The site-specific ribosomal insertion element type II of Bombyx mori (R2Bm) contains the coding sequence for a reverse transcriptase-like enzyme.

Abstract

Two classes of DNA elements interrupt a fraction of the rRNA repeats of Bombyx mon. We have analyzed by genomic blotting and sequence analysis one class of these elements which we have named R2. These elements occupy approximately 9% of the rDNA units of B. mon and appear to be homologous to the type II rDNA insertions detected in Drosophila melanogaster. Approximately 25 copies of R2 exist within the B. mori genome, of which at least 20 are located at a precise location within otherwise typical rDNA units. Nucleotide sequence analysis has revealed that the 4.2-kilobase-pair R2 element has a single large open reading frame, occupying over 82% of the total length of the element. The central region of this 1,151-amino-acid open reading frame shows homology to the reverse transcriptase enzymes found in retroviruses and certain transposable elements. Amino acid homology of this region is highest to the mobile line 1 elements of mammals, followed by the mitochondrial type II introns of fungi, and the pol gene of retroviruses. Less homology exists with transposable elements of D. melanogaster and Saccharomyces cerevisiae. Two additional regions of sequence homology between LI and R2 elements were also found outside the reverse transcriptase region. We suggest that the R2 elements are retrotransposons that are site specific in their insertion into the genome. Such mobility would enable these elements to occupy a small fraction of the rDNA units of B. mori despite their continual elimination from the rDNA locus by sequence turnover.A fraction of the 28S ribosomal genes in several insect species is interrupted by segments of non-rDNA approximately 5 kilobases (kb) in length (see the review by Beckingham [3]). Based on the nucleotide sequences of their junction regions, these insertions have been divided into two classes. Type I elements have been reported in Drosophila virilis (34), D. melanogaster (7, 37), Calliphora erythrocephala (43), and Bombyx mori (12,16). They interrupt the 28S rRNA gene at a location approximately two-thirds of the distance from the 5' end of the gene and are flanked by a 14-base-pair (bp) duplication of rDNA sequences. Type II elements have only been reported in D. melanogaster (7,37) and B. mori (12,16). They interrupt the 28S gene 75 bp upstream of the type I elements and do not contain flanking duplications of rDNA sequences. In D. melanogaster, rDNA units containing either of these elements are transcribed at a significantly lower level than are the remaining rDNA units (20,23,28). To be consistent with the singleletter nomenclature frequently used to describe repetitive or transposable DNA elements and to avoid possible confusion with the type I and II intron sequences of fungal mitochondrial DNAs, we suggest that these elements be referred to as the Ri (type I) and R2 (type II) elements (R referring to rDNA units).Disruption of the large rRNA genes has also been detected in noninsect species. In Ascaris lumbricoides, a 4.5-kb element interrupts a small fraction of the 26S rRNA genes at ...

Evolutionary conservation and molecular characteristics of repetitive sequences of Drosophila koepferae

“…Finally, a report of sequences related to the D. melanogasten Jockey nonviral retroposon in the species Apis mellifera and Bombyx mon has appeared, although this evidence is also indirect, obtained by hybridizations with a D. melanogaster probe (Kimura et a!., 1993). Our study is the second direct demonstration, by means of sequencing, of retrotransposable sequences found in very distant species, after the finding of related Ri and R2 elements (ribosomal DNA insertions) in B. mon and D. melanogaster (Burke et at., 1987;Jacubczak et at., 1990) and later in other insect species (Jacubczak et a!., 1991). Although the low similarity at the nucleotide level is compatible with an old origin of both sequences, the protein similarities (75-79 per cent, identities ranging from 31 to 36 per cent) are quite high, if the fact that the sequenced regions are expected to be diverging rapidly is taken into account.…”

Rte‐1, a retrotransposon‐like element in Caenorhabditis elegans

“…Non-LTR elements are usually organized with two overlapping ORFs whereas Rte-1 has only one ORF. Other non-LTR elements with a single ORF besides Rte-1 have been reported, for example R2Bm [22]. There is no A-rich region at the 3' end of Rte-1, as would be expected for a non-LTR retrotransposon.…”

“…Amino acid sequence analysis of the longer ORF (ORF2) shows significant homology with reverse transcriptases of retroviruses [21], while the shorter ORF (ORF1) often has homology with the nucleic acid binding domain of the gag genes. There are also some elements which contain only one long ORF with homology to reverse transcriptase-like sequences [22,23]. Recently, the non-LTR retrotransposon from Bombyx mori (R2Bm) has been shown to encode an endonuclease that also contains reverse transcriptase activity [24,25].…”

High Processivity of the Reverse Transcriptase from a Non-long Terminal Repeat Retrotransposon

“…The intensity of the R2 band was compared with known concentrations of bovine serum albumin using the fluoroimaging function of a Storm 860 PhosphorImager and ImageQuant. Avian myeloblastosis virus (AMV) reverse transcriptase was obtained from Promega, poly(rA)/oligo(dT) [13][14][15][16][17][18] was from Amersham Biosciences, and poly(rA) was from Sigma.…”

“…Polymerization reactions were for 4 -7 min, depending on the length of the template. Reverse transcription reactions conducted under processive conditions were started by the simultaneous addition of 20 g of heparin and 2 g of poly(rA)/poly(dT) [13][14][15][16][17][18] along with the dNTP at the start of the polymerization reaction ("trap" conditions). The trap with poly(rA) templates included 20 g of heparin and 2 g of poly(dIdC), 6 g of E. coli RNA, and 0.1 g of oligo(dT) 18 .…”