An evolutionary analysis of trypanosomatid GP63 proteases

Variation in Leishmania chemokine suppression driven by diversification of the GP63 virulence factor

Leishmaniasis is a neglected tropical disease with diverse outcomes ranging from self-healing lesions, to progressive non-healing lesions, to metastatic spread and destruction of mucous membranes. Although resolution of cutaneous leishmaniasis is a classic example of type-1 immunity leading to self-healing lesions, an excess of type-1 related inflammation can contribute to immunopathology and metastatic spread. Leishmania genetic diversity can contribute to variation in polarization and robustness of the immune response through differences in both pathogen sensing by the host and immune evasion by the parasite. In this study, we observed a difference in parasite chemokine suppression between the Leishmania (L.) subgenus and the Viannia (V.) subgenus, which is associated with severe immune-mediated pathology such as mucocutaneous leishmaniasis. While Leishmania (L.) subgenus parasites utilize the virulence factor and metalloprotease glycoprotein-63 (gp63) to suppress the type-1 associated host chemokine CXCL10, L. (V.) panamensis did not suppress CXCL10. To understand the molecular basis for the inter-species variation in chemokine suppression, we used in silico modeling to identify a putative CXCL10-binding site on GP63. The putative CXCL10 binding site is in a region of gp63 under significant positive selection, and it varies from the L. major wild-type sequence in all gp63 alleles identified in the L. (V.) panamensis reference genome. Mutating wild-type L. (L.) major gp63 to the L. (V.) panamensis sequence at the putative binding site impaired cleavage of CXCL10 but not a non-specific protease substrate. Notably, Viannia clinical isolates confirmed that L. (V.) panamensis primarily encodes non-CXCL10-cleaving gp63 alleles. In contrast, L. (V.) braziliensis has an intermediate level of activity, consistent with this species having more equal proportions of both alleles. Our results demonstrate how parasite genetic diversity can contribute to variation in immune responses to Leishmania spp. infection that may play critical roles in the outcome of infection.

Leishmaniasis is a neglected tropical disease caused by Leishmania parasites and spread by the bites of infected sand flies. Most cases of leishmaniasis present as self-healing sores that are resolved by a balanced immune response. Other cases of leishmaniasis involve spread to sites distant from the original bite, including damage of the inner surfaces of the mouth and nose. These cases of leishmaniasis involve an excessive immune response. Leishmania parasites produce virulence factor proteins, such as GP63, to trick the immune system into mounting a weaker response. GP63 specifically degrades signaling proteins that attract and activate certain immune cells. Here, we demonstrate that Leishmania parasite species have evolved to differ in their ability to degrade signaling proteins. In Leishmania species known to cause more immune-mediated tissue damage, the GP63 virulence factor has evolved to not degrade specific immune signaling proteins, thus attracting, and activating more immune cells. Our results demonstrate how diversity among Leishmania parasite species can contribute to variation in immune responses that may play critical roles in the outcome of infection.

Update on relevant trypanosome peptidases: Validated targets and future challenges

Trypanosoma cruzi, the agent of the American Trypanosomiasis, Chagas disease, and Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, the agents of Sleeping sickness (Human African Trypanosomiasis, HAT), as well as Trypanosoma brucei brucei, the agent of the cattle disease nagana, contain cysteine, serine, threonine, aspartyl and metallo peptidases. The most abundant among these enzymes are the cysteine proteases from the Clan CA, the Cathepsin L-like cruzipain and rhodesain, and the Cathepsin B-like enzymes, which have essential roles in the parasites and thus are potential targets for chemotherapy. In addition, several other proteases, present in one or both parasites, have been characterized, and some of them are also promising candidates for the developing of new drugs. Recently, new inhibitors, with good selectivity for the parasite proteasomes, have been described and are very promising as lead compounds for the development of new therapies for these neglected diseases. This article is part of a Special Issue entitled: "Play and interplay of proteases in health and disease".

Repositioning of HIV Aspartyl Peptidase Inhibitors for Combating the Neglected Human Pathogen Trypanosoma cruzi

Chagas disease, caused by the flagellate parasite Trypanosoma cruzi, is a wellknown neglected tropical disease. This parasitic illness affects 6-7 million people and can lead to severe myocarditis and/or complications of the digestive tract. The changes in its epidemiology facilitate co-infection with the Human Immunodeficiency Virus (HIV), making even more difficult the diagnosis and prognosis. The parasitic infection is reactivated in T. cruzi/HIV co-infection, with the appearance of unusual manifestations in the chronic phase and the exacerbation of classical clinical signs. The therapeutic arsenal to treat Chagas disease, in all its clinical forms, is restricted basically to two drugs, benznidazole and nifurtimox. Both drugs are extremely toxic and the therapeutic efficacy is still unclear, making the clinical treatment a huge issue to be solved. Therefore, it seems obvious the necessity of new tangible approaches to combat this illness. In this sense, the repositioning of approved drugs appears as an interesting and viable strategy. The discovery of Human Immunodeficiency Virus Aspartyl Peptidase Inhibitors (HIV-PIs) represented a milestone in the treatment of Acquired Immune Deficiency Syndrome (AIDS) and, concomitantly, a marked reduction in both the incidence and prevalence of important bacterial, fungal and parasitic co-infections was clearly observed. Taking all these findings into consideration, the present review summarizes the promising and beneficial data concerning the effects of HIV-PIs on all the evolutionary forms of T. cruzi and in important steps of the parasite's life cycle, which highlight their possible application as alternative drugs to treat Chagas disease.

Exoproteome profiling of Trypanosoma cruzi during amastigogenesis early stages

Chagas disease is caused by the protozoan Trypanosoma cruzi, affecting around 8 million people worldwide. After host cell invasion, the infective trypomastigote form remains 2–4 hours inside acidic phagolysosomes to differentiate into replicative amastigote form. In vitro acidic-pH-induced axenic amastigogenesis was used here to study this step of the parasite life cycle. After three hours of trypomastigote incubation in amastigogenesis promoting acidic medium (pH 5.0) or control physiological pH (7.4) medium samples were subjected to three rounds of centrifugation followed by ultrafiltration of the supernatants. The resulting exoproteome samples were trypsin digested and analysed by nano flow liquid chromatography coupled to tandem mass spectrometry. Computational protein identification searches yielded 271 and 483 protein groups in the exoproteome at pH 7.4 and pH 5.0, respectively, with 180 common proteins between both conditions. The total amount and diversity of proteins released by parasites almost doubled upon acidic incubation compared to control. Overall, 76.5% of proteins were predicted to be secreted by classical or non-classical pathways and 35.1% of these proteins have predicted transmembrane domains. Classical secretory pathway analysis showed an increased number of mucins and mucin-associated surface proteins after acidic incubation. However, the number of released trans-sialidases and surface GP63 peptidases was higher at pH 7.4. Trans-sialidases and mucins are anchored to the membrane and exhibit an enzyme-substrate relationship. In general, mucins are glycoproteins with immunomodulatory functions in Chagas disease, present mainly in the epimastigote and trypomastigote surfaces and could be enzymatically cleaved and released in the phagolysosome during amastigogenesis. Moreover, evidence for flagella discard during amastigogenesis are addressed. This study provides the first comparative analysis of the exoproteome during amastigogenesis, and the presented data evidence the dynamism of its profile in response to acidic pH-induced differentiation.

In silico characterization of multiple genes encoding the GP63 virulence protein from Leishmania braziliensis: identification of sources of variation and putative roles in immune evasion

Background

The leishmaniasis are parasitic diseases caused by protozoans of the genus Leishmania, highly divergent eukaryotes, characterized by unique biological features. To survive in both the mammalian hosts and insect vectors, these pathogens make use of a number of mechanisms, many of which are associated with parasite specific proteases. The metalloprotease GP63, the major Leishmania surface antigen, has been found to have multiple functions required for the parasite’s survival. GP63 is encoded by multiple genes and their copy numbers vary considerably between different species and are increased in those from the subgenus Viannia, including L. braziliensis.

Results

By comparing multiple sequences from Leishmania and related organisms this study sought to characterize paralogs in silico, evaluating their differences and similarities and the implications for the GP63 function. The Leishmania GP63 genes are encoded on chromosomes 10, 28 and 31, with the genes from the latter two chromosomes more related to genes found in insect or plant parasites. Those from chromosome 10 have experienced independent expansions in numbers in Leishmania, especially in L. braziliensis. These could be clustered in three groups associated with different mRNA 3′ untranslated regions as well as distinct C-terminal ends for the encoded proteins, with presumably distinct expression patterns and subcellular localizations. Sequence variations between the chromosome 10 genes were linked to intragenic recombination events, mapped to the external surface of the proteins and predicted to be immunogenic, implying a role against the host immune response.

Conclusions

Our results suggest a greater role for the sequence variation found among the chromosome 10 GP63 genes, possibly related to the pathogenesis of L. braziliensis and closely related species within the mammalian host. They also indicate different functions associated to genes mapped to different chromosomes. For the chromosome 10 genes, variable subcellular localizations were found to be most likely associated with multiple functions and target substrates for this versatile protease.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5465-z) contains supplementary material, which is available to authorized users.

The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees

Trypanosomatids (Trypanosomatidae, Kinetoplastida) are flagellated protozoa containing many parasites of medical or agricultural importance. Among those, Crithidia bombi and C. expoeki, are common parasites in bumble bees around the world, and phylogenetically close to Leishmania and Leptomonas. They have a simple and direct life cycle with one host, and partially castrate the founding queens greatly reducing their fitness. Here, we report the nuclear genome sequences of one clone of each species, extracted from a field-collected infection. Using a combination of Roche 454 FLX Titanium, Pacific Biosciences PacBio RS, and Illumina GA2 instruments for C. bombi, and PacBio for C. expoeki, we could produce high-quality and well resolved sequences. We find that these genomes are around 32 and 34 MB, with 7,808 and 7,851 annotated genes for C. bombi and C. expoeki, respectively-which is somewhat less than reported from other trypanosomatids, with few introns, and organized in polycistronic units. A large fraction of genes received plausible functional support in comparison primarily with Leishmania and Trypanosoma. Comparing the annotated genes of the two species with those of six other trypanosomatids (C. fasciculata, L. pyrrhocoris, L. seymouri, B. ayalai, L. major, and T. brucei) shows similar gene repertoires and many orthologs. Similar to other trypanosomatids, we also find signs of concerted evolution in genes putatively involved in the interaction with the host, a high degree of synteny between C. bombi and C. expoeki, and considerable overlap with several other species in the set. A total of 86 orthologous gene groups show signatures of positive selection in the branch leading to the two Crithidia under study, mostly of unknown function. As an example, we examined the initiating glycosylation pathway of surface components in C. bombi, finding it deviates from most other eukaryotes and also from other kinetoplastids, which may indicate rapid evolution in the extracellular matrix that is involved in interactions with the host. Bumble bees are important pollinators and Crithidia-infections are suspected to cause substantial selection pressure on their host populations. These newly sequenced genomes provide tools that should help better understand host-parasite interactions in these pollinator pathogens.

Deep sequencing of the Trypanosoma cruzi GP63 surface proteases reveals diversity and diversifying selection among chronic and congenital Chagas disease patients

Background

Chagas disease results from infection with the diploid protozoan parasite Trypanosoma cruzi. T. cruzi is highly genetically diverse, and multiclonal infections in individual hosts are common, but little studied. In this study, we explore T. cruzi infection multiclonality in the context of age, sex and clinical profile among a cohort of chronic patients, as well as paired congenital cases from Cochabamba, Bolivia and Goias, Brazil using amplicon deep sequencing technology.

Methodology/ Principal Findings

A 450bp fragment of the trypomastigote TcGP63I surface protease gene was amplified and sequenced across 70 chronic and 22 congenital cases on the Illumina MiSeq platform. In addition, a second, mitochondrial target—ND5—was sequenced across the same cohort of cases. Several million reads were generated, and sequencing read depths were normalized within patient cohorts (Goias chronic, n = 43, Goias congenital n = 2, Bolivia chronic, n = 27; Bolivia congenital, n = 20), Among chronic cases, analyses of variance indicated no clear correlation between intra-host sequence diversity and age, sex or symptoms, while principal coordinate analyses showed no clustering by symptoms between patients. Between congenital pairs, we found evidence for the transmission of multiple sequence types from mother to infant, as well as widespread instances of novel genotypes in infants. Finally, non-synonymous to synonymous (dn:ds) nucleotide substitution ratios among sequences of TcGP63Ia and TcGP63Ib subfamilies within each cohort provided powerful evidence of strong diversifying selection at this locus.

Conclusions/Significance

Our results shed light on the diversity of parasite DTUs within each patient, as well as the extent to which parasite strains pass between mother and foetus in congenital cases. Although we were unable to find any evidence that parasite diversity accumulates with age in our study cohorts, putative diversifying selection within members of the TcGP63I gene family suggests a link between genetic diversity within this gene family and survival in the mammalian host.

Trypanosoma cruzi, the causal agent of Chagas disease in Latin America, infects several million people in some of the most economically deprived regions of Latin America. T. cruzi infection is lifelong and has a variable prognosis: some patients never exhibit symptoms while others experience debilitating and fatal complications. Available data suggest that parasite genetic diversity within and among disease foci can be exceedingly high. However, little is know about the frequency of multiple genotype infections in humans, as well as their distribution among different age classes and possible impact on disease outcome. In this study we develop a next generation amplicon deep sequencing approach to profile parasite diversity within chronic Chagas Disease patients from Bolivia and Brazil. We were also able to compare parasite genetic diversity present in eleven congenitally infants with parasite genetic diversity present in their mothers. We did not detect any specific association between the number and diversity of parasite genotypes in each patient with their age, sex or disease status. We were, however, able to detect the transmission of multiple parasite genotypes between mother and foetus. Furthermore, we also detected powerful evidence for natural selection at the antigenic locus we targeted, suggesting a possible interaction with the host immune system.

The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite

Leishmaniasis is an infectious disease caused by Leishmania species. Leishmania amazonensis is a New World Leishmania species belonging to the Mexicana complex, which is able to cause all types of leishmaniasis infections. The L. amazonensis reference strain MHOM/BR/1973/M2269 was sequenced identifying 8,802 codifying sequences (CDS), most of them of hypothetical function. Comparative analysis using six Leishmania species showed a core set of 7,016 orthologs. L. amazonensis and Leishmania mexicana share the largest number of distinct orthologs, while Leishmania braziliensis presented the largest number of inparalogs. Additionally, phylogenomic analysis confirmed the taxonomic position for L. amazonensis within the “Mexicana complex”, reinforcing understanding of the split of New and Old World Leishmania. Potential non-homologous isofunctional enzymes (NISE) were identified between L. amazonensis and Homo sapiens that could provide new drug targets for development.

Genome evolution in trypanosomatid parasites

A decade of genome sequencing has transformed our understanding of how trypanosomatid parasites have evolved and provided fresh impetus to explaining the origins of parasitism in the Kinetoplastida. In this review, I will consider the many ways in which genome sequences have influenced our view of genomic reduction in trypanosomatids; how species-specific genes, and the genomic domains they occupy, have illuminated the innovations in trypanosomatid genomes; and how comparative genomics has exposed the molecular mechanisms responsible for innovation and adaptation to a parasitic lifestyle.

GP63 function in the interaction of trypanosomatids with the invertebrate host: facts and prospects

The GP63 of the protozoan parasite Leishmania is a highly abundant zinc metallopeptidase, mainly glycosylphosphatidylinositol-anchored to the parasite surface, which contributes to a myriad of well-established functions for Leishmania in the interaction with the mammalian host. However, the role of GP63 in the Leishmania-insect vector interplay is still a matter of controversy. Data from GP63 homologues in insect and plant trypanosomatids strongly suggest a participation of GP63 in this interface, either through nutrient acquisition or through binding to the insect gut receptors. GP63 has also been described in the developmental forms of Trypanosoma cruzi, Trypanosoma brucei and Trypanosoma rangeli that deal with the vector. Here, the available data from GP63 will be analyzed from the perspective of the interaction of trypanosomatids with the invertebrate host.

Mitogen-activated protein kinases in innate immunity

Following pathogen infection or tissue damage, the stimulation of pattern recognition receptors on the cell surface and in the cytoplasm of innate immune cells activates members of each of the major mitogen-activated protein kinase (MAPK) subfamilies--the extracellular signal-regulated kinase (ERK), p38 and Jun N-terminal kinase (JNK) subfamilies. In conjunction with the activation of nuclear factor-κB and interferon-regulatory factor transcription factors, MAPK activation induces the expression of multiple genes that together regulate the inflammatory response. In this Review, we discuss our current knowledge about the regulation and the function of MAPKs in innate immunity, as well as the importance of negative feedback loops in limiting MAPK activity to prevent host tissue damage. We also examine how pathogens have evolved complex mechanisms to manipulate MAPK activation to increase their virulence. Finally, we consider the potential of the pharmacological targeting of MAPK pathways to treat autoimmune and inflammatory diseases.

The Trypanosoma rangeli trypomastigote surfaceome reveals novel proteins and targets for specific diagnosis

Sympatric distribution and sharing of hosts and antigens by Trypanosoma rangeli and Trypanosoma cruzi, the etiological agent of Chagas' disease, often incur in misdiagnosis and improper epidemiological inferences. Many secreted and surface proteins (SP) have been described as important antigens shared by these species. This work describes the T. rangeli surfaceome obtained by gel-free (LC-ESI-MS/MS) and gel-based (GeLC-ESI-MS/MS) proteomic approaches, and immunoblotting analyses and the comparison of these SP with T. cruzi. A total of 138 T. rangeli proteins and 343 T. cruzi proteins were obtained, among which, 42 and 157 proteins were exclusively identified in T. rangeli or T. cruzi trypomastigotes, respectively. Immunoblotting assays using sera from experimentally infected mice revealed a distinct band pattern for each species. MS/MS analysis of T. rangeli exclusive bands revealed two unique GP63-related proteins and flagellar calcium-binding protein. Also, a ~32kDa band composed of 12 distinct proteins was exclusively recognized by anti-T. cruzi serum. This highly sensitive proteomic assessment of surface proteins characterized the T. rangeli surfaceome, revealing several differences and similarities between these two parasites. The study reports new T. rangeli-specific proteins with promising use in differential diagnosis from T. cruzi.

BIOLOGICAL SIGNIFICANCE

In this manuscript, we report the first proteomic analysis of the T. rangeli surface (surfaceome), a non-pathogenic parasite occurring in sympatry with T. cruzi, the etiological agent of Chagas disease. This comparative proteomic analysis was performed using high-throughput in-gel and gel-free proteomic approaches combined with immunoblotting, allowing us to identify new T. rangeli-specific proteins with promising use in differential serodiagnosis, among several other protein not previously reported for this taxon. Additionally, cross-recognition assays showed that T. cruzi surface proteins were recognized by heterologous serum (anti-T. rangeli) that strengthens the possibility of misdiagnosis of Chagas disease in humans and other mammals. Thus, this work provides new insights to understand the serological cross-reactivity between T. cruzi and T. rangeli, as well as, the identification of targets for specific T. rangeli diagnosis as revealed by the comparative surfaceome analysis. We strongly believe that this research is of importance to the readers of Journal of Proteomics since it provides new potential markers for diagnosis of both T. cruzi and T. rangeli parasites increasing the spectrum of specific targets for unambiguous diagnosis of T. rangeli and T. cruzi infections, besides describing new approaches to assess the trypanosomatids proteome.

Host-parasite interaction: parasite-derived and -induced proteases that degrade human extracellular matrix

Parasitic protozoa are among the most important pathogens worldwide. Diseases such as malaria, leishmaniasis, amoebiasis, giardiasis, trichomoniasis, and trypanosomiasis affect millions of people. Humans are constantly threatened by infections caused by these pathogens. Parasites engage a plethora of surface and secreted molecules to attach to and enter mammalian cells. The secretion of lytic enzymes by parasites into host organs mediates critical interactions because of the invasion and destruction of interstitial tissues, enabling parasite migration to other sites within the hosts. Extracellular matrix is a complex, cross-linked structure that holds cells together in an organized assembly and that forms the basement membrane lining (basal lamina). The extracellular matrix represents a major barrier to parasites. Therefore, the evolution of mechanisms for connective-tissue degradation may be of great importance for parasite survival. Recent advances have been achieved in our understanding of the biochemistry and molecular biology of proteases from parasitic protozoa. The focus of this paper is to discuss the role of protozoan parasitic proteases in the degradation of host ECM proteins and the participation of these molecules as virulence factors. We divide the paper into two sections, extracellular and intracellular protozoa.

Impact of Leishmania metalloprotease GP63 on macrophage signaling

The intramacrophage protozoan parasites of Leishmania genus have developed sophisticated ways to subvert the innate immune response permitting their infection and propagation within the macrophages of the mammalian host. Several Leishmania virulence factors have been identified and found to be of importance for the development of leishmaniasis. However, recent findings are now further reinforcing the critical role played by the zinc-metalloprotease GP63 as a virulence factor that greatly influence host cell signaling mechanisms and related functions. GP63 has been found to be involved not only in the cleavage and degradation of various kinases and transcription factors, but also to be the major molecule modulating host negative regulatory mechanisms involving for instance protein tyrosine phosphatases (PTPs). Those latter being well recognized for their pivotal role in the regulation of a great number of signaling pathways. In this review article, we are providing a complete overview about the role of Leishmania GP63 in the mechanisms underlying the subversion of macrophage signaling and functions.

Recombinant glycoprotein 63 (Gp63) of Trypanosoma carassii suppresses antimicrobial responses of goldfish (Carassius auratus L.) monocytes and macrophages

We previously reported that proteins secreted by Trypanosoma carassii play a role in evasion of fish host immune responses. To further understand how these parasites survive in the host, we cloned and expressed T. carassii glycoprotein 63 (Tcagp63), and generated a rabbit polyclonal antibody to the recombinant protein (rTcagp63). Tcagp63 was similar to gp63 of other trypanosomes and grouped with Trypanosoma cruzi and Trypanosoma brucei gp63 in phylogenetic analysis. We showed that rTcagp63 down-regulated Aeromonas salmonicida and recombinant goldfish TNFα2-induced production of reactive oxygen and nitrogen intermediates. Macrophages treated with rTcagp63 also exhibited significant reduction in the expression of inducible nitric oxide synthase (iNOS)-A, TNFα-1 and TNFα-2. Recombinant Tcagp63 bound to and was internalised by goldfish macrophages. The Tcagp63 may act by altering the signalling events important in downstream monocyte/macrophage antimicrobial and other cytokine-induced functions. We believe that this is the first report on downregulation of antimicrobial responses by trypanosome gp63.

Immune evasion strategies of trypanosomes: a review

Trypanosomes are digenetic protozoans that infect domestic and wild animals, as well as humans. They cause important medical and veterinary diseases, making them a major public health concern. There are many species of trypanosomes that infect virtually all vertebrate taxa. They typically cycle between insect or leech vectors and vertebrate hosts, and they undergo biochemical and morphological changes in the process. Trypanosomes have received much attention in the last 4 decades because of the diseases they cause and their remarkable armamentarium of immune evasion mechanisms. The completed genome sequences of trypanosomes have revealed an extensive array of molecules that contribute to various immune evasion mechanisms. The different species interact uniquely with their vertebrate hosts with a wide range of evasion strategies and some of the most fascinating immune evasion mechanisms, including antigenic variation that was first described in the trypanosomes. This review focuses on the variety of strategies that these parasites have evolved to evade or modulate immunity of endothermic and ectothermic vertebrates.