Les trois complexes SMC Cohésine, Condensine et SMC5/6 sont principalement étudiés pour leurs rôles mitotiques, cependant tous trois sont localisés à proximité des fourches de réplication en condition de stress réplicatif. Au cours de cette thèse, nous nous sommes particulièrement intéressés aux complexes Cohésine et Condensine. Dans une première partie, nous décrivons un nouveau rôle des condensines dans la progression des fourches de réplication en condition de stress réplicatif à l’hydroxyurée (HU) et au Méthyl-Méthane-Sulfonate (MMS). Nos données montrent que dans ces conditions, les condensines limitent l’accumulation de la protéine de liaison à l’ADN simple-brin RPA (Replication Protein A) à proximité des fourches de réplication. Ces résultats révèlent que les condensines limitent l’exposition d’ADN simple brin et pourraient ainsi protéger l’intégrité des fourches de réplication et la stabilité du génome. Dans une seconde partie nous décrivons le mécanisme de recrutement du complexe Cohésine aux fourches de réplication en condition de stress réplicatif. Dans ces conditions, les cohésines renforcent la cohésion des chromatides sœurs afin de faciliter le redémarrage des fourches de réplication par recombinaison homologue. Nous montrons que le complexe SMC-like MRX (Mre11-Rad50-Xrs2), l’histone méthyle-transférase Set1 et l’histone acétyle-transférase Gcn5 sont requis pour le recrutement des cohésines aux fourches de réplication. Nos données révèlent qu’en réponse au stress réplicatif, Gcn5, Set1 et MRX modifient la dynamique des histones. Gcn5 et MRX réduisent la densité d’histone sur l’ADN répliqué alors que Set1 maintient la mobilité des nucléosomes. La modification de la dynamique des histones semble importante pour une réponse cellulaire efficace au stress réplicatif et pour le chargement de complexes SMC aux fourches de réplication. / The three SMC complexes Cohesin, Condensin and SMC5/6 are mainly studied for their role in mitosis, nevertheless they all localize at replication forks in replicative stress conditions. During this thesis, we focused on Cohesin and Condensin. In the first part we describe a new role for the condensin complex in response to replicative stress. In the presence of Hydroxyurea (HU) and Methyl-Methan-Sulfonate (MMS), condensin is required for cell growth and replication fork progression. Moreover, our results show that condensin limits the accumulation of the specific single-strand DNA (ssDNA) binding protein RPA (Replication Protein A) in the vicinity of replication forks under HU treatment, revealing that condensin limits ssDNA accumulation during replicative stress. In this way, Condensin could protect replication fork integrity and genome stability in response to replicative stress. In the second part, we decipher the cohesin recruitment mechanisms at replication fork under replicative stress. In that context, cohesin reinforces sister chromatid cohesion and facilitates homologous recombination (HR) dependent replication fork restart pathways. We show here that the SMC-like MRX complex, the histone methyl transferase Set1 and the histone acetyl transferase Gcn5 are required for cohesin recruitment at stalled replication forks. Our results show that these three proteins affect histone H3 dynamics on replicated DNA in response to replicative stress. Gcn5 and MRX reduce H3 density whereas Set1 maintains nucleosome mobility. These two parameters seem to be important for efficient response to replicative stress and for SMC complexes loading close to stressed replication forks.

Meiotic recombination is a prerequisite for exchange of genetic information in all Sexually reproducing organisms. This process is initiated by the formation of double stranded breaks (DSBs) in DNA followed by homology directed repair. The process is subjected to surveillance mechanisms that control DSB formation and allow for repair of DSBs by halting cell cycle progression. Interestingly, though generation of DSBs is an Essential event in meiosis they are nevertheless regarded as the most lethal forms of DNA damage. If left unrepaired a single DSB can lead to gene deletion, duplication, translocations and missegregation of large chromosome fragments leading to cell death. In Saccharomyces cerevisiae, genetic screens for mutants defective in meiotic recombination led to the identification of a group of genes called the RAD52 epistasis group which includes RAD50, RAD51, RAD52, RAD54, RAD55, RAD57, RAD59, MRE11 and XRS2. A subset of these genes, namely MRE11, RAD50 and XRS2, have been shown by genetic studies to be essential for several nuclear events including sensing DSBs, double strand break repair (DSBR) by homologous recombination (HR) and non homologous end joining (NHEJ), telomere length maintenance, cell cycle activation in response to DSBs, mitotic and meiotic recombination. In vitro, Mre11 displays Mn2+-dependent endonuclease activity on ssDNA, 3'-5' Exonuclease on single- and double-stranded DNA, strand annealing and weak hairpin Opening activities. Mutational analyses have revealed two functional domains in Mre11- Then terminal nuclease domain involved in telomere length maintenance and DSB Processing and the C terminal DNA binding domain involved in DSB formation during Meiosis. Rad50, a 153 kDa protein shares homology with the SMC (Structural Maintenance of Chromosome) family of proteins which are involved in chromosome Condensation and cohesion. It consists of a bipartite N- and C terminal Walker A and Walker B motifs separated by a heptad repeat sequence which folds into an antiparallel Coiled-coil structure. The heptad repeats are separated by a metal binding globular region the Zn hook. Rad50 is an ATP-dependent DNA-binding protein. hRad50 regulates the exonuclease activity of hMre11. Unlike Mre11 and Rad50, which are evolutionarily conserved, Xrs2 is found only in S. cerevisiae and Nbs1 in mammals. Xrs2 appears to be sequence non-specific DNA- binding protein. Xrs2 in yeast or Nbs1 is its counterpart in mammals target Mre11 and Rad50 to the sites of DNA damage and mediate S-phase cell cycle checkpoint activation. Mutations in either one of the MRX subunits results in defects in repair of DSBs, activation of cell cycle checkpoint and shortened telomeres leading to genomic instability. Hypomorphic mutations in MRE11 and NBS1 lead to genetic disorders- A-TLD (ataxia-telangiectasia-like disorder) and NBS (Nijmegen breakage syndrome) respectively, that are phenotypic ally related to AT (ataxia-telangiectasia) caused by mutations in ATM. Patients with AT, A-TLD or NBS syndromes are hypersensitive to radiomimetic agents and are predisposed to cancer. Several lines of evidence suggest that S. cerevisiae strains bearing mre11Δ, rad50Δ or xrs2Δ display shortening of telomeres. Telomeres are the nucleoprotein ends of all linear eukaryotic chromosomes that are important in maintaining the integrity of the genome.Telomeres are comprised of repetitive G rich sequence most of which is double stranded but the extreme 3' end protrudes to form 3' single stranded overhang called the G tail. elopers are essential in preventing end-end fusion of chromosome, are important for chromosome replication, segregation and genome stability. Genetic studies have implicated the MRX complex in both telomerase-dependent and independent telomere length maintenance. Studies have indicated a direct role for S. cerevisiae MRE11 in the proper establishment of telomere end-structure. However, the molecular mechanism of MRX at telomeres is poorly understood. To understand the role(s) of MRX complex at telomeres, it is important to elucidate the biochemical activities of MRX complex as well as its individual subunits on the telomere DNA structures. Since, Mre11 complex is known to function in several processes related to DNA metabolism it becomes imperative to study the function of Mre11 complex on DNA substrates in the context of a given nuclear process. The 3' single trended telomeric sequence is capable of acquiring folded conformation(s) as a mechanism of end protection which is mediated by several telomere-specific and nonspecific ending proteins. In mammals, the 3' ssDNA has been demonstrated to fold into tloop configuration mediated by some of the components of sheltrin protein complex, wherein the ssDNA invades the duplex DNA resulting in the formation of a displacement loop (D loop). Evidence for the formation of t-loop has been shown in vitro with human telomeres. However, the formation of t-loops has not been demonstrated in S. cerevisiae. Nevertheless, there is growing body of evidence which suggests the formation of alternative DNA structures such as G4 DNA at the yeast telomeres. G quadruplexes (G quartets or G4 DNA) are thermodynamically stable structures formed by Hoogsteen base pairing between guanine residues. In a G quartet the four guanine residues are paired, where each guanine residue is an electron acceptor and a donor and stabilized by a metal cation. The presence of G rich motifs at the promoter regions, rDNA, telomeres and recombination hot spots indicate that G4 DNA has important functions in vivo. Although the existence of G4 DNA has been the subject of much debate, the identification of several proteins that promote (Rap1, Hop1, Topo I, TEBPβ), modify and resolve (POT1, TERT, KEM1, GQN1, BLM, WRN, Rte1) G4 DNA, together with the direct visualization of G4 DNA using G4 DNA specific antibodies and RNA interference have provided compelling for the existence of G4 DNA in vivo. To elucidate the function of MRX complex or its individual subunits at telomeres, the biochemical activities of purified MRX complex and its individual subunits on G4 DNA, D loop, duplex DNA and G rich ssDNA has been analyzed in this study. G4 DNA was assembled from S. cerevisiae telomeric sequence. G4 DNA was isolated and its identity was ascertained by chemical probing and circular dichroism. S. cerevisiae MRE11 and XRS2 was cloned and expressed in E. coli BL21 (DE3)plysS. S. cerevisiae RAD50 in pPM231 vector in S. cerevisiae BJ5464 strain was a gift from Dr. Patrick Sung (Yale University). Mre11, Rad50 and Xrs2 were overexpressed and purified to >98% homogeneity. The identity of the proteins was ascertained by Western bloting using polyclonal antibodies. Using purified proteins heterotrimeric MRX and heterodimeric MR and MX protein complexes were formed in the absence of ATP, DNA or Mn2+. The ability of M/R/X to bind to telomeric DNA substrates was studied by electrophoretic mobility shift assays. Mre11, Rad50, Xrs2 and MRX displayed higher binding affinity for G4 DNA over D loop, ss- or dsDNA. MRX bound G4 DNA more efficiently compared to its individual subunits as 10-fold lower concentration of MRX was able to shift the DNA into the protein-DNA complex. The protein-G4 DNA complexes were stable as >0.8 M NaCl as required to dissociate 50% of protein-G4 DNA complexes. Efficient competition by poly(dG), which is known to fold into G4 DNA, suggested that the protein-G4 DNA complex was specific. Competition experiments with tetra-[N-methyl- pyridyl]-porphyrin suggested that M/R/X recognizes distinct determinants and makes specific interactions with G4 DNA. G4 DNA is highly polymorphic and can exist as intramolecular or intermolecular (parallel and antiparallel) structures. High affinity binding of Mre11 to G4 DNA (parallel) over G2' DNA (antiparallel), ss- and dsDNA suggests the existence of parallel G4 DNA structures at the telomeres and that G4 DNA may be the natural substrate for MRX complex in vivo. Telomeres are elongated by telomerase that requires access to the 3' G-tail for its activity. Formation of G4 DNA structures renders the 3' G-tail inaccessible to telomerase thereby inhibiting telomere elongation. To elucidate the functional relevance of high affinity of M/R/X for G4 DNA, the ability of the complex to generate the appropriate DNA structure for telomere elongation has been analyzed. In this study, I considered the possibility that MRX could act as: (a) a helicase that opens up the G4 DNA structures making it accessible to telomerase or (b) as a nuclease that cleaves the G4 DNA generating substrates for telomerase. Helicase assay with Mre11, Xrs2, MX and MRX on G4 DNA and duplex DNA showed no detectable DNA unwinding activity. Interestingly, nuclease assays with Mre11 on G4 DNA showed that Mre11 cleaved G4 DNA in Mn2+-dependent manner and the cleavage was mapped to the G residues at the stacks of G quartets. Mre11 cleaved telomeric duplex DNA in the center of TGTG repeat sequence, G rich ssDNA at 5' G residue in an array of 3 G residues and D loop structure preferentially at the 5' ends at TG residues. Significantly, the endonuclease activity of Mre11 was abrogated by Rad50. Xrs2 had no effect on the endonuclease activity of Mre11. Structural studies on Rad50 and Mre11 showed that binding of ATP by Rad50 positions the Rad50 catalytic domain in close proximity to the nuclease active site of Mre11. In yeast, disruption of ATP binding Walker motifs results in a null phenotype, suggesting that ATP is required for Rad50 functions in vivo. hRad50 is known to regulate the exonuclease activity of hMre11 in the presence of ATP. Therefore, can ATP modulate the effect of S. cerevisiae (Sc) Rad50 on ScMre11? To address this question, I monitored the ATPase activity of Rad50 in the absence or presence of DNA. Rad50 hydrolyzed ATP in a DNA-independent manner; however, ATPase activity was enhanced in the presence of Mre11 and Xrs2. However, Rad50 exhibited a low turnover indicating that ATP could function as a switch molecule. Based on these observations, the effect of ATP on the nuclease activity was examined. The binding of ATP and its hydrolysis by Rad50 attenuated the inhibition exerted by Rad50 on the Mre11 endonuclease activity. Cleavage of G4 DNA, D loop, duplex DNA and ssDNA required ATP hydrolysis, since no cleavage product was observed when ADP or ATPγS was substituted for ATP. This observation was corroborated using a hairpin DNA substrate that mimics a intermediate in VDJ recombination, thereby confirming the generality of regulation of Rad50 on the endonuclease activity of Mre11. Does Rad50 regulate the exonuclease activity of Mre11 as well? To address this question, exonuclease activity of Mre11, MR and MRX on 3' labeled duplex DNA and G4 DNA was assayed. Rad50 had no measurable effect on the exonuclease activity of Mre11. Based on previous studies and my observations, I propose a model for the role of MRX in telomere length maintenance and its regulation by the ATP-binding pocket of Rad50. MRX binds telomeric DNA substrates in a non-productive complex, which is converted to a catalytically active complex upon binding of ATP by Rad50. ATP induces conformational changes, repositioning the complex such that the catalytic site of Mre11 now has access to the substrate. Following cleavage of DNA by Mre11, the release of ADP and inorganic phosphate, generate the cleaved product. The cleaved DNA is now accessible to telomerase or telomere binding proteins. In summary, the data presented in my PhD thesis demonstrates that Mre11 is a structure- and sequence-specific endonuclease. The natural substrate for telomerase is the 3' ssDNA. G quartets at telomeres not only protect the ends from degradation but also make the ends inaccessible for telomerase activity. Genetic studies have shown that cells proficient for telomerase activity but lacking any one of the components of the MRX complex display shortening in telomere length. The ability of Mre11 to cleave G4 DNA at the stacks of G quartets therefore, suggests a mechanism by which the 3' ssDNA is rendered accessible to telomerase or other telomere binding proteins. Yeast telomeres are characterized by the presence of subtelomeric Y' elements proximal to the terminal TG1- 3 repeat sequences. The Y' element has been shown to be amplified by telomerase in a fraction of mutants with short telomeres. The mechanism by which Y' DNA is amplified is unclear. The ability of Mre11 to cleave telomere duplex DNA at the center of TGTG repeats could contribute to the generation of appropriate substrate for elongation by telomerase, thereby contributing to Y' DNA amplification. Telomere length is maintained by homeostasis between processes that contribute to telomere elongation and those that cause attrition in telomeric ends. Overelongated telomeres are brought to wild type telomere size by a unique recombinational single step deletion process termed telomere rapid deletion (TRD). TRD involves invasion of the elongated 3' G tail into the proximal telomeric tract resulting in the formation of the D loop structure. Following branch migration the D-loop is nicked and resolved into a deleted telomere and a circular liner product. Cells deleted for MRE11, RAD50 or XRS2 are deficient in TRD process. It has been hypothesized that Mre11 could be a candidate for cleaving the D-loop structure. The endonuclease activity of Mre11 on D-loop structure, preferentially at the 5' ends at TG residues demonstrated in this study, show that Mre11 could function as the nuclease required to generate the deleted telomere in TRD. MRX complex is involved in several processes involving DNA metabolism. It is important that the activities of the complex are regulated in the in vivo context. Complex formation and the interaction of the individual subunits with nucleotide cofactors and metal ions constitute a mode of regulation. This study shows that Rad50 regulates the endonuclease, but not exonuclease activity of Mre11. The binding of ATP and its hydrolysis by Rad50 brings in the regulatory factor necessary to keep the uncontrolled nuclease activity of MRX in check, thus preventing any deleterious effects on telomere length. Telomere maintenance by telomerase is activated in 80% of cancer cells. Inhibition of telomerase by G quartets provides a new drug targets for potential anti-cancer drugs. It is, therefore, likely that understanding the biological consequences of G quadruplex interactions would provide a better insight in development of therapeutics for cancer.

Repair of double-strand DNA breaks (DSBs) by the homologous recombination (HR) pathway results in crossovers (COs) required for a successful first meiotic division. DSB resection is the nucleic degradation of DSB ends to expose 3’ single strand DNA (ssDNA), an intermediate required for HR. To investigate genes involved in meiosis, a forward genetic screen was performed to search for novel genes or informative new mutant alleles of known genes. Mre11 is one member of the MRX/N (Mre11-Rad50-Xrs2/Nbs1) complex required for meiotic DSB formation and for resection in budding yeast. In Caenorhabditis elegans, evidence for the MRX/N’s role in DSB resection is limited. We isolated the first separation of function allele in C. elegans , mre 11(iow1), isolated from our forward genetic screen. The mre-11(iow1) mutants are specifically defective in meiotic DSB resection but not in DSB formation. The mre 11(iow1) mutants display chromosomal fragmentation and aggregation in late prophase I. Recombination intermediates and crossover formation is greatly reduced in mre 11(iow1) mutants. Irradiation induced DSBs during meiosis fail to be repaired from the early to middle prophase I in mre 11(iow1) mutants. Our data suggest that some DSBs in mre 11(iow1) mutants are repaired by the non homologous end joining (NHEJ) pathway because removing NHEJ partially suppresses some meiotic defects conferred by mre 11(iow1). In the absence of NHEJ and a functional MRX/N, meiotic DSBs are channeled to an EXO 1 dependent form of recombination repair. Overall, our analysis supports a role for MRE-11 in the resection of DSBs in early to middle meiotic prophase I and in blocking NHEJ. A reverse genetic screen and a yeast two hybrid screen were performed to search for genes with genetic and/or physical interactions with mre-11. The reverse genetic screen isolated a novel meiotic gene, nhr-2, as a partial suppressor of the meiotic defects conferred by mre-11(iow1). The yeast two hybrid screen identified kin-18 interacting with mre-11. KIN-18 is the C. elegans homolog of mammalian Thousand And One kinase (TAO) kinase. KIN-18/TAO is MAPK kinase kinase whose meiotic role was unknown. We have found that KIN-18 is essential for normal meiotic progression as kin-18 mutants exhibit accelerated meiotic recombination, ectopic germ cell differentiation, and enhanced levels of germline apoptosis. In C.elegans MPK-1 activation in late pachytene is required for physiological apoptosis (nuclei removed by apoptosis serve as nursing cells for oocytes) and oocyte differentiation. The kin-18 mutants also showed absence of MPK-1 activation and aberrant MPK-1 activation that includes ectopic activation in the wrong regions in the germline or more than one time of activation. The progression defects in kin-18 mutants are suppressed by inhibiting an upstream activator, KSR-2, of the canonical MPK-1 signaling. Our data suggest KIN-18 affects meiotic progression by modulating the timing of MPK-1 activation. This regulation ensures the proper timing of recombination and normal apoptosis, which is required for the formation of functional oocytes. Meiosis is a conserved process; revealing that KIN-18 is a novel regulator of meiotic progression in C. elegans will motivate hypothesis for TAO kinase’s role in the germline development in higher eukaryotes. Meiosis is a crucial for sexually reproducing organisms to maintain ploidy level from one generation to the next. Accurate chromosome segregation in the meiosis requires meiotic recombination between homologous chromosomes. Failure in recombination can lead to abnormal segregation of chromosomes in meiosis, which leads to aneuploidy. Anueploidy is a leading cause of miscarriages and attributes to chromosomal related birth defects. Meiotic recombination starts with programmed DNA double strand breaks (DSBs), followed by repair of these DSBs by homologous recombination (HR) pathway. One key step in HR is resection, a process to covert DSB ends into single strand DNA (ssDNA). To broaden our understanding of meiotic DSB resection, we used a nematode, C. elegans, as a model to investigate genes in DSB resection. We have isolated a specific mutant allele of a meiotic gene, mre-11. Our data suggest meiotic DSB resection in C. elegans requires collaboration of mre-11 and another gene exo-1; efficient resection of DSB ends is important to safeguard repair of DSB by HR against other illegitimate repair pathway. In addition, we identified a gene kin-18 by looking for genes interacting with mre-11. Characterization of kin-18 show meiotic recombination is tightly coordinated with germ cell progression. Our analysis provides significant improvement in the understanding of meiotic recombination in C. elegans. Given the high conservation of the two genes, mre-11 and kin-18, our finding may be applied to other organisms.

In Saccharomyces cerevisiae DNA postreplication repair (PRR) functions to bypass replication-blocking lesions to prevent damage-induced cell death. PRR employs two different mechanisms to bypass damaged DNA. While translesion synthesis (TLS) has been well characterized, little is known about the molecular events involved in error-free bypass although it has been assumed that homologous recombination (HR) is required for such a mode of lesion bypass. We undertook a genome-wide, synthetic genetic array (SGA) screen for novel genes involved in PRR and observed evidence of genetic interactions between error-free PRR and HR. We were screening for synthetic lethality which occurs when the combination of two mutations leads to an inviable organism, however, either single mutation allows for cell viability. In addition, we screened for conditionally synthetic lethal interaction which occurs when the combination of two mutations is inviable only in the presence of a DNA-damaging agent. This screen identified and assigned four genes, CSM2, PSY3, SHU1 and SHU2, whose products form a stable Shu complex, to the error-free PRR pathway. Previous studies have indicated that the Shu complex is required for efficient HR and that inactivation of any one of these genes is able to suppress the severe phenotypes of top3 and sgs1. We confirmed and further extended some of the reported observations and demonstrated that error-free PRR mutations are also epistatic to sgs1. Based on the above analyses, we propose a model in which error-free PRR utilizes the Shu complex to recruit HR to facilitate template switching, followed by double-Holliday junction resolution by Sgs1-Top3. Null mutations of HR genes including rad51, 52, 54, 55 and 57 are known to confer characteristic synergistic interactions with TLS mutations. To our surprise, null mutations of genes encoding the Mre11-Rad50-Xrs2 (MRX) complex, which is also required for HR, are epistatic to TLS mutations. The MRX complex confers an endo/exonuclease activity required for the detection and processing of DNA double-strand breaks (DSBs). Our results suggest that the MRX complex functions in both TLS and error-free PRR and that this function requires the nuclease activity of Mre11. This is in sharp contrast to other known HR genes that only function downstream of error-free PRR. Furthermore, we found that inactivation of SGS1 significantly inhibits proliferating cell nuclear antigen (PCNA) monoubiquitination and is epistatic to mutations in TLS, suggesting that Sgs1 also functions at earlier steps in DNA lesion bypass. We also examined the roles of Sae2 and Exo1, two accessory nucleases involved in DSB resection, in PRR. We found that while Sae2 is primarily required for TLS, Exo1 is exclusively involved in error-free PRR. In light of the distinct and overlapping activities of the above nucleases in the resection of DSBs, we propose that the distinct single-strand nuclease activities of MRX, Sae2 and Exo1 dictate the preference between TLS and error-free PRR for lesion bypass. While both PRR pathways are dependent on the ubiquitination of PCNA, error-free PRR utilizes non-canonical Lys63-linked polyubiquitinated PCNA to signal lesion bypass. This mechanism is dependent on the Mms2-Ubc13 complex being in close proximity to PCNA, a process thought to be dependent on Rad5. Rad5 is a member of the SWI/SNF family of ATPases that contains a RING finger motif characteristic of an E3 Ub ligase. Previous in vitro experiments demonstrated the ability of Rad5 to promote replication fork regression, a function dependent on its helicase/ATPase activity. We therefore created site-specific mutants defective in either Rad5 RING finger or helicase/ATPase activity, or both, in order to examine their genetic interactions with known TLS and error-free PRR genes. Our results indicate that both the Rad5 RING finger motif and the helicase/ATPase activity are exclusively involved in error-free PRR. To our surprise, like the Rad5 RING finger, lack of the helicase/ATPase activity also abolishes the Lys63-linked PCNA polyubiquitin chain formation, suggesting that either the Rad5 helicase/ATPase-promoted replication fork regression signals PCNA polyubiquitination or this domain has a yet unidentified activity. In summary, results obtained from this thesis dissertation have revealed novel mechanisms of yeast PRR in S. cerevisiae, a mechanism that appears to be evolutionarily conserved throughout eukaryotes, from yeast to humans.

In Saccharomyces cerevisiae DNA postreplication repair (PRR) functions to bypass replication-blocking lesions to prevent damage-induced cell death. PRR employs two different mechanisms to bypass damaged DNA. While translesion synthesis (TLS) has been well characterized, little is known about the molecular events involved in error-free bypass although it has been assumed that homologous recombination (HR) is required for such a mode of lesion bypass. We undertook a genome-wide, synthetic genetic array (SGA) screen for novel genes involved in PRR and observed evidence of genetic interactions between error-free PRR and HR. We were screening for synthetic lethality which occurs when the combination of two mutations leads to an inviable organism, however, either single mutation allows for cell viability. In addition, we screened for conditionally synthetic lethal interaction which occurs when the combination of two mutations is inviable only in the presence of a DNA-damaging agent. This screen identified and assigned four genes, CSM2, PSY3, SHU1 and SHU2, whose products form a stable Shu complex, to the error-free PRR pathway. Previous studies have indicated that the Shu complex is required for efficient HR and that inactivation of any one of these genes is able to suppress the severe phenotypes of top3 and sgs1. We confirmed and further extended some of the reported observations and demonstrated that error-free PRR mutations are also epistatic to sgs1. Based on the above analyses, we propose a model in which error-free PRR utilizes the Shu complex to recruit HR to facilitate template switching, followed by double-Holliday junction resolution by Sgs1-Top3. Null mutations of HR genes including rad51, 52, 54, 55 and 57 are known to confer characteristic synergistic interactions with TLS mutations. To our surprise, null mutations of genes encoding the Mre11-Rad50-Xrs2 (MRX) complex, which is also required for HR, are epistatic to TLS mutations. The MRX complex confers an endo/exonuclease activity required for the detection and processing of DNA double-strand breaks (DSBs). Our results suggest that the MRX complex functions in both TLS and error-free PRR and that this function requires the nuclease activity of Mre11. This is in sharp contrast to other known HR genes that only function downstream of error-free PRR. Furthermore, we found that inactivation of SGS1 significantly inhibits proliferating cell nuclear antigen (PCNA) monoubiquitination and is epistatic to mutations in TLS, suggesting that Sgs1 also functions at earlier steps in DNA lesion bypass. We also examined the roles of Sae2 and Exo1, two accessory nucleases involved in DSB resection, in PRR. We found that while Sae2 is primarily required for TLS, Exo1 is exclusively involved in error-free PRR. In light of the distinct and overlapping activities of the above nucleases in the resection of DSBs, we propose that the distinct single-strand nuclease activities of MRX, Sae2 and Exo1 dictate the preference between TLS and error-free PRR for lesion bypass. While both PRR pathways are dependent on the ubiquitination of PCNA, error-free PRR utilizes non-canonical Lys63-linked polyubiquitinated PCNA to signal lesion bypass. This mechanism is dependent on the Mms2-Ubc13 complex being in close proximity to PCNA, a process thought to be dependent on Rad5. Rad5 is a member of the SWI/SNF family of ATPases that contains a RING finger motif characteristic of an E3 Ub ligase. Previous in vitro experiments demonstrated the ability of Rad5 to promote replication fork regression, a function dependent on its helicase/ATPase activity. We therefore created site-specific mutants defective in either Rad5 RING finger or helicase/ATPase activity, or both, in order to examine their genetic interactions with known TLS and error-free PRR genes. Our results indicate that both the Rad5 RING finger motif and the helicase/ATPase activity are exclusively involved in error-free PRR. To our surprise, like the Rad5 RING finger, lack of the helicase/ATPase activity also abolishes the Lys63-linked PCNA polyubiquitin chain formation, suggesting that either the Rad5 helicase/ATPase-promoted replication fork regression signals PCNA polyubiquitination or this domain has a yet unidentified activity. In summary, results obtained from this thesis dissertation have revealed novel mechanisms of yeast PRR in S. cerevisiae, a mechanism that appears to be evolutionarily conserved throughout eukaryotes, from yeast to humans.

In eukaryotes, the repair of DSBs is accomplished through two broadly defined processes: Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR). The central step of HR is pairing and exchange of strands between two homologous DNA molecules, which is catalyzed by the conserved Rad51/RecA family of proteins. Prior to this step, an essential step in all HR pathways i.e. 5'→3' resection of broken DNA ends to generate 3' single stranded DNA tails. At the molecular level, initiation of DNA end resection is accomplished through the concerted action of MRX complex (Mre11, Rad50 and Xrs2) and Sae2 protein. To elucidate the molecular basis underlying DSB end resection in S. cerevisiae mre11 nuclease deficient mutants, we have performed a comprehensive analysis of the role of S. cerevisiae Mre11 (henceforth called as ScMre11) in the processing of DSB ends using a variety of DNA substrates. We observed that S. cerevisiae Mre11(ScMre11) exhibits higher binding affinity for single- over double-stranded DNA and intermediates of recombination and repair and catalyzes robust unwinding of substrates possessing a3' single-stranded DNA overhang but not of 5' overhangs or blunt-ended DNA fragments. Furthermore, reconstitution of DSB end resection network in-vitro revealed that Rad50, Xrs2, and Sae2 potentiated the DNA unwinding activity of Mre11. Since the exonuclease activity of Mre11 is of the opposite polarity to that expected for resection of DSBs, unwinding activity of Mre11 in conjunction with Rad50, Xrs2, and Sae2 might provide an alternate mechanism for the generation of ssDNA intermediates for DSB end repair and HR. Additionally, ScMre11 displays strong homotypic as well as heterotypic interaction with Sae2. In summary, our results revealed important insights into the mechanism of DSB end processing and support a model in which Sae2, Rad50, and Xrs2 positively regulate the ScMre11-mediated DNA unwinding activity via their direct interactions or through allosteric effects on the DNA or cofactors. Prompted by the closer association of MRX and Sae2 during DSB end processing, we asked whether Sae2 and its endonuclease activity is required for cellular response to replication stress caused by DNA damage. Toward this end, we examined the sensitivity of S. cerevisiae wild type, sae2Δ and various SAE2 mutant strains defective in phosphorylation and nuclease activity in the presence of different genotoxic agents, which directly or indirectly generate DSBs during replication. We found that S. cerevisiae lacking SAE2 show decreased cell viability, altered cell cycle dynamics after DNA damage, and more specifically, that Sae2 endonuclease activity is essential for these biological functions. To corroborate the genetic evidences for role of SAE2 during replicative stress, we investigated SAE2 functions in-vitro. For this, we purified native Sae2 protein and nuclease dead mutant of Sae2 i.e. sae2G270D. Our studies revealed dimeric forms of both the wild type and mutant forms of Sae2. Furthermore, Sae2 displays higher binding affinity and catalytic activity with branched DNA structures, such as Holliday junction and replication forks. By using nuclease dead Sae2 protein i.e. sae2G270D, we confirmed that the endonuclease activity is not fortuitous and is intrinsic to Sae2 polypeptide. Furthermore, nuclease-defective Mre11 stimulates Sae2endonuclease activity. Mapping of the cleavage sites of Sae2 revealed a distinct preference for cleavage on the 5' end of the Holliday junction, suggesting the importance of Sae2 nuclease during recombination mediated restart of the reversed replication fork. In summary, our data clearly demonstrate a previously uncharacterized role for Sae2 nuclease activity in resection of DSB ends, processing of intermediates of DNA replication/repair and attenuation of DNA replication stress-related defects in S. cerevisiae.