Dynamics of Protein-Protein Interaction Network in Plasmodium Falciparum

Integration of organism-wide protein interactome data with information on expression of genes, cellular localization of proteins and their functions has proved extremely useful in developing biologically intuitive interaction networks. This chapter highlights the dynamics in protein interaction network across different stages in the lifecycle of Plasmodium falciparum, a malarial parasite, and the implication of the network dynamics in different physiological processes. The main focus of the chapter is the integration of information on experimentally derived interactions of P.falciparum proteins with expression data and analysis of the implications of interactions in different cellular processes. Extensive analysis has been made to quantify the interaction dynamics across various stages, as well as correlating it with the dynamics of the cellular pathways involving the interacting proteins. The authors’ analysis demonstrates the power of strategic integration of genome-wide datasets in extracting information on dynamics of biological pathways and processes.

[1]  Patricia De la Vega,et al.  Discovery of Gene Function by Expression Profiling of the Malaria Parasite Life Cycle , 2003, Science.

[2]  Pierre Legrain,et al.  Prediction, assessment and validation of protein interaction maps in bacteria. , 2002, Journal of molecular biology.

[3]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[4]  J. Kuźnicki,et al.  Sgt1 has co-chaperone properties and is up-regulated by heat shock. , 2008, Biochemical and biophysical research communications.

[5]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

[6]  V. Fischetti,et al.  A major surface protein on group A streptococci is a glyceraldehyde-3- phosphate-dehydrogenase with multiple binding activity , 1992, The Journal of experimental medicine.

[7]  L. Aravind,et al.  Plasmodium Biology Genomic Gleanings , 2003, Cell.

[8]  Stefan Wuchty,et al.  Rich-Club Phenomenon in the Interactome of P. falciparum—Artifact or Signature of a Parasitic Life Style? , 2007, PloS one.

[9]  James R. Knight,et al.  A Protein Interaction Map of Drosophila melanogaster , 2003, Science.

[10]  J. O'connor,et al.  The glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase of Candida albicans is a surface antigen , 1997, Journal of bacteriology.

[11]  G. Kopperschläger,et al.  Interaction of 6‐phosphofructokinase with cytosolic proteins of Saccharomyces cerevisiae , 2004, Yeast.

[12]  Shmuel Sattath,et al.  How reliable are experimental protein-protein interaction data? , 2003, Journal of molecular biology.

[13]  Lawrence Hunter,et al.  Assessing and Combining Reliability of Protein Interaction Sources , 2007, Pacific Symposium on Biocomputing.

[14]  M. Gerstein,et al.  Genomic analysis of regulatory network dynamics reveals large topological changes , 2004, Nature.

[15]  Benjamin A. Shoemaker,et al.  Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners , 2007, PLoS Comput. Biol..

[16]  Narayanan Eswar,et al.  Host–pathogen protein interactions predicted by comparative modeling , 2007, Protein science : a publication of the Protein Society.

[17]  J. Breman,et al.  The intolerable burden of malaria: a new look at the numbers. , 2001, The American journal of tropical medicine and hygiene.

[18]  Zohar Itzhaki,et al.  Evolutionary conservation of domain-domain interactions , 2006, Genome Biology.

[19]  M A Sirover,et al.  New insights into an old protein: the functional diversity of mammalian glyceraldehyde-3-phosphate dehydrogenase. , 1999, Biochimica et biophysica acta.

[20]  S. Báo,et al.  Glyceraldehyde-3-Phosphate Dehydrogenase of Paracoccidioides brasiliensis Is a Cell Surface Protein Involved in Fungal Adhesion to Extracellular Matrix Proteins and Interaction with Cells , 2006, Infection and Immunity.

[21]  Chi V Dang,et al.  Multifaceted roles of glycolytic enzymes. , 2005, Trends in biochemical sciences.

[22]  Burkhard Rost,et al.  Protein–Protein Interactions More Conserved within Species than across Species , 2006, PLoS Comput. Biol..

[23]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[24]  Jörg Stülke,et al.  Regulatory links between carbon and nitrogen metabolism. , 2006, Current opinion in microbiology.

[25]  D. Winzor,et al.  Interactions of glycolytic enzymes with erythrocyte membranes. , 1990, Biochimica et biophysica acta.

[26]  Timo K. Korhonen,et al.  pH-Dependent Association of Enolase and Glyceraldehyde-3-Phosphate Dehydrogenase of Lactobacillus crispatus with the Cell Wall and Lipoteichoic Acids , 2007, Journal of bacteriology.

[27]  J M Gauthier,et al.  Protein--protein interaction maps: a lead towards cellular functions. , 2001, Trends in genetics : TIG.

[28]  C. Deane,et al.  Protein Interactions , 2002, Molecular & Cellular Proteomics.

[29]  A. Vaid,et al.  PfPKB, a Protein Kinase B-like Enzyme from Plasmodium falciparum , 2006, Journal of Biological Chemistry.

[30]  J. O'connor,et al.  The glyceraldehyde-3-phosphate dehydrogenase polypeptides encoded by the Saccharomyces cerevisiae TDH1, TDH2 and TDH3 genes are also cell wall proteins. , 2001, Microbiology.

[31]  S. Barik,et al.  Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics , 2004, BMC Molecular Biology.

[32]  P. Brown,et al.  Shotgun DNA microarrays and stage‐specific gene expression in Plasmodium falciparum malaria , 2000, Molecular microbiology.

[33]  M. Vignali,et al.  A protein interaction network of the malaria parasite Plasmodium falciparum , 2005, Nature.

[34]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Li Li,et al.  PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data , 2003, Nucleic Acids Res..

[36]  David L. Tabb,et al.  A proteomic view of the Plasmodium falciparum life cycle , 2002, Nature.

[37]  D. di Bernardo,et al.  How to infer gene networks from expression profiles , 2007, Molecular systems biology.

[38]  Emmanuelle Le Chatelier,et al.  Genetic Evidence for a Link Between Glycolysis and DNA Replication , 2007, PloS one.

[39]  B. Schwikowski,et al.  A network of protein–protein interactions in yeast , 2000, Nature Biotechnology.

[40]  E Roth,et al.  Plasmodium falciparum carbohydrate metabolism: a connection between host cell and parasite. , 1990, Blood cells.

[41]  D. Chakrabarti,et al.  Characterization of protein Ser/Thr phosphatases of the malaria parasite, Plasmodium falciparum: inhibition of the parasitic calcineurin by cyclophilin-cyclosporin complex. , 1999, Molecular and biochemical parasitology.

[42]  B. Snel,et al.  Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.

[43]  S. L. Wong,et al.  A Map of the Interactome Network of the Metazoan C. elegans , 2004, Science.

[44]  V. Schächter Construction and prediction of protein-protein interaction maps. , 2002, Ernst Schering Research Foundation workshop.

[45]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[46]  Rajinder Kumar,et al.  Plasmodium falciparum calcineurin and its association with heat shock protein 90: mechanisms for the antimalarial activity of cyclosporin A and synergism with geldanamycin. , 2005, Molecular and biochemical parasitology.

[47]  G. Church,et al.  Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae , 2001, Nature Genetics.

[48]  Andrey Rzhetsky,et al.  Towards the Prediction of Complete Protein-Protein Interaction Networks , 2001, Pacific Symposium on Biocomputing.

[49]  Ogobara K. Doumbo,et al.  The pathogenic basis of malaria , 2002, Nature.

[50]  Sheng-tian Li,et al.  Critical Role of Calpain-mediated Cleavage of Calcineurin in Excitotoxic Neurodegeneration* , 2004, Journal of Biological Chemistry.

[51]  J. Rothberg,et al.  Gaining confidence in high-throughput protein interaction networks , 2004, Nature Biotechnology.

[52]  E. Golemis,et al.  The yeast two-hybrid system: criteria for detecting physiologically significant protein-protein interactions. , 1999, Current issues in molecular biology.

[53]  Christian Hott,et al.  Co‐ordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasite Plasmodium falciparum revealed by microarray analysis , 2001, Molecular microbiology.

[54]  Albert-László Barabási,et al.  Statistical mechanics of complex networks , 2001, ArXiv.

[55]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[56]  B. Alberts The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists , 1998, Cell.

[57]  Neil Hall,et al.  Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry , 2002, Nature.

[58]  P. Uetz,et al.  The elusive yeast interactome , 2006, Genome Biology.

[59]  Ting Chen,et al.  An integrated approach to the prediction of domain-domain interactions , 2006, BMC Bioinformatics.

[60]  T. Barrette,et al.  Probabilistic model of the human protein-protein interaction network , 2005, Nature Biotechnology.

[61]  I. Kurland,et al.  Covalent control of 6‐phosphofructo‐2‐kinase/fructose‐2,6‐bisphosphatase: Insights into autoregulation of a bifunctional enzyme , 1995, Protein science : a publication of the Protein Society.

[62]  T. Sittler,et al.  The Plasmodium protein network diverges from those of other eukaryotes , 2005, Nature.

[63]  Benjamin A. Shoemaker,et al.  Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases , 2007, PLoS Comput. Biol..

[64]  L. Mirny,et al.  Protein complexes and functional modules in molecular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.