Projects

GlycoPar is setup to provide a comprehensive, timely and multidisciplinary training of young European researchers (10 Early Stage Researchers and 3 Experienced Researchers) with the skills and knowledge demanded to address the challenges involved in the study of parasite glycobiology.

Jessica Bevan (PhD student project 1), IMM, Portugal

A systems biology approach to uncover new key glycan-processing enzymes essential for complex N-glycosylation in T. brucei

Main objective: To develop tools to characterise the effects of knockdown of crucial enzymes involved in N-glycosylation metabolism in T. brucei


This project proposes to use Activity Base Proteomic Profiling (ABPP) in order to identify the remaining uncharacterised glycosyltransferases present in Trypanosoma brucei. Their role in T. brucei will then be established through the use of functional genomics and biochemical characterisation in order to assess their essentiality and hopefully find new targets for therapeutics against African sleeping sickness.

Duration: 36 months
Secondments to: SilicoLife, ETH Zürich, University of Dundee, LSTM
Contact: Joao Rodrigues, Instituto de Medicina Molecular-Lisbon[j.rodrigues@fm.ul.pt]

 

Elda iljazi (PhD student project 2), U. Dundee, Scotland

The origin and role of D-arabinopyranose (D-Ara) in kinetoplastids

Main objective: To define the de novo pathway to D-Ara from D-glucose in trypanosomatids


The cell surface glycoconjugates of Leishmania major and Crithidia are involved in parasites survival, infectivity and virulence in their insect vectors and mammalian host. Both the parasites express surface glycoconjugates that contain the rare sugar, D-arabinopyranose. The source is GDP-α-D-Arapyranose but origin of D-Ara itself is unknown. The project is to define the de novo pathway to D-Ara from D-glucose (D-Glc) using a combination of classical biochemistry and state-of-the art analytical methodology.


Duration: 36 months
Secondments to: MH Hannover, Ludger
Contact: Michael Ferguson, University of Dundee [m.a.j.ferguson@dundee.ac.uk]

 

Marta Cova (PhD student project 3), CRESIB, Spain


Sugar nucleotide metabolism and the roles of GDP-fucose and UDP-galactose in P. falciparum


Main objective: To assess the essentiality and role of sugar nucleotide metabolic routes in the malaria parasite


Protozoan parasites surfaces are usually rich in glycoconjugates, some of which play vital roles in their survival, infectivity or virulence. Sugar nucleotides are the building blocks of glycoconjugates. The project focuses on the exploration of the sugar nucleotides and their biosynthetic pathways in Plasmodium falciparum, the most deadly parasite that causes Malaria. Characterization of these essential pathways will enhance our understanding of the parasite’s glycobiology and may provide novel/urgently needed new targets for chemotherapeutic intervention.


Duration: 36 months
Secondments to: University of Dundee, MH Hannover, Ludger
Contact: Luis Izquierdo, CRESIB-Barcelona [luis.izquierdo@cresib.cat]

 

Nathalie Cornillie (PhD student project 4), ETH, Switzerland


Substrate-specificity of single-subunit oligosaccharyltransferases (OSTs) of T. brucei


Main objective: To define protein and oligosaccharide substrate specificity of T. brucei OSTs

N-linked glycosylation is one of the most common protein modifications in eukaryotic organisms. In the central reaction of the pathway, the oligosaccharyltransferase (OST), located at the endoplasmatic reticulum, transfers a preassembled oligosaccharide to asparagine residues within the consensus sequence asparagine-X-serine/threonine. The project focuses on the expression and characterization of the OST of Entamoeba histolytica and Plasmodium falciparum, which are deadly human parasites. Functional analysis of the OST complex will be done by studying in vitro N-linked glycosylation. Furthermore, a purified OST complex will be used in X-ray crystallization studies to gain structural information.


Duration: 36 months
Secondments to: SilicoLife, LSTM
Contact: Markus Aebi, ETH Zurich [markus.aebi@micro.biol.ethz.ch]

 

Andreia Albuquerque (PhD student project 5), MH-H, Germany


C-mannosylation in Apicomplexan parasites: Potential new targets for drug design


Main objective: To characterize C-mannosylation in Apicomplexan parasites.


The aim is to characterize and understand the importance of C-mannosylation in Apicomplexan parasites.Our model organism Toxoplasma gondii is a parasite of humans and some animals, and a model for other Apicomplexans including Plasmodium sp., the causative agents of Malaria. To date, very little is known about C-mannosylation of proteins in eukaryotes. Here, we wish to identify C-mannosylated proteins and define the effect of loss of C-mannosylation on the parasite biology.


Duration: 36 months
Secondments to: Biognos, University of Dundee
Contact: Rita Gerardy-Schahn & Françoise Routier, MH Hannover [gerardy-schahn.rita@mh-hannover.de & routier.francoise@mh-hannover.de]

 

Aitor Casas (PhD student project 6), LSTM, England


Structural and functional characterization of surface glycans from T. brucei metacyclics


Main objective: To characterize the structure, transfer and role of N-glycans from metacyclics

 

Trypanosoma brucei is an insect-borne parasite that causes sleeping sickness, which is a fatal disease affecting thousands of people in Africa every year. It also kills livestock and consequently has placed a severe economic burden on Sub-Saharan Africa as there is no vaccine. This parasite alternates its life cycle between a vertebrate host and a blood-feeding insect vector, the tsetse fly. The infectious stage of the parasite (the metacyclic form) develops in the salivary glands of the infected tsetse and is only transmitted to a mammalian host through the infected fly’s bite. So far, the metacyclic stage of T. brucei has been underinvestigated at the molecular level partly due to the difficulties culturing this form in vitro. However, access to large tsetse facilities and the recent development of an in vitro culture system make possible the characterization of this important parasite stage. This project aims to determine the structure and function of the glycocalyx (sugar coat on the parasite surface) from the T. brucei metacyclic stage. This is important as metacyclic surface sugars may be involved in the recognition of host tissues and cells or may be essential for establishing a mammalian infection after transmission by the tsetse. Unlike the metacyclic variant surface glycoprotein (VSG) coat, the surface sugars attached to the VSG proteins are thought to remain unaltered, thus making them a potential target for developing a glycovaccine against sleeping sickness.

 

Duration: 36 months
Secondments to: University of Dundee, ETH Zurich, Malcisbo
Contact: Alvaro Acosta-Serrano, LSTM-Liverpool [A.F.Acosta-Serrano@liverpool.ac.uk]

 

Matthew Calvert (ER postdoc project 7), HIPS, Germany

 

Substrate specificity, inhibition and structural analysis of the nematode enzyme GalT-1

 

Main objective: To assess the specificity of GalT-1 and to design and obtain inhibitors against the enzyme by chemical synthesis of complex oligosaccharide acceptor molecules and glycomimetic derivatives

 

The galactosyltransferase enzyme GalT-1 was recently identified in the model nematode Caenorhabditis elegans, and has been shown to catalyse galactosylation of the core fucose residue in N-glycans. In order to gain insight into the structure and reactivity of this enzyme, mimics of the native octasaccharide substrate will be synthesised, with these molecules enabling characterisation of the enzyme by enzymology. With the results obtained from these studies, an effective inhibitor of GalT-1 will be designed and synthesised, ultimately enabling crystallisation of the enzyme in complex with an inhibitor and analysis of its structure by X-ray crystallography.

 

Contact: Alexander Titz, HIPS-Saarbrücken [alexander.titz@helmholtz-hzi.de]

 

Francesca Martini (PhD student project 8), Malcisbo, Switzerland

 

Recombinant expression of Dirofilaria immitis proteins with nematode-specific N-linked glycans


Main objective: To develop a vaccine against D. immitis based on recombinantly expressed parasite-specific glycoproteins.


The goal of this project is to develop a novel vaccine protective against the dog’s heartworm Dirofilaria immitis, a parasite distributed worldwide. The characterization of this D. immitis’ glycome in the early stages of this project is of primary importance for the identification of potentially immunogenic glycan structures. Moreover, various in vitro and in silico approaches will be used aiming at the establishment of a glycotarget and its subsequent production and testing.


Duration: 36 months
Secondments to: BOKU
Contact: Irene Schiller, Malcisbo AG-Zurich [irene.schiller@postmail.ch]

 

Ohm Prakash (PhD student project 9), MH-H, Germany


Structure-based Inhibitor Design and Glycoinformatics


Main objective: Inhibitor design for Leishmania pyrophosphorylase; Virtual screening of small molecule libraries against P. falciparum enzymes and C. elegans enzymes to detect potential inhibitors.


Leishmania are protozoan parasites that cause severe diseases in humans and animals. They expresses two pyrophosphorylases responsible for the synthesis of UDP-glucose, which are essential for parasite survival. The aim of this work is to gain detailed structural information about these enzymes in order to design structure based inhibitors affecting exclusively the parasite pyrophosphorylases.


Duration: 36 months
Secondments to: MH Hannover or HZI (X-ray crystallography), CRESIB (in vitro testing of inhibitors)
Contact: Rita Gerardy-Schahn & Françoise Routier, MH Hannover [gerardy-schahn.rita@mh-hannover.de & routier.francoise@mh-hannover.de]

 

Sushil Kumar (PhD student project 10), SilicoLife, Portugal


Development of software tools for the analysis and integration of experimental data obtained from glycoproteomic approaches.

Main objective: To integrate glycomics data with genome scale models to identify physiologically relevant nodes in metabolic and regulatory networks


The objective of the project is to produce a state-of-the-art review on the current glycomics data resources and analytical tools as no standardization methods for representation, storage or analysis of glycomics data has been adopted by the glycobiology community so far. The report will focus on technical difficulties in existing glycomics databases and analytical tools for data access and performing data analysis respectively. Further, state-of-the-art knowledge will be used to tackle the challenging task of developing effective strategy for integrating glycomics data with genome-scale models (GSMs) of human parasites to investigate the metabolism and predict the effect of glycans/glycoconjugates biosynthesis in their survival strategies. The project will utilize available GSMs of parasites and glycomics data from various glycomics resources to develop methodology for performing integrative analysis using Flux Balance Analysis (FBA).

 

Duration: 36 months
Secondments to: Instituto de Medicina Molecular
Contact: Simão Soares, SilicoLife Lda.-Guimarães [ssoares@silicolife.com]

 

Eleonora Aquilini (ER postdoc project 11), IMM, Portugal


ER postdoc project 11: Comprehensive glycoproteomic analysis of P. falciparum


Main objective: To fully characterize the putative N- and O-glycoproteome of P. falciparum across several stages of the parasite life cycle.


More than 40% of the world’s population lives at risk of contracting malaria. Human malaria is caused by protozoa of the genus Plasmodium. By using a comprehensive, fully characterization of the N-glycome of P. falciparum across several stages of its life cycle, it will be possible to acquire new insights into parasite evolution, molecular biology, and host-pathogen interactions, but also move one-step closer to the development of a malarial vaccine.


Duration: 24 months
Secondments to: CRESIB, Ludger, SilicoLife
Contact: Joao Rodrigues, Instituto de Medicina Molecular-Lisbon [j.rodrigues@fm.ul.pt]

 

Jorick Vanbeselaere (ER postdoc project 12), BOKU, Austria


Characterization of the structure and biosynthesis of parasite glycans.


Main objective: Analysis of amoebal glycoconjugates and assay of key glycoenzyme activities by HPLC and mass spectrometry.

 

This research project aims to characterize the fine structures of N-glycans and lipophosphoglycans (LPG) in amoebae and to investigate the metabolism pathways required for the biosynthesis of these structures. Some amoebae are responsible for severe human infections, like amoebic keratitis in the eyes or granulomatous amoebic encephalitis (GAE) in the brain. The structural studies will be realized by HPLC (High Performance Liquid Chromatography) purification and MS (Mass Spectrometry) analyses to collect and identify all the glycan structures of interest. The metabolic studies will be based on identification by HPLC and LC-MS of the required cellular building blocks, as well as on cloning of selected amoebae genes using standard approaches of molecular
biology. Recombinant protein expression will allow the assay of relevant enzymes in order
to investigate their specificities. This project will provide structural and metabolic information about N-glycans and lipophosphoglycans that could be directly involved in the pathogenicity of Amoebae species.


Duration: 24 months
Secondments to: CRESIB, University of Dundee, Malcisbo
Contact: Iain Wilson, BOKU-Vienna [iain.wilson@boku.ac.at]

 

Katherine Wongtrakul-Kish (ER postdoc project 13), Ludger Ltd, England


Characterization of the structure and biosynthesis of parasite glycans.


Main objective: Analysis of amoebal glycoconjugates and assay of key glycoenzyme activities by HPLC and mass spectrometry.


As part of her work in GlycoPar, Katherine will be involved in the development of high throughput, automatable analytical technologies to aid in the analysis of parasite glycans at various levels of glycomics analysis. This work will focus mainly on methods for monosaccharide and released O-glycan analysis, including a comparison of different glycan labels. In addition to this, her project will also focus on the optimisation of linkage analysis methodologies to further probe the parasite glycome.


Duration: 24 months
Secondments to: BOKU, CRESIB, Instituto de Medicina Molecular
Contact: Daniel Spencer, Ludger Ltd.-Abingdon [Daniel.Spencer@ludger.com]