Differential gene expression in the ookinete stage of the malaria parasite Plasmodium berghei

Systems Biology-Based Investigation of Host-Plasmodium Interactions

Malaria is a serious, complex disease caused by parasites of the genus Plasmodium. Plasmodium parasites affect multiple tissues as they evade immune responses, replicate, sexually reproduce, and transmit between vertebrate and invertebrate hosts. The explosion of omics technologies has enabled large-scale collection of Plasmodium infection data, revealing systems-scale patterns, mechanisms of pathogenesis, and the ways that host and pathogen affect each other. Here, we provide an overview of recent efforts using systems biology approaches to study host-Plasmodium interactions and the biological themes that have emerged from these efforts. We discuss some of the challenges in using systems biology for this goal, key research efforts needed to address those issues, and promising future malaria applications of systems biology.

Characterization of Plasmodium developmental transcriptomes in Anopheles gambiae midgut reveals novel regulators of malaria transmission

The passage through the mosquito is a major bottleneck for malaria parasite populations and a target of interventions aiming to block disease transmission. Here, we used DNA microarrays to profile the developmental transcriptomes of the rodent malaria parasite Plasmodium berghei in vivo, in the midgut of Anopheles gambiae mosquitoes, from parasite stages in the midgut blood bolus to sporulating oocysts on the basal gut wall. Data analysis identified several distinct transcriptional programmes encompassing genes putatively involved in developmental processes or in interactions with the mosquito. At least two of these programmes are associated with the ookinete development that is linked to mosquito midgut invasion and establishment of infection. Targeted disruption by homologous recombination of two of these genes resulted in mutant parasites exhibiting notable infection phenotypes. GAMER encodes a short polypeptide with granular localization in the gametocyte cytoplasm and shows a highly penetrant loss-of-function phenotype manifested as greatly reduced ookinete numbers, linked to impaired male gamete release. HADO encodes a putative magnesium phosphatase with distinctive cortical localization along the concave ookinete periphery. Disruption of HADO compromises ookinete development leading to significant reduction of oocyst numbers. Our data provide important insights into the molecular framework underpinning Plasmodium development in the mosquito and identifies two genes with important functions at initial stages of parasite development in the mosquito midgut.

The role of MACPF proteins in the biology of malaria and other apicomplexan parasites

Apicomplexans are eukaryotic parasites of major medical and veterinary importance. They have complex life cycles through frequently more than one host, interact with many cell types in their hosts, and can breach host cell membranes during parasite traversal of, or egress from, host cells. Some of these parasites make a strikingly heavy use of the pore-forming MACPF domain, and encode up to 10 different MACPF domain-containing proteins. In this chapter, we focus on the two most studied and medically important apicomplexans, Plasmodium and Toxoplasma, and describe the known functions of their MACPF polypeptide arsenal. Apicomplexan MACPF proteins appear to be involved in a variety of membrane-damaging events, making them an attractive model to dissect the structure-function relationships of the MACPF domain.

Identification of differentially expressed genes in American cockroach ovaries and testes by suppression subtractive hybridization and the prediction of its miRNAs

Studies on the cockroach have contributed to our understanding of several important developmental processes, especially those that can be easily studied in the embryo. However, our knowledge on late events such as gonad differentiation in the cockroach is still limited. The major aim of the present study was to identify sex-specific genes between adult female and male Periplaneta americana. Two cDNA libraries were constructed using the suppression subtractive hybridization method; a total of 433 and 599 unique sequences were obtained from the forward library and the reverse library, respectively, by cluster assembly, and sequence alignment of 1,032 expressed sequence tags. The analysis of the differentially expressed gene functions allowed these genes to be categorized into three groups: biological process, molecular function, and cellular component. The differentially expressed genes were suggested to be related to the development of the gonads of P. americana. Twelve differentially expressed genes were randomly selected and verified using relative quantitative real-time polymerase chain reaction (qRT-PCR). Meanwhile, by adopting a range of filtering criteria, we predicted two potential microRNA sequences for P. americana, pam-miR100-3p and pam-miR7. To confirm the expression of potential microRNAs (miRNAs) in American cockroach, a qRT-PCR approach was also employed. The data presented here offer the insights into the molecular foundation of sex differences in American cockroach, and the first report for the miRNAs in this species. In addition, the results can be used as a reference for unraveling candidate genes associated with the sex and reproduction of cockroaches.

A perforin-like protein mediates disruption of the erythrocyte membrane during egress of Plasmodium berghei male gametocytes

Successful gametogenesis of the malaria parasite depends on egress of the gametocytes from the erythrocytes within which they developed. Egress entails rupture of both the parasitophorous vacuole membrane and the erythrocyte plasma membrane, and precedes the formation of the motile flagellated male gametes in a process called exflagellation. We show here that egress of the male gametocyte depends on the function of a perforin-like protein, PPLP2. A mutant of Plasmodium berghei lacking PPLP2 displayed abnormal exflagellation; instead of each male gametocyte forming eight flagellated gametes, it produced gametocytes with only one, shared thicker flagellum. Using immunofluorescence and transmission electron microscopy analysis, and phenotype rescue with saponin or a pore-forming toxin, we conclude that rupture of the erythrocyte membrane is blocked in the mutant. The parasitophorous vacuole membrane, on the other hand, is ruptured normally. Some mutant parasites are still able to develop in the mosquito, possibly because the vigorous motility of the flagellated gametes eventually leads to escape from the persisting erythrocyte membrane. This is the first example of a perforin-like protein in Plasmodium parasites having a role in egress from the host cell and the first parasite protein shown to be specifically required for erythrocyte membrane disruption during egress.

Effects of MACPF/CDC proteins on lipid membranes

Recent work on the MACPF/CDC superfamily of pore-forming proteins has focused on the structural analysis of monomers and pore-forming oligomeric complexes. We set the family of proteins in context and highlight aspects of their function which the direct and exclusive equation of oligomers with pores fails to explain. Starting with a description of the distribution of MACPF/CDC proteins across the domains of life, we proceed to show how their evolutionary relationships can be understood on the basis of their structural homology and re-evaluate models for pore formation by perforin, in particular. We furthermore highlight data showing the role of incomplete oligomeric rings (arcs) in pore formation and how this can explain small pores generated by oligomers of proteins belonging to the family. We set this in the context of cell biological and biophysical data on the proteins' function and discuss how this helps in the development of an understanding of how they act in processes such as apicomplexan parasites gliding through cells and exiting from cells.

Plasmodium falciparum: epigenetic control of var gene regulation and disease

Plasmodium falciparum, one of the deadliest parasites on earth causes human malaria resulting one million deaths annually. Central to the parasite pathogenicity and morbidity is the switching of parasite virulence (var) gene expression causing host immune evasion. The regulation of Plasmodium var gene expression is poorly understood. The complex life cycle of Plasmodium and mutually exclusive expression pattern of var genes make this disease difficult to control. Recent studies have demonstrated the pivotal role of epigenetic mechanism for control of coordinated expression of var genes, important for various clinical manifestations of malaria. In this review, we discuss about different Plasmodium histones and their various modifications important for gene expression and gene repression.Contribution of epigenetic mechanism to understand the var gene expression is also highlighted. We also describe in details P. falciparum nuclear architecture including heterochromatin, euchromatin and telomeric regions and their importance in subtelomeric and centrally located var gene expression. Finally, we explore the possibility of using Histone Acetyl Transferase (HAT) and Histone Deacetylase (HDAC)inhibitors against multi-drug resistance malaria parasites to provide another line of treatment for malaria.

Apicomplexan perforin-like proteins

Numerous perforin-like proteins are encoded in the genomes of apicomplexan parasites, where they are expressed in various life-cycle stages and play critical roles in pathogenesis and lifecycle progression. These ApiPLPs are characterized by the presence of a MACPF domain, responsible for pore-formation in target membranes in a number of systems, including many bacterial pathogens and effector cells of the immune response. ApiPLP MACPF domains maintain the critical structural elements but are often present in new and intriguing domain arrangements. Recent work in Toxoplasma and Plasmodium has shown that ApiPLPs are important for breaching membranes during parasite egress and cell traversal. Here we present an overview of this important protein family from a structural, functional and phylogenetic perspective across the Apicomplexa.

Epigenetics in Plasmodium: what do we really know?

In the burgeoning field of Plasmodium gene expression, there are--to borrow some famous words from a former U.S. Secretary of Defense--"known knowns, known unknowns, and unknown unknowns." This is in itself an important achievement, since it is only in the past decade that facts have begun to move from the third category into the first. Nevertheless, much remains in the middle ground of known or suspected "unknowns." It is clear that the malaria parasite controls vital virulence processes such as host cell invasion and cytoadherence at least partly via epigenetic mechanisms, so a proper understanding of epigenetic transcriptional control in this organism should have great clinical relevance. Plasmodium, however, is an obligate intracellular parasite: it operates not in a vacuum but rather in the complicated context of its metazoan hosts. Therefore, as valuable data about the parasite's basic epigenetic machinery begin to emerge, it becomes increasingly important to relate in vitro studies to the situation in vivo. This review will focus upon the challenge of understanding Plasmodium epigenetics in an integrated manner, in the human and insect hosts as well as the petri dish.

Mitochondrial gene cytochrome b developmental and environmental expression in Aedes aegypti (Diptera: Culicidae)

Cytochrome b, coded by mitochondrial DNA, is one of the cytochromes involved in electron transport in the respiratory chain of mitochondria. Cytochrome b is a critical intermediate in a mitochondrial death pathway. To reveal whether cytochrome b of the mosquito Aedes aegypti (L.) (Diptera: Culicidae) (AeaCytB) is developmentally regulated, we used real-time quantitative polymerase chain reaction (qPCR) to examine AeaCytB gene expression levels in different developmental stages of Ae. aegypti. The qPCR showed that AeaCytB was expressed in each developmental stage, with peaks at first and second instars and was highly expressed in teneral male and female Ae. aegypti adults. Because mitochondrial genes exist as multiple copies, AeaCytB has much higher expression levels in all developmental stages in Ae. aegypti compared with nuclear genes. We also investigated the effect of abiotic environmental factors (e.g., high temperatures, ultraviolet radiation, and pesticide) on AeaCytB gene expression. Taken together, these results suggest that AeaCytB gene plays an important role in the development of Ae. aegypti and its response to environmental stress.

Cytochrome c gene and protein expression: developmental regulation, environmental response, and pesticide sensitivity in Aedes aegypti

Cytochrome c is a highly conserved protein that is found in many multicellular and unicellular organisms. Cytochrome c is a critical intermediate in apoptosis: a controlled form of cell death that kills cells as part of their natural process of development and in response to environmental condition. To detect whether cytochrome c of the mosquito Aedes aegypti (L.) (AeaCytC) is developmentally regulated, we used quantitative real-time polymerase chain reaction (PCR) to examine AeaCytC gene expression levels in different developmental stages ofAe. aegypti. Quantitative real-time PCR showed that AeaCytC was expressed in each developmental stage, at different points in time, and it was highly expressed in teneral female Ae. aegypti. Ae. aegypti cytochrome c protein (AeaCYTC) was detected only in adult mosquitoes, not in early developmental stages of Ae. aegypti. We also investigated the effect of certain environmental factors (e.g., temperature, UV-light, and permethrin insecticide) on AeaCytC gene and AeaCYTC protein expression in adult mosquitoes, and we found that response varied with age. These results suggest that AeaCytC gene and AeaCYTC protein play functional roles in the development of Ae. aegypti and the differential expression of cytochrome c has potential as a biomarker for environmental and chemical stress.

Evidence-based annotation of the malaria parasite's genome using comparative expression profiling

A fundamental problem in systems biology and whole genome sequence analysis is how to infer functions for the many uncharacterized proteins that are identified, whether they are conserved across organisms of different phyla or are phylum-specific. This problem is especially acute in pathogens, such as malaria parasites, where genetic and biochemical investigations are likely to be more difficult. Here we perform comparative expression analysis on Plasmodium parasite life cycle data derived from P. falciparum blood, sporozoite, zygote and ookinete stages, and P. yoelii mosquito oocyst and salivary gland sporozoites, blood and liver stages and show that type II fatty acid biosynthesis genes are upregulated in liver and insect stages relative to asexual blood stages. We also show that some universally uncharacterized genes with orthologs in Plasmodium species, Saccharomyces cerevisiae and humans show coordinated transcription patterns in large collections of human and yeast expression data and that the function of the uncharacterized genes can sometimes be predicted based on the expression patterns across these diverse organisms. We also use a comprehensive and unbiased literature mining method to predict which uncharacterized parasite-specific genes are likely to have roles in processes such as gliding motility, host-cell interactions, sporozoite stage, or rhoptry function. These analyses, together with protein-protein interaction data, provide probabilistic models that predict the function of 926 uncharacterized malaria genes and also suggest that malaria parasites may provide a simple model system for the study of some human processes. These data also provide a foundation for further studies of transcriptional regulation in malaria parasites.

Serial Analysis of Gene Expression in Plasmodium berghei salivary gland sporozoites

BACKGROUND

The invasion of Anopheles salivary glands by Plasmodium sporozoites is an essential step for transmission of the parasite to the vertebrate host. Salivary gland sporozoites undergo a developmental programme to express genes required for their journey from the site of the mosquito bite to the liver and subsequent invasion of, and development within, hepatocytes. A Serial Analysis of Gene Expression was performed on Anopheles gambiae salivary glands infected or not with Plasmodium berghei and we report here the analysis of the Plasmodium sporozoite transcriptome.

RESULTS

Annotation of 530 tag sequences homologous to Plasmodium berghei genomic sequences identified 123 genes expressed in salivary gland sporozoites and these genes were classified according to their transcript abundance. A subset of these genes was further studied by quantitative PCR to determine their expression profiles. This revealed that sporozoites modulate their RNA amounts not only between the midgut and salivary glands, but also during their storage within the latter. Among the 123 genes, the expression of 66 is described for the first time in sporozoites of rodent Plasmodium species.

CONCLUSION

These novel sporozoite expressed genes, especially those expressed at high levels in salivary gland sporozoites, are likely to play a role in Plasmodium infectivity in the mammalian host.

Identification of differentially expressed genes in female Culex pipiens pallens

Culex pipiens pallens is the mosquito vector of a number of human pathogens such as Wuchereria bancrofti, Brugia malayi, and epidemic encephalitis B virus. Female C. pipiens pallens play an important role in transmitting pathogens by sucking blood, which is essential for reproduction. In the present study, a subtractive cDNA library for female C. pipiens pallens was constructed by the suppression subtractive hybridization (SSH) technique and then 100 clones from the female SSH library were sequenced and analyzed. Female-differentially expressed genes in C. pipiens pallens were screened using semiquantitative RT-PCR. The full-length cDNA of an EST sequence (fs68) that was specifically expressed in female C. pipiens pallens was characterized by 3' and 5' rapid amplification of cDNA ends (RACE). The characteristics of the female-specific gene were further analyzed using bioinformatics and Northern blot. It was shown that the female-specific gene was a previously uncharacterized gene and may encode a salivary peptide. This putative salivary peptide could be a very important molecule in the blood feeding of female C. pipiens pallens.

Plasmodium berghei: plasmodium perforin-like protein 5 is required for mosquito midgut invasion in Anopheles stephensi

During its life cycle the malarial parasite Plasmodium forms three invasive stages which have to invade different and specific cells for replication to ensue. Invasion is vital to parasite survival and consequently proteins responsible for invasion are considered to be candidate vaccine/drug targets. Plasmodium perforin-like proteins (PPLPs) have been implicated in invasion because they contain a predicted pore-forming domain. Ookinetes express three PPLPs, and one of them (PPLP3) has previously been shown to be essential for mosquito midgut invasion. In this study we show through phenotypic analysis of loss-of-function mutants that PPLP5 is equally essential for mosquito infection. Δpplp5 ookinetes cannot invade midgut epithelial cells, but subsequent parasite development is rescued if the midgut is bypassed by injection of ookinetes into the hemocoel. The indistinguishable phenotypes of Δpplp5 and Δpplp3 ookinetes strongly suggest that these two proteins contribute to a common process.