Chapter 23 : Genomic and Postgenomic Approaches to Understanding the Pathogenesis of the Enteric Protozoan Parasite

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Elaborate regulation of membrane trafficking is essential for the targeting of molecules necessary for pathogenesis (e.g., lectin and CPs) to precise intracellular compartments such as the surface membrane and lysosomes. This chapter discusses the diversification of cysteine proteases (CPs) and Rab in the context of their diverse localization and function. Encystation and excystation are fundamental processes required for the transmission and development of amebiasis. The current assembly predicts that the genome contains 8,160 genes, almost 1.5-fold more than the number of genes in (5,268) or (5,538), and close to that in (12,500). The majority of ribosomal protein genes are well conserved, and only the gene for the large subunit protein L41 has not been identified. The chapter focuses only on several important pathways closely related to the parasite's molecular epidemiology, biology, and virulence. It also talks about the insights obtained from comparing their genome information with that of to understand the conservation and unique evolution of the species. Insights into the developmental regulation of CPs and Rab small GTPases during encystation are also discussed as examples of transcriptomic approaches to understand the biology and pathogenesis of this group of enteric protozoa. To gain insights into the mechanisms of encystation-specific membrane trafficking, the authors also investigated the transcriptomic changes of Rab genes during the encystation of . The kinetics of the steady-state levels of mRNA for individual Rab genes were categorized into cyst-specific, trophozoite-specific, or constitutive genes.

Citation: Nakada-Tsukui K, Nozaki T. 2011. Genomic and Postgenomic Approaches to Understanding the Pathogenesis of the Enteric Protozoan Parasite , p 321-341. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch23
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Figure 1

Phylogenetic analysis of CPs from and Phylogenetic analysis of CPs from the C1 family of and was performed using CLUSTAL W. Trees were drawn using MEGA4. The consensus phylogenetic trees of the CP-A, CP-B, and CP-C families are shown. The numbers at the nodes represent the bootstrap values for 1,000 iterations shown in percentages. The scale bar indicates 0.1 or 0.2 substitutions at each amino acid position.

Citation: Nakada-Tsukui K, Nozaki T. 2011. Genomic and Postgenomic Approaches to Understanding the Pathogenesis of the Enteric Protozoan Parasite , p 321-341. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch23
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Figure 2

Phylogenetic analysis of Rab genes from and Phylogenetic analysis was performed as described in the legend to Fig. 1 . An overview of the whole phylogenetic tree is shown on the left, while magnifed portions (A to D) of the tree are shown separately on the right.

Citation: Nakada-Tsukui K, Nozaki T. 2011. Genomic and Postgenomic Approaches to Understanding the Pathogenesis of the Enteric Protozoan Parasite , p 321-341. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch23
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Figure 3

Kinetics of CP and Rab gene expression during encystation in trophozoites were cultured in encystation medium. Total RNA was extracted at 0, 0.5, 2, 8, 24, 48, and 120 h, and subjected to transcriptome analysis using DNA microarrays. The normalized relative fluorescence intensity of each gene is shown.

Citation: Nakada-Tsukui K, Nozaki T. 2011. Genomic and Postgenomic Approaches to Understanding the Pathogenesis of the Enteric Protozoan Parasite , p 321-341. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch23
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Generic image for table
Table 1

CPs from and

Citation: Nakada-Tsukui K, Nozaki T. 2011. Genomic and Postgenomic Approaches to Understanding the Pathogenesis of the Enteric Protozoan Parasite , p 321-341. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch23
Generic image for table
Table 2

Rab genes from and

Citation: Nakada-Tsukui K, Nozaki T. 2011. Genomic and Postgenomic Approaches to Understanding the Pathogenesis of the Enteric Protozoan Parasite , p 321-341. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch23

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