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.

Evolutionary structure of Plasmodium falciparum major variant surface antigen genes in South America: Implications for epidemic transmission and surveillance

“…Among the different DBL domains characterized, DBLα is the most conserved and is involved in the adherence of infected red blood cells (RBCs) to uninfected RBCs (Chen et al., 1998; Vogt et al., 2003). Bioinformatic analyses have shown that var gene diversity is of ancient origin and maintained by balancing selection, and that through the process of shuffling homology blocks during recombination var genes are able to diversify (Rask et al., 2010; Zilversmit et al., 2013). Moreover, it has been demonstrated that var gene repertoire diversity within and between parasite genomes is also generated by meiosis during sexual recombination (Chen et al., 2011; Zilversmit et al., 2013) and by mitotic recombination during asexual division (Bopp et al., 2013; Claessens et al., 2014; Duffy et al., 2009).…”

Towards an anti-disease malaria vaccine

“…It also leads to inflammation, occlusion of blood vessels and to the symptoms of severe malaria, including cerebral malaria and pregnancy-associated malaria, which are characterized by marked sequestration of parasites in the brain and placenta [12]. Endothelial tethering is mediated by the P. falciparum erythrocyte membrane protein 1, PfEMP1, a large protein family with ∼60 members encoded in each genome [13,14]. Each PfEMP1 is formed from multiple copies of two parasite-specific domain types, the CIDR and DBL domains, which are most often spatially arranged in a linear array (Figure 1) [15].…”

“…As proteins that are constantly exposed to the immune system, selection pressure has caused them to expand into a large and antigenically variant protein family that varies significantly between different isolates [13,14]. The population of parasites released from the liver expresses most PfEMP1s, with a reduced repertoire found later in infection [22,23].…”

“…Narrowing down the search required extensive sequence analysis and PfEMP1 domain classification [14]. First, the PfEMP1s were arranged into groups A, B and C, depending on their chromosomal location and the domain types encoded [31].…”

Molecular basis of severe malaria

“…The studies by Avril et al (1) and Claessens et al (2) identify narrow subsets of group A var genes that were expressed by parasites selected to adhere with high affinity to endothelial cells derived from human brain tissue. When the encoded PfEMP1s were classified according to their domain architecture, they were found to possess one of two specific combinations of binding domain cassettes, referred to as DC8 or DC13, at their N-terminal ends (19). Interestingly, parasites expressing these var genes also bound to endothelial cells derived from nonbrain tissues; however, they did not bind intracellular adhesion molecule 1 (ICAM1), a host surface molecule previously proposed to be the endothelial receptor bound by infected erythrocytes in the brain.…”