The budding yeast, Saccharomyces cerevisiae, serves as an excellent model for identifying fundamental mechanisms of DNA repair. A Local Coherence Detection (LCD) algorithm that uses biclustering to assign genes to multiple functional sub-groups was applied on the chromosome E-MAP containing genetic interactions among genes involved in nuclear processes. Using this method, we found that Asf1 and Rtt109, genes that are together required for histone H3K56 acetylation, cluster together with Ctf4, Ctf18, Ctf8 and Dcc1, genes important for efficient sister chromatid cohesion. It is known that H3K56 acetylation is required for post-repair chromatin reassembly at sites of DNA double-strand breaks (DSBs). The cohesion genes were previously implicated in the repair of some DNA DSBs, but the nature of their involvement has not been reported. The experimental data in my thesis work suggest that Ctf4, Ctf8, Ctf18 and Dcc1 function in the post-repair chromatin reassembly pathway.

The budding yeast, Saccharomyces cerevisiae, serves as an excellent model for identifying fundamental mechanisms of DNA repair. A Local Coherence Detection (LCD) algorithm that uses biclustering to assign genes to multiple functional sub-groups was applied on the chromosome E-MAP containing genetic interactions among genes involved in nuclear processes. Using this method, we found that Asf1 and Rtt109, genes that are together required for histone H3K56 acetylation, cluster together with Ctf4, Ctf18, Ctf8 and Dcc1, genes important for efficient sister chromatid cohesion. It is known that H3K56 acetylation is required for post-repair chromatin reassembly at sites of DNA double-strand breaks (DSBs). The cohesion genes were previously implicated in the repair of some DNA DSBs, but the nature of their involvement has not been reported. The experimental data in my thesis work suggest that Ctf4, Ctf8, Ctf18 and Dcc1 function in the post-repair chromatin reassembly pathway.

Indiana University-Purdue University Indianapolis (IUPUI) / DNA double strand breaks (DSB), particularly those induced by ionizing radiation (IR) are complex lesions and if not repaired, these breaks can lead to genomic instability, chromosomal abnormalities and cell death. IR-induced DSB often have DNA termini modifications including thymine glycols, ring fragmentation, 3' phosphoglycolates, 5' hydroxyl groups and abasic sites. Non-homologous end joining (NHEJ) is a major pathway responsible for the repair of these complex breaks. Proteins involved in NHEJ include the Ku 70/80 heterodimer, DNA-PKcs, processing proteins including Artemis and DNA polymerases µ and λ, XRCC4, DNA ligase IV and XLF. The precise molecular mechanism of DNA-PK activation and Artemis processing at the site of a DNA DSB has yet to be elucidated. We have investigated the effect of DNA sequence and structure on DNA-PK activation and results suggest a model where the 3' strand of a DNA terminus is responsible for annealing and the 5' strand is involved in activation of DNA-PK. These results demonstrate the influence of DNA structure and orientation on DNA-PK activation and provide a molecular mechanism of activation resulting from compatible termini, an essential step in microhomology-mediated NHEJ. Artemis, a nuclease implicated in processing of DNA termini at a DSB during NHEJ, has been demonstrated to have both DNA-PK independent 5'-3' exonuclease activities and DNA-PK dependent endonuclease activity. Evidence suggests that either the enzyme contains two different active sites for each of these distinct processing activities, or the exonuclease activity is not intrinsic to the Artemis polypeptide. To distinguish between these possibilities, we sought to determine if it was possible to biochemically separate Artemis endonuclease activity from exonuclease activity. An exonuclease-free fraction of Artemis was obtained that retained DNA-PK dependent endonuclease activity, was phosphorylated by DNA-PK and reacted with an Artemis specific antibody. These data demonstrate that the exonuclease activity thought to be intrinsic to Artemis can be biochemically separated from the Artemis endonuclease. These results reveal novel mechanisms of two critical NHEJ proteins, and further enhance our understanding of DNA-PK and Artemis activity and their role in NHEJ.

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The lexA protein in E. coli is a specific repressor of the recA gene. The lexA protein is cleaved by the recA protein in response to DNA damage. Cleavage derepresses the recA gene resulting in high level synthesis of recA protein and the expression of other DNA damage inducible functions (SOS functions). The lexA3 mutation makes the lexA protein resistant to cleavage and thus inhibits expression of DNA damage inducible functions. A mutant of E. coli has been isolated which exhibits many of the properties expected of a strain carrying an operator-constitutive mutation in the recA gene. The mutation partially suppresses the UV sensitivity of lexA3 strains, maps near the recA structural gene, allows constitutive synthesis of the recA protein and the recA message, and is cis-acting. Strains carrying the recAo('c) mutation were used to study the role of amplified levels of recA protein in the expression of certain SOS functions. The recAo('c) mutation did not suppress the UV inhibitory effect of the lexA3 mutation on the expression of UV induced cellular mutagenesis, and the reactivation and mutagenesis of UV irradiated phage (lamda). The expression of these functions in lexA('+) strains was not enhanced by the recAo('c) mutation. Constitutive recA synthesis did not result in lethal filamentous growth. These results are consistent with those reported elsewhere that the expression of SOS function is not dependent on high levels of recA protein and that the various "SOS genes" are repressed by the lexA protein as is the recA gene. Thus, recA protein is required in SOS expression for the inactivation of lexA protein and recA amplification is a consequence, not a cause of SOS expression. The DNA sequence of the recA operator region from a (lamda)precA transducing phage thought to carry the recAo('c) mutation isolated here, was determined. No difference was detected between the supposed mutant DNA and wild type controls. The significance of these results and the possibility that the recAo('c) mutation was not transferred to the phage are discussed.

The product of the Escherichia coli lexA gene has been identified, and the regulation of lexA gene expression in vivo has been examined. A series of specialized transducing phages carring lexA⁺ and 3 different amber lexA alleles was constructed by in vivo recombination between λlexA3 and host lexA alleles. These phages were characterized extensively to confirm that they carried the appropriate lexA allele. The lexA gene product was identified by comparison of the polypeptides encoded by λlexA3 and the amber lexA phages. A 24,000 dalton polypeptide, synthesized after infection of both amber-suppressor and non-suppressor hosts by λlexA3 was not synthesized following amber lexA phage infection of non-suppressor hosts. Synthesis of this polypeptide following amber lexA phage infection was restored by the presence of an amber suppressor mutation in the host. On the basis of these data, the 24,000 dalton polypeptide was identified as the lexA gene product. Regulation of lexA gene expression in vivo was examined by hybridization experiments to measure lexA mRNA levels. The basla level of lexA mRNA in wild type E. coli was found to be .006% of total mRNA. Treatment of the bacteria with 100 erglmm² ultraviolet irradiation (UV) led to an eight-fold increase in lexA mRNA levels within 10 minutes, the lexA mRNA remained elevated until 70 minutes after irradiation, then slowly declined. By comparison, the level of recA mRNA increased from .05% to .51% of total mRNA within 10 minutes following UV irradiation, then declined. Both lexA and recA genes were induced by nalidixic acid treatment; the induction was not as rapid as UV induction and different relative induction kinetics of the two genes were seen. The levels of lexA and recA mRNAS were measured in several mutant strains following UV-irradiation.

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