Metabolomic analysis of entamoeba biology

Abstract

Whole genome or transcriptome information provides the annotation of genes and proteins and predicts metabolic pathways, but unequivocal demonstration of the functionalities of the enzymes and metabolic pathways remains challenging. Because nearly 56 % of the Entamoeba histolytica genes remain unannotated, correlative “omics” analyses of genomics, transcriptomics, proteomics, and biochemical metabolic profiling can be useful in uncovering new, or poorly understood, metabolisms and metabolic pathways. Current understanding of metabolic pathways constructed by genes and pathway predictions are based on homology search of the genome, transcriptome, and proteome databases and conventional biochemical demonstration of enzymatic activities. However, it is well known that there are large disparities between the pathways predicted in silico and the pathways actually operating in vivo. Thus, it is important to demonstrate the presence and kinetics (flow or flux) of the metabolites involved in the pathways. To this end, a variety of analytical methods and platforms for metabolomics and metabolite profiling has been developed, in which intracellular and extracellular metabolites can be selectively or globally analyzed. Global metabolomics analysis of Entamoeba histolytica under environmental stress conditions, in different life-cycle stages, and heterogenic (i.e., clinical) isolates, should potentially uncover unpredictable metabolic pathways, interaction and regulation of pathways, and also directly demonstrate the role of individual genes on metabolic pathways, and thus helps our understanding of the physiological and biological roles of metabolic pathways and a network of regulatory interactions between them. Metabolomics of Entamoeba is still in its infancy and only a handful of studies have been reported thus far. In this chapter, we summarize a few examples of the application of metabolomics, combined with transcriptomic analysis, to the analysis of global changes in metabolism in response to three representative physiological conditions: Encystation, oxidative stress, and cysteine deprivation. We also discuss future applications of metabolomics to understand the biology and pathogenesis of E. histolytica. Furthermore, because major metabolic differences between the parasite and its host provide rational drug targets, which are either selectively present in pathogens or highly divergent from humans, multi-“omics” approaches, including metabolomics, should lead to important discoveries of unique exploitable metabolic networks crucial to develop new effective drugs against amebiasis.