The adaptive roles of aneuploidy and polyclonality in Leishmania in response to environmental stress

Abstract

Aneuploidy is generally considered harmful, but in some microorganisms, it can act as an adaptive mechanism against environmental stress. Here, we use Leishmania—a protozoan parasite with remarkable genome plasticity—to study the early steps of aneuploidy evolution under high drug pressure (using antimony or miltefosine as stressors). By combining single‐cell genomics, lineage tracing with cellular barcodes, and longitudinal genome characterization, we reveal that aneuploidy changes under antimony pressure result from polyclonal selection of pre‐existing karyotypes, complemented by further and rapid de novo alterations in chromosome copy number along evolution. In the case of miltefosine, early parasite adaptation is associated with independent point mutations in a miltefosine transporter gene, while aneuploidy changes only emerge later, upon exposure to increased drug levels. Therefore, polyclonality and genome plasticity are hallmarks of parasite adaptation, but the scenario of aneuploidy dynamics depends on the nature and strength of the environmental stress as well as on the existence of other pre‐adaptive mechanisms.

R-loops acted on by RNase H1 are a determinant of chromosome length-associated DNA replication timing and genome stability inLeishmania

“…The loss of subtelomere, ribosomal and SL sequences suggests that RNase H1 is required for the maintenance of repetitive DNA, possibly by preventing R-loops accumulation at DNA replication stress-prone regions. It is also possible that at least some of the stable changes in karyotype may explain reversion of the short-term growth defect after RNase H1 loss, consistent with the idea that aneuploidy is an adaptative strategy relying on polyclonal selection of pre-existing karyotypes 129, 130 .…”

“…Alternatively, or in addition, earlier traversal of DNA replication across R-loops in the smaller chromosomes relative to the larger could explain the increasing burden of SNPs and InDels as chromosome size decreases. It will be interesting to determine how RNase H1 mutation affects the ability of Leishmania to adapt to changing environments, which has been associated with genome instability 129, 154, 155 .…”

Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites

“…The presence of a polysomy in Chromosome 8 in long-term mammalian infection, undetected in the original culture isolate, suggests that different environments may favor specific combinations of chromosomal duplications (Dumetz et al 2017). In fact, preadapted Leishmania donovani karyotypes were further modulated de novo under strong antimony pressure, potentially providing resistance in vitro (Negreira et al 2023). Aneuploidy, more specifically chromosome duplication followed by loss, was also associated with loss of heterozygosity (LoH) in Leishmania (Prieto Barja et al 2017).…”