No description available.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2015-11-12T13:13:21Z No. of bitstreams: 1 RitaDeCassiaBarretoDaSilva_TESE.pdf: 3291914 bytes, checksum: 557593d073ed5762546f566b1d7e415d (MD5) / Approved for entry into archive by Elisangela Moura (lilaalves@gmail.com) on 2015-11-16T15:20:00Z (GMT) No. of bitstreams: 1 RitaDeCassiaBarretoDaSilva_TESE.pdf: 3291914 bytes, checksum: 557593d073ed5762546f566b1d7e415d (MD5) / Made available in DSpace on 2015-11-16T15:20:00Z (GMT). No. of bitstreams: 1 RitaDeCassiaBarretoDaSilva_TESE.pdf: 3291914 bytes, checksum: 557593d073ed5762546f566b1d7e415d (MD5) Previous issue date: 2014-03-27 / 2019-05-27 / A abordagem metagen?mica tem permitido o acesso ao material gen?tico de microrganismos n?o cultivados e tem sido usada para identifica??o de novos genes. Apesar da import?ncia dos mecanismos de reparo de DNA para a manuten??o da integridade gen?mica nosso conhecimento sobre mecanismos de reparo de DNA ? baseado em organismos modelo como E. coli e pouco ? conhecido sobre os organismos de vida livre e n?o cultivados. Neste trabalho, a abordagem metagen?mica foi aplicada para descobrir novos genes envolvidos com a manuten??o da integridade gen?mica. Um clone positivo foi identificado por replicar a biblioteca metagen?mica em meio seletivo contendo H2O2. O clone metagen?mico foi capaz de complementar parcialmente a defici?ncia em reparo de DNA de cepas simples e duplo-mutantes de E.coli (recA e xthA nfo, respectivamente) submetidas ao estresse gerado por H2O2 e MMS.A an?lise de sequ?ncia mostrou uma ORF codificando para uma prote?na hipot?tica membro da superfam?lia Exo_Endo_Phos (PF03372) e, a filogenia indicou que a mesma n?o est? inclusa em nenhuma das subfam?lias EEP. Assim, uma nova nuclease foi identificada e experimentalmente caracterizada in vivo e in vitro. Ensaios espec?ficos utilizando a nuclease purificada e oligonucleotideos fluorescentemente marcados revelaram sua atividade 3?-5?exonuclease, em substratos simples e dupla-fita, dependente de Magn?sio e sens?vel a EDTA. Uma vez que este ? o primeiro relato e caracteriza??o de uma enzima obtida a partir de abordagem metagen?mica mostrando uma atividade exonuclease, foi nomeada EXOMEG1

No description available.

Metastasis is the spread of cancer cells from the primary tumor to distant sites. It is the most dangerous attribute of cancer, and also the principle cause of cancerrelated morbidity and mortality. Metastasis suppressor genes are a group of genes that suppress tumor metastasis without significant effect on tumorigenicity. NM23 was the first identified metastasis suppressor gene, and loss of its expression is a frequent hallmark of metastatic growth in multiple cancers (e.g. melanoma, carcinomas of breast, stomach and liver). NM23-H1 possesses at least three enzymatic activities, including nucleoside diphosphate kinase (NDPK), histidine kinase (hisK), and a more recently described 3f-5f exonuclease (EXO). While the hisK has been shown to be linked to the suppression of cell motility, the NDPK has been reported to be unrelated to the suppression of metastatic potential indirectly. Relevance of EXO has not been addressed. Other known 3f-5f exonuclease are closely associated with DNA repair functions, suggesting NM23-H1 may suppress mutations required for metastasis. As a transcription factor, NM23 has been shown to modestly downregulate the transcription on PDGF-A chain, a growth factor oncogene, either alone or in association with another transcriptional factor, Pur@. At the same time, identification of NM23-H1 as a 3f-5fexonuclease suggests the role of NM23-H1 in DNA repair. Etoposide and cisplatin elicited nuclear translocation of H1 within 4 h in HeLa and HepG2 cells, seen as accumulation of H1 in small intranuclear foci, strongly suggesting the DNA repair function of H1. To investigate the enzymatic function contributing to metastasis suppressor activity of H1, complementation system was used by transfecting NM23-H1 with individually disrupted enzymatic function into 2 melanoma cell lines, 1205LU and WM793. Overexpression of H1 in 1205LU suppressed lung metastasis in vivo without effect on indices of transformation (e.g. proliferation, soft agar colonization). EXO- deficient H1 and NDPK-deficient H1 lost suppression of lung metastasis, while hisK-deficient H1 maintained suppressor activity. Consistent with the results in 1205LU cells, EXO-deficient H1 and NDPKdeficient H1 lost suppression of the progression of WM793 cells in protein-free medium, while WT and hisK-deficient H1 prevented the progression. Taken together, these data suggest that the NDPK and/or 3f-5fEXO activity of H1 inhibits the progression of premetastatic cells to the metastatic phenotype, possibly via a DNA repair function or other structural transactions with DNA.

No description available.

NM23-H1 represents the first identified metastasis suppressor, exhibiting reduced expression in breast carcinoma and melanoma, and an ability to inhibit metastatic growth without significant impact on the transformed phenotype. Although its molecular mechanism of action is not fully understood, NM23-H1 possesses at least three enzymatic activities that may mediate metastasis suppressor function. It catalyzes nucleoside diphosphate kinase (NDPK) activity, as well as protein histidine kinase and 3’-5’ exonuclease activities. As 3’-5’ exonucleases are generally required for maintenance of genomic integrity, this activity represents a plausible mediator to underlie the metastasis suppressor function of NM23-H1 protein. To investigate the relevant activity of NM23-H1 in metastasis suppression, we constructed a panel of NM23-H1 mutant variants with selective enzymatic lesions. Previous studies have identified some key amino acid residues important for the enzymatic characteristics of NM23-H1. However, none of them are selective for disrupting the 3’-5’ exonuclease activity. In this study, we show that a substitution of Glu5 to alanine results in a dramatic, selective loss in 3’-5’ exonuclease property without significant affecting other enzymatic activities. To measure the extent to which the exonuclease function opposes mutation and metastasis, NM23-deficient and metastatic cell lines with forced expression of NM23-H1 variants are analyzed in nude mice. In spontaneous metastasis models, NM23-H1 mutants deficient in 3‘-5’ exonuclease activity significantly disrupt the capacity of metastasis suppression of wild-type protein, indicating that the 3’-5’ exonuclease activity of NM23-H1 is necessary for the spontaneous metastasis-suppressing effects. As 3'-5' exonucleases are generally associated with DNA repair process, we have also studied the contributions of yeast NM23 homologue YNK1 to genomic integrity in Saccharomyces cerevisiae. Consistent with an antimutator function, ablation of YNK1 significantly results in increased mutation rates following exposure to UV irradiation and the alkylating agent methyl methanesulfonate (MMS). The impaired DNA-damage response of ynk1Δ cells suggests a role of human homologue NM23 in DNA repair. More evidence is being collected in our laboratory to demonstrate a role for NM23-H1 in maintaining genomic integrity. Collectively, our findings of DNA repair activity of NM23-H1 will contribute to the understandings of the mechanisms in metastasis suppression and new drug discoveries.

Orientador: Maria Isabel Nogueira Cano / Resumo: Entre as espécies do gênero Leishmania estão os protozoários que causam leishmaniose, uma doença tropical negligenciada endêmica em muitos países, incluindo o Brasil. Métodos de controle e tratamento ainda são ineficientes e a resistência a drogas é um desafio. Por isso, pesquisas para entender melhor a biologia molecular desses parasitos são encorajadas. Uma possível estratégia para isso, é o estudo dos telômeros, estrutura fundamental para a homeostase do genoma. Os telômeros são estruturalmente diferentes do resto do cromossomo, e contam com proteínas específicas que realizam sua manutenção. A Replication Protein A subunit 1 (RPA-1) é uma proteína que interage de DNA de simples fita que tem diversas funções relacionadas com o metabolismo do DNA eucarioto, incluindo os telômeros. A RPA-1 é parte de um complexo heterotrimérico conservado nos eucariotos, incluindo Leishmania spp.. Recentemente nós mostramos por modelagem molecular que a estrutura terciária da LaRPA-1 difere dos seus ortólogos em humanos e leveduras, além de mostrar interações específicas nos telômeros dos parasitos, que na ausência de homólogos canônicos para telomere-end binding protein (TEP) elegem a LaRPA-1 como um potencial candidato para essa função. Neste trabalho, avaliamos a capacidade da LaRPA-1 como uma TEP, cujo papel principal é proteger a extremidade 3' dos telômeros de ataques por exonucleases. Uma busca estrutural por proteínas que compartilham com as TEP domínios de interação proteína-DNA, mos... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Among the protozoa parasites of the Leishmania genus are the causative agents of leishmaniasis, a neglected tropical disease endemic in many countries, including Brazil. Disease control and treatment are still inefficient and parasite drug resistance is a challenge. Therefore, efforts for the establishment of intensive research to better understand the molecular biology of these parasites are encouraged. One possible strategy is to study parasite telomeres, a vital chromosome structure important to maintain genome homeostasis. Telomeres are significantly different from the rest of the chromosome and are associated with proteins involved in their maintenance. Replication Protein A subunit 1 (RPA1), a single-stranded DNA-binding protein that plays multiple roles in eukaryotic DNA metabolism, including telomeres, is part of a conserved heterotrimeric complex which is present in most eukaryotes including Leishmania spp. Recently, using molecular dynamics simulations we have shown that the tertiary structure of LaRPA-1 differs from human and yeast RPA-1 and that it also shows parasitespecific interactions with telomeric DNA. In the absence of real homologues to telomere-end binding proteins, LaRPA-1 could be considered a potential candidate. If LaRPA-1 is a telomere-end binding protein, one of its main role would be to protect the telomeric 3`-end termini from nuclease attack. A structural search for proteins that share with the TEP domains of protein-DNA interaction, showed that ... (Complete abstract click electronic access below) / Mestre

Submitted by Gabriel Arantes Galvão Dias dos Santos (arantes_gabriel@hotmail.com) on 2018-05-14T15:21:05Z No. of bitstreams: 1 Dissertação pós defesa.pdf: 3303163 bytes, checksum: 01b3ceab15b6016a9aaca279d39ebdc5 (MD5) / Approved for entry into archive by Sulamita Selma C Colnago null (sulamita@btu.unesp.br) on 2018-05-14T17:46:54Z (GMT) No. of bitstreams: 1 santos_gagd_me_bot.pdf: 3303163 bytes, checksum: 01b3ceab15b6016a9aaca279d39ebdc5 (MD5) / Made available in DSpace on 2018-05-14T17:46:54Z (GMT). No. of bitstreams: 1 santos_gagd_me_bot.pdf: 3303163 bytes, checksum: 01b3ceab15b6016a9aaca279d39ebdc5 (MD5) Previous issue date: 2018-04-27 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Entre as espécies do gênero Leishmania estão os protozoários que causam leishmaniose, uma doença tropical negligenciada endêmica em muitos países, incluindo o Brasil. Métodos de controle e tratamento ainda são ineficientes e a resistência a drogas é um desafio. Por isso, pesquisas para entender melhor a biologia molecular desses parasitos são encorajadas. Uma possível estratégia para isso, é o estudo dos telômeros, estrutura fundamental para a homeostase do genoma. Os telômeros são estruturalmente diferentes do resto do cromossomo, e contam com proteínas específicas que realizam sua manutenção. A Replication Protein A subunit 1 (RPA-1) é uma proteína que interage de DNA de simples fita que tem diversas funções relacionadas com o metabolismo do DNA eucarioto, incluindo os telômeros. A RPA-1 é parte de um complexo heterotrimérico conservado nos eucariotos, incluindo Leishmania spp.. Recentemente nós mostramos por modelagem molecular que a estrutura terciária da LaRPA-1 difere dos seus ortólogos em humanos e leveduras, além de mostrar interações específicas nos telômeros dos parasitos, que na ausência de homólogos canônicos para telomere-end binding protein (TEP) elegem a LaRPA-1 como um potencial candidato para essa função. Neste trabalho, avaliamos a capacidade da LaRPA-1 como uma TEP, cujo papel principal é proteger a extremidade 3' dos telômeros de ataques por exonucleases. Uma busca estrutural por proteínas que compartilham com as TEP domínios de interação proteína-DNA, mostrou que no genoma de Leishmania spp. não existem homólogos estruturais para as mesmas. Aqui mostramos por diferentes abordagens que a LaRPA-1 tem a capacidade de interagir com no mínimo uma repetição telomérica e também é capaz de proteger in vitro a simples fita telomérica rica em G (5’ TTAGGG 3’) da digestão por Exonuclease I bacteriana cuja atividade é no sentido 3’-5’. Somando esses dados, com dados anteriores que mostram que a LaRPA-1 tem preferência pela fita telomérica rica em G e o fato dela ter sido co-purificada com a atividade de telomerase sugerem fortemente que ela está diretamente relacionada com a manutenção da maquinaria telomérica, podendo inclusive ser considerada a principal ligante de simples fita telomérica rica em G (3’ G-overhang) em Leishmania spp. / Among the protozoa parasites of the Leishmania genus are the causative agents of leishmaniasis, a neglected tropical disease endemic in many countries, including Brazil. Disease control and treatment are still inefficient and parasite drug resistance is a challenge. Therefore, efforts for the establishment of intensive research to better understand the molecular biology of these parasites are encouraged. One possible strategy is to study parasite telomeres, a vital chromosome structure important to maintain genome homeostasis. Telomeres are significantly different from the rest of the chromosome and are associated with proteins involved in their maintenance. Replication Protein A subunit 1 (RPA1), a single-stranded DNA-binding protein that plays multiple roles in eukaryotic DNA metabolism, including telomeres, is part of a conserved heterotrimeric complex which is present in most eukaryotes including Leishmania spp. Recently, using molecular dynamics simulations we have shown that the tertiary structure of LaRPA-1 differs from human and yeast RPA-1 and that it also shows parasitespecific interactions with telomeric DNA. In the absence of real homologues to telomere-end binding proteins, LaRPA-1 could be considered a potential candidate. If LaRPA-1 is a telomere-end binding protein, one of its main role would be to protect the telomeric 3`-end termini from nuclease attack. A structural search for proteins that share with the TEP domains of protein-DNA interaction, showed that in the genome of Leishmania spp. there are no structural homologues for them. In this work, we show by different methods, that in vitro LaRPA-1 can bind at least one telomeric repeat and it can also protect the telomeric G-rich sequence (5’ TTAGGG 3’) from the bacterial 3’-5’Exonuclease I digestion. These data compiled to previous data showing that LaRPA-1 preferentially binds the G-rich telomeric DNA and that it co-purifies with telomerase activity strongly suggest that LaRPA-1 is directly involved with parasite telomere maintenance and, possibly, is the main G-rich single-stranded (3’ G-overhang) telomere-binding protein in Leishmania spp.

Aptamers are short oligonucleotide sequences (DNA or RNA) capable of high affinity and specific binding to a molecule or a family of molecules. Aptamers are lower in cost and exhibit higher reproducibility when compared to antibodies and thus are well-suited for recognition and detection of small molecular targets such as drugs of abuse and small medical biomarkers. While aptamers have been extensively utilized for development of small molecule sensors, several limitations prevent measurements of complex or real-world samples. This dissertation describes methods, technologies, and assays that were developed with the goal of producing and/or improving aptamer-based sensors for target detection in complex samples. Aptamer engineering is detailed as an important facet of maximizing aptamer-sensor sensitivity and specificity, along with adaptation to various read-out mechanisms for improved selectivity. In chapter 3, an aptamer vii sensor for cocaine is developed based on binding between the fluorophore ATMND to the cocaine aptamer which results in quenching (i.e., ‘turn-off’) of the fluorescence of ATMND. Cocaine binding results in displacement of the ATMND and recovery of the fluorescence signal. Detection of cocaine is demonstrated with an engineered cocaine aptamer with higher affinity for cocaine, permitting over a 50-fold increase in sensitivity over other aptamer-based sensors. The method can be used in dilute biological fluids (e.g., saliva) with a single step reaction (seconds) and robust signal output. In chapter 4, a new adenosine specific aptamer is identified through rational engineering of a previously reported ATP-binding aptamer. The new adenosine aptamer is utilized to develop an electrochemical sensor for detection of adenosine in undiluted serum. The method displays 40-fold higher sensitivity in undiluted serum measurements over previously reported aptamer-based sensors for adenosine but also demonstrates specificity for adenosine over ATP, ADP and AMP that has not been previously reported. In chapter 5, a nuclease-guided truncation method is developed to yield optimal structure-switching aptamer sequences for the emergent illicit drug methylenedioxypyrovalerone (MDPV) and medical biomarkers ATP and deoxycorticosterone 21-glucoside (DOG). The method intelligently removes unessential nucleotides, producing truncated aptamer sequences with structure-switching functionality. This technique will be immediately useful for simple and low-cost development of aptamer-based electrochemical sensors.

DNA double-strand breaks (DSBs) are lethal in eukaryotic cells if left unrepaired. In Saccharomyces cerevisiae the Mre11/Rad50/Xrs2 (MRX) complex is required for repair of DSBs through homologous recombination and nonhomologous end joining. Although Mre11 complexes exhibit 3'[rightwards arrow]5' exonuclease activity and endonuclease activity on DNA hairpin and single-stranded DNA overhang substrates in vitro, the role of the MRX complex in homologous recombination in vivo is not well understood. It has been shown to be specifically required for the processing of protein-conjugated DNA ends at DSBs during meiosis and hairpin-capped DSBs in mitotic cells and has been suggested that the Mre11 nuclease functions to remove damaged DNA ends. Recently, the Sae2 protein has been demonstrated to be involved in hairpin-capped DSBs and DNA end processing along with MRX in vivo. However, the Sae2 protein has no known homologs outside of fungi and no obvious motifs to suggest the function(s) of the Sae2 protein. We have purified recombinant Sae2 and MRX and report that the Sae2 protein itself is a single-stranded DNA endonuclease. The Sae2 protein stimulates the 3[rightwards arrow]5' exonuclease activity of the MRX complex. Also, the MRX complex can stimulate Sae2 nuclease activity to cleave ssDNA adjacent to DNA hairpin structures. The Sae2 protein also binds independently to double-stranded DNA and forms higher order protein-DNA complexes with MRX. These results provide biochemical evidence for functional cooperatively between MRX and Sae2 on DSBs and hairpin-capped DNA ends. / text