Made available in DSpace on 2015-07-22T20:50:40Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-03-31 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Conselho Nacional de Pesquisas (CNPq e INV) / National Institute of Health (NIH) / Protozoários do gênero Trypanosoma possuem um complexo ciclo de vida, alternando entre hospedeiros vertebrados e invertebrados. A adaptação a essas diversas condições ambientais necessita de rápidas mudanças na expressão gênica para preencher os requerimentos metabólicos ou morfológicos para sobrevivência. Muito pouco se sabe sobre os mecanismos que controlam estas transformações e sobre as vias de sinalização celular implicadas. Como nestes organismos o controle da expressão gênica ocorre ao nível pós transcricional, decidimos neste trabalho estudar a função de proteínas quinases envolvidas no controle da síntese protéica e no crescimento destes parasitas. Em diversos eucariotos a proteína quinase TOR (Target Of Rapamycin) está envolvida no controle da síntese protéica e crescimento celular frente à disponibilidade de nutrientes ou fatores de crescimento. Por análise de seqüências de T. brucei disponíveis nos bancos de dados do genoma desses parasitas encontramos quatro candidatos para TOR (TbTOR1, TbTOR2, TbTOR-like1 and TbTOR-like 2). Dois complexos TOR em T. brucei (TbTORC1 e TbTORC2) foram descritos previamente. No primeiro capítulo desta tese estudamos: TbTOR-like 1 e a comparamos com TbTOR2. TbTOR-like 1 não se encontra em nenhum dos complexos TORC e possui um domínio PDZ não encontrado nas outras TORs de T. brucei ou de outros eucariotos. Ela se localiza em grânulos no citosol que após estresse hiperosmótico migram para a periferia celular. Depleção de TbTOR-like 1 causa uma inibição progressiva do crescimento celular, gerando células de tamanho maior que se acumulam na fase S/G2 do ciclo celular. Estas células também apresentam um aumento no número de acidocalcissomos assim como aumentos nos níveis de polifosfato e pirofosfato. Estes dados indicam que TbTOR-like1 parece estar envolvida no controle do crescimento celular e na biogênese de acidocalcissomos respondendo a variações osmóticas do meio. No segundo capítulo da tese estudamos proteínas quinases envolvidas no controle da síntese protéica através da fosforilação da subunidade  do fator de iniciação eucariótico 2 da tradução (eIF2α. Estas quinases são ativadas por distintos tipos de estresse. T. brucei codifica para três potenciais proteínas quinases de eIF2α (TbeIF2K1, K2 e K3). Estudamos mais especificamente a K2. Mostramos que ela é uma glicoproteína transmembrânica localizada na região da bolsa flagelar em ambas as formas de T. brucei e nos compartimentos endossomais de Trypanosoma cruzi. Estes compartimentos endossomais são denominados de reservossomos e se formam apenas no estágio do parasita que vive no lúmen do tubo digestivo do inseto vetor. Este fato sugere que em ambos os parasitas esta proteína quinase possa estar funcionando como um sensor no transporte de nutrientes e proteínas. De maneira geral revelamos a existência de pelo menos dois mecanismos pelos quais os tripanossomas percebem e resistem às modificações ambientais durante seu ciclo de vida. / Protozoa of the genus Trypanosoma have a complex life cycle alternating between vertebrate and invertebrate hosts. The adaptation to different environmental conditions requires rapid changes in gene expression to fill up the morphological and metabolic requirements for survival. Very little is known about the mechanisms that control these changes and the signaling pathways involved. As in these organisms the control of gene expression occurs at post-transcriptional level, in this work we decided to investigate the function of protein kinases involved in the control of protein synthesis and growth of these parasites. In several eukaryotes TOR (target of rapamycin) protein kinases are involved in protein synthesis control and cell growth in response of the availability of nutrients or growth factors. By searching T. brucei genomic database we found four candidates for TOR (TbTOR1, TbTOR2, TbTOR-like1 and TbTOR-like 2). Two TOR complexes were previously described in T. brucei (TbTORC1 and TbTORC2). In the first chapter of this thesis we study: TbTOR-like 1 and compared it with TbTOR2. TbTOR-like 1 is not present in any of the TORC complexes and has a PDZ domain not found in any of other TORs of T brucei, or other eukaryotes. It is located cytosolic granules that migrate to the cell periphery after hyperosmotic stress. Depletion TbTOR-like 1 causes a progressive inhibition of cell growth, generating enlarged cells that accumulate in S/G2 phase of the cell cycle. These cells also show increased number of acidocalcisomes and augmented levels of polyphosphate and pyrophosphate. These data indicate that TbTOR-like seems to be involved in controlling cell growth and biogenesis of acidocalcisomes responding to osmotic changes in the medium. In the second chapter of the thesis we studied protein kinases involved in protein synthesis control through the phosphorylation of the  subunit of the eukaryotic translation initiation factor 2 (eIF2α).These kinases are activated by different types of stress. T. brucei encodes three potential eIF2α protein kinases (TbeIF2K1, K2 and K3). We studied more specifically the K2. We showed that it is a transmembrane glycoprotein located in the region of the flagellar pocket in both forms of T. brucei, and in the endosomal compartments of Trypanosoma cruzi. These endosomal compartments are known as reservosomes and they are formed only in the parasite’s stage that li ves in the digestive tract lumen of the insect vector. This fact suggests that in both parasites this protein kinase may be acting as a sensor in the transport of nutrients and proteins. In conclusion we revealed the existence of at least two mechanisms by which trypanosomes perceive and resist to environmental changes during their life cycle. / TEDE / BV UNIFESP: Teses e dissertações

Orientador: Regina Maria Barretto Cicarelli / Banca: Maria Teresa Marques Novo / Banca: Cleslei Fernando Zanelli / Banca: Marcia Aparecida Silva Graminha / Banca: Otávio Henrique Thiemann / Resumo: A família Trypanosomatidae inclui diversos parasitas protozoários responsáveis por diferentes doenças humanas. Várias evidências sugerem importantes diferenças entre a maquinária de tradução e processamento de mRNA (trans-splicing) em Tripanosomatídeos quando comparados com eucariótos superiores. Neste contexto, alguns fatores importantes para o funcionamento da célula eucarióticas são os pequenos complexos constituídos de proteínas e RNA, chamados de ribonucleoproteínas (U snRNPs). Esta partículas possuem papel essencial no processamento de RNA mensageiros e durante a reação de splicing apresenta um core comum composto por proteínas (proteínas Sm) and RNAs estruturais (U snRNAs) e um conjunto de proteínas específicas de cada complexo. Embora bem definidas em mamíferos, snRNPs permanecem pouco caracterizadas em Tripanosomatídeos. Ferramentos de bioinformática identificaram quatro possíveis proteínas específicas do complexo U5 snRNP (U5-15K, U5-40K, U5-102K e U5-116K), e importantes parâmetros foram determinados, como peso molecular estimado, domínios e motivos conservados. Este trabalho demonstrou que U5-15K e 45-102K são altamente conservadas entre o Tripanosomatídeos e os domínios Dim1 and Prp1 foram identificados, respectivamente. Técnicas de purificação de complexos (PTP-tag) revelaram que estas proteínas interagem com o U5 snRNA, sugerindo que participem do complexo U5 snRNP. Análises funcionais demonstraram que U5-15K é essencial para viabilidade celular e que de alguma forma esta asssociada tanta a reação de cis quanto de tras-splcing. Experimentos de imunolocalização de U5-15K and U5-102K corroboram este dados, uma vez que as protínas em questão possuem localização nuclear. / Abstract:There are several protozoan parasites in Trypanosomatidae family, including different agents responsible for human diseases. Several evidences suggest important differences in the translational system and mRNA processing (trans-splicing) in Trypanosomatids when compared to higher eukaryotes. In this context, some important factors for the functioning of eukaryotic cells are the small complexes of RNA and proteins; these particles of ribonucleoproteins (UsnRNPs) have an essential role in the pre-mRNA processing, mainly during splicing. UsnRNP presents a common protein core associated between itself and with the snRNA, named Sm proteins and specific proteins of each snRNP. Even though they are well defined in mammals, snRNPs are still not well characterized in certain Trypanosomatids. Bioinformatics analysis identified four possible U5 snRNP specific proteins (U5-15K, U5-40K, U5-102K and U5-116K), and important parameters were determinated, as estimated molecular weight, motifs and conserved domains. This work shows that the U5-15K and U5-102K proteins are highly conserved among different Tryponosomatids species and Dim1 and Prp1 domains were identified, respectively. Tandem affinity pull-down assay revealed that these proteins interact with U5snRNA, suggesting its participation in U5snRNP particle, and functional analysis showed that U5-15K is essential for cell viability and it is associated in some way to trans and cis-splicing machinery. Immunolocalization experiments corroborated those data, showed U5-15K and U5-102K in the nucleus of the cell. / Doutor

Aim of this thesis was to shed light on the function(s) of Iba57 and Ssc1 proteins in both life cycle stages of T. brucei using RNA interference. Depletion of Ssc1 resulted in severe grow phenotype, decrease in activities of iron-sulphur cluster-containing enzyme aconitase but no increase in oxidative stress sensitivity or accumulation of ROS in mitochondrion. Down regulation of Iba57, specialized maturation factor of aconitase and homoaconitase, lead to depletion of aconitase, destabilization of Isa1 and increased sensitivity to oxidative stress and accumulation of ROS in both stages.

Lipid metabolism in Trypanosoma brucei, the causative agent of African sleeping sickness, differs from its human host, allowing a plethora of novel drug targets to be discovered and validated. Cytidine diphosphate diacylglycerol (CDP-DAG) is a central lipid intermediate produced by the enzyme CDP-DAG synthase (CDS), but nothing was known about CDS in T. brucei. Only one gene encodes CDS in Trypanosoma brucei (Tb927.7.220) and this was shown to encode a functional CDS by overexpression in E. coli and complementation of a yeast CDS null, which was created during this study. Expression and activity of TbCDS was confirmed in T. brucei, and was shown to be essential in both life cycle stages. Disruption of TbCDS altered the lipid profile of T. brucei, confirming a central role for CDP-DAG in phospholipid synthesis. Biochemical and morphological characterisation of mutants in TbCDS expression elucidated at least two separately localised and regulated pools of CDP-DAG and phosphatidylinositol in T. brucei. In bloodstream form these pools are localised to the Golgi and the ER, however in procyclics it is possible that both of these pools are localised to the Golgi, since no phosphatidylinositol synthase protein was detected in the ER of procyclics. Reduction in TbCDS was shown to affect cell cycle regulation and Golgi segregation possibly due to a depletion of phosphorylated phosphatidylinositols (PIPs). These studies also indicate that phosphatidylglycerol may be synthesised by the phosphatidylglycerol-phosphate synthase which may be capable of using phosphatidylserine as a substrate in a headgroup swapping reaction. TbCDS has now been genetically validated as a drug target, and has highlighted novel aspects of lipid biosynthesis in T. brucei. Collectively, these findings highlight the central role played by TbCDS and the new knowledge gained here may lead to the discovery and validation of other novel drug targets against African sleeping sickness.

Human African Trypanosomiasis (HAT) is an infectious, vector-borne protozoal disease which is amongst the so-called neglected diseases. In 2000, at a summit of the United Nations, eight Millennium Development Goals (MDGs) were set, to be achieved by 2015. MDG 6 states “to combat HIV/AIDS, malaria & other diseases”. With just under 2 years to go before the end of 2015, HAT is still thriving in developing countries. The drugs currently used for the treatment of HAT are in short supply, have severe side effects and those used to treat late stages of the disease are very difficult to administer. The aforementioned challenges call for research into this neglected disease in order to develop new, safe and easy-to-use medicines. Naphthoquinones are a class of compounds shown to possess anti-parasitic activity, amongst a variety of other biological activities, and therefore this pharmacophore was selected for this study. The purpose of this study was to synthesise derivatives of 2,3-dichloro-1,4- naphthoquinone to be tested for anti-trypanosomal activity and thereafter conduct structureactivity relationship studies. A series of reactions were carried out using thiophenol, phenol and aniline nucleophiles to synthesise thioether (-S-), ether (-O-) and amino (-NH-) derivatives of 2,3-dichloro-1,4-naphthoquinone with various halogen or methyl substituents. Purification of the products was carried out by recrystallisation. Nuclear magnetic resonance (NMR), infra-red (IR) and high pressure liquid chromatography coupled to an electro-spray ionisation mass spectrometer (HPLC-ESI-MS) were the analytical methods used for structural confirmation of the products. There were eighteen 1,4-naphthoquinone derivatives that were successfully synthesised using ethanolic solutions. Unfortunately, attempts to synthesise 1,4-naphthoquinones in reactions involving 2-(trifluoro-methyl)aniline and 2-isopropyl-5-methylphenol were unsuccessful, presumably due to steric hindrance by the bulky ortho-substituents. Although the aims of the synthetic procedures were to obtain both mono- and disubstituted products by nucleophilic displacement of the chlorine atom(s) of 2,3-dichloro-1,4- naphthoquinone, only monosubstituted products were obtained from substitution with aniline and phenol nucleophiles. Thiol nucleophiles, however, selectively yielded disubstituted products only. Synthesised naphthoquinone derivatives were tested against Trypanosoma brucei and calculation of the EC₅₀ values from the obtained dose-response curves was carried out using the four parametric equation. All the 1,4-naphthoquinones showed a degree of potency, except compounds 1b, 3c and 3e, which had little or lack of potency. Structure-activity relationship studies (SARs and QSARs) were carried out to determine which structural features or functional group substituents of the naphthoquinone derivatives contribute or take away from the desired anti-trypanosomal activity. It was found that compounds with the best in vitro anti-trypanosomal potencies in the series of analogous 1,4-naphthoquinone derivatives had EC₅₀ values in the range 2.137 to 2.884 μM. The most potent compound in the series was 2-chloro-3-(4-(trifluoromethyl)phenylamino)-1,4- naphthoquinone 1e; but it was 142-fold less potent than the reference standard of melarsoprol.

Les progrès récents dans la modélisation informatique des réseaux biologiques permettent maintenant aux chercheurs d'étudier le métabolisme cellulaire des organismes. Dans ce projet, ces approches ont été utilisées pour analyser le métabolisme de Trypanosoma brucei. Ce parasite protozoaire est responsable de la trypanosomiase africaine, une maladie mortelle chez l'homme et qui entraine des dégâts importants dans les élevages. Ce parasite est principalement retrouvé dans les régions d'Afrique sub-sahariennes. Durant cette thèse, des informations sur le métabolisme de T. brucei ont été recueillies à partir d'études publiées, bases de données et de communication personnelle avec des experts qui étudient les différents aspects du métabolisme des trypanosomatides. Cette information a été mise à disposition de la communauté à travers la base de données TrypanoCyc. La base de données a été publiée en Novembre 2014 et a eu plus de 4200 visiteurs provenant de plus de cent pays depuis Novembre 2015. Un modèle métabolique à l'échelle du génome de T. brucei a également été reconstruit sur la base des informations recueillies. Ce modèle a permis de faciliter l'étude du métabolisme de T. brucei en utilisant une approche de biologie des systèmes. Des algorithmes basés sur l'analyse de balance des flux ont été conçus pour optimiser la visualisation et l'étude des propriétés métaboliques du parasite. En utilisant l'algorithme iMat, des modèles spécifiques de la forme sanguine de T. brucei ont été générés à partir des informations fournies par les études publiées et les annotations présentent dans. Enfin, un algorithme a été conçu pour optimiser encore ces modèles spécifiques afin d'améliorer la cohérence de leurs prédictions avec les résultats publiés. Les modèles ainsi créés, spécifiques à la forme sanguine, ont montré une meilleure puissance prédictive que le modèle initial à l'échelle du génome, en particulier pour prédire le comportement métabolique spécifique de différents mutants de T. brucei. / Recent advances in computational modelling of biological networks have helped researchers study the cellular metabolism of organisms. In this project, these approaches were used to analyze Trypanosoma brucei metabolism. This protozoan parasite is the causative agent of African trypanosomiasis, a lethal disease which has been responsible for huge loss of lives and livestock in Sub- Saharan Africa since ancient times. Information on T. brucei metabolism was gathered from published studies, databases and from personal communication with experts studying different areas of Trypanosomatid research. This information has been presented to the public through the TrypanoCyc Database, a community annotated T. brucei database. The database was published in November 2014 and has had over 4200 visitors from more than 100 countries as of November 2015. A manually curated genome-scale metabolic model for T. brucei was also built based on the gathered information to facilitate the study of T. brucei metabolism using systems biology approaches. Flux balance analysis based algorithms were designed to optimize visualization and study interesting metabolic properties. Blood-stream form specific metabolic models were generated using information available from published studies and the TrypanoCyc annotations with the help of the iMAT algorithm. Finally, an algorithm was designed to further optimize these stage specific models to improve the consistency of their predictions with results published in previous studies. These stage-specific models were observed to have a clear advantage over the genome-scale model when predicting stage-specific behaviour of T. brucei, particularly when predicting mutant behaviour.

Trypanosomatid parasites such as Trypanosoma brucei have unusual mechanisms of gene expression including polycistronic transcription, mitochondrial RNA editing and trans-splicing. Additionally, these protists rely mainly on post-transcriptional regulation where RNA-binding proteins (RBP) have shown to play a major role. RBP6 and RBP10 are two examples of RBPs that play crucial roles in procyclic and bloodstream form parasites differentiation respectively, by post-transcriptional regulation. Over-expression of RBP6 is enough to promote differentiation into metacyclic trypomastigotes that are infective to mice. However, continuous expression is required, and this pattern does not reflect the natural expression in the tsetse fly or the influence of other RNA-binding proteins. RBP5 is a RBP with a single RNA-recognition motif similar to RBP6 and RBP10, whose expression is upregulated during the life stages within the salivary glands of tsetse flies. We hypothesize the RBP5 facilitates metacyclogenesis in the tsetse fly. To evaluate possible contributions to T. brucei differentiation, we will over-express RBP5 in procyclic cells alone and in combination with RBP6. Initial screening of cells over-expressing PTP-tagged RBP5 resulted in parasites with a moderate growing defect, and the scoring of nuclei and kinetoplasts in fixed cells showed a progressive accumulation of cells with 2 nuclei and 2 kinetoplasts (2N2K) and appearance of multinucleated cells. On the other hand, over-expression of non-tagged RBP5 generated a more severe growing defect, starting immediately after the first day of induction. The scoring of nuclei and kinetoplasts resulted in a drastic increase of 2N2K cells and a greater appearance of multinucleated cells, which suggests an irregular cell cycle progression. When developing the dual over-expression system, our cells over-expressing RBP6 were not able to differentiate into any stage, and when over-expressing RBP5 and RBP6 coordinately, no differentiation process was observed either. Together these data suggest that RBP5 might be a regulator of genes involved in the initiation of cytokinesis in T. brucei parasites, however a role in metacyclogenesis cannot be discarded since we were not able to obtain metacyclic parasites. This study helped us to get a better understanding of the post-transcriptional regulatory mechanisms that repress and regulate T. brucei cell cycle progression.

The cilium/flagellum is a complex organelle protruding from the cell body and functioning in motility, sensing, and signalling. It is composed of hundreds of protein constituents, the majority of which comprise the flagellar cytoskeleton - the microtubule-based axoneme. Because the flagellum lacks ribosomes, its protein constituents have to be imported from the cell body and delivered to proper locations. Moreover, these proteins have to retain their function over a considerable length of time, despite the mechanical stress caused by flagellar beating and due to environmental exposure. This raises the question whether and where protein turnover occurs. Previously, it was established that Chlamydomonas reinhardtii flagella are dynamic structures (Marshall & Rosenbaum, 2001). In contrast, in the Trypanosoma brucei flagellum axonemal proteins are remarkably stable (Vincensini et al., 2018). However, the questions of axonemal assembly and stability were so far investigated only for a small number of proteins and during relatively short periods. Moreover, in these experiments expression of studied proteins was controlled by non-native regulatory elements. To elucidate the site of incorporation of proteins from all major axonemal complexes and to find out if and where the protein turnover occurs, T....

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