京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第18176号 / 医博第3896号 / 新制||医||1003(附属図書館) / 31034 / 京都大学大学院医学研究科医学専攻 / (主査)教授 小松 賢志, 教授 髙田 穣, 教授 萩原 正敏 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

One major pathway to overcome DNA damage induced replication blocks is translesion DNA synthesis, which is the replicative bypass of DNA damage by non-classical polymerases. For the cell to utilize translesion synthesis the non-classical DNA polymerase is recruited to sites of DNA damage, and a polymerase switch occurs between the stalled classical polymerase and the incoming non-classical polymerase. This process requires the replication accessory factor proliferating cell nuclear antigen (PCNA) and its monoubiquitination at Lys-164. To better understand the role of PCNA during translesion synthesis, I biochemically and structural characterized two PCNA mutant proteins, G178S and E113G PCNA, which are defective in translesion synthesis. The X-ray crystal structure of both mutant proteins showed a shift in an extended loop, called loop J, compared to the wild type PCNA structure. Steady state kinetic studies determined that in contrast to wild type PCNA which stimulates the non-classical polymerases, the two PCNA mutant proteins fail to stimulate the activity of the non-classical polymerase pol η. These results indicate that loop J in PCNA plays an essential role in facilitating translesion synthesis. During the structural studies of the E113G PCNA mutant protein I observed a unique PCNA structure that failed to form the characteristic PCNA ring shape structure, through traditional intersubunit interactions of domain A and domain B on neighboring subunits. Instead this non-trimeric PCNA structure formed A-A and B-B intersubunit interactions. The B-B interface is structurally similar to the A-B interface observed for the trimeric ring shaped form. In contrast the A-A interface is stabilized by hydrophobic interactions. The location of the E113G substitution is directly within this hydrophobic surface and would not be favorable in the wild type protein. This suggests that the side chain of Glu-113 promotes trimer formation by destabilizing these possible alternate subunit interactions. To biochemically and structurally characterize the impact of monoubiquitinating PCNA (Ub-PCNA), I developed an Ub-PCNA analog by splitting the protein into two self-assembling polypeptides. This analog supports cell growth and translesion synthesis in vivo, and steady state kinetic studies showed that the Ub-PCNA analog stimulates the catalytic activity of pol η in vitro. The X-ray crystal structure of Ub-PCNA showed that the ubiquitin moieties are located on the back face of PCNA. Surprisingly, the attachment of ubiquitin does not change PCNA's conformation. This implies that PCNA ubiquitination does not cause an allosteric change to PCNA, and instead facilitates non-classical polymerase recruitment to the back of PCNA by forming a new binding surface for the non-classical polymerases.

All living organisms are made of cells, within which genetic information is stored on long strands of deoxyribonucleic acid (DNA). The DNA encodes thousands of different genes and provides the blueprint for all of the structures and activities occurring within the cell. The building blocks of DNA are the four deoxyribonucleotides, dATP, dGTP, dTTP, and dCTP, which are collectively referred to as dNTPs. The key enzyme in the production of dNTPs is ribonucleotide reductase (RNR). In the budding yeast Saccharomyces cerevisiae, the concentrations of the individual dNTPs are not equal and it is primarily RNR that maintains this balance. Maintenance of the dNTP pool balance is critical for accurate DNA replication and DNA repair since elevated and/or imbalanced dNTP concentrations increase the mutation rate and can ultimately lead to genomic instability and cancer. In response to DNA damage, the overall dNTP concentration in S. cerevisiae increases. Cell survival rates increase as a result of the elevated concentration of dNTPs, but the cells also suffer from a concomitant increase in mutation rates. When the replication machinery encounters DNA damage that it cannot bypass, the replication fork stalls and recruits specialized translesion synthesis (TLS) polymerases that bypass the damage so that replication can continue. We hypothesized that elevated dNTP levels in response to DNA damage may allow the TLS polymerases to more efficiently bypass DNA damage. To explore this possibility, we deleted all known TLS polymerases in a yeast strain in which we could artificially increase the dNTP concentrations. Surprisingly, even though all TLS polymerases had been deleted, elevated dNTP concentrations led to increased cell survival after DNA damage. These results suggest that replicative DNA polymerases may be involved in the bypass of certain DNA lesions under conditions of elevated dNTPs. We confirmed this hypothesis in vitro by demonstrating that high dNTP concentrations result in an increased efficiency in the bypass of certain DNA lesions by DNA polymerase epsilon, a replicative DNA polymerase not normally associated with TLS activity. We asked ourselves if it would be possible to create yeast strains with imbalanced dNTP concentrations in vivo, and, if so, would these imbalances be recognized by the checkpoint control mechanisms in the cell. To address these questions, we focused on the highly conserved loop2 of the allosteric specificity site of yeast Rnr1p. We introduced several mutations into RNR1-loop2 that resulted in changes in the amino acid sequence of the protein. Each of the rnr1-loop2 mutation strains obtained had different levels of individual dNTPs relative to the others. Interestingly, all of the imbalanced dNTP concentrations led to increased mutation rates, but these mutagenic imbalances did not activate the S-phase checkpoint unless one or several dNTPs were present at concentrations that were too low to sustain DNA replication. We were able to use these mutant yeast strains to successfully correlate amino acid substitutions within loop2 of Rnr1p to specific ratios of dNTP concentrations in the cells. We also demonstrated that specific imbalances between the individual dNTP levels result in unique mutation spectra. These mutation spectra suggest that the mutagenesis that results from imbalanced dNTP pools is due to a decrease in fidelity of the replicative DNA polymerases at specific DNA sequences where they are more likely to make a mistake. The mutant rnr1-loop2 strains that we have created with defined dNTP pool imbalances will be of great value for in vivo studies of polymerase fidelity, translesion synthesis by specialized DNA polymerases, and lesion recognition by the DNA repair machinery.

Master of Science / Division of Biology / Nicholas A. Wallace / Cancer is not a single story, but rather numerous often interwoven tales, each with its own characters and progression. In the case of human papillomavirus (HPV) induced cervical cancer (CaCx), the narrative is about the relationship between virus and host, with the consequences of evolution’s shortsightedness driving the plot. Along with the increased proliferative state characteristic of cancer, cells experience frequent, inaccurate replication and replication stresses (ex. DNA damage and nucleotide starvation). To prevent replication fork stall and collapse generated by these stresses, the cell employs translesion synthesis (TLS). Notably, most of the genes in this pathway are upregulated in CaCx; however, the key protein polymerase eta is not. We have observed that upregulation in this pathway is complicated. It occurs at numerous levels, increasing both mRNA and protein abundance. This research further dissects how TLS upregulation occurs. Data shows that in CaCx-derived cell lines, the stability of some TLS proteins is increased, while the stability of other TLS proteins is unchanged. The increased proliferation, typical of these cell lines, cannot account for the enhanced stability. Despite increased TLS protein stability, these cells fail to adequately activate TLS increasing the risk of DNA damage. Genomic instability is a driving factor in HPV genome integration that prevents viral propagation and leads to cell transformation. It also raises mutagenesis rates, likely creating a selective pressure for tolerating failed TLS. The elevated mutation rate known to be associated with failed TLS could also provide a mechanism for acquired resistance to the drugs commonly used to treat CaCx. Changes in protein abundance are routinely used as biomarkers that can lead to the improved outcomes associated with early cancer detection. Elevated TLS protein could be leveraged to ensure cervical cancers are detected during Stage 1, when the 5-year survival rate is 80-90%, rather than at Stage IV, when the rate dips to around 15%.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20559号 / 医博第4244号 / 新制||医||1022(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 高田 穣, 教授 萩原 正敏, 教授 松本 智裕 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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No description available.

<p>Translesion synthesis is a fundamental biological process that enables DNA replication across lesion sites to ensure timely duplication of genetic information at the cost of replication fidelity, and it is implicated in development of cancer drug resistance after chemotherapy. The eukaryotic Y-family polymerase Rev1 is an essential scaffolding protein in translesion synthesis. Its C-terminal domain (CTD), which interacts with translesion polymerase &#950; through the Rev7 subunit and with polymerases &#954;, &#953; and &#951; in vertebrates through the Rev1-interacting region (RIR), is absolutely required for function. </p><p>In chapter 1, the solution structures of the mouse Rev1 CTD and its complex with the Pol &#954; RIR are reported, revealing an atypical four-helix bundle. Yeast two-hybrid assays were used to identify a Rev7-binding surface centered at the &#945;2-&#945;3 loop and N-terminal half of &#945;3 of the Rev1 CTD. Binding of the mouse Pol &#954; RIR to the Rev1 CTD induces folding of the disordered RIR peptide into a three-turn &#945;-helix, with the helix stabilized by an N-terminal cap. RIR-binding also induces folding of a disordered N-terminal loop of the Rev1 CTD into a &#946;-hairpin that projects over the shallow &#945;1-&#945;2 surface and creates a deep hydrophobic cavity to interact with the essential FF residues juxtaposed on the same side of the RIR helix. The combined structural and biochemical studies reveal two distinct surfaces of the Rev1 CTD that separately mediate the assembly of extension and insertion translesion polymerase complexes.</p><p>The multifaceted abilities of the Rev1 CTD are further explicated in chapter 2 where the purification and structure determination of a quaternary translesion polymerase complex consisting of the Rev1 CTD, the heterodimeric Pol &#950; complex, and the Pol &#954; RIR is reported. Yeast two-hybrid assays were employed to identify important interface residues of the translesion polymerase complex. The structural elucidation of such a quaternary translesion polymerase complex encompassing both insertion and extension polymerases bridged by the Rev1 CTD provides the first molecular explanation of the essential scaffolding function of Rev1 and highlights the Rev1 CTD as a promising target for developing novel cancer therapeutics to suppress translesion synthesis. Our studies support the notion that vertebrate insertion and extension polymerases could structurally cooperate within a mega translesion polymerase complex (translesionsome) nucleated by Rev1 to achieve efficient lesion bypass without incurring an additional switching mechanism.</p><p>Chapter 3 explores the ubiquitin-binding capacity of the FAAP20 UBZ in an effort to begin understanding its requirement for recruitment of the Fanconi anemia complex to interstrand DNA crosslink sites and for interaction with the translesion synthesis machinery through recognition of monoubiquitinated Rev1. FAAP20 is an integral component of the Fanconi anemia core complex that mediates the repair of DNA interstrand crosslinks. Although the UBZ-ubiquitin interaction is thought to be exclusively encapsulated within the &#946;&#946;&#945; module of UBZ, it is revealed that the FAAP20-ubiquitin interaction extends beyond such a canonical zinc-finger motif. Instead, ubiquitin-binding by FAAP20 is accompanied by transforming a disordered tail C-terminal to the UBZ of FAAP20 into a rigid, extended &#946;-loop that latches onto the complex interface of the FAAP20 UBZ and ubiquitin, with the invariant C-terminal tryptophan emanating toward I44Ub for enhanced binding specificity and affinity. Substitution of the C-terminal tryptophan with alanine in FAAP20 not only abolishes FAAP20-ubiquitin binding in vitro, but also causes profound cellular hypersensitivity to DNA interstrand crosslink lesions in vivo, highlighting the indispensable role of the C-terminal tail of FAAP20, beyond the compact zinc finger module, toward ubiquitin recognition and Fanconi anemia complex-mediated DNA interstrand crosslink repair.</p><p>Having structurally elucidated the molecular basis of the essential scaffolding function of the Rev1 CTD, the search for small molecule inhibitors of the Rev1-Rev7 interaction has been initiated toward the goal of developing novel adjuvants to DNA targeting chemotherapeutics. Screening efforts have led to the discovery of a lead compound, JH-RE-06*NaOH, that specifically targets the Rev7-binding hydrophobic pocket of the Rev1 CTD with low micromolar affinity, effectively inhibiting the Rev1-Rev7 interaction in an in vitro ELISA assay developed for high-throughput screening of small molecule libraries. With the potential for positive outcomes in future in vivo assays, we hope to develop JH-RE-06*NaOH into the first potent inhibitor of translesion synthesis in cancer patients being treated with DNA-targetng chemotherapeutics to aid in sensitization and prevention of chemoresistance development in malignancies.</p> / Dissertation

La protéine PCNA est un facteur d'échafaudage polyvalent pour plus de cinquante protéines impliquées dans le métabolisme d'ADN, notamment dans la réplication et la réparation. Comment les échanges entre les partenaires de PCNA sont régulés est actuellement mal compris. Parmi ses partenaires, CDT1, p21 et PR-Set7/Set8 possèdent un motif d'interaction avec PCNA particulier, nommé « PIP degron », qui favorise leur protéolyse d'une manière dépendante de l'E3 ubiquitine ligase CRL4Cdt2. Après irradiation aux UV-C, le facteur d'initiation de la réplication CDT1 est rapidement détruit d'une manière dépendante de son PIP degron, mais le rôle de cette dégradation est inconnu. Dans cette étude, j'ai analysé la fonction du PIP degron de CDT1 et fourni des évidences expérimentales qui montrent que l'inhibition de la dégradation de Cdt1 par CRL4Cdt2 dans les cellules de mammifères compromet la relocalisation de l'ADN polymérase translesionnelle eta en foyers nucléaires induits par les irradiations UV-C. En élargissant cette étude à d'autres partenaires de PCNA, nous avons constaté que seuls les protéines qui contiennent un PIP degron, et pas un PIP box canonique comme celui de FEN1 et p15 (PAF), interfèrent avec la formation de foyers de pol eta. La mutagenèse du PIP degron de CDT1 a révélé qu'un résidu de thréonine conservé parmi les PIP degrons est essentiel pour l'inhibition de la formation des foyers de pol eta. Les résultats obtenus suggèrent que l'élimination de protéines contenant des PIP degrons par la voie CRL4Cdt2 régule le recrutement de pol eta au niveau des sites de dommages induits par les UV-C. / The sliding clamp PCNA is a versatile scaffold for more than fifty proteins involved in DNA metabolism such as replication and repair. How the switch between PCNA partners is regulated is currently not fully understood. Among its partners, Cdt1, p21 and PR-Set7/Set8 contain a specialized PCNA-binding motif named « PIP degron » that promotes their proteolysis in a fashion dependent on the E3 ubiquitin ligase CRL4Cdt2. Upon UV-irradiation, the replication initiation factor Cdt1 is rapidly destroyed in a PIP degron-dependent manner but the role of this degradation is unknown. Here we have analyzed the function of Cdt1 PIP degron and we provide evidence that interference with CRL4Cdt2-mediated destruction of Cdt1 in mammalian cells compromises PCNA-dependent relocalisation of the DNA translesion polymerase eta into UV-induced nuclear foci. By extending this analysis to other PCNA partners, we found that only PIP degrons, as compared to canonical PCNA-binding motifs of Fen1 and p15(PAF), interfere with pol eta focus formation. Mutagenesis of Cdt1 PIP degron revealed that a threonine residue conserved in PIP degrons is critical for inhibition of pol eta focus formation. Our results suggest that removal of high-affinity PIP degron-containing proteins from PCNA by CRL4Cdt2 pathway regulates pol eta recruitment to sites of UV-damage.

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.