Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France.
The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel.
PLoS Pathog. 2022 Mar 16;18(3):e1010375. doi: 10.1371/journal.ppat.1010375. eCollection 2022 Mar.
The protozoan parasite Leishmania donovani causes fatal human visceral leishmaniasis in absence of treatment. Genome instability has been recognized as a driver in Leishmania fitness gain in response to environmental change or chemotherapy. How genome instability generates beneficial phenotypes despite potential deleterious gene dosage effects is unknown. Here we address this important open question applying experimental evolution and integrative systems approaches on parasites adapting to in vitro culture. Phenotypic analyses of parasites from early and late stages of culture adaptation revealed an important fitness tradeoff, with selection for accelerated growth in promastigote culture (fitness gain) impairing infectivity (fitness costs). Comparative genomics, transcriptomics and proteomics analyses revealed a complex regulatory network associated with parasite fitness gain, with genome instability causing highly reproducible, gene dosage-independent and -dependent changes. Reduction of flagellar transcripts and increase in coding and non-coding RNAs implicated in ribosomal biogenesis and protein translation were not correlated to dosage changes of the corresponding genes, revealing a gene dosage-independent, post-transcriptional mechanism of regulation. In contrast, abundance of gene products implicated in post-transcriptional regulation itself correlated to corresponding gene dosage changes. Thus, RNA abundance during parasite adaptation is controled by direct and indirect gene dosage changes. We correlated differential expression of small nucleolar RNAs (snoRNAs) with changes in rRNA modification, providing first evidence that Leishmania fitness gain in culture may be controlled by post-transcriptional and epitranscriptomic regulation. Our findings propose a novel model for Leishmania fitness gain in culture, where differential regulation of mRNA stability and the generation of modified ribosomes may potentially filter deleterious from beneficial gene dosage effects and provide proteomic robustness to genetically heterogenous, adapting parasite populations. This model challenges the current, genome-centric approach to Leishmania epidemiology and identifies the Leishmania transcriptome and non-coding small RNome as potential novel sources for the discovery of biomarkers that may be associated with parasite phenotypic adaptation in clinical settings.
原生动物寄生虫利什曼原虫在没有治疗的情况下会导致致命的人类内脏利什曼病。基因组不稳定性已被认为是利什曼虫在适应环境变化或化疗时获得适应性的驱动因素。尽管潜在的有害基因剂量效应，但基因组不稳定性如何产生有益的表型尚不清楚。在这里，我们通过对适应体外培养的寄生虫进行实验进化和综合系统方法来解决这个重要的开放性问题。对早期和晚期培养适应阶段的寄生虫进行表型分析表明存在一个重要的适应性权衡，即在原虫培养中选择加速生长（适应性增益）会损害感染力（适应性代价）。比较基因组学、转录组学和蛋白质组学分析揭示了与寄生虫适应性增益相关的复杂调控网络，基因组不稳定性导致高度可重复、基因剂量非依赖性和依赖性变化。鞭毛转录物减少，编码和非编码 RNA 增加，这些 RNA 参与核糖体生物发生和蛋白质翻译，与相应基因的基因剂量变化无关，揭示了一种基因剂量非依赖性、转录后调控机制。相反，参与转录后调控本身的基因产物丰度与相应的基因剂量变化相关。因此，寄生虫适应过程中的 RNA 丰度受直接和间接基因剂量变化的控制。我们将小核仁 RNA（snoRNA）的差异表达与 rRNA 修饰的变化相关联，首次提供了证据表明，利什曼虫在培养中的适应性增益可能受到转录后和转录后修饰的调控。我们的研究结果提出了一个新的利什曼虫在培养中获得适应性的模型，其中 mRNA 稳定性的差异调节和修饰核糖体的产生可能潜在地从有害基因剂量效应中筛选出有利的基因剂量效应，并为遗传异质性、适应寄生虫群体提供蛋白质组稳健性。该模型挑战了当前利什曼虫流行病学的基因组中心方法，并确定了利什曼转录组和非编码小 RNA 组作为发现可能与临床环境中寄生虫表型适应相关的生物标志物的潜在新来源。
