UCSF

The recent advances in genomic sequencing technologies in the past decade have enabled the unprecedented ability to investigate infectious diseases and organisms that were traditionally difficult to study in the laboratory. In particular, the human malaria parasite, Plasmodium falciparum, is a unique challenge because of the difficulty to grow these obligate intracellular parasites during the complex blood stages. Yet despite these challenges, genomic approaches have allowed us to investigate the parasite in an unbiased and comprehensive manner. The work described here uses DNA sequencing, RNA sequencing, high-throughput screening, and bioinformatics tools to understand the fundamental biological processes of the malaria parasite such as mechanisms of drug resistance, regulation of translation, and determinants of translational efficiency. A mechanistic understanding of how the parasite can escape antimalarial drug pressure is valuable for future drug development and the design of new drugs that avoid known parasite resistance mechanisms. To this end, we have developed a bioinformatics pipeline that will identify mutations such as copy number variations or single nucleotide polymorphisms that confer resistance to various drugs in vitro. The process of translation in malaria is poorly understood as the technologies for measuring translation or protein products are limited to measuring only the most abundant proteins. To address this problem, we took a genome-wide approach of ribosome profiling which quantitatively measures transcription and translation simultaneously for the entire genome. This study led to many interesting questions revolving around how the P. falciparum ribosome functions differently from other eukaryotic ribosomes and what cis-acting sequences determine the efficiency of translation. To answer these questions, we developed an in vitro translation system derived from cell free lysates of P. falciparum to both screen for drug compounds that specifically inhibit malaria translation and not other eukaryotic translation and we have employed this assay to find specific sequences found primarily on the 5’ untranslated region of an mRNA that can modulate translation. In total, this work addresses the regulation of gene expression in the asexual blood stages of this medically relevant parasite.