Plasmodium research in the postgenomic era

Helicases involved in splicing from malaria parasite Plasmodium falciparum

An interesting element of eukaryotic genomes is the large quantity of non-coding intervening sequences commonly known as introns, which regularly interrupt functional genes and therefore must be removed prior to the use of genetic information by the cell. After splicing, the mature RNA is exported from the nucleus to the cytoplasm. Any error in the process of recognition and removal of introns, or splicing, would lead to change in genetic message and thus has potentially catastrophic consequences. Thus splicing is a highly complex essential step in eukaryotic gene expression. It takes place in spliceosome, which is a dynamic RNA-protein complex made of snRNPs and non-snRNP proteins. The splicing process consists of following sequential steps: spliceosome formation, the first transesterification and second transesterification reactions, release of the mature mRNA and recycling of the snRNPs. The spliceosomal components produce a complex network of RNA-RNA, RNA-protein and protein-protein interactions and spliceosome experience remodeling during each splicing cycle. Helicases are essentially required at almost each step for resolution of RNA-RNA and/or RNA-protein interactions. RNA helicases share a highly conserved helicase domain which includes the motif DExD/H in the single letter amino acid code. This article will focus on members of the DExD/H-box proteins involved specially in splicing in the malaria parasite Plasmodium falciparum.

Potential and limits of in silico target discovery - Case study of the search for new antimalarial chemotherapeutic targets

In medical sciences, a target is a broad concept to qualify a biological entity and/or a biological phenomenon, on which one aims to act as part of a therapy. It follows that a target can be defined as a phenotype, a biological process, a subcellular organelle, a protein or a protein domain. It also follows that a target cannot be defined independently of the type of intervention one considers implementing. In this brief review, we describe how in silico organization of genomic and post-genomic information of all partners involved in malaria (human patient, Plasmodium parasite and Anopheles vector), complying with knowledge of the disease in etiologic terms, appears as an efficient source of information not only to help selecting but also discarding target candidates. Some limitations in our capacity to explore the stored biological information, due to the current quality of genomic annotation, level of database integration, or to the performances of existing analytic and mining tools, are discussed. In silico strategies to assess the feasibility of bringing a target to a therapeutic development pipeline, in terms of target "druggability", are introduced.

Ethnopharmacology and malaria: New hypothetical leads or old efficient antimalarials?

New treatments are urgently needed to curb and eradicate malaria in developing countries. As most people living in malarial endemic areas use traditional medicine to fight this disease, why have new treatments not emerged recently from ethnopharmacology-oriented research? The rationale and limitations of the ethnopharmacological approach are discussed in this paper, focusing on ethnopharmacology methodologies and techniques used for assessing botanical samples for their antimalarial properties. Discrepancies often observed between strong ethnopharmacological reputation and laboratory results are discussed, as well as new research perspectives.

Unraveling the components of protein translocation pathway in human malaria parasite Plasmodium falciparum

The targeting and translocation of proteins is an essentially required and conserved process in all the living organisms. This complex process involves multiple steps and requires a variety of factors before the protein reaches its final destination. The major components of translocation machinery are signal recognition particle (SRP) and secretory (Sec) complex. These are composed of highly conserved components. SRP contains SRP RNA and other polypeptides such as SRP9, SRP14, SRP19 and SRP54. Sec complex is composed of Sec61alphabetagamma, Sec62 and Sec63. In this review using bioinformatics approach we have shown that the P. falciparum genome contains the homologues for all of these and other factors such as SRP receptor, and TRAM (translocation associated membrane protein), which are required for post- and co-translational protein translocation. We have also shown the various steps of translocation in a hypothetical model.

Spectrin-based skeleton in red blood cells and malaria

PURPOSE OF REVIEW

Malaria represents one of the most important selective factors affecting human populations. Several inherited diseases of red blood cells lead to resistance at the erythrocytic stage. Among patients who experience hereditary elliptocytosis related to mutations of erythrocyte membrane proteins, molecular studies have shown the prevalence of particular spectrin mutations in patients from black ethnic extraction, leading one to question the selection of new malaria-resistant genes.

RECENT FINDINGS

Prospective epidemiological and molecular studies in West Africa have confirmed the prevalence (between 0.6 and 1.6%) of particular spectrin mutations related to hereditary elliptocytosis. These studies have also revealed the frequency of alpha-spectrin chain polymorphisms, associated in cis with elliptocytogenic spectrin mutations and defining particular spectrin allele haplotypes. Culture studies of Plasmodium falciparum in elliptocytes bearing such elliptocytogenic alleles of spectrin showed that these alleles are supplementary genetic factors of malaria resistance in vitro.

SUMMARY

Certain instances of spectrin mutations or polymorphisms have not yet been shown to constitute new factors of innate resistance to malaria in vivo. Epidemiological surveys of hereditary elliptocytosis and parasite culture studies, however, have argued that the relationships between parasite and spectrin-based skeleton should be examined more closely and the molecular interactions between parasite ligands and particular spectrin chain domains should be characterized.

Lessons in the genomic diversity of malaria

Genome-wide characterization of Plasmodium falciparum genetic diversity represents an important step in malaria genetics. The organizational and collaborative efforts to reach this goal and the results on linkage disequilibrium and genetic diversity among worldwide isolates provide general lessons.

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is important to significantly increase the knowledge of the biology of its causative agents, and is motivated, on a longer term, by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should, therefore, be as reliable and versatile as possible. In this context, five aspects of the organization and mining of malaria genomic and post-genomic data were examined: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes, particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Recent progress towards a grid-enabled chemogenomic knowledge space is discussed.

PlasmoDB v5: new looks, new genomes

Version 5.1 of PlasmoDB, a resource for malaria parasite genomic and functional genomics datasets, was released in August 2006. This new release includes additional Plasmodium genomes and a newly designed website. The new site reflects the status of PlasmoDB as a member of a linked family of Apicomplexan databases.

Plasmodium falciparum DNA helicase 60. dsRNA- and antibody-mediated inhibition of malaria parasite growth and downregulation of its enzyme activities by DNA-interacting compounds

Helicases are ubiquitous enzymes that play important roles in all types of DNA transaction in the cells. Recently we have reported the characterization of the first DEAD-box helicase [Plasmodium falciparum DNA helicase 60 (PfDH60)] from Plasmodium falciparum and have shown that it is a unique, dual bipolar helicase expressed in a stage-specific manner. In this study, we show the further characterization of PfDH60. For analyzing the significance of this enzyme in parasite growth, we studied the effect of dsRNA and specific antibodies on growth of the parasite. The studies indicate that the parasite cultures treated with PfDH60 dsRNA exhibited approximately 50% growth inhibition when compared with either untreated cultures or cultures treated with unrelated dsRNA. It was interesting to note that purified immunoglobulins against PfDH60 induced approximately 62% inhibition of in vitro growth of P. falciparum and that this inhibitory effect was associated with morphologic damage to the parasite. DNA-interacting compounds inhibit DNA helicase and ssDNA-dependent ATPase activities of PfDH60. Of various compounds tested, only actinomycin, daunorubicin, ethidium bromide, netropsin and nogalamycin were able to inhibit the enzyme activities of PfDH60, with apparent IC50 values for helicase inhibition of 0.8, 0.3, 2.0, 1.2 and 1.5 microm, respectively. It may be proposed that these compounds form a complex with DNA and specifically inhibit helicases due to obstruction in the translocation of the enzyme. These compounds also inhibited parasite growth in culture. This is the first study to show inhibition of growth of the parasite by the dsRNA of a helicase, and most probably this is due to interference with cognate mRNA expression.