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Beverley, S. M.

Publications and source records attributed to Beverley, S. M..

12 recordsLinked to original sources
bioRxiv2023

Parasite hybridization promotes spreading of endosymbiotic viruses

Viruses are the most abundant biological entities on Earth and play a significant role in the evolution of many organisms and ecosystems. In pathogenic protozoa, the presence of endosymbiotic viruses has been linked to an increased risk of treatment failure and severe clinical outcome. Here, we studied the molecular epidemiology of the zoonotic disease cutaneous leishmaniasis in Peru and Bolivia through a joint evolutionary analysis of Leishmania braziliensis parasites and their endosymbiotic Leishmania RNA virus. We show that parasite populations circulate in isolated pockets of suitable habitat and are associated with single viral lineages that appear in low prevalence. In contrast, groups of hybrid parasites were geographically and ecologically dispersed, and commonly infected from a pool of genetically diverse viruses. Our results suggest that parasite hybridization, likely due to increased human migration and ecological perturbations, increased the frequency of endosymbiotic interactions known to play a key role in disease severity.

evolutionary biology↗
bioRxiv2022

An RNA interference (RNAi) toolkit and its utility for functional genetic analysis of Leishmania ( Viannia )

RNA interference (RNAi) is a powerful tool whose efficacy against a broad range of targets enables functional genetic tests individually or systematically. However, the RNAi pathway has been lost in evolution by a variety of eukaryotes including most Leishmania sp. RNAi was retained in species of the Leishmania subgenus Viannia, and here we describe the development, optimization, and application of RNAi tools to the study of L. (Viannia) braziliensis. We developed vectors facilitating generation of long-hairpin or "stem-loop" (StL) RNAi knockdown constructs, using Gateway site-specific recombinase technology. A survey of applications of RNAi in L. braziliensis included genes interspersed within multigene tandem arrays such as QDPR, a potential target or modulator of antifolate sensitivity. Other tests include genes involved in cell differentiation and amastigote proliferation (A600), and essential genes of the intraflagellar transport (IFT) pathway. We tested a range of stem lengths targeting the L. braziliensis hypoxanthine-guanine phosphoribosyltransferase (HGPRT) and reporter firefly luciferase (LUC) genes and found that the efficacy of RNAi increased with stem length, and fell off greatly below about 128 nt. We used the StL length dependency to establish a useful hypomorphic approach not possible with other gene ablation strategies, with shorter IFT140 stems yielding viable cells with compromised flagellar morphology. We showed that co-selection for RNAi against adenine phosphoryl transferase (APRT1) using 4-aminopyrazolpyrimidine (APP) could increase the efficacy of RNAi against reporter constructs, a useful tool that may facilitate improvements in future work. Thus, for many genes, RNAi provides a useful tool for studying Leishmania gene function with some unique advantages.

microbiology↗
bioRxiv2022

An expanded proteomic survey of the human parasite Leishmania major focusing on changes in null mutants of the Golgi GDP-Mannose/Fucose/Arabinopyranose transporter LPG2 or the mitochondrial fucosyltransferase FUT1

The trypanosomatid protozoan parasite Leishmania has a significant impact on human health globally. Understanding the pathways associated with virulence within this significant pathogen is critical for identifying novel vaccination and chemotherapy targets. Within this study we leverage an ultradeep proteomic approach to improve our understanding of two virulence associated genes in Leishmania, encoding the Golgi Mannose/Arabinopyranose/Fucose nucleotide-sugar transporter LPG2, and the mitochondrial fucosyltransferase FUT1. Using deep peptide fractionation followed by complementary fragmentation approaches with higher energy collisional dissociation (HCD) and Electron-transfer dissociation (ETD) allowed the identification of over 6500 proteins, nearly doubling the experimentally known Leishmania major proteome. This deep proteomic analysis revealed significant quantitative differences in both{Delta} lpg2- and{Delta} fut1s mutants with FUT1-dependent changes linked to marked alterations within mitochondrial associated proteins while LPG2-dependent changes impacted many pathways including the secretory pathway. While the FUT1 enzyme has been shown to fucosylate peptides in vitro, no evidence for protein fucosylation was identified within our ultradeep analysis nor did we observe fucosylated glycans within Leishmania glycopeptides isolated using HILIC enrichment. Combined this work provides a critical resource for the community on the observable Leishmania proteome as well as highlights phenotypic changes associated with LPG2 or FUT1 ablation which may guide the development of future therapeutics. ImportanceLeishmania is a widespread trypanosomatid protozoan parasite of humans with [~]12 million cases ranging from mild to fatal, and hundreds of millions asymptomatically infected. This work advances knowledge of the experimental proteome by nearly 2 fold, to more than 6500 proteins a great resource to investigators seeking to decode how this parasite is transmitted and causes disease, and new targets for therapeutic intervention. The ultradeep proteomics approach identified potential proteins underlying the persistence without pathology phenotype of deletion mutants of the Golgi nucleotide transporter LPG2, showing many alterations and several candidates. Studies of a rare deletion mutant of the mitochondrial fucosyltransferase FUT1 revealed changes underlying its strong mitochondrial dysfunction, but did not reveal examples of fucosylation of either peptides or N-glycans. This suggests this vital proteins elusive target(s) may be more complex than the methods used could detect, or may not be a protein, perhaps another glycoconjugate or glycolipid.

microbiology↗
bioRxiv2022

Quantitative single-cell analysis of Leishmania major amastigote differentiation demonstrates variably extended expression of the lipophosphoglycan (LPG) virulence factor in different host cell types

Immediately following their deposition into the mammalian host by an infected sand fly vector, Leishmania parasites encounter and are engulfed by a variety of cell types. From there, parasites may transit to other cell types, primarily macrophages or dendritic cells, where they replicate and induce pathology. During this time, Leishmania cells undergo a dramatic transformation from the motile non-replicating metacyclic stage to the non-motile replicative amastigote stage, a differentiative process that can be termed amastigogenesis. To follow this at the single cell level, we identified a suite of experimental landmarks delineating different stages of amastigogenesis qualitatively or quantitatively, including new uses of amastigote-specific markers that showed interesting cellular localizations at the anterior or posterior ends. We compared amastigogenesis in synchronous infections of peritoneal and bone-marrow derived macrophages (PEM, BMM) or dendritic cells (BMDC). Overall, the marker suite expression showed an orderly transition post-infection with similar kinetics between host cell types, with the emergence of several amastigote traits within 12 hours, followed by parasite replication after 24 hours, with parasites in BMM or BMDC initiating DNA replication more slowly. Lipophosphoglycan (LPG) is a Leishmania virulence factor that facilitates metacyclic establishment in host cells but declines in amastigotes. Whereas LPG expression was lost by parasites within PEM by 48 hours, >40% of the parasites infecting BMM or BMDC retained metacyclic-level LPG expression at 72 hr. Thus L. major may prolong LPG expression in different intracellular environments, thereby extending its efficacy in promoting infectivity in situ and during cell-to-cell transfer of parasites expressing this key virulence factor. Author SummaryLeishmaniasis caused by species of the trypanosomatid protozoan parasite Leishmania is an important widespread global health problem. Humans become infected by Leishmania following the bite of sand flies bearing the flagellated metacyclic promastigote stage, and the first 24-48 hours thereafter are critical to the outcome of infection. During this time, parasites are engulfed by several host cell types, where they differentiate into the rounded amastigote stage, adapted for intracellular survival and proliferation, with concomitant changes in metabolism and virulence factor expression. We developed a suite of markers that allowed us to monitor promastigote-to-amastigote differentiation (amastigogenesis) on a single-cell level. Two showed amastigote-specific expression and localized to the anterior or posterior regions. Our marker suite allowed us to chart the course of amastigogenesis in different host cell environments and to determine the timing of amastigote development relative to the initiation of parasite replication and the expression of the virulence factor lipophosphoglycan (LPG). We report that the amastigogenesis process follows a determined sequence of events that occurs prior to parasite replication. In contrast, parasites may respond to different host cell environments by prolonging LPG expression, thereby extending the duration of its pro-infectivity functions within or in transit between host cell destinations.

microbiology↗
bioRxiv2022

Sphingolipids protect ergosterol in the Leishmania major membrane from sterol-binding toxins

Susceptibility of Leishmania to the first line treatment amphotericin B remains poorly understood. Amphotericin B targets ergosterol, so one approach to improving drug efficacy and reducing side effects could be improving access to ergosterol. While the surface exposure of ergosterol in Leishmania is unknown, sterols in mammalian cells can be sheltered from sterol-binding agents by membrane components, including sphingolipids. Here, we tested the ability of the Leishmania major sphingolipids inositol phosphorylceramide (IPC), and ceramide to shelter ergosterol by preventing binding and cytotoxicity of the sterol-specific toxins streptolysin O and perfringolysin O using flow cytometry. In contrast to mammalian systems, Leishmania sphingolipids did not preclude toxin binding to sterols in the membrane. However, IPC interfered with cytotoxicity. Ceramide reduced perfringolysin O, but not streptolysin O, cytotoxicity in cells. Ceramide sensing was controlled by the toxin L3 loop. Ceramide was sufficient to protect L. major promastigotes from amphotericin B. We propose a mechanism whereby pore-forming toxins engage additional lipids like ceramide to determine the optimal environment to sustain pore formation. Thus, L. major offers a genetically tractable model organism for understanding toxin-membrane interactions. Furthermore, our findings suggest targeting ceramide may enhance the efficacy of ergosterol-targeting anti-leishmanial drugs. Abstract ImportanceLeishmaniasis is a neglected tropical disease with [~]1.5-2 million new cases and [~]70,000 deaths annually. One first-line treatment for leishmaniasis is liposomal amphotericin B, which is expensive and damages the kidneys. Cost and side effects can be minimized by improving efficacy. To improve efficacy, we must learn how amphotericins target--ergosterol--is protected by other components of Leishmania. The human ergosterol equivalent is protected by components called sphingolipids. We tested the ability of sphingolipids to protect ergosterol using pore-forming toxins. Pore-forming toxins use ergosterol to bind and kill Leishmania. Unlike human cells, toxins bound to ergosterol--indicating that they had access--when sphingolipids were present. However, sphingolipids protected Leishmania from toxins and amphotericin. Thus, Leishmania organizes sterol-protective components differently from humans. Further, toxins and Leishmania serve as a system to understand fundamental rules governing sterol-protecting component membrane organization. We can use this information to help improve drugs targeting sterols.

microbiology↗
bioRxiv2022

Inositol Phosphorlyceramide Synthase null Leishmania major (Δipcs-) are viable and virulent in animal infections where salvage of host sphingomyelin predominates

Many pathogens synthesize inositolphosphorylceramide (IPC) as the major sphingolipid (SL), differing from the mammalian host where sphingomyelin (SM) or more complex SLs predominate, and the divergence between IPCS and mammalian sphingolipid synthases has prompted interest as a potential drug target. However, in the trypanosomatid protozoan Leishmania, cultured insect stage promastigotes lacking de novo sphingolipid synthesis ({Delta}spt2-) and sphingolipids entirely survive and remain virulent, as infective amastigotes salvage host sphingolipids and continue to produce IPC. To further understand the role of IPC, we generated null IPCS mutants in L. major ({Delta}ipcs-). Unexpectedly and unlike fungi where IPCS is essential, {Delta}ipcs- was remarkably normal in culture and highly virulent in mouse infections. Both IPCS activity and IPC were absent in {Delta}ipcs- promastigotes and amastigotes, arguing against an alternative route of IPC synthesis. Notably, salvaged mammalian sphingomyelin (SM) was highly abundant in purified amastigotes from both WT and {Delta}ipcs-, and salvaged SLs could be further metabolized into IPC. SM was about 7-fold more abundant than IPC in WT amastigotes, establishing that SM is the dominant amastigote SL, thereby rendering IPC partially redundant. These data suggest that SM salvage likely plays key roles in the survival and virulence of both WT and {Delta}ipcs- parasites in the infected host, confirmation of which will require the development of methods or mutants deficient in host SL/SM uptake in the future. Our findings call into question the suitability of IPCS as a target for chemotherapy, instead suggesting that approaches targeting SM/SL uptake or catabolism may warrant further emphasis.

microbiology↗
bioRxiv2022

Genetic exchange in Leishmania is facilitated by IgM natural antibodies

Host factors mediating Leishmania genetic exchange are not well defined. Here, we demonstrate that IgM antibodies, but not IgG or IgA, facilitate parasite genetic hybridization in vitro and in vivo. IgM induces the gradual and transient formation of a structured parasite clump in a process essential for L. major and L. tropica hybridization in vitro. Parasite hybrids and 3-nucleated parasites were observed inside this structure, named the Leishmania mating clump. IgM was also required for or significantly increased Leishmania hybrid formation in vivo. At minimum, we observed a 12-fold increase in the proportion of hybrids recovered from sand flies provided a second blood meal containing IgM compared to controls. Notably, genetic backcross events in sand flies were only observed in the presence of IgM, and were reproducibly recovered, reinforcing the relevance of IgM for Leishmania genetic exchange in vivo. The in vitro and in vivo Leishmania crosses from these studies resulted in full genome hybrids. Leishmania co-option of a host antibody to facilitate mating in the insect vector establishes a new paradigm of parasite-host-vector coevolution that promotes parasite diversity and fitness through genetic exchange.

microbiology↗
bioRxiv2021

A broadly active fucosyltransferase LmjFUT1 whose mitochondrial localization and catalytic activity is essential in parasitic Leishmania major

Glycoconjugates play major roles in the infectious cycle of the trypanosomatid parasite Leishmania. While GDP-Fucose synthesis is essential (Guo et al 2017), fucosylated glycoconjugates have not been reported in Leishmania major. Four predicted fucosyltransferases appear conventionally targeted to the secretory pathway; SCA1/2 play a role in side-chain modifications of lipophosphoglycan, while gene deletion studies here showed that FUT2 and SCAL were not essential. Unlike most eukaryotic glycosyltransferases, the predicted 1-2 fucosyltransferase encoded by FUT1 localized to the mitochondrion. A quantitative plasmid segregation assay, expressing FUT1 from the multicopy episomal pXNG vector in a chromosomal null {Delta}fut1- background, established that FUT1 is essential. Similarly "plasmid shuffling" confirmed that both enzymatic activity and mitochondrial localization were required for viability, comparing import-blocked or catalytically inactive enzymes respectively. Enzymatic assays of tagged proteins expressed in vivo or of purified recombinant FUT1 showed it had a broad fucosyltransferase activity including glycan and peptide substrates. Unexpectedly a single rare {Delta}fut1-s segregant ({Delta}fut1s) was obtained in rich media, which showed severe growth defects accompanied by mitochondrial dysfunction and loss, all of which were restored upon FUT1 re-expression. Thus, FUT1 along with the similar Trypanosoma brucei enzyme TbFUT1 (Bandini et al 2021) joins the eukaryotic O-GlcNAc transferase isoform as one of the few glycosyltransferases acting within the mitochondrion. Trypanosomatid mitochondrial FUT1s may offer a facile system for probing mitochondrial glycosylation in a simple setting and their essentiality renders it an attractive target for chemotherapy of these serious human pathogens. Significance StatementAbundant surface glycoconjugates play key roles in the infectious cycle of protozoan parasites including Leishmania. Through defining biosynthetic pathways we identified a fucosyltransferase FUT1 that was localized to the parasite mitochondrion, an atypical compartment for glycosyltransferases. FUT1 was essential for normal growth, requiring both mitochondrial localization and enzymatic activity. Loss of FUT1 in a unique segregant showed extensive mitochondrial defects. Enzymatic tests showed FUT1 could fucosylate glycan and peptide substrates in vitro, although as yet the native substrate is unknown. Trypanosomatid mitochondrial FUT1s may offer a facile system in the future for probing mitochondrial glycosylation in a setting uncomplicated by multiple isoforms targeted to diverse compartments, and its essentiality renders it an attractive target for chemotherapy of these deadly parasites.

microbiology↗
bioRxiv2020

Interplay of the Trypanosome Lytic Factor and innate immune cells in the resolution of cutaneous Leishmania infection

Trypanosome Lytic Factor (TLF) is a primate-specific high-density lipoprotein complex that contains APOL1, the lytic component. Human TLF confers sterile immunity to many animal-infective extracellular Trypanosoma Ssp, which have been extensively investigated. Here, we have dissected the underappreciated role of TLF and neutrophils against intracellular Leishmania in intradermal infection. Our data show that mice producing human or baboon TLF have reduced parasite burdens when infected intradermally with metacyclic promastigotes of L. major. This TLF-mediated reduction in parasite burden was lost in neutrophil-depleted TLF mice, suggesting that early recruitment of neutrophils is required for TLF-mediated killing of L. major. Neutrophils and macrophages are the predominant phagocytes recruited to the site of infection. Our data show that acidification of the macrophage phagosome is essential for TLF-mediated lysis of metacyclic promastigotes. In vitro we find that only metacyclic promastigotes co-incubated with TLF in an acidic milieu were lysed. However, amastigotes were not killed by TLF at any pH. These findings correlated with binding experiments, revealing that labeled TLF binds specifically to the surface of metacyclic promastigotes, but not to amastigotes. During differentiation to the amastigote stage, the parasites shed their surface glycoconjugates. Metacyclic promastigotes of L. major deficient in the synthesis of surface glycoconjugates (lpg1- and lpg5A-/lpg5B-) were partially resistant to TLF lysis. We propose that TLF binds to the outer surface glycoconjugates of metacyclic promastigotes, whereupon APOL1 forms a pH-gated ion channel in the plasma membrane, resulting in osmotic lysis. We hypothesize that resistance to TLF requires shedding of the surface glycoconjugates, which occurs upon phagocytosis by immune cells. Author SummaryLeishmaniasis is a common term used for disease caused by parasites of the genus Leishmania. Depending on the parasite species and the clinical outcome of the disease, leishmaniasis can be divided into cutaneous, muco-cutaneous and visceral. Of the three, cutaneous leishmaniasis is the most common form, which is usually characterized by a localized lesion due to the infection of immune cells, primarily macrophages of the dermis and local lymph nodes. Sometimes, infected individuals can remain asymptomatic and do not show visible lesions. Moreover, the time between the infection and appearance of lesions are also variable and range from a few weeks to months and a few years in some cases. This subclinical stage of leishmaniasis depends on a variety of factors: parasite virulence, infectious dose, and host immune response. Therefore, it is important to understand the host-parasite interaction and its role in the clinical outcome of the disease. Here, we analyze the interaction between a cutaneous strain of Leishmania and a host innate immune factor called Trypanosome Lytic Factor (TLF). TLF is a type of High-Density Lipoprotein (HDL) complex that circulates in our plasma. TLF kills extracellular African Trypanosomes by lysing the parasites. The lytic ability of TLF is due to the primate specific protein APOL1 that forms pH gated ion channels. APOL1 inserts into biological membranes at acidic pH and forms a closed ion-channel that opens when the membrane associated APOL1 is exposed to neutral pH. Using transgenic mice producing primate TLF, we show both human and baboon TLFs ameliorate cutaneous Leishmania major infection. The reduction in parasite burden correlated with: 1. infectious dose of metacyclic promastigotes and 2. the concentration of circulating TLF in mouse plasma. The early recruitment of neutrophils at the site of infection was required for the reduction of parasite burden by TLF. Macrophages, another major cell that phagocytoses metacyclic promastigotes at the site of infection require an acidified phagosome for TLF mediated killing of L. major. The acidification step is also essential for TLF mediated lysis of axenic metacyclic promastigotes of Leishmania in vitro. The susceptibility of metacyclic promastigotes to TLF mediated lysis is governed by the surface glycoconjugates of Leishmania. We find that surface glycoconjugate deficient Leishmania are resistant to TLF mediated killing. Based on these data, we conclude that the shedding of surface glycoconjugates while transitioning from metacyclic promastigotes to amastigotes results in parasite resistance to TLF mediated lysis. Whether TLF is effective at killing metacyclic promastigotes of other experimentally tractable Leishmania sp. such as L. infantum, and L. donovani, which have slightly different surface glycoconjugate structures is yet to be tested. Our data raise the possibility that TLF can have lytic activity against a broad range of pathogens such as bacteria, viruses, fungi and parasites with surface glycoconjugates that transit through intracellular acidic compartments.

microbiology↗
bioRxiv2019

An essential GDP-Fuc: β-D-Gal α-1,2-fucosyltransferase is located in the mitochondrion of Trypanosoma brucei

Fucose is a common component of eukaryotic cell-surface glycoconjugates, generally added by Golgi-resident fucosyltransferases. Whereas fucosylated glycoconjugates are rare in kinetoplastids, the biosynthesis of the nucleotide sugar GDP-Fuc has been shown to be essential in Trypanosoma brucei. Here we show that the single identifiable T. brucei fucosyltransferase (TbFUT1) is a GDP-Fuc: {beta}-D-galactose -1,2-fucosyltransferase with an apparent preference for a Gal{beta}1,3GlcNAc{beta}1-O-R acceptor motif. Conditional null mutants of TbFUT1 demonstrated that it is essential for both the mammalian-infective bloodstream form and the insect vector-dwelling procyclic form. Unexpectedly, TbFUT1 was localized in the mitochondrion of T. brucei and found to be required for mitochondrial function in bloodstream form trypanosomes. Finally, the TbFUT1 gene was able to complement a Leishmania major mutant lacking the homologous fucosyltransferase gene (Guo et al., 2021). Together these results suggest that kinetoplastids possess an unusual, conserved and essential mitochondrial fucosyltransferase activity that may have therapeutic potential across trypanosomatids.

microbiology↗
bioRxiv2018

Concentration of 2’C-methyladenosine triphosphate by Leishmania guyanensis enables specific inhibition of Leishmania RNA virus 1 via its RNA polymerase

Leishmania is a widespread trypanosomatid protozoan parasite causing significant morbidity and mortality in humans. The endobiont dsRNA virus Leishmania RNA virus 1 (LRV1) chronically infects some strains, where it increases parasite numbers and virulence in murine leishmaniasis models, and correlates with increased treatment failure in human disease. Previously, we reported that 2-C-methyladenosine (2CMA) potently inhibited LRV1 in Leishmania guyanensis (Lgy) and L. braziliensis, leading to viral eradication at concentrations above 10 {micro}M. Here we probed the cellular mechanisms of 2CMA inhibition, involving metabolism, accumulation and inhibition of the viral RNA dependent RNA polymerase (RDRP). Activation to 2CMA triphosphate (2CMATP) was required, as 2CMA showed no inhibition of RDRP activity from virions purified on cesium chloride gradients. In contrast, 2CMA-TP showed IC50s ranging from 150 to 910 {micro}M, depending on the CsCl density of the virion (empty, ssRNA- and dsRNA-containing). Lgy parasites incubated in vitro with 10 {micro}M 2CMA accumulated 2CMA-TP to 410 {micro}M, greater than the most sensitive RDRP IC50 measured. Quantitative modeling showed good agreement between the degree of LRV1 RDRP inhibition and LRV1 levels. These results establish that 2CMA activity is due to its conversion to 2CMA-TP, which accumulates to levels that inhibit RDRP and cause LRV1 loss. This attests to the impact of the Leishmania purine uptake and metabolism pathways, which allow even a weak RDRP inhibitor to effectively eradicate LRV1 at micromolar concentrations. Future RDRP inhibitors with increased potency may have potential therapeutic applications for ameliorating the increased Leishmania pathogenicity conferred by LRV1.

microbiology↗