title: Protease-associated cellular networks in malaria parasite Plasmodium falciparum.
abstract: BACKGROUND
  Malaria continues to be one of the most severe global infectious diseases, responsible for 1-2 million deaths yearly. The rapid evolution and spread of drug resistance in parasites has led to an urgent need for the development of novel antimalarial targets. Proteases are a group of enzymes that play essential roles in parasite growth and invasion. The possibility of designing specific inhibitors for proteases makes them promising drug targets. Previously, combining a comparative genomics approach and a machine learning approach, we identified the complement of proteases (degradome) in the malaria parasite Plasmodium falciparum and its sibling species 123, providing a catalog of targets for functional characterization and rational inhibitor design. Network analysis represents another route to revealing the role of proteins in the biology of parasites and we use this approach here to expand our understanding of the systems involving the proteases of P. falciparum.
  
  
  RESULTS
  We investigated the roles of proteases in the parasite life cycle by constructing a network using protein-protein association data from the STRING database 4, and analyzing these data, in conjunction with the data from protein-protein interaction assays using the yeast 2-hybrid (Y2H) system 5, blood stage microarray experiments 678, proteomics 9101112, literature text mining, and sequence homology analysis. Seventy-seven (77) out of 124 predicted proteases were associated with at least one other protein, constituting 2,431 protein-protein interactions (PPIs). These proteases appear to play diverse roles in metabolism, cell cycle regulation, invasion and infection. Their degrees of connectivity (i.e., connections to other proteins), range from one to 143. The largest protease-associated sub-network is the ubiquitin-proteasome system which is crucial for protein recycling and stress response. Proteases are also implicated in heat shock response, signal peptide processing, cell cycle progression, transcriptional regulation, and signal transduction networks.
  
  
  CONCLUSIONS
  Our network analysis of proteases from P. falciparum uses a so-called guilt-by-association approach to extract sets of proteins from the proteome that are candidates for further study. Novel protease targets and previously unrecognized members of the protease-associated sub-systems provide new insights into the mechanisms underlying parasitism, pathogenesis and virulence.
authors.affiliation: Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA.
authors.forename: Timothy G
authors.initials: TG
authors.lastname: Lilburn
authors.forename: Hong
authors.initials: H
authors.lastname: Cai
authors.forename: Zhan
authors.initials: Z
authors.lastname: Zhou
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000818:Animals; D057225:Data Mining; D030562:Databases, Protein; D004912:Erythrocytes / Q000469:parasitology; D010447:Peptide Hydrolases / Q000378:metabolism*; D010963:Plasmodium falciparum / Q000201:enzymology* / Q000378:metabolism; D040081:Protein Array Analysis; D025941:Protein Interaction Mapping; D040901:Proteomics; D015800:Protozoan Proteins / Q000378:metabolism*; D017385:Sequence Homology; D020798:Two-Hybrid System Techniques; D014452:Ubiquitins / Q000378:metabolism
chemical_list: D015800:Protozoan Proteins; D014452:Ubiquitins; D010447:Peptide Hydrolases