Recently, hydrogen peroxide (H₂O₂), and its free-radical product the hydroxyl radical (OH·), have been identified as major sources of DNA damage in living organisms. We examined DNA repair of hydrogen peroxide damage, using a standard bacteriophage T4 test system in which several different types of repair could be determined. Post-replication recombinational repair and denV-dependent excision repair had little or no effect on H₂O₂ damage. Also, an enzyme important in repair of H₂O₂-induced DNA damage in the E. coli host cells, exonuclease III, was not utilized in repair of lethal H₂O₂ damage to the phage. However, multiplicity reactivation, a form of recombinational repair between multiply infecting phage genomes, was found to repair H₂O₂ damages efficiently. The RAD52 gene of Saccharomyces cerevisiae and genes 46 and 47 of bacteriophage T4 are essential for most recombination and recombinational repair in their respective organisms. The RAD52 gene was introduced into expression vectors which were used to transform E. coli. RAD52 expression was induced, and its ability to complement either gene 46 or gene 47 phage mutants was determined with respect to phage growth, recombination, and recombinational repair. RAD52 gene expression allowed growth of gene 46 and gene 47 mutants under otherwise restrictive conditions, as measured by plaque formation and burst size. The RAD52 gene also restored the ability of gene 46 and gene 47 mutants to undergo recombination of rII markers. Furthermore, the RAD52 gene restored recombinational repair after UV irradiation of gene 46 and gene 47 mutants. The published DNA sequence of RAD52 was compared with the published sequences of genes 46 and 47. Although overall homologies were only marginally significant, RAD52 and gene 46 had substantial sequence similarity over a limited region. These results indicate that the recombinational repair pathway found in phage T4 may be ubiquitous for DNA damage caused by endogenous exidative reactions. Furthermore, they indicated that an essential element of the recombination mechanism in both procaryotic viruses and eucaryotes arose from a common ancestor. Procaryotes and eucaryotes are thought to have diverged at least one billion years ago. Thus, recombination apparently arose early in evolution.

No description available.

No description available.

No description available.

No description available.

No description available.

Human rhinoviruses (HRV) are extremely common human respiratory pathogens, most commonly associated with mild upper respiratory tract infections. The three known species of HRV (HRV-A, -B and –C) are members of the family Picornaviridae and genus Enterovirus. In contrast to the enterovirus (EV-A-D) species that commonly infect the gut, HRV are generally thought to be acid labile with replication restricted to the respiratory tract. Investigations of the clinical correlations of HRV infections detected on diagnostic screening of respiratory specimens demonstrated no specific association between HRV variant and clinical presentation. For example, similar species distributions were observed in patients admitted to the ITU and those discharged with minor illness. Unexpectedly, screening of stool specimens for HRV showed a prevalence of 10% with viral loads similar to EV infections. These findings suggested that a reappraisal of HRV tropism and disease associations may be warranted. HRV-A and -B isolates were originally classified into 100 serotypes by serological neutralisation properties. As HRV-C is difficult to isolate, no attempt had been previously made to classify the wealth of available HRV-C sequences. To facilitate definition of novel HRV types and classification of HRV-C, a system was devised to divide HRV sequences into genotypically defined types. Pairwise VP1 nucleotide p-distance analysis revealed distinct thresholds between inter- and intra- type divergence and available sequences were classified into 77 HRV-A, 29 -B and 51 -C types. This provides a standardised basis for type definition and identification, allowing consistency in studies of genetic diversity, epidemiology and evolution. It has been adopted by the ICTV Picornavirus Study Group for classification of HRV. Although the occurrence of recombination has been documented within the coding region of EV, analysis of dated HRV sequences revealed an overall lack of intra-species recombination between three coding regions of HRV-B and -C. In contrast, full HRV-A type groups appeared to have been subject to a large number of recombination events, suggesting extensive recombination during the period of its diversification into types. Putative recombination breakpoints localised to the non-structural region. Within HRV-A and HRV-B, recombination within the 5ˈUTR was infrequent. However, over 60% of analysed HRV-C strains grouped within the HRV-A clade and two recombination hotspots were identified. An additional interspecies recombination event was detected between HRV-A/C in the 2A coding region, with putative breakpoints mapping to the boundaries of the C-terminal domain of the proteinase. The studies within this thesis provide evidence for a broadened understanding of the clinical significance of HRV. In addition, the assignment of HRV sequences into genotypically defined types allowed description of the observed genetic diversity and completion of analysis which reaffirmed the sporadic nature of recombination within the coding region of HRV.

φC31 integrase (Int) and other site-specific recombinases enable controlled and precise genetic manipulations of complex genomes. Int mediates integration of the φC31 genome into the genome of its Streptomyces host. Recombination occurs between specific attachment sites; attB and attP. Int binds attP and attB with similar affinities, despite significant sequence differences. The mechanism through which Int recognises its substrates is not fully understood. To study DNA binding in vivo in the absence of recombination, we employed the challenge phage assay. In this assay, binding by Int to attP or attB results in a high frequency of P22-1000 lysogen formation in Salmonella. When Int has lost binding activity, fewer lysogens are generated. A randomly mutated integrase library has been screened using this assay. A number of the mutants showed a reduction in binding to both attB and attP or just to attB. Point mutations in these integrases largely clustered either a putative zinc finger or to the pfam07508 ‘recombinase' domain. To validate the phage challenge assay data, the binding defective Int mutants were purified and tested in in vitro DNA binding experiments. Int mutants displayed reduced binding to attB and/or attP compared to attL or attR. The purified proteins were used in in vitro recombination assays. Mutants in the recombinase domain generally showed reduced integration whilst demonstrating almost wild type gp3 dependant excision. These data combined with data from others suggested two DNA binding domains in Int; the recombinases domain and the zinc finger. A truncated mutant Int, IntV371SUGA had previously been shown to bind DNA with low affinity. The mutations in the recombinase domain were transferred to IntV371SUGA to test their effect on DNA binding. I suggest that the recombinase motif is intimately involved in DNA recognition and discrimination between the att sites required for phage integratation and excision.

<p>The genomes of many strains of baker’s yeast, Saccharomyces cerevisiae, contain multiple repeats of the copper-binding protein Cup1. Cup1 is a member of the metallothionein family, and is found in a tandem array on chromosome VIII. In this thesis, I describe studies that characterized these tandem arrays and their mechanism of formation across diverse strains of yeast. I show that CUP1 arrays are an illuminating model system for observing recombination in eukaryotes, and describe insights derived from these observations. </p><p>In our first study, we analyzed 101 natural isolates of S. cerevisiae in order to examine the diversity of CUP1-containing repeats across different strains. We identified five distinct classes of repeats that contain CUP1. We also showed that some strains have only a single copy of CUP1. By comparing the sequences of all the strains, we were able to elucidate the mechanism of formation of the CUP1 tandem arrays, which involved unequal non-homologous recombination events starting from a strain that had only a single CUP1 gene. Our observation of CUP1 repeat formation allows more general insights about the formation of tandem repeats from single-copy genes in eukaryotes, which is one of the most important mechanisms by which organisms evolve.</p><p>In our second study, we delved deeper into our mechanistic investigations by measuring the relative rates of inter-homolog and intra-/inter-sister chromatid recombination in CUP1 tandem arrays. We used a diploid strain that is heterozygous both for insertion of a selectable marker (URA3) inside the tandem array, and also for markers at either end of the array. The intra-/inter-sister chromatid recombination rate turned out to be more than ten-fold greater than the inter-homolog rate. Moreover, we found that loss of the proteins Rad51 and Rad52, which are required for most inter-homolog recombination, did not greatly reduce recombination in the CUP1 tandem repeats. Additionally, we investigated the effects of elevated copper levels on the rate of each type of recombination at the CUP1 locus. Both types of recombination are increased at high concentrations of copper (as is known to be the case for CUP1 transcription). Furthermore, the inter-homolog recombination rate at the CUP1 locus is higher than the average over the genome during mitosis, but is lower than the average during meiosis. </p><p>The research described in Chapter 2 is published in 2014.</p> / Dissertation

This thesis describes a method of determining the recombination rate coefficient experimentally, which does not depend on a specific model of the recombination process. With this method established, results are presented for the recombination rate coefficient measurements at 44.6 Torr.