All living cells are dependent on nucleic acids for their survival. The genetic information stored in DNA is translated into functional proteins via a messenger molecule, the ribonucleic acid (RNA). Since DNA and RNA can be considered as polymers of nucleotides (NTPs), balanced pools of NTPs are crucial to nucleic acid synthesis and repair. The de novo reduction of ribonucleoside diphosphates (NDPs) to deoxyribonucleoside diphosphates (dNDPs), the precursors for DNA synthesis, is catalyzed by the enzyme ribonucleotide reductase (RNR). In cycling cells the dominant form of mammalian RNR consists of two proteins called R1 and R2. A proteasome-mediated degradation completely deprives postmitotic cells of R2 protein. The nonproliferating cells use instead a p53 inducible small RNR subunit, called p53R2 to synthesize dNTPs for mitochondrial DNA replication and DNA repair. To address the ongoing controversy regarding the localization and subsequently function and regulation of RNR subunits, the subcellular localization of all the mammalian RNR subunits during the cell cycle and after DNA damage was followed as a part of this thesis. Irrespective of the employed methodology, only a cytosolic localization could be observed leading to a conclusion that the dNTPs are synthesized in the cytosol and transported into the nucleus or mitochondria for DNA synthesis and repair. Thus, our data do not support the suggestion that nuclear translocation is a new additional mechanism regulating ribonucleotide reduction in mammalian cells. In an attempt to find a cure for African sleeping sickness, a lethal disease caused by a human pathogen, Trypanosoma brucei, nucleotide metabolism of the parasite was studied. The trypanosomes exhibit strikingly low CTP pools compared with mammalian cells and they also lack salvage of cytidine/cytosine making the parasite CTP synthetase a potential target for treatment of the disease. Following expression, purification and kinetic studies of the recombinant T. brucei CTP synthetase it was found that the enzyme has a higher Km value for UTP than the mammalian CTP synthetase. In combination with a lower UTP pool the high Km may account for the low CTP pool in trypanosomes. The activity of the trypanosome CTP synthetase was irreversibly inhibited by the glutamine analog acivicin, a drug extensively tested as an antitumor agent. Daily injections of acivicin to trypanosome-infected mice were sufficient to suppress the parasite infections. The drug was shown to be trypanocidal when added to cultured bloodstream T. brucei for four days at 1 uM concentration. Therefore, acivicin may qualify as a drug with “desirable” properties, i.e. cure within 7 days, according to the current Target Product Profiles of WHO and DNDi. Trypanosomes lack de novo purine biosynthesis and are therefore dependent on exogenous purines such as adenosine that is taken up from the blood by high-affinity transporters. We found that besides the cleavage-dependent pathway, where adenosine is converted to adenine by inosine-adenosine-guanosine-nucleoside hydrolase, T. brucei can also salvage adenosine by adenosine kinase (AK). The efficient adenosine transport combined with a high-affinity AK yields a strong salvage system in T. brucei, but on the other hand makes the parasites highly sensitive to adenosine analogs such as adenine arabinoside (Ara-A). The cleavage-resistant Ara-A was shown to be readily taken up by the parasites and phosphorylated by the TbAK-dependent pathway, inhibiting trypanosome proliferation and survival by incorporation into nucleic acids and by affecting nucleotide levels in the parasite.

Computer-aided drug discovery involves the application of computer science and programming to solve chemical and biological problems. Specifically, the QSAR (Quantitative Structure Activity Relationships) methodology is used in drug development to provide a rational basis of drug synthesis, rather than a trial and error approach. Molecular dynamics (MD) studies focus on investigating the details of drug-target interactions to elucidate various biophysical characteristics of interest. Infectious diseases like Trypanosoma brucei rhodesiense (TBR) and P. falciparum (malaria) are responsible for millions of deaths annually around the globe. This necessitates an immediate need to design and develop new drugs that efficiently battle these diseases. As a part of the initiatives to improve drug efficacy QSAR studies accomplished the formulation of chemical hypothesis to assist development of drugs against TBR. Results show that CoMSIA 3D QSAR models, with a Pearson’s correlation coefficient of 0.95, predict a compound with meta nitrogens on the phenyl groups, in the combinatorial space based on a biphenyl-furan diamidine design template, to have higher activity against TBR relative to the existing compound set within the same space. Molecular dynamics study, conducted on a linear benzimidazole-biphenyl diamidine that has non-classical structural similarity to earlier known paradigms of minor groove binders, gave insights into the unique water mediated interactions between the DNA minor groove and this ligand. Earlier experiments suggested the interfacial water molecules near the terminal ends of the ligand to be responsible for the exceptianlly high binding constant of the ligand. Results from MD studies show two other modes of binding. The first conformation has a single water molecule with a residency time of 6ns (average) that is closer to the central part of the ligand, which stabilizes the structure in addition to the terminal water. The second conformation that was detected had the ligand completely away from the floor of the minor groove, and hydrogen bonded to the sugar oxygens.

Trypanosoma brucei and T. congolense are protozoan parasites that infect humans, domestic livestock and wildlife in Africa. These parasites undergo complex morphological and biochemical changes, during the various stages of their life cycle. These changes correlate with alterations in the levels of trypanosomal lysosomal cysteine proteases, suggesting a role for transcriptional regulation of the cysteine protease in these parasites. The mechanism of this regulation is not yet understood nor have the promoter regions of the cloned trypanosome cysteine protease genes been investigated. This study involved an attempt to clone the T. brucei and T. congolense DNA fragments containing the promoter regions as the initial step in the investigation of the control elements of the cysteine protease gene. Trypanosomes were isolated from infected rat blood employing a combination of the methods of isopicnic isolation on Percoll gradients and DEAE-cellulose anion exchange resin chromatography. Approximately 5 x 10⁹ viable trypanosome cells were isolated from the infected rat blood and chromosomal DNA (approximately 500 μg) was extracted by alkaline-lysis method. Trypanosome genomic libraries were initially constructed in Eschericia coli HB101 employing the positive selection vector pEcoR251. The Trypanosoma brucei pEcoR251 library contained 6 000 recombinants and the Trypanosoma congolense library contained 15 000 recombinants. Plasmid DNA was then extracted from pools of recombinants, employing the alkaline-lysis method, digested with EcoRl restriction endonuclease and resolved by agarose gel electrophoresis. After Southern hybridisation, the pEcoR251 libraries did not reveal any putative clones containing the fragment of interest when probed with both an oligonucleotide probe and the PCR generated dsDNA probe. Genomic libraries were then constructed in the phagemid pUC119. The T. brucei and T. congolense genomic libraries contained 33 000 and 27 000 recombinants respectively. Recombinants from the T. brucei and T. congolense libraries were pooled in lots of 400 and 300 respectively. Of the 80 T. brucei plasmid pools that were screened 30 pools contained fragments that hybridised with the probe whilst 12 pools from the 90 T. congolense library pools that were screened contained fragments that hybridised with the probe. Putative clones identified appeared to contain inserts, ranging between two and seven kb in size. A partial T. congolense library consisting of approximately 12 pools was screened by colony hybridisation for identification of individual clones and 76 putative clones were identified. After confirmation of these putative clones on a dot blot using a DIG-labelled dsDNA probe, a selection of 30 putative clones were subjected to Southern hybridisation using a DIG-labelled DNA probe. Following Southern hybridisation 23 putative clones were identified to contain DNA inserts of interest in the range of two to seven kb. Five clones, designated pCPC1, pCPC2, pCPC3, pCPC4 and pCPC5 were then selected for further restriction mapping. Clone pCPC4 contains a seven kb fragment of T. congolense genomic DNA. A partial T. brucei library consisting of approximately 30 pools was screened by colony hybridisation for the identification of individual putative clones. Although plasmid pools containing putative clones were identified repeatedly by Southern blotting and DNA/DNA hybridisation, it was not possible to identify individual putative clones following transformation into E. coli MV1184 and colony hybridisation. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 1997.

This thesis comprises of diverse projects all focused towards analysis of mitochondrial translation in unicellular parasites. As only two mitochondrially encoded genes are required during the life cycle stage when Trypanosoma brucei resides in the bloodstream of a mammalian host, this protist provides a simplified background in which to study mitochondrial translation termination phase. The leading project utilizes T. brucei to examine mitochondrial translation termination factor TbMrf1 by gene knockout. Subsequently, it is suggested that the peptidyl-tRNA hydrolase TbPth4 is able to abate the TbMrf1 knockout phenotype by its ability to rescue mitoribosomes that become stalled when TbMrf1 is absent. Additionally, modifying methyltransferase of TbMrf1, the TbMTQ1, was characterized. And finally, this work contributed to the development of the protein expression regulation method in Leishmania parasites, a protocol for measurement of proton pumping activity of FoF1 ATPase complex in native mitochondria, and optimization of purification protocol for hydrophobic recombinant proteins.

Made available in DSpace on 2016-06-02T20:20:33Z (GMT). No. of bitstreams: 1 4383.pdf: 5759644 bytes, checksum: 0a6a6bb722062f7934be619267686311 (MD5) Previous issue date: 2012-04-24 / Universidade Federal de Minas Gerais / Selenium (Se) is an essential element found in selenoproteins as the 21st amino acid (Selenocysteine Sec).For the Sec incorporation and the related biosynthetic pathaway, several elements are required: tRNASec, a UGA codon and a Sec insertion sequence (SECIS), a conserved motif downstream of the selenoprotein encoding gene. Selenoproteins generally participate in the cellular redox balance, playing an important role on cell growth and proliferation. These proteins, as well as the the Sec synthesis pathway, are present in members of the Bacteria, Archaea and Eukarya domains, being identified in several protozoa, including the kinetoplastids. Auranofin, a gold-contaning antirheumatic drug, is a known selenoproteins inhibitorand Trypanosoma brucei and Leishmania majorcells are sensitive to this compound, with a LD50 in nanomolar range. This indicates a possible dependence of these parasites on selenoproteins. Theselenophosphate synthetase (SELD/SPS2) is responsible for the formation of monoselenophosphate from selenide and ATP, being essencial for selenoprotein biosynthesis. SPS2 knockdown led to apoptosis under sub-optimal growth conditions. The selenoproteome of these flagellated protozoa consists of distant homologs of the mammalian SelK and SelT, and a novel selenoprotein designated SelTryp, a kinetoplastidspecific protein. The functions of any of these selenoproteins are not known.We have investigated the effect of their downregulation in T. brucei to interpret their possible physiological role. The TbSelK depletion shows no effect on growth under optimal conditions, but the cells became more sensitive to endoplasmic reticulum stress agents and oxidative stress, suggesting that SelK is an ER stress-regulated protein and plays an important role in protecting T. brucei cells from ER stress agent. The TbSelT gene silence by RNA interference hampers the parasite survival, but the sensitivity to the agents tested was not asevident as it was forTbSelK, suggesting a role for TbSelT in protection against stress, but not specifically ER stress. Our results show the importance of selenocysteine and selenoproteins to parasite survival. / Selênio (Se) é um elemento essencial encontrado em selenoproteínas na forma do 21º aminoácido selenocisteína (Sec U). A incorporação co-traducional de Sec depende de uma complexa via de síntese, de um códon de terminação UGA em fase de leitura e uma estrutura terciária do RNA mensageiro conhecida como elemento SECIS. A maioria das selenoproteínas conhecidas participa de processos de manutenção do estado redox das células, tendo um importante papel no crescimento e proliferação celular. Essas proteínas, bem como os componentes da via de síntese de Sec, estão presentes em membros dos domínios de Bactérias, Arquéais e Eucaria, tendo sido identificada em diversos protozoários, incluindo os kinetoplastidas. Auranofin, um composto de ouro usado como agente antireumático, tem sido descrito como um inibidor de selenoproteínas através de sua ligação com o aminoácido selenocisteína e células de Trypanosoma brucei e Leishmania major são altamente sensíveis a este composto, apresentando um LD50 na faixa de nanomolar. Esta evidência indica uma possível dependência destes parasitas por selenoproteínas e consequentemente pela sua via de síntese. A selenofosfato sinetase (SELD/SPS2) é a enzima responsável pela síntese de monoselenofosfato a partir de seleneto e ATP, sendo, portanto uma proteína fundamental na síntese de selenocisteína. Sua depleção levou a apoptose celular quando mantidas em condições de estresse. Esse efeito pode ser causado pela consequente falta das selenoproteínas ou pelo acúmulo de espécies tóxicas de selênio, como o seleneto. Os protozoários apresentam número reduzido de selenoproteínas e kinetoplastidas apresentam 3, duas homólogas distantes de mamíferos, SelK e SelT, e uma nova proteína exclusiva denominada SelTryp, que não apresentam homologia com nenhuma outra proteína descrita. O papel dessas proteínas não é conhecido, e nós investigamos suas possíveis funções através da inibição de sua expressão. A depleção de TbSelK não mostrou efeito sob condições normais, mas tornou as células mais sensíveis a agentes indutores de estresse de retículo endoplasmático, o que nos permite inferir uma função de manutenção da homeostase dessa organela. A depleção de TbSelT causou uma diminuição no crescimento celular, mas o aumento da sensibilidade aos agentes indutores de estresse não foi tão pronunciada como em TbSelK. Nossos resultados revelam a importância de selenocisteína para parasitas, uma vez que esses organismos enfrentam diversos tipos de estresses para manter a viabilidade e a progressão da doença nos diferentes hábitats encontrados ao longo do seu ciclo de vida.

Le trypanosome sud américain, Trypanosoma cruzi, transmis par un insecte hématophage de type triatome est le protozoaire connus pour causer la maladie de Chagas chez l’Homme. Le cycle de vie de ce parasite alterne à la fois sur le type d’hôte, insecte ou hôte vertébré, et sur la forme :trypomastigote pour la forme quiescente et amastigote et épimastigote pour les formes prolifératives. Concernant la forme, seuls les parasites épimastigotes évoluent et prolifèrent dans le tube digestif des triatomes et possèdent un système endocytaire actif nécessaire à leur besoin énergétique. Toutefois, cette endocytose est restreinte à deux sites membranaires, la poche flagellaire et le cytostome, à partir desquels se créent des cargos endocytaires. Ces cargos endocytaires fusionnent ensuite avec un réseau vésiculaire endosomal qui délivre son contenu dans des réservosomes, compartiments similaires aux lysosomes.Chez le trypanosome africain (Trypanosoma brucei brucei), l’endocytose ne se réalise qu’au niveau de la poche flagellaire. Certaines protéines appartenant à cette voie endocytaire sont modifiées par de longues chaines de résidus poly-N-acétyllactosamine (pNAL) de manière post-traductionnelle. Initialement, il a été proposé que ces résidus puissent agir en tant que signal de tri dans le processus d’endocytose chez ces parasites.En nous basant sur les travaux qui ont été réalisés chez le trypanosome africain, nous nous sommes proposés d’approfondir les connaissances sur la voie endocytaire du trypanosome sud américain (Trypanosoma cruzi) qui est beaucoup moins étudié. Pour ce faire, à l’aide de deux lectines, la tomatolectine et la lectine de Griffonia simplicifolia qui présentent respectivement une affinité pour les résidus pNAL et les résidus N-acétylglucosamine (GlcNAc) en fin de chaine, nous avons pu enrichir et caractériser par LC-MS², 173 glycoprotéines putatives dont plus de 13% sont localisées dans la voie endocytaire. Parmi les protéines identifiées, en plus des nombreuses hydrolases lysosomiales, nous avons pu identifier une lectine de type C localisée dans la partie antérieure des parasites, au niveau des principaux sites endocytaires. Cette dernière possédant de nombreux résidus en commun avec les récepteurs de type scavengers, elle pourrait donc jouer un rôle important dans la fixation et l’endocytose de certains nutriments.Nos travaux ont ainsi permis d’établir que similairement aux trypanosomes africains, Trypanosoma cruzi possèdent des glycoprotéines modifiées par des N-glycanes contenant des pNAL. Nos travaux ont également permis d’établir que ces résidus s’associent préférentiellement aux glycoprotéines de la voie endocytaire (au niveau du cytostome et du réservosome) de la forme épimastigote. L’ensemble des résultats obtenus durant cette thèse tendent à montrer que les résidus pNAL des glycoprotéines présentes dans la voie endocytaire ont été conservées entre les deux parasites étudiés (Trypanosoma cruzi et Trypanosoma brucei brucei). / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

This thesis aimed to identify the trypanocidal mode of action of non-natural chamuvarinin analogs, and to assess the previously uncharacterized secondary alternative oxidase (AOX2) as a possible drug target of the trypanosomatids. The drugs used to treat infections with Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. are highly toxic and are increasingly becoming less effective as the parasites develop resistance, therefore new drugs against the diseases are desperately needed. Non-natural analogs of chamuvarinin were tested for trypanocidal activity to determine the structure activity relationships of the compounds against insect-form T. cruzi and Leishmania spp. This identified several potent and selective analogs, which retained good activity against the medically relevant intracellular forms of the parasites. Photoaffinity labeling was utilized to identify the mode of action and protein target(s) of the chamuvarinin analogs. The analogs were shown to deplete ATP levels and to induce mitochondrial dysmorphia and mitochondrial oxidative stress. Photoaffinity labeling confirmed the mitochondrial localization of the protein target(s) of these compounds, however the exact protein target(s) were unable to be identified by protein pull-down and mass spectrometry. The previously uncharacterized secondary alternative oxidases (AOX2) are conserved throughout the human-infective trypanosomatids and are absent from mammalian cells, thus making an attractive drug target if the protein is essential. The AOX2 of T. brucei, T. cruzi and L. major were expressed in Escherichia coli to characterize the enzymatic activity of the proteins. T. brucei AOX2 was successfully purified and shown to be an ubiquinol oxidase, which contains bound iron (III). The role of AOX2 within the trypanosomatids was determined by biochemical phenotyping and genetic manipulation of T. brucei, T. cruzi and L. major, which indicated that AOX2 is an essential mitochondrial oxidase in the three trypanosomatids, with a putative role in energy production, and therefore is an attractive multi-trypanosomatid drug target.

No description available.

Trypanosoma brucei and related protists are distinguished from all other eukaryotes by an unusual mitochondrial genome known as kinetoplast DNA (kDNA) that is a catenated network composed of minicircles and maxicircles. Replication of this single nucleoid involves a release, replicate, and reattach mechanism for the thousands of catenated minicircles and requires at least three DNA polymerase (POLIB, POLIC and POLID) with similarity to E. coli DNA polymerase I. Like other proofreading replicative DNA polymerases, POLIB has both an annotated polymerase domain and an exonuclease domain. Predictive modelling of POLIB indicates that it has the canonical right hand polymerase structure with a unique and large 369 amino acid insertion within the polymerase domain (thumb region) homologous to E. coli RNase T. The goal of this study was to evaluate whether the polymerase domain is necessary for the essential replicative role of POLIB. To study the structure-function relationship, an RNAi-complementation system was designed to ectopically express POLIB variants in T. brucei that has endogenous POLIB silenced by RNAi.Control experiments expressing an ectopic copy of POLIB wildtype (IBWTPTP) or polymerase domain mutant (IBPol-PTP) in the absence of RNAi did not impact fitness in procyclic cells despite protein levels being 5 - 8.5 fold higher than endogenous POLIB levels. Immunofluorescence detection of the tagged variants indicated homogenous expression of the variants in a population of cells and negligible changes in kDNA morphology. Lastly, Southern blot analyses of cells expressing the IBWTPTP or IBPol-PTP variants indicated no changes in free minicircle species. A dually inducible RNAi complementation system was designed and tested with the IBWTPTP and IBPol-PTP variants. Inductions of POLIB RNAi accompanied by ectopic expression of either variant using the standard 1 mg/ml tetracycline resulted in low protein levels of both variants while knockdown of the endogenous POLIB mRNA was greater than 85%. Increasing the tetracycline concentration to 4 mg/ml improved expression levels of both variants. However, levels of the ectopically expressed variants never exceeded that of endogenous POLIB. Using the 4 mg/ml induction conditions, complementation with IBWTPTP resulted in a partial rescue of the POLIB RNAi phenotype based on fitness curves, quantification of kDNA content and Southern blot analysis of free minicircles. IBWTPTP complementation resulted in gradual increase of IBWTPTP protein levels over the 10 day induction, and a small kDNA phenotype instead of the progressive loss of kDNA normally associated with POLIB RNAi. Additionally, the loss of free minicircles was delayed. Complementation with the IBPol-PTP variant produced more consistent levels of IBPol-PTP protein although still below endogenous POLIB levels. Loss of fitness was similar to POLIB RNAi alone. However, a small kDNA phenotype emerged early after just four days of complementation and persisted for the remainder of the induction. The majority of the IBRNAi + IBPol-PTP population (70%) contained small kDNA compared to the parental POLIB RNAi or IBWTPTP complementation that had only 45% and 50% small kDNA, respectively. Lastly, the pattern of free minicircle loss closely resembled POLIB RNAi alone. Together, these data suggest that the dually inducible system results in a partial rescue with the IBWTPTP variant. Rescue with IBPol-PTP variant results in a noticeably different phenotype from either POLIB RNAi alone or IBWTPTP complementation indicating that the POLIB polymerase domain is likely essential for the in vivo role of POLIB during kDNA replication.

Trypanosoma brucei species are vector-borne protozoan parasites that cause Human African typanosomiasis (HAT) and nagana in cattle. In humans, the diseases caused by these parasites are fatal if left untreated. Treatments for these diseases are complicated because the approved drugs for treatment are ineffective against the parasites and have many toxic side effects associated with their use. There is a clear need to identify new therapeutics that are less toxic and more effective against T. brucei. Our approach for identifying new therapies is to identify novel targets in the parasite that can be modulated by small molecules. The mitogen-activated protein kinases (MAPK) pathway is a three-tiered signaling cascade that regulates cell responses to stimuli and are involved in essential processes. MAPKs can regulate differentiation, virulence, apoptosis, cell cycle and gene expression, which makes MAPKs interesting drug targets in T. brucei. The extracellular-signal regulated kinase 8 homolog in T. brucei (TbERK8) is essential for survival in bloodstream form T. brucei. The work in this dissertation involves characterizing this T. brucei MAPK to better understand its biological function and identify small molecules that can inhibit its activity to kill the parasite. Here, we report that TbERK8 is an atypical MAPK kinase that is able to autophosphorylate and no upstream kinases that activate TbERK8 have been identified. We have demonstrated that TbERK8 is able to phosphorylate the proliferating cell nuclear antigen homolog in T. brucei (TbPCNA). This is in contrast to the reported function the human ERK8 and PCNA homologs that form a stable complex in normal breast cells which does not result in PCNA phosphorylation. We also report here that TbPCNA is phosphorylated on three residues localized to a unique insertion loop by TbERK8. TbPCNA is tightly regulated in the parasites such that either upregulating or downregulating its expression arrests T. brucei proliferation. Although, this mechanism of phosphorylation is unique to TbPCNA, the role that such phosphorylation has in regulating TbPCNA is not known. Finally, we have identified small molecules that can selectively inhibit either TbERK8 or HsERK8, demonstrating that TbERK8 can be selectively inhibited to kill the parasite. The unique properties of TbERK8 can be exploited by small molecules that can be developed into new parasite-specific therapies that kill T. brucei with fewer side effects to the patients. / Ph. D.