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1.  Molecular control of irreversible bistability during trypanosome developmental commitment 
The Journal of Cell Biology  2015;211(2):455-468.
Phosphoproteomic and functional analysis of the developmental progression of Trypanosomes demonstrates that this transition shows bistability, with commitment to differentiation requiring new protein synthesis, and that the protein kinase NRK is a key regulator.
The life cycle of Trypanosoma brucei involves developmental transitions that allow survival, proliferation, and transmission of these parasites. One of these, the differentiation of growth-arrested stumpy forms in the mammalian blood into insect-stage procyclic forms, can be induced synchronously in vitro with cis-aconitate. Here, we show that this transition is an irreversible bistable switch, and we map the point of commitment to differentiation after exposure to cis-aconitate. This irreversibility implies that positive feedback mechanisms operate to allow commitment (i.e., the establishment of “memory” of exposure to the differentiation signal). Using the reversible translational inhibitor cycloheximide, we show that this signal memory requires new protein synthesis. We further performed stable isotope labeling by amino acids in cell culture to analyze synchronized parasite populations, establishing the protein and phosphorylation profile of parasites pre- and postcommitment, thereby defining the “commitment proteome.” Functional interrogation of this data set identified Nek-related kinase as the first-discovered protein kinase controlling the initiation of differentiation to procyclic forms.
doi:10.1083/jcb.201506114
PMCID: PMC4621835  PMID: 26483558
2.  Leishmania major UDP-sugar pyrophosphorylase salvages galactose for glycoconjugate biosynthesis 
Graphical abstract
Highlights
•Galactose salvage in Leishmania major is mediated by UDP-sugar pyrophosphorylase (USP).•USP is not rate limiting for glycocalyx biosynthesis under standard growth conditions.•Salvage by USP contributes to glycoconjugate biosynthesis but is insufficient on its own.
Leishmaniases are a set of tropical and sub-tropical diseases caused by protozoan parasites of the genus Leishmania whose severity ranges from self-healing cutaneous lesions to fatal visceral infections. Leishmania parasites synthesise a wide array of cell surface and secreted glycoconjugates that play important roles in infection. These glycoconjugates are particularly abundant in the promastigote form and known to be essential for establishment of infection in the insect midgut and effective transmission to the mammalian host. Since they are rich in galactose, their biosynthesis requires an ample supply of UDP-galactose. This nucleotide-sugar arises from epimerisation of UDP-glucose but also from an uncharacterised galactose salvage pathway. In this study, we evaluated the role of the newly characterised UDP-sugar pyrophosphorylase (USP) of Leishmania major in UDP-galactose biosynthesis. Upon deletion of the USP encoding gene, L. major lost the ability to synthesise UDP-galactose from galactose-1-phosphate but its ability to convert glucose-1-phosphate into UDP-glucose was fully maintained. Thus USP plays a role in UDP-galactose activation but does not significantly contribute to the de novo synthesis of UDP-glucose. Accordingly, USP was shown to be dispensable for growth and glycoconjugate biosynthesis under standard growth conditions. However, in a mutant seriously impaired in the de novo synthesis of UDP-galactose (due to deficiency of the UDP-glucose pyrophosphorylase) addition of extracellular galactose increased biosynthesis of the cell surface lipophosphoglycan. Thus under restrictive conditions, such as those encountered by Leishmania in its natural habitat, galactose salvage by USP may play a substantial role in biosynthesis of the UDP-galactose pool. We hypothesise that USP recycles galactose from the blood meal within the midgut of the insect for synthesis of the promastigote glycocalyx and thereby contributes to successful vector infection.
doi:10.1016/j.ijpara.2015.06.004
PMCID: PMC4722067  PMID: 26215058
Leishmania; Trypanosomatid; Nucleotide-sugar; Galactose metabolism; Galactose salvage; Glycoconjugates
3.  Proteomic Identification of Immunodiagnostic Antigens for Trypanosoma vivax Infections in Cattle and Generation of a Proof-of-Concept Lateral Flow Test Diagnostic Device 
PLoS Neglected Tropical Diseases  2016;10(9):e0004977.
Trypanosoma vivax is one of the causative agents of Animal African Trypanosomosis in cattle, which is endemic in sub-Saharan Africa and transmitted primarily by the bite of the tsetse fly vector. The parasite can also be mechanically transmitted, and this has allowed its spread to South America. Diagnostics are limited for this parasite and in farm settings diagnosis is mainly symptom-based. We set out to identify, using a proteomic approach, candidate diagnostic antigens to develop into an easy to use pen-side lateral flow test device. Two related members the invariant surface glycoprotein family, TvY486_0045500 and TvY486_0019690, were selected. Segments of these antigens, lacking N-terminal signal peptides and C-terminal transmembrane domains, were expressed in E. coli. Both were developed into ELISA tests and one of them, TvY486_0045500, was developed into a lateral flow test prototype. The tests were all evaluated blind with 113 randomised serum samples, taken from 37 calves before and after infection with T. vivax or T. congolense. The TvY486_0045500 and TvY486_0019690 ELISA tests gave identical sensitivity and specificity values for T. vivax infection of 94.5% (95% CI, 86.5% to 98.5%) and 88.0% (95% CI, 75.7% to 95.5%), respectively, and the TvY486_0045500 lateral flow test prototype a sensitivity and specificity of 92.0% (95% CI, 83.4% to 97.0%) and 89.8% (95% CI, 77.8% to 96.6%), respectively. These data suggest that recombinant TvY486_0045500 shows promise for the development of a pen-side lateral flow test for the diagnosis of T. vivax animal African trypanosomosis.
Author Summary
African Animal Trypanosomosis presents a significant problem for agricultural development in sub-Saharan Africa and leads to large economic losses. One of the main parasites responsible is Trypanosoma vivax. Current diagnostic methods are either symptom-based or too costly and technologically demanding for use in endemic regions. Here, we identified T. vivax proteins selectively recognized by infected cattle sera and developed two related proteins into ELISA tests and one of these into a lateral flow test prototype. All three tests performed well when tested against randomised calf sera, suggesting good potential for the development of a pen-side T. vivax animal African trypanosomosis diagnostic device for use in endemic regions.
doi:10.1371/journal.pntd.0004977
PMCID: PMC5015970  PMID: 27606593
4.  Identification of sVSG117 as an Immunodiagnostic Antigen and Evaluation of a Dual-Antigen Lateral Flow Test for the Diagnosis of Human African Trypanosomiasis 
Background
The diagnosis of human African trypanosomiasis (HAT) caused by Trypanosoma brucei gambiense relies mainly on the Card Agglutination Test for Trypanosomiasis (CATT). There is no immunodiagnostic for HAT caused by T. b. rhodesiense. Our principle aim was to develop a prototype lateral flow test that might be an improvement on CATT.
Methodology/Principle Findings
Pools of infection and control sera were screened against four different soluble form variant surface glycoproteins (sVSGs) by ELISA and one, sVSG117, showed particularly strong immunoreactivity to pooled infection sera. Using individual sera, sVSG117 was shown to be able to discriminate between T. b. gambiense infection and control sera by both ELISA and lateral flow test. The sVSG117 antigen was subsequently used with a previously described recombinant diagnostic antigen, rISG65, to create a dual-antigen lateral flow test prototype. The latter was used blind in a virtual field trial of 431 randomized infection and control sera from the WHO HAT Specimen Biobank.
Conclusion/Significance
In the virtual field trial, using two positive antigen bands as the criterion for infection, the sVSG117 and rISG65 dual-antigen lateral flow test prototype showed a sensitivity of 97.3% (95% CI: 93.3 to 99.2) and a specificity of 83.3% (95% CI: 76.4 to 88.9) for the detection of T. b. gambiense infections. The device was not as good for detecting T. b. rhodesiense infections using two positive antigen bands as the criterion for infection, with a sensitivity of 58.9% (95% CI: 44.9 to 71.9) and specificity of 97.3% (95% CI: 90.7 to 99.7). However, using one or both positive antigen band(s) as the criterion for T. b. rhodesiense infection improved the sensitivity to 83.9% (95% CI: 71.7 to 92.4) with a specificity of 85.3% (95% CI: 75.3 to 92.4). These results encourage further development of the dual-antigen device for clinical use.
Author Summary
Human African Trypanosomiasis (HAT) is caused by infection with Trypanosoma brucei gambiense or T. b. rhodesiense. The diagnosis of T. b. gambiense infections currently relies primarily on a Card Agglutination Test for Trypanosomiasis (CATT), which has acknowledged limitations, and there is no simple test for T. b. rhodesiense infection. Our overall aim is to produce a simple lateral flow test device with a similar or better sensitivity and specificity than CATT but with better stability and ease of use at point of care. In this study, we identified a particular variant surface glycoprotein, sVSG117, with good diagnostic potential and combined it with a previously identified recombinant diagnostic antigen, rISG65, to produce a prototype dual-antigen lateral flow test. We performed a virtual field trial by testing the device blind with 431 randomized serum samples provided by the WHO HAT Specimen Biobank. The results show that, although the prototype lateral flow test is un-optimized, it was able to diagnose T. b. gambiense HAT with a sensitivity and specificity of 97.3% and 83.3% and T. b. rhodesiense HAT with a sensitivity and specificity of 83.9% and 85.3%.
doi:10.1371/journal.pntd.0002976
PMCID: PMC4102454  PMID: 25033401
5.  TbGT8 is a bifunctional glycosyltransferase that elaborates N-linked glycans on a protein phosphatase AcP115 and a GPI-anchor modifying glycan in Trypanosoma brucei 
Parasitology International  2014;63(3):513-518.
The procyclic form of Trypanosoma brucei expresses procyclin surface glycoproteins with unusual glycosylphosphatidylinositol-anchor side chain structures that contain branched N-acetyllactosamine and lacto-N-biose units. The glycosyltransferase TbGT8 is involved in the synthesis of the branched side chain through its UDP-GlcNAc: βGal β1-3N-acetylglucosaminyltransferase activity. Here, we explored the role of TbGT8 in the mammalian bloodstream form of the parasite with a tetracycline-inducible conditional null T. brucei mutant for TbGT8. Under non-permissive conditions, the mutant showed significantly reduced binding to tomato lectin, which recognizes poly-N-acetyllactosamine-containing glycans. Lectin pull-down assays revealed differences between the wild type and TbGT8 null-mutant T. brucei, notably the absence of a broad protein band with an approximate molecular weight of 110 kDa in the mutant lysate. Proteomic analysis revealed that the band contained several glycoproteins, including the acidic ecto-protein phosphatase AcP115, a stage-specific glycoprotein in the bloodstream form of T. brucei. Western blotting with an anti-AcP115 antibody revealed that AcP115 was approximately 10 kDa smaller in the mutant. Enzymatic de-N-glycosylation demonstrated that the underlying protein cores were the same, suggesting that the 10-kDa difference was due to differences in N-linked glycans. Immunofluorescence microscopy revealed the colocalization of hemagglutinin epitope-tagged TbGT8 and the Golgi-associated protein GRASP. These data suggest that TbGT8 is involved in the construction of complex poly-N-acetyllactosamine-containing type N-linked and GPI-linked glycans in the Golgi of the bloodstream and procyclic parasite forms, respectively.
Graphical abstract
Highlights
•TbGT8 is involved in N-linked glycan synthesis in the bloodstream form.•AcP115 is a target glycoprotein of TbGT8-dependent glycan processing.•TbGT8 is localized in the Golgi and modified by N-linked glycan(s).
doi:10.1016/j.parint.2014.01.007
PMCID: PMC4003530  PMID: 24508870
CBB, Coomassie brilliant blue; cKO, conditional double knockout; FP, flagellar pocket and lysosome/endosome system; GlcNAc, N-acetylglucosamine; GPI, glycosylphosphatidylinositol; HA, hemagglutinin epitope; LacNAc, N-acetyllactosamine; PBS, phosphate buffered saline; PNGase, peptide N-glycosidase; VSG, variant surface glycoprotein; Glycosyltransferase; Trypanosoma brucei; N-linked glycan; GPI-anchor; Tomato lectin
6.  GPI-anchored Proteins and Free GPI Glycolipids of Procyclic Form Trypanosoma brucei Are Nonessential for Growth, Are Required for Colonization of the Tsetse Fly, and Are Not the Only Components of the Surface Coat 
Molecular Biology of the Cell  2006;17(12):5265-5274.
The procyclic form of Trypanosoma brucei exists in the midgut of the tsetse fly. The current model of its surface glycocalyx is an array of rod-like procyclin glycoproteins with glycosylphosphatidylinositol (GPI) anchors carrying sialylated poly-N-acetyllactosamine side chains interspersed with smaller sialylated poly-N-acetyllactosamine–containing free GPI glycolipids. Mutants for TbGPI12, deficient in the second step of GPI biosynthesis, were devoid of cell surface procyclins and poly-N-acetyllactosamine–containing free GPI glycolipids. This major disruption to their surface architecture severely impaired their ability to colonize tsetse fly midguts but, surprisingly, had no effect on their morphology and growth characteristics in vitro. Transmission electron microscopy showed that the mutants retained a cell surface glycocalyx. This structure, and the viability of the mutants in vitro, prompted us to look for non-GPI–anchored parasite molecules and/or the adsorption of serum components. Neither were apparent from cell surface biotinylation experiments but [3H]glucosamine biosynthetic labeling revealed a group of previously unidentified high apparent molecular weight glycoconjugates that might contribute to the surface coat. While characterizing GlcNAc-PI that accumulates in the TbGPI12 mutant, we observed inositolphosphoceramides for the first time in this organism.
doi:10.1091/mbc.E06-08-0702
PMCID: PMC1679689  PMID: 17035628
7.  Fragment screening reveals salicylic hydroxamic acid as an inhibitor of Trypanosoma brucei GPI GlcNAc-PI de-N-acetylase 
Carbohydrate Research  2014;387(100):54-58.
Graphical abstract
Highlights
•First non-substrate analogue inhibitor of the trypanosome GPI pathway.•Active against recombinant enzyme and cell-free system.•Low molecular weight and good ligand efficiency.
The zinc-metalloenzyme GlcNAc-PI de-N-acetylase is essential for the biosynthesis of mature GPI anchors and has been genetically validated in the bloodstream form of Trypanosoma brucei, which causes African sleeping sickness. We screened a focused library of zinc-binding fragments and identified salicylic hydroxamic acid as a GlcNAc-PI de-N-acetylase inhibitor with high ligand efficiency. This is the first small molecule inhibitor reported for the trypanosome GPI pathway. Investigating the structure activity relationship revealed that hydroxamic acid and 2-OH are essential for potency, and that substitution is tolerated at the 4- and 5-positions.
doi:10.1016/j.carres.2013.12.016
PMCID: PMC3991331  PMID: 24589444
GPI; Trypanosoma brucei; Hydroxamic acid; Inhibitor; N-Deacetylase
8.  Investigation of copper(II) tetrafluoroborate catalysed epoxide opening 
Tetrahedron Letters  2011;52(52):7091-7094.
Graphical abstract
We report the extension of the copper(II) tetrafluoroborate catalysed opening of epoxides with alcohols to include a wider variety of alcohols, a range of solvents and a method to purify the products from the reaction.
doi:10.1016/j.tetlet.2011.10.090
PMCID: PMC3314918  PMID: 22505782
Epoxide; Copper(II) tetrafluoroborate; Lewis acid; Alcohols
9.  Preclinical Evidence for the Use of Sunitinib Malate in the Treatment of Plexiform Neurofibromas 
Pediatric blood & cancer  2015;63(2):206-213.
Purpose
Plexiform neurofibromas (pNF) are pathognomonic nerve and soft tissue tumors of neurofibromatosis type I (NF1), which are highly resistant to conventional chemotherapy and associated with significant morbidity/mortality. Disruption of aberrant SCF/c-Kit signaling emanating from the pNF microenvironment induced the first ever objective therapeutic responses in a recent phase 2 trial. Sunitinib malate is a potent, highly selective RTK inhibitor with activity against c-Kit, PDGFR, and VEGFR, which have also been implicated in the pathogenesis of these lesions. Here, we evaluate the efficacy of sunitinib malate in a preclinical Krox20;Nf1flox/− pNF murine model.
Experimental Design
Proliferation, β-hexosaminidase release (degranulation), and Erk1/2 phosphorylation were assessed in sunitinib treated Nf1+/− mast cells and fibroblasts, respectively. Krox20;Nf1flox/− mice with established pNF were treated sunitinib or PBS-vehicle control for a duration of 12 weeks. pNF metabolic activity was monitored by serial [18F]DG-PET/CT imaging.
Results
Sunitinib suppressed multiple in vitro gain-in-functions of Nf1+/− mast cells and fibroblasts and attenuated Erk1/2 phosphorylation. Sunitinib treated Krox20;Nf1flox/− mice exhibited significant reductions in pNF size, tumor number, and FDG uptake compared to control mice. Histopathology revealed reduced tumor cellularity and infiltrating mast cells, markedly diminished collagen deposition, and increased cellular apoptosis in sunitinib treated pNF.
Conclusions
Collectively, these results demonstrate the efficacy of sunitinib in reducing tumor burden in Krox20;Nf1flox/− mice. These preclinical findings demonstrate the utility of inhibiting multiple RTKs in pNF and provide insights into the design of future clinical trials.
doi:10.1002/pbc.25763
PMCID: PMC4862309  PMID: 26375012
Sunitinib malate; Receptor tyrosine kinase; Neurofibromatosis type 1; Plexiform neurofibroma; Therapy; Preclinical mouse model
10.  A Gene of the β3-Glycosyltransferase Family Encodes N-Acetylglucosaminyltransferase II Function in Trypanosoma brucei* 
The Journal of Biological Chemistry  2016;291(26):13834-13845.
The bloodstream form of the human pathogen Trypanosoma brucei expresses oligomannose, paucimannose, and complex N-linked glycans, including some exceptionally large poly-N-acetyllactosamine-containing structures. Despite the presence of complex N-glycans in this organism, no homologues of the canonical N-acetylglucosaminyltransferase I or II genes can be found in the T. brucei genome. These genes encode the activities that initiate the elaboration of the Manα1–3 and Manα1–6 arms, respectively, of the conserved trimannosyl-N-acetylchitobiosyl core of N-linked glycans. Previously, we identified a highly divergent T. brucei N-acetylglucosaminyltransferase I (TbGnTI) among a set of putative T. brucei glycosyltransferase genes belonging to the β3-glycosyltransferase superfamily (Damerow, M., Rodrigues, J. A., Wu, D., Güther, M. L., Mehlert, A., and Ferguson, M. A. (2014) J. Biol. Chem. 289, 9328–9339). Here, we demonstrate that TbGT15, another member of the same β3-glycosyltransferase family, encodes an equally divergent N-acetylglucosaminyltransferase II (TbGnTII) activity. In contrast to multicellular organisms, where GnTII activity is essential, TbGnTII null mutants of T. brucei grow in culture and are still infectious to animals. Characterization of the large poly-N-acetyllactosamine containing N-glycans of the TbGnTII null mutants by methylation linkage analysis suggests that, in wild-type parasites, the Manα1–6 arm of the conserved trimannosyl core may carry predominantly linear poly-N-acetyllactosamine chains, whereas the Manα1–3 arm may carry predominantly branched poly-N-acetyllactosamine chains. These results provide further detail on the structure and biosynthesis of complex N-glycans in an important human pathogen and provide a second example of the adaptation by trypanosomes of β3-glycosyltransferase family members to catalyze β1–2 glycosidic linkages.
doi:10.1074/jbc.M116.733246
PMCID: PMC4919465  PMID: 27189951
glycobiology; glycosyltransferase; parasite; post-translational modification (PTM); Trypanosoma brucei; N-acetylglucosamine
11.  Synthesis of potential metal-binding group compounds to examine the zinc dependency of the GPI de-N-acetylase metalloenzyme in Trypanosoma brucei 
Carbohydrate Research  2011;346(6):708-714.
Graphical abstract
A small zinc-binding group (ZBG) library of deoxy-2-C-branched-monosaccharides, for example, 1,5-anhydroglucitols, consisting of either monodentate ligand binding carboxylic acids or bidentate ligand binding hydroxamic acids, were prepared to assess the zinc affinity of the putative metalloenzyme 2-acetamido-2-deoxy-α-d-glucopyranosyl-(1→6)-phosphatidylinositol de-N-acetylase (EC 3.5.1.89) of glycosylphosphatidylinositol biosynthesis. The N-ureido thioglucoside was also synthesised and added to the ZBG library because a previous N-ureido analogue, synthesised by us, had inhibitory activity against the aforementioned de-N-acetylase, presumably via the N-ureido motif.
doi:10.1016/j.carres.2011.02.004
PMCID: PMC3125106  PMID: 21377660
Glycosylphosphatidylinositol (GPI) biosynthesis; Zinc metalloenzyme inhibitor; Zinc-binding group; Branched monosaccharides, Phosphatidylinositol de-N-acetylase
12.  Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling* 
We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754).
doi:10.1074/mcp.O115.055467
PMCID: PMC4937518  PMID: 27114452
13.  Glycotyping of Trypanosoma brucei variant surface glycoprotein MITat1.8 
Graphical abstract
VSG MITat1.8 was characterized with respect to its N-glycosylation, GPI anchor structure and found to be a disulfide-linked homodimer.
Following a switch from variant surface glycoprotein MITat1.4 to variant surface glycoprotein MITat1.8 expression by Lister strain 427 Trypanosoma brucei brucei parasites, the latter uncharacterized variant surface glycoprotein was analysed. Variant surface glycoprotein MITat1.8 was found to be a disulphide-linked homodimer, containing a complex N-linked glycan at Asn58 and a glycosylphosphatidylinositol membrane anchor attached to Asp419. Mass spectrometric analyses demonstrated that the N-glycan is exclusively Galβ1-4GlcNAcβ1-2Manα1-3(Galβ1-4GlcNAcβ1-2Manα1-6)Manβ1-4GlcNAcβ1-4GlcNAc and that the conserved Man3GlcN-myo-inositol glycosylphosphatidylinositol anchor glycan core is substituted with an average of 4 hexose, most likely galactose, residues. The presence of a complex N-glycan at Asn58 is consistent with the relatively acidic environment of the Asn58 N-glycosylation sequon, that predicts N-glycosylation by T. brucei oligosaccharyltransferase TbSTT3A with a Man5GlcNAc2 structure destined for processing to a paucimannose and/or complex N-glycan (Izquierdo L, Schulz B, Rodrigues JA et al. EMBO J 2009;28:2650–61 [12]).
doi:10.1016/j.molbiopara.2010.06.007
PMCID: PMC2935967  PMID: 20558211
Trypanosoma brucei; N-linked oligosaccharides; N-glycosylation; Glycosylphosphatidylinositol; GPI; Mass spectrometry
14.  Prophossi: automating expert validation of phosphopeptide–spectrum matches from tandem mass spectrometry 
Bioinformatics  2010;26(17):2153-2159.
Motivation: Complex patterns of protein phosphorylation mediate many cellular processes. Tandem mass spectrometry (MS/MS) is a powerful tool for identifying these post-translational modifications. In high-throughput experiments, mass spectrometry database search engines, such as MASCOT provide a ranked list of peptide identifications based on hundreds of thousands of MS/MS spectra obtained in a mass spectrometry experiment. These search results are not in themselves sufficient for confident assignment of phosphorylation sites as identification of characteristic mass differences requires time-consuming manual assessment of the spectra by an experienced analyst. The time required for manual assessment has previously rendered high-throughput confident assignment of phosphorylation sites challenging.
Results: We have developed a knowledge base of criteria, which replicate expert assessment, allowing more than half of cases to be automatically validated and site assignments verified with a high degree of confidence. This was assessed by comparing automated spectral interpretation with careful manual examination of the assignments for 501 peptides above the 1% false discovery rate (FDR) threshold corresponding to 259 putative phosphorylation sites in 74 proteins of the Trypanosoma brucei proteome. Despite this stringent approach, we are able to validate 80 of the 91 phosphorylation sites (88%) positively identified by manual examination of the spectra used for the MASCOT searches with a FDR < 15%.
Conclusions:High-throughput computational analysis can provide a viable second stage validation of primary mass spectrometry database search results. Such validation gives rapid access to a systems level overview of protein phosphorylation in the experiment under investigation.
Availability: A GPL licensed software implementation in Perl for analysis and spectrum annotation is available in the supplementary material and a web server can be assessed online at http://www.compbio.dundee.ac.uk/prophossi
Contact: d.m.a.martin@dundee.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btq341
PMCID: PMC2922888  PMID: 20651112
15.  Synthetic glycovaccine protects against the bite of Leishmania-infected sand flies 
The Journal of infectious diseases  2006;194(4):512-518.
Leishmaniasis is a vector-borne disease transmitted to human and other mammalian hosts by sand fly bite. Here we show that immunization with Leishmania mexicana promastigote secretory gel (PSG) or a chemically defined synthetic glycovaccine containing the glycans found in L. mexicana PSG can both provide significant protection against challenge by the bite of infected sand flies. Only the glycan from L. mexicana was protective, those found in other species did not protect against L. mexicana infection. Further, neither PSG nor the glycovaccine protected against artificial needle challenge, which is traditionally used in antileishmanial vaccine development. Conversely, an antigen preparation that was effective against needle challenge offered no protection against sand fly bite. These findings provide a new target for Leishmania vaccine development and demonstrate the critical role of the vector in the evaluation of candidate vaccines for leishmaniasis and other vector-borne diseases.
doi:10.1086/505584
PMCID: PMC2839923  PMID: 16845636
leishmaniasis; vaccine; sand fly; promastigote secretory gel
16.  Application of electrospray mass spectrometry to the structural determination of glycosylphosphatidylinositol membrane anchors 
Glycobiology  2010;20(5):576-585.
The addition of glycosylphosphatidylinositol (GPI) anchors to proteins is an important posttranslational modification in eukaryotic cells. The complete structural elucidation of GPI anchors is a complex process that requires relatively large amounts of starting material. In this paper, we assess the degree of structural information that can be obtained by applying electrospray mass spectrometry and tandem mass spectrometry to permethylated GPI glycans prepared from a well-characterized GPI-anchored glycoprotein, the variant surface glycoprotein from Trypanosoma brucei. All GPI glycans contain a non-N-acetylated glucosamine residue, and permethylation leads to the formation of a fixed positive charge on the glycans, in the form of a quaternary amine. The permethylated glycans were detected as [M +- Na]2+- ions, and tandem mass spectrometry of these ions produced substantial, albeit incomplete, structural information on the branching patterns and linkage types for various GPI glycoforms of the variant surface glycoprotein.
doi:10.1093/glycob/cwq007
PMCID: PMC2850939  PMID: 20100693
glycosylphosphatidylinositol; GPI anchor; mass spectrometry; Trypanosoma brucei; variant surface glycoprotein
17.  Myristoyl-CoA:protein N-myristoyltransferase depletion in trypanosomes causes avirulence and endocytic defects 
The enzyme myristoyl-CoA:protein N-myristoyltransferase (NMT) catalyses the co-translational covalent attachment of the fatty acid myristate to the N-terminus of target proteins. NMT is known to be essential for viability in Trypanosoma brucei and Leishmania major. Here we describe phenotypic analysis of T. brucei bloodstream form cells following knockdown of NMT expression by tetracycline-inducible RNA interference. Cell death occurs from 72 h post-induction, with approximately 50% of cells displaying a defect in endocytic uptake by this time. The majority of these induced cells do not have an enlarged flagellar pocket typical of a block in endocytosis but vesicle accumulation around the flagellar pocket indicates a defect in vesicular progression following endocytic fusion. Induced parasites have a wild-type or slightly enlarged Golgi apparatus, unlike the phenotype of cells with reduced expression of a major N-myristoylated protein, ARL1. Critically we show that following NMT knockdown, T. brucei bloodstream form cells are unable to establish an infection in a mouse model, therefore providing further validation of this enzyme as a target for drug development.
doi:10.1016/j.molbiopara.2009.09.006
PMCID: PMC2789243  PMID: 19782106
Arf, ADP-ribosylation factor; Arl, ADP-ribosylation factor-like; BSF, bloodstream form; ConA, concanavalin A; NMT, myristoyl-CoA:protein N-myristoyltransferase; RNAi, RNA interference; T. brucei, Trypanosoma brucei; VSG, variant surface glycoprotein; Myristoyl-CoA:protein N-myristoyltransferase; N-Myristoylation; Trypanosoma brucei; Endocytosis; RNA interference; Drug target
18.  Challenging nickel-catalysed amine arylations enabled by tailored ancillary ligand design 
Nature Communications  2016;7:11073.
Palladium-catalysed C(sp2)–N cross-coupling (that is, Buchwald–Hartwig amination) is employed widely in synthetic chemistry, including in the pharmaceutical industry, for the synthesis of (hetero)aniline derivatives. However, the cost and relative scarcity of palladium provides motivation for the development of alternative, more Earth-abundant catalysts for such transformations. Here we disclose an operationally simple and air-stable ligand/nickel(II) pre-catalyst that accommodates the broadest combination of C(sp2)–N coupling partners reported to date for any single nickel catalyst, without the need for a precious-metal co-catalyst. Key to the unprecedented performance of this pre-catalyst is the application of the new, sterically demanding yet electron-poor bisphosphine PAd-DalPhos. Featured are the first reports of nickel-catalysed room temperature reactions involving challenging primary alkylamine and ammonia reaction partners employing an unprecedented scope of electrophiles, including transformations involving sought-after (hetero)aryl mesylates for which no capable catalyst system is known.
The development of highly effective Earth-abundant catalysts for C(sp 2)-N cross-coupling represents an on-going challenge in synthetic chemistry. Here, the authors report a nickel complex containing a bisphosphine ancillary ligand allowing room-temperature couplings of amines and ammonia with a range of electrophiles.
doi:10.1038/ncomms11073
PMCID: PMC4814586  PMID: 27004442
19.  Surface Sialic Acids Taken from the Host Allow Trypanosome Survival in Tsetse Fly Vectors 
The Journal of Experimental Medicine  2004;199(10):1445-1450.
The African trypanosome Trypanosoma brucei, which causes sleeping sickness in humans and Nagana disease in livestock, is spread via blood-sucking Tsetse flies. In the fly's intestine, the trypanosomes survive digestive and trypanocidal environments, proliferate, and translocate into the salivary gland, where they become infectious to the next mammalian host. Here, we show that for successful survival in Tsetse flies, the trypanosomes use trans-sialidase to transfer sialic acids that they cannot synthesize from host's glycoconjugates to the glycosylphosphatidylinositols (GPIs), which are abundantly expressed on their surface. Trypanosomes lacking sialic acids due to a defective generation of GPI-anchored trans-sialidase could not survive in the intestine, but regained the ability to survive when sialylated by means of soluble trans-sialidase. Thus, surface sialic acids appear to protect the parasites from the digestive and trypanocidal environments in the midgut of Tsetse flies.
doi:10.1084/jem.20030635
PMCID: PMC2211819  PMID: 15136592
Trypanosoma brucei; trypanosomiasis; glycosylphosphatidylinositol; trans-sialidase; GPI transamidase
22.  Depletion of UDP-Glucose and UDP-Galactose Using a Degron System Leads to Growth Cessation of Leishmania major 
PLoS Neglected Tropical Diseases  2015;9(11):e0004205.
Interconversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal) by the UDP-Glc 4´-epimerase intimately connects the biosynthesis of these two nucleotide sugars. Their de novo biosynthesis involves transformation of glucose-6-phosphate into glucose-1-phosphate by the phosphoglucomutase and subsequent activation into UDP-Glc by the specific UDP-Glc pyrophosphorylase (UGP). Besides UGP, Leishmania parasites express an uncommon UDP-sugar pyrophosphorylase (USP) able to activate both galactose-1-phosphate and glucose-1-phosphate in vitro. Targeted gene deletion of UGP alone was previously shown to principally affect expression of lipophosphoglycan, resulting in a reduced virulence. Since our attempts to delete both UGP and USP failed, deletion of UGP was combined with conditional destabilisation of USP to control the biosynthesis of UDP-Glc and UDP-Gal. Stabilisation of the enzyme produced by a single USP allele was sufficient to maintain the steady-state pools of these two nucleotide sugars and preserve almost normal glycoinositolphospholipids galactosylation, but at the apparent expense of lipophosphoglycan biosynthesis. However, under destabilising conditions, the absence of both UGP and USP resulted in depletion of UDP-Glc and UDP-Gal and led to growth cessation and cell death, suggesting that either or both of these metabolites is/are essential.
Author Summary
Leishmaniases are a set of tropical and sub-tropical diseases caused by protozoan parasites of the genus Leishmania. They affect about 12 million people and cause a high morbidity. Since treatments against all forms of leishmaniasis are limited in number and efficacy, many efforts are made to identify potential drug targets and develop new therapies. Although considerable progress in genetic manipulation of Leishmania parasites have been made, it remains difficult to study molecules or metabolic pathways essential for parasite viability and growth. In the present work, we used a combination of gene deletion and conditional protein destabilization to demonstrate that biosynthesis of the nucleotide sugar UDP-glucose and its derivative UDP-galactose is essential for parasite growth. Addition of a specific ligand to the culture medium of the engineered parasite protected the targeted enzyme from degradation and enabled cell growth and viability. However, removal of the stabilizing compound led to depletion of UDP-glucose and UDP-galactose, growth arrest and cell death. This work thus opens a new possibility for the study of essential proteins.
doi:10.1371/journal.pntd.0004205
PMCID: PMC4631452  PMID: 26529232
23.  Evaluation of the Diagnostic Accuracy of Prototype Rapid Tests for Human African Trypanosomiasis 
Background
Diagnosis of human African trypanosomiasis (HAT) remains a challenge both for active screening, which is critical in control of the disease, and in the point-of-care scenario where early and accurate diagnosis is essential. Recently, the first field deployment of a lateral flow rapid diagnostic test (RDT) for HAT, “SD BIOLINE HAT” has taken place. In this study, we evaluated the performance of “SD BIOLINE HAT” and two new prototype RDTs.
Methodology/Principal Findings
The performance of “SD BIOLINE HAT” and 2 prototype RDTs was tested using archived plasma from 250 Trypanosoma brucei gambiense patients, and 250 endemic controls. As well as comparison of the sensitivity and specificity of each device, the performance of individual antigens was assessed and the hypothetical performance of novel antigen combinations extrapolated. Neither of the prototype devices were inferior in sensitivity or specificity to “SD BIOLINE HAT” (sensitivity 0.82±0.01, specificity 0.97±0.01, 95% CI) at the 5% margins, while one of the devices (BBI) had significantly superior sensitivity (0.88±0.03). Analysis of the performance of individual antigens was used to model new antigen combinations to be explored in development of the next generation of HAT RDTs. The modelling showed that an RDT using two recombinant antigens (rLiTat1.5 and rISG65) would give a performance similar to the best devices in this study, and would also offer the most robust performance under deteriorating field conditions.
Conclusions/Significance
Both “SD BIOLINE HAT” and the prototype devices performed comparably well to one another and also to the published performance range of the card agglutination test for trypanosomiasis in sensitivity and specificity. The performance of individual antigens enabled us to predict that an all-recombinant antigen RDT can be developed with an accuracy equivalent to “ SD BIOLINE HAT.” Such an RDT would have advantages in simplified manufacture, lower unit cost and assured reproducibility.
Author Summary
The most prevalent species of trypanosome causing human African trypanosomiasis (HAT), Trypanosoma brucei gambiense, presents a diagnostic challenge. While early diagnosis is essential for effective treatment and also to control transmission, symptoms are non-specific and parasitological diagnosis is laborious and technically difficult. Screening for HAT suspects has until now been done using the card agglutination test for trypanosomiasis (CATT), which requires a cold chain and equipment, making it difficult to deploy. Thus there is an urgent need for sensitive point of care diagnostic tests that are suitable for use in rural areas in terms of stability, simplicity and cost. We describe the evaluation of 3 rapid diagnostic tests (RDTs) for HAT based on lateral flow devices that detect antibodies against defined parasite antigens in blood samples. We demonstrate that the SD BIOLINE HAT RDT currently being deployed in HAT endemic regions, as well as two new prototype devices, are accurate in screening for HAT. By analysing the sensitivity of each of the antigens used in the devices tested, we predict that a highly sensitive RDT based on recombinant antigens can be developed. An all-recombinant antigen RDT offers significant benefits in manufacturing reproducibility and cost, and would dramatically simplify HAT diagnosis.
doi:10.1371/journal.pntd.0003373
PMCID: PMC4270746  PMID: 25521120
24.  TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei 
Nucleic Acids Research  2014;43(Database issue):D637-D644.
The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome. Metabolic network databases are of increasing importance in allowing us to contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments. Here we present a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have also implemented a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite.
doi:10.1093/nar/gku944
PMCID: PMC4384016  PMID: 25300491
25.  Proteomic Selection of Immunodiagnostic Antigens for Trypanosoma congolense 
Animal African Trypanosomosis (AAT) presents a severe problem for agricultural development in sub-Saharan Africa. It is caused by several trypanosome species and current means of diagnosis are expensive and impractical for field use. Our aim was to discover antigens for the detection of antibodies to Trypanosoma congolense, one of the main causative agents of AAT. We took a proteomic approach to identify potential immunodiagnostic parasite protein antigens. One hundred and thirteen proteins were identified which were selectively recognized by infected cattle sera. These were assessed for likelihood of recombinant protein expression in E. coli and fifteen were successfully expressed and assessed for their immunodiagnostic potential by ELISA using pooled pre- and post-infection cattle sera. Three proteins, members of the invariant surface glycoprotein (ISG) family, performed favorably and were then assessed using individual cattle sera. One antigen, Tc38630, evaluated blind with 77 randomized cattle sera in an ELISA assay gave sensitivity and specificity performances of 87.2% and 97.4%, respectively. Cattle immunoreactivity to this antigen diminished significantly following drug-cure, a feature helpful for monitoring the efficacy of drug treatment.
Author Summary
Animal African Trypanosomosis (AAT) is a set of diseases whereby animals are infected with single-cell parasites that replicate in their bloodstream. The disease in cattle results in weight-loss and death, and AAT is a significant veterinary problem for sub-Saharan Africa. One of the principal trypanosome species responsible for AAT in cattle is Trypanosoma congolense and, although there are drug-treatments for these infections, current diagnostic methods are impractical for field use. Our aim was to discover protein molecules from the parasite to which infected animals make antibodies, to then make these proteins in bacteria and to subsequently demonstrate that they can be used to detect antibodies in cattle serum, thus diagnosing AAT. To discover the diagnostic proteins, we dissolved parasites in a detergent solution and applied them to beads coated with antibodies from infected cattle and to beads coated with antibodies from un-infected cattle. We then compared the proteins bound to each and selected those proteins that were at least 100-fold enriched by the infected cattle antibodies. We refined this list, according to practical and performance considerations, and settled on one protein, called Tc38630. Testing Tc38630 with cattle sera showed that it can detect about nine out of ten AAT infections.
doi:10.1371/journal.pntd.0002936
PMCID: PMC4055490  PMID: 24922510

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