Systems analysis of chaperone networks in the malarial parasite Plasmodium falciparum

Abstract

Molecular chaperones participate in the maintenance of cellular protein homeostasis, cell growth and differentiation, signal transduction, and development. Although a vast body of information is available regarding individual chaperones, few studies have attempted a systems level analysis of chaperone function. In this paper, we have constructed a chaperone interaction network for the malarial parasite, Plasmodium falciparum. P. falciparum is responsible for several million deaths every year, and understanding the biology of the parasite is a top priority. The parasite regularly experiences heat shock as part of its life cycle, and chaperones have often been implicated in parasite survival and growth. To better understand the participation of chaperones in cellular processes, we created a parasite chaperone network by combining experimental interactome data with in silico analysis. We used interolog mapping to predict protein-protein interactions for parasite chaperones based on the interactions of corresponding human chaperones. This data was then combined with information derived from existing high-throughput yeast two-hybrid assays. Analysis of the network reveals the broad range of functions regulated by chaperones. The network predicts involvement of chaperones in chromatin remodeling, protein trafficking, and cytoadherence. Importantly, it allows us to make predictions regarding the functions of hypothetical proteins based on their interactions. It allows us to make specific predictions about Hsp70-Hsp40 interactions in the parasite and assign functions to members of the Hsp90 and Hsp100 families. Analysis of the network provides a rational basis for the anti-malarial activity of geldanamycin, a well-known Hsp90 inhibitor. Finally, analysis of the network provides a theoretical basis for further experiments designed toward understanding the involvement of this important class of molecules in parasite biology.

Figure 1. Prediction of Functions for Hypothetical Proteins

(A) Involvement of PF14_0510 in transcriptional regulation. (B) PF14_0324 may be involved in haemoglobin metabolism. (C) Participation of PF14_0700 in membrane protein trafficking. The node for which the function is being predicted is highlighted in yellow in each case.

Figure 2. Chaperone Function during Parasite Development

(A) Numerical comparison of the various stage-specific chaperone networks. (B) Top panel. Quantitation of the amounts of the major parasite heat shock proteins in various parasite stages. Bottom panel. Quantitation of the abundance of actin, tubulin, and centrin proteins in the different stages.

Figure 3. Network of PfHsp90 and PfHsp70 Interactions

(A) Subnetwork of PfHsp90 (PF07_0029) and PfHsp70 interactions. Green lines indicate protein–protein interactions derived from yeast two-hybrid screens, while the red lines indicate interactions predicted through interolog analysis. PfHsp90 client proteins indicating involvement of PfHsp90 in particular cellular processes are underlined by blue and red lines. The black lines indicate PfHsp90 co-chaperones while the star indicates casein kinase II alpha subunit, a protein that may be involved in the phosphorylation of PfHsp90. The boxed protein is Cg4, a PfHsp90 interactor that may be associated with drug resistance while the pink lines mark the three Hsp40 proteins that may function as PfHsp70 co-chaperones. (B) Schematic representation of the involvement of Hsp70, Hsp90, and Hsp40 in the biological processes of a typical eukaryotic cell.

Figure 4. Inferences from Networks Analysis

(A) Network of interacting proteins for PfHsp101 (PF11_0175). (B) Left panel. Subnetwork of calnexin, calreticulin, BiP, and Grp94 in the ER of human cells. Underlined proteins indicate interactions between BiP, Grp94, protein disulfide isomerases (P4HB, PDIA4, PDIA6), peptidyl prolyl isomerases (PPIA, PPIB), and ERP29. Right panel. Subnetwork of the parasite ER chaperones, PfBiP and PfGrp94. Proteins indicated by blue lines mark interactions between PfBiP, PfGrp94, peptidyl prolyl isomerase (PF11_0164), and protein disulfide isomerases (MAL8P1.17 and PF11_0352). The protein marked with the red line is PfEMP1 ((PFI1830c).