Dataset Information

Proteogenomic analysis of Toxoplasma gondii (comparing genome releases 6 and 10) to demonstrate the performance of the ProteoAnnotator software

ABSTRACT: Testing the performance of the ProteoAnnotator software via comparing analysis of annotating the Toxoplasma gondii gene models 6 and 10

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Toxoplasma Gondii Me49

SUBMITTER: Fawaz Ghali

LAB HEAD: Andrew R. Jones

PROVIDER: PXD001042 | Pride | 2014-10-20

REPOSITORIES: Pride

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Publications

ProteoAnnotator--open source proteogenomics annotation software supporting PSI standards.

Ghali Fawaz F Krishna Ritesh R Perkins Simon S Collins Andrew A Xia Dong D Wastling Jonathan J Jones Andrew R AR

Proteomics 20141119 23-24

The recent massive increase in capability for sequencing genomes is producing enormous advances in our understanding of biological systems. However, there is a bottleneck in genome annotation--determining the structure of all transcribed genes. Experimental data from MS studies can play a major role in confirming and correcting gene structure--proteogenomics. However, there are some technical and practical challenges to overcome, since proteogenomics requires pipelines comprising a complex set o ...[more]

PMID: 25297486

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Project description:Phosphorylation is a regulatory mechanism by which intracellular apicomplexan parasites control the process of invading and modifying host cells. However, the sporulated oocysts’ phosphoprotein repertoires between virulent and avirulent strains of Toxoplasma gondii and the underlying mechanisms contributing to virulence is still a mystery. A quantitative analysis of the sporulated oocysts’ phosphoproteome profile of T. gondii virulent and avirulent strains belonging to different genotypes was conducted to reveal phosphoprotein expression patterns that contribute to the virulence of a particular phenotype. Phosphopeptides from the sporulated oocysts of the virulent strain PYS (Chinese ToxoDB#9) and the avirulent strain type II (PRU strain) were enriched by titanium dioxide (TiO2) affinity chromatography and quantified using iBT technology. A total of 10,645 unique phosphopeptides, 8,181 nonredundant phosphorylation sites and 2,792 phosphoproteins were identified. The quantitative analysis identified 4,129 differentially expressed phosphopeptides (DEPs) between sporulated oocysts of the PYS strain and PRU strain (|log1.5 fold change| > 1 and P < 0.05), including 2,485 upregulated and 1,644 downregulated phosphopeptides. Motif analysis identified 24 motifs from the upregulated phosphorylated peptides including 22 serine motifs and two threonine motifs (TPE and TP), and 15 motifs from the downregulated phosphorylated peptides including 12 serine motifs and three threonine motifs (TP, RxxT and KxxT) in PYS strain when comparing PYS/PRU. Several kinases were consistent with motifs of overrepresented phosphopeptides, such as PKA, PKG, CKII, IKK, MAPK, EGFR, INSR, Jak, Syk, Src, Ab1. GO analysis, KEGG pathway analysis and STRING analysis revealed differentially expressed phosphoproteins (DEPs) exhibiting significant functional properties. Kinase associated network analysis showed that AGC kinase had the greatest connected peptides. Our findings reveal significant difference in phosphopeptides of sporulated oocysts between virulent and avirulent T. gondii strains, which provides solid foundation for further exploring the mechanisms contributing to the virulence of T. gondii.

Dataset Information

Proteogenomic analysis of Toxoplasma gondii (comparing genome releases 6 and 10) to demonstrate the performance of the ProteoAnnotator software

Publications

ProteoAnnotator--open source proteogenomics annotation software supporting PSI standards.

Similar Datasets

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