Genome deletions to overcome the directed loss of gene function in Leishmania

Evolutionary duplication of the leishmanial adaptor protein α-SNAP plays a role in its pathogenicity

Essential-gene duplication during evolution promotes specialized functions beyond the typical role. Our in-silico study unveiled two α-SNAP paralogs in Leishmania, a crucial component that, along with NSF, triggers disassembly of the cis-SNARE complex, formed during vesicle fusion with target membranes. While multiple α-SNAPs are common in many flagellated protists, including the trypanosomatids, they are unusual among other eukaryotes. This study explores the evolutionary and functional relevance of α-SNAP gene duplication in Leishmania donovani, emphasizing both subfunctionalization and neofunctionalization. We discovered that Leishmania donovani α-SNAP (Ldα-SNAP) genes are transcribed in promastigote and amastigote stages, indicating they are not pseudogenes. Although the two paralogs share essential residues and structural features, only Ldα-SNAP1660 (Ldα-SNAP1) can effectively substitute the function of its yeast counterpart, while Ldα-SNAP3040 (Ldα-SNAP2) cannot. This functional difference is attributed to a replacement of alanine with phosphorylatable-serine in Ldα-SNAP1 during evolution from the most common ancestral ortholog. This modification is rarely observed in corresponding orthologs of other trypanosomatids. Incidentally, Ldα-SNAP paralogs exhibit differential localization in the ER and flagellar pocket. However, both paralogs, either actively or passively, regulate the secretion of exosomes and PM blebs, containing the virulence protein GP63. This indicates functional division and their indirect participation in host's macrophage inactivation. Moreover, a small fraction of Ldα-SNAP1's presence in flagellum hints at a potential role in sensing environmental cues and aiding parasite's attachment to the sandfly's hindgut. Our findings underscore that duplicated Ldα-SNAPs have retained ancestral functions through subfunctionalization, and subsequently, they acquired parasite-specific neofunction(s) through accumulation of natural mutation(s).

Evaluation of the Leishmania Inositol Phosphorylceramide Synthase as a Drug Target Using a Chemical and Genetic Approach

The lack of effective vaccines and the development of resistance to the current treatments highlight the urgent need for new anti-leishmanials. Sphingolipid metabolism has been proposed as a promising source of Leishmania-specific targets as these lipids are key structural components of the eukaryotic plasma membrane and are involved in distinct cellular events. Inositol phosphorylceramide (IPC) is the primary sphingolipid in the Leishmania species and is the product of a reaction mediated by IPC synthase (IPCS). The antihistamine clemastine fumarate has been identified as an inhibitor of IPCS in L. major and a potent anti-leishmanial in vivo. Here we sought to further examine the target of this compound in the more tractable species L. mexicana, using an approach combining genomic, proteomic, metabolomic and lipidomic technologies, with molecular and biochemical studies. While the data demonstrated that the response to clemastine fumarate was largely conserved, unexpected disturbances beyond sphingolipid metabolism were identified. Furthermore, while deletion of the gene encoding LmxIPCS had little impact in vitro, it did influence clemastine fumarate efficacy and, importantly, in vivo pathogenicity. Together, these data demonstrate that clemastine does inhibit LmxIPCS and cause associated metabolic disturbances, but its primary target may lie elsewhere.

Disruption of the inositol phosphorylceramide synthase gene affects Trypanosoma cruzi differentiation and infection capacity

Sphingolipids (SLs) are essential components of all eukaryotic cellular membranes. In fungi, plants and many protozoa, the primary SL is inositol-phosphorylceramide (IPC). Trypanosoma cruzi is a protozoan parasite that causes Chagas disease (CD), a chronic illness for which no vaccines or effective treatments are available. IPC synthase (IPCS) has been considered an ideal target enzyme for drug development because phosphoinositol-containing SL is absent in mammalian cells and the enzyme activity has been described in all parasite forms of T. cruzi. Furthermore, IPCS is an integral membrane protein conserved amongst other kinetoplastids, including Leishmania major, for which specific inhibitors have been identified. Using a CRISPR-Cas9 protocol, we generated T. cruzi knockout (KO) mutants in which both alleles of the IPCS gene were disrupted. We demonstrated that the lack of IPCS activity does not affect epimastigote proliferation or its susceptibility to compounds that have been identified as inhibitors of the L. major IPCS. However, disruption of the T. cruzi IPCS gene negatively affected epimastigote differentiation into metacyclic trypomastigotes as well as proliferation of intracellular amastigotes and differentiation of amastigotes into tissue culture-derived trypomastigotes. In accordance with previous studies suggesting that IPC is a membrane component essential for parasite survival in the mammalian host, we showed that T. cruzi IPCS null mutants are unable to establish an infection in vivo, even in immune deficient mice.

Life in plastic, it's fantastic! How Leishmania exploit genome instability to shape gene expression

Leishmania are kinetoplastid pathogens that cause leishmaniasis, a debilitating and potentially life-threatening infection if untreated. Unusually, Leishmania regulate their gene expression largely post-transcriptionally due to the arrangement of their coding genes into polycistronic transcription units that may contain 100s of functionally unrelated genes. Yet, Leishmania are capable of rapid and responsive changes in gene expression to challenging environments, often instead correlating with dynamic changes in their genome composition, ranging from chromosome and gene copy number variations to the generation of extrachromosomal DNA and the accumulation of point mutations. Typically, such events indicate genome instability in other eukaryotes, coinciding with genetic abnormalities, but for Leishmania, exploiting these products of genome instability can provide selectable substrates to catalyse necessary gene expression changes by modifying gene copy number. Unorthodox DNA replication, DNA repair, replication stress factors and DNA repeats are recognised in Leishmania as contributors to this intrinsic instability, but how Leishmania regulate genome plasticity to enhance fitness whilst limiting toxic under- or over-expression of co-amplified and co-transcribed genes is unclear. Herein, we focus on fresh, and detailed insights that improve our understanding of genome plasticity in Leishmania. Furthermore, we discuss emerging models and factors that potentially circumvent regulatory issues arising from polycistronic transcription. Lastly, we highlight key gaps in our understanding of Leishmania genome plasticity and discuss future studies to define, in higher resolution, these complex regulatory interactions.