pido , a non-long terminal repeat retrotransposon of the chicken repeat 1 family from the genome of the Oriental blood fluke, Schistosoma japonicum

Laha, Thewarach; Brindley, Paul J.; Verity, Christiana K.; McManus, Donald P.; Loukas, Alex

doi:10.1016/s0378-1119(02)00381-5

Cited by 25 publications

(19 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The disease is endemic in 74 developing countries, infecting about 200 million individuals, and it is estimated that an additional 500 to 600 million are at risk (59). The Schistosoma genome has approximately 270 Mbp (54), and a considerable portion (more than 20%) is believed to be composed of retrotransposons (31). Four retroelements belonging to LTR and non-LTR classes have been previously characterized for S. mansoni (10,14,15).…”

mentioning

confidence: 99%

Saci-1, -2, and -3 and Perere, Four Novel Retrotransposons with High Transcriptional Activities from the Human Parasite Schistosoma mansoni

DeMarco¹,

Kowaltowski²,

Machado

et al. 2004

J Virol

View full text Add to dashboard Cite

Using the data set of 180,000 expressed sequence tags (ESTs) of the blood fluke Schistosoma mansoni generated recently by our group, we identified three novel long-terminal-repeat (LTR)-and one novel non-LTR-expressed retrotransposon, named Saci-1, -2, and -3 and Perere, respectively. Full-length sequences were reconstructed from ESTs and have deduced open reading frames (ORFs) with several uncorrupted features, characterizing them as possible active retrotransposons of different known transposon families. Alignment of reconstructed sequences to available preliminary genome sequence data confirmed the overall structure of the transposons. The frequency of sequenced transposon transcripts in cercariae was 14% of all transcripts from that stage, twofold higher than that in schistosomula and three-to fourfold higher than that in adults, eggs, miracidia, and germ balls. We show by Southern blot analysis, by EST annotation and tallying, and by counting transposon tags from a Social Analysis of Gene Expression library, that the four novel retrotransposons exhibit a 10-to 30-fold lower copy number in the genome and a 4-to 200-fold-higher transcriptional rate per copy than the four previously described S. mansoni retrotransposons. Such differences lead us to hypothesize that there are two different populations of retrotransposons in S. mansoni genome, occupying different niches in its ecology. Examples of retrotransposon fragment inserts were found into the 5 and 3 untranslated regions of four different S. mansoni target gene transcripts. The data presented here suggest a role for these elements in the dynamics of this complex human parasite genome.

show abstract

mentioning

confidence: 99%

Saci-1, -2, and -3 and Perere, Four Novel Retrotransposons with High Transcriptional Activities from the Human Parasite Schistosoma mansoni

DeMarco¹,

Kowaltowski²,

Machado

et al. 2004

J Virol

View full text Add to dashboard Cite

show abstract

“…Mobile genetic elements colonizing the genome of S. mansoni are of interest both for their potential in developing tools for schistosome transgenesis and for their influence on the evolution and structure of the schistosome genome [13,14]. Previously characterized schistosome MGEs include SINE-like retroposons [15,16], long terminal repeat (LTR) retrotransposons [12,17,18], non-LTR retrotransposons [10,11], and DNA transposons related to bacterial IS1016 insertion sequences [19]. Boudicca , the first LTR retrotransposon characterized from the genome of S. mansoni [20] belongs to the gypsy -like retrotransposons, one of three highly divergent groups of LTR retrotransposons: the Gypsy/Ty3 group, the Copia/Ty1 group and the Pao/BEL group [21].…”

Section: Introductionmentioning

confidence: 99%

Untitled

et al. 2005

Self Cite

View full text Add to dashboard Cite

BackgroundOf the major families of long terminal repeat (LTR) retrotransposons, the Pao/BEL family is probably the least well studied. It is becoming apparent that numerous LTR retrotransposons and other mobile genetic elements have colonized the genome of the human blood fluke, Schistosoma mansoni.ResultsA proviral form of Sinbad, a new LTR retrotransposon, was identified in the genome of S. mansoni. Phylogenetic analysis indicated that Sinbad belongs to one of five discreet subfamilies of Pao/BEL like elements. BLAST searches of whole genomes and EST databases indicated that members of this clade occurred in species of the Insecta, Nematoda, Echinodermata and Chordata, as well as Platyhelminthes, but were absent from all plants, fungi and lower eukaryotes examined. Among the deuterostomes examined, only aquatic species harbored these types of elements. All four species of nematode examined were positive for Sinbad sequences, although among insect and vertebrate genomes, some were positive and some negative. The full length, consensus Sinbad retrotransposon was 6,287 bp long and was flanked at its 5'- and 3'-ends by identical LTRs of 386 bp. Sinbad displayed a triple Cys-His RNA binding motif characteristic of Gag of Pao/BEL-like elements, followed by the enzymatic domains of protease, reverse transcriptase (RT), RNAseH, and integrase, in that order. A phylogenetic tree of deduced RT sequences from 26 elements revealed that Sinbad was most closely related to an unnamed element from the zebrafish Danio rerio and to Saci-1, also from S. mansoni. It was also closely related to Pao from Bombyx mori and to Ninja of Drosophila simulans. Sinbad was only distantly related to the other schistosome LTR retrotransposons Boudicca, Gulliver, Saci-2, Saci-3, and Fugitive, which are gypsy-like. Southern hybridization and bioinformatics analyses indicated that there were about 50 copies of Sinbad in the S. mansoni genome. The presence of ESTs representing transcripts of Sinbad in numerous developmental stages of S. mansoni along with the identical 5'- and 3'-LTR sequences suggests that Sinbad is an active retrotransposon.ConclusionSinbad is a Pao/BEL type retrotransposon from the genome of S. mansoni. The Pao/BEL group appears to be comprised of at least five discrete subfamilies, which tend to cluster with host species phylogeny. Pao/BEL type elements appear to have colonized only the genomes of the Animalia. The distribution of these elements in the Ecdysozoa, Deuterostomia, and Lophotrochozoa is discontinuous, suggesting horizontal transmission and/or efficient elimination of Pao-like mobile genetic elements from some genomes.

show abstract

“…Both the evolution and size of this genome may be highly influenced by mobile genetic elements. Indeed, more than half of the schistosome genome appears to be composed of or derived from repetitive sequences, to a large extent from retrotransposable elements (34)(35)(36).…”

mentioning

confidence: 99%

“…Previously characterized schistosome mobile genetic elements include SINE-like retrotransposons (60,18), LTR retrotransposons (36), and at least two families of non-LTR retrotransposons (35). Although active replication of these elements has not been definitively proven, mRNA transcripts encoding reverse transcriptase and endonuclease have been detected (34,36), as has reverse transcriptase activity in schistosome extracts (29), suggesting that at least some of these elements are actively mobile within the genome.…”

mentioning

confidence: 99%

Boudicca , a Retrovirus-Like Long Terminal Repeat Retrotransposon from the Genome of the Human Blood Fluke Schistosoma mansoni

Copeland

Brindley

Heyers

et al. 2003

J Virol

View full text Add to dashboard Cite

pido , a non-long terminal repeat retrotransposon of the chicken repeat 1 family from the genome of the Oriental blood fluke, Schistosoma japonicum

Cited by 25 publications

References 38 publications

Saci-1, -2, and -3 and Perere, Four Novel Retrotransposons with High Transcriptional Activities from the Human Parasite Schistosoma mansoni

Saci-1, -2, and -3 and Perere, Four Novel Retrotransposons with High Transcriptional Activities from the Human Parasite Schistosoma mansoni

Untitled

Boudicca , a Retrovirus-Like Long Terminal Repeat Retrotransposon from the Genome of the Human Blood Fluke Schistosoma mansoni

Contact Info

Product

Resources

About