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Identification of proteins secreted by malaria parasite into erythrocyte using SVM and PSSM profiles.

ABSTRACT: BACKGROUND: Malaria parasite secretes various proteins in infected RBC for its growth and survival. Thus identification of these secretory proteins is important for developing vaccine/drug against malaria. The existing motif-based methods have got limited success due to lack of universal motif in all secretory proteins of malaria parasite. RESULTS: In this study a systematic attempt has been made to develop a general method for predicting secretory proteins of malaria parasite. All models were trained and tested on a non-redundant dataset of 252 secretory and 252 non-secretory proteins. We developed SVM models and achieved maximum MCC 0.72 with 85.65% accuracy and MCC 0.74 with 86.45% accuracy using amino acid and dipeptide composition respectively. SVM models were developed using split-amino acid and split-dipeptide composition and achieved maximum MCC 0.74 with 86.40% accuracy and MCC 0.77 with accuracy 88.22% respectively. In this study, for the first time PSSM profiles obtained from PSI-BLAST, have been used for predicting secretory proteins. We achieved maximum MCC 0.86 with 92.66% accuracy using PSSM based SVM model. All models developed in this study were evaluated using 5-fold cross-validation technique. CONCLUSION: This study demonstrates that secretory proteins have different residue composition than non-secretory proteins. Thus, it is possible to predict secretory proteins from its residue composition-using machine learning technique. The multiple sequence alignment provides more information than sequence itself. Thus performance of method based on PSSM profile is more accurate than method based on sequence composition. A web server PSEApred has been developed for predicting secretory proteins of malaria parasites,the URL can be found in the Availability and requirements section.

SUBMITTER: Verma R

PROVIDER: S-EPMC2358896 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Identification of proteins secreted by malaria parasite into erythrocyte using SVM and PSSM profiles.

Verma Ruchi R Tiwari Ajit A Kaur Sukhwinder S Varshney Grish C GC Raghava Gajendra Ps GP

BMC bioinformatics 20080416

<h4>Background</h4>Malaria parasite secretes various proteins in infected RBC for its growth and survival. Thus identification of these secretory proteins is important for developing vaccine/drug against malaria. The existing motif-based methods have got limited success due to lack of universal motif in all secretory proteins of malaria parasite.<h4>Results</h4>In this study a systematic attempt has been made to develop a general method for predicting secretory proteins of malaria parasite. All ...[more]

PMID: 18416838

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Project description:Malaria parasites modify their host erythrocyte in multiple ways, leading to changes in the deformability, adhesiveness, and permeability of the host erythrocyte. Most of these changes are mediated by proteins exported from the parasite to the host erythrocyte, where these proteins interact with the host cell cytoskeleton or form complexes in the plasma membrane of the infected erythrocyte. In addition, malaria parasites induce the formation of membranous compartments-the parasitophorous vacuole, the tubovesicular network (TVN), the Maurer's clefts and small vesicles-within the infected erythrocyte, a cell that is normally devoid of internal membranes. After infection, changes also occur in the composition and asymmetry of the erythrocyte plasma membrane. Although many aspects of the mechanism of export of parasite proteins have become clear, the mechanism by which these membranous compartments are formed and expanded is almost entirely unknown. To determine whether parasite-derived phospholipids play a part in these processes, we applied a metabolic labeling technique that allows phosphatidylcholine to be labeled with a fluorophore. As the host erythrocyte cannot synthesize phospholipids, within infected erythrocytes, only parasite-derived phosphatidylcholine will be labeled with this technique. The results revealed that phosphatidylcholine produced by the parasite is distributed throughout the infected erythrocyte, including the TVN and the erythrocyte plasma membrane, but not Maurer's clefts. Interestingly, labeled phospholipids were also detected in the erythrocyte plasma membrane very soon after invasion of the parasites, indicating that the parasite may add phospholipids to the host erythrocyte during invasion. IMPORTANCE Here, we describe a previously unappreciated way in which the malaria parasite interacts with the host erythrocyte, namely, by the transfer of parasite phospholipids to the erythrocyte plasma membrane. This likely has important consequences for the survival of the parasite in the host cell and the host organism. We show that parasite-derived phospholipids are transferred from the parasite to the host erythrocyte plasma membrane and that other internal membranes that are produced after the parasite has invaded the cell are produced, at least in part, using parasite-derived phospholipids. The one exception to this is the Maurer's cleft, a membranous organelle that is involved in the transport of parasite proteins to the surface of the erythrocyte. This reveals that the Maurer's cleft is produced in a different manner than the other parasite-induced membranes. Overall, these findings provide a platform for the study of a new aspect of the host-parasite interaction.

Dataset Information

Identification of proteins secreted by malaria parasite into erythrocyte using SVM and PSSM profiles.

Publications

Identification of proteins secreted by malaria parasite into erythrocyte using SVM and PSSM profiles.

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