Les cellules exposent à leurs surface glycoconjugués qui jouent important dans des événements biologiques importants tels que la communication entre cellules, la croissance de cellules saines ou cancéreuses et les processus d'infection d'agents pathogènes. Certaines structures polysaccharidiques qui contiennent le résidu Galf ont attiré beaucoup d’intérêt au cours des dernières décennies. En effet, le galactofuranose peut être exprimé chez de nombreuses espèces pathogènes, telles que Mycobacterium tuberculosis, Aspergillus et Leishmania, mais il est absent chez les mammifères. Par conséquent, ces glycoconjugués sont considérés comme des cibles intéressantes pour des approches thérapeutiques.Les galactofuranosyltransférases (GalfT) catalysent le transfert des résidus de galactofuranose dans les structures des glycoconjugués. Cependant, ces GalfT sont des enzymes faiblement décrites, malgré leur rôle crucial dans la virulence ainsi que dans la pathogénicité de nombreux micro-organismes. Jusqu'à présent, seule la GalfT2 de Mycobacterium tuberculosis a été entièrement caractérisée.Dans cette thèse, quatre GalfTs de Leishmania major, l'agent responsable de la leishmaniose, ont été caractérisées. Elles ont été d'abord clonées, surexprimées dans E. coli et purifiées. Ensuite, leurs paramètres cinétiques respectifs ont été déterminés. De plus, puisque ces GalfT sont situées dans l'appareil de Golgi de Leishmania, nous avons supposé que leur glycosylation pourrait être un élément important pour leur stabilité etleur activité. Ainsi, des GalfT glycosylés ont été produites à l'aide de Leishmania tarentolae et les résultats préliminaires de leur activité enzymatiques ont été obtenus.Les GalfT leishmaniennes démontrent des résultats prometteurs pour le développement de nouvelles stratégies chimio-enzymatiques pour la synthèse de glycoconjugués contenant du Galf, ainsi que pour la conception de nouveaux médicaments contre la leishmaniose. / Cells are heavily decorated by diverse glycoconjugates that are involved in important biological events such ascell-cell communication, growth of healthy or cancerous cells and pathogens infection process. Among these polysaccharidic structures, Galf-containing glycans have been the subject of increasing interest in the last decades. Indeed, the galactofuranose can be found in many pathogenic species, such as Mycobacteriumtuberculosis, Aspergillus and Leishmania, but is absent in mammals. Therefore, these glycoconjugates are considered as interesting targets for therapeutic approaches.Galactofuranosyltransferases (GalfTs) catalyse the transfer of galactofuranose residues into glycoconjugatesstructures. However, GalfTs are poorly described enzymes despite their crucial role in the virulence and the pathogenicity of numerous microorganisms. Up to date, only one mycobacterial GalfT has been fully characterized.In this thesis, four putative GalfTs of Leishmania major, the causing agent of leishmaniosis diseases, were characterized. They were first cloned, overexpressed in E. coli and purified. Then, their respective kineticparameters were determined. In addition, since these GalfT are located in the Golgi apparatus of Leishmania, we assumed that their glycosylation could be an important element for their stability and activity. So, glycosylatedGalfTs were produced using, Leishmania tarentolae, and preliminary results of their enzymatic activity were obtained.Still, leishmanian GalfTs demonstrate promising results for the development of new chemoenzymatic strategies for Galf-containing glycoconjugates synthesis, as well as the design of new drugs against leishmaniasis.

Human systemic fungal infections are increasing, and causing high morbidity and mortality. Treatment is challenging because fungi share many metabolic pathways with mammals. Current antifungals are losing effectiveness due to drug resistance. In immunocompromised patients Aspergillus fumigatus causes systemic aspergillosis, the most important airborne fungal disease. Mortality from aspergillosis exceeds 50% even with aggressive treatment. We need novel antifungal drug targets. Fungal cell wall components are promising targets for antifungal therapy as they are essential for fungi and absent from humans. The sugar galactofuranose (Galf) is a 5-memberd ring form of galactose that is found in the cell walls of many fungi, but not in mammals. I used molecular biology and microscopy techniques to characterize Galf biosynthesis enzymes in the model species A. nidulans. I studied three enzymes that catalyze sequential steps in Galf biosynthesis: UgmA, UgtA and UgeA. UDP-galactopyranose mutase (UgmA) creates UDP-galactofuranose (UDP-Galf) from UDP galactopyranose (UDP-Galp) in the cytoplasm. The UDP-Galf transporter (UgtA) moves UDP Galf into membrane bound organelles for incorporation into cell wall compartments. Upstream of UgmA, UDP-glucose/galactose epimerase (UgeA) interconverts UDP-glucose into UDP-Galp, the UgmA substrate. Neither UgmA nor UgtA has a human counterpart; UgeA is in the Leloir galactose metabolism pathway that found in many organisms from bacteria to humans. None of UgeA, UgmA and UgtA is essential for viability of A. nidulans, but deleting any one of them substantially reduces colony growth and sporulation (Figure i). Wild type and Galf defective strains (ugeA∆, ugmA∆ and ugtA∆) were quantified for colony growth, cell morphometry, spore formation and germination, as well as wall architecture. The abundance of these proteins was regulated using the alcA promoter. Galf content was assessed by immunolocalization in the Galf defective strains, showing that those strains lacked immunodetectable Galf. Gene products were localized with fluorescent protein tags; both UgmA and UgeA were cytoplasmic, whereas UgtA was Golgi localized. Wall surfaces were imaged and force-probed using transmission electron microscopy and atomic force microscopy. Overall, Galf deletion strains had aberrant wall maturation, and poorly consolidated surfaces. Our results indicate that Galf is necessary for abundant sporulation, wild type growth and full maturation of Aspergillus cell wall. Galf deletion strains were assessed for sensitivity to antifungal agents in clinical use. They were significantly more sensitive to caspofungin and amphotericin B that target cell wall synthesis and cell membrane chemistry, respectively. Thus, anti-Galf drugs (once created) may be useful in combination with existing antifungal drugs. In summary, Galf biosynthesis pathway appears to be promising as an antifungal drug development target.

Human systemic fungal infections are increasing, and causing high morbidity and mortality. Treatment is challenging because fungi share many metabolic pathways with mammals. Current antifungals are losing effectiveness due to drug resistance. In immunocompromised patients Aspergillus fumigatus causes systemic aspergillosis, the most important airborne fungal disease. Mortality from aspergillosis exceeds 50% even with aggressive treatment. We need novel antifungal drug targets. Fungal cell wall components are promising targets for antifungal therapy as they are essential for fungi and absent from humans. The sugar galactofuranose (Galf) is a 5-memberd ring form of galactose that is found in the cell walls of many fungi, but not in mammals. I used molecular biology and microscopy techniques to characterize Galf biosynthesis enzymes in the model species A. nidulans. I studied three enzymes that catalyze sequential steps in Galf biosynthesis: UgmA, UgtA and UgeA. UDP-galactopyranose mutase (UgmA) creates UDP-galactofuranose (UDP-Galf) from UDP galactopyranose (UDP-Galp) in the cytoplasm. The UDP-Galf transporter (UgtA) moves UDP Galf into membrane bound organelles for incorporation into cell wall compartments. Upstream of UgmA, UDP-glucose/galactose epimerase (UgeA) interconverts UDP-glucose into UDP-Galp, the UgmA substrate. Neither UgmA nor UgtA has a human counterpart; UgeA is in the Leloir galactose metabolism pathway that found in many organisms from bacteria to humans. None of UgeA, UgmA and UgtA is essential for viability of A. nidulans, but deleting any one of them substantially reduces colony growth and sporulation (Figure i). Wild type and Galf defective strains (ugeA∆, ugmA∆ and ugtA∆) were quantified for colony growth, cell morphometry, spore formation and germination, as well as wall architecture. The abundance of these proteins was regulated using the alcA promoter. Galf content was assessed by immunolocalization in the Galf defective strains, showing that those strains lacked immunodetectable Galf. Gene products were localized with fluorescent protein tags; both UgmA and UgeA were cytoplasmic, whereas UgtA was Golgi localized. Wall surfaces were imaged and force-probed using transmission electron microscopy and atomic force microscopy. Overall, Galf deletion strains had aberrant wall maturation, and poorly consolidated surfaces. Our results indicate that Galf is necessary for abundant sporulation, wild type growth and full maturation of Aspergillus cell wall. Galf deletion strains were assessed for sensitivity to antifungal agents in clinical use. They were significantly more sensitive to caspofungin and amphotericin B that target cell wall synthesis and cell membrane chemistry, respectively. Thus, anti-Galf drugs (once created) may be useful in combination with existing antifungal drugs. In summary, Galf biosynthesis pathway appears to be promising as an antifungal drug development target.

Forma epimastigotas de T. cruzi são aglutinadas especificamente por baixas concentrações de concanavalina A. A aglutinação é linear com o tempo até aproximadamente10 minutos, para um número de células maior que 1 x 108 células/ml. Nessas condições a aglutinação é dependente da concentração de con A. As formas tripomastigotas sanguícolas e matecíclicas não são aglutináveis por con A. O complexo glicoproteico isolado de formas epimastigotas de T. cruzi por tratramentofenólico de extrato celular, apresenta na sua composição ácida siálico, glicosamina, galactose, glicose e manose, além de xilose em algumas frações. Os aminoácidos constituintes são principalmente lisina, ácido aspártico (e/ou asparagina), alanina, treonina, ácido glutâmico (e/ou glutamina). serina, prolina e glicina. Esse complexo pode ser separado em três componentes em colunas de DEAE-celulose. Dois desses componentes, selecionados para estudo, inibem a reação de aglutinação por con A das formas epimastigotas, assim como a fração não cromatografada. Essas frações isoladas fornecem quatro componentes glicoproteicos por eletroforese em gel de poliacrilamida na presença de SDS. / Epimastigote forms of T. cruzi are agglutinated by low con A concentrations. The agglutinabillity is linear up to 10 minutes. Under these conditions the agglutination is dependent on the con A concentration providing the cell density is 108/ml or higher. The blood forms and culture trypomastigotes are not agglutinated by con A. A glycoprotein complex was isolated from epimastigote forms of T. cruzi by aqueous phenol extraction. This complex is composed by sialic acid, glucosamine, galactose, glucose, mannose and xylose. The latter appears only in some fractions of the complex. The amino acids found are lysine, aspartic acid (and/or asparagine), alanine, threonine, glutamic acid (and/or glutamine), serine, proline and glycine. The glycoproteins render three components in DEAE-cellulose columns (peaks 1, 2 and 3). The peaks 2 and 3 are able to inhibit the agglutination of epimastigotes by con A. These fractions are separated in four glycoprotein components by polyacrylamide gel electrophoresis in the presence of SDS.

Forma epimastigotas de T. cruzi são aglutinadas especificamente por baixas concentrações de concanavalina A. A aglutinação é linear com o tempo até aproximadamente10 minutos, para um número de células maior que 1 x 108 células/ml. Nessas condições a aglutinação é dependente da concentração de con A. As formas tripomastigotas sanguícolas e matecíclicas não são aglutináveis por con A. O complexo glicoproteico isolado de formas epimastigotas de T. cruzi por tratramentofenólico de extrato celular, apresenta na sua composição ácida siálico, glicosamina, galactose, glicose e manose, além de xilose em algumas frações. Os aminoácidos constituintes são principalmente lisina, ácido aspártico (e/ou asparagina), alanina, treonina, ácido glutâmico (e/ou glutamina). serina, prolina e glicina. Esse complexo pode ser separado em três componentes em colunas de DEAE-celulose. Dois desses componentes, selecionados para estudo, inibem a reação de aglutinação por con A das formas epimastigotas, assim como a fração não cromatografada. Essas frações isoladas fornecem quatro componentes glicoproteicos por eletroforese em gel de poliacrilamida na presença de SDS. / Epimastigote forms of T. cruzi are agglutinated by low con A concentrations. The agglutinabillity is linear up to 10 minutes. Under these conditions the agglutination is dependent on the con A concentration providing the cell density is 108/ml or higher. The blood forms and culture trypomastigotes are not agglutinated by con A. A glycoprotein complex was isolated from epimastigote forms of T. cruzi by aqueous phenol extraction. This complex is composed by sialic acid, glucosamine, galactose, glucose, mannose and xylose. The latter appears only in some fractions of the complex. The amino acids found are lysine, aspartic acid (and/or asparagine), alanine, threonine, glutamic acid (and/or glutamine), serine, proline and glycine. The glycoproteins render three components in DEAE-cellulose columns (peaks 1, 2 and 3). The peaks 2 and 3 are able to inhibit the agglutination of epimastigotes by con A. These fractions are separated in four glycoprotein components by polyacrylamide gel electrophoresis in the presence of SDS.

UDP-galactopyranose mutase (UGM) is a flavoenzyme which catalyzes the interconversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDPGalf). UDP-Galf is the active precursor of Galf residues. Glycoconjugates of Galf residues are found in the cell wall of bacteria and on the cell surface of higher eukaryotes. Galf residues have not been found in humans and the fact that they are essential for the growth of pathogenic bacteria makes UGM a potential antibacterial target. In the present study, crystal structures of UGM from Deinocococcus radiodurans (drUGM) in complex with substrate (UDP-Galp) were determined. UDP-Galp is buried in the active site and bound in a U-shaped conformation. The binding mode and active site interactions of UDP-Galp are consistent with the previous biochemical and mechanistic studies. The mobile loops in the substrate complex structures exist in a closed conformation and Arg198 on one of the mobile loops stabilizes the phosphate groups of the substrate. The anomeric carbon of galactose is 2.8 Å from the N5 of FAD (in the reduced complex) favorable to form FAD-galactosyl adduct. In addition to substrate complex structures, the crystal structures of drUGM in complex with UDP, UMP, and UDP-Glc have been determined. The mobile loops in all these complexes exist in a closed conformation. Inhibitors for UGM were identified by ligand-based and structure-based methods. The phosphonate analog of UDP-Galp (GCP) showed only weak inhibition against various bacterial UGMs. The structure of drUGM in complex with GCP provided a basis for its inhibitory activity. Poor stabilization of the phosphate groups by conserved arginines (Arg198 and Arg305) and altered sugar binding mode account for its activity. Novel indole-based (LQ1, LQ6 and LQ10) inhibitors of UGM were identified through structure-based virtual screening (SBVS) of a chemical library. Inhibition studies also allowed the identification of an active site aspartic acid that plays role in inhibitor binding. The structural studies on drUGM provided a basis for understanding substrate binding to UGM. In vitro enzyme inhibition studies allowed the identification of novel indole-based inhibitors. The structural and inhibition studies reported here enhance the understanding of UGM-ligand interactions and will assist in the development of more potent inhibitors of UGM.

UDP-galactopyranose mutase (UGM) is a flavoenzyme which catalyzes the interconversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDPGalf). UDP-Galf is the active precursor of Galf residues. Glycoconjugates of Galf residues are found in the cell wall of bacteria and on the cell surface of higher eukaryotes. Galf residues have not been found in humans and the fact that they are essential for the growth of pathogenic bacteria makes UGM a potential antibacterial target. In the present study, crystal structures of UGM from Deinocococcus radiodurans (drUGM) in complex with substrate (UDP-Galp) were determined. UDP-Galp is buried in the active site and bound in a U-shaped conformation. The binding mode and active site interactions of UDP-Galp are consistent with the previous biochemical and mechanistic studies. The mobile loops in the substrate complex structures exist in a closed conformation and Arg198 on one of the mobile loops stabilizes the phosphate groups of the substrate. The anomeric carbon of galactose is 2.8 Å from the N5 of FAD (in the reduced complex) favorable to form FAD-galactosyl adduct. In addition to substrate complex structures, the crystal structures of drUGM in complex with UDP, UMP, and UDP-Glc have been determined. The mobile loops in all these complexes exist in a closed conformation. Inhibitors for UGM were identified by ligand-based and structure-based methods. The phosphonate analog of UDP-Galp (GCP) showed only weak inhibition against various bacterial UGMs. The structure of drUGM in complex with GCP provided a basis for its inhibitory activity. Poor stabilization of the phosphate groups by conserved arginines (Arg198 and Arg305) and altered sugar binding mode account for its activity. Novel indole-based (LQ1, LQ6 and LQ10) inhibitors of UGM were identified through structure-based virtual screening (SBVS) of a chemical library. Inhibition studies also allowed the identification of an active site aspartic acid that plays role in inhibitor binding. The structural studies on drUGM provided a basis for understanding substrate binding to UGM. In vitro enzyme inhibition studies allowed the identification of novel indole-based inhibitors. The structural and inhibition studies reported here enhance the understanding of UGM-ligand interactions and will assist in the development of more potent inhibitors of UGM.

The cell wall is essential for fungal survival in natural environments. Galactofuranose (Galf) decorates certain carbohydrates and lipids of Aspergillus cell wall, is absent in humans and appears to play a role in fungal cell wall maturation. Previous studies in our lab showed that deletion of any of three sequential-acting genes (ugeA, ugmA, and ugtA) of Galf pathway caused substantially reduced growth and spore production. Two genes upstream of the Galf pathway, galD and galE are essential for galactose metabolism in many systems including the budding yeast, Saccharomyces cerevisiae. Interestingly, characterization of galD and galE in A. nidulans using cell and molecular techniques showed that unlike yeast, neither of these genes was essential for growth at physiological pH 7.5. Nevertheless for each case, their expressions were up-regulated by growth on galactose, revealing the relative complexity of galactose metabolism in A. nidulans. Our study also showed that repression of the three sequentially acting Galf pathway genes by conditional promoters phenocopied previously characterized deletion morphology. Using anti-Galf (L10) we also showed that deletion and repression of these genes caused no Galf in the hyphal wall. Gene deletion or repression also increased sensitivity to the wall-targeting drug, caspofungin. Related results from qPCR showed that deletion or repression of ugmA increased gene expression of α-glucan synthase agsB and decreased that of β-glucan synthase fksA. Therefore, Galf is non-essential but important for many aspects of Aspergillus growth, sporulation, and wall maturation. Aspergillosis, the most common airborne systemic fungal disease, is typically caused by Aspergillus fumigatus. Several A. fumigatus UgmA (AfUgmA) mutants with altered enzyme activity due to single amino acid changes were used to assess their effect on growth and wall composition in A. nidulans. Wild type AfugmA complemented the phenotypic defects in an A. nidulans ugmAΔ strain, consistent with these two genes being homologous. The AfUgmA crystal structure has been solved, and the in vitro enzymatic effects of specific mutations in the enzyme active site have been published. AfUgmA mutated strains with reduced activity in vitro impaired A. nidulans growth in a manner substantially similar to gene deletion and gene down-regulation. Site directed mutagenesis showed that AfUgmA residues R182 and R327 were critical for Galf generation both in vivo and in vitro. This supports previous results showing that UgmA is essential for Galf biosynthesis. Using fluorescent latex beads, we showed that reduction of wall Galf increased hyphal surface adhesion. Consistent with qPCR studies, immunofluorescence and ELISA results showed that loss or absence of Galf increased wall α-glucan but reduced wall β -glucan. Galf is important for wall surface integrity and for maintaining dynamic co-ordination with other pathways. To begin to assess this dynamic co-ordination, Tandem Affinity Purification (TAP) tagging combined with LC-MS/MS was used to identify the interacting partners of UgmA. Our results showed that UgmA interacted with proteins that are involved in cytoskeleton generation, osmotic adaptation, and cell signalling pathway. Further study will help us to understand the dynamic coordination of Galf biosynthesis pathway with other wall carbohydrate polymers for Aspergillus wall formation. In summary, my thesis results have clearly shown that Galf plays important roles in Aspergillus growth, and wall surface integrity. We also showed that Galf deficient strains are hypersensitive to wall-targeting drugs, indicating that Galf biosynthesis pathway could be potential target for combination therapy. The Galf pathway also maintained a dynamic co-ordination with alpha-glucan and beta-glucan carbohydrate pathways. Future study may include developing an inhibitor against UgmA and exploring the relationship of Galf pathway with alpha-glucan and beta-glucan carbohydrate pathways.

Galactofuranose (Galf) is the five membered ring form of galactose. It is found on the cell wall and surface of many pathogens including Mycobacterium tuberculosis, Aspergillus fumigatus, Leishmania major, and Trypanosoma cruzi. Galf has been implicated in pathogenesis in these organisms; thus the biosynthetic pathway of Galf is a target for drug design. Galf is synthesized by the enzyme UDP-galactopyranose mutase (UGM), which converts UDP-galactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf). Solving the mechanism and structure of UGMs will aid in the development of specific inhibitors against these enzymes. Herein we present the detailed functional analysis of UGMs from A. fumigatus, T. cruzi, and L. major. The mechamism and structure these eukaryotic UGMs were examined by steady-state kinetics, rapid-reaction kinetics, trapping of reaction intermediates, fluorescence anisotropy, and X-ray crystallography. The mechanism first involves reduction of the required flavin by NADPH, followed by UDP-Galp binding and subsequent SN2 attack by the flavin on galactose displacing UDP to form a flavin N5-C1 galactose adduct. Next, the galactose ring opens forming an iminium ion allowing isomerization to occur. Lastly, the product is released and UGM is available to bind another substrate or be reoxidized by molecular oxygen. The three-dimensional structure of A. fumigatus UGM was solved using X-ray crystallography in four conformations: oxidized in complex with sulfate ions, reduced, reduced in complex with UDP, and reduced in complex with UDP-Galp, giving valuable information on the unique features of eukaryotic UGMs including features important for oligomerization and for substrate binding. The novel mechanism and structure provide valuable information for the development of specific inhibitors of eukaryotic UGMs. / Ph. D.

UDP-galactopyranose mutase (EC 5.4.99.9; UGM), the product of the glf gene, is an enzyme that catalyzes the conversion of uridine diphosphate galactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf). UGM activity is found in bacteria, parasites and fungi, however is absent in higher eukaryotes. This enzyme is essential for the viability of many pathogenic organisms, such as Mycobacterium tuberculosis and Escherichia coli, due to the broad distribution of Galf in crucial structures such as the cell wall or capsular polysaccharide. Not surprisingly, galactofuranose biosynthesis has become an attractive antimicrobial target due to the absence of these sugars in higher eukaryotes. The UGM homologue, UDP-Nacetylgalactopyranose mutase (UNGM), was identified in Campylobacter jejuni 11168, encoded for by the cj1439c gene. UNGM is known to function as a bifunctional mutase, which catalyzes the reversible ring contraction between the pyranose-furanose forms of UDPgalactose (UDP-Gal) and UDP-N-acetylgalactosamine (UDP-GalNAc). UNGM is essential for the virulence of C. jejuni, due to the incorporation of UDP-N-acetylgalactofuranose into the capsular polysaccharide. We report the first structure of UNGM determined by X-ray crystallography, to a resolution of 1.9 Å. Analysis of the dimeric, holoenzyme structure of UNGM has identified that the cofactor flavin adenine dinucleotide is bound within each monomer of the enzyme. Comparative analysis with UGM homologues has confirmed the conserved active site residues involved in the binding of various substrates. Docking studies suggest that UNGM binds its natural substrates in a productive binding mode for catalysis with the flavin cofactor, which is consistent with the proposed mechanism for UNGM. The mobile loops are essential for substrate binding, and we have identified that the conserved arginine residue, Arg169, and the neighboring Arg168, function to stabilize the diphosphate region of UDP, although not concurrently. The non-conserved arginine residue, Arg168, appeared to favor the stabilization of N-acetylated sugars, which is in agreement with the enzyme’s higher binding affinity for UDP-GalNAc over UDP-Gal by a factor of 0.9. We have also identified that the active site Arg59 exists in two conformations in the structure of UNGM, with one conformation directed toward the active site. Arg59 is 2.5 to 3.0 Å from the acetamido moiety of GalNAc, which is favorable for stabilization and is believed to confer specificity for this substrate.