No description available.

Conjugation is a fundamentally important mechanism of horizontal DNA transfer between bacteria, bacteria x archea, and bacteria x eukaryotes. This work has concentrated on conjugation between bacteria x eukaryotes, specifically Escherichia coli x Saccharomyces cerevisiae. Four hypotheses were tested, investigating the barriers to this particular form of DNA transfer. The first investigated if a mutation that altered the cell-surface of the recipient S. cerevisiae could inhibit DNA transfer. The final three utilised a recombination-dependent-conjugation assay to investigate the barrier to DNA transmission through recombination. The hypotheses tested if the frequency of recombination, in this recombination-dependent-conjugation assay, differed when using similar or diverged DNA substrates, if a mismatch repair mutation within the recipient could affect the frequencies of recombination observed, and if the position on the plasmid of the gene of interest affected the frequency of transmission. Transmission of the Ura3 DNA sequence in the recipient S. cerevisiae was used to test all four hypotheses. The cell wall mutants mnn9, knr4, fks1 and kre6 were utilised to investigate if the cell-surface of the recipient could affect the frequency of transmission. The similar and diverged substrates utilised in the investigation of the affect of sequence similarity on recombination were the DNA sequences of ura3 from S. cerevisiae and Saccharomyces carlsbergensis, respectively and the MMR mutants utilised were msh2, pms1 and pol30-52. Cell wall mutants were not found to limit the frequency of transfer once donor-recipient contact was induced through the solid surface mating procedure. Sequence similarity, MMR and the relative position of the ura3 DNA sequence on the conjugative plasmids were shown to have little effect on the frequency of transmission in S. cerevisiae. This suggests that any DNA that enters the nucleus of S. cerevisiae (eukaryotes) can recombine with the chromosome and alter it to the same extent. However, trends within the data also suggest that DNA is transferred into the recipient and then transported to the nucleus to recombine with the chromosome as a single-stranded DNA molecule.

Conjugation is a fundamentally important mechanism of horizontal DNA transfer between bacteria, bacteria x archea, and bacteria x eukaryotes. This work has concentrated on conjugation between bacteria x eukaryotes, specifically Escherichia coli x Saccharomyces cerevisiae. Four hypotheses were tested, investigating the barriers to this particular form of DNA transfer. The first investigated if a mutation that altered the cell-surface of the recipient S. cerevisiae could inhibit DNA transfer. The final three utilised a recombination-dependent-conjugation assay to investigate the barrier to DNA transmission through recombination. The hypotheses tested if the frequency of recombination, in this recombination-dependent-conjugation assay, differed when using similar or diverged DNA substrates, if a mismatch repair mutation within the recipient could affect the frequencies of recombination observed, and if the position on the plasmid of the gene of interest affected the frequency of transmission. Transmission of the Ura3 DNA sequence in the recipient S. cerevisiae was used to test all four hypotheses. The cell wall mutants mnn9, knr4, fks1 and kre6 were utilised to investigate if the cell-surface of the recipient could affect the frequency of transmission. The similar and diverged substrates utilised in the investigation of the affect of sequence similarity on recombination were the DNA sequences of ura3 from S. cerevisiae and Saccharomyces carlsbergensis, respectively and the MMR mutants utilised were msh2, pms1 and pol30-52. Cell wall mutants were not found to limit the frequency of transfer once donor-recipient contact was induced through the solid surface mating procedure. Sequence similarity, MMR and the relative position of the ura3 DNA sequence on the conjugative plasmids were shown to have little effect on the frequency of transmission in S. cerevisiae. This suggests that any DNA that enters the nucleus of S. cerevisiae (eukaryotes) can recombine with the chromosome and alter it to the same extent. However, trends within the data also suggest that DNA is transferred into the recipient and then transported to the nucleus to recombine with the chromosome as a single-stranded DNA molecule.

Submitted by Reginaldo Soares de Freitas (reginaldo.freitas@ufv.br) on 2017-03-29T11:03:04Z No. of bitstreams: 1 texto completo.pdf: 3774617 bytes, checksum: 197f3ca5359c93c3476e850581110d85 (MD5) / Made available in DSpace on 2017-03-29T11:03:04Z (GMT). No. of bitstreams: 1 texto completo.pdf: 3774617 bytes, checksum: 197f3ca5359c93c3476e850581110d85 (MD5) Previous issue date: 2013-04-16 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O arsênio (As) é um elemento não só tóxico, mas também altamente genotóxico aos seres vivos. Muitas lacunas precisam ser preenchidas com relação aos processos causadores de toxidade do As em plantas, bem como os mecanismos de tolerância e sensibilidade a este metalóide. Para isso, plantas de Arabidopsis thaliana (WT, mutantes msh2 e transgênicas repórteres em mutações) e Allium cepa foram expostas a 0, 2, 8 e 16 mg As L -1, durante cinco dias, em sistema hidropônico ou em meio de cultura. As plantas acumularam grandes teores de As nas raízes e apresentaram elevado fator de translocação para a parte aérea, e também alterações no acúmulo de nutrientes. Os sintomas visuais se intensificaram com o aumento da concentração de As na solução nutritiva. As raízes adquiriram coloração escura e aspecto gelatinoso, danificado e aumento no comprimento e densidade dos pêlos; a parte aérea apresentou aumento dos teores de antocianinas e sinais de senescência precoce, bem como alterações na espessura de tecidos. O estresse oxidativo e a redução dos teores de fósforo foram apontados como os principais efeitos do As capazes de causar toxidez, evidenciando os danos indiretos deste elemento no organismo. Foram verificadas importantes alterações fotossintéticas, bem como indícios de danos ao processo de respiração celular devido o aumento da expressão de genes codificantes de oxidases alternativas. Também foram observadas alterações nos teores de açúcares em folhas jovens, maduras e raízes. O As promoveu fragmentação do DNA nos ápices radiculares de A. cepa e aumento das taxas de mutação pontual e de recombinação-não homóloga em A. thaliana. O significativo aumento da expressão dos genes msh2 e msh7, codificadores de enzimas-chave do processo mismatch repair, que realiza o reparo de bases danificadas ou erroneamente inseridas no DNA, sugeriu a importância deste mecanismo no combate à genotoxidade do As em A. thaliana. Isso foi confirmado pela maior sensibilidade observada nas plantas mutantes msh2 ao As, detectada visualmente via aumento da peroxidação de lipídios. Observou-se inibição da atividade da protease caspase-3, associada ao processo de morte celular programada, reforçando a capacidade de inibição da atividade enzimática pelo As. / Arsenic (As) is not only a toxic element, but also highly genotoxic to living organisms. Several gaps in our understanding of As toxicity in plants need to be filled, including the mechanisms that result in tolerance and sensitivity to this metalloid. For this reason Arabidopsis thaliana plants (WT, msh2 mutants and transgenic reporters in mutation process) and Allium cepa were exposed to 0, 2, 8 e 16 mg As L -1, for five days, in a hydroponic system or in culture medium. The plants accumulated large amounts of As in roots and presented a high translocation factor to the shoot, and also showed changes in nutrient accumulation. The visual symptoms have intensified with the increasing of As concentration in the nutritive solution. Roots showed dark coloration and a damaged and gelatinous aspect, with increased roots hair length and density. The shoots showed accumulation of anthocyanins and signs of early senescence, as well as changes in tissue thickness. Oxidative stress and reduction of phosphorus concentration in tissues have been implicated as the main cause of toxicity, evidencing the indirect damage from this element in the organism. Important changes in photosynthesis were observed, as signs of damage to respiration, due to increased expression of alternative oxidase genes. Thus, changes in the levels of synthesis and utilization of sugars by plants were observed. As promoted DNA fragmentation in A. cepa and increased rates of point mutation and nonhomologous recombination. The significant increase in the expression pattern of the msh2 and msh7 genes, which encode key enzymes in DNA repair process, suggests the importance of this mechanism in defense against As genotoxicity in A. thaliana. This was confirmed by the greater sensitivity observed in msh2 mutants to As as indicated by visual symptoms and by an increase in lipid peroxidation. Inhibition of the activity of the caspase-3 protease was also observed, evidencing the As capacity of enzyme activity inhibition. / Tese enviada pela secretaria do curso por e-mail, em 28-03-17.

Escherichia coli MutS is a DNA binding repair protein (97 kDa, monomer) and its biological significance arises from its recognition of mismatches which occur as errors during DNA replication. Mismatches and mutagenic bases represent a fascinating and diverse range of shapes and sizes and it is not obvious how a single protein (MutS) can recognise such molecular diversity against a huge background of canonical Watson-Crick base pairs. In this project, the structure of a 17mer mismatch GT DNA was carried out using NMR spectroscopy to identify the differences caused by the introduction of a non-canonical base pair on helical structure. The resulting structure was B-form in conformation and local helical distortions were observed about the GT mispair due primarily to its sheared orientation. The effect of mismatch orientation, sequence context and oligonucleotide length on mismatch stability was also investigated using UV absorbance melting and NMR spectroscopy. The results showed that substitution of a TG mispair for a GT mispair was accompanied by a small drop in melting temperature. It was also discovered that sequences in which purine-purine or pyrimidine-pyrimidine stacking occurred induced additional stability of the mismatch resulting in a higher melting temperature of the duplex.Affinity of mismatch GT DNA and its mismatch orientation, sequence context and length analogues for MutS was investigated by monitoring changes to the chemical shifts and linewidths of imino protons resonances during NMR titration. The results showed that MutS displayed higher affinity towards sequences which involved better stacking between the flanking base pairs and the GT/TG mispair.Analogous NMR structural investigations of 6-thioguanine modified 13mer GC DNA and its oxidised derivatives have been successfully carried out. The NMR structure was successfully determined of the former and the results obtained showed the effect on helical structure induced by the substitution of a different DNA lesion.Although the crystal structures of MutS bound to DNA mismatches have been known for a number of years, the analogous crystal structures of uncomplexed apo MutS have not been determined to date. Consequently, vital structural knowledge on the large change in conformation of MutS upon binding to the DNA mismatch is seriously lacking. We have successfully isolated the structurally and functionally important NTD of E. coli MutS and its labelled (13C, 15N) analogues and have shown that it is endowed with a stable, tertiary structural fold and well suited to NMR structure determination. This is exemplified by the assignments of several backbone amide and side chain resonances using isotope aided 3D NMR techniques.

DNA encodes the genetic information of the cell, therefore, every single living organism has a precise DNA damage response mechanism to safeguard DNA integrity. Base mismatches are endogenous DNA lesions introduced by the replicative polymerase during DNA replication. The conserved DNA mismatch repair pathway corrects these base mismatches. Mismatch repair initiation is orchestrated by two proteins, MutS and MutL. MutS recognizes and binds to base mismatches and relays the presence of the lesion to MutL. MutL, in turn, interacts with downstream factors to coordinate mismatch excision. The processivity clamp, typically known for its role in tethering the DNA polymerase to DNA during replication, is also involved in several steps of this repair process including MutL endonuclease activation and strand resynthesis. The dynamics of the MutS-MutL and MutL-processivity clamp interactions present one of the bottlenecks to uncovering the spatial and time organization of these protein assemblies. Therefore, little is known about the interactions that orchestrate the early steps of mismatch repair. The biochemical and structural work included in this thesis outlines a precise series of molecular cues that activate MutL. / Thesis / Doctor of Philosophy (PhD)

The fidelity of DNA replication prevents mutations that may lead to cancer predisposition or neurodegenerative diseases. One mechanism that enhances DNA replication fidelity is DNA mismatch repair, which corrects mismatches and small insertion/deletion loops that have escaped polymerase proofreading. In all eukaryotes and most prokaryotes, MutL (a key mismatch repair protein) has an intrinsic endonuclease activity that nicks the newly synthesized strand and recruits downstream factors to remove and correct errors. It has been proposed that ATP binding promotes a series of conformational changes that induce structural order within MutL and stimulates its endonuclease activity. The C-terminal domain of MutL, which harbors the endonuclease site, does not bind to DNA. This has prevented the molecular characterization of its endonuclease activity. In this thesis, we first show that MutL in B. subtilis exhibits asymmetric conformations similar to yeast and human MutL homologs. We also devise a novel approach to bypass the binding defect of the C-terminal domain by using fusion proteins. We find that these fusions bind to DNA specifically and, in the presence of the processivity clamp, can nick DNA. One of these fusion proteins in particular stimulates the nicking activity much more efficiently than the C-terminal domain alone. This work lays the foundation for the mechanistic characterization of the MutL endonuclease and provides a method to stabilize transient protein-DNA interactions. / Thesis / Master of Science (MSc)

No description available.

DNA mismatch repair corrects base-base mismatches and small insertion/deletion loops generated during normal DNA replication. If left unrepaired, these errors become permanent mutations and can lead to increased susceptibility to cancer. In most prokaryotes and all eukaryotes, the mismatch repair protein MutL is a sequence-unspecific endonuclease that plays an essential role in the strand discrimination step of this pathway. Prokaryotic MutL forms homodimers with two endonuclease sites, whereas eukaryotic MutL homologs form heterodimers with a single active site. To elucidate the mechanistic differences between prokaryotic and eukaryotic MutL, we tested whether both endonuclease sites are necessary for prokaryotic MutL nicking activity. MutL interaction with the processivity clamp is required to stimulate endonuclease activity. Therefore, we also tested whether both subunits of the MutL dimer needed to interact with the processivity clamp. To this end, we engineered a system to independently manipulate each protomer of the homodimer. We demonstrated that prokaryotic MutL is regulated by the processivity clamp to act in a similar manner to eukaryotic MutL with only one functional site contributing to the endonuclease activity. We also devised a strategy to stabilize the transient interactions between MutL, the β-clamp, and DNA through disulfide bridge crosslinking and heterobifunctional crosslinking. Stabilizing transient protein-protein and protein-DNA interactions will help optimize future structural studies in obtaining the ternary complex for mechanistic insights to the MutL endonuclease activity and regulation imposed by the β-clamp. / Thesis / Master of Science (MSc)

The von Hippel-Lindau (VHL) tumor suppressor pVHL is lost in 90% of clear-cell renal-cell carcinomas (ccRCCs). Jade-1 is a renal tumor suppressor that is normally stabilized by pVHL. MutS Homolog2 (MSH2) is a key initiator in DNA mismatch repair (MMR). Defects in MMR are associated with genome-wide instability and predisposition to certain types of cancer. Mass spectrometry data of immunoprecipitated Flag-tagged Jade-1 lysates showed signal for MSH2, suggesting Jade-1 may participate in MMR. Here, we confirmed an interaction between endogenous MSH2 and endogenous Jade-1 by coimmunoprecipitation. Using cell fractionation, we found that MSH2 and Jade-1 translocated to the nucleus in response to alkylating agent MNNG in kidney proximal tubule cells. We also visualized the translocation of Jade-1 by immunofluorescence. Silencing JADE1 also influenced the kinetics of MSH2 translocation. In addition, by colony forming assay, JADE1-silenced cells were resistant to mismatch damage induced by MNNG, which is a feature of cells with an MMR defect. Furthermore, reintroducing pVHL into renal cancer cells also changed the amount of translocated MSH2 and Jade-1. In contrast to wild-type mice, Jade1 heterozygous mice got spontaneous tumors, and those tumors continued to show heterozygosity for Jade1. Taken together, our results identify a mechanism for Jade-1 regulation of MMR through its nuclear translocation. pVHL may also contribute to MSH2 and Jade-1 translocation by increasing Jade-1 abundance. These findings establish an early role for Jade-1 in MMR, provide further indication that Jade-1 helps maintain genomic stability in the kidney and support that Jade-1 is a haploinsufficient renal tumor suppressor.