Efficient and accurate repair of DNA double strand breaks (DSBs) is required to maintain genomic stability in both eukaryotes and prokaryotes. In Escherichia coli, DSBs are repaired by homologous recombination (HR). During this process, DNA synthesis needs to be primed and templated from an intact homologous sequence to restore any information that may have been lost on the broken DNA molecule. Two critical late stages of the pathway are repair DNA synthesis and the processing of Holliday junctions (HJs). However, our knowledge of the detailed mechanisms of these steps is still limited. Our laboratory has developed a system that permits the induction of a site-specific DSB in the bacterial chromosome. This break forms in a replication dependent manner on one of the sister chromosomes, leaving the second sister chromosome intact for repair by HR. Unlike previously available systems, the repairable nature of these breaks has made it possible to physically investigate the different stages of DNA double-strand break repair (DSBR) in a chromosomal context. In this thesis, I have addressed some fundamental questions relating to repair DNA synthesis and processing of HJs by using a combination of mutants defective in specific biochemical reactions and an assay that I have developed to detect repair DNA synthesis, using a polar termination sequence (terB). First, by using terB sites located at different locations around the break point, it was shown that the DnaB-dependent repair forks are established in a coordinated manner, meaning that the collision of the repair forks occurs between two repair DNA synthesis initiation sites. Second, DSBR was shown to require the PriB protein known to transduce the DNA synthesis initiation signal from PriA protein to DnaT. Conversely, the PriC protein (known as an alternative to PriB in some reactions) was not required in this process. PriB was also shown to be required to establish DnaB-dependent repair synthesis using the terB assay. Third, the establishment and termination of repair DNA synthesis by collision of converging repair forks were shown to occur independently of HJ resolution. This conclusion results from the comparison of the viability of single and double mutants, deficient in either the establishment of DNA synthesis, HJ resolution or in both reactions, subjected to DSBs and from the study of the DNA intermediates that accumulated in these mutants as detected by two-dimensional gel electrophoresis. Fourth, the role of RecG protein during DSB repair was investigated. Solexa sequencing analyses showed that recG null mutant cells undergoing DSBs accumulate more DNA around the break point (Mawer and Leach, unpublished data). This phenomenon was further investigated by two different approaches. Using terB sites in different locations around the break point and ChIP-Seq analyses to investigate the distribution of RecA in a recG null mutant demonstrating that the establishment of repair forks depends on the presence of RecG. Further studies using PriA helicase-dead mutant showed that the interplay between RecG and PriA proteins is essential for the establishment of correctly oriented repair forks during DSBR. As a whole, this work provides evidence on the coordinated nature of the establishment and termination of DNA synthesis during DSBR and how this requires a correct interplay between PriA-PriB and RecG. A new adapted model of homologous recombination is presented.

Como é de suma importância a integridade da informação contida no DNA, este recebe proteção contra agentes danosos que podem prejudicar sua estrutura. Mesmo em caso de dano, a célula possui um grupo de proteínas que estão envolvidas na correção e mitigação destes danos. O primeiro grupo é um conjunto de proteínas envolvidas no reparo de DNA livre de erro. Caso estas proteínas não consigam minimizar os danos, outro conjunto de proteínas é expresso como uma alternativa ao reparo. Dentre estas, estão as DNA polimerases especializadas em usar uma fita de DNA danificada como molde para replicação. Este mecanismo possibilita à célula sobreviver aos danos potencialmente citotóxicos, às custas de mutagênese. Em bactérias, a reposta ao dano de DNA envolve um conjunto de proteínas que são expressas como parte da resposta SOS. Dentre elas estão enzimas envolvidas na síntese translesão (TLS). Diferentemente de Escherichia coli que possui três polimerases propensas a erro especializadas em TLS, Caulobacter crescentus possui um cassete mutagênico imuABC que está implicado na síntese de DNA usando como molde uma fita danificada. Neste trabalho, estudamos o mecanismo de TLS mediado por ImuABC nesta bactéria, e encontramos uma série de diferenças com o mecanismo de bypass realizado pela principal polimerase implicada em TLS em E. coli (Pol V). As proteínas ImuABC quando expressas em níveis máximos da resposta SOS não são capazes de aumentar as taxas de mutagênese espontânea. O produto do operon imuABC, diferentemente da Pol V, não necessita de RecA para realizar TLS. Apenas a expressão destas proteínas em um background sem o gene recA já é suficiente para que ocorra a mutagênese induzida por UVC. Ao estudar a mutagênese como resposta ao dano de DNA induzido por radiação UVC em níveis genômicos em C. crescentus, notamos que a maioria das mutações encontradas está presente em regiões que possuem pirimidinas adjacentes que sabidamente são extremamente reativas à radiação UVC, levando à formação de fotoprodutos. Nossos dados sugerem que existe uma região no cromossomo circular de C. crescentus que é preferencialmente mutada, e este acúmulo de mutações pode ser consequência do reparo que acontece próximo à origem replicativa, deixando as mutações acumuladas próximas à região de término da replicação. / As the integrity of information contained in DNA is of utmost importance, it receives protection against harmful agents that may harm its structure. Even in case of damage, the cell has a group of proteins that are involved in the correction and mitigation of these damages. The first group is a set of proteins involved in error-free DNA repair. If these proteins fail to minimize damage, another set of proteins is expressed as an alternative to repair. Among these are DNA polymerases that specialize in using a damaged DNA strand as a template for replication. This mechanism enables the cell to survive potentially cytotoxic damage at the expense of mutagenesis. In bacteria, the DNA damage response involves a set of proteins that are expressed as part of the SOS response. Among them are enzymes involved in translesion synthesis (TLS). Unlike Escherichia coli that has three TLS error-prone polymerases, Caulobacter crescentus bears the imuABC mutagenic cassette that is involved in DNA synthesis using a damaged template. In this work, we studied the mechanism of TLS mediated by ImuABC in this bacterium, and we found a number of differences relative to the characteristics of the principal polymerase involved in TLS in E. coli (Pol V). ImuABC proteins when expressed at maximum levels of the SOS response are not able to increase the rates of spontaneous mutagenesis. ImuABC, unlike Pol V, does not require RecA to perform TLS. The presence of these proteins in a background without the recA gene is sufficient for UVC-induced mutagenesis to occur. In studying mutagenesis as a response to DNA damage induced by UVC radiation at genomic levels in C. crescentus, we noted that most of the mutations found are present in regions that have adjacent pyrimidines, which are known to be extremely reactive to UVC radiation, leading to the formation of photoproducts. Our data suggest that there is a region on the circular chromosome of C. crescentus that is preferably mutated, and this accumulation of mutations may be a consequence of the repair occurring near the replicative origin, leaving the accumulated mutations close to the replication termination region.

The purpose of this study was to identify the effects of the neurotransmitter, serotonin (SE), on the immune function of peripheral blood mononuclear cells (PBMC) of normal, healthy subjects. This was done as a preliminary investigation to studies on the association of SE with immune changes in autistic subjects. The PBMC isolated from normal male subjects were treated with various concentrations of SE for 48 hrs. Their incubation in SE at a concentration of 10-3 M induced about a 35% decrease in DNA synthesis. However, incubation of the cells in lower concentrations (10-4 to 10-10) of SE produced no significant effect. The ability of natural killer (NK) cells to lyse K562 target cells was also examined after incubation with SE for 48 hrs. The NK activity was almost completely eliminated following incubation in 10-3M of SE, but the activity was not significantly decreased by exposure to lower concentrations of SE. The viability of PBMC was not altered following incubation with SE under identical conditions as those utilized in the NK assay. Preliminary analysis using a fluorescence-activated cell sorter (FACS) of monoclonal antibodies directed against Tll (total T cell), T4 (helper T cell), T8 (suppressor and cytotoxic T cells), B-cell and NK cell markers indicated that the suppressive effect exerted by SE could be attributed to a decrease in the density of these markers or receptors on the cell surface. These findings provide additional evidence for a possible link between neurotransmitters, specifically SE, and immune function.

Bibliography: leaves 267-287.

Graduation date: 1993

Structural analyses of DNA oligonucleotides indicate the presence of bound water molecules in the major and minor grooves of DNA. These water molecules participate in DNA charge transfer by their reaction with guanosine radical cation to form 7,8-dihydro-8-oxo-guanine (8-oxoG), which when treated with a base leads to DNA strand cleavage. We probed the reaction of guanosine radical cation with water with series of alkyl substituted cytidines and thymidines by incorporating the modified nucleosides into anthraquinone linked DNA duplexes and irradiating them with UV light at 350 nm. The incorporation of these hydrophobic substituents disrupt the DNA spine of hydration, and we have observed that these modifications in the major and minor groove do not effect the trapping or long distance hopping of radical cations in DNA. The second part of the work reported herein examines the role of charged nucleosides in long range charge transfer in duplex DNA. DNA methylation is a naturally occurring process mediated by enzymes responsible for such functions in biological systems. Hypermethylation of DNA can also occur as a result of environmental alkylating agents leading to mutation of the affected cells. Methylation of the ring nitrogen of a purine base can introduce a positive charge in the ring resulting in the cleavage of the glycosidic bond of the nucleoside. To understand the role of a charged nucleoside on charge transfer in DNA, we designed and synthesized cationic nucleoside mimics, which were incorporated into anthraquinone-linked DNA strands and irradiated at 350 nm. The presence of the cationic bases on the duplexes inhibits the migrating hole from hopping along the DNA strand, and induces a prominent local structural distortion of the DNA as a result of the charged nucleobase.

DNA condensation is the process in which an anionic polymer in combination with condensing agents undergoes a drastic reduction in volume and collapses into ordered structures. Double-stranded DNA has a uniform helical secondary structure, whereas single-stranded DNA is complex and adopts numerous different conformations. Novel mixed-stranded DNA molecules, with defined regions of both single-stranded and double-stranded secondary structures attached to one another in the same molecule, were created in this body of work. Mixed-stranded DNA was designed to be intermediate between its parent secondary structures in order to discover if mixed-stranded DNA will find a balance in terms of condensation properties as well. Mixed-stranded DNA was found to condense into minimally aggregated, globular particles in the presence of low mM concentrations of divalent transition metals in aqueous solvent at room temperature, a property not observed for either pure dsDNA or ssDNA. A model is presented to describe how mixed-stranded DNA -Mn2+, -Ni2+, and -Cd2+ condensates with the observed properties are produced. Multivalent-induced condensation of mixed-stranded DNA is also characterized and found to involve an unusual rod-like morphology in order to accommodate the secondary structures condensing independent of one another at different concentrations of multivalent cations. The attachment of a ss region to an otherwise ds molecule was found to greatly influence condensation properties of the entire molecule.

R1162 is a broad-host range, mobilizable plasmid conferring resistance to streptomycin and sulfonamides. Efficient conjugative mobilization of R1162 requires three plasmid-encoded proteins: MobA, MobB and MobC. MobA binds plasmid DNA at the origin of transfer (oriT), nicks the subsequently transferred strand and ligates the ends of the strand after transfer into the recipient. The N-terminal region of this protein carries out this DNA processing. The C-terminal half is a primase required to initiate DNA synthesis at two single-stranded priming sites sites, oriL and oriR, during vegetative plasmid replication. The primase region of MobA is not necessary for DNA processing by the N-terminal part of the protein, however its role in strand replacement during conjugation is not clearly defined. This study demonstrates that R1162 can undergo multiple rounds of transfer from a single plasmid molecule. The presence of oriL increases the frequency of second-round transfer, presumably due to initiation of replacement strand synthesis at this site by R1162 primase in the donor. Priming at oriR by the primase region of MobA is required for efficient replacement strand synthesis in the recipient when the plasmid is transferred to Salmonella. When the plasmid is transferred into E. coli, the plasmid-encoded priming system is not required for strand replacement in the recipient, presumably due to a host-encoded mechanism capable of priming the transferred strand. Transport of MobA through the R751 conjugative pore was also investigated. The two domains of MobA can be transported to recipient cells independently of each other. However, MobB is required for the transport of either fragment. Two sites, named the R-site and the P-site, are located in the relaxase and primase domains of MobA, respectively, and make up part of the signals required for MobA transport. Unlike previously described type IV transport signals, domain structure is required for the MobA transport signals to be active. / text

Access to abstract restricted until 12/14/2014. / Access to thesis restricted until 12/14/2014. / Department of Biology

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