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京都大学 / 新制・課程博士 / 博士(農学) / 甲第23247号 / 農博第2454号 / 新制||農||1084(附属図書館) / 学位論文||R3||N5337(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 三芳 秀人, 教授 宮川 恒, 教授 森 直樹 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

ATP-binding cassette (ABC) transporters use the power of ATP binding and hydrolysis to deliver a wide variety of molecules across membrane bilayers. Crystal structures in the past two decades have provided snapshots of these transporters under various conditions, which revealed conformational changes of transporters upon substrate and ATP binding along the transport pathway. However, understanding of kinetics of substate translocation and the knowledge of transient intermediates along the transport pathway remain primitive, especially for Type II ABC importers. In this thesis work, I employed fluorescence resonance energy transfer (FRET) to study the transport mechanism of BtuCD, a model type II ABC importer that transports vitamin B12. I also exploited the photophysical property of the transport substrate, B12, that quenches the fluorescence of certain fluorophores nearby through FRET, which enables the monitoring of B12 binding and release. Our ensemble FRET data showed the binding of B12 and nucleotide both weaken the interaction between BtuCD and BtuF. Our single-molecule FRET (smFRET) experiments not only revealed stepwise movement of substrate molecule through the transporter in real-time and at the single-molecule level, but also yielded the rates of transition between individual conformational states, which had not been previously characterized in any other transporters. The results showed that ATP hydrolysis, instead of ATP binding, drives the power-stroke for the transport cycle. They also showed two sequential ATP hydrolysis events are required to complete a transport cycle, with the first ATP hydrolysis event delivering B12 into the cavity of BtuCD and the second resetting the BtuCD-F complex for a new cycle of transport.

Acyldepsipeptide (ADEP1) is an antibiotic that binds to Escherichia coli ClpP, mimicking the interaction that the protease typically establishes with ClpA/ClpX ATPases in bacterial cells. Binding of ADEP1 causes the N-terminal end of the ClpP to adopt a structured β-hairpin and triggers opening of the axial gate in the tetradecameric ClpP. Open conformation of the axial gate causes translocation of the substrates into the catalytic chamber of ClpP and the resultant uncontrolled proteolysis renders cellular death making ADEP1 a potent antibiotic. Our current understanding about the ADEP1-induced open conformation of the axial gate is limited. Based on the existing X-ray structures, it is unclear whether the mechanism of ADEP1-mediated activation of ClpP is conserved in Gram-positive and Gram-negative bacteria. To understand the activation mechanism of ClpP by ADEP1, we obtained Bacillus subtilis ClpP variants with amino acid substitutions in the N-terminal region and tested the effect of these mutations on substrate translocation using fluorescence-based proteolytic assays and cryo-electron microscopy. We found that compromising the integrity of the β-hairpin adopted by the N-terminal region prevented translocation of the substrate into the catalytic chamber of B. subtilis ClpP. These results suggest that the structural requirements for a functional axial channel are conserved in Gram-positive and Gram-negative bacteria. This study defines the structural requirements for ADEP1-mediated activation of the ClpP protease and serves as a model for the functioning of ClpP in the context of the ClpAP and ClpXP complexes. / Thesis / Master of Science (MSc)

Aggregatibacter actinomycetemcomitans is strongly associated with aggressive periodontitis and one of several virulence factors is a leukotoxin (LtxA). The toxin has a consequential impact on human leukocytes which leads to an interference with the host ́s defences due to a chain reaction involving activation and release of a pro-inflammatory cytokine; interleukin-1β (IL-1β). As an early phase in this reaction chain the toxin stimulates a massive release of adenosine triphosphate (ATP) from human leukocytes. We hypothesize that leukotoxin-induced pro- inflammatory cell death is initiated by ATP release through pannexin channels in the human monocyte cell membrane. The aim of this study was to investigate if blocking of pannexin channels with carbenoxolone (Cbx) results in a reduction of ATP release. A human monocyte cell line (THP-1 cells) was exposed to purified LtxA, Cbx and oxidized ATP. Colorimetric ATP kit was used to evaluate levels of ATP release and thereafter the samples were read in a spectrophotometer. This study confirms that LtxA induces an ATP release from THP-1 cells. Our conclusion is that blocking of pannexin channels does not result in a statistically significant reduction in ATP release, which indicates that ATP is released by one or several other undetected pathways.

Purinerge P2X3-Rezeptoren spielen eine bedeutende Rolle in der Vermittlung chronischer Schmerzen, welche ein führendes Problem des Gesundheitswesens mit vielen sozioökonomischen Konsequenzen darstellen. Die Tatsache, dass P2X3-Rezeptoren fast ausschließlich von nozizeptiven Neuronen exprimiert werden, macht sie trotz ihres besonderen Desensitisierungsverhaltens zu vielversprechenden Angriffspunkten zukünftiger Schmerztherapien, beispielsweise mithilfe kompetitiver Antagonisten an diesen Rezeptoren. Zur Analyse der Wechselwirkungen zwischen Agonist und kompetitivem Antagonist wird meist der Schild-Plot benutzt. Jedoch ist dieser im Falle der sehr schnell desensitisierenden P2X3-Rezeptoren ungeeignet, da die Vorbedingung eines stabilen Gleichgewichts zwischen Agonist und Antagonist aufgrund der Desensitisierung nicht erfüllt ist. Ziel der vorliegenden Arbeit war es, eine neue Methode zur Analyse der Interaktion kompetitiver Antagonisten mit ihrer Bindungsstelle am Beispiel des P2X3-Rezeptors zu entwickeln und so für die Antagonistenbindung bedeutende Aminosäuren der Bindungsstelle zu identifizieren. Mittels der Patch-Clamp-Technik wurden die Effekte der Antagonisten A-317491, TNP-ATP und PPADS auf die vom P2X1,3-Rezeptor-selektiven Agonisten α,β-MeATP induzierten Ströme am P2X3-Wildtyp-Rezeptor und an fünf Rezeptormutanten mit veränderter Ligandenbindungsstelle untersucht. Alle Rezeptoren wurden in HEK293-Zellen exprimiert. Anhand der gemessenen Daten wurde ein Hidden Markov Model (HMM) erstellt, welches die sequentiellen Übergänge des Rezeptors von geschlossen zu offen und desensitisiert in An- und Abwesenheit des Antagonisten miteinander kombiniert. Die am P2X3-Rezeptor induzierten Ströme konnten mithilfe dieses Modells korrekt gefittet und die für die Antagonistenbindung wichtigen Aminosäuren innerhalb der Bindungsstelle bestimmt werden. Als Resultat dieser Arbeit konnte außerdem gezeigt werden, dass das HMM eine geeignete Methode zur Analyse der Wirkung kompetitiver Antagonisten an schnell desensitisierenden Rezeptoren darstellt. Die untersuchten Antagonisten A-317491 und TNP-ATP haben einen kompetitiven Wirkmechanismus, während PPADS eine pseudoirreversible Blockade verursacht.

The thesis is concerning with the road transport of goods under controlled temperature. Under such goods we mean foodstuffs. The aim of the thesis is to describe the issue of road transport of foodstuffs on the whole logistic chain using the production of Danone company as an example for illustration.

ATPDases ou ATP-difosfohidrolases são enzimas que clivam o ATP e o ADP a AMP e Pi e estão envolvidos em inibição da agregação plaquetária. No parasita Schistosoma mansoni nosso grupo identificou e clonou o gene da ATPDase1, e a proteína foi localizada na superfície do tegumento. Recentemente, clonamos o gene da ATPDase2 usando a informação do banco de dados de ESTs de S. mansoni e imunolocalizamos a sua proteína também no tegumento. ATPDase2 foi encontrada em ambas as membranas do tegumento basal e apical juntamente com a ATPDase1, entretanto ATPDase2 somente foi encontrada no espaço sincicial do tegumento. A presença de ambas as enzimas sobre a superfície externa do tegumento sugere um maior papel sobre a regulação de abundância de nucleotídeos. Análise da expressão de ambos os genes foram realizadas por RT- PCR em tempo real usando RNA de ovos, miracídeo, cercária, esquistossômulo e verme adulto. Os resultados mostraram que o gene da ATPDase1 foi mais expresso em ovos (7 vezes), adulto (6 vezes), cercária (3,5 vezes) e esquistossômulo (1,5 vezes) quando comparado ao miracídio, que foi tomado como referência. O gene da ATPDase2 foi mais expresso em ovos (16 vezes), cercária (11 vezes), miracídio (7 vezes) e verme adulto (2 vezes) quando comparado a esquistossômulo, mostrando que ambos os genes são modulados ao longo de seus estágios de ciclo de vida . Para maior caracterização destas enzimas, elas foram expressas heterologamente na levedura Pichia pastoris como proteínas de fusão com cauda de 6 histidinas e as proteínas recombinantes foram purificadas por cromatografia de afinidade com resina de Ni-NTA. As ATPDases recombinantes foram obtidas de forma ativa e medições de atividade enzimática foram realizadas. ATPDase1 - mostrou atividades ATPásica e ADPásica em torno de 650 e 160 nmoles Pi.min -1. mg-1 , respectivamente. ATPDase2 teve atividades ATPásica e ADPásica na faixa de 1050 e 250 nmoles Pi.min-1.mg-1 , respectivamente. Adicionalmente, atividades UTPásica e UDPásica também foram encontradas nestas enzimas. Estudos de dicroísmo circular com estas duas enzimas elucidaram suas estruturas secundárias. Com isto, ATPDase1 (S66 to Q507 ) teve alfa-hélice (7 %), folha-beta (45 %) e estrutura randômica (48 %), e a ATPDase2 (N83 a K564 ) mostrou conter alfa-hélice (14 %), folha-beta (33 %) e estrutura randômica (53 %). Nós mostramos que a ATPDase2 é secretada pelo parasita no meio, de forma similar como descrito para as ATP-difosfohidrolases humanas CD39L2 e CD39L4. Adicionalmente, em ensaios de inibição de penetração (cercária em camundongo) usando anticorpo anti- ATPDase1 foi mostrada uma redução em 20 % da capacidade de penetração através da pele das cercárias previamente incubadas com o anti-soro. Devido a que a expressão do gene da ATPDase2 estava mais alta em miracídio e cercária, estágios que infectam caramujos e humanos, respectivamente, postulamos que ATPDase2 poderia ajudar no processo de invasão do parasita. No estágio ovo ambos os genes estão altamente expressados sugerindo um possível envolvimento das ATPDases na resposta de proteção contra o sistema imune humano. Ensaios de proteção contra S. mansoni em camundongos, usando as ATPDases 1 e 2 como antígenos, resultaram em uma baixa proteção obtendo-se não mais que 20% na redução da carga parasitária. / ATPDases or ATP-diphosphohydrolases are enzymes that cleave ATP and ADP to AMP and Pi and are involved in inhibition of platelet aggregation. In the parasite Schistosoma mansoni our group had identified and cloned the ATPDase1 gene and localized the protein on the tegument surface. Recently, we cloned the ATPDase2 gene using S. mansoni EST databank information and we immunolocalized it also in the tegument. ATPDase 2 was found on both the apical and basal tegument membranes together with ATPDase1, but only ATPDse2 was found in the syncytium space of the tegument. The presence of both enzymes on the tegumental outer surface suggests a major role in regulation of nucleotides abundance. Expression analysis of both genes was performed by Real Time RT- PCR using RNA from eggs, miracidia, cercariae, schistosomula and adult worms. The results showed that ATPDase1 gene was more expressed in eggs (7-fold), adults (6-fold), cercariae (3.5-fold) and schistosomula (1.5-fold) when compared to miracidia, which was taken as the reference. ATPDase2 gene was more expressed in eggs (16-fold), cercariae (11-fold), miracidia (7-fold) and adult worms (2-fold) when compared to schistosomula, showing that both genes are modulated along the life cycle stages. For further characterization of these enzymes, they were expressed heterologously in the yeast Pichia pastoris as fusion proteins with hexa-histidine tags and the recombinant proteins were purified by Ni-NTA affinity chromatography. The recombinant ATPDases were obtained in active form and activity measurements were performed. ATPDase1 did show ATPase and ADPase activities about 650 and 160 nmoles Pi.min-1.mg-1 , respectively. ATPDase2 had ATPase and ADPase activities in the range of 1050 and 250 nmoles Pi.min-1.mg-1 , respectively. These results were obtained in the presence of calcium as cofactor. Additionally, UTPase and UDPase activities were found for both enzymes. Circular dichroism studies with these enzymes elucidated their secondary structures; ATPDase1 (S66 to Q507 ) has alpha helix (7%), beta sheet (45%) and random coil (48%), whereas ATPDase2 (N83 a K564 ) showed alpha helix (14%), beta sheet (33%) and random coil (53%). We found that ATPDase2 was secreted by the parasite to the medium, similar to what has been described for human CD39-L2 and CD39-L4 ATP-diphosphohydrolases. Additionally, a penetration assay (cercaria to mice) using antibody anti-ATPDase1 did show a decrease of 20% in the penetration capacity through mice skin of cercaria previously incubated with this antiserum. Because ATPDase2 gene expression was increased in miracidia and cercariae, the stages that infect snail and human, respectively, we postulate that ATPDase2 may help the parasite\'s invasion process. In the egg stage both genes were highly expressed suggesting a possible involvement of the ATPDases in the protection response of eggs against the human immune system. Assays of protection against S. mansoni in mice, using recombinant ATPDase1 and 2 as antigens, resulted in low protection obtaining no more than 20% of parasite burden reduction.

O Complexo de pré-replicação em T.brucei é composto por Orc1/Cdc6 e as helicases MCMs. Em um trabalho anterior mostramos que TbOrc1/Cdc6 pode ligar e hidrolisar ATP in vitro. Neste sentido, o objetivo deste trabalho é avaliar a importância da hidrólise e ligação de ATP para a formação e estabilidade do complexo pré-replicação de T.brucei. Para tanto, foram geradas proteínas recombinantes Orc1/Cdc6 de T. brucei mutadas nas regiões Walker A (TbOrc1/Cdc6K79T) ou sensor 2 (TbOrc1/Cdc6R251,252E) incapazes de ligar ou hidrolisar ATP, respectivamente. Finalmente, as células expressando TbOrc1/Cdc6K79T ou TbOrc1/Cdc6R251,252E foram avaliadas quanto a (i ) estabilidade da interação Orc1/Cdc6 -DNA, (ii) capacidade de estabilizar MCM no DNA, (iii) capacidade de replicar seu DNA. A mutação na região sensor 2 de T.brucei (TbOrc1/Cdc6R251,252E) reduziu drasticamente a atividade de ATPase em comparação com a proteína selvagem . TbOrc1/Cdc6 mutado no sitio de ligação ao ATP perdeu a capacidade de interagir com o ATP (TbOrc1/Cdc6K79T). A super expressão desses genes inibiu de forma significativa a proliferação celular, causou ineficiência no carregamento de MCM para o DNA e ocasionou falhas na progressão do ciclo celular, atrasando a fase S. / The pre-replication complex in T.brucei is composed of at Orc1/Cdc6 and MCMs helicases. In a previous paper we showed that TbOrc1/Cdc6 can bind and hydrolyze ATP in vitro. Based on that, the objective of this study is to evaluate the importance of ATP binding and hydrolysis to the formation and stability of the pre - replication complex in T.brucei. For this purpose, T. brucei Orc1/Cdc6 recombinant proteins were generated mutated at regions on Walker A (TbOrc1/Cdc6K79T) and sensor 2 (TbOrc1/Cdc6R251 , 252E) in order to unable the ATP binding and hydrolyzation respectively . Finally , cells expressing TbOrc1/Cdc6K79T or TbOrc1/Cdc6R251 , 252E were evaluated for (i) stability of Orc1/Cdc6 - DNA interaction , (ii) ability to stabilize MCM in DNA , (iii) ability to replicate its DNA . The mutation in the sensor 2 region of T.brucei (TbOrc1/Cdc6R251 , 252E) drastically reduced the ATPase activity compared to the wild-type protein. TbOrc1/Cdc6 mutated in the ATP binding site has lost the ability to interact with ATP (TbOrc1/Cdc6K79T). The overexpression of these genes significantly inhibited cell proliferation causing inefficient loading of MCM DNA and led to failure in cell cycle progression by delaying the phase S.