Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1

Amambua-Ngwa, Alfred; Button-Simons, Katrina A.; Li, Xue; Kumar, Sudhir; Brenneman, Katelyn Vendrely; Ferrari, Marco; Checkley, Lisa A; Haile, Meseret T.; Shoue, Douglas A; McDew-White, Marina; Tindall, Sarah M; Reyes, Ann; Delgado, Elizabeth; Dalhoff, Hayley; Larbalestier, James K.; Amato, Roberto; Pearson, Richard D.; Taylor, Alexander B.; Nosten, François H.; D'Alessandro, Umberto; Kwiatkowski, Dominic; Cheeseman, Ian H.; Kappe, Stefan H.I.; Avery, Simon V.; Conway, David J.; Vaughan, Ashley M.; Ferdig, Michael T.; Anderson, Timothy J.C.

Abstract

Malaria parasites break down host haemoglobin into peptides and amino acids in the digestive vacuole for export to the parasite cytoplasm for growth: interrupting this process is central to the mode of action of several antimalarial drugs. Mutations in the chloroquine (CQ) resistance transporter, pfcrt, located in the digestive vacuole membrane, confer CQ resistance in Plasmodium falciparum, and typically also affect parasite fitness. However, the role of other parasite loci in the evolution of CQ resistance is unclear. Here we use a combination of population genomics, genetic crosses and gene editing to demonstrate that a second vacuolar transporter plays a key role in both resistance and compensatory evolution. Longitudinal genomic analyses of the Gambian parasites revealed temporal signatures of selection on a putative amino acid transporter (pfaat1) variant S258L, which increased from 0% to 97% in frequency between 1984 and 2014 in parallel with the pfcrt1 K76T variant. Parasite genetic crosses then identified a chromosome 6 quantitative trait locus containing pfaat1 that is selected by CQ treatment. Gene editing demonstrated that pfaat1 S258L potentiates CQ resistance but at a cost of reduced fitness, while pfaat1 F313S, a common southeast Asian polymorphism, reduces CQ resistance while restoring fitness. Our analyses reveal hidden complexity in CQ resistance evolution, suggesting that pfaat1 may underlie regional differences in the dynamics of resistance evolution, and modulate parasite resistance or fitness by manipulating the balance between both amino acid and drug transport.

Citation

Amambua-Ngwa, A., Button-Simons, K. A., Li, X., Kumar, S., Brenneman, K. V., Ferrari, M., …Anderson, T. J. (2023). Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1. Nature Microbiology, https://doi.org/10.1038/s41564-023-01377-z

• Journal Article Type: Article
• Acceptance Date: Mar 29, 2023
• Online Publication Date: May 11, 2023
• Publication Date: May 11, 2023
• Deposit Date: Mar 2, 2023
• Publicly Available Date: May 12, 2023
• Journal: Nature Microbiology
• Electronic ISSN: 2058-5276
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• DOI: https://doi.org/10.1038/s41564-023-01377-z
• Keywords: Cell Biology; Microbiology (medical); Genetics; Applied Microbiology and Biotechnology; Immunology; Microbiology
• Public URL: https://nottingham-repository.worktribe.com/output/17942934
• Publisher URL: https://www.nature.com/articles/s41564-023-01377-z
• Additional Information: Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.