Over the past decade, we have discovered a system of translational control of gene expression in all living organisms, involving dozens of RNA modifications – the epitranscriptome – coupled with an alternative genetic code of synonymous codon usage. Profs. Preiser and Dedon have defined the set of RNA modifications in Plasmodium falciparumand identified two epitranscriptome behaviors in the red blood cell life cycle of the parasite. One involves simultaneous up-regulation of ~20 modifications during the maturation of the parasite, in concert with developmental up-regulation of protein production and metabolism in general. The other facet of epitranscriptomic behavior involved the model for translational control of gene expression. Analysis of proteome and tRNA modifications across the RBC life cycle revealed coordinated up-and down-regulation of tRNA isoacceptors and proteins coded by genes enriched with the cognate codons of these tRNAs.

Building on these observations, preliminary analyses show stress-specific reprogramming of the epitranscriptome, including patterns unique to exposure to antimicrobial agents such as artemisinin. We now propose to define the role of translationalcontrol mechanisms in the emerging resistance to artemisinin in malaria parasites in Southeast Asia. Mutations in the kelch K13 gene were identified in artemisinin-resistant clinical isolates in SE Asia, while kelch mutations and artemisinin resistance have not emerged in Africa, which raises questions about the potential for other parasite mechanisms to play a role in artemisinin resistance. Here we will define one such mechanism: a link between tRNA modifications, an alternative genetic code, and artemisinin resistance in P. falciparum. Using wild-type and kelch mutant P. falciparum strains, we will quantify changes in tRNA modification, protein, and transcript levels during the RBC life cycle. Preliminary studies are consistent with the idea that strains with kelch-mediated artemisinin resistance prefer a metabolically and translationally "less active" state when encountering artemisinin stress and respond by down-regulating the general tRNA modification levels that would normally increase during the RBCphase of parasite development. We propose to characterize these pathways to identify potential targets for therapeutic intervention to reverse the drug resistance.