Comparative Transcriptional and Genomic Analysis of Plasmodium falciparum Field Isolates

Abstract

Mechanisms for differential regulation of gene expression may underlie much of the phenotypic variation and adaptability of malaria parasites. Here we describe transcriptional variation among culture-adapted field isolates of Plasmodium falciparum, the species responsible for most malarial disease. It was found that genes coding for parasite protein export into the red cell cytosol and onto its surface, and genes coding for sexual stage proteins involved in parasite transmission are up-regulated in field isolates compared with long-term laboratory isolates. Much of this variability was associated with the loss of small or large chromosomal segments, or other forms of gene copy number variation that are prevalent in the P. falciparum genome (copy number variants, CNVs). Expression levels of genes inside these segments were correlated to that of genes outside and adjacent to the segment boundaries, and this association declined with distance from the CNV boundary. This observation could not be explained by copy number variation in these adjacent genes. This suggests a local-acting regulatory role for CNVs in transcription of neighboring genes and helps explain the chromosomal clustering that we observed here. Transcriptional co-regulation of physical clusters of adaptive genes may provide a way for the parasite to readily adapt to its highly heterogeneous and strongly selective environment.

Plasmodium Helical Interspersed Subtelomeric (PHIST) Proteins, at the Center of Host Cell Remodeling

“…Variable expression generally has also been observed in field isolates (50). Figure 6 presents expression data obtained only from asexual blood stage parasites, but a proteomic study revealed that a number of PHIST proteins are enriched in early gametocytes, the sexual blood stage of P. falciparum.…”

“…Genes annotated "phista-like" or as "phist" genes were grouped together as "phist others." Yellow boxes to the right of the heat map indicate PHIST proteins present in the early gametocyte proteome (35), differentially expressed phist genes in pregnancy-associated malaria (29,49,50,84,92,112) and in cerebral malaria (32,34), or if variant expression has been reported (55). Green to red colors represent fold changes (log fold changes from Ϫ3 to 3).…”

Transcriptional variation in the malaria parasitePlasmodium falciparum

“…Some studies have compared global blood stages transcription between different P. falciparum lines, but their sample size and experimental design resulted in the identification of only a small number of variantly expressed genes: One study compared two isogenic lines selected to display different antigenic and adhesive properties (Mok et al 2007), whereas another study compared the transcriptome of three genetically different parasite lines, focusing on the comparison of patterns of expression along the life cycle rather than comparing transcript levels (Llinas et al 2006). Genome-wide transcriptional differences have also been analyzed in field isolates Lemieux et al 2009;Mackinnon et al 2009), but these studies suffer intrinsic limitations such as the inability to distinguish between spontaneous variation and selection, and the common occurrence of mixed infections. Furthermore, some of the transcript-level differences observed may be attributable to genetic polymorphism.…”

NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children

“…We did not detect peptides corresponding to this protein using mass spectrometry, but reanalysis of our existing microarray data sets (15) indicated that probable protein PF10_0350 expression levels are significantly higher in parasites isolated from children's versus those isolated from pregnant mothers (log 2 fold = -3.15, P = 4.66 × 10 -8 ; Supplemental Table 13). Probable protein PF10_0350 was previously reported to be downregulated in placental parasites when compared with parasites from nonpregnant women and children (17) and has been reported to be expressed at higher levels in field isolates than in laboratory-adapted strains (29), suggesting that its function might be important for binding of pRBC to nonplacental receptors in the human host. As with garp and Gbph2, this protein has no orthologs in other Plasmodium species (although it does have a paralog in P. falciparum, predicted exported protein of unknown function MAL7P1.171) (22).…”

“…Three of the genes upregulated in children's parasites (garp, Gbph2, and probable protein PF10_0350) are unique to P. falciparum (22), which causes the most severe form of human malaria, suggesting that these proteins could have a role in virulence that is absent in other parasite species. Finally, the expression of these 4 genes has been reported to vary in parasites selected for their ability to bind particular host receptors (26,27) and in field parasites when compared with laboratory strains (28,29). Future experiments will attempt to validate these proteins as biomarkers of disease severity and as targets for intervention strategies designed to reduce the severity of childhood malaria.…”