ToxoDB: an integrated Toxoplasma gondii database resource

Gajria, Bindu; Bahl, Amit; Brestelli, John; Dommer, Jennifer; Fischer, Steven H.; Gao, Xin; Heiges, Mark; Iodice, John; Kissinger, Jessica C.; Mackey, Aaron J.; Pinney, Deborah F.; Roos, David S.; Stoeckert, Christian J.; Wang, Haiming; Brunk, Brian P.

doi:10.1093/nar/gkm981

Cited by 416 publications

(453 citation statements)

References 14 publications

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“…gondii Nuclear Fucosylation Is Dependent on the de Novo GDPFucose Biosynthetic Pathway. Because T. gondii and other apicomplexans have no salvage pathway for fucose (25,26), GDPfucose is synthesized from GDP-mannose in a three-step process catalyzed by GDP-mannose dehydratase (GMD, TGGT1_238940) and GDP-fucose synthase (Fig. S2D) (21).…”

Section: Significancementioning

confidence: 99%

O -fucosylated glycoproteins form assemblies in close proximity to the nuclear pore complexes of Toxoplasma gondii

Bandini

Haserick

Motari

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Toxoplasma gondii is an intracellular parasite that causes disseminated infections in fetuses and immunocompromised individuals. Although gene regulation is important for parasite differentiation and pathogenesis, little is known about protein organization in the nucleus. Here we show that the fucose-binding Aleuria aurantia lectin (AAL) binds to numerous punctate structures in the nuclei of tachyzoites, bradyzoites, and sporozoites but not oocysts. AAL also binds to Hammondia and Neospora nuclei but not to more distantly related apicomplexans. Analyses of the AAL-enriched fraction indicate that AAL binds O-linked fucose added to Ser/Thr residues present in or adjacent to Ser-rich domains (SRDs). Sixty-nine Ser-rich proteins were reproducibly enriched with AAL, including nucleoporins, mRNA-processing enzymes, and cell-signaling proteins. Two endogenous SRDs-containing proteins and an SRD-YFP fusion localize with AAL to the nuclear membrane. Superresolution microscopy showed that the majority of the AAL signal localizes in proximity to nuclear pore complexes. Host cells modify secreted proteins with O-fucose; here we describe the O-fucosylation pathway in the nucleocytosol of a eukaryote. Furthermore, these results suggest O-fucosylation is a mechanism by which proteins involved in gene expression accumulate near the NPC.toxoplasma | fucose | nuclear glycosylation | nuclear pore complex T he apicomplexan parasite Toxoplasma gondii causes disseminated infections in humans, and these infections can lead to severe damage in immunocompromised individuals and fetuses (1, 2). There is no human vaccine against T. gondii, and recently the price of pyrimethamine, the drug used to treat toxoplasmosis in the United States, has increased more than 50-fold (2).T. gondii has a complex life cycle, and the parasite's ability to differentiate through its life stages in response to stresses and environmental conditions is fundamental for its pathogenicity and transmission (3). Transcriptome analyses have revealed that a large percentage of mRNAs show life stage-specific expression (4) and/or cell cycle regulation (5). Recent studies have increased our understanding of gene expression in T. gondii by identifying the AP2 family of transcription factors (6-8) and by describing posttranslational modifications (PTMs) of histones and some of the enzymes responsible for them (9-11). However, little is known about protein organization at the nuclear periphery, a subnuclear compartment that plays a critical role in transcriptional regulation in many eukaryotes. In particular, the gene-gating model (12) suggests that the nuclear pore complex (NPC) has a role in transcriptional regulation and chromatin organization as well as in protein and mRNA transport (13,14).In T. gondii chromodomain protein 1 localizes with heterochromatin at the nuclear periphery (15), and centromeres sequester to an apical nuclear region (16). Although the nuclear localization signal (NLS) and importin-α system are present, key nuclear import and export molecules are...

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Section: Significancementioning

confidence: 99%

O -fucosylated glycoproteins form assemblies in close proximity to the nuclear pore complexes of Toxoplasma gondii

Bandini

Haserick

Motari

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…The apicomplexan peptide datasets were downloaded from the following public databases: PlasmoDB [120] (release 8.2) for the annotated peptides of all Plasmodium species investigated here, CryptoDB (release 4.6) [120,121] for the annotated peptides of C. parvum and C. hominis, the Wellcome Trust Sanger Institute's FTP site (ftp.sanger.ac.uk) for T. annulata, the EMBL database for B. bovis (accession number AAXT00000000), and ToxoDB release 7.2 [36] for the annotated peptides of T. gondii type II strain (ME49). The T. parva peptide dataset had previously been downloaded from the now discontinued TIGR website (www.tigr.org/tdb/e2k1/tpa1/).…”

Section: Identification and Classification Of Apicomplexan Pksmentioning

confidence: 99%

“…These include five species, whose kinomes have been described in detail: P. falciparum [10,11], P. yoelii [33], P. berghei [34], T. gondii [35,36] and C. parvum [37]. Furthermore, we report the initial characterization of seven apicomplexan kinomes, including P. chabaudi, P. knowlesi, and P. vivax, C. hominis, T. annulata and T. parva, as well as B. bovis.…”

Section: Introductionmentioning

confidence: 99%

The kinomes of apicomplexan parasites

Miranda‐Saavedra

Gabaldón

Barton

et al. 2012

Microbes and Infection

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Protein phosphorylation plays a fundamental role in the biology and invasion strategies of apicomplexan parasites. Many apicomplexan protein kinases are substantially different from their mammalian orthologues, and thus constitute a landscape of potential drug targets. Here, we integrate genomic, biochemical, genetic and evolutionary information to provide an integrated and up-to-date analysis of twelve apicomplexan kinomes. All kinome sequences are available through the Kinomer database.2

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“…BLASTP and TBLASTN analyses (Altschul et al 1997) were performed on protein and nucleotide sequences available at the NCBI website, http://www.ncbi.nlm.nih.gov/BLAST/. Additional search was carried out at specific apicomplexan web sites, GeneDB, ApiDB, CryptoDB, PiroplasmaDB, ToxoDB, and PlasmoDB (Aurrecoechea et al 2007(Aurrecoechea et al , 2009Gajria et al 2008;Heiges et al 2006;Hertz-Fowler et al 2004; http://www.genedb.org/; http://eupathdb.org/eupathdb/). Nucleotide sequences identified in BLASTN searches were translated in the reading frames denoted in the BLASTN hit, taking frame shifts or introns of genomic sequences into account.…”

Section: Database Homology Searchmentioning

confidence: 99%

Wider than Thought Phylogenetic Occurrence of Apicortin, A Characteristic Protein of Apicomplexan Parasites

Orosz

2016

J Mol Evol

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ToxoDB: an integrated Toxoplasma gondii database resource

Cited by 416 publications

References 14 publications

O -fucosylated glycoproteins form assemblies in close proximity to the nuclear pore complexes of Toxoplasma gondii

O -fucosylated glycoproteins form assemblies in close proximity to the nuclear pore complexes of Toxoplasma gondii

The kinomes of apicomplexan parasites

Wider than Thought Phylogenetic Occurrence of Apicortin, A Characteristic Protein of Apicomplexan Parasites

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