Determining the sequence of parasite DNA

PCR-based technology in veterinary parasitology

DNA technology is having a major impact in many areas of veterinary parasitology. In particular, the polymerase chain reaction (PCR) has found broad applicability because its sensitivity permits enzymatic amplification of gene fragments from minute quantities of nucleic acids derived from limited amounts of parasite material. This paper discusses some recent applications of PCR-based methods to parasites and highlights their usefulness or potential for those of veterinary importance. The focus is on PCR tools for the accurate identification of parasites and their genetic characterisation, the diagnosis of infections, the isolation and characterisation of expressed genes, the detection of anthelmintic resistance, and mutation scanning approaches for the high resolution analysis of PCR products.

Karyotype and synteny among the chromosomes of all four species of human malaria parasite

The karyotype and chromosomes of the human malaria parasite Plasmodium falciparum have been well characterized in recent years. Here we present karyotype maps of the three other human malaria species, P. vivax, P. malariae and P. ovale. Chromosomes of these species were found to be of significantly higher molecular weight than those of P. falciparum. Some 14 P. vivax chromosomes were distinguishable, and 12-14 P. malariae and P. ovale chromosomes. The chromosome location of 15 genes, known to be present within five synteny groups between P. falciparum and the rodent malarias, were analyzed, and four of these synteny groups were found to be conserved between all of the human malaria species. In addition, a more detailed genome map of P. vivax was made using ten housekeeping and antigen genes. These data represent the first karyotype maps of all species of malaria which infect man.

Genomics and the biology of parasites

Despite the advances of modern medicine, the threat of chronic illness, disfigurement, or death that can result from parasitic infection still affects the majority of the world population, retarding economic development. For most parasitic diseases, current therapeutics often leave much to be desired in terms of administration regime, toxicity, or effectiveness and potential vaccines are a long way from market. Our best prospects for identifying new targets for drug, vaccine, and diagnostics development and for dissecting the biological basis of drug resistance, antigenic diversity, infectivity and pathology lie in parasite genome analysis, and international mapping and gene discovery initiatives are under way for a variety of protozoan and helminth parasites. These are far from ideal experimental organisms, and the influence of biological and genomic characteristics on experimental approaches is discussed, progress is reviewed and future prospects are examined.

Gene synteny in species of Plasmodium

We have attempted to establish the degree of linkage conservation between different species of the malaria parasite Plasmodium. Initially, the chromosome locations of 42 homologous genes were established in parasites from a rodent malaria species and the human malaria parasite P. falciparum. Of these genes, 26 appeared to be conserved within ten synteny groups between the two genomes. Several synteny groups were analysed further by long-range restriction mapping of digested chromosomes. Finally, a fine restriction map of one of the linkage groups was made from the rodent malaria parasites P. berghei and from P. falciparum and from the simian malaria parasite P. knowlesi. The fine-scale organisation of this linkage group appears to have remained intact among the three species, despite the evolutionary distance between them. This provides the first example of linkage conservation between the rodent, simian and human malaria species, which represent three different branches of the inferred phylogenetic tree of the genus Plasmodium.

Mutation scanning methods for the analysis of parasite genes

Molecular variation is widespread in parasite populations, and its analysis has important implications for studying aspects relating to the function and organisation of genes, and the taxonomy, phylogeny and population genetics of parasites. This article reviews some PCR-based mutation scanning techniques that have advantages over currently used DNA methods for the analysis of genetic variation in parasites. The review is technical and describes briefly the principles of relevant techniques, examines some of their advantages and disadvantages and gives several examples for possible applications.

Construction and initial analysis of a representative lambda ZAPII expression library of the intracellular rickettsia Cowdria ruminantium: cloning of map1 and three other Cowdria genes

The causative agent of heartwater, the rickettsia Cowdria ruminantium, is very poorly understood at the molecular level owing to a profound lack of suitable tools. We have developed an immunoaffinity chromatographic method to purify C. ruminantium from host cell components and the purified rickettsial cells have been used to prepare substantially pure Cowdria DNA. This DNA has been used to construct what we believe to be the first fully representative C. ruminantium expression library. A clone containing the complete Cowdria map1 gene has been isolated and sequenced. This gene has been expressed in E. coli cells from the native Cowdria promoter, suggesting that the mechanisms for gene transcription and translation are similar between these two organisms. Parts of three other Cowdria genes have also been isolated and sequenced.

Application of molecular biology in veterinary parasitology

The number of applications of molecular biology in veterinary parasitology is increasing rapidly. The techniques used with eukaryotic cells are generally applicable to the study of parasites and their hosts. The polymerase chain reaction is particularly important for identification and diagnosis of parasites, as well as for many other applications. With species and type specific probes or primers, sensitivities and specificities unheard of with conventional techniques can be achieved. The accumulation of more information on the DNA sequences of parasites will reveal many more unique sequences which can be used for identification, diagnosis, molecular epidemiology, vaccine development and for studying the evolutionary biology and the physiology of parasites and the host-parasite relationship. Similarly, the completion of genome projects on host organisms will greatly assist efforts to select for hosts that are genetically resistant to parasite infection. The study of the molecular biology of antiparasitic drug receptors, potential targets for chemotherapy, and the molecular genetics of drug resistance will allow molecular screens to be used with combinatorial chemistry in the search for new antiparasitic drugs, improvements to existing chemotherapeutic families and better diagnosis and monitoring of drug resistance. While there is a proliferation of molecular biology techniques, the availability of simple kits and of automated techniques and services for sequencing, library construction and oligonucleotide synthesis and other procedures is making it easier for non-specialists to apply many of the common techniques of molecular biology. Molecular biology and the benefits from its application are relevant for veterinary parasitologists in developing countries as well as developed countries and we should introduce aspects of molecular biology to the teaching and training of veterinary parasitologists.

Hemoglobin catabolism and iron utilization by malaria parasites

Erythrocytic malaria parasites transport large quantities of erythrocyte cytoplasm to an acidic food vacuole, where hemoglobin is degraded. Globin is hydrolysed to free amino acids, which are subsequently incorporated into parasite proteins. Potentially toxic heme moieties are polymerized to hemozoin and also probably provide necessary parasite iron. Our understanding of the precise mechanisms of hemoglobin processing is incomplete. However, it is clear that hemoglobin catabolism and related events in the malarial food vacuole are the likely targets of both important antimalarial drugs and of promising new compounds. Thus, a more precise characterization of the metabolism of hemoglobin and iron by malaria parasites should expedite the development of new modes of antimalarial chemotherapy.

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.

Cloning and characterization of a Plasmodium falciparum cyclophilin gene that is stage-specifically expressed

An immunosuppressive agent, cyclosporin A (CsA), has antimalarial activity in several Plasmodium species. Cyclophilins of several species including Plasmodium falciparum exhibit peptidyl-prolyl cis-trans isomerase activity which is inhibited by CsA. A gene encoding P. falciparum cyclophilin (PFCyP) was cloned and characterized. This gene has the entire coding sequence for the mature protein plus a 39-amino-acid-long N-terminal extension. Most of the amino acids predicted to be involved in the peptidyl-prolyl cis-trans isomerase activity and CsA binding are present in the cloned gene. The PFCyP also has the single highly conserved tryptophan residue that is a major determinant in the inhibition of PPIase activity by CsA. The PFCyP coding sequence with or without the N-terminal amino-acid extension was used to construct recombinant expression vectors which were transformed into E. coli. Both vectors produced enzymatically active mature PFCyP proteins that were sensitive to CsA. Northern blot analysis of RNA isolated from the synchronized parasite cultures verified the expression of PFCyP in all erythrocytic stages of the parasite, but at variable levels. The highest level of expression was observed in ring-stage parasites, a stage shown to be more susceptible to CsA. Inhibition of P. falciparum growth in vitro by CsA was re-evaluated for chloroquine-sensitive and chloroquine-resistant strains of the parasite. Essentially, there was no difference between the two strains for the concentration of CsA required to yield 50% inhibition in 48 h of exposure (0.25-0.4 microM).