Introns and their flanking sequences of<i>Bombyx mori</i>rDNA

Fujiwara, Haruhiko; Ogura, Teru; Takada, Naoko; Miyajima, Naoko; Ishikawa, Hajime; Maekawa, Hideaki

doi:10.1093/nar/12.17.6861

Cited by 51 publications

(42 citation statements)

References 30 publications

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“…6). In an area of 60 amino acids, 16 positions were identical between R2 and Li, corresponding to 27% homology. This VOL.…”

Section: Resultsmentioning

confidence: 99%

“…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.…”

mentioning

confidence: 99%

“…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.…”

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confidence: 99%

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

Burke¹,

Calalang²,

Eickbush³

1987

Mol. Cell. Biol.

130

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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 ...

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“…6). In an area of 60 amino acids, 16 positions were identical between R2 and Li, corresponding to 27% homology. This VOL.…”

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

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

Burke¹,

Calalang²,

Eickbush³

1987

Mol. Cell. Biol.

130

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“…The region analyzed consisted of positions 467 to 787 of the VOL. 15,1995 STRUCTURAL ANALYSIS OF TRAS1 4547 TRAS1-ORF2 (from SFTV to DKLT) and includes the four conserved amino acid motifs identified by Poch et al (40). A phylogenetic tree constructed from the alignment is shown in Fig.…”

mentioning

confidence: 99%

Structural Analysis of TRAS1, a Novel Family of Telomeric Repeat-Associated Retrotransposons in the Silkworm, Bombyx mori

Okazaki

Ishikawa

Fujiwara

1995

Molecular and Cellular Biology

106

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We characterized TRAS1, a retrotransposable element which was inserted into the telomeric repetitive sequence (CCTAA) n of the silkworm, Bombyx mori. The complete sequence of TRAS1, a stretch of 7.8 kb with a poly(A) tract at the 3 end, was determined. No long terminal repeat (LTR) was found at the termini of the element. TRAS1 contains gag-and pol-like open reading frames (ORFs) which are similar to those of non-LTR retrotransposons. The two ORFs overlap but are one nucleotide out of frame (؉1 frameshift). Most of the approximately 250 copies of TRAS1 elements in the genome were highly conserved in the structure. Chromosomal in situ hybridization showed that TRAS1 elements are clustered at the telomeres of Bombyx chromosomes. A phylogenetic analysis using the amino acid sequence of the reverse transcriptase domain within the pol-like ORF revealed that TRAS1 falls into one lineage with R1, which is a family of non-LTR retrotransposons inserted into the same site within the 28S ribosomal DNA unit in most insects. TRAS1 may have been derived from R1 and changed the target specificity so that TRAS1 inserts into the telomeric repetitive sequence (CCTAA) n . Southern hybridization and Bal 31 exonuclease analyses showed that TRAS1 elements are clustered proximal to the terminal long tract of (CCTAA) n . TRAS1 is a novel family of non-LTR retrotransposons which are inserted into the telomeric repetitive sequences as target sites.

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“…3A and Table 1). R7 in R1 clade (16) and R8 in R2 clade (77) insert into 18S rDNA, while the remaining seven R elements, R1 (78,79), R2 (7,78), R4 (24), R5 (80), R6 (16), R9 (81), and RT (82), are inserted into the 28S rDNA. It is of interest that all R-element target sites within 28S and 18S rDNA are highly conserved among organisms.…”

Section: Rdna-specific Non-ltr Elements (R-elements)mentioning

confidence: 99%

Site-specific non-LTR retrotransposons

Fujiwara

2015

Microbiol Spectr

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Although most of non-long terminal repeat (non-LTR) retrotransposons are incorporated in the host genome almost randomly, some non-LTR retrotransposons are incorporated into specific sequences within a target site. On the basis of structural and phylogenetic features, non-LTR retrotransposons are classified into two large groups, restriction enzyme-like endonuclease (RLE)-encoding elements and apurinic/apyrimidinic endonuclease (APE)-encoding elements. All clades of RLE-encoding non-LTR retrotransposons include site-specific elements. However, only two of more than 20 APE-encoding clades, Tx1 and R1, contain site-specific non-LTR elements. Site-specific non-LTR retrotransposons usually target within multi-copy RNA genes, such as rRNA gene (rDNA) clusters, or repetitive genomic sequences, such as telomeric repeats; this behavior may be a symbiotic strategy to reduce the damage to the host genome. Site-and sequence-specificity are variable even among closely related non-LTR elements and appeared to have changed during evolution. In the APE-encoding elements, the primary determinant of the sequence-specific integration is APE itself, which nicks one strand of the target DNA during the initiation of target primed reverse transcription (TPRT). However, other factors, such as interaction between mRNA and the target DNA, and access to the target region in the nuclei also affect the sequence-specificity. In contrast, in the RLE-encoding elements, DNA-binding motifs appear to affect their sequence-specificity, rather than the RLE domain itself. Highly specific integration properties of these site-specific non-LTR elements make them ideal alternative tools for sequence-specific gene delivery, particularly for therapeutic purposes in human diseases.

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Introns and their flanking sequences ofBombyx morirDNA

Cited by 51 publications

References 30 publications

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

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

Structural Analysis of TRAS1, a Novel Family of Telomeric Repeat-Associated Retrotransposons in the Silkworm, Bombyx mori

Site-specific non-LTR retrotransposons

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