Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer

Abstract

The var gene encoded hyper-variable Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family mediates cytoadhesion of infected erythrocytes to human endothelium. Antibodies blocking cytoadhesion are important mediators of malaria immunity acquired by endemic populations. The development of a PfEMP1 based vaccine mimicking natural acquired immunity depends on a thorough understanding of the evolved PfEMP1 diversity, balancing antigenic variation against conserved receptor binding affinities. This study redefines and reclassifies the domains of PfEMP1 from seven genomes. Analysis of domains in 399 different PfEMP1 sequences allowed identification of several novel domain classes, and a high degree of PfEMP1 domain compositional order, including conserved domain cassettes not always associated with the established group A–E division of PfEMP1. A novel iterative homology block (HB) detection method was applied, allowing identification of 628 conserved minimal PfEMP1 building blocks, describing on average 83% of a PfEMP1 sequence. Using the HBs, similarities between domain classes were determined, and Duffy binding-like (DBL) domain subclasses were found in many cases to be hybrids of major domain classes. Related to this, a recombination hotspot was uncovered between DBL subdomains S2 and S3. The VarDom server is introduced, from which information on domain classes and homology blocks can be retrieved, and new sequences can be classified. Several conserved sequence elements were found, including: (1) residues conserved in all DBL domains predicted to interact and hold together the three DBL subdomains, (2) potential integrin binding sites in DBLα domains, (3) an acylation motif conserved in group A var genes suggesting N-terminal N-myristoylation, (4) PfEMP1 inter-domain regions proposed to be elastic disordered structures, and (5) several conserved predicted phosphorylation sites. Ideally, this comprehensive categorization of PfEMP1 will provide a platform for future studies on var/PfEMP1 expression and function.

Author Summary

About one million African children die from malaria every year. The severity of malaria infections in part depends on which type of the parasitic protein PfEMP1 is expressed on the surface of the infected red blood cells. Natural immunity to malaria is mediated through antibodies to PfEMP1. Therefore hopes for a malaria vaccine based on PfEMP1 proteins have been raised. However, the large sequence variation among PfEMP1 molecules has caused great difficulties in executing and interpreting studies on PfEMP1. Here, we present an extensive sequence analysis of all currently available PfEMP1 sequences and show that PfEMP1 variation is ordered and can be categorized at different levels. In this way, PfEMP1 belong to group A–E and are composed of up to four components, each component containing specific DBL or CIDR domain subclasses, which in some cases form entire conserved domain combinations. Finally, each PfEMP1 can be described in high detail as a combination of 628 homology blocks. This dissection of PfEMP1 diversity also enables predictions of several functional sequence motifs relevant to the fold of PfEMP1 proteins and their ability to bind human receptors. We therefore believe that this description of PfEMP1 diversity is necessary and helpful for the design and interpretation of future PfEMP1 studies.