京都大学 / 0048 / 新制・課程博士 / 博士(生命科学) / 甲第21400号 / 生博第401号 / 新制||生||53(附属図書館) / 京都大学大学院生命科学研究科高次生命科学専攻 / (主査)教授 松崎 文雄, 教授 石川 冬木, 教授 松本 智裕 / 学位規則第4条第1項該当 / Doctor of Philosophy in Life Sciences / Kyoto University / DFAM

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Yes / Multiple pathways participate in the AMPA receptor trafficking that underlies long-term potentiation (LTP) of synaptic transmission. Here we demonstrate that protein SUMOylation is required for insertion of the GluA1 AMPAR subunit following transient glycine-evoked increase in AMPA receptor surface expression (ChemLTP) in dispersed neuronal cultures. ChemLTP increases co-localisation of SUMO-1 and the SUMO conjugating enzyme Ubc9 and with PSD95 consistent with the recruitment of SUMOylated proteins to dendritic spines. In addition, we show that ChemLTP increases dendritic levels of SUMO-1 and Ubc9 mRNA. Consistent with activity dependent translocation of these mRNAs to sites near synapses, levels of the mRNA binding and dendritic transport protein CPEB are also increased by ChemLTP. Importantly, reducing the extent of substrate protein SUMOylation by overexpressing the deSUMOylating enzyme SENP-1 or inhibiting SUMOylation by expressing dominant negative Ubc9 prevent the ChemLTP-induced increase in both AMPAR surface expression and dendritic SUMO-1 mRNA. Taken together these data demonstrate that SUMOylation of synaptic protein(s) involved in AMPA receptor trafficking is necessary for activity-dependent increases in AMPAR surface expression. / Medical Research Council, the European Research Council and the Wellcome Trust

This thesis investigates the integration of vehicles with differing levels of automation and connectivity within suburban traffic systems, focusing on their impact on road safety, traffic efficiency, and risk, particularly concerning vulnerable road users. By employing a Cooperative and Connected Automotive Mobility (CCAM) framework, the study examines how vehicles that share real-time information and intentions under different CCAM configurations influence the dynamics of suburban mobility. Utilizing simulation tools like SUMO and Artery, this research conducts multiple traffic scenario simulations to capture the interactions between automated, connected, and conventional vehicles. The simulations specifically target the implementation of Intelligent Transport Systems (ITS) protocols such as ETSI ITS-G5, directed by the European standard, assessing their efficacy in fostering safer and more efficient suburban environments. The parameters used to determine the performance of a scenario are number of emergency brakes, collisions, average vehicle speed, average relative speed and ratio of departed speed. The findings aim to provide actionable insights into deploying advanced vehicular technologies, ensuring their beneficial integration into increasingly complex suburban traffic networks, thus supporting global road safety initiatives like Vision Zero. This project shows that safety-wise, the general mix of vehicles that provide the safest traffic conditions are the heterogenous mix of 50% automated, with higher levels of connectivity contributing to better metric scores from an efficiency standpoint.

PML et les corps nucléaires (CN) sont impliqués dans la défense antivirale. En effet, notre équipe a montré que la surexpression de PMLIII confère la résistance au virus de la stomatite vésiculaire, au virus de l'influenza, au virus foamy mais pas au virus de l’encéphalomyocardite (EMCV). J’ai montré dans mon travail de thèse que l’EMCV contrecarre le pouvoir antiviral de PMLIII en induisant sa dégradation par un processus dépendant du protéasome et de SUMO. Cependant, les cellules de souris invalidées pour PML sont plus sensibles à l’infection par l’EMCV que les cellules issues de souris parentales. Pour déterminer l’isoforme de PML responsable de cet effet antiviral, j’ai analysé l’effet des sept isoformes de PML (PMLI-VII) et j’ai montré que seule l’expression en stable de PMLIV confère la résistance à l’EMCV en séquestrant la polymérase virale 3Dpol au sein des CN PML. De plus la déplétion de PMLIV augmente la production de l’EMCV dans les cellules traitées par l’interféron. Ces données indiquent le mécanisme par lequel PML confère la résistance à l’EMCV et révèlent que PML est l’une des protéines médiatrices des effets anti-EMCV de l’interféron. / PML and nuclear bodies (NBs) are implicated in antiviral defense. Indeed, our team showed that overexpression of PMLIII confers resistance to vesicular stomatitis virus, influenza virus, foamy virus but not to encephalomyocarditis virus (EMCV). I have shown during my thesis that EMCV counteracts the antiviral effect of PMLIII by inducing its degradation in SUMO and proteasome-dependent way. However, cells derived from PML knockout mice are more susceptible to EMCV infection than wild-type cells. To determine the isoforme of PML implicated in this antiviral effect, I analysed the effect of the seven PML isoforms (PMLI-PMLVII) and I showed that only stable expression of PMLIV confers resistance to EMCV by sequestring the viral polymérase 3Dpol in PML Nbs. In addition, depletion of PMLIV boosted EMCV production in interferon-treated cells. These finding sindicate the mechanism by which PML confers resistance to EMCV and reveal a new pathway mediating the antiviral activity of interferon against EMCV.

ATP-dependent chromatin remodelers have been proposed to act sequentially, and to a certain extent non-redundantly, in the priming stages of the DNA Damage Response pathways by establishing chromatin in lesion sites ready to act as a scaffold for repair factors or to be displaced in order to allow DNA repair. Among remodeling factors proposed to play a role in DNA repair is SMARCAD1, a poorly characterized, non-canonical member of the SWR1-like family of SNF2/SWI2 superfamily of ATPases, which has recently been identified as a potential target for ATM/ATR phosphorylation at canonical and non-canonical sites upon DNA damage. The actual mechanism for SMARCAD1 recruitment and involvement in DNA remodeling is still unknown, and unlike most other chromatin remodelers, SMARCAD1 does not contain DNA- or histone-binding domains frequently accompanying such proteins. Instead, in addition to the core ATPase domain, only two CUE domains (a type of helical ubiquitin-binding domain) have been identified. This thesis presents the findings of an investigation intended to structurally characterize SMARCAD1 by dissecting and identifying its domain architecture, and examining the activity and ligand selectivity of its binding domains in the functional context of DNA damage repair. The solution NMR structure of the CUE1 domain is presented, describing a triple helix bundle consistent with other members of the family. Furthermore, a novel SUMO interacting motif was identified and through a combination of NMR titrations and phospho-proteomics analysis, shown to be constitutively phosphorylated which excludes the possibility of DNA damage dependent ATM targeting as the recruitment mechanism for DNA repair. Additionally, it is demonstrated that both CUE domains are poor binders of mono-ubiquitin, however CUE1 specifically mediates the high affinity binary interaction with the transcriptionally repressive master regulator KAP1. This interaction was shown to be independent of post-translational ubiquitylation but rather sustained through direct interaction with the dimeric RBCC domain of KAP1. Finally, mass spectrometry profiling of domain-dependent interactions (based on differential abundance relative to changes due to chemically induced DNA damage) suggests SMARCAD1 may be involved in p53 transcriptional regulation through interactions maintained with CUE1 prior to DNA damage, whereas the SIM domain selectively targets protein interactions upon DNA damage that simultaneously activate p53 transcriptional control and recruit SMARCAD1 to DNA damage repair pathways.

La latence post-intégrative du VIH-1 génère des réservoirs qui empêchent l'éradication du virus avec les thérapies actuelles. La compréhension des mécanismes moléculaires de la latence servirait à l'identification de nouvelles cibles thérapeutiques et le développement de molécules de type LRA (Latency Reversing Agent) permettant la guérison fonctionnelle des patients et un arrêt des traitements. Nous avons démontré que la combinaison de deux types différents de LRAs à base de composés libérant P-TEFb (JQ1, I-BET, I-BET151 et HMBA) ou des agonistes de PKC (prostratine, bryostatine-1 et Ing-B) conduit à une robuste activation synergique de la production du VIH-1 dans divers modèles cellulaires de latence post-intégrative et dans des réservoirs de lymphocytes T CD4+ primaires. Le répresseur transcriptionnel CTIP2 recrute des complexes multienzymatiques pour favoriser l'établissement et la persistance de la latence du VIH-1 dans les cellules microgliales, le principal réservoir viral du système nerveux central. De plus, CTIP2 s’associe au complexe 7SK snRNP pour inhiber P-TEFb, un facteur d’élongation indispensable à l’expression du VIH-1 et à la réactivation des provirus latents. Des expériences d’immunoprécipitations de CTIP2, couplées à la spectrométrie de masse, nous ont permis d’identifier près de 900 partenaires protéiques de CTIP2. Parmi ces nouveaux partenaires, nous avons identifié la SUMO E3 ligase KAP1. Nous montrons que KAP1 réprime les phases précoce et tardive Tat dépendante de la transcription du VIH-1. KAP1 induit une dégradation de Tat, qui est sensible aux modulations de la voie SUMO. En effet, la sumoylation favorise l'association de Tat avec KAP1, de même que sa dégradation. Globalement, nos résultats suggèrent que KAP1 contribue à l'établissement et à la persistance des réservoirs latents du VIH-1. Cibler les voies SUMO constituerait un nouveau champ d'investigation dans le cadre du développement de nouvelles classes de LRAs. / The HIV-1 post-integration latency generates reservoirs that prevent the eradication of the virus with the current therapies. The understanding of the molecular mechanisms of this latency enable the identification of new therapeutic targets and the development of LRA (Latency Reversing Agent) for functional cure and treatments interruption. We have demonstrated that the combination of two different LRAs based on P-TEFb releasing compounds (JQ1, I-BET, I- BET151 and HMBA) or PKC agonists (prostratin, bryostatin-1 and Ing-B) leads to robust synergistic activation of HIV-1 production in various cellular models of post-integration latency and in primary CD4+ T cells reservoirs. The transcriptional repressor CTIP2 recruits multienzymatic complexes to promote the establishment and persistence of HIV-1 latency in microglial cells, the main viral reservoir of the central nervous system. Furthermore, CTIP2 binds to the 7SK snRNP complex to inhibit P-TEFb, an elongation factor essential for HIV-1 expression and reactivation of latent proviruses. Immunoprecipitation experiments of CTIP2 coupled to mass spectrometry allowed us to identify almost 900 proteins partners of CTIP2. Among these new partners, we have identified the E3 SUMO ligase KAP1. We found that KAP1 contributes to HIV-1 gene silencing by repressing the initiation and the Tat–dependent steps of the viral gene transcription. KAP1 induces Tat degradation via a SUMO-sensitive pathway. Indeed, favoring the sumoylation promotes Tat association with KAP1 and the resulted Tat degradation. Altogether, our results suggest that KAP1 contributes to the establishment and the persistence of the latently infected HIV-1 reservoirs. Moreover, these results suggest that targeting the SUMO pathways may be a new field of investigation to develop new classes of LRAs for cure strategies.

DNA repair pathways have evolved to protect the genome from damage caused by intrinsic and extrinsic factors. Although numerous DNA repair mechanisms have been studied and reported, information regarding how they coordinate with the necessary changes in chromatin structure is scarce. Smc (structural maintenance of chromosomes) proteins are a conserved, essential family of proteins required for chromosome organization and accurate segregation. The budding yeast, Saccharomyces cerevisiae has three Smc-protein complexes: Smc1/3 complex (cohesin), Smc2/4 complex (condensin) and the Smc5/6 complex, required for sister chromatid cohesion, condensation and DNA repair, respectively. The chromatin associated Smc5/6 complex consists of Smc5, Smc6 and six non-smc elements (Nse1-Nse6). Smc5 and Smc6 are required for stability of repetitive chromosomal regions and sister chromatid recombination-mediated repair of double-strand breaks. Mms21/Nse2, a subunit of the Smc5/6 complex, is a SUMO E3-ligase, which conjugates SUMO (small ubiquitin-like modifier) to Smc5 and Yku70 (DNA repair protein) and its SUMO ligase activity protects the cells from extrinsic DNA damage. To address the role of Nse2 SUMO ligase in cellular events, we isolated mutants (nse2∆sl and nse2C221A) defective in the E3-ligase domain of Nse2 and found that these mutants are sensitive to genotoxic agents, for example MMS, UV or bleomycin, as expected. We found that cysteine 221 present in the SP-RING domain of Nse2 is required in the function of Nse2 in resisting genotoxic stress. We found that nse2∆sl cultures are slow growing and show increased abundance of cells having 2N DNA content (indicative of a G2-M cell cycle delay or arrest) relative to wild type cells. The DNA damage checkpoint pathway is activated to a limited extent in unchallenged nse2∆sl mutant cells indicating that cells lacking the SUMO ligase activity of Nse2 incur spontaneous DNA damage. Furthermore nse2∆sl cells are exquisitely sensitive to caffeine, an agent known to override the DNA damage checkpoint in a number of organisms by inhibiting the DNA damage checkpoint transducer ATR (Homo sapiens), Mec1 (Saccharomyces cerevisiae) and Rad3 (Schizosaccharomyces pombe). In order to investigate the importance of the DNA damage checkpoint pathway for nse2∆sl cells, we employed a genetic approach. We found that nse2∆sl exhibits synthetic sick interaction with mec1∆ but not tel1∆ (defective in Mec1 or Tel1 PI kinases) or mrc1∆ (defective in Mrc1 or mediator of replication checkpoint 1) indicating that the DNA damage induced Mec1 dependent checkpoint pathway is selectively required but the replication stress checkpoint pathway is dispensable for optimal growth of unchallenged nse2∆sl cells. In order to further investigate the role of Nse2 in S phase events, we used camptothecin (CPT), a drug that induces S phase specific double strand breaks. CPT inhibits topoisomerase I by trapping the covalent Top1-DNA intermediate. Collision of a DNA replication fork with such a complex results in double-strand and single-strand breaks in DNA. We found that nse2∆sl is CPT-sensitive and that nse2∆sl top1-8 has a synthetic sick phenotype. Thus, our chemical and genetic interaction studies suggest that the SUMO ligase activity of Nse2 may be required when Top1 function is compromised. Interestingly, human and yeast Top1 proteins are known to be sumoylated. Our findings suggest that MMS-induced enhancement of Top1 sumoylation in budding yeast is partially dependent on SUMO ligase activity of Nse2. Since both sumoylation and Top1 play a role in telomere maintenance, we also examined the telomere length in single as well as double mutants and found that there is slight telomere lengthening in nse2∆sl top1-8 double mutant. To gain further insight into the genetic interaction between Nse2 and other proteins which affect DNA topology, we also investigated genetic interaction of Nse2 with other topoisomerases. We found that top3-2 nse2∆sl exhibited a synthetic sick phenotype but nse2∆sl top2-4 showed partial rescue of temperature sensitivity. In order to investigate whether chromosome integrity is compromised in nse2∆sl cells we employed a YAC (yeast artificial chromosome) based assay to examine GCRs (gross chromosomal rearrangements). We found elevated levels of GCR in nse2∆sl cells compared to wild type cells. Furthermore, deletion of DNA Topoisomerase1 in nse2∆sl background selectively destabilizes a longer YAC relative to shorter YACs. We also examined the effect of varying origin number on YAC stability in nse2∆sl as well as top1∆ and nse2∆sl top1∆ cells. We found that a YAC having fewer origins is not destabilized in nse2∆sl and top1∆ single mutants but is destabilized in the nse2∆sl top1∆ double mutant. Since Nse2 is a non-SMC member of the Smc5/6 complex, we also investigated the effect of varying origin number on YAC stability in smc6-56 and smc656 top1∆ mutants. We found that the stability of a YAC is modestly compromised in the smc6-56 mutant but its derivative having fewer origins is not further destabilized, rather it seems to be stabilized. In order to gain molecular insights into the involvement of the SUMO ligase activity of Nse2 in maintenance of chromosome integrity, we examined sumoylation of specific substrates following a candidate approach. Smc5 and Yku70 are known targets of Nse2dependent sumoylation. We found that Smc6 is also sumoylated and that the MMS-induced enhancement of Smc6 sumoylation in budding yeast is partially dependent on Nse2. To understand the functional significance of Smc5 sumoylation, we mutated lysine residues of all the four predicted sumoylation sites ψKXE/D, individually as well as all four together. We found that all the single as well as quadruple mutants were weakly sensitive to MMS suggesting that these putative sumoylation sites of Smc5 may contribute towards countering MMS-induced DNA damage. Interestingly, we found that Smc5 sumoylation is enhanced when treated with MMS (methyl methane sulfonate) but not significantly with HU (hydroxyurea) and CPT (camptothecin). We also generated putative ATP-binding defective mutants in Smc5. Previous studies suggest that the ATPase motif is required for the essential function of some Smc proteins (for example, Smc1 and Smc6). We found that smc5K75E and smc5K75Q, having a mutation in the lysine residue of the conserved GXGKS motif present in the Walker A type box at the Nterminus exhibited a null phenotype implying that this conserved lysine residue is required for essential function of Smc5. In this study, employing genetic and biochemical methods, we have characterized the Nse2 SUMO ligase defective mutant and analyzed its role in the unperturbed mitotic cell cycle and in genome maintenance. We have also employed genetic methods to study the involvement of both Nse2 and DNA Topoisomerase I in maintaining genomic stability. Lastly, we have addressed the functional significance of Lysine residues of putative sumoylation sites and the conserved ATP-binding motif of Smc5 by mutational analysis. In conclusion, our study highlights an important role for the SUMO ligase activity of Nse2 in maintaining genomic stability and suggests that sumoylation of Smc5 may be important for resisting MMS-induced genotoxic stress.

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Durch ein zunehmendes Verkehrsaufkommen wächst die Notwendigkeit den Verkehr in irgendeiner Form "intelligent" zu organisieren. In diesem Kontext sind die sogenannten Intelligent Transportation Systems (ITS) in den Fokus der Forschung gerückt. Diese Systeme zielen in der Regel auf die dynamische Optimierung der Routenwahlen von Verkehrsteilnehmern ab und sollen dadurch die Effizienz des Verkehrs verbessern. Grundsätzlich kann die Vorstellung einer optimalen Routenwahl in eine von zwei Kategorien eingeteilt werden: das Nash Gleichgewicht und die systemoptimale Routenwahl. Während Nash Gleichgewichte vergleichsweise einfach erzielt werden können-beispielsweise dadurch, dass jeder Fahrer seine Route egoistisch optimiert-ist das Erreichen des Systemoptimums ungleich schwerer. Dieses setzt nämlich voraus, dass alle Fahrer miteinander kooperieren und gemeinsam eine Lösung finden, von der die Gesamtheit als solche profitiert. In dieser Dissertation diskutieren wir das Design eines dezentralisierten ITS, welches in der Lage ist, eine systemoptimale Routenzuweisung im Straßennetzwerk zu approximieren, so dass die Fahrzeuge den price of anarchy nicht mehr in voller Höhe bezahlen müssen. Der besondere Fokus liegt hierbei auf der Anwendbarkeit des Ansatzes in realistischen Umgebungen, in denen eine Vielzahl von Schwierigkeiten zu erwarten ist. Dies beinhaltet beispielsweise eine unvollständige oder inkorrekte Sicht auf die aktuelle Verkehrssituation, das Fehlen von Wissen über Fahrzeuge, die erst in der Zukunft das Straßennetz betreten sowie ein nicht perfekter oder ressourcenlimitierter Kommunikationskanal. / The increasing amount of road traffic necessitates approaches that somehow "intelligently" organize traffic. In this context, the study of intelligent transportation systems (ITS) has been performed for some time. The goals of such systems include, e.g., is the dynamic optimization of route choices in a road network and hence the improvement of traffic conditions. There are two main methodologies how an optimization can be performed: the optimization towards a Nash equilibrium or towards a system optimum. While Nash equilibria can be easily reached, e.g., when every driver selfishly optimizes his own route, reaching the system optimum is a challenging task and requires all drivers to cooperate in an altruistic manner in favor of the system from a global perspective. In this work, we discuss the design of a decentralized ITS that is capable of approximating system optimal route choices in the network avoiding that the drivers have to pay the full price of anarchy. The focus, in this context, lies on the applicability to real life situations where a number of difficulties has to be expected, e.g., an incomplete or incorrect view on the current traffic situation, the lack of future knowledge and an imperfect or limited communication channel. Facing these challenging questions, we develop solutions to a number of research questions, that arise from the aforementioned difficulties. Before we can do so, we focus on the fundamental concepts of traffic optimization with an emphasis both on the theoretical concepts as well as their applicability in real world environments.