Quantitative protein expression profiling reveals extensive post-transcriptional regulation and post-translational modifications in schizont-stage malaria parasites

Foth, Bernardo J.; Zhang, Neng; Mok, Sachel; Preiser, Peter R.; Bozdech, Zbynek

doi:10.1186/gb-2008-9-12-r177

Cited by 116 publications

(116 citation statements)

References 70 publications

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“…a total of 150 g protein per strip) during rehydration, whereas for preparative silver-stained gels each strip was loaded with 500 -1000 g protein. Addition of IPG buffer and DeStreak Solution (GE Healthcare), strip rehydration, IEF, strip equilibration, and second-dimension protein separation by SDS-PAGE were carried out as described (13). Gels were scanned on a Typhoon Trio scanner (GE Healthcare) at 100 m resolution and the resulting images analyzed with DeCyder 2D software, Version 6.5 (GE Healthcare).…”

Section: Methodsmentioning

confidence: 99%

“…Cell Culture and Parasite Sampling-Parasites of P. falciparum strain Dd2 (MR4, http://www.mr4.org/) were initially grown at 1-14% parasitaemia in plastic flasks under standard conditions (27) and as described previously (13). Parasites were synchronized by sorbitol treatments (5% sorbitol for 5-10 min at room temperature) over several generations at 4 -5 or at 20 h after the start of erythrocyte invasion.…”

Section: Methodsmentioning

confidence: 99%

“…The protocol to prepare the peptides for, matrix-assisted laser desorption ionization/time-of-flight (MALDI-TOF(/TOF)) mass spectrometry (i.e. destaining, washing, ingel trypsin-digestion, concentration using micro-C18-ZipTips, and spotting onto MALDI target plates) was as described (13) except that here 0.1% trifluoroacetic acid was used instead of 0.5% formic acid during the ZipTip-procedure. Peptide mass fingerprints and tandem MS (MS/MS) fragment ion masses were recorded by MALDI-TOF/ TOF mass spectrometry with a 4800 Plus MALDI TOF/TOF Analyzer (Applied Biosystems, Forster City, CA) at the proteomics core center of Nanyang Technological University, Singapore.…”

Section: Methodsmentioning

confidence: 99%

“…Two-dimensional Protein Gel Electrophoresis and DIGE-Protein preparations were carried out as described (13). Further details and the DIGE CyDye labeling regimen employed are described in the Supplemental Data.…”

Section: Methodsmentioning

confidence: 99%

“…has been shown to be up-regulated on a translational but not on a transcriptional level following drug treatment (10). Other studies have evaluated the links between transcription and translation during the Plasmodium life cycle progression in more general terms by employing different types of large scale proteomics assays (7,(11)(12)(13)(14)(15)(16)(17)(18)(19). These studies thus complemented the transcriptome analyses and demonstrated that each developmental stage of Plasmodium is characterized also by a unique protein content that is linked to the specialized functionalities of that particular stage.…”

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confidence: 99%

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Quantitative Time-course Profiling of Parasite and Host Cell Proteins in the Human Malaria Parasite Plasmodium falciparum

Foth

Zhang

Chaal

et al. 2011

Molecular & Cellular Proteomics

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Studies of the Plasmodium falciparum transcriptome have shown that the tightly controlled progression of the parasite through the intra-erythrocytic developmental cycle (IDC) is accompanied by a continuous gene expression cascade in which most expressed genes exhibit a single transcriptional peak. Because the biochemical and cellular functions of most genes are mediated by the encoded proteins, understanding the relationship between mRNA and protein levels is crucial for inferring biological activity from transcriptional gene expression data. Although studies on other organisms show that <50% of protein abundance variation may be attributable to corresponding mRNA levels, the situation in Plasmodium is further complicated by the dynamic nature of the cyclic gene expression cascade. In this study, we simultaneously determined mRNA and protein abundance profiles for P. falciparum parasites during the IDC at 2-hour resolution based on oligonucleotide microarrays and two-dimensional differential gel electrophoresis protein gels. We find that most proteins are represented by more than one isoform, presumably because of post-translational modifications. Like transcripts, most proteins exhibit cyclic abundance profiles with one peak during the IDC, whereas the presence of functionally related proteins is highly correlated. In contrast, the abundance of most parasite proteins peaks significantly later (median 11 h) than the corresponding transcripts and often decreases slowly in the second half of the IDC. Computational modeling indicates that the considerable and varied incongruence between transcript and protein abundance may largely be caused by the dynamics of translation and protein degradation. Furthermore, we present cyclic abundance profiles also for parasite-associated human proteins and confirm the presence of five human proteins with a potential role in antioxidant defense within the parasites.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Quantitative Time-course Profiling of Parasite and Host Cell Proteins in the Human Malaria Parasite Plasmodium falciparum

Foth

Zhang

Chaal

et al. 2011

Molecular & Cellular Proteomics

Self Cite

135

145

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Quantitative Proteomics

Chance

Chang

Schlatzer

et al. 2009

Encyclopedia of Analytical Chemistry

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Quantitative proteomics technologies have been evolving rapidly, but have reached a level of maturity where reliable results of well‐understood statistical significance can be expected from experiments intended to measure changes in protein abundance in paired samples of case versus control or in multiple comparison studies with substantial numbers of biological replicates and multiple treatments. This review provides an overview of the progress and challenges in the field and highlights specific methods to examine changes in protein abundance where the intact protein species are separated and quantified (top‐down proteomics) and where proteins are digested and separated and peptide abundance is quantified (bottom‐up or shotgun proteomics) to infer relative protein abundance. This paper provides specific examples of two‐dimensional (2‐D) gel‐based quantification along with shotgun methods using 18 O‐labeling and label‐free quantification methods. In each case, issues of sample numbers, target variance, sample prefractionation, and other considerations that are informative to the practical use of these techniques are highlighted. The future prospects of this field are bright, but the challenges of integrating the wealth of proteomics data available into an informative biological context remain an area of important future development.

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