title: Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications.
abstract: Malaria drug resistance contributes to up to a million annual deaths. Judicious deployment of new antimalarials and vaccines could benefit from an understanding of early molecular events that promote the evolution of parasites. Continuous in vitro challenge of Plasmodium falciparum parasites with a novel dihydroorotate dehydrogenase (DHODH) inhibitor reproducibly selected for resistant parasites. Genome-wide analysis of independently-derived resistant clones revealed a two-step strategy to evolutionary success. Some haploid blood-stage parasites first survive antimalarial pressure through fortuitous DNA duplications that always included the DHODH gene. Independently-selected parasites had different sized amplification units but they were always flanked by distant A/T tracks. Higher level amplification and resistance was attained using a second, more efficient and more accurate, mechanism for head-to-tail expansion of the founder unit. This second homology-based process could faithfully tune DNA copy numbers in either direction, always retaining the unique DNA amplification sequence from the original A/T-mediated duplication for that parasite line. Pseudo-polyploidy at relevant genomic loci sets the stage for gaining additional mutations at the locus of interest. Overall, we reveal a population-based genomic strategy for mutagenesis that operates in human stages of P. falciparum to efficiently yield resistance-causing genetic changes at the correct locus in a successful parasite. Importantly, these founding events arise with precision; no other new amplifications are seen in the resistant haploid blood stage parasite. This minimizes the need for meiotic genetic cleansing that can only occur in sexual stage development of the parasite in mosquitoes.
authors.affiliation: Department of Chemistry, University of Washington, Seattle, Washington, United States of America.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Guler
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Freeman
authors.forename: Vida
authors.initials: V
authors.lastname: Ahyong
authors.forename: Rapatbhorn
authors.initials: R
authors.lastname: Patrapuvich
authors.forename: John
authors.initials: J
authors.lastname: White
authors.forename: Ramesh
authors.initials: R
authors.lastname: Gujjar
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Phillips
authors.forename: Joseph
authors.initials: J
authors.lastname: DeRisi
authors.forename: Pradipsinh K
authors.initials: PK
authors.lastname: Rathod
mesh_terms: D000818:Animals; D009033:Culicidae / Q000469:parasitology; D016054:DNA, Protozoan / Q000096:biosynthesis / Q000235:genetics; D000090722:Dihydroorotate Dehydrogenase; D004351:Drug Resistance / Q000235:genetics*; D056426:Genetic Loci / Q000235:genetics; D006801:Humans; D044925:Oxidoreductases Acting on CH-CH Group Donors / Q000235:genetics / Q000378:metabolism; D010963:Plasmodium falciparum / Q000235:genetics / Q000378:metabolism; D011003:Ploidies; D015800:Protozoan Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D016054:DNA, Protozoan; D000090722:Dihydroorotate Dehydrogenase; D015800:Protozoan Proteins; D044925:Oxidoreductases Acting on CH-CH Group Donors