The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation

Xia, Dong; Sanderson, Sanya J.; Jones, Andrew R.; Prieto, Judith Helena; Yates, John R.; Bromley, Elizabeth H. C.; Tomley, Fiona M.; Lal, Kalpana; Sinden, Robert E.; Brunk, Brian P.; Roos, David S.; Wastling, Jonathan M.

doi:10.1186/gb-2008-9-7-r116

Cited by 114 publications

(106 citation statements)

References 52 publications

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“…Proteomic data was available for P. falciparum (Florens et al 2002), P. berghei , P. yoelii (Tarun et al 2008), T. gondii (Bradley et al 2005;Xia et al 2008), and C. parvum . The data was downloaded from ApiDB (Aurrecoechea et al 2007).…”

Section: Functional Annotationmentioning

confidence: 99%

The origins of apicomplexan sequence innovation

Wasmuth¹,

Daub²,

Peregrín-Alvarez³

et al. 2009

Genome Res.

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The Apicomplexa are a group of phylogenetically related parasitic protists that include Plasmodium, Cryptosporidium, and Toxoplasma. Together they are a major global burden on human health and economics. To meet this challenge, several international consortia have generated vast amounts of sequence data for many of these parasites. Here, we exploit these data to perform a systematic analysis of protein family and domain incidence across the phylum. A total of 87,736 protein sequences were collected from 15 apicomplexan species. These were compared with three protein databases, including the partial genome database, PartiGeneDB, which increases the breadth of taxonomic coverage. From these searches we constructed taxonomic profiles that reveal the extent of apicomplexan sequence diversity. Sequences without a significant match outside the phylum were denoted as apicomplexan specialized. These were collated into 9134 discrete protein families and placed in the context of the apicomplexan phylogeny, identifying the putative origin of each family. Most apicomplexan families were associated with an individual genus or species. Interestingly, many genera-specific innovations were associated with specialized host cell invasion and/or parasite survival processes. Contrastingly, those families reflecting more ancestral relationships were enriched in generalized housekeeping functions such as translation and transcription, which have diverged within the apicomplexan lineage. Protein domain searches revealed 192 domains not previously reported in apicomplexans together with a number of novel domain combinations. We highlight domains that may be important to parasite survival.

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Section: Functional Annotationmentioning

confidence: 99%

The origins of apicomplexan sequence innovation

Wasmuth¹,

Daub²,

Peregrín-Alvarez³

et al. 2009

Genome Res.

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“…Such analyses can provide information about specificity and virulence, and contribute to the development of therapeutic agents and an effective vaccine. A number of studies based on 2-dimensional electrophoresis (2-DE) and mass spectrometry have been performed on T. gondii [8][9][10][11][12]. For example, Cohen et al [8] characterized global protein expression of the T. gondii RH strain by 2-DE and matrixassisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, while Xia et al [11] analyzed the proteome of 3 strains of Toxoplasma (ME49, GT1, and VEG) using 2-DE, gel liquid chromatography-linked tandem mass spectrometry, and multidimensional protein identification technology (Mud-PIT).…”

Section: Introductionmentioning

confidence: 99%

Proteomic Analysis ofToxoplasma gondiiKI-1 Tachyzoites

et al. 2010

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Abstract:We studied on the proteomic characteristics of Toxoplasma gondii KI-1 tachyzoites which were originally isolated from a Korean patient, and compared with those of the well-known virulent RH strain using 2-dimensional electrophoresis (2-DE), mass spectrometry, and quantitative real-time PCR. Two-dimensional separation of the total proteins isolated from KI-1 tachyzoites revealed up to 150 spots, of which 121 were consistent with those of RH tachyzoites. Of the remaining 29 spots, 14 showed greater than 5-fold difference in density between the KI-1 and RH tachyzoites at a pH of 5.0-8.0. Among the 14 spots, 5 from the KI-1 isolate and 7 from the RH strain were identified using MALDI-TOF mass spectrometry and database searches. The spots from the KI-1 tachyzoites were dense granule proteins (GRA 2, 3, 6, and 7), hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGRPTase), and uracil phosphoribosyltransferase (UPRTase). The spots from the RH strain were surface antigen 1 (SAG 1), L-lactate dehydrogenase (LDH), actin, chorismate synthase, peroximal catalase, hexokinase, bifunctional dihydrofolate reductase-thymidylate synthase (DHTR-TS), and nucleosidetriphosphatases (NTPases). Quantitative real-time PCR supported our mass spectrometric results by showing the elevated expression of the genes encoding GRA 2, 3, and 6 and UPRTase in the KI-1 tachyzoites and those encoding GRA 7, SAG 1, NTPase, and chorismate synthase in the RH tachyzoites. These observations demonstrate that the protein compositions of KI-1 and RH tachyzoites are similar but differential protein expression is involved in virulence.

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“…Although still in its infancy, proteogenomics has been applied to date for improving genome annotation of various pathogenic microbes, including Plasmodium falciparum [38], Toxoplasma gondii [39], Leishmania donovani [40], Candida glabrata [41], Mycoplasma pneumoniae [33], Mycobacterium tuberculosis [30], Shigella flexneri [42], and Yersinia spp. [43,44].…”

Section: Improving Gene Annotation By Proteogenomics In a Quest For Mmentioning

confidence: 99%

High throughput genomic and proteomic technologies in the fight against infectious diseases

Tanca

Deligios

Addis

et al. 2013

J Infect Dev Ctries

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New technologies have shown significant promise in the fight against infectious diseases, with the discovery of novel molecular targets for in vitro diagnostics and the improved design of vaccines. In developing countries, especially in areas of neglected diseases and resources-poor settings, a number of technological innovations are further needed, such as the integration of old and new biomarkers in suitable analysis platforms, the simplification of existing analysis systems, and the improvement of sample preservation and management. However, in these areas, identification of new biomarkers for infectious diseases is still a core issue in the diagnostic quest. Similarly, new technologies will allow scientists to design vaccines with improved immunogenicity, efficacy and safety in the local area, according to the circulating pathogenic strains and the genetic background of the population to be immunized. In this work we review the current omics-based technologies and their potential for accelerating the development of next generation vaccines and the identification of biomarkers suitable for point-of-care (POC) diagnostic applications.

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The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation

Cited by 114 publications

References 52 publications

The origins of apicomplexan sequence innovation

The origins of apicomplexan sequence innovation

Proteomic Analysis ofToxoplasma gondiiKI-1 Tachyzoites

High throughput genomic and proteomic technologies in the fight against infectious diseases

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