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Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

Sela N, Stern A, Makalowski W, Pupko T, Ast G - Biol. Direct (2008)

Bottom Line: Transduplication of protein-coding genes is common in plants, but is unknown of in animals.The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM) that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene.Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel. noasela@post.tau.ac.il

ABSTRACT
Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR) sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM) that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif.

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Y48G1BL.4 gene with predicted RRM domain. (A) A schematic illustration of the Y48G1BL.4 gene with predicted exons and an intron, and the position of the Turmoil-1 sequence within the genome. (B) Pairwise alignment (using bl2seq) between Turmoil-1 and the Y48G1BL.4 DNA sequence. The intron sequence is indicated by lower-case letters and the protein-coding region by upper-case letters. The potential new 5' splice site is marked in red and the 5' splice site position within the original RRM domain is marked with an arrow. (C) The predicted three-dimensional structure of the RRM domain generated from Y48G1BL.4.
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Figure 3: Y48G1BL.4 gene with predicted RRM domain. (A) A schematic illustration of the Y48G1BL.4 gene with predicted exons and an intron, and the position of the Turmoil-1 sequence within the genome. (B) Pairwise alignment (using bl2seq) between Turmoil-1 and the Y48G1BL.4 DNA sequence. The intron sequence is indicated by lower-case letters and the protein-coding region by upper-case letters. The potential new 5' splice site is marked in red and the 5' splice site position within the original RRM domain is marked with an arrow. (C) The predicted three-dimensional structure of the RRM domain generated from Y48G1BL.4.

Mentions: One of the Turmoil-1 copies (number 1 in Table 1) contains within it an open reading frame (ORF) with the accession number Y48G1BL.4. It contains two putative exons and an intron (Figure 3), which are similar to the RRM domain. The 5' splice site that corresponds to that in the rsp-2 transcript has been mutated. A novel 5' splice site is most likely located nine nucleotides downstream from the original one. At this site, a point mutation changed an AT into a GT dinucleotide (marked in red in Figure 3). Usage of this 5' splice site maintains the ORF equivalent to that of the RRM domain of rsp-2 with the exception of the addition of three amino acids. These additional residues should have a negligible effect on the three-dimensional structure of the RRM domain (Figure 3C). This ORF, however, may not be transcriptionally active as its sequence is only found in the UNIPROT database (accession number Q9N3P9), and there is no EST or cDNA supporting evidence. If this is the case, it would be consistent with reports that indicate that all known transduplicates in rice, in spite of their genomic abundance, are pseudogenes [16].


Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

Sela N, Stern A, Makalowski W, Pupko T, Ast G - Biol. Direct (2008)

Y48G1BL.4 gene with predicted RRM domain. (A) A schematic illustration of the Y48G1BL.4 gene with predicted exons and an intron, and the position of the Turmoil-1 sequence within the genome. (B) Pairwise alignment (using bl2seq) between Turmoil-1 and the Y48G1BL.4 DNA sequence. The intron sequence is indicated by lower-case letters and the protein-coding region by upper-case letters. The potential new 5' splice site is marked in red and the 5' splice site position within the original RRM domain is marked with an arrow. (C) The predicted three-dimensional structure of the RRM domain generated from Y48G1BL.4.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2572040&req=5

Figure 3: Y48G1BL.4 gene with predicted RRM domain. (A) A schematic illustration of the Y48G1BL.4 gene with predicted exons and an intron, and the position of the Turmoil-1 sequence within the genome. (B) Pairwise alignment (using bl2seq) between Turmoil-1 and the Y48G1BL.4 DNA sequence. The intron sequence is indicated by lower-case letters and the protein-coding region by upper-case letters. The potential new 5' splice site is marked in red and the 5' splice site position within the original RRM domain is marked with an arrow. (C) The predicted three-dimensional structure of the RRM domain generated from Y48G1BL.4.
Mentions: One of the Turmoil-1 copies (number 1 in Table 1) contains within it an open reading frame (ORF) with the accession number Y48G1BL.4. It contains two putative exons and an intron (Figure 3), which are similar to the RRM domain. The 5' splice site that corresponds to that in the rsp-2 transcript has been mutated. A novel 5' splice site is most likely located nine nucleotides downstream from the original one. At this site, a point mutation changed an AT into a GT dinucleotide (marked in red in Figure 3). Usage of this 5' splice site maintains the ORF equivalent to that of the RRM domain of rsp-2 with the exception of the addition of three amino acids. These additional residues should have a negligible effect on the three-dimensional structure of the RRM domain (Figure 3C). This ORF, however, may not be transcriptionally active as its sequence is only found in the UNIPROT database (accession number Q9N3P9), and there is no EST or cDNA supporting evidence. If this is the case, it would be consistent with reports that indicate that all known transduplicates in rice, in spite of their genomic abundance, are pseudogenes [16].

Bottom Line: Transduplication of protein-coding genes is common in plants, but is unknown of in animals.The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM) that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene.Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel. noasela@post.tau.ac.il

ABSTRACT
Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR) sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM) that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif.

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