S. kluyveri.     

Intermolecular mRNA-rRNA hybridization and the distribution of potential interaction regions in murine 18S rRNA.

Intermolecular hybridization experiments show that murine 18S rRNA and 28S rRNA are capable of forming stable hybrid structures with mRNA from genes p53, c-myc and c-mos from the same species. Both 5'-uncoding and coding oncogene p53 mRNA regions contain fragments interacting with rRNA. Computer analysis revealed 18S rRNA fragments complementary to oligonucleotides frequently met in mRNA, which are potential hybridization regions (clinger-fragments). The distribution of clinger-fragments along 18S rRNA sequence is universal at least for one hundred murine mRNA sequences analyzed. Maximal frequencies of oligonucleotides complementary to 18S rRNA clinger-fragments are reliably (2-3 times) higher for mRNA than for intron sequences and randomly generated sequences. The results obtained suggest a possible role of clinger-fragments in translation processes as universal regions of mRNA binding.     

Sequence and secondary structure of mouse 28S rRNA 5''terminal domain. Organisation of the 5.8S-28S rRNA complex.

We present the sequence of the 5' terminal 585 nucleotides of mouse 28S rRNA as inferred from the DNA sequence of a cloned gene fragment. The comparison of mouse 28S rRNA sequence with its yeast homolog, the only known complete sequence of eukaryotic nucleus-encoded large rRNA (see ref. 1, 2) reveals the strong conservation of two large stretches which are interspersed with completely divergent sequences. These two blocks of homology span the two segments which have been recently proposed to participate directly in the 5.8S-large rRNA complex in yeast (see ref. 1) through base-pairing with both termini of 5.8S rRNA. The validity of the proposed structural model for 5.8S-28S rRNA complex in eukaryotes is strongly supported by comparative analysis of mouse and yeast sequences: despite a number of mutations in 28S and 5.8S rRNA sequences in interacting regions, the secondary structure that can be proposed for mouse complex is perfectly identical with yeast's, with all the 41 base-pairings between the two molecules maintained through 11 pairs of compensatory base changes. The other regions of the mouse 28S rRNA 5'terminal domain, which have extensively diverged in primary sequence, can nevertheless be folded in a secondary structure pattern highly reminiscent of their yeast' homolog. A minor revision is proposed for mouse 5.8S rRNA sequence.     

Intermolecular hybridization of 5S rRNA with 18S rRNA: identification of a 5'-terminally-located nucleotide sequence in mouse 5S rRNA which base-pairs with two specific complementary sequences in 18S rRNA.

Eukaryotic 5S rRNA hybridizes specifically with 18S rRNA in vitro to form a stable intermolecular RNA:RNA hybrid. We have used 5S rRNA/18S rRNA fragment hybridization studies coupled with ribonuclease digestion and primer extension/chain termination analysis of 5S rRNA:18S rRNA hybrids to more completely map those mouse 5S rRNA and 18S rRNA sequences responsible for duplex formation. Fragment hybridization analysis has defined a 5'-terminal region of 5S rRNA (nucleotides 6-27) which base-pairs with two independent sequences in 18S rRNA designated Regions 1 (nucleotides 1157-1180) and 2 (nucleotides 1324-1339). Ribonuclease digestion of isolated 5S rRNA:18S rRNA hybrids with both single-strand- and double-strand-specific nucleases supports the involvement of this 5'-terminal 5S rRNA sequence in 18S rRNA hybridization. Primer extension/chain termination analysis of isolated 5S rRNA:18S rRNA hybrids confirms the base-pairing of 5S rRNA to the designated Regions 1 and 2 of 18S rRNA. Using these results, 5S rRNA:18S rRNA intermolecular hybrid structures are proposed. Comparative sequence analysis revealed the conservation of these hybrid structures in higher eukaryotes and the same but smaller core hybrid structures in lower eukaryotes and prokaryotes. This suggests that the 5S rRNA:16S/18S rRNA hybrids have been conserved in evolution for ribosome function.     

A very large repeating unit of mouse DNA containing the 18S, 28S and 5.8S rRNA genes

The organization of the 18S, 28S and 5.8S rRNA genes in the mouse has been elucidated by mapping with restriction endonucleases Eco RI, Hind III and Bam HI. Ribosomal DNA fragments were detected in electrophoretically fractionated digests of total nuclear DNA by in situ hybridization with radioiodinated rRNAs or with complementary RNA synthesized directly on rRNA templates. A map of the rDNA which includes 13 restriction sites was constructed from the sizes of rDNA fragments and their labeling by different probes The map indicates that the rRNA genes lie within remarkably large units of reiterated DNA, at least 44,000 base pairs long. At least two, and possibly four, classes of repeating unit can be distinguished, the heterogeneity probably residing in the very large nontranscribed spacer region. The 5.8S rRNA gene lies in the transcribed region between the 18S and 28S genes.     

Complete nucleotide sequence of the 16S rRNA gene of Mycobacterium bovis BCG.

The complete nucleotide sequence of the 16S rRNA gene of Mycobacterium bovis BCG was determined. Its coding region was estimated to be 1,536 base pairs long. The nucleotide sequence of the gene in M. bovis BCG has homologies of 75 and 89% with those of Escherichia coli and Streptomyces lividans, respectively.     

Turnover of ribosomal 28S and 18S rRNA during rat liver regeneration

The turnover of 28S and 18S rRNA was studied in the course of 12 d after partial hepatectomy, including the proliferative (1st to 5th d) and post-proliferative (6th to 12th d) phases of liver regeneration. Turnover data, as the day-to-day rates of synthesis and degradation of 28S and 18S rRNA, were obtained by employing a suitable experimental procedure for the estimation of the increase of the amount of rRNA in the regenerating liver. It was found that 28S and 18S rRNA are accumulated into the cytoplasm and degraded at identical rates both in the proliferative and post proliferative phases. The turnover of both rRNA moieties is markedly slower during the first 3 d of liver regeneration.     

Analysis of DNA encoding 23S rRNA and 16S–23S rRNA intergenic spacer regions from Plesiomonas shigelloides

Amplification of the gene encoding 23S rRNA of Plesiomonas shigelloides by polymerase chain reaction (PCR), with primers complementary to conserved regions of 16S and the 3' end of 23S rRNA genes, resulted in a DNA fragment of approximately 3 kb. This fragment was cloned in Escherichia coli and its nucleotide sequence determined. The region encoding 23S rRNA shows high homology with the published sequences of 23S rRNA from other members of the gamma division of Proteobacteria. The sequence of the intergenic spacer region, between the 16S and 23S rRNA genes, was determined in a further two clones. In one the sequence of a single tRNA(Glu) was found which was absent from the other two. This variation in sequence suggests that the different clones may be derived from different ribosomal RNA operons.