Faculty of Science School of Pathology 9903547r robyn.brakin@gmail.com / Mycobacterium tuberculosis is an important human pathogen, claiming more lives per annum than any other single infectious organism. The host environment of M. tuberculosis contains DNA-damaging agents that pose a constant threat to the M. tuberculosis genome, and as a result, the ability to repair damaged DNA is likely to play an important role in bacterial survival. Y-family polymerases perform translesional synthesis and replicate DNA in an error-prone manner. By characterising the Y-family polymerases in mycobacteria, a better understanding the organism’s adaptive mutagenesis may be established. Through gene expression studies, it was found that UV irradiation of Mycobacterium smegmatis resulted in the up-regulation of dinP3, which was determined to be a Y-family polymerase by sequence analysis. DinP3 expression was found to be under control of the SOS response and is the first example of a Y-family polymerase in mycobacteria forming part of the SOS regulon. However, loss of DinP3 did not change the ability of M. smegmatis to tolerate UV irradiation. Mutagenesis studies revealed a complex interaction between the different Y-family polymerases in M. smegmatis. It was shown that spontaneous mutagenesis was increased in the absence of DinP3, whereas UV-targeted mutagenesis was increased in the absence of DinP, another Y-family polymerase. In conclusion, these results reflect the differences in control and in the mutational profiles of the Y-family polymerases in M. smegmatis. Moreover, these polymerases exhibit distinctive features from other bacterial Y-family polymerases, highlighting the different way in which bacteria have adapted to deal with lesions in their genetic material.

Cells have lesion bypass DNA polymerases (DNAPs), often in the Y-Family, which synthesize passed DNA damage. One class of Y-Family DNAPs includes hDNAP k, EcDNAP IV and SsDbh, which insert accurately opposite N2-dG adducts, including BP-N2-dG formed from benzo[a]pyrene (BP). Another class includes hDNAP h, EcDNAP V and SsDpo4, which insert accurately opposite UV-damage. For correct Watson-Crick pairing between BP-N2-dG and dCTP, the BP moiety must be in the minor groove. On the minor groove side of the active site, k/IV/Dbh-class DNAPs have large openings that accommodate the BP moiety. Primer extension assays with purified proteins show that DNAP IV correctly inserts dCTP opposite BP more than 10-fold faster than it mis-inserts dATP, dGTP, or dTTP. In contrast, h/V/Dpo4-class DNAPs have small active site openings, which cannot accommodate BP and lead to a distorted structure and increased mutagenesis; e.g., Dpo4 has dGTP and dATP insertion rates that are 10-fold greater than those of dCTP. The opening in Dpo4 is plugged and bulky, whereas DNAP IV has a relatively spacious cavity. Consistent with this model, mutants of Dpo4 with a larger opening insert up to 10-fold more accurately opposite BP-N2-dG. Near the active site, Dpo4 has a single non-covalent bridge (NCB) between the little finger domain and the thumb-palm-fingers domain. DNAP IV and Dbh have a second, distal NCB that is 8 angstroms away from the active site towards the 3' end of the template DNA. Dpo4 becomes nearly 5-fold more accurate when mutated to carry a distal NCB, suggesting that NCB's also help control mutagenesis. Lastly, the active site of Dpo4 has a cavity in the major groove side, which may allow base flipping and dGTP insertion opposite -BP, while k/IV/Dbh-type polymerases do not. When this cavity is plugged in Dpo4 by mutagenesis or the introduction of an N-clasp motif, dGTP rates increase by nearly 20-fold. In conclusion, this data suggests that three structural regions contribute to accurate dCTP insertion opposite BP-N2-dG by k/IV/Dbh-class DNAPs: a large opening on the minor groove side near the active site, a cavity on the major groove side, and the number of non-covalent bridges between the little finger domain and the thumb-palm-fingers domain.

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Young adults of the twenty-first century face a long path to adulthood marked by uncertainty and lack of stability. In response, young adults are heading back to or failing to leave their family homes in higher numbers than generations before (Jacobsen and Mather 2011; Qian 2012). These macro-level trends bring about questions about their impact on family relationships as well as how these relationships have evolved over time. My thesis investigates parent-child relationships during co-residence with a specific focus on generation and gender differences. Through secondary data analysis of the National Survey of Families and Households, I explore how parent-child relationships during co-residence differ between parents of Generation Xer young adults (born between 1965-1980) and Millennial young adults (born between 1981-1996). Additionally, I examine gender differences between these two generational cohorts. My findings offer support that intergenerational relationships are not necessary closer, but look different for parents of Millennials as compared to Generation Xers. I also find that there are significant gender differences between mothers and fathers of Generation Xers versus those of Millennials. I find that mothers of Generation Xers report more time shared with co-residing young adults and increased frequency of perceived emotional support from their child than fathers; yet, fathers of Millennials report more perceived support than mothers. I suggest these findings offer support for the notion that gendered roles play out into young adulthood and potentially have more flexibility for fathers across time. As the economic and social landscape continues to change and present more uncertainty, family relationships become a form of social security; thus it becomes increasingly important to understand these dynamics. My findings are significant as they contribute to a better understanding of parent-child relationships over time and offer discussion on the potential implications.

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