Identification of novel rhoptry proteins in Neospora caninum by LC/MS-MS analysis of subcellular fractions

Proteomics Applications in Toxoplasma gondii: Unveiling the Host-Parasite Interactions and Therapeutic Target Discovery

Toxoplasma gondii, a protozoan parasite with the ability to infect various warm-blooded vertebrates, including humans, is the causative agent of toxoplasmosis. This infection poses significant risks, leading to severe complications in immunocompromised individuals and potentially affecting the fetus through congenital transmission. A comprehensive understanding of the intricate molecular interactions between T. gondii and its host is pivotal for the development of effective therapeutic strategies. This review emphasizes the crucial role of proteomics in T. gondii research, with a specific focus on host-parasite interactions, post-translational modifications (PTMs), PTM crosstalk, and ongoing efforts in drug discovery. Additionally, we provide an overview of recent advancements in proteomics techniques, encompassing interactome sample preparation methods such as BioID (BirA*-mediated proximity-dependent biotin identification), APEX (ascorbate peroxidase-mediated proximity labeling), and Y2H (yeast two hybrid), as well as various proteomics approaches, including single-cell analysis, DIA (data-independent acquisition), targeted, top-down, and plasma proteomics. Furthermore, we discuss bioinformatics and the integration of proteomics with other omics technologies, highlighting its potential in unraveling the intricate mechanisms of T. gondii pathogenesis and identifying novel therapeutic targets.

Molecular characterization of NCLIV_011700 of Neospora caninum, a low sequence identity rhoptry protein

Neospora caninum is an obligate intracellular parasite related to abortion in cattle, goats and sheep. The life cycle of N. caninum is characterized by the time-coordinated secretion of proteins contained in micronemes, rhoptries and dense granules, allowing the active invasion and the adaptation of the parasite in the cell environment. Thus, the proteins of the secretome have the potential to be considered as targets for N. caninum control. Despite the importance of neosporosis in the livestock-related economy, no commercial treatment is available. Furthermore, the process of invasion, propagation and immune evasion are not completely elucidated. In this study, we initiated the characterization of NCLIV_011700 of N. caninum, a protein with low sequence identity to NcROP15 or TgROP15 (<15%). Our goal was the detection and molecular characterization of the NCLIV_011700, once homology (with low identity >20%) was observed within the Apicomplexa. The NCLIV_011700 sequence was aligned and compared to the closer apicomplexan homologues (ROP15 from N. caninum, T. gondii, Hammondia hammondi, Cystospores suis), including the predicted domains. In general, the NCLIV_011700 demonstrated low identity with ROP15 of apicomplexan (<20%) and had a ubiquitin domain. On the other side, the NCLIV_011700 homologues were composed of a non-cytoplasmic domain, suggesting different functions between NcROP15 (or homologues) and NCLIV_011700 during the parasite life cycle. Moreover, the NCLIV_011700 was amplified by PCR, ligated to a pET28a plasmid and expressed in Escherichia coli. The recombinant form of NCLIV_011700 was purified in a nickel-Sepharose resin and applied for polyclonal antibody production in mice. The antiserum against NCLIV_011700 (anti-r NCLIV_011700) was used to localize the native form of the protein using Western blot and confocal microscopy. Also, the NCLIV_011700 antiserum partially inhibited the parasite adhesion/invasion process, indicating an active role of the protein in the N. caninum cycle. Thus, the initial NCLIV_011700 characterization will contribute to enlarging the comprehension of N. caninum, aiming at the future development of tools to control the parasite infection/propagation.

Next-Generation Technologies and Systems Biology for the Design of Novel Vaccines Against Apicomplexan Parasites

Parasites of the phylum Apicomplexa are the causative agents of important diseases such as malaria, toxoplasmosis or cryptosporidiosis in humans, and babesiosis and coccidiosis in animals. Whereas the first human recombinant vaccine against malaria has been approved and recently recommended for wide administration by the WHO, most other zoonotic parasitic diseases lack of appropriate immunoprophylaxis. Sequencing technologies, bioinformatics, and statistics, have opened the "omics" era into apicomplexan parasites, which has led to the development of systems biology, a recent field that can significantly contribute to more rational design for new vaccines. The discovery of novel antigens by classical approaches is slow and limited to very few antigens identified and analyzed by each study. High throughput approaches based on the expansion of the "omics", mainly genomics and transcriptomics have facilitated the functional annotation of the genome for many of these parasites, improving significantly the understanding of the parasite biology, interactions with the host, as well as virulence and host immune response. Developments in genetic manipulation in apicomplexan parasites have also contributed to the discovery of new potential vaccine targets. The present minireview does a comprehensive summary of advances in "omics", CRISPR/Cas9 technologies, and in systems biology approaches applied to apicomplexan parasites of economic and zoonotic importance, highlighting their potential of the holistic view in vaccine development.

From Signaling Pathways to Distinct Immune Responses: Key Factors for Establishing or Combating Neospora caninum Infection in Different Susceptible Hosts

: Neospora caninum is an intracellular protozoan parasite affecting numerous animal species. It induces significant economic losses because of abortion and neonatal abnormalities in cattle. In case of infection, the parasite secretes numerous arsenals to establish a successful infection in the host cell. In the same context but for a different purpose, the host resorts to different strategies to eliminate the invading parasite. During this battle, numerous key factors from both parasite and host sides are produced and interact for the maintaining and vanishing of the infection, respectively. Although several reviews have highlighted the role of different compartments of the immune system against N. caninum infection, each one of them has mostly targeted specific points related to the immune component and animal host. Thus, in the current review, we will focus on effector molecules derived from the host cell or the parasite using a comprehensive survey method from previous reports. According to our knowledge, this is the first review that highlights and discusses immune response at the host cell-parasite molecular interface against N. caninum infection in different susceptible hosts.

Characterization of the Neospora caninum NcROP40 and NcROP2Fam-1 rhoptry proteins during the tachyzoite lytic cycle

Virulence factors from the ROP2-family have been extensively studied in Toxoplasma gondii, but in the closely related Neospora caninum only NcROP2Fam-1 has been partially characterized to date. NcROP40 is a member of this family and was found to be more abundantly expressed in virulent isolates. Both NcROP2Fam-1 and NcROP40 were evaluated as vaccine candidates and exerted a synergistic effect in terms of protection against vertical transmission in mouse models, which suggests that they may be relevant for parasite pathogenicity. NcROP40 is localized in the rhoptry bulbs of tachyzoites and bradyzoites, but in contrast to NcROP2Fam-1, the protein does not associate with the parasitophorous vacuole membrane due to the lack of arginine-rich amphipathic helix in its sequence. Similarly to NcROP2Fam-1, NcROP40 mRNA levels are highly increased during tachyzoite egress and invasion. However, NcROP40 up-regulation does not appear to be linked to the mechanisms triggering egress. In contrast to NcROP2Fam-1, phosphorylation of NcROP40 was not observed during egress. Besides, NcROP40 secretion into the host cell was not successfully detected by immunofluorescence techniques. These findings indicate that NcROP40 and NcROP2Fam-1 carry out different functions, and highlight the need to elucidate the role of NcROP40 within the lytic cycle and to explain its relative abundance in tachyzoites.

Neospora caninum tachyzoite immunome study reveals differences among three biologically different isolates

Pathogenesis of bovine neosporosis is determined by different host- and parasite-dependent factors, including isolate virulence. A previous study identified that several Neospora caninum tachyzoite proteins were more abundant in virulent isolates, Nc-Liv and Nc-Spain7, compared with the low-virulent isolate Nc-Spain1H. Herein, we explored differences in the immunomes of these three isolates. Protein extracts from the Nc-Liv, Nc-Spain1H and Nc-Spain7 isolates were analysed in a 3×3 design by 2-DE immunoblot using sera from experimentally infected mice with these same three isolates. All isolates displayed a highly similar antigenic pattern when they were assessed using the same serum. Most of the reactive spots were located in the acidic region (pH 3-7) and grouped in 3 antigenic areas (250-70, 45-37 and 35-15 KDa). Differences found in the immunome depended on the sera used, regardless of the extract employed. In this sense, sera from Nc-Liv and Nc-Spain7 infected mice recognized the highest number of antigens, followed by Nc-Spain1H infected mice sera. In fact, 4 proteins identified by MS were not consistently detected in each isolate extract by sera from low-virulent Nc-Spain1H-infected mice: serine-threonine phosphatase 2C and superoxide dismutase (related to metabolism), gliding associated protein GAP45 (related to tachyzoites invasion), and NcGRA1 (located on dense granules). Similarly, 4 non-identified spots and another 2 spots chains located in 45-37 kDa area were not detected by this pooled sera. Variations between virulent Nc-Spain7 and Nc-Liv were limited to the absence of recognition by sera from Nc-Spain7-infected mice of GAP45 and the spot chains located in the 45-37 kDa area. These results suggest that variations in the immunome profiles rely on the immune response induced by each isolate and that these differentially recognized antigens could be investigated as putative virulence markers of neosporosis.

A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum

Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large-scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data against a panel of official and alternate gene models generated directly from RNASeq data, using several newly generated and some previously published MS datasets for this meta-analysis. We identified a total of 201 996 and 39 953 peptide-spectrum matches for T. gondii and N. caninum, respectively, at a 1% peptide FDR threshold. This equated to the identification of 30 494 distinct peptide sequences and 2921 proteins (matches to official gene models) for T. gondii, and 8911 peptides/1273 proteins for N. caninum following stringent protein-level thresholding. We have also identified 289 and 140 loci for T. gondii and N. caninum, respectively, which mapped to RNA-Seq-derived gene models used in our analysis and apparently absent from the official annotation (release 10 from EuPathDB) of these species. We present several examples in our study where the RNA-Seq evidence can help in correction of the current gene model and can help in discovery of potential new genes. The findings of this study have been integrated into the EuPathDB. The data have been deposited to the ProteomeXchange with identifiers PXD000297and PXD000298.

Vaccines against neosporosis: what can we learn from the past studies?

Neospora caninum is an intracellular apicomplexan parasite, which is a leading cause of abortion in cattle; thus neosporosis represents an important veterinary health problem and is of high economic significance. The parasite can infect cattle via trans-placental transmission from an infected cow to its fetus (vertical transmission), or through the oral route via ingestion of food or water contaminated with oocysts that were previously shed with the feces of a canid definitive host (horizontal transmission). Although vaccination was considered a rational strategy to prevent bovine neosporosis, the only commercialized vaccine (Neoguard®) produced ambiguous results with relatively low efficacy, and was recently removed from the market. Therefore, there is a need to develop an efficient vaccine capable of preventing both, the horizontal transmission through infected food or water to a naïve animal as well as the vertical transmission from infected but clinically asymptomatic dams to the fetus. Different vaccine strategies have been investigated, including the use of live attenuated vaccines, killed parasite lysates, total antigens or antigen fractions from killed parasites, and subunit vaccines. The vast majority of experimental studies were performed in mice, and to a certain extent in gerbils, but there is also a large number of investigations that were conducted in cattle and sheep. However, it is difficult to directly compare these studies due to the high variability of the parameters employed. In this review, we will summarize the recent advances made in vaccine development against N. caninum in cattle and in mice and highlight the most important factors, which are likely to influence the degree of protection mediated by vaccination.

Molecular cloning and characterization of NcROP2Fam-1, a member of the ROP2 family of rhoptry proteins in Neospora caninum that is targeted by antibodies neutralizing host cell invasion in vitro

Recent publications demonstrated that a fragment of a Neospora caninum ROP2 family member antigen represents a promising vaccine candidate. We here report on the cloning of the cDNA encoding this protein, N. caninum ROP2 family member 1 (NcROP2Fam-1), its molecular characterization and localization. The protein possesses the hallmarks of ROP2 family members and is apparently devoid of catalytic activity. NcROP2Fam-1 is synthesized as a pre-pro-protein that is matured to 2 proteins of 49 and 55 kDa that localize to rhoptry bulbs. Upon invasion the protein is associated with the nascent parasitophorous vacuole membrane (PVM), evacuoles surrounding the host cell nucleus and, in some instances, the surface of intracellular parasites. Staining was also observed within the cyst wall of 'cysts' produced in vitro. Interestingly, NcROP2Fam-1 was also detected on the surface of extracellular parasites entering the host cells and antibodies directed against NcROP2Fam-1-specific peptides partially neutralized invasion in vitro. We conclude that, in spite of the general belief that ROP2 family proteins are intracellular antigens, NcROP2Fam-1 can also be considered as an extracellular antigen, a property that should be taken into account in further experiments employing ROP2 family proteins as vaccines.

Unravelling the Neospora caninum secretome through the secreted fraction (ESA) and quantification of the discharged tachyzoite using high-resolution mass spectrometry-based proteomics

BACKGROUND

The apicomplexan parasite Neospora caninum causes neosporosis, a disease that leads to abortion or stillbirth in cattle, generating an economic impact on the dairy and beef cattle trade. As an obligatory intracellular parasite, N. caninum needs to invade the host cell in an active manner to survive. The increase in parasite cytosolic Ca2+ upon contact with the host cell mediates critical events, including the exocytosis of phylum-specific secretory organelles and the activation of the parasite invasion motor. Because invasion is considered a requirement for pathogen survival and replication within the host, the identification of secreted proteins (secretome) involved in invasion may be useful to reveal interesting targets for therapeutic intervention.

METHODS

To chart the currently missing N. caninum secretome, we employed mass spectrometry-based proteomics to identify proteins present in the N. caninum tachyzoite using two different approaches. The first approach was identifying the proteins present in the tachyzoite-secreted fraction (ESA). The second approach was determining the relative quantification through peptide stable isotope labelling of the tachyzoites submitted to an ethanol secretion stimulus (discharged tachyzoite), expecting to identify the secreted proteins among the down-regulated group.

RESULTS

As a result, 615 proteins were identified at ESA and 2,011 proteins quantified at the discharged tachyzoite. We have analysed the connection between the secreted and the down-regulated proteins and searched for putative regulators of the secretion process among the up-regulated proteins. An interaction network was built by computational prediction involving the up- and down-regulated proteins. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD000424.

CONCLUSIONS

The comparison between the protein abundances in ESA and their measure in the discharged tachyzoite allowed for a more precise identification of the most likely secreted proteins. Information from the network interaction and up-regulated proteins was important to recognise key proteins potentially involved in the metabolic regulation of secretion. Our results may be helpful to guide the selection of targets to be investigated against Neospora caninum and other Apicomplexan organisms.

Identification of three novel Toxoplasma gondii rhoptry proteins

The rhoptries are key secretory organelles from apicomplexan parasites that contain proteins involved in invasion and modulation of the host cell. Some rhoptry proteins are restricted to the posterior bulb (ROPs) and others to the anterior neck (RONs). As many rhoptry proteins have been shown to be key players in Toxoplasma invasion and virulence, it is important to identify, understand and characterise the biological function of the components of the rhoptries. In this report, we identified putative novel rhoptry genes by identifying Toxoplasma genes with similar cyclical expression profiles as known rhoptry protein encoding genes. Using this approach we identified two new rhoptry bulb (ROP47 and ROP48) and one new rhoptry neck protein (RON12). ROP47 is secreted and traffics to the host cell nucleus, RON12 was not detected at the moving junction during invasion. Deletion of ROP47 or ROP48 in a type II strain did not show major influence in in vitro growth or virulence in mice.

Identification of Besnoitia besnoiti proteins that showed differences in abundance between tachyzoite and bradyzoite stages by difference gel electrophoresis

Bovine besnoitiosis is a chronic and debilitating disease, caused by the apicomplexan parasite Besnoitia besnoiti. Infection of cattle by B. besnoiti is governed by the tachyzoite stage, which is related to acute infection, and the bradyzoite stage gathered into macroscopic cysts located in subcutaneous tissue in the skin, mucosal membranes and sclera conjunctiva and related to persistence and chronic infection. However, the entire life cycle of this parasite and the molecular mechanisms underlying tachyzoite-to-bradyzoite conversion remain unknown. In this context, a different antigenic pattern has been observed between tachyzoite and bradyzoite extracts. Thus, to identify stage-specific proteins, a difference gel electrophoresis (DIGE) approach was used on tachyzoite and bradyzoite extracts followed by mass spectrometry (MS) analysis. A total of 130 and 132 spots were differentially expressed in bradyzoites and tachyzoites, respectively (average ratio ± 1.5, P<0.05 in t-test). Furthermore, 25 differentially expressed spots were selected and analysed by MALDI-TOF/MS. As a result, 5 up-regulated bradyzoite proteins (GAPDH, ENO1, LDH, SOD and RNA polymerase) and 5 up-regulated tachyzoite proteins (ENO2; LDH; ATP synthase; HSP70 and PDI) were identified. The present results set the basis for the identification of new proteins as drug targets. Moreover, the role of these proteins in tachyzoite-to-bradyzoite conversion and the role of the host cell environment should be a subject of further research.

Subversion of host cellular functions by the apicomplexan parasites

Rhoptries are club-shaped secretory organelles located at the anterior pole of species belonging to the phylum of Apicomplexa. Parasites of this phylum are responsible for a huge burden of disease in humans and animals and a loss of economic productivity. Members of this elite group of obligate intracellular parasites include Plasmodium spp. that cause malaria and Cryptosporidium spp. that cause diarrhoeal disease. Although rhoptries are almost ubiquitous throughout the phylum, the relevance and role of the proteins contained within the rhoptries varies. Rhoptry contents separate into two intra-organellar compartments, the neck and the bulb. A number of rhoptry neck proteins are conserved between species and are involved in functions such as host cell invasion. The bulb proteins are less well-conserved and probably evolved for a particular lifestyle. In the majority of species studied to date, rhoptry content is involved in formation and maintenance of the parasitophorous vacuole; however some species live free within the host cytoplasm. In this review, we will summarise the knowledge available regarding rhoptry proteins. Specifically, we will discuss the role of the rhoptry kinases that are used by Toxoplasma gondii and other coccidian parasites to subvert the host cellular functions and prevent parasite death.

Proteome expression changes among virulent and attenuated Neospora caninum isolates

Neospora caninum is a cyst-forming parasite that has been recognised worldwide as a cause of cattle abortion and neuromuscular disease in dogs. Variations in genetic profiles, behaviour in vitro, and pathogenicity have been established among N. caninum isolates. However, it is unclear which parasite factors are implicated in this intra-specific diversity. Comparative analysis of protein expression patterns may define the determinants of biological diversity in N. caninum. Using DIGE and MALDI-TOF MS techniques, we quantified and identified differentially expressed proteins in the tachyzoite stage across three N. caninum isolates: the virulent Nc-Liv and Nc-Spain 7 isolates, and the attenuated Nc-Spain 1H isolate. Comparison between Nc-Spain 7 and Nc-Spain 1H extracts revealed 39 protein spots that were more abundant in Nc-Spain 7 and 21 in Nc-Spain 1H. Twenty-four spots were also increased in Nc-Spain 7 and 12 in Nc-Liv. Three protein spots were more abundant in the Nc-Liv extracts than in the Nc-Spain 1H extracts. MS analysis identified 11 proteins differentially expressed that are potentially involved in gliding motility and the lytic cycle of the parasite, and oxidative stress. These differences could help to explain variations in behaviour between isolates and provide a better knowledge of mechanisms associated with virulence.