Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 03-023

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Titel:
Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon

Author(s):
Claudia S. Copeland, Oliver Heyers, Bernd H. Kalinna, Andreas Bachmair, Peter F. Stadler, Ivo L. Hofacker, Paul J. Brindley

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Abstract:
Boudicca is a gypsy-like, long terminal repeat (LTR) retrotransposon that has colonized the genome of the human blood fluke, Schistosoma mansoni. Previous studies have indicated that more than 1000 copies of Boudicca reside within the S. mansoni genome, although many of them may be degenerate and inactive. Messenger RNAs transcribed from proviral, genomic copies of Boudicca were investigated by reverse-transcription PCR. Overlapping RTPCR products corresponding to the gag and pol polyproteins of Boudicca, along with relevant sequences of genomic fragments of Boudicca, were assembled into contigs. Consensus sequences from these contigs were used to predict the sequence and structure of transpositionally active copies of the Boudicca retrotransposon. They verified that Boudicca has a kabuki-like Cys-His box motif at the active site of its gag protein, a classic DTG motif as the active site of the protease domain of the pol ORF2, and indicated a contiguous integrase domain at the Cterminus of pol with strong identity to integrase from the LTR retrotransposons CsRn1 and kabuki, as well as to the Genbank conserved domain rve (pfam 00665) integrase core domain. Models of the secondary structure of the Boudicca transcript suggested that the first AUG was occluded by a stem loop structure, which in turn suggested a method of regulation of expression of Boudicca proteins at the level of translation. In addition, phylogenetic analysis targeting discrete domains of Boudicca revealed a generalized radiation in sequences among the multiple copies of Boudicca resident in the schistosome genome.

Keywords:
Long terminal repeat (LTR), secondary structure, post-transcriptional regulation, multiple AUG codons, CsRn1, Kabuki

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