abstract: The Heliobacterial reaction center (HbRC) is generally regarded as the most primitive photosynthetic reaction center (RC) known. Even if the HbRC is structurally and functionally simple compared to higher plants, the mechanisms of energy transduction preceding, inside the core, and from the RC are not totally established. Elucidating these structures and mechanisms are paramount to determining where the HbRC is in the grand scheme of RC evolution. In this work, the function and properties of the solubilized cyt c553, PetJ, were investigated, as well as the role HbRC localized menaquinone plays in light-induced electron transfer, and the interaction of the Nif-specific ferredoxin FdxB with reaction center particles devoid of bound FA/FB proteins. In chapter 2, I successfully express and purify a soluble version of PetJ that functions as a temperature dependent electron donor to P800+. Recombinant PetJ retains the spectroscopic characteristics of membrane-bound PetJ. The kinetics were characteristic of a bimolecular reaction with a second order rate of 1.53 x 104 M-1s-1 at room temperature and a calculated activation energy of 91 kJ/mol. In chapter 4, I use reverse phase high-performance liquid chromatography (HPLC) to detect the light-induced generation of Menaquinol-9 (MQH2) in isolated heliobacterial membranes. This process is dependent on laser power, pH, temperature, and can be modified by the presence of the artificial electron acceptor benzyl viologen (BV) and the inhibitors azoxystrobin and terbutryn. The addition of the bc complex inhibitor azoxystrobin decreases the ratio of MQ to MQH2. This indicates competition between the HbRC and the bc complex, and hints toward a truncated cyclic electron flow pathway. In chapter 5, the Nif-Specific ferredoxin FdxB was recombinantly expressed and shown to oxidize the terminal cofactor in the HbRC, FX-, in a concentration-dependent manner. This work indicates the HbRC may be able to reduce a wide variety of electron acceptors that may be involved in specific metabolic processes. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2015

abstract: The heliobacterial reaction center (HbRC) is widely considered the simplest and most primitive photosynthetic reaction center (RC) still in existence. Despite the simplicity of the HbRC, many aspects of the electron transfer mechanism remain unknown or under debate. Improving our understanding of the structure and function of the HbRC is important in determining its role in the evolution of photosynthetic RCs. In this work, the function and properties of the iron-sulfur cluster FX and quinones of the HbRC were investigated, as these are the characteristic terminal electron acceptors used by Type-I and Type-II RCs, respectively. In Chapter 3, I develop a system to directly detect quinone double reduction activity using reverse-phase high pressure liquid chromatography (RP-HPLC), showing that Photosystem I (PSI) can reduce PQ to PQH2. In Chapter 4, I use RP-HPLC to characterize the HbRC, showing a surprisingly small antenna size and confirming the presence of menaquinone (MQ) in the isolated HbRC. The terminal electron acceptor FX was characterized spectroscopically and electrochemically in Chapter 5. I used three new systems to reduce FX in the HbRC, using EPR to confirm a S=3/2 ground-state for the reduced cluster. The midpoint potential of FX determined through thin film voltammetry was -372 mV, showing the cluster is much less reducing than previously expected. In Chapter 7, I show light-driven reduction of menaquinone in heliobacterial membrane samples using only mild chemical reductants. Finally, I discuss the evolutionary implications of these findings in Chapter 7. / Dissertation/Thesis / M.S. Biochemistry 2012

A malária é uma das principais e a mais disseminada das parasitoses humanas. A falta de uma vacina eficaz e o problema da resistência aos fármacos tem contribuído para o adiamento da solução do controle desta infecção. A busca de novos alvos biológicos tem se concentrado, em parte, na compreensão de vias metabólicas. Em P. falciparum, identificamos a biossíntese das duas formas da vitamina K (filoquinona e menaquinona). Na via MEP foram caracterizadas duas importantes enzimas bifuncionais, a farnesil difosfato sintase/geranilgeranil difosfato sintase (FPPS/GGPPS) capaz de formar farnesil difosfato e geranilgeranil difosfato e octaprenil pirofosfato sintase/fitoeno sintase (OPP/PSY) responsável pela biossíntese da cadeia isoprênica que se liga ao anel da via de ubiquinona, como também forma o primeiro caroteno na via de carotenóides. Este projeto tem como objetivo caracterizar o gene MenA da biossíntese de MQ, determinar a localização de FPPS/GGPPS em P. falciparum e investigar a importância de OPP/PSY e de FPPS/GGPPS no ciclo intraeritrocítico de P. falciparum. / Malaria is one of the main widespread human parasites. The lack of an effective vaccine and the problem of drug resistance haves contributed to the delay of the control solution of this infection. The search for new biological targets has focused in part on the understanding of metabolic pathways. In P. falciparum, identified the biosynthesis of the two forms of vitamin K (phylloquinone and menaquinone). In the MEP pathway were characterized two important bifunctional enzyme, farnesyl diphosphate synthase/geranylgeranyl diphosphate synthase (FPPS/GGPPS) able to form farnesyl diphosphate and geranylgeranyl diphosphate and octaprenyl pyrophosphate synthase/phytoene synthase (OPP/PSY) responsible for the biosynthesis of isoprenic side chains attached to the benzoquinone ring of ubiquinones, but also forms the first carotene in the carotenoid pathway. This project aims to characterize the MenA gene from the MQ biosynthesis, determine the localization of FPPS/GGPPS and investigate the importance of OPP/PSY and FPPS/GGPPS in intra-erythrocytic cycle of P. falciparum.

A malária é uma das principais e a mais disseminada das parasitoses humanas. A falta de uma vacina eficaz e o problema da resistência aos fármacos tem contribuído para o adiamento da solução do controle desta infecção. A busca de novos alvos biológicos tem se concentrado, em parte, na compreensão de vias metabólicas. Em P. falciparum, identificamos a biossíntese das duas formas da vitamina K (filoquinona e menaquinona). Na via MEP foram caracterizadas duas importantes enzimas bifuncionais, a farnesil difosfato sintase/geranilgeranil difosfato sintase (FPPS/GGPPS) capaz de formar farnesil difosfato e geranilgeranil difosfato e octaprenil pirofosfato sintase/fitoeno sintase (OPP/PSY) responsável pela biossíntese da cadeia isoprênica que se liga ao anel da via de ubiquinona, como também forma o primeiro caroteno na via de carotenóides. Este projeto tem como objetivo caracterizar o gene MenA da biossíntese de MQ, determinar a localização de FPPS/GGPPS em P. falciparum e investigar a importância de OPP/PSY e de FPPS/GGPPS no ciclo intraeritrocítico de P. falciparum. / Malaria is one of the main widespread human parasites. The lack of an effective vaccine and the problem of drug resistance haves contributed to the delay of the control solution of this infection. The search for new biological targets has focused in part on the understanding of metabolic pathways. In P. falciparum, identified the biosynthesis of the two forms of vitamin K (phylloquinone and menaquinone). In the MEP pathway were characterized two important bifunctional enzyme, farnesyl diphosphate synthase/geranylgeranyl diphosphate synthase (FPPS/GGPPS) able to form farnesyl diphosphate and geranylgeranyl diphosphate and octaprenyl pyrophosphate synthase/phytoene synthase (OPP/PSY) responsible for the biosynthesis of isoprenic side chains attached to the benzoquinone ring of ubiquinones, but also forms the first carotene in the carotenoid pathway. This project aims to characterize the MenA gene from the MQ biosynthesis, determine the localization of FPPS/GGPPS and investigate the importance of OPP/PSY and FPPS/GGPPS in intra-erythrocytic cycle of P. falciparum.

In 1998 the genome sequence of Mycobacterium tuberculosis H37Rv was published1. M. tuberculosis is the primary causative agent of tuberculosis, a disease with a long history in humans, which still has a great impact on human mortality today. As part of the M. tuberculosis Structural Genomics Consortium we selected nine target genes (Rv0534c (menA); Rv0548c (menB); Rv0553 (menC); Rv0555 (menD); Rv0542c (menE); Rv3853 (menG); Rv0558 (ubiE); Rv0989c (grcC2) and Rv0990c) from M. tuberculosis, including all known members of the menaquinone biosynthesis pathway, for structural studies. All nine genes were taken through the structural genomics “pipeline”, either becoming stuck at various “bottlenecks” or continuing successfully to structure solution. At the initial bioinformatics analysis step, eight of the nine targeted genes were deemed suitable for further study. PCR amplification and cloning of these genes into several different expression vectors followed. Expression of the gene products for the seven successfully cloned genes was undertaken in an E. coli expression host, followed by experiments (refolding, lysis buffer and expression temperature screens) aimed at obtaining soluble protein in sufficient quantities for crystallisation. Of the seven proteins successfully overexpressed, five remain at this stage as they could not be obtained in soluble form. The remaining two, Rv3853 (MenG), solubilised by refolding, and MenB, solubilised by 24ºC expression, were purified and both successfully produced diffracting crystals. The crystal structure of Rv3853 was determined by isomorphous replacement (SIRAS) and refined at 1.9 Å resolution (R = 19.0% and Rfree = 22.0%). The structure of several different crystal forms of MenB, were determined by molecular replacement. Refinement of two of these structures, MenB_P43212 at 2.15Å resolution (R = 20.3% and Rfree = 23.1%) and MenB_C2-NCoA at 2.3 Å resolution (R = 19.7% and Rfree = 22.5%), has been completed. The structure of Rv3853, combined with the discovery that UbiE was more likely to catalyse the final, S-adenosylmethionine-dependent, methyltransfer step of menaquinone biosynthesis, led to the conclusion that Rv3853 had been misannotated as MenG. Combined with further bioinformatics analysis the Rv3853 structure has been useful in providing new ideas as to the real function of Rv3853. In contrast, the structure of MenB confirmed its place as a member of the crotonase superfamily although the C-terminus was located in a position not observed in other crotonase superfamily structures. Several flexible regions likely to be important in MenB function have been identified by examination of the various MenB structures / Author was the recipient of a University of Auckland Doctoral Scholarship and a Foundation of Research Science & Technology Top Achiever Doctoral Scholarship

In 1998 the genome sequence of Mycobacterium tuberculosis H37Rv was published1. M. tuberculosis is the primary causative agent of tuberculosis, a disease with a long history in humans, which still has a great impact on human mortality today. As part of the M. tuberculosis Structural Genomics Consortium we selected nine target genes (Rv0534c (menA); Rv0548c (menB); Rv0553 (menC); Rv0555 (menD); Rv0542c (menE); Rv3853 (menG); Rv0558 (ubiE); Rv0989c (grcC2) and Rv0990c) from M. tuberculosis, including all known members of the menaquinone biosynthesis pathway, for structural studies. All nine genes were taken through the structural genomics “pipeline”, either becoming stuck at various “bottlenecks” or continuing successfully to structure solution. At the initial bioinformatics analysis step, eight of the nine targeted genes were deemed suitable for further study. PCR amplification and cloning of these genes into several different expression vectors followed. Expression of the gene products for the seven successfully cloned genes was undertaken in an E. coli expression host, followed by experiments (refolding, lysis buffer and expression temperature screens) aimed at obtaining soluble protein in sufficient quantities for crystallisation. Of the seven proteins successfully overexpressed, five remain at this stage as they could not be obtained in soluble form. The remaining two, Rv3853 (MenG), solubilised by refolding, and MenB, solubilised by 24ºC expression, were purified and both successfully produced diffracting crystals. The crystal structure of Rv3853 was determined by isomorphous replacement (SIRAS) and refined at 1.9 Å resolution (R = 19.0% and Rfree = 22.0%). The structure of several different crystal forms of MenB, were determined by molecular replacement. Refinement of two of these structures, MenB_P43212 at 2.15Å resolution (R = 20.3% and Rfree = 23.1%) and MenB_C2-NCoA at 2.3 Å resolution (R = 19.7% and Rfree = 22.5%), has been completed. The structure of Rv3853, combined with the discovery that UbiE was more likely to catalyse the final, S-adenosylmethionine-dependent, methyltransfer step of menaquinone biosynthesis, led to the conclusion that Rv3853 had been misannotated as MenG. Combined with further bioinformatics analysis the Rv3853 structure has been useful in providing new ideas as to the real function of Rv3853. In contrast, the structure of MenB confirmed its place as a member of the crotonase superfamily although the C-terminus was located in a position not observed in other crotonase superfamily structures. Several flexible regions likely to be important in MenB function have been identified by examination of the various MenB structures / Author was the recipient of a University of Auckland Doctoral Scholarship and a Foundation of Research Science & Technology Top Achiever Doctoral Scholarship

In 1998 the genome sequence of Mycobacterium tuberculosis H37Rv was published1. M. tuberculosis is the primary causative agent of tuberculosis, a disease with a long history in humans, which still has a great impact on human mortality today. As part of the M. tuberculosis Structural Genomics Consortium we selected nine target genes (Rv0534c (menA); Rv0548c (menB); Rv0553 (menC); Rv0555 (menD); Rv0542c (menE); Rv3853 (menG); Rv0558 (ubiE); Rv0989c (grcC2) and Rv0990c) from M. tuberculosis, including all known members of the menaquinone biosynthesis pathway, for structural studies. All nine genes were taken through the structural genomics “pipeline”, either becoming stuck at various “bottlenecks” or continuing successfully to structure solution. At the initial bioinformatics analysis step, eight of the nine targeted genes were deemed suitable for further study. PCR amplification and cloning of these genes into several different expression vectors followed. Expression of the gene products for the seven successfully cloned genes was undertaken in an E. coli expression host, followed by experiments (refolding, lysis buffer and expression temperature screens) aimed at obtaining soluble protein in sufficient quantities for crystallisation. Of the seven proteins successfully overexpressed, five remain at this stage as they could not be obtained in soluble form. The remaining two, Rv3853 (MenG), solubilised by refolding, and MenB, solubilised by 24ºC expression, were purified and both successfully produced diffracting crystals. The crystal structure of Rv3853 was determined by isomorphous replacement (SIRAS) and refined at 1.9 Å resolution (R = 19.0% and Rfree = 22.0%). The structure of several different crystal forms of MenB, were determined by molecular replacement. Refinement of two of these structures, MenB_P43212 at 2.15Å resolution (R = 20.3% and Rfree = 23.1%) and MenB_C2-NCoA at 2.3 Å resolution (R = 19.7% and Rfree = 22.5%), has been completed. The structure of Rv3853, combined with the discovery that UbiE was more likely to catalyse the final, S-adenosylmethionine-dependent, methyltransfer step of menaquinone biosynthesis, led to the conclusion that Rv3853 had been misannotated as MenG. Combined with further bioinformatics analysis the Rv3853 structure has been useful in providing new ideas as to the real function of Rv3853. In contrast, the structure of MenB confirmed its place as a member of the crotonase superfamily although the C-terminus was located in a position not observed in other crotonase superfamily structures. Several flexible regions likely to be important in MenB function have been identified by examination of the various MenB structures / Author was the recipient of a University of Auckland Doctoral Scholarship and a Foundation of Research Science & Technology Top Achiever Doctoral Scholarship

In 1998 the genome sequence of Mycobacterium tuberculosis H37Rv was published1. M. tuberculosis is the primary causative agent of tuberculosis, a disease with a long history in humans, which still has a great impact on human mortality today. As part of the M. tuberculosis Structural Genomics Consortium we selected nine target genes (Rv0534c (menA); Rv0548c (menB); Rv0553 (menC); Rv0555 (menD); Rv0542c (menE); Rv3853 (menG); Rv0558 (ubiE); Rv0989c (grcC2) and Rv0990c) from M. tuberculosis, including all known members of the menaquinone biosynthesis pathway, for structural studies. All nine genes were taken through the structural genomics “pipeline”, either becoming stuck at various “bottlenecks” or continuing successfully to structure solution. At the initial bioinformatics analysis step, eight of the nine targeted genes were deemed suitable for further study. PCR amplification and cloning of these genes into several different expression vectors followed. Expression of the gene products for the seven successfully cloned genes was undertaken in an E. coli expression host, followed by experiments (refolding, lysis buffer and expression temperature screens) aimed at obtaining soluble protein in sufficient quantities for crystallisation. Of the seven proteins successfully overexpressed, five remain at this stage as they could not be obtained in soluble form. The remaining two, Rv3853 (MenG), solubilised by refolding, and MenB, solubilised by 24ºC expression, were purified and both successfully produced diffracting crystals. The crystal structure of Rv3853 was determined by isomorphous replacement (SIRAS) and refined at 1.9 Å resolution (R = 19.0% and Rfree = 22.0%). The structure of several different crystal forms of MenB, were determined by molecular replacement. Refinement of two of these structures, MenB_P43212 at 2.15Å resolution (R = 20.3% and Rfree = 23.1%) and MenB_C2-NCoA at 2.3 Å resolution (R = 19.7% and Rfree = 22.5%), has been completed. The structure of Rv3853, combined with the discovery that UbiE was more likely to catalyse the final, S-adenosylmethionine-dependent, methyltransfer step of menaquinone biosynthesis, led to the conclusion that Rv3853 had been misannotated as MenG. Combined with further bioinformatics analysis the Rv3853 structure has been useful in providing new ideas as to the real function of Rv3853. In contrast, the structure of MenB confirmed its place as a member of the crotonase superfamily although the C-terminus was located in a position not observed in other crotonase superfamily structures. Several flexible regions likely to be important in MenB function have been identified by examination of the various MenB structures / Author was the recipient of a University of Auckland Doctoral Scholarship and a Foundation of Research Science & Technology Top Achiever Doctoral Scholarship

Vitamin K belongs to the family of fat-soluble vitamins, which is not determinated in clinical laboratories. It is a cofactor necessary for posttranslational γ-carboxylation of glutamyl residues in selected proteins such as the osteocalcin, and procoagulation factors II, VII, IX, X. Vitamin K deficient individuals appear to have more undercarboxylated proteins, which are functionally defective. Lack of this vitamin has been associated with risk of developing osteoporosis and cardiovascular diseases. The aim of this work was to develop and validate the HPLC method and the LC-MS/MS method for determination of three vitamin K's forms - vitamin K1, MK-4 and MK-7 in serum. After successful validation of both methods, patient samples and healthy population samples were measured. There were measured 350 patient samples by HPLC method. These samples were divided into two groups - patients with diagnostic of osteoporosis and patients without osteoporosis. We measured 946 samples by LC-MS/MS method. Samples were divided into groups: patients with osteoporosis, patients without osteoporosis, healthy population, patients with osteopenia and patients with cystic fibrosis. The reference range of vitamin K in healthy population was obtained by LC-MS/MS method. The next aim was to compare the effectiveness of...

La vitamine K permet l’activation biologique de 14 protéines identifiées à ce jour et qualifiées de vitamines K dépendantes (PVKD). Un recyclage très efficient de la vitamine K par l’enzyme VKORC1 permet d’en limiter grandement les besoins nutritionnels. Chez certaines personnes, une subcarence pourrait exister et contribuer au développement de calcifications de la média des parois vasculaires et augmenter ainsi le facteur de risque cardio-vasculaire. Ce type de calcification est retrouvé chez les personnes hémodialysées, présentant un diabète ou tout simplement au cours du vieillissement. Le lien entre cette subcarence et les calcifications vasculaires est difficilement étudiable chez l’Homme du fait d’une évolution lente et d’effets pouvant être masqués par d’autres facteurs environnementaux. Pour pouvoir étudier directement ce phénomène, un modèle murin a été développé et caractérisé. Les rats développés dans de ce modèle ont des besoins fortement augmentés en vitamine K du fait d’un recyclage fortement altéré. Après 12 semaines d’administration déficient en vitamine K, les rats mâles présentaient des calcifications vasculaires médiales importantes de l’aorte, des poumons, des testicules et du cœur. La coagulation est maintenue bien qu’une diminution de l’activité des facteurs de la coagulation vitamine K dépendants soit observée. La matrix-gla-protéine tissulaire ainsi que l’ostéocalcine plasmatique sont retrouvées accumulées sous leur forme inactive. Dans le même temps, la concentration en vitamine K tissulaire est très fortement diminuée. Ces résultats ne sont pas observés chez les rats non mutés subcarencés ni chez les rats mutés non-subcarencé. Ce travail permet pour la première fois de montrer l’existence d’un lien fort entre subcarence en vitamine K et calcifications vasculaires. Ce modèle de subcarence pourrait servir à une meilleure compréhension du rôle des différentes PVKD extra-hépatiques. Il constitue également un modèle de choix pour l’étude des calcifications médiales et de leurs évolutions / Vitamin K allows the biological activation of 14 proteins identified to date and called K-dependent vitamins (PVKD). A highly efficient recycling of vitamin K by the enzyme VKORC1 greatly limits the nutritional requirements. In some people, subcarence may exist and contribute to the development of vascular wall medial calcification and thus increase the cardiovascular risk factor. This type of calcification is found in people with hemodialysis, diabetes or simply during aging. The link between this subcarence and vascular calcification is difficult to study in humans because of a slow evolution and effects that can be masked by other environmental factors. To study this phenomenon directly, a murine model has been developed and characterized. The rats developed in this model have a greatly increased need for vitamin K because of a highly altered recycling. After 12 weeks of vitamin K deficiency, male rats had significant medial vascular calcification of the aorta, lungs, testes and heart. Coagulation is maintained although a decrease in activity of vitamin K-dependent coagulation factors is observed. Matrix-gla-tissue protein as well as plasma osteocalcin are found accumulated in their inactive form. At the same time, the concentration of tissue vitamin K is greatly reduced. These results are not observed in the non-mutated subcarenated rats nor in the non-subcarated mutated rats. This work allows for the first time to show the existence of a strong link between vitamin K subcarence and vascular calcifications. This subcarency model could be used to better understand the role of the different extrahepatic PVKDs. It is also a model of choice for the study of medial calcifications and their evolution