Characterization of promoters and stable transfection by homologous and nonhomologous recombination in Plasmodium falciparum

Genetic studies of the protozoan parasite Plasmodium falciparum have been severely limited by the inability to introduce or modify genes. In this paper we describe a system of stable transfection of P. falciparum using a Toxoplasma gondii dihydrofolate reductase-thymidylate synthase gene, modified to confer resistance to pyrimethamine, as a selectable marker. This gene was placed under the transcriptional control of the P. falciparum calmodulin gene flanking sequences. Transfected parasites generally maintained plasmids episomally while under selection; however, parasite clones containing integrated forms of the plasmid were obtained. Integration occurred by both homologous and nonhomologous recombination. In addition to the flanking sequence of the P. falciparum calmodulin gene, the 5' sequences of the P. falciparum and P. chabaudi dihydrofolate reductase-thymidylate synthase genes were also shown to be transcriptionally active in P. falciparum. The minimal 5' sequence that possessed significant transcriptional activity was determined for each gene and short sequences containing important transcriptional control elements were identified. These sequences will provide considerable flexibility in the future construction of plasmid vectors to be used for the expression of foreign genes or for the deletion or modification of P. falciparum genes of interest.

Current status of the Plasmodium falciparum genome project

The Plasmodium falciparum Genome Project is a collaborative effort by many laboratories that will provide detailed molecular information about the parasite, which may be used for developing practical control measures. Initial goals are to prepare an electronically indexed clone bank containing partially sequenced clones representing up to 80% of the parasite's genes and to prepare an ordered set of overlapping clones spanning each of the parasite's 14 chromosomes. Currently, clones of genomic DNA, prepared as yeast artificial chromosomes, are arranged into contigs covering approximately 70% of the genome of parasite clone 3D7, gene sequence tags are available from more than contigs covering approximately 70% of the genome of parasite clone 3D7, gene sequence tags are available from more than 20% of the parasite's genes, and approximately 5% of the parasite's genes are tentatively identified from similarity searches of entries in the international sequence databases. A total of > 0.5 Mb of P. falciparum sequence tag data is available. The gene sequence tags are presently being used to complete YAC contig assembly and localize the cloned genes to positions on the physical map in preparation for sequencing the genome. Routes of access to project information and services are described.

The ATP-binding cassette (ABC) gene family of Plasmodium falciparum

Multidrug resistance (MDR) in mammalian tumour cells is mediated by P-glycoproteins. The apparent similarities between MDR and the chloroquine-resistance phenotype (CQR) in Plasmodium falciparum suggests that homologous proteins may be involved. In mammals, P-glycoproteins are encoded by mdr genes that are a subset of a super-family characterized by ATP-binding cassettes (ABC). Three genes, pfmdr1, pfmdr2 and pfef3-rl, have been identified in P. falciparum that have homology to the ABC transporter gene family. Each protein encoded by these genes has a distinct structure, suggesting functional differences between the three. Justin Rubio and Alan Cowman here discuss the structure and possible function of the ABC proteins from P. falciparum and evidence that the protein encoded by the pfmdr1 gene can influence quinoline-containing antimalarial drug-resistance phenotypes.

Mechanisms of drug resistance in malaria

Plasmodium falciparum causes the most severe form of human malaria which directly results in over two million deaths per year. As there is not yet a useful vaccine against this disease the major form of treatment and control is the use of chemotherapeutic agents. Unfortunately the parasite has managed to devise mechanisms that allow it to evade the action of almost all the antimalarials in our arsenal. The antifolate drugs include the dihydrofolate inhibitors pyrimethamine and proguanil as well as the sulfones and sulfonamides. These antimalarials act on enzymes in the folate pathway. The mechanism of resistance to these compounds involve mutations in the target enzyme that decrease the affinity of binding of the drug. A second major group of antimalarials include the quinine-like compounds. Quinine was one of the first compounds used to treat malaria and the related drug chloroquine is the most important antimalarial. Mefloquine and halofantrine were developed in response to major problems with the spread of chloroquine resistance. Chloroquine resistance is due to the ability of the parasite to decrease the accumulation of the drug in the cell. The exact mechanism that allows this is still under investigation although at least one protein has been identified that affects the accumulation of this important antimalarial.

Molecular cloning of a gene from Plasmodium falciparum that codes for a protein sharing motifs found in adhesive molecules from mammals and plasmodia

Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria-associated pathology. We report here the molecular cloning of a putative adhesive molecule from P. falciparum that shares both sequence and structural similarities with a sporozoite surface molecule from Plasmodium termed the thrombospondin-related anonymous protein (TRAP) and, to a lesser extent, with the circumsporozoite (CS) protein. The gene, which is present on chromosome 3 as a single copy, was termed CTRP for CS protein-TRAP-related protein. The full-length CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The putative extracellular region of CTRP is defined by two separated adhesive domains. The first domain contains six 210-amino acid-long homologous repeats, the sequence of which is related to the A-type domain found in adhesive molecules including the alpha subunits of several integrins and a number of extracellular matrix glycoproteins. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. Interstrain analysis of eight different parasite isolates revealed that CTRP does not show size polymorphism except in repetitive regions flanking potential adhesive domains.

Functional complementation of the ste6 gene of Saccharomyces cerevisiae with the pfmdr1 gene of Plasmodium falciparum

The pfmdr1 gene has been associated with a drug-resistant phenotype in Plasmodium falciparum, and overexpression of pfmdr1 has been associated with mefloquine- and halofantrine-resistant parasites, but little is known about the functional role of pfmdr1 in this process. Here, we demonstrate that the pfmdr1 gene expressed in a heterologous yeast system functions as a transport molecule and complements a mutation in ste6, a gene which encodes a mating pheromone a-factor export molecule. In addition, the pfmdr1 gene containing two mutations which are associated with naturally occurring chloroquine resistance abolishes this mating phenotype, suggesting that these genetic polymorphisms alter this transport function. Our results support the functional role of pfmdr1 as a transport molecule in the mediation of drug resistance and provide an assay system to address the nature of this transport function.

Characterization of the gene family encoding a host-protective antigen of the tapeworm Taenia ovis

Genomic structure has been determined for a gene encoding a host-protective antigen of the parasitic platyhelminth Taenia ovis. An incomplete cDNA, known as 45W, encodes the protective antigen. Southern hybridisation experiments using 45W cDNA as a probe, revealed that the 45W gene was a member of a multigene family. Differential Southern hybridisation and rapid amplification of cDNA end (RACE) experiments were used to characterise the related genes, allowing the full-length coding region of the 45W encoded antigen to be determined. The gene family comprises a minimum of four members per haploid genome with each member showing varying degrees of 5' and 3' homology with respect to the 45W cDNA. A close homologue of the 45W gene, designated 45S, differed from 45W at 11 of 985 nt comprising the full-length mRNA. Sequencing of several independent RACE products for both 45W and 45S identified a cDNA which may be a product of homologous recombination between these genes, suggesting that the two genes may be alleles. Homologous recombination in genes which encode a host protective antigen such as 45W would provide a mechanism by which antigenic variants could arise.

Cloning of a new cation ATPase from Plasmodium falciparum: conservation of critical amino acids involved in calcium binding in mammalian organellar Ca(2+)-ATPases

In order to study molecules that may be involved in pH gradient formation in Plasmodium, we have identified a novel cation-translocating ATPase (P-type ATPase) gene from P. falciparum (Pf). We report the full-length nucleotide and deduced amino acid (aa) sequences of this gene that we called PfATPase4. The PfATPase4 protein shares features with the different members of eukaryotic P-type ATPases, such as a similar transmembrane (TM) organization and aa identity in functionally important regions. Interestingly, the PfATPase4 protein possesses conserved aa involved in calcium binding in mammalian organellar Ca(2+)-ATPases.

A YAC contig map of Plasmodium falciparum chromosome 4: characterization of a DNA amplification between two recently separated isolates

We have generated a physical map of Plasmodium falciparum chromosome 4 using yeast artificial chromosomes (YACs). The map is defined by a YAC contig spanning approximately 1.05 Mb, which has been restriction mapped to a resolution of 30 kb and is punctuated by 22 sequence-tagged sites. The physical information obtained has enabled us to compare and contrast the structure of chromosome 4 in detail between FCR3 and B8, two recently separated isolates of P. falciparum, leading to characterization of a novel chromosome polymorphism occurring in a subtelomeric region. Comparison of chromosomes 4 from 10 different isolates has shown that chromosome size polymorphisms are restricted to both subtelomeric regions. These analyses provide a high-resolution physical map that will be important to complement genetic analysis of this human pathogen.

Molecular cloning and sequence of two novel P-type adenosinetriphosphatases from Plasmodium falciparum

We have identified two novel P-type ATPase genes from Plasmodium falciparum and report the full-length nucleotide and derived amino acid sequence of the ATPase2 gene from P. falciparum (PfATPase2). PfATPase2 is phylogenetically remote from the different members of prokaryotic and mammalian P-type ATPases but shares features with a putative membrane-spanning Ca2+ ATPase involved in ribosome function in yeast. PfATPase2 is expressed during the intraerythrocytic life cycle of the parasite and appears to be required in the late stages of its asexual development. We also present the partial sequence of another malarial gene displaying sequence similarity with the family of P-type transporting ATPases (PfATPase4). We have analysed the organisation of the genes encoding the P-type ATPases of P. falciparum and show that they are a highly dispersed gene family.

Synthesis and activity of some antimalarial bisquinolines

A new type of bisquinoline antimalarial, in which the basic side chain of chloroquine is retained, has been evaluated. Nine bisamides were prepared from aliphatic diacids with 6-amino- and 8-amino-((4-(diethylamino)-1-methylbutyl)amino)quinoline, and screened against chloroquine-sensitive and -resistant strains of Plasmodium falciparum in vitro. The resistance indices for all compounds were lower than for chloroquine. The position of attachment and length of the linker chain markedly affected activity. The most active (IC50 = 120 nM against the chloroquine-resistant FAC8 strain) was the -(O)C(CH2)4C(O)- linked 8-amino compound.

Plasmodium falciparum: the pfmdr2 protein is not overexpressed in chloroquine-resistant isolates of the malaria parasite

We have isolated and sequenced a full-length gene (pfmdr2) that has homology to the ABC (ATP-binding cassette)-type transport proteins which includes the mammalian P-glycoproteins, CFTR, and the protein product of the Plasmodium falciparum pfmdr1 gene. The protein encoded by the pfmdr2 gene has 10 hydrophobic domains followed by a region homologous to the nucleotide binding fold of the ABC transport proteins. The pfmdr2 protein also shows homology outside the nucleotide binding fold and some structural similarity to HMT1, a protein involved in heavy metal tolerance in Schizosaccharomyces pombe. Antibodies raised to the pfmdr2 protein react with a 110-kDa band and localization by immunofluorescence suggests that protein is expressed over the whole parasite and may be located on the plasma membrane of the parasite. Comparison of the level of expression of the pfmdr2 protein in chloroquine-resistant and -sensitive parasites show that it is present at approximately equal levels which is in contrast to previous results that determined the level of the pfmdr2 transcript. These results support the evidence that pfmdr2 is not involved in the chloroquine resistance phenotype.

Primary structure and expression of the dihydropteroate synthetase gene of Plasmodium falciparum

The enzyme dihydropteroate synthetase (DHPS) from Plasmodium falciparum is involved in the mechanism of action of the sulfone/sulfonamide group of drugs. We describe the cloning and sequencing of the gene encoding the P. falciparum DHPS enzyme and show that it is a bifunctional enzyme that includes dihydro-6-hydroxymethylpterin pyrophosphokinase (PPPK) at the N terminus of DHPS. The gene encodes a putative protein of 83 kDa that contains two domains that are homologous with the DHPS and PPPK enzymes of other organisms. The PPPK-DHPS gene is encoded on chromosome 8 and has two introns. An antibody raised to the PPPK region of the protein was found to recognize a 68-kDa protein that is expressed throughout the asexual life cycle of the parasite. We have determined the sequence of the DHPS portion of the gene from sulfadoxine-sensitive and -resistant P. falciparum clones and identified sequence differences that may have a role in sulfone/sulfonamide resistance.

Cloning and characterization of the vacuolar ATPase B subunit from Plasmodium falciparum

The transvacuolar pH gradient determines, to a significant extent, the distribution of the antimalarial drug chloroquine in Plasmodium falciparum. A proton pump, similar to the vacuolar ATPase found in many cell types, appears to regulate a pH gradient across the membranes of acidic compartments of the parasite. In order to understand and define the components involved in the maintenance of the vacuolar pH gradient, we have cloned and characterized a gene, designated VAP B, encoding a P. falciparum homologue of the B subunit of the vacuolar ATPase. The VAP B gene encodes a protein of 494 amino acids which has between 69% and 74% amino acid identity with the sequences of vacuolar ATPase B subunits of other organisms. The VAP B gene exists as a single copy gene on chromosome 4 that gives rise to a RNA transcript of 2.4 kb. Antibodies raised to the VAP B protein react specifically with a protein of 56-kDa, consistent with the size predicted from the gene sequence and with the homologous protein from other organisms. The 56-kDa protein is expressed throughout the asexual life cycle and subcellular localization by indirect immunofluorescence shows that the protein has a heterogeneous distribution over most of the parasite. This suggests that the function of the vacuolar proton ATPase is not confined to the regulation of the pH of the digestive vacuole.

Expression of the plasmodial pfmdr1 gene in mammalian cells is associated with increased susceptibility to chloroquine

Chloroquine (CQ)-resistant (CQR) Plasmodium falciparum malaria parasites show a strong decrease in CQ accumulation in comparison with chloroquine-sensitive parasites. Controversy exists over the role of the plasmodial pfmdr1 gene in the CQR phenotype. pfmdr1 is a member of the superfamily of ATP-binding cassette transporters. Other members of this family are the mammalian multidrug resistance genes and the CFTR gene. We have expressed the pfmdr1-encoded protein, Pgh1, in CHO cells and Xenopus oocytes. CHO cells expressing the Pgh1 protein demonstrated an increased, verapamil-insensitive susceptibility to CQ. Conversely, no increase in drug susceptibility to primaquine, quinine, adriamycin, or colchicine was observed in Pgh1-expressing cells. CQ uptake experiments revealed an increased, ATP-dependent accumulation of CQ in Pgh1-expressing cells over the level in nonexpressing control cells. The increased CQ accumulation in Pgh1-expressing cells coincided with an enhanced in vivo inhibition of lysosomal alpha-galactosidase by CQ. CHO cells expressing Pgh1 carrying two of the CQR-associated Pgh1 amino acid changes (S1034C and N1042D) did not display an increased CQ sensitivity. Immunofluorescence experiments revealed an intracellular localization of both mutant and wild-type forms of Pgh1. We conclude from our results that wild-type Pgh1 protein can mediate an increased intracellular accumulation of CQ and that this function is impaired in CQR-associated mutant forms of the protein. We speculate that the Pgh1 protein plays an important role in CQ import in CQ-sensitive malaria parasites.

Photoaffinity labeling of chloroquine-binding proteins in Plasmodium falciparum

A photoreactive analog of chloroquine, N-(4-(4-diethylamino-1-methylbutylamino)quinolin-6-yl)-4- azi do-2- hydroxybenzamide (referred to as ASA-Q), has been synthesized and shown to mimic the action of chloroquine in possessing substantial antimalarial activity against a chloroquine-sensitive strain of Plasmodium falciparum. As for chloroquine, ASA-Q is less effective at killing drug-resistant strains of malaria, and the resistance can be modulated using the reagent verapamil. ASA-Q has been radiolabeled with Na125I and used as a photoaffinity probe for labeling chloroquine-binding proteins in malaria-infected erythrocytes. Two proteins have been identified with apparent molecular masses of 42 and 33 kDa in both chloroquine-sensitive and chloroquine-resistant strains of malaria. Photoaffinity labeling of the two proteins by iodo-ASA-Q was competitively inhibited by an excess of unlabeled chloroquine. The structurally related antimalarials amodiaquine and quinine also inhibited labeling of the two proteins, while verapamil and doxycycline had no effect. We suggest that the two labeled proteins are the macromolecular targets of chloroquine action in malaria parasites.

The mode of action and the mechanism of resistance to antimalarial drugs

The mechanism of action of the antifolate and quinoline antimalarials has been investigated over the last few decades, and recent advances should aid the development of new drugs to combat the increasingly refractile parasite. The molecular description of resistance to the antifolates has been well characterised and is due to structural changes in the target enzymes, but the factors involved in the parasite's ability to circumvent the action of the quinoline antimalarials have yet to be fully elucidated. This review discusses the mode of action of these drugs and the means used by the parasite to defeat our therapeutic ingenuity.

Selection for mefloquine resistance in Plasmodium falciparum is linked to amplification of the pfmdr1 gene and cross-resistance to halofantrine and quinine

Two chloroquine-resistant cloned isolates of Plasmodium falciparum were subjected to mefloquine selection to test if this resulted in alterations in chloroquine sensitivity and amplification of the pfmdr1 gene. The mefloquine-resistant lines derived by this selection were shown to have amplified and overexpressed the pfmdr1 gene and its protein product (Pgh1). Macrorestriction maps of chromosome 5, where pfmdr1 is encoded, showed that this chromosome has increased in size in response to mefloquine selection, indicating the presence of a gene(s) in this area of the genome that confers a selective advantage in the presence of mefloquine. Concomitant with the increase in mefloquine resistance was a corresponding increase in the level of resistance to halofantrine and quinine, suggesting a true multidrug-resistance phenotype. The mefloquine-selected parasite lines also showed an inverse relationship between the level of chloroquine resistance and increased pfmdr1 gene copy number. These results have important implications for the derivation of amplified copies of the pfmdr1 gene in field isolates, as they suggest that quinine pressure may be involved.

Phosphorylation of a P-glycoprotein homologue in Plasmodium falciparum

A P-glycoprotein homologue has been previously identified in Plasmodium falciparum and was termed PGH 1. This paper describes studies analyzing the phosphorylation of the PGH 1 molecule. It was found, by metabolic labeling with [32P]orthophosphate, that PGH 1 was phosphorylated throughout the entire asexual erythrocytic life cycle of the parasite, with the maximum level of 32P incorporation during the trophozoite and schizont stages. Incubation of trophozoites with modulators of mammalian protein kinases suggests that a Ca(2+)-dependent protein kinase is involved in phosphorylation of PGH 1. PGH 1 could also be phosphorylated in the presence of gamma-32P ATP on purified digestive vacuoles where this protein has previously been localized. Two-dimensional phospho-amino acid analysis revealed that PGH 1 was phosphorylated on serine and threonine residues and the pattern of amino acid phosphorylation was similar for PGH 1 phosphorylated in infected red blood cells and on purified digestive vacuoles. PGH 1 phosphorylation in the presence of some antimalarial drugs was analyzed and it was found that neither chloroquine nor compounds that modulate chloroquine resistance had any effect on PGH 1 phosphorylation.

Cloning and characterization of a vacuolar ATPase A subunit homologue from Plasmodium falciparum

The distribution of the antimalarial drug chloroquine is determined to a significant extent by a transvacuolar pH gradient in Plasmodium falciparum. A proton pump similar to the vacuolar ATPase found in many cell types has been suggested to maintain a pH gradient across the membranes of acidic compartments in the parasite. In order to understand and define the components involved in the mechanism of acidification of parasite vesicles, we have cloned and characterized a gene, designated VAP-A, encoding a P. falciparum homologue of the catalytic A subunit of the vacuolar ATPase. The VAP-A gene encodes a polypeptide of 611 amino acids which shows between 56 to 61% amino acid identity over its entire length with the sequences of vacuolar ATPase A subunits from several species. The VAP-A gene exists as a single copy gene on P. falciparum chromosome 13 and gives rise to a transcript of 3.7 kb. Antibodies raised against a VAP-A gene segment expressed in Escherichia coli react specifically with a 67-kDa polypeptide, consistent with the size predicted from the sequence and with the size of the corresponding polypeptide in other organisms. The 67-kDa protein is present throughout the asexual erythrocytic cycle and is expressed at similar levels in 5 P. falciparum isolates of differing chloroquine sensitivity. Sequence analysis of the coding region of the VAP-A gene from 2 chloroquine-sensitive and 3 chloroquine-resistant isolates has shown no changes that are linked to chloroquine resistance. Therefore, a proposed chloroquine resistance-linked vacuolar acidification defect does not involve mutations in the VAP-A gene in the isolates we have studied.

Nucleotide binding properties of a P-glycoprotein homologue from Plasmodium falciparum

The Plasmodium falciparum P-glycoprotein homologue 1 (PGH1) is structurally similar to several members of the ATP-binding cassette (ABC) superfamily of membrane transporters. We have examined whether the nucleotide binding domains predicted from the deduced amino sequence are functional by photoaffinity labeling of purified parasite digestive vacuoles with the analogue 8-azido-alpha-[32P]ATP (8-N3-ATP). This reagent labels a 160-kDa protein in vacuoles from both a chloroquine sensitive and a chloroquine-resistant parasite isolate. The 160-kDa protein could be immunoprecipitated with affinity-purified antibodies against the P. falciparum P-glycoprotein homologue (PGH1). Inhibition of photoaffinity labeling of PGH1 could be achieved with ATP, ADP, GTP and GDP but not with AMP or GMP. In order to map the 8-N3-ATP binding sites on PGH1, photoaffinity-labeled PGH1 was digested with trypsin and immunoprecipitated with site-specific antibodies. Taken together, these results indicate that 8-N3-ATP specifically labels PGH1 and that one binding site resides within the amino terminal half of the molecule. This supports the contention that PGH1 is involved in a nucleotide-regulated transport function across the membrane of the digestive vacuole.

Drug resistance and the P-glycoprotein homologues of Plasmodium falciparum

The chloroquine resistance phenotype of Plasmodium falciparum shares many similarities to multi-drug resistance in tumour cells and this has led to the identification of two mdr-like genes (pfmdr1, pfmdr2) from this human pathogen. The pfmdr1 gene has been linked to the chloroquine resistance phenotype, although a genetic cross appears to contradict these results. Analysis of drug resistant mutants selected in vitro has shown that the level of expression of the pfmdr1 gene can affect resistance to chloroquine, mefloquine, halofantrine and quinine. Mefloquine isolates from the field appear to always contain amplified levels of the pfmdr1 gene and also overexpress the transcript. They are also resistant to halofantrine suggesting a true multi-drug resistant phenotype.

Cloning and analysis of the RESA-2 gene: a DNA homologue of the ring-infected erythrocyte surface antigen gene of Plasmodium falciparum

We have cloned and sequenced a homologue of the ring-infected erythrocyte surface antigen (RESA) gene from Plasmodium falciparum designated RESA-2. Two reading frames with high homology to exon 1 and exon 2 of RESA at both the nucleotide and amino acid levels were identified in the RESA-2 sequence. However, RESA-2 does not contain either of the blocks of tandem repeats present in RESA. The lack of an RNA transcript in either asexual or sexual stage parasites and the presence of an in-frame stop codon in the second reading frame suggests RESA-2 could be a pseudogene. Its lack of expression in asexual stages demonstrates that it does not complement the RESA deletion in isolate FCR3.