Revealing the mystery of metabolic adaptations using a genome scale model of Leishmania infantum

The immunomicrotope of Leishmania control and persistence

Leishmania is an intracellular protozoan transmitted by sand fly vectors; it causes cutaneous, mucocutaneous, or visceral disease. Its growth and survival are impeded by type 1 T helper cell responses, which entail interferon (IFN)-γ-mediated macrophage activation. Leishmania partially escapes this host defense by triggering immune cell and cytokine responses that favor parasite replication rather than killing. Novel methods for in situ analyses have revealed that the pathways of immune control and microbial evasion are strongly influenced by the tissue context, the micro milieu factors, and the metabolism at the site of infection, which we collectively term the 'immunomicrotope'. Understanding the components and the impact of the immunomicrotope will enable the development of novel strategies for the treatment of chronic leishmaniasis.

An anti-leishmanial compound 4',7-dihydroxyflavone elicits ROS-mediated apoptosis-like death in Leishmania parasite

The treatment for leishmaniasis is currently plagued by side effects such as toxicity and the emergence of drug resistance to the available repertoire of drugs, as well as the expense of these drugs. Considering such rising concerns, we report the anti-leishmanial activity and mechanism of a flavone compound 4',7-dihydroxyflavone (TI 4). Four flavanoids were initially screened for anti-leishmanial activity and cytotoxicity. The results showed that the compound TI 4 exhibited higher activity and selectivity index at the same time as maintaining low cytotoxicity. Preliminary microscopic studies and fluorescence-activated cell sorting analysis reported that the parasite underwent apoptosis on TI 4 treatment. Further in-depth studies revealed high reactive oxygen species (ROS) production and thiol levels in the parasites, suggesting ROS-mediated apoptosis in the parasites upon TI 4 treatment. Other apoptotic indicators such as intracellular Ca²⁺ and mitochondrial membrane potential also indicated the onset of apoptosis in the treated parasites. The mRNA expression levels signified that the redox metabolism genes were upregulated by two-fold along with the apoptotic genes. In summary, the use of TI 4 on Leishmania parasites induces ROS-mediated apoptosis; therefore, the compound has immense potential to be an anti-leishmanial drug. However, in vivo studies would be required to ascertain its safety and efficacy before we can exploit the compound against the growing leishmaniasis crisis.

Delineating infection strategies of Leishmania donovani secretory proteins in Human through host-pathogen protein Interactome prediction

Interactions of Leishmania donovani secretory virulence factors with the host proteins and their interplay during the infection process in humans is poorly studied in Visceral Leishmaniasis. Lack of a holistic study of pathway level de-regulations caused due to these virulence factors leads to a poor understanding of the parasite strategies to subvert the host immune responses, secure its survival inside the host and further the spread of infection to the visceral organs. In this study, we propose a computational workflow to predict host-pathogen protein interactome of L.donovani secretory virulence factors with human proteins combining sequence-based Interolog mapping and structure-based Domain Interaction mapping techniques. We further employ graph theoretical approaches and shortest path methods to analyze the interactome. Our study deciphers the infection paths involving some unique and understudied disease-associated signaling pathways influencing the cellular phenotypic responses in the host. Our statistical analysis based in silico knockout study unveils for the first time UBC, 1433Z and HS90A mediator proteins as potential immunomodulatory candidates through which the virulence factors employ the infection paths. These identified pathways and novel mediator proteins can be effectively used as possible targets to control and modulate the infection process further aiding in the treatment of Visceral Leishmaniasis.

Determinants of Innate Immunity in Visceral Leishmaniasis and Their Implication in Vaccine Development

Leishmaniasis is endemic to the tropical and subtropical regions of the world and is transmitted by the bite of an infected sand fly. The multifaceted interactions between Leishmania, the host innate immune cells, and the adaptive immunity determine the severity of pathogenesis and disease development. Leishmania parasites establish a chronic infection by subversion and attenuation of the microbicidal functions of phagocytic innate immune cells such as neutrophils, macrophages and dendritic cells (DCs). Other innate cells such as inflammatory monocytes, mast cells and NK cells, also contribute to resistance and/or susceptibility to Leishmania infection. In addition to the cytokine/chemokine signals from the innate immune cells, recent studies identified the subtle shifts in the metabolic pathways of the innate cells that activate distinct immune signal cascades. The nexus between metabolic pathways, epigenetic reprogramming and the immune signaling cascades that drive the divergent innate immune responses, remains to be fully understood in Leishmania pathogenesis. Further, development of safe and efficacious vaccines against Leishmaniasis requires a broader understanding of the early interactions between the parasites and innate immune cells. In this review we focus on the current understanding of the specific role of innate immune cells, the metabolomic and epigenetic reprogramming and immune regulation that occurs during visceral leishmaniasis, and the strategies used by the parasite to evade and modulate host immunity. We highlight how such pathways could be exploited in the development of safe and efficacious Leishmania vaccines.

Deletion of Glutamine Synthetase Gene Disrupts the Survivability and Infectivity of Leishmania donovani

Glutamine synthetase (GS) is one of the most important metabolic enzymes which catalyzes ligation of glutamate and ammonia to form glutamine. Previous studies from our lab had revealed significant differences in parasite and host GS enzyme which warranted us to further work on its relevance in parasite. To analyze glutamine synthetase function in Leishmania, we generated GS overexpressors and knockout mutants and evaluated their ability to grow in vitro in monocyte differentiated macrophage and in vivo by infections in BALB/c mice. GS knocked out strain showed significant growth retardation with delayed cell cycle progression and morphological alteration. Null mutants exhibited attenuated infectivity both in in vitro and in vivo experiments and the effect was reverted back when infected with GS complemented parasites. This indicated that the alterations in phenotype observed were indeed due to GS knockout. GS knockout also made the parasite increasingly sensitive to Miltefosine. Detailed investigation of mode of parasite death upon Miltefosine treatment by dual staining with Annexin-V conjugated FITC and propidium iodide, pointed towards apoptotic or necrotic mode of cell death. This is the first report to confirm that GS is essential for the survivability and infectivity of Leishmania donovani, and can be exploited as a potential drug-target.

Nutrition, malnutrition, and leishmaniasis

Leishmaniasis is a vector-borne infectious disease with a long history of infecting humans and other animals. It is a known emerging or resurging disease. The host nutritional state has an indispensable role in defense against pathogens. The host defense system disorganization as a result of undernutrition is responsible for asymptomatic infections and even severe diseases. Host susceptibility and pathophysiologic severity to infection can be aggravated owing to undernourishment in a number of pathways, and infection also may aggravate preexisting poor nutrition or further increase host susceptibility. This study suggests that there may be some relationship between malnutrition and the endemicity of the parasite. The susceptibility to and severity of leishmanial infection can be altered by the body weight and serum levels of micronutrients. Nutrition not only affects the vulnerability of the host but also may affect the desire of sandfly to bite a specific host. Apart from host defense mechanism, nutritional stress also greatly influences vector competence and host-seeking behavior, especially during larvae development. The host and sandfly vector nutritional states could also influence the evolution of the parasite. It is essential to elucidate the roles that diets and nutrition play in the leishmanial life cycle. The aim of this article is to review the influences of nutrition and diets on the host susceptibility and severity of infection, preemptive and therapeutic strategy feedback, parasite evolution, and vector competence.

Integrative Computational Framework for Understanding Metabolic Modulation in Leishmania

Background: The integration of computational and mathematical approaches is used to provide a key insight into the biological systems. Through systems biology approaches we seek to find detailed and more robust information on Leishmanial metabolic network. Forman/Forman-Ricci curvature measures were applied to identify important nodes in the network(s). This was followed by flux balance analysis (FBA) to decipher important drug targets. Results: Our results revealed several key high curvature nodes (metabolites) belonging to common yet crucial metabolic networks, thus, maintaining the integrity of the network which signifies its robustness. Further analysis revealed the presence of some of these metabolites, MGO, in redox metabolism of the parasite. Being a component in the glyoxalase pathway and highly cytotoxic, we further attempted to study the outcome of the deletion of the key enzyme (GLOI) mainly involved in the neutralization of MGO by utilizing FBA. The model and the objective function kept as simple as possible demonstrated an interesting emergent behavior. The non-functional GLOI in the model contributed to "zero" flux which signifies the key role of GLOI as a rate limiting enzyme. This has led to several fold increase production of MGO, thereby, causing an increased level of MGO•- generation. Conclusions: The integrated computational approaches have deciphered GLOI as a potential target both from curvature measures as well as FBA which could further be explored for kinetic modeling by implying various redox-dependent constraints on the model. Furthermore, a constraint-based FBA on a larger model could further be explored to get broader picture to understand the exact underlying mechanisms. Designing various in vitro experimental perspectives could churn the therapeutic importance of GLOI.

Efflux pumps and antimicrobial resistance: Paradoxical components in systems genomics

Efflux pumps play a major role in the increasing antimicrobial resistance rendering a large number of drugs of no use. Large numbers of pathogens are becoming multidrug resistant due to inadequate dosage and use of the existing antimicrobials. This leads to the need for identifying new efflux pump inhibitors. Design of novel targeted therapies using inherent complexity involved in the biological network modeling has gained increasing importance in recent times. The predictive approaches should be used to determine antimicrobial activities with high pathogen specificity and microbicidal potency. Antimicrobial peptides, which are part of our innate immune system, have the ability to respond to infections and have gained much attention in making resistant strain sensitive to existing drugs. In this review paper, we outline evidences linking host-directed therapy with the efflux pump activity to infectious disease.

Evolutionary Perspectives of Genotype-Phenotype Factors in Leishmania Metabolism

The sandfly midgut and the human macrophage phagolysosome provide antagonistic metabolic niches for the endoparasite Leishmania to survive and populate. Although these environments fluctuate across developmental stages, the relative changes in both these environments across parasite generations might remain gradual. Such environmental restrictions might endow parasite metabolism with a choice of specific genotypic and phenotypic factors that can constrain enzyme evolution for successful adaptation to the host. With respect to the available cellular information for Leishmania species, for the first time, we measure the relative contribution of eight inter-correlated predictors related to codon usage, GC content, gene expression, gene length, multi-functionality, and flux-coupling potential of an enzyme on the evolutionary rates of singleton metabolic genes and further compare their effects across three Leishmania species. Our analysis reveals that codon adaptation, multi-functionality, and flux-coupling potential of an enzyme are independent contributors of enzyme evolutionary rates, which can together explain a large variation in enzyme evolutionary rates across species. We also hypothesize that a species-specific occurrence of duplicated genes in novel subcellular locations can create new flux routes through certain singleton flux-coupled enzymes, thereby constraining their evolution. A cross-species comparison revealed both common and species-specific genes whose evolutionary divergence was constrained by multiple independent factors. Out of these, previously known pharmacological targets and virulence factors in Leishmania were identified, suggesting their evolutionary reasons for being important survival factors to the parasite. All these results provide a fundamental understanding of the factors underlying adaptive strategies of the parasite, which can be further targeted.

Integrative Approaches to Understand the Mastery in Manipulation of Host Cytokine Networks by Protozoan Parasites with Emphasis on Plasmodium and Leishmania Species

Diseases by protozoan pathogens pose a significant public health concern, particularly in tropical and subtropical countries, where these are responsible for significant morbidity and mortality. Protozoan pathogens tend to establish chronic infections underscoring their competence at subversion of host immune processes, an important component of disease pathogenesis and of their virulence. Modulation of cytokine and chemokine levels, their crosstalks and downstream signaling pathways, and thereby influencing recruitment and activation of immune cells is crucial to immune evasion and subversion. Many protozoans are now known to secrete effector molecules that actively modulate host immune transcriptome and bring about alterations in host epigenome to alter cytokine levels and signaling. The complexity of multi-dimensional events during interaction of hosts and protozoan parasites ranges from microscopic molecular levels to macroscopic ecological and epidemiological levels that includes disrupting metabolic pathways, cell cycle (Toxoplasma and Theileria sp.), respiratory burst, and antigen presentation (Leishmania spp.) to manipulation of signaling hubs. This requires an integrative systems biology approach to combine the knowledge from all these levels to identify the complex mechanisms of protozoan evolution via immune escape during host-parasite coevolution. Considering the diversity of protozoan parasites, in this review, we have focused on Leishmania and Plasmodium infections. Along with the biological understanding, we further elucidate the current efforts in generating, integrating, and modeling of multi-dimensional data to explain the modulation of cytokine networks by these two protozoan parasites to achieve their persistence in host via immune escape during host-parasite coevolution.

The role of membrane transporters in Leishmania virulence

Leishmania are parasitic protozoa which infect humans and cause severe morbidity and mortality. Leishmania parasitise as extracellular promastigotes in the insect vector and as intracellular amastigotes in the mammalian host. Cycling between hosts involves implementation of stringent and co-ordinated responses to shifting environmental conditions. One of the key dynamic aspects of Leishmania biology is substrate acquisition and metabolism. Genomic analyses have revealed that Leishmania encode many putative membrane transporters, many of which are differentially expressed during the parasite life cycle. Only a small fraction of these transporters, however, have been functionally characterised. Currently, most information is available about nutrient transporters, mainly involved in carbohydrate, amino acid, nucleobase and nucleoside, cofactor, and ion acquisition. Several have apparent roles in Leishmania virulence and will be discussed in this perspective.