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Distinct physiological states of Plasmodium falciparum in malaria infected patients

ABSTRACT: Patients infected with Plasmodium falciparum sustain diverse disease outcome; we wanted to determine if parasites derived ex vivo have diverse biological states. To explore parasite in vivo biology we measured parasite steady state whole genome transcription using a previously reported custom made Affy array (Scrmalaria) based on the laboratory strain 3D7. Extensive bioinformatic analysis was carried out including cross species comparisions to yeast. For sample cluster analysis, a filtered gene list containing 3937 genes was generated by thresholding gene expression levels to a minimum of 50 EU and removing any genes that varied less than 3 fold or 100 EU across the dataset. To minimize potential effects of different dates of collection and hybridizations, the data was rank ordered by expression level and each gene was given an ordinal value. Keywords: ex vivo

ORGANISM(S): Plasmodium falciparum

PROVIDER: GSE9152 | GEO | 2007/12/13

SECONDARY ACCESSION(S): PRJNA102703

REPOSITORIES: GEO

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Project description:Background Dickeya dadantii is a necrotrophic pathogen causing disease in many plants. Previous studies have demonstrated that the type III secretion system (T3SS) of D. dadantii is required for full virulence. HrpL is an alternative sigma factor that binds to the hrp box promoter sequence of T3SS genes to up-regulate their expression. Methodology/Principal Findings To explore the inventory of HrpL-regulated genes of D. dadantii 3937 (3937), transcriptome profiles of wild-type 3937 and a hrpL mutant grown in a T3SS-inducing medium were examined. Using a cut-off value of 1.5, significant differential expression was observed in sixty-three genes, which are involved in various cellular functions such as type III secretion, chemotaxis, metabolism, regulation, and stress response. A hidden Markov model (HMM) was used to predict candidate hrp box binding sites in the intergenic regions of 3937, including the promoter regions of HrpL-regulated genes identified in the microarray assay. In contrast to biotrophic phytopathgens such as Pseudomonas syringae, among the HrpL up-regulated genes in 3937 only those within the T3SS were found to contain a hrp box sequence. Moreover, direct binding of purified HrpL protein to the hrp box was demonstrated for hrp box-containing DNA fragments of hrpA and hrpN using the electrophoretic mobility shift assay (EMSA). In this study, a putative T3SS effector DspA/E was also identified as a HrpL-upregulated gene, and shown to be translocated into plant cells in a T3SS-dependent manner. Conclusion/Significances We provide the genome-wide study of HrpL-regulated genes in a necrotrophic phytopathogen (D. dadantii 3937) through a combination of transcriptomics and bioinformatics, which led to identification of several effectors. Our study indicates the extent of differences for T3SS effector protein inventory requirements between necrotrophic and biotrophic pathogens, and may allow the development of different strategies for disease control for these different groups of pathogens.

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Distinct physiological states of Plasmodium falciparum in malaria infected patients

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