Characterisation of a sexual stage-specific gene encoding ORC1 homologue in the human malaria parasite Plasmodium falciparum

The Cryptosporidium parvum transcriptome during in vitro development

Cryptosporidiosis is caused by an obligate intracellular parasite that has eluded global transcriptional or proteomic analysis of the intracellular developmental stages. The transcript abundance for 3,302 genes (87%) of the Cryptosporidium parvum protein coding genome was elucidated over a 72 hr infection within HCT8 cells using Real Time-PCR. The parasite had detectable transcription of all genes in vitro within at least one time point tested, and adjacent genes were not co-regulated. Five genes were not detected within the first 24 hr of infection, one containing two AP2 domains. The fewest genes detected were at 2 hr post infection, while 30% (985) of the genes have their highest expression at 48 and/or 72 hr. Nine expression clusters were formed over the entire 72 hr time course and indicate patterns of transcriptional increases at each of the 7 time points collected except 36 hr, including genes paralleling parasite 18S rRNA transcript levels. Clustering within only the first 24 hr of infection indicates spikes in expression at each of the 4 time points, a group paralleling 18S rRNA transcript levels, and a cluster with peaks at both 6 and 24 hr. All genes were classified into 18 functional categories, which were unequally distributed across clusters. Expression of metabolic, ribosomal and proteasome proteins did not parallel 18S rRNA levels indicating distinct biochemical profiles during developmental stage progression. Proteins involved in translation are over-represented at 6 hr, while structural proteins are over-represented at 12 hr. Standardization methods identified 107 genes with <80% at a single of its total expression at a single time point over 72 hr. This comprehensive transcriptome of the intracellular stages of C. parvum provides insight for understanding its complex development following parasitization of intestinal epithelial cells.

Functional dissection of the catalytic carboxyl-terminal domain of origin recognition complex subunit 1 (PfORC1) of the human malaria parasite Plasmodium falciparum

Origin recognition complex subunit 1 (ORC1) is essential for DNA replication in eukaryotes. The deadly human malaria parasite Plasmodium falciparum contains an ORC1/CDC6 homolog with several interesting domains at the catalytic carboxyl-terminal region that include a putative nucleoside triphosphate-binding and hydrolysis domain, a putative PCNA-interacting-protein (PIP) motif, and an extreme C-terminal region that shows poor homology with other ORC1 homologs. Due to the unavailability of a dependable inducible gene expression system, it is difficult to study the structure and function of essential genes in Plasmodium. Using a genetic yeast complementation system and biochemical experiments, here we show that the putative PIP domain in ORC1 that facilitates in vitro physical interaction with PCNA is functional in both yeast (Saccharomyces cerevisiae) and Plasmodium in vivo, confirming its essential biological role in eukaryotes. Furthermore, despite having less sequence homology, the extreme C-terminal region can be swapped between S. cerevisiae and P. falciparum and it binds to DNA directly, suggesting a conserved role of this region in DNA replication. These results not only provide us a useful system to study the function of the essential genes in Plasmodium, they help us to identify the previously undiscovered unique features of replication proteins in general.

Differential association of Orc1 and Sir2 proteins to telomeric domains in Plasmodium falciparum

Telomeres have the capacity to recruit proteins that facilitate the spreading of heterochromatin into subtelomeric DNA regions. In the human protozoan pathogen Plasmodium falciparum, the telomere-associated protein Sir2 has been shown to control the silencing of members of virulence genes at some, but not all, chromosome-end loci, indicating that additional proteins are involved in telomere position effect. Here, we identified, in P. falciparum, a novel telomere-associated protein that displays homology with the origin-of-recognition-complex 1 protein Orc1. Antibodies raised against this P. falciparum protein localized to telomeric clusters in the nuclear periphery and the nucleolus. It was found that, prior to DNA replication, P. falciparum Orc1 and Sir2 undergo drastic subcellular reorganization, such as dissociation from the telomere cluster and spreading into the nucleus and parasite cytoplasm. Relocation of Orc1 and Sir2 was also linked to the partial dissociation of telomere clusters. Super gel-shift and chromatin-immunoprecipitation experiments showed the physical association of Orc1 with telomere repeats but revealed a differential association with adjacent non-coding repeat DNA elements. Our data suggest that Plasmodium telomeres might fold back and that Orc1 cooperates with Sir2 in telomeric silencing.

Expression and subcellular localization of ORC1 in Leishmania major

The mechanism of DNA replication is highly conserved in eukaryotes, with the process being preceded by the ordered assembly of pre-replication complexes (pre-RCs). Pre-RC formation is triggered by the association of the origin replication complex (ORC) with chromatin. Leishmania major appears to have only one ORC ortholog, ORC1. ORC1 in other eukaryotes is the largest of the ORC subunits and is believed to play a significant role in modulating replication initiation. Here we report for the first time, the cloning of ORC1 from L. major, and the analysis of its expression in L. major promastigotes. In human cells ORC1 levels have been found to be upregulated in G1 and subsequently degraded, thus playing a role in controlling replication initiation. We examine the subcellular localization of L. major ORC1 in relation to the different stages of the cell cycle. Our results show that, unlike what is widely believed to be the case with ORC1 in human cells, ORC1 in L. major is nuclear at all stages of the cell cycle.

Pre-replication complex organization in the atypical DNA replication cycle of Plasmodium falciparum: Characterization of the mini-chromosome maintenance (MCM) complex formation

The overall organization of cell division in Plasmodium is unique compared to that observed in model organisms because DNA replicates more than once per cell cycle at several points of its life cycle. The sequencing of the Plasmodium genome has also revealed the apparent absence of many key components (e.g. Cdt1, DDK and Cdc45) of the eukaryotic cell cycle machinery that are responsible for the formation of the pre-replication complex (pre-RC). We have characterized the Plasmodium falciparum minichromosome maintenance complex (MCM) that plays a key role in the transition of pre-RC to the RC. Similar to other eukaryotes, the Plasmodium genome encodes six MCM subunits. Here, we show that expression levels of at least three of the PfMCM subunits, the homologues of MCM2, MCM6 and MCM7, change during the intraerythrocytic development cycle, peaking in schizont and decreasing in the ring and trophozoite stages. PfMCM2, 6 and 7 subunits interact with each other to form a developmentally regulated complex: these interactions are detectable in rings and schizonts, but not in trophozoites. PfMCM2, 6 and 7 subunits are localized in both cytosolic and nucleosolic fractions during all intraerythrocytic stages of P. falciparum development, with increased nuclear localization in schizonts. Only PfMCM6 is associated with the chromatin fraction at all stages of growth. No phosphorylation of PfMCM2, 6 and 7 was detected, but two as yet unidentified threonine-phosphosphorylated proteins were present in the complex, whose pattern of phosphorylation varied during parasite development.

Expression and characterization of human malaria parasite Plasmodium falciparum origin recognition complex subunit 1

In eukaryotes, the origin recognition complex (ORC) is essential for the initiation of DNA replication. The largest subunit of this complex (ORC1) has a regulatory role in origin activation. Here we report the cloning and functional characterization of Plasmodium falciparum ORC1 homolog. Using immunofluorescence and immunoelectron microscopy, we show here that PfORC1 is expressed in the nucleus during the late trophozoite and schizont stages where maximum amount of DNA replication takes place. Homology modelling of the carboxy terminal region of PfORC1 (781-1033) using Saccharomyces pombe Cdc6/Cdc18 homolog as a template reveals the presence of a similar AAA+ type nucleotide-binding fold. This region shows ATPase activity in vitro that is important for the origin activity. To our knowledge, this is the first evidence of an individual ORC subunit that shows ATPase activity. These observations strongly suggest that PfORC1 might be involved in DNA replication initiation during the blood stage of the parasitic life cycle.

Identification of a second proliferating cell nuclear antigen in the human malarial pathogen Plasmodium falciparum

Proliferating cell nuclear antigen seems to exist as a single form in higher eukaryotic cells and plays multiple roles in nucleic acid metabolism. We have identified a second additional proliferating cell nuclear antigen (PfPCNA2) in Plasmodium falciparum on the basis of several lines of evidence. (1) PfPCNA2, consisting of 264 amino acid residues with a predicted molecular mass of 30.2kDa, shares only 29% identity and 53% similarity with PfPCNA1 at the amino acid level. (2) Southern blot analyses revealed that the hybridisation pattern of the Pfpcna2 gene is completely different from that of the Pfpcna1 gene. (3) Chromosomal localisation studies showed that Pfpcna2 is located on chromosome 12 while Pfpcna1 is located on chromosome 13. Northern blot analyses revealed two different transcripts of Pfpcna2, one expressed in both asexual and sexual erythrocytic stages, while the other existed only in the sexual stage, implying that PfPCNA2 may play multiple roles in DNA metabolism in different stages of the parasite. Recombinant protein of PfPCNA2, overexpressed in Escherichia coli, has been purified to near homogeneity and shown to form an oligomer, probably a trimer, as revealed by a size-exclusion chromatography and a native gel electrophoresis, suggesting that PfPCNA2, like its higher eukaryotic counterparts, may serve as a sliding platform which is capable of interaction with diverse proteins and regulation of their activities.