Genome sequence of the human malaria parasite Plasmodium falciparum

Abstract

The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria.

Figure 1

Schematic representation of the P. falciparum 3D7 genome. Q Protein-encoding genes are indicated by open diamonds. All genes are depicted at the same scale regardless of their size or structure. The labels indicate the name for each gene. The rows of coloured rectangles represent, from top to bottom for each chromosome, the high-level Gene Ontology assignment for each gene in the ‘biological process’, ‘molecular function’, and ‘cellular component’ ontologies; the life-cycle stage(s) at which each predicted gene product has been detected by proteomics techniques^,; and Plasmodium yoelii yoelii genes that exhibit conserved sequence and organization with genes in P. falciparum, as shown by a position effect analysis. Rectangles surrounding clusters of P. yoelii genes indicate genes shown to be linked in the P. y. yoelii genome. Boxes containing coloured arrowheads at the ends of each chromosome indicate subtelomeric blocks (SBs; see text and Fig. 2).

Figure 2

Alignment of subtelomeric regions of chromosomes 1, 3, 6 and 11. MUMmer2 alignments showing exact matches between the left subtelomeric regions of chromosome 6 (horizontal axis) and chromosomes 11 (red), 1 (blue) and 3 (green), illustrating the conserved synteny between all telomeres. Each point represents an exact match of 40 bp or longer that is shared by two chromosomes and is not found anywhere else on either chromosome. Each collinear series of points along a diagonal represents an aligned region. SB, subtelomeric block; TARE, telomere-associated repetitive element.

Figure 3

Gene Ontology classifications. Classification of P. falciparum proteins according to the ‘biological process’ (a) and ‘molecular function’ (b) ontologies of the Gene Ontology system.

Figure 4

Overview of metabolism and transport in P. falciparum. Glucose and glycerol provide the major carbon sources for malaria parasites. Metabolic steps are indicated by arrows, with broken lines indicating multiple intervening steps not shown; dotted arrows indicate incomplete, unknown or questionable pathways. Known or potential organellar localization is shown for pathways associated with the food vacuole, mitochondrion and apicoplast. Small white squares indicate TCA (tricarboxylic acid) cycle metabolites that may be derived from outside the mitochondrion. Fuschia block arrows indicate the steps inhibited by antimalarials; grey block arrows highlight potential drug targets. Transporters are grouped by substrate specificity: inorganic cations (green), inorganic anions (magenta), organic nutrients (yellow), drug efflux and other (black). Arrows indicate direction of transport for substrates (and coupling ions, where appropriate). Numbers in parentheses indicate the presence of multiple transporter genes with similar substrate predictions. Membrane transporters of unknown or putative subcellular localization are shown in a generic membrane (blue bar). Abbreviations: ACP, acyl carrier protein; ALA, aminolevulinic acid; CoA, coenzyme A; DHF, dihydrofolate; DOXP, deoxyxylulose phosphate; FPIX²⁺ and FPIX³⁺, ferro- and ferriprotoporphyrin IX, respectively; pABA, para-aminobenzoic acid; PEP, phosphoenolpyruvate; P_i, phosphate; PP_i, pyrophosphate; PRPP, phosphoribosyl pyrophosphate; THF, tetrahydrofolate; UQ, ubiquinone.

Figure 5

Analysis of transporters in P. falciparum. a, Comparison of the numbers of transporters belonging to the major facilitator superfamily (MFS), ATP-binding cassette (ABC) family, P-type ATPase family and the amino acid/polyamine/choline (APC) family in P. falciparum and other eukaryotes. Analyses were performed as previously described. b, Comparison of the numbers of proteins with ten or more predicted transmembrane segments (TMS) in P. falciparum and other eukaryotes. Prediction of membrane spanning segments was performed using TMHMM.

Figure 6

Organization of multi-gene families in P. falciparum. a, Telomeric regions of all chromosomes showing the relative positions of members of the multi-gene families: rif (blue) stevor (yellow) and var (colour coded as indicated; see b and c). Grey boxes represent pseudogenes or gene fragments of any of these families. The left telomere is shown above the right. Scale: ~0.6 mm = 1 kb. b, c, var gene domain structure. var genes contain three domain types: DBL, of which there are six sequence classes; CIDR, of which there are two sequence classes; and conserved 2 (C2) domains (see text). The relative order of the domains in each gene is indicated (c). var genes with the same domain types in the same order have been colour coded as an identical class and given an arbitrary number for their type (b) and the total number of members of each class in the genome of P. falciparum clone 3D7. d, Internal multi-gene family clusters. Key as in a.