Orientador: Anete Pereira de Souza / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-14T21:21:36Z (GMT). No. of bitstreams: 1 Saraiva_AntonioMarcos_D.pdf: 12032714 bytes, checksum: 1262a05ca10735e855fa138a2093d04b (MD5) Previous issue date: 2009 / Resumo: A linhagem 9a5c da bactéria Xylella fastidiosa foi o primeiro fitopatógeno a ter seu genoma completamente sequenciado, o qual gerdu diversas informações sobre seu metabolismo e patogenicidade. Das orfs codificadas por esta bactéria, destaca-se; no presente trabalho, a XF0703, cuja proteína correlata (com 28,3 kDa) possui similaridade com proteínas SurE de várias outras bactérias. Proteínas SurEs são nucleotidases que desfosforilam diversos nucleosideos monofosforilados para seus respectivos nucleosideos. Tal função é de fundamental importância para manter o pool balanceado dos quatro (deoxi)ribonucleosideos para síntese de DNA e RNA, respectivamente. Este trabalho descreve a clonagem da orfXF0703 no vetor pET29a, a expressão da proteína recombinante (XfSurE) em Escheríchia coli BL21(DE3) e a purificação da mesma por cromatografia de afinidade ao níquel. A análise da estrutura secundária foi feita por dicroísmo circular e realizou-se a determinação do estado oligomérico por cromatografia de gel filtração e espalhamento de luz a baixo ângulo (SAXS), os quais revelaram que a proteína é um tetrâmero. Dados de caracterização funcional indicam que a proteína possui maior atividade em pH neutro na presença do íon manganês como cofator, com uma maior afinidade pelo substrato 3'-AMP (K0,5=0,16 mM). Além disso, ensaios cinéticos mostram que a proteína possui um comportamento alostérico com alta cooperatividade positiva (coeficiente de Hill em torno de 2,6) com todos os quatro substratos naturais testados (3'-AMP, 5'-dAMP, 5'-AMP e 5-GMP). Experimentos com a técnica de SAXS permitiram calcular o raio de giro (32,7 ± 0.2 A), distância máxima intramolecular (100 A) e a simetria do envelope da molécula (222). A estrutura de diversas SurEs homólogas já cristalizadas foram superpostas ao envelope obtido, sendo que StSurE (SurE de Salmonella com maior idenjidade de aminoácidos) mostrou ter o melhor ajuste. No entanto, notou-se que havia espaços vazios no envelope de XfSurE e tais espaços podiam ser preenchidos a partir do afastamento das alças responsáveis pela tetramerização e pela rotação dos f dímeros. Estes movimentos (translação e rotação) podem explicar o comportamento alostérico da proteína, facilitando a entrada de substrato ao sítio catalítico da molécula. / Abstract: The 9a5c strain from bacterium Xylella fastidiosa was the first phytopathogen to have its genome completely sequenced, which revealed a lot of information about its metabolism and its pathogenicity. 'From a variety of orfs encoded by this bacterium, we highlight, in this work, the XF0703, which correlated protein (with 28.3 kDa) has similarity with SurE proteins from several other bacteria. The SurE proteins *are nucleotidases that dephosphorylate various monophosphorylated nucleosides to their respective nucleosides. This function is critical for maintaining the balanced pool of four (deoxy) ribonucleosides for DNA and RNA synthesis. In this work, we describes the cloning of the XF0703 orf into the vector pET29a, the recombinant protein overexpression (XfSurE) in Escherichia coli BL21(DE3) and the protein purification by nickel affinity chromatography. The secondary structure analysis was done by circular dichroism, while oligomeric state determination was achieved by gel filtration chromatography and small-angle X-ray light scattering (SAXS), which showed that the protein is a tetramer. Functional characterization data indicate that the protein has a highest activity at neutral pH in the presence of manganese as a cofactor, with a highest affinity for the 3-AMP substrate (K0,5 = 0,16 mM). Furthermore, kinetic tests showed that the protein has a allosteric behavior with a high positive cooperativity (Hill coefficient around 2.6) for all natural substrates screened (3-AMP, 5'-dAMP, 5'-AMP and 5'-GMP). Experiments with SAXS technique have allowed to calculate the radius of gyration (32.7 ± 0.2 A), maximum intramolecular distance (100 A) and molecule symmetry. / Doutorado / Genetica de Microorganismos / Doutor em Genetica e Biologia Molecular

As peçonhas de artrópodos são ricas fontes de neurotoxinas, verdadeiras ferramentas moleculares com ação seletiva e específica sobre o Sistema Nervoso Central (SNC) de mamíferos, e de grande relevância clínico-científica. Demonstramos recentemente que a peçonha de P. bistriata, quando injetada por via intracerebroventricular (i.c.v.), desencadeava crises convulsivas em ratos, um indício da existência de neurotoxinas pró-convulsivantes na peçonha dessa aranha. O grupo do Prof. Dr. Joaquim Coutinho-Netto isolou da peçonha dessa aranha várias neurotoxinas, dentre as quais uma denominada PbTx 2.2.1, que possui a capacidade de inibir a captação do neurotransmissor GABA em sinaptosomas corticais de ratos (in vitro), uma ação considerada como potencialmente anticonvulsivante. As frações PbTx 2.2.1 e 1.2.3 protegem retinas de ratos após isquêmia. Mas, não se testou o efeito anticonvulsivante dessa fração em experimentos in vivo. O presente trabalho teve dois objetivos: 1- Propor um método cromatográfico para isolar da peçonha de aranhas, neurotoxinas pró-convulsivantes não protéicas e de baixo peso molecular. Isolar e caracterizar parcialmente estas neurotoxinas da peçonha da aranha P.bistriata; 2- verificar se a fração PbTx 2.2.1 possui efeito anticonvulsivante in vivo. O isolamento da peçonha de P. bistriata, realizado com filtração em gel (Sephadex G-50 e G-25), cromatografia líquida de alta eficiência (CLAE) (colunas de fase reversa e troca catiônica), e CLAE-acoplado a espectrometria de massa (CLAE-MS) produziu uma fração (fração 7) e um subcomponente (fração 7.1) com atividade pró-convulsivante, após injeção i.c.v. Tal fração apresenta características típicas de ácidos nucléicos. Confirmou-se, através de ressonância magnética nuclear (RMN) que o constituinte majoritário desta fração é o nucleosídeo inosina. O método cromatográfico mostrou-se muito lento. Uma outra fração (fração 6) da mesma peçonha inibiu as crises causadas por bicuculina i.c.v., ao passo que a fração 1 apresentou atividade de fosfatase ácida e alcalina. A injeção i.c.v. da fração PbTx 2.2.1, 20 min antes do convulsivante bicuculina também i.c.v., bloqueou as crises convulsivas em 71,4% dos animais, o que caracteriza um efeito anticonvulsivante in vivo desta fração. Conclui-se que: 1- A peçonha de P. bistriata possui, dentre muitas, uma fração (fração 7) com efeito pró-convulsivante quando injetada i.c.v. em ratos. Nesta fração, aparentemente o composto majoritário é o nucleosídeo inosina. A peçonha da mesma aranha possui também uma fração com atividade anticonvulsivante (fração 6) e outra com atividade de fosfatase ácida e alcalina (fração 1). 2- o método cromatográfico proposto pode ser otimizado talvez pelo uso de ultrafiltração; 3- a fração PbTx 2.2.1 apresenta efeito anticonvulsivante in vivo no modelo de indução de crises por injeção i.c.v. de bicuculina. / Arthropod venoms are rich sources of neurotoxins, molecular tools with selective and specific actions over the mamalian central nervous system with great clinical and scientific importance. Previous work of our laboratory showed that the spider venom of Parawixia bistriata, when injected by intracerebroventricular (i.c.v.) route, induced convulsive seizures in rats, a sign of convulsant neurotoxins. The group of Professor Joaquim Coutinho-Netto isolated from this spider venom a neurotoxin called PbTx 2.2.1 which is a GABA transporter inhibitor in the rat cortical synaptosomal preparation (in vitro), a potencially anticonvulsant property. The fractions PbTx 2.2.1 and 1.2.3 protected retinal cells against isquemy. But, it has not been tested if the PbTx 2.2.1 fraction also has an in vivo anticonvulsant action. Present work has two objectives: 1- to propose a chromatographic methodology to isolate non-proteic low molecular weigh convulsant neurotoxins from spider venoms. Isolate and partially characterize these neurotoxins from P. bistriata venom; 2- test if PbTx 2.2.1 has in vivo anticonvulsant effect. Biochemical venom isolation by gel filtration (Sephadex G-50 and G-25), reverse phase and cationic exchange in high pressure liquid cromatography (HPLC) and also HPLC coupled to mass spectrometry (HPLC-MS), has pointed that the P. bistriata spider venom has a fraction (fraction 7) and a subfraction (7.1) with convulsant activity when injected i.c.v. in rats. Fraction 7 has nucleosidic characteristics. Nuclear magnetic ressonance (NMR) has showed that the principal component of this fraction is the nucleoside iosine. An other fraction (fraction 6) isolated from the same venom, inhibited seizures induced by i.c.v. bicuculine and the fraction 1 showed acid and basic phosphatase activity PbTx 2.2.1, when injected i.c.v. 20 min prior to the convulsant bicuculline (i.c.v.), has blocked seizures in 71.4 % of the animals, what was considered an anticonvulsant effect. The conclusions are: 1- the spider venom of P. bistriata has a fraction (fraction 7) with convulsant action when injected i.c.v. in rats. The major component of this fraction is the nucleoside iosine. This spider venom also has another fraction (fraction 6) with anticonvulsant activity and one with acid and alcaline phosphatase (fraction 1); 2- the chomatographic methodology can be improved, perhaps by ultrafiltration methods; 3- the PbTx 2.2.1 fraction has anticonvulsant effect in vivo.

The three ways of synthesis of 5'-deoxy and 5'deoxy-5'-fluoromodified nucleosides derived from known cytostatic compounds was designed. Two routes were successfully developed and target substances were prepared. Third one was unsuccessful due to difficulties with deprotection of the key intermediate.

Metabolic differences in the strategies used for pyrimidine base and nucleoside salvage were studied in the pseudomonads and enteric bacteria. Fluoro--analogs were used to select mutant strains of E. coli, S. typhimurium, P. putida, and P. aeruginosa blocked in one or more of the uracil and uridine salvage enzymes. HPLC analysis of cell-free extracts from wild-type and mutant strains examined the effectiveness of the selections. Evidence was found for cytidine kinase in Pseudomonas and for an activity that converted uracil compounds to cytosine compounds. Using media supplemented with 150 μg of orotic acid per ml, P. putida SOC 1, a Pyr, upp mutant which utilizes orotic acid as a pyrimidine source was isolated for the first time in any study.

No description available.

Orientador: Ana Valéria Colnaghi Simionato / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-24T11:07:57Z (GMT). No. of bitstreams: 1 Buzatto_AdrianaZardini_M.pdf: 6706551 bytes, checksum: 371c3400224fcd4031972f241185d555 (MD5) Previous issue date: 2014 / Resumo: O câncer está entre as maiores causas de óbitos no mundo, porém, se a enfermidade for detectada no início, grande parte dos casos pode atingir a cura. Os nucleosídeos são moléculas originadas da degradação do RNA e suas concentrações em fluidos biológicos são alteradas na presença de tumores devido à maior taxa de replicação celular, portanto são potenciais biomarcadores tumorais. A investigação do perfil de tais metabólitos pode auxiliar no diagnóstico e no tratamento do câncer. Neste trabalho, um novo método para a análise de nucleosídeos em soro sanguíneo por eletroforese capilar (CE-UV) no modo cromatografia micelar eletrocinética capilar (MECK) foi desenvolvido e validado. O surfactante catiônico brometo de cetiltrimetilamônio (CTAB) foi empregado, com consequente inversão do fluxo eletrosmótico. Os analitos foram extraídos da matriz de soro sanguíneo através de extração em fase sólida (SPE) e um amplo estudo sobre estratégias de pré-concentração foi realizado para obtenção de limites de quantificação mais baixos e adequados. Sete padrões de nucleosídeos mais o padrão interno foram separados em c.a. 25 min sob as condições de análise otimizadas, i.e. eletrólito de corrida composto por ácido bórico 30 mmol/L, CTAB 50 mmol/L e metanol 10% (v/v) em pH 9,90; tensão de -10 kV; temperatura de 20°C; injeção hidrodinâmica a 50 mbar por 120 s seguida por aplicação 25 kV entre vials de eletrólito por 15 s; e capilar de sílica fundida com 50 µm de diâmetro interno e 56 cm de comprimento efetivo. Foram atingidas eficiências entre 4,3 ? 104 e 1,0 ? 105 e resolução mínima de 1,5. A metodologia foi validada em um pool de soro sanguíneo de indivíduos sadios e foram obtidos limites de quantificação entre 1,0 e 4,0 µmol/L, coeficientes de correlação linear entre 0,9801 e 0,9969 e precisões e exatidões menores que 20%. O método foi aplicado a amostras de 60 indivíduos sadios e 66 portadores de câncer de próstata e um estudo quimiométrico foi realizado para avaliação da potencialidade dos nucleosídeos como biomarcadores tumorais, com obtenção de especificidade acima de 90%. Tal metodologia, portanto, pode ser empregada em conjunto com as já bem estabelecidas para o diagnóstico do câncer de próstata / Abstract: Cancer is amongst the major causes of death worldwide, but, if the disease is detected early, most cases can be cured. Nucleosides are molecules originated from RNA degradation and their concentrations in biological fluids are altered during tumor development due to a higher rate of cell replication; therefore, they are putative tumor biomarkers. The investigation of the profile of such metabolites may aid in the diagnosis and treatment of cancer. In this work, a novel method for the analysis of nucleosides in blood serum by capillary electrophoresis (CE-UV) under micellar electrokinetic capillary chromatography (MECK) mode was developed and validated. The cationic surfactant cetyltrimethyl ammonium bromide (CTAB) was employed, with consequent reversal of the electrosmotic flow. The analytes were extracted from blood serum samples by solid phase extraction (SPE) and a wide study on pre-concentration strategies was accomplished in order to obtain lower and more adequate limits of quantification. Seven nucleoside standards plus the internal standard were separated within c.a. 25 min under the optimized conditions, i.e. electrolyte composed by 30 mmol/L boric acid, 50 mmol/L CTAB and 10% methanol (v/v) with pH 9,90; voltage of -10 kV; temperature of 20°C; hydrodynamic injection under 50 mbar for 120 s followed by 25 kV for 15 s between electrolyte vials; and fused silica capillary with 50 µm internal diameter and 56 cm of effective length. Efficiencies between 4.3 ? 104 and 1.0 ? 105 and a minimum resolution of 1.5 were achieved. The methodology was validated in a pool of blood serum samples from healthy individuals and limits of quantification between 1,0 and 4,0 µmol/L were obtained, as well as linear correlation coefficients between 0,9801 and 0,9969 and precision and accuracy lower than 20%. The method was applied to samples from 60 healthy individuals and 66 prostate cancer patients and a chemometric study was employed in order to evaluate the potentiality of the nucleosides as tumor biomarkers, with specificity higher than 90%. Therefore, this methodology may be applied in conjunction with those already established for prostate cancer diagnosis / Mestrado / Quimica Analitica / Mestra em Química

The overall objective of this study has been to address some of the longstanding questions concerning functional organization of the interphase nucleus. This was achieved by using recently developed high-resolution fluorescence in situ hybridization techniques for a precise localization of specific DNA and RNA sequences in conjunction with immunocytochemistry and biochemical fractionation. This study is based on the philosophy that new insights may be gained by an approach that attempts to interrelate genomic organization, spatial arrangement of RNA metabolism, and nuclear substructure within the mammalian cell nucleus. The nuclear distribution of an exogenous, viral RNA (Epstein-Barr Virus, EBV) within nuclear matrix preparations was studied by developing an approach which couples in situhybridization with biochemical fractionation procedures. EBV RNA molecules accumulate in highly localized foci or elongated tracks within the nucleus of lymphoma cells. These RNA tracks were retained with spatial and quantitative fidelity in nuclear matrix preparations even after biochemical fractionation which removes 95% of cellular protein, DNA, and phospholipid. This provided direct evidence that the primary transcripts are localized via their binding to, or comprising part of, a non-chromatin nuclear substructure. Then the nuclear distribution of RNA from an endogenous gene, fibronectin, was investigated using fluorescence techniques modified for more sensitive detection of endogenous RNAs within nuclear morphology. A series of in situhybridization experiments were performed using different combinations of intron, cDNA, and genomic probes for RNA/RNA or RNA/DNA analysis in intact cells. Fibronectin RNAs were highly localized in the nucleus, forming foci or tracks. Both intron and exon sequences were highly concentrated at the same site within the nucleus, indicating the presence of primary unspliced transcripts. Double-color hybridization using a nontranscribed 5' flanking sequence probe and a genomic DNA probe showed that the gene and RNA track for fibronectin were spatially overlapped, with the gene consistently towards one end of the track. These results provided evidence that the accumulation of RNA molecules occurs directly at or near the site of transcription, and further indicated a structural polarity to the RNA track formation with the gene towards one end. It was further discovered that within a single cell, cDNA probes produced longer tracks than those formed with intron probes, i.e. intron signals were generally confined to a smaller part of the track than the exon signals, indicating that splicing occurs within the RNA track. Additional experiments using poly(A) RNA hybridization or anti-SC-35 antibody staining combined with fibronectin RNA hybridization have shown that the fibronectin tracks were associated with recently discovered transcript domains enriched in poly(A) RNA and splicing factors. To further determine whether other specific genes and RNAs are functionally organized within the nucleus, the nuclear distribution of several active or inactive genes was analyzed in terms of their spatial relationship to transcript domains. The results indicated that in addition to fibronectin, the genes or their primary transcripts from two other active genes, collagen and actin, were also closely associated with the domains. For both of these, over 90% of the gene/RNA sites were either overlapping or directly contacting the domains. In contrast. for two inactive genes, cardiac myosin heavy chain and neurotensin, it was found that both genes were separated from the domains in the majority of nuclei. Histone genes, which have several unique features, showed a relatively complex result with about half of the gene signals extremely close to the domains. Therefore, three actively expressed genes were demonstrated to be tightly associated with the domains and, moreover, their RNAs showed distinct and characteristic spatial relationships with the domains. In contrast, two inactive genes were not associated with the domains. One potential implication of these finding is that active genes may be preferentially localized in and around these transcript domains. The nuclear localization of another RNA, XIST, standing for X-inactivation specific transcript, was studied because of its potentially unique biological role. XIST is the only gene which is known to be expressed from the inactive human X chromosome but not from the active X chromosome, and was believed to be important in X inactivation. Using fluorescence in situhybridization, it was found that XIST RNA was highly localized within the nucleus and always completely overlapped the Barr body which is the condensed, inactive X chromosome. The different fine distribution pattern of XIST RNA within the nucleus as compared to other protein coding RNAs suggested a unique function for this RNA, possibly involving a structural role in inactivating the X chromosome. The final area of my thesis research was to study and acquire expertise in the applications of fluorescence in situ hybridization in gene mapping and cancer genetics. A retinoblastoma (RB)-related putative tumor suppressor gene, p107, was mapped to human chromosome 20 in band q11.2. Localization of p107 to 20q11.2 was of particular interest because of the correlation of breakpoints in this area with specific myeloid disorders such as acute nonlymphocytic leukemia and myelodysplastic syndrome. Other applications of in situ hybridization including the search for unknown genes at a known chromosomal breakpoint, detection of deletions, translocations or other chromosomal rearrangements associated with specific tumors were also explored and reviewed.

In previous work I described the purification and properties of the microtubule-based mechanochemical ATPase cytoplasmic dynein. Cytoplasmic dynein was found to produce force along microtubules in the direction corresponding to retrograde axonal transport. Cytoplasmic dynein has been identified in a variety of eukaryotes including yeast and human, and there is a growing body of evidence suggesting that this "molecular motor" is responsible for the transport of membranous organelles and mitotic chromosomes. The first part of this thesis investigates the molecular basis of microtubule-activation of the cytoplasmic dynein ATPase. By analogy with other mechanoenzymes, this appears to accelerate the rate-limiting step of the cross-bridge cycle, ADP release. Using limited proteolysis, site-directed antibodies, and N-terminal microsequencing, I identified the acidic C-termini of α and β-tubulin as the domains responsible for activation of the dynein ATPase. The second part of this thesis investigates the structure of the 74 kDa subunit of cytoplasmic dynein. The amino acid sequence deduced from cDNA clones predicts a 72,753 dalton polypeptide which includes the amino acid sequences of nine peptides determined by microsequencing. Northern analysis of rat brain poly(A) revealed an abundant 2.9 kb mRNA. However, PCR performed on first strand cDNA, together with the sequence of a partially matching tryptic peptide, indicate the existence of three isoforms. The C-terminal half is 26.4% identical and 47.7% similar to the product of the Chlamydomonas ODA6 gene, a 70 kDa subunit of flagellar outer arm dynein. Based on what is known about the Chlamydomonas70 kDa subunit, I suggest that the 74 kDa subunit is responsible for targeting cytoplasmic dynein to membranous organelles and kinetochores of mitotic chromosomes. The third part of this thesis investigates a 50 kDa polypeptide which co-purifies with cytoplasmic dynein on sucrose density gradients. Monoclonal antibodies were produced against the 50 kDa subunit and used to show that it is a component of a distinct 20S complex which contains additional subunits of 45 and 150 kDa. Moreover, like cytoplasmic dynein, the 50 kDa polypeptide localizes to kinetochores of metaphase chromosomes by light and electron microscopy. The 50 kDa-associated complex is reported to stimulate cytoplasmic dynein-mediated organelle motility in vitro. The complex is, therefore, a candidate for modulating cytoplasmic dynein activity during mitosis.

Members of the Argonaute family of proteins, which interact with small RNAs, are the key players of RNAi and other related pathways. The C. elegans genome encodes 27 members of the Argonaute family. During this thesis research, we sought to understand the functions of the members of this gene family in C. elegans. Among the Argonaute family members, rde-1 and alg-1/2have previously been shown to be essential for RNAi and development, respectively. In this work, we wanted to assign functions to the remaining members of this large family of proteins. Here, we describe the phenotype of 31 deletion alleles representing all of the previously uncharacterized Argonaute members. In addition to rde-1, our analysis revealed that two other Argonaute members csr-1 and prg-1 are also essential for development. csr-1 is partially required for RNAi, and essential for proper chromosome segregation. prg-1, a member of PIWI subfamily of Argonaute genes, exhibits reduced brood size and temperature-sensitive sterile phenotype, implicating that it is required for germline maintenance. Additionally, we showed that RDE-1 interacts with trigger-derived sense and antisense siRNAs (primary siRNAs) to initiate RNAi, while several other Argonaute proteins, SAGO-1, SAGO-2, and perhaps others, functioning redundantly, interact with amplified siRNAs (secondary siRNAs) to mediate downstream silencing. Moreover, our analysis uncovered that another member of Argonaute gene family, ergo-1, is essential for the endogenous RNAi pathway. Furthermore, we built an eight-fold Argonaute mutant, MAGO8, and analyzed its developmental phenotype and sensitivity to RNAi. Our analysis revealed that the genes deleted in the MAGO8 mutant function redundantly with each other, and are required for RNAi and the maintenance of the stem cell totipotency.

This thesis deals with the synthesis of prodrugs based on analogs of nucleoside phosphonates derived from 6-fluoro-3-hydroxypyrazine-2-carboxamide (T-705) and 3- hydroxypyrazine-2-carboxamide (T-1105). T-705 and T-1105 act as inhibitors of an influenza RNA polymerase. Both compounds mimic naturally occurring nucleobases, so their fluorinated nucleoside phosphonates could also be biologically active. Derivatives of 2-deoxy-2-fluoro-D-ribose (2-FdR) were prepared in this work. Because of complications during the syntthesis of 3-deoxy-3-fluoro-D-ribose (3-FdR) derivatives, 5- deoxy-5-fluoro-D-xylose (5-FdX) derivatives were prepared instead. Deoxyfluorination was done after incorporation of suitable protecting groups followed by selective deprotection and phosphonate binding. Furthermore nucleosides were synthetised using silyl-Hilbert-Johnson method and their bis-POM derivattives were also prepared. Key words: favipiravir (T-705), T-1105, prodrugs, phosphonates, fluorinated nucleosides