title: Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon.
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 genomic copies of Boudicca were investigated by reverse transcription PCR. Overlapping RT-PCR 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 C-terminus of pol with strong identity to integrase from the LTR retrotransposons CsRn1 and kabuki, as well as to the conserved integrase core domain, GenBank rve (). 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, at the level of translation, of Boudicca proteins. 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.
authors.affiliation: Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin, Berlin, Germany.
authors.forename: Claudia S
authors.initials: CS
authors.lastname: Copeland
authors.forename: Oliver
authors.initials: O
authors.lastname: Heyers
authors.forename: Bernd H
authors.initials: BH
authors.lastname: Kalinna
authors.forename: Andreas
authors.initials: A
authors.lastname: Bachmair
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Brindley
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D003001:Cloning, Molecular; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D018509:DNA, Helminth / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D018628:Gene Dosage; D005786:Gene Expression Regulation; D015683:Gene Products, gag / Q000235:genetics; D016678:Genome; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D020815:Polyproteins / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics; D018510:RNA, Helminth / Q000737:chemistry / Q000235:genetics; D018626:Retroelements / Q000235:genetics*; D012550:Schistosoma mansoni / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D018509:DNA, Helminth; D015683:Gene Products, gag; D020815:Polyproteins; D018510:RNA, Helminth; D018626:Retroelements