Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania

Abstract

Aneuploidy causes broad-scale disruption in the stochiometric balances of transcripts, proteins, and metabolites. These disruptions often lead to detrimental effects for the organism, but for some organisms and in certain environments, it can also cause a fitness advantage. Understanding the complex trade-off between aneuploidy fitness gains and losses requires a systems biological comprehension of its molecular impact. The protozoan parasite Leishmania provides a unique study angle to this problem, as the pathogen lacks transcriptional regulation of individual protein-coding genes and has an unusually high tolerance for aneuploidy. Here, we present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. This 4 layer multi-omics analysis unambiguously establishes that despite this tolerance, aneuploidy in Leishmania globally and drastically impacts the transcriptome and proteome of affected chromosomes, ultimately explaining the degree of metabolic differences between strains. This impact appears to be present throughout the life cycle of the parasite as we observed it in both its proliferative and infectious life stages. We show that, through dosage compensation, protein complex subunits, secreted proteins, and non-cytoplasmic proteins responded less or even not at all to aneuploidy. In contrast to other Eukaryotes, we did not observe the widespread regulation at the transcript level that typically modulate some of the negative effects of aneuploidy. Instead, Leishmania features a surprisingly high number of regulated proteins encoded by non-aneuploid chromosomes, suggesting that aneuploidy results in extensive post-transcriptionally modulation of protein levels. Our results provide the foundation for the integrated molecular understanding of aneuploidy in Leishmania. They also highlight that the parasite is an attractive model to study processes of post-transcriptional modulation of protein levels in the context of aneuploidy and beyond.

Nitric Oxide Resistance in Leishmania (Viannia) braziliensis Involves Regulation of Glucose Consumption, Glutathione Metabolism and Abundance of Pentose Phosphate Pathway Enzymes

“…In addition, we demonstrated that the rapid modulation of NO-resistant parasites’ proteome upon NO challenge involves an increase in total protein content, which is suggestive of ploidy alterations in response to nitrosative stress. In line with this proposal, recently it was reported that aneuploidy in L. donovani is followed by proteome modulation and could explain metabolic differences between strains [ 53 ]. Aneuploidy and karyotypic mosaicism are common in Leishmania spp., and such genome plasticity allow parasites to explore fitness possibilities for survival [ 54 , 55 , 56 ].…”

Transcriptional Shift and Metabolic Adaptations during Leishmania Quiescence Using Stationary Phase and Drug Pressure as Models

“…In contrast, the abundance of carbon sources such as sucrose and 3 hexose-multimers (labelled as cellopentaose, cellohexaose and celloheptaose) were identified as increasing in quiescent cells. These penta, hexa and hepta-hexoses have previously been inferred [45] to derive from mannogen, a polymannose carbohydrate reserve used by Leishmania [46]. Interestingly, while most structural phospholipids were not modulated, a number of free fatty acyls and also sphingolipids were increased in quiescent promastigotes, while no clear trend was observed in amastigotes.…”

High throughput single-cell genome sequencing gives insights into the generation and evolution of mosaic aneuploidy inLeishmania donovani

“…By investigating which chromosomes were more prone to somy alterations in rare and common karyotypes, we gathered evidence suggesting that all chromosomes can be stochastically amplified during population expansion, potentially at different rates, but we hypothesize that selective forces likely dictate the higher frequency of polysomies observed in some chromosomes. Changes in the average chromosome copy numbers of cell populations are directly reflected in the average amount of transcripts encoded by the genes present on these chromosomes ( 19 , 23 ) and to a certain degree also affect the average amount of certain proteins ( 24 ). Consequently, aneuploidy might lead to dosage imbalances between the product of genes located in chromosomes that display different somies.…”

“…In fact, changes in average aneuploidy pattern and not variation in nucleotide sequence are the first genomic modifications observed at populational level during the course of experimental selection of drug resistance ( 21 , 22 ). Given that these alterations in average somies are reflected in the average amount of corresponding transcripts ( 19 , 23 ), and to a certain degree, of proteins ( 24 ), it has been proposed that aneuploidy allows Leishmania to adapt by means of rapid changes in gene dosage.…”