TY - JOUR T1 - Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology Y1 - 2006 A1 - Bringaud, Frederic A1 - Ghedin, Elodie A1 - Blandin, Gaëlle A1 - Bartholomeu, Daniella C. A1 - Caler, Elisabet A1 - Levin, Mariano J. A1 - Baltz, Théo A1 - Najib M. El‐Sayed KW - Degenerate retroelement KW - Evolution KW - Ingi KW - L1Tc KW - Leishmania major KW - Non-LTR retrotransposon KW - Retroposon KW - Trypanosoma brucei KW - Trypanosoma cruzi AB - The ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5'-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs. VL - 145 SN - 0166-6851 ER - TY - JOUR T1 - Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology Y1 - 2002 A1 - Diehl, Susanne A1 - Diehl, Frank A1 - Najib M. El‐Sayed A1 - Clayton, Christine A1 - Hoheisel, Jörg D. KW - Expression KW - Gene KW - Microarray KW - Regulation KW - Trypanosoma brucei AB - A microarray comprising 21[punctuation space]024 different PCR products spotted on glass slides was constructed for gene expression studies on Trypanosoma brucei. The arrayed fragments were generated from a T. brucei shotgun clone library, which had been prepared from randomly sheared and size-fractionated genomic DNA. For the identification of stage-specific gene activity, total RNA from in vitro cultures of the human, long slender form and the insect, procyclic form of the parasite was labelled and hybridised to the microarray. Approximately 75% of the genomic fragments produced a signal and about 2% exhibited significant differences between the transcript levels in the bloodstream and procyclic forms. A few results were confirmed by Northern blot analysis or reverse-transcription and PCR. Three hundred differentially regulated clones have been selected for sequencing. So far, of 33 clones that showed about 2-fold or more over-expression in bloodstream forms, 15 contained sequences similar to those of VSG expression sites and at least six others appeared non-protein-coding. Of 29 procyclic-specific clones, at least eight appeared not to be protein-coding. A surprisingly large proportion of known regulated genes was already identified in this small sample, and some new ones were found, illustrating the utility of genomic arrays. VL - 123 SN - 0166-6851 ER - TY - JOUR T1 - Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi JF - Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology Y1 - 2002 A1 - Bringaud, Frederic A1 - García-Pérez, José Luis A1 - Heras, Sara R. A1 - Ghedin, Elodie A1 - Najib M. El‐Sayed A1 - Andersson, Björn A1 - Baltz, Théo A1 - Lopez, Manuel C. KW - Ingi KW - L1Tc KW - Non-LTR retrotransposon KW - RIME KW - Trypanosoma brucei KW - Trypanosoma cruzi AB - As observed for most eukaryotic cells, trypanosomatids contains non-LTR retrotransposons randomly inserted in the nuclear genome. Autonomous retroelements which, code for their own transposition, have been characterized in Trypanosoma brucei (ingi) and Trypanosoma cruzi (L1Tc), whereas non-autonomous retroelements have only been characterized in T. brucei (RIME). Here, we have characterized in the genome of Trypanosoma cruzi four complete copies of a non-autonomous non-LTR retrotransposon, called NARTc. This 0.26 kb NARTc element has the characteristics of non-LTR retrotransposons: the presence a poly(dA) tail and of a short flanking duplicated motif. Analysis of the Genome Survey Sequence databases indicated that the Trypanosoma cruzi haploid genome contains about 140 NARTc copies and about twice as many L1Tc copies. Interestingly, the NARTc and L1Tc retroelements share, with the Trypanosoma brucei ingi and RIME retrotransposons, a common sequence (the first 45 bp with 91% identity), whereas the remaining sequences are very divergent. This suggests that these four trypanosome non-LTR retrotransposons were derived from the same common ancester and the sequence of their 5'-extremity may have a functional role. In addition, the genome of Leishmania major contains the same conserved motif present in the trypanosome retroelements, whicle no transposable elements have been detected so far in Leishmania sp. VL - 124 SN - 0166-6851 ER -