Artemisinin resistance in Plasmodium falciparum threatens global efforts to control and eliminate malaria. Polymorphisms in the kelch domain–carrying protein K13 are associated with artemisinin resistance, but the underlying molecular mechanisms are unknown. We analyzed the in vivo transcriptomes of 1043 P. falciparum isolates from patients with acute malaria and found that artemisinin resistance is associated with increased expression of unfolded protein response (UPR) pathways involving the major PROSC and TRiC chaperone complexes. Artemisinin-resistant parasites also exhibit decelerated progression through the first part of the asexual intraerythrocytic development cycle. These findings suggest that artemisinin-resistant parasites remain in a state of decelerated development at the young ring stage, whereas their up-regulated UPR pathways mitigate protein damage caused by artemisinin. The expression profiles of UPR-related genes also associate with the geographical origin of parasite isolates, further suggesting their role in emerging artemisinin resistance in the Greater Mekong Subregion.

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Malaria genetic variation has been extensively characterized, but the level of epigenetic plasticity remains largely unexplored. Here we provide a comprehensive characterization of transcriptional variation in the most lethal malaria parasite, Plasmodium falciparum, based on highly accurate transcriptional analysis of isogenic parasite lines grown under homogeneous conditions. This analysis revealed extensive transcriptional heterogeneity within genetically homogeneous clonal parasite populations. We show that clonally variant expression controlled at the epigenetic level is an intrinsic property of specific genes and gene families, the majority of which participate in host-parasite interactions. Intrinsic transcriptional variability is not restricted to genes involved in immune evasion, but also affects genes linked to lipid metabolism, protein folding, erythrocyte remodeling, or transcriptional regulation, among others, indicating that epigenetic variation results in both antigenic and functional variation. We observed a general association between heterochromatin marks and clonally variant expression, extending previous observations for specific genes to essentially all variantly expressed gene families. These results suggest that phenotypic variation of functionally unrelated P. falciparum gene families is mediated by a common mechanism based on reversible formation of H3K9me3-based heterochromatin. In changing environments, diversity confers fitness to a population. Our results support the idea that P. falciparum uses a bethedging strategy, as an alternative to directed transcriptional responses, to adapt to common fluctuations in its environment. Consistent with this idea, we found that transcriptionally different isogenic parasite lines markedly differed in their survival to heat-shock mimicking febrile episodes and adapted to periodic heat-shock with a pattern consistent with natural selection of pre-existing parasites.

Functions have yet to be defined for the majority of genes of Plasmodium falciparum, the agent responsible for the most serious form of human malaria. Here we report changes in P. falciparum gene expression induced by 20 compounds that inhibit growth of the schizont stage of the intraerythrocytic development cycle. In contrast with previous studies, which reported only minimal changes in response to chemically induced perturbations of P. falciparum growth, we find that approximately 59% of its coding genes display over three-fold changes in expression in response to at least one of the chemicals we tested. We use this compendium for guilt-by-association prediction of protein function using an interaction network constructed from gene co-expression, sequence homology, domain-domain and yeast two-hybrid data. The subcellular localizations of 31 of 42 proteins linked with merozoite invasion is consistent with their role in this process, a key target for malaria control. Our network may facilitate identification of novel antimalarial drugs and vaccines.

Plasmodium vivax causes over 100 million clinical infections each year. Primarily because of the lack of a suitable culture system, our understanding of the biology of this parasite lags significantly behind that of the more deadly species P. falciparum. Here, we present the complete transcriptional profile throughout the 48-h intraerythrocytic cycle of three distinct P. vivax isolates. This approach identifies strain specific patterns of expression for subsets of genes predicted to encode proteins associated with virulence and host pathogen interactions. Comparison to P. falciparum revealed significant differences in the expression of genes involved in crucial cellular functions that underpin the biological differences between the two parasite species. These data provide insights into the biology of P. vivax and constitute an important resource for the development of therapeutic approaches.comparative genomics ͉ Plasmodium falciparum I t is now increasingly recognized that P. vivax infections contribute significantly to the burden of malaria (1, 2). In all endemic areas except for Africa, P. vivax is often the dominant species, and at least 100 million cases are reported annually (2, 3). Although vivax malaria is clinically less likely than P. falciparum to develop into a life threatening disease, it exerts a substantial toll on the individual's health and economic well being. The chronic, long-lasting nature of the infection contributes substantially to morbidity. Chronicity is because of hypnozoites, dormant liver stages from which fresh blood infection or relapses originate up to 2 years after the infectious bite (4). The presence of hypnozoites make infections by P. vivax difficult to cure radically and pose a serious obstacle to the control and eventual eradication of this parasite.The description of the P. falciparum genome (5) and staged erythrocytic transcriptome (6, 7) has provided an invaluable resource for the study of this important species. It would be of fundamental and practical interest to do the same for P. vivax because there are important biological and clinical differences between this species and P. falciparum, whose basis is currently unknown (8). For example, the presence of circulating mature erythrocytic stages of P. vivax would suggest that multigene families and processes implicated in antigenic variation and immune evasion are quite different to P. falciparum, whose mature asexual red cell stages generally sequester. Unlike P. falciparum, P. vivax has a selective preference for infecting reticulocytes (9), strongly suggesting an alternate red cell attachment invasion mechanism. In contrast to the rigid, sticky and knobby P. falciparum infected red cell, P. vivax remodels the host-cell membranes to produce a highly deformable erythrocyte characterized by numerous caveola-vesicle complexes (10-12). Finally, the kinetics of gametocyte production in P. vivax is also different than P. falciparum, with P. vivax gametocytes appearing much earlier and being relatively short lived (8). Aside ...

SummaryHeterochromatin-dependent gene silencing is central to the adaptation and survival of Plasmodium falciparum malaria parasites, allowing clonally variant gene expression during blood infection in humans. By assessing genome-wide heterochromatin protein 1 (HP1) occupancy, we present a comprehensive analysis of heterochromatin landscapes across different Plasmodium species, strains, and life cycle stages. Common targets of epigenetic silencing include fast-evolving multi-gene families encoding surface antigens and a small set of conserved HP1-associated genes with regulatory potential. Many P. falciparum heterochromatic genes are marked in a strain-specific manner, increasing the parasite's adaptive capacity. Whereas heterochromatin is strictly maintained during mitotic proliferation of asexual blood stage parasites, substantial heterochromatin reorganization occurs in differentiating gametocytes and appears crucial for the activation of key gametocyte-specific genes and adaptation of erythrocyte remodeling machinery. Collectively, these findings provide a catalog of heterochromatic genes and reveal conserved and specialized features of epigenetic control across the genus Plasmodium.

Summary Variant surface antigens play an important role in the pathogenesis of Plasmodium falciparum malaria. To date, intensive work has mainly focused on the role in parasite virulence of the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) encoded by the var multigene family. Two other multigene families coding for STEVOR and RIFIN have recently also been shown to be expressed in the invasive merozoite as well as on the surface of the infected erythrocyte, implicating them as potential parasite virulence factors. Here we report that STEVOR is an erythrocyte-binding protein recognizing Glycophorin C on the red blood cell (RBC) surface. STEVOR expression on the RBC leads to PfEMP1-independent rosette formation, while antibodies targeting STEVOR in the merozoite can effectively inhibit invasion. Our results suggest a novel role of STEVOR in enabling infected erythrocytes at the schizont stage to bind uninfected erythrocytes to form rosettes, thereby protecting released merozoites from immune detection.

AbstractAchievement of malaria elimination requires development of novel strategies interfering with parasite transmission, including targeting the parasite sexual stages (gametocytes). The formation of Plasmodium falciparum gametocytes in the human host takes several days during which immature gametocyte-infected erythrocytes (GIEs) sequester in host tissues. Only mature stage GIEs circulate in the peripheral blood, available to uptake by the Anopheles vector. Mechanisms underlying GIE sequestration and release in circulation are virtually unknown. We show here that mature GIEs are more deformable than immature stages using ektacytometry and microsphiltration methods, and that a switch in cellular deformability in the transition from immature to mature gametocytes is accompanied by the deassociation of parasite-derived STEVOR proteins from the infected erythrocyte membrane. We hypothesize that mechanical retention contributes to sequestration of immature GIEs and that regained deformability of mature gametocytes is associated with their release in the bloodstream and ability to circulate. These processes are proposed to play a key role in P falciparum gametocyte development in the host and to represent novel and unconventional targets for interfering with parasite transmission.