Genetic investigation of tricarboxylic acid metabolism during the Plasmodium falciparum life cycle

Abstract

New antimalarial drugs are urgently needed to control drug-resistant forms of the malaria parasite Plasmodium falciparum. Mitochondrial electron transport is the target of both existing and new antimalarials. Herein, we describe 11 genetic knockout (KO) lines that delete six of the eight mitochondrial tricarboxylic acid (TCA) cycle enzymes. Although all TCA KOs grew normally in asexual blood stages, these metabolic deficiencies halted life-cycle progression in later stages. Specifically, aconitase KO parasites arrested as late gametocytes, whereas α-ketoglutarate-dehydrogenase-deficient parasites failed to develop oocysts in the mosquitoes. Mass spectrometry analysis of (13)C-isotope-labeled TCA mutant parasites showed that P. falciparum has significant flexibility in TCA metabolism. This flexibility manifested itself through changes in pathway fluxes and through altered exchange of substrates between cytosolic and mitochondrial pools. Our findings suggest that mitochondrial metabolic plasticity is essential for parasite development.

Figure 1. TCA architecture in the asexual blood stages of WT P. falciparum

Bar graphs show the percent isotopic enrichment (y-axes) for ¹³C isotopomers (x-axes) of TCA metabolites extracted from D10 WT parasites incubated for 4 h with either U-¹³C glucose (blue bars) or U-¹³C glutamine (orange bars). Please note different scales for distinct metabolites. These data are the average of three biological replicates, each carried out in triplicate. The molecular structures corresponding to the most abundant glucose and glutamine-derived isotopomers are shown (*). Abbreviations: KDH, α-ketoglutarate dehydrogenase; SCS, succinyl-CoA synthase; SDH, succinate dehydrogenase; FH, fumarate hydratase; MQO, malate quinone oxidoreductase; CS, citrate synthase; ACO, aconitase; IDH, isocitrate dehydrogenase. Cofactors: Q, ubiquinone; QH₂, ubiquinol; NAD⁺, nicotinamide adenine dinucleotide; NADH, reduced nicotinamide adenine dinucleotide; NADP⁺, nicotinamide adenine dinucleotide phosphate; NADPH, reduced nicotinamide adenine dinucleotide phosphate.

Figure 2. Metabolic consequences of TCA cycle disruptions in the asexual blood stages

(Top) A linearized depiction of oxidative TCA metabolism showing each of the expected isotopomers produced from U-¹³C glutamine labeling. Among them, aspartate (*) undergoes rapid exchange with oxaloacetate (oxaloacetate cannot be stably measured by the methods used in this work); +2 succinate (far right) is derived from a second round of the TCA cycle. Levels of isotopically enriched metabolites observed in extracts from uninfected RBCs, D10 WT and 9 different TCA KO lines are shown. For each line, data are averaged from at least three biological replicates, which were carried out in duplicate or triplicate. Each row shows a complete profile of the TCA cycle metabolites. Each column corresponds to the ratio of isotopomer in each KO line relative to the D10 WT. Orange circles show the positions of carbons labeled by U-¹³C glutamine. Red triangles represent the ratio of each individual measurement relative to the D10 WT. Grey triangles indicate metabolites that are below the threshold of detection. Blue Xs indicate the enzymatic steps that were disrupted in the KO lines. Abbreviations: Glu, glutamate; αKG, α-ketoglutarate; Suc, succinate; Fum, fumarate; Mal, malate; Asp, aspartate; Cit, citrate. For genetic and phenotypic analyses of these KOs, see Figures S1, S2 and Table S3.

Figure 3. Anaplerotic compensation for impaired glutamine metabolism

(A) A schematic representation of the cytosolic and mitochondrial pathways used by PEPC-derived oxaloacetate. Blue arrows depict glucose utilization without mitochondrial participation (pre-mitochondrial flux) and red arrows indicate glucose utilization involving mitochondrial processes (post-mitochondrial flux). (B) Extracellular concentrations of individual metabolites in D10 WT, ΔKDH, ΔKDH/ΔIDH lines. (C) Pre- and post-mitochondrial metabolites excreted into the medium by the D10 WT and various KO lines. The total excretion of glucose-derived carbon through PEPC is the sum of the concentrations of +3 malate and +3 aspartate (pre-mitochondrial, blue bars), and +5 citrate, +4/+5 α-ketoglutarate and +4/+5 glutamate (post-mitochondrial, red bars). Data are derived from three biological replicates. The glucose labeling patterns in other TCA KO lines from the parasite pellet samples are shown in Figure S4 and Table S4.

Figure 4. mtETC inhibition blocks the TCA flux

(A) A schematic representation of carbon input from glucose into the TCA metabolites. Blue arrows/circles show anaplerotic input through PEPC reaction, while gold arrows/circles indicate flux from acetyl-CoA. Atovaquone (ATV) blocks the mtETC, thereby inhibiting MQO. (B) Enrichment of each metabolite in yDHOD transgenic parasites in the presence or absence of ATV is shown. The +2 and +5 citrate isotopomers are diagnostic of flux through the citrate synthase reaction. Data are the average of three biological replicates. A more comprehensive set of TCA cycle isotopomers is presented in Figure S5.

Figure 5. TCA cycle is essential to mosquito stage development of P. falciparum

(A) Gametocytemia of NF54 WT and NF54-ΔKDH parasites on days 14–20 post induction. (B) Exflagellation percentage in NF54 WT and NF54-ΔKDH lines on days 14–20 post induction. (C) Infectivity of NF54 WT and NF54-ΔKDH parasites as measured by the number of oocysts per mosquito on day 8 after blood feeding. Panels D to F correspond to panels A to C, respectively, showing results from NF54-ΔAco line. In (C) and (F), data are from two independent feeding experiments. Morphological data are shown in Figure S6.

Figure 6. Models for TCA metabolism under various conditions

A schematic representation of TCA flux is shown for (A) WT, (B) ΔAco, (C) ΔKDH, and (D) atovaquone-treated parasites. Metabolic fluxes are depicted qualitatively as major (thick blue lines), minor (thin black lines), or zero (dotted lines). Some minor fluxes have been excluded for clarity of presentation. At the bottom of each panel, the progression of the parasite lifecycle is indicated. IDC, intra-erythrocytic development cycle, is comprised of ring (R), trophozoite (T) and schizont (S). Gametocyte development progresses from stage I to stage V. Mosquito stages include gamete (G), zygote (Z), ookinete (OK) and oocyst (OC). Proposed reasons for developmental arrest at each of these s tages are indicated by numbers within red octagons.