La carnitine, un acide aminé crucial pour le transfert intracellulaire des acides gras chez les animaux et les micro-organismes, est présente chez les plantes mais son mode d'implication dans le métabolisme lipidique et dans le développement reste à déterminer. Afin d'étudier le rôle biologique de la carnitine chez Arabidopsis nous avons initié une recherche bioinformatique d'enzymes susceptibles de participer à sa synthèse dans le but d'obtenir des mutants à teneur réduite en carnitine. Des serines hydroxyméthyl transférases (SHMT), des thréonines aldolases (THA) et des aldéhydes déshydrogénases (ALDH) candidates ont été identifiées. Une recherche de mutants, soit caractérisés, soit dans les collections disponibles, ainsi qu'une approche de mutagénèse par micro-ARN artificiel ont été initiées. Ces mutants ont été étudiés sur le plan de leur teneur en carnitine, en précurseur y-butyrobétaïne, et en esters de carnitine. Les enzymes THA ne semblent pas impliquées dans la synthèse de la carnitine et si un mutant faible de SHMT1 présente une réduction de sa teneur, et de la y-butyrobétaïne, l'implication de cette protéine reste à démontrer. L'étude d'un mutant perte de fonction du gène ALDH10A8, et de mutants baisse de fonction du gène ALDH10A9, et une complémentation fonctionnelle de mutants de levure, nous ont permis de montrer que les enzymes ALDH10 sont impliquées dans la voie de biosynthèse de la carnitine en permettant la synthèse de la y-butyrobétaïne. Les mutants des protéines ALDH10, présentant des teneurs réduites en carnitine et en acyl-carnitine, sont désormais disponibles comme outil du rôle de la carnitine chez Arabidopsis. / Carnitine, a crucial amino acid for the intacellular transfer of fatty acids in animals and microorganisms, is present in plants but its mode of implication in lipid metabolism and development remains to be determined. In order to investigate the biological function of carnitine in Arabidopsis, we initiated a bioinformatic search for enzymes that could be involved in its synthesis in order to obtain mutants with a reduced carnitine content. Serine hydroxymethyl transferases (SHMT), threonine aldolase (THA) and aldehyde dehydrogenase (ALDH) were identified as candidates. A search for mutants, either characterized or in available collections ans an amiRNA mutagenesis approach were carried out. In these mutants, the y-butyrobetaine as carnitine precursor, the carnitine, and carnitine esters were quantified. The THA enzymes do not appear to be involved in the carnitine synthesis and even if a weak mutant of SHMT1 has reduced contents of carnitine and y-butyrobetaine, the involvement of this protein remains to be demonstrated. A study of a knock-out mutant of the ALDH10A8 gene, of knock-down mutants of ALDH10A9 and a functional complementation of a C. albicans ALDH mutant, has confirmed the implication of ALDH10A8 and ALDH10A9 enzymes in the synthesis of y-butyrobetaine within the cartinine biosynthesis pathway. Mutants of the ALDH10 proteins, having significantly reduced carnitine and acyl-carnitine amounts, are now available as tools for studying the role of carnitine in Arabidopsis.

A doença de Chagas é uma doença causada pelo protozoário parasita Trypanosoma cruzi, que afeta cerca de 10 milhões de pessoas, principalmente nas Américas. O T. cruzi utiliza aminoácidos como importante fonte de energia e em vários processos biológicos como diferenciação, resistência a condições de estresse e invasão de células hospedeiras. A serina está envolvida em muitas vias biosintéticas. Uma das funções relevantes da serina é a formação de compostos C1 para a biossíntese de nucleotídeos. O uso de serina para esse fim é iniciado pela Serina Hidroximetiltransferase, cuja atividade foi detectada em T. cruzi, mas seu papel na biologia do parasita permanece pouco explorado. Neste trabalho, identificamos um gene que codifica uma Serina Hidroximetiltransferase putativa com dupla localização (citoplasmática e mitocondrial). Por recombinação homóloga, obtemos parasitas knockouts heterozigotos nos quais um alelo de SHMT foi substituído pelo gene da neomicina fosfotransferase. Os parasitas knockouts não mostraram diferenças na taxa de crescimento das formas epimastigotas ou na metaciclogênese in vitro. Porém, os parasitas knockouts mostraram uma diminuição significativa tanto no índice de infecção como no número de tripomastigotas liberados de células CHO-K1 infectadas com formas metacíclicas knockout. / Chagas disease is a disorder caused by the protozoa parasite Trypanosoma cruzi, which affects about 10 million people, mainly in the Americas. T. cruzi uses amino acids as an important energy source and in several biological processes such as differentiation, resistance to stress conditions and in the host-cell invasion. Serine is involved in many biosynthetic pathways. One of the relevant functions of serine is the formation of C1 compounds for the biosynthesis of nucleotides. The use of serine for that purpose is initiated by Serine Hydroxymethyltransferase, whose activity was detected in T. cruzi but its role in the biology of parasite remains poorly explored. In this work we identified a putative gene encoding a SHMT with dual localization, cytoplasmic and mitochondrial. We generated a single knockout cell line by homologous recombination in which one allele of SHMT was replaced by the neomycin phosphotransferase gene. Knockout parasites showed no difference in epimastigote growth rate or in in vitro metacyclogenesis. However, knockout parasites showed a significant decrease in both, infection index and in the number of trypomastigotes released from CHO-K1cells infected with knockout metacyclic forms.

A doença de Chagas é uma doença causada pelo protozoário parasita Trypanosoma cruzi, que afeta cerca de 10 milhões de pessoas, principalmente nas Américas. O T. cruzi utiliza aminoácidos como importante fonte de energia e em vários processos biológicos como diferenciação, resistência a condições de estresse e invasão de células hospedeiras. A serina está envolvida em muitas vias biosintéticas. Uma das funções relevantes da serina é a formação de compostos C1 para a biossíntese de nucleotídeos. O uso de serina para esse fim é iniciado pela Serina Hidroximetiltransferase, cuja atividade foi detectada em T. cruzi, mas seu papel na biologia do parasita permanece pouco explorado. Neste trabalho, identificamos um gene que codifica uma Serina Hidroximetiltransferase putativa com dupla localização (citoplasmática e mitocondrial). Por recombinação homóloga, obtemos parasitas knockouts heterozigotos nos quais um alelo de SHMT foi substituído pelo gene da neomicina fosfotransferase. Os parasitas knockouts não mostraram diferenças na taxa de crescimento das formas epimastigotas ou na metaciclogênese in vitro. Porém, os parasitas knockouts mostraram uma diminuição significativa tanto no índice de infecção como no número de tripomastigotas liberados de células CHO-K1 infectadas com formas metacíclicas knockout. / Chagas disease is a disorder caused by the protozoa parasite Trypanosoma cruzi, which affects about 10 million people, mainly in the Americas. T. cruzi uses amino acids as an important energy source and in several biological processes such as differentiation, resistance to stress conditions and in the host-cell invasion. Serine is involved in many biosynthetic pathways. One of the relevant functions of serine is the formation of C1 compounds for the biosynthesis of nucleotides. The use of serine for that purpose is initiated by Serine Hydroxymethyltransferase, whose activity was detected in T. cruzi but its role in the biology of parasite remains poorly explored. In this work we identified a putative gene encoding a SHMT with dual localization, cytoplasmic and mitochondrial. We generated a single knockout cell line by homologous recombination in which one allele of SHMT was replaced by the neomycin phosphotransferase gene. Knockout parasites showed no difference in epimastigote growth rate or in in vitro metacyclogenesis. However, knockout parasites showed a significant decrease in both, infection index and in the number of trypomastigotes released from CHO-K1cells infected with knockout metacyclic forms.

This thesis combines four published research papers and a book chapter investigating aspects of central metabolism in the human malaria parasite Plasmodium falciparum. The publications are preceded by a statement which explores features of the research not fully described in the published texts, incorporates a review of the development over time and the present state of relevant scientific knowledge, and discusses the place of the individual papers and book chapter within malaria research. An assessment of the impact of each publication on its field of study is also included. A general discussion of the combination of papers as representative of the progress of research into the metabolism of malaria parasites concludes the statement section. The first publication is a chapter from a book, which describes detailed methods for the in vitro cultivation of P. falciparum. Such methodology, both robust and reliable, is a prerequisite for any investigation of parasite metabolism. The following publications are all primary research papers. The second publication describes the isolation and characterisation of the gene encoding the glycolytic pathway enzyme enolase from P. falciparum. The inferred amino acid sequence included peptide insertions found only in the enolases of higher plants and other photosynthetic organisms. This raised implications concerning the deep evolutionary history of the malaria parasite and related species. The third is concerned with the elucidation of the molecular basis of resistance to the antimalarial drug sulfadoxine. Resistance was found to result from point mutations within the dihydropteroate synthetase domain of the bifunctional protein hydroxymethylpterin pyrophosphokinase-dihydroptero¬ate synthetase, an enzyme of the parasite folate pathway. Additionally, it was discovered that the presence of exogenous folate has an antagonistic effect on sulfadoxine in some parasites of a defined genotype. This highlighted the importance of folate salvage in parasite metabolism. Fourth is a paper representing the discovery of a novel metabolism in both P. falciparum and the related apicomplexan parasite Toxoplasma gondii. The use of parasite genes in rescuing an Escherichia coli tyrosine auxotroph resulted in a proof of function of the products of these genes as pterin-4a-carbinolaminedehydratases. Pterin recycling, hitherto undetected in apicomplexans, was therefore added to the known metabolic processes of these organisms. The final paper describes an investigation into the subcellular distribution of the folate pathway enzyme serine hydroxymethyltransferase (SHMT) within P. falciparum erythrocytic stage parasites. The use of confocal laser scanning microscopy and immunofluorescent techniques showed that SHMTc, the sole enzymatically active parasite SHMT protein, was found in the cytoplasm but also showed a stage-specific localisation to both the mitochondrion and apicoplast organelles. The otherwise enigmatic, enzymatically inert, SHMTm paralogue revealed a possible function, when in complex, in allowing targeted localisation of SHMTc to the mitochondrion. The spatial distribution of SHMTm also suggested a possible role in the morphogenesis of elongating apicoplasts during schizogony.

Pyridoxal 5’-phosphate (PLP), the active form of vitamin B6, is a cofactor for many enzymes involved in the metabolism of amino acids, amino acid derived metabolites and some amino sugars. PLP is one of the most versatile cofactors and the PLP-dependent enzymes catalyze a variety of reactions including transamination, decarboxylation, inter-conversion of L-and D-amino acids and removal or replacement of chemical groups bound at β or γ carbon of amino acids. The thesis describes the structural studies carried out on three PLP-dependent enzymes; N-acetylornithine aminotransferase (AcOAT), serine hydroxymethyltransferase (SHMT) and diaminopropionate ammonia lyase (DAPAL). Chapter 1 of the thesis begins with a brief introduction to PLP-dependent enzymes and their classification. This is followed by a review of structures of enzymes belonging to the subgroup II aminotransferases. The last section of chapter I contains a detailed description of the structures available till date for SHMT from various sources and the mutational studies carried out on SHMT. All the common experimental procedures and computational methods used for the current investigations are described in chapter II, as most of these are applicable to all structure determinations and analyses. The experimental procedures described include cloning, overexpression, purification, crystallization, and X-ray diffraction data collection. Computational methods include details of various programs used during data processing, structure determination, refinement, model building, structure validation and analysis. AcOAT is one of the key enzymes in arginine and lysine metabolism. AcOAT belongs to the fold type I (αfamily) subgroup II family of PLP dependent enzymes. Both S. typhimurium and E. coli have two genes each, one involved in the biosynthesis of arginine and another in the biodegradation of arginine. Biosynthetic AcOAT catalyzes the conversion of N-acetylglutamate semialdehyde to N-acetylornithine (AcOrn) in the presence of L-glutamate and the conversion of N-succinyl-L-2-amino-6-oxopimelate to N-succinyl-L,L-diaminopimelate in lysine biosynthesis. Meso-DAP and lysine, the products of lysine biosynthesis pathway, are known to function as cross-linking moieties in the peptidoglycan component of bacterial cell wall. Therefore N-acetylornithine aminotransferase could serve as a target for designing antibacterials. Chapter III gives the details of the work carried out on AcOAT. Two genes each from S. typhimurium and E. coli coding for biosynthetic and biodegradative AcOAT were cloned in E. coli, overexpressed and purified by Ni-NTA affinity chromatography. Of the four enzymes, biosynthetic AcOAT from S. typhimurium (sArgD) crystallized in the unliganded form and in the presence of the inhibitor gabaculine or one of the substrates L-glutamate, diffracted to a maximum resolution of 1.90 Å and contained a dimer in the asymmetric unit. The structure was determined by the molecular replacement method using human ornithine aminotransferase (hOAT) as the starting model. The structure of unliganded sAcOAT showed significant electron density for PLP in only one of the subunits (subunit A). The asymmetry in PLP binding could be attributed to the ordering of the loop Lαk-βm in only one subunit. The Km and kcat/Km values determined with the purified sArgD suggested that the enzyme could accept both acetylornithine (AcOrn) and ornithine (Orn) as the substrates and had much higher affinity for AcOrn than for Orn. However, OAT accepts only Orn as the substrate. Comparison of the structurte of sArgD with T. thermophilus AcOAT and hOAT suggested that the higher specificity of sArgD towards AcOrn may not be due to specific differences in the active site residues but could result from minor conformational changes in some of them. sArgD was inhibited by gabaculine with an inhibition constant (Ki) of 7 µM and a second order rate constant (k2) of 0.16 mM-1s-1. The crystal structure of sArgD obtained in the presence of gabaculine and the spectral studies of sArgD with gabaculine suggested that the enzyme might have a low affinity for the PLP-gabaculine complex. Biosynthetic AcOAT from E. coli (eArgD) crystallized in the presence of gabaculine in hanging drop vapor diffusion method and diffracted X-rays only to a resolution of 3.5 Å. Two data sets were collected for the eArgD crystals. One of the data sets belonged to P1 (data 1) and the other to P321 space group (data 2) with a solvent content of ~70%. Data 1 was twinned and the unit cell was unusually large and could accommodate ~24 molecules in the asymmetric unit where as data 2 had four molecules in the asymmetric unit. Biodegradataive AcOAT from E. coli also crystallized in presence of gabaculine in hanging drop vapor diffusion method and suffered from low diffraction quality, where as that from S. typhimurium did not yield crystals. In chapter IV, X-ray crystallographic studies on various site specific mutants of SHMT from Bacillus stereotherophilus (bs) and a detailed comparison of structural data with the biochemical results in relation to mechanism of catalysis are presented. SHMT is a member of the α-class of PLP-dependent enzymes and catalyzes the reversible conversion of L-Ser and THF to glycine and 5,10-methylene THF. 5,10-methylene THF serves as a major source of one-carbon units in the biosynthesis of nucleotides and a few amino acids. SHMT also catalyses the cleavage of β-hydroxy amino acids like L-allo-threonine, transamination, racemization and decarboxylation reactions. SHMT shows increased activity along with enhanced nucleotide synthesis and therefore is a potential target for cancer chemotherapy. The availability of structural and biochemical data on SHMT from different sources ranging from human to E. coli enabled the identification of active site residues and a more critical examination of the role of these residues in the different steps of catalysis. The important mutants studied in the present investigation are E53Q, Y51F, Y61F, Y61A, Y60A, N341A and F351G of bsSHMT. The crystal structures of all these mutants are solved in the presence of various ligands, which gave many interesting results. E53, one of the active residues, interacts with the side chain hydroxyl group of serine bound to PLP in the wild type serine complex and N10 and formyl oxygen in the wild type glycine-FTHF complex. In E53Q glycine and serine complexes, glycine carboxyl and serine side chain were in two conformations, respectively, the new conformation being stabilized by their interaction with the mutated residue Q53. The structure of E53Q-Gly complex obtained in the presence and absence of 5-formyl THF(FTHF) showed an interesting case of enzyme memory in which the final conformational state depends on the way it was obtained and suggested that E53 is crucial for FTHF/THF binding. Though the spectrum showed that FTHF binds to the mutant initially, no density was observed for FTHF in the final structure. FTHF is believed to dissociate from the active site with prolonged incubation leaving behind a few significant conformational changes. Y51, one of the highly conserved tyrosines in SHMT, has hydrogen bonding interactions with the phosphate group of PLP and the active site lysine (K226) in bsSHMT. Mutation of Y51 to F resulted in significant changes at the active site. In all the structures of Y51F complexes, the phosphate group is in two conformations and F51 has moved away from the phosphate and in turn changed the position of Y61, another tyrosine in the active site. The residue Y61 is hydrogen bonded to R357 in the internal aldimine complex of bsSHMT. Addition of glycine/serine to bsSHMT resulted in the conformational change of Y61 away from R357 and towards E53, allowing the added glycine/serine to interact with R357. Mutation of Y61 to A did not bring significant structural changes. Structures of Y51F and Y61A mutants complexed with L-allo-Thr (cleaved to Gly by the wild type enzyme) showed that L-allo-Thr was not cleaved to glycine and acetaldehyde and confirmed the biochemical observation that these two residues are essential even for the THF-independent reaction. Residues Y60 and N341 are also highly conserved residues among SHMTs. Y60 stacks over PABA ring of FTHF in the wild type glycine-FTHF ternary complex. N341 has strong hydrogen bonding interactions with N1 and N8 atoms of the pteridine ring of FTHF. Mutation of either Y60 or N341 to A destroys the binding ability of FTHF/THF to the enzyme according to the biochemical and structural observations. The residue F351 exhibits different conformations in the two subunits of wild type glycine-FTHF ternary complex and is thought to be an important residue in determining the asymmetric binding of FTHF. Mutation of F351 to G did not affect the catalytic activity. Surprisingly, in the crystal structure obtained in the presence of L-allo-Thr, the ligand did not get cleaved to glycine, though in solution, the mutant is as active as the wild type enzyme. Chapter V describes the preliminary structural studies carried out on DAPAL from E. coli and S. typhimurium. DAPAL catalyzes the α, βelimination of both L-and D-diaminopropionate (DAP). DAP is the immediate precursor of two neurotoxins 3oxalyl and 2,3-dioxalyl DAP present in Lathyrus sativus, a grain legume rich in proteins and capable of growing well in drought conditions. The presence of these two neurotoxins precludes its use as a source of protein rich food. This enzyme is present only in bacteria and few species of actinomycetes. Unlike many other PLP-dependent enzymes, DAPAL does not catalyze any side reaction and is the only enzyme known to remove an amino group from the βcarbon of the substrate. The enzymes from E. coli (eDAPAL) and S. typhimurium (sDAPAL) produced diffraction quality crystals. However, crystals of sDAPAL did not survive heavy atom soaking and eDAPAL crystals suffered from poor reproducibility and severe non-isomorphism making it difficult to obtain suitable heavy atom derivatives for structure determination. Production of selenomethionine labelled proteins for these enzymes was initiated and thin crystals were obtained for eDAPAL. Improvement of the quality of these crystals is necessary in order to solve the structure of DAPAL by MAD method.

Myc transcriptionally regulates genes involved in processes such as cell proliferation, metabolism, differentiation, and angiogenesis.  MYC expression is deregulated in many types of human cancer; therefore discovering the mechanisms behind MYCs role in tumorigenesis is essential.  In this dissertation, I have focused on several Myc target genes, Spermidine synthase (Srm); Lactate dehydrogenase (Ldh); 3-phosphoglycerate dehydrogenase (Phgdh); Serine hydroxymethyltransferase (SHMT) 1 and 2; and Pim-3 (a member of the Pim family of serine/threonine kinases).  These enzymes play a role in various functions: Spermidine synthase (polyamine synthesis); Lactate dehydrogenase (glycolysis); Phgdh and Shmt (serine metabolism); and Pim-3 (cell signaling).  In order to elucidate the impact Myc over-expression has on metabolism in tumorigenesis, we use human cell lines, and transgenic mice as well as cell lines and tissues derived from these mice.  The impact of inhibition of these target genes on Myc-driven tumorigenesis was done by genetically inhibiting the target gene (using RNAi or mouse models) or inhibiting the protein with a chemical inhibitor.  Investigating these Myc target genes will help determine if inhibition of Myc target genes is a viable approach for chemotherapeutics, and under what conditions this inhibition may be the most valuable.  In paper I, we examine SRM; a highly expressed enzyme in the polyamine synthesis pathway that converts putrescine to spermidine, and is important for actively growing cells.  Genetic inhibition via RNAi against Srm, or chemical inhibition of Srm, resulted in decreased proliferation of B-cell tumor lines from transgenic mice in vitro.  In vivo treatment of λ-Myc transgenic mice with a chemical SRM inhibitor exhibited a significant chemopreventative effect on tumor formation. These results support previous findings that inhibition of polyamine synthesis pathway enzymes has a place in cancer therapy.  Many Myc target genes have been suggested as attractive targets in battling Myc-driven tumorigenesis.  Surprisingly in paper II, when we analyzed the inhibition of other Myc target genes, such as Ldh, Shmt, and Phgdh, we found that inhibition of these genes did not inhibit Myc-driven tumorigenesis to any significant degree. However, inhibition of Ldh, Phgdh and Shmt2 had a notable effect on in vitro Ras-driven transformation.  These findings suggest that chemotherapeutic inhibition of metabolic genes such as Ldh, Phgdh and Shmt2 may be effective in genetically defined settings, keeping in mind the oncogenic lesion behind the tumor.  The Pim kinase family consists of three serine/threonine kinases, Pim1-3.  In paper III, we found that Pim-3 is a direct Myc target gene and that Pim-3 expression is high in Burkitt Lymphoma samples taken from human patients, as well as spontaneously arising lymphomas from Myc transgenic mice. We also found that inhibition of Pim-3 using a pan-Pim kinase inhibitor, Pimi, in these spontaneously arising Myc lymphomas resulted in caspase independent cell death.  These results indicate that Pim kinase inhibition may be a potential chemotherapeutic strategy in human lymphomas that rely on Pim-3 kinase expression.

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