Cell fractionation of parasitic protozoa: a review

The parabasal filaments of Trichomonas vaginalis: A new filament and observations using 0.8 nm-resolution scanning electron microscopy

Trichomonas vaginalis is the etiologic agent of trichomoniasis, the most common nonviral sexually transmitted infection worldwide, with an estimated 260 million new cases annually. T. vaginalis contains organelles common to all eukaryotic cells, uncommon cell structures such as hydrogenosomes, and a complex and elaborate cytoskeleton constituting the mastigont system. The mastigont system is mainly formed by several proteinaceous structures associated with basal bodies, the pelta-axostylar complex made of microtubules, and striated filaments named the costa and the parabasal filaments (PFs). Although the structural organization of trichomonad cytoskeletons has been analyzed using several techniques, observation using a new generation of scanning electron microscopes with a resolution exceeding 1 nm has allowed more detailed visualization of the three-dimensional organization of the mastigont system. In this study, we have investigated the cytoskeleton of T. vaginalis using a diverse range of scanning probe microscopy techniques, which were complemented by electron tomography and Fast-Fourier methods. This multi-modal approach has allowed us to characterize an unknown parabasal filament and reveal the ultrastructure of other striated fibers that have not been published before. Here, we show the differences in origin, striation pattern, size, localization, and additional details of the PFs, thus improving the knowledge of the cell biology of this parasite.

Microbial Pathogenesis in the Era of Spatial Omics

The biology of a cell, whether it is a unicellular organism or part of a multicellular network, is influenced by cell type, temporal changes in cell state, and the cell's environment. Spatial cues play a critical role in the regulation of microbial pathogenesis strategies. Information about where the pathogen is-in a tissue or in proximity to a host cell-regulates gene expression and the compartmentalization of gene products in the microbe and the host. Our understanding of host and pathogen identity has bloomed with the accessibility of transcriptomics and proteomics techniques. A missing piece of the puzzle has been our ability to evaluate global transcript and protein expression in the context of the subcellular niche, primary cell, or native tissue environment during infection. This barrier is now lower with the advent of new spatial omics techniques to understand how location regulates cellular functions. This review will discuss how recent advances in spatial proteomics and transcriptomics approaches can address outstanding questions in microbial pathogenesis.

Proteomic Profiling of Leishmania donovani Promastigote Subcellular Organelles

To facilitate a greater understanding of the biological processes in the medically important Leishmania donovani parasite, a combination of differential and density-gradient ultracentrifugation techniques were used to achieve a comprehensive subcellular fractionation of the promastigote stage. An in-depth label-free proteomic LC-MS/MS analysis of the density gradients resulted in the identification of ∼50% of the Leishmania proteome (3883 proteins detected), which included ∼645 integral membrane proteins and 1737 uncharacterized proteins. Clustering and subcellular localization of proteins was based on a subset of training Leishmania proteins with known subcellular localizations that had been determined using biochemical, confocal microscopy, or immunoelectron microscopy approaches. This subcellular map will be a valuable resource that will help dissect the cell biology and metabolic processes associated with specific organelles of Leishmania and related kinetoplastids.

The Cytoskeleton of Parabasalian Parasites Comprises Proteins that Share Properties Common to Intermediate Filament Proteins

Certain protist lineages bear cytoskeletal structures that are germane to them and define their individual group. Trichomonadida are excavate parasites united by a unique cytoskeletal framework, which includes tubulin-based structures such as the pelta and axostyle, but also other filaments such as the striated costa whose protein composition remains unknown. We determined the proteome of the detergent-resistant cytoskeleton of Tetratrichomonas gallinarum. 203 proteins with homology to Trichomonas vaginalis were identified, which contain significantly more long coiled-coil regions than control protein sets. Five candidates were shown to associate with previously described cytoskeletal structures including the costa and the expression of a single T. vaginalis protein in T. gallinarum induced the formation of accumulated, striated filaments. Our data suggests that filament-forming proteins of protists other than actin and tubulin share common structural properties with metazoan intermediate filament proteins, while not being homologous. These filament-forming proteins might have evolved many times independently in eukaryotes, or simultaneously in a common ancestor but with different evolutionary trajectories downstream in different phyla. The broad variety of filament-forming proteins uncovered, and with no homologs outside of the Trichomonadida, once more highlights the diverse nature of eukaryotic proteins with the ability to form unique cytoskeletal filaments.

Leishmania (Viannia) braziliensis: insights on subcellular distribution and biochemical properties of heparin-binding proteins

Leishmaniasis is a vector-borne disease and an important public health issue. Glycosaminoglycan ligands in Leishmania parasites are potential targets for new strategies to control this disease. We report the subcellular distribution of heparin-binding proteins (HBPs) in Leishmania (Viannia) braziliensis and specific biochemical characteristics of L. (V.) braziliensis HBPs. Promastigotes were fractionated, and flagella and membrane samples were applied to HiTrap Heparin affinity chromatography columns. Heparin-bound fractions from flagella and membrane samples were designated HBP Ff and HBP Mf, respectively. Fraction HBP Ff presented a higher concentration of HBPs relative to HBP Mf, and SDS-PAGE analyses showed 2 major protein bands in both fractions (65 and 55 kDa). The 65 kDa band showed gelatinolytic activity and was sensitive to inhibition by 1,10-phenanthroline. The localization of HBPs on the promastigote surfaces was confirmed using surface plasmon resonance (SPR) biosensor analysis by binding the parasites to a heparin-coated sensor chip; that was inhibited in a dose-dependent manner by pre-incubating the parasites with variable concentrations of heparin, thus indicating distinct heparin-binding capacities for the two fractions. In conclusion, protein fractions isolated from either the flagella or membranes of L. (V.) braziliensis promastigotes have characteristics of metallo-proteinases and are able to bind to glycosaminoglycans.

Plant organelle proteomics: collaborating for optimal cell function

Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.

Subcellular proteomics of Trypanosoma cruzi reservosomes

Reservosomes are the endpoint of the endocytic pathway in Trypanosoma cruzi epimastigotes. These organelles have the particular ability to concentrate proteins and lipids obtained from medium together with the main proteolytic enzymes originated from the secretory pathway, being at the same time a storage organelle and the main site of protein degradation. Subcellular proteomics have been extensively used for profiling organelles in different cell types. Here, we combine cell fractionation and LC-MS/MS analysis to identify reservosome-resident proteins. Starting from a purified reservosome fraction, we established a protocol to isolate reservosome membranes. Transmission electron microscopy was applied to confirm the purity of the fractions. To achieve a better coverage of identified proteins we analyzed the fractions separately and combined the results. LC-MS/MS analysis identified in total 709 T. cruzi-specific proteins; of these, 456 had predicted function and 253 were classified as hypothetical proteins. We could confirm the presence of most of the proteins validated by previous work and identify new proteins from different classes such as enzymes, proton pumps, transport proteins, and others. The definition of the reservosome protein profile is a good tool to assess their molecular signature, identify molecular markers, and understand their relationship with different organelles.

A soluble pyrophosphatase, a key enzyme for polyphosphate metabolism in Leishmania

We report the functional characterization in Leishmania amazonensis of a soluble pyrophosphatase (LaVSP1) that localizes in acidocalcisomes, a vesicular acidic compartment. LaVSP1 is preferentially expressed in metacyclic forms. Experiments with dominant negative mutants show the requirement of LaVSP1 functional expression for metacyclogenesis and virulence in mice. Depending on the pH and the cofactors Mg2+ or Zn2+, both present in acidocalcisomes, LaVSP1 hydrolyzes either inorganic pyrophosphate (Km = 92 microM, kcat = 125 s(-1)), tripolyphosphate (Km = 1153 microM, kcat = 131 s(-1)), or polyphosphate of 28 residues (Km = 123 microM, kcat = 8 s(-1)). Predicted structural analysis suggests that the structural orientation of the residue Lys78 in LaVSP1 accounts for the observed increase in Km compared with the yeast pyrophosphatase and for the ability of trypanosomatid VSP1 enzymes to hydrolyze polyphosphate. These results make the VSP1 enzyme an attractive drug target against trypanosomatid parasites.