TriTrypDB: a functional genomic resource for the Trypanosomatidae

Abstract

TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ‘User Comments’ may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.

Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit

“…However, the total size of the six rRNA pieces is about one-fourth larger than the 25S rRNA in yeast (4,225 vs. 3,392 nts) (11,12). This increase is accounted for by the larger size of ESs and the addition of trypanosome-specific ESs.…”

“…The references were initially fitted as rigid bodies into the negative B-factor-sharpened density map using Chimera (43). The rRNA sequences were obtained from TriTrypDB Kinetoplastid Genomics Resource (tritrypdb.org/tritrypdb/) (11). Regions of rRNA conserved between T. cruzi and yeast were used as starting points, followed by extensive manual building using Coot (44).…”

Adenylosuccinate Synthetase and Adenylosuccinate Lyase Deficiencies Trigger Growth and Infectivity Deficits in Leishmania donovani

“…Primary Structures of L. donovani ADSS and ASL-The L. donovani ADSS (ABS11225) and ASL (ABS11226) genes and their flanking sequences were isolated from purified cosmid clones that hybridized to the putative ADSS (LmjF.13.1190) and ASL (LmjF.04.0460) ORFs, respectively, from L. major (38 (38) as well as two internal insertions of 20 and 55 residues, which render the leishmanial ADSSs much longer than ADSSs from other organisms (supplemental Fig. S1A).…”

“…Two putative coding sequences, one for ADSS (LmjF13.1190) and one for ASL (LmjF04.0460), were retrieved from a search of the Leishmania major genome (38). Oligonucleotide primers were designed against the L. major putative ADSS and ASL ORFs and utilized to amplify gene fragments from L. major genomic DNA via standard PCR methodology (39,40).…”

Trypanosome Letm1 Protein Is Essential for Mitochondrial Potassium Homeostasis

“…To shed light on this situation, we have undertaken functional analysis of Letm1 (TriTrypDB genome database accession number Tb927.3.4920 (19)) in the protozoan flagellate Trypanosoma brucei. As a member of the Kinetoplastea, it has a long and independent evolutionary history, perhaps due to its early branching from other eukaryotic lineages (20,21).…”