This is an investigation into alcohol dehydrogenases (ADHs) from Geobacillus thermoglucosidasius. Eighteen ADHs have been studied, with seven taken for closer inspection. Characterisation was carried out to determine the industrial significance of these enzymes, starting with the substrate scope of the ADHs. The key results obtained are as follows: ADH A is the alcohol dehydrogenase domain of the bifunctional ADHE enzyme (Extance, 2012; Extance et al., 2013). It has been determined that the substrate scope, whilst restricted to linear aliphatic aldehydes, extends at least to dodecanal. Also, with a specificity constant of 167 mM-1 min-1 it appears that ADH A could prefer butanal to shorter-chain aldehydes such as ethanal and propanal with specificity constants of 38 mM-1 min-1 and 35 mM-1 min-1, respectively. Thus ADH A may have a preference for longer aldehydes than previously believed due to its native role in the production of ethanol from acetyl-coA. ADH B was previously investigated for its potential role in the production of butanol. Here it was confirmed as an NADH-dependent ADH, with a substrate scope limited to five carbon length substrates and smaller, with residual activity with C6 substrates. ADH B demonstrated activity with ethyl 4-chloroacetoacetate, an intermediate in the production of statins. Further, an estimated half-life whilst stored at 4°C of 770 days; retention of 86% activity with 10vol% ethyl acetate and 92% activity with 10vol% acetonitrile; and a specific activity of 27 U mg-1 with 3M 2-butanone are all indications that ADH B is a potentially useful enzyme for industry. The last enzyme to be previously investigated was ADH C, which in this work was confirmed to be an acetoin reductase with a very small substrate scope exclusively based around the acetoin motif, and therefore no further work was conducted. ADH D and ADH F both have broad substrate scopes including the industrially-relevant substrates, 5-norbornene-2-carboxaldehyde, 1-phenyl-1,2-propanedione, ethyl 4-chloroacetoacetate and ethyl-2-oxo-4-phenylbutyrate. ADH D is an NADPH-dependent enzyme whereas ADH F can utilise both NADH and NADPH. Both enzymes are annotated as aldo-keto reductases, which is further indicated by multiple sequence alignment with the most similar available protein sequences and crystal structures. Thus, these two enzymes are the first aldo-keto reductases to be examined from moderate thermophiles, and are tentatively assigned in the AKR family as AKR6D1 and AKR5G4 respectively. ADH D has a very low KM (≤0.1 μM) with NADPH, giving a specificity constant of 2,800,000 mM-1 min-1, substantially higher than any other noted. ADH D showed >80% activity from pH 5.0 - 8.0. The enzyme was resistant to solvents DMSO (at 5 vol%) and ethyl acetate, acetonitrile and cyclopentyl methyl ether (at 20vol%). ADH F had the broadest substrate scope of any ADH tested, with 1-phenyl-1,2-propanedione the most preferred substrate with a KM of 0.010 mM and a specificity constant of 54,000 mM-1 min-1. It greatly preferred sodium phosphate at pH 7.0, as almost any deviation resulted in a substantial loss of activity. Activity of ≥70% was recorded in 5vol% DMSO, ethyl acetate, acetonitrile, cyclopentyl methyl ether and 50vol% hexane . Both ADH D and F have optimal activities at 70 °C and both may have application in the biotechnology industry for the production of pharmaceutical intermediates and other high value chemicals. ADH E acts solely as an aldehyde reductase, with Vmax using NADH of 74, 331, 320 and 281 U mg-1 for methanal, ethanal, propanal and butanal, respectively. Activity with NADPH was limited (< 1% compared with NADH). Activity was also noted with higher aldehydes such as octanal and furfural. ADH G is an NADPH-dependent ADH utilizing aldehydes only. It has an optimal temperature of 60°C with a half-life of under two hours at that temperature. In conclusion, this thesis reports a feasibility study into the potential industrial use of specific enzymes for a variety of purposes ranging from the production of pharmaceutical intermediates to bioremediation. ADHs D and F are most likely to have use in the biotechnology industry, and ADHs B and E may be suitable for cofactor regeneration. ADH E may additionally be useful in the bioremediation industry. In addition, the anticipated biological significance of these enzymes is described.

O nitrato é uma das principais fontes de nitrogênio disponível para as plantas, sendo a nitrato redutase (NR) a enzima responsável pela sua redução a nitrito. O nitrito é considerado tóxico em altas concentrações e, por esse motivo, a atividade da NR possui uma regulação complexa, principalmente em nível transcricional e pós-traducional. Trabalhos anteriores do nosso grupo, utilizando plantas de abacaxizeiro cultivadas in vitro, demonstraram que, em condições de termoperíodo de 28ºC dia/15ºC noite, as raízes apresentaram um estímulo positivo de atividade da NR na ausência de luz quando comparado às plantas crescidas em temperatura constante de 28ºC, associado posteriormente à atividade da NR de membrana plasmática (NRPM). Baseado nesses resultados questionou-se qual seria a influência da aplicação do estímulo de frio associado ou não à presença de luz na atividade da NR em folhas e raízes de abacaxizeiro. Este trabalho teve como objetivos investigar os efeitos do frio na atividade da NR em folhas e raízes de abacaxizeiro em diferentes tempos de exposição, na presença ou ausência da luz e em diferentes fases do ciclo de 24 horas (claro/escuro). Buscou-se averiguar qual NR estaria envolvida nessas respostas: a NR citossólica (NRc) ou de membrana plasmática (NRPM), assim como verificar o envolvimento do NO na sinalização pela baixa temperatura. O ritmo diário de atividade da NR também foi avaliado, logo após a exposição ao frio, em diferentes fases do ciclo de claro/escuro. As plantas foram expostas a 1, 3, 6 ou 9 horas a 10ºC ou 25ºC (controle) na luz ou no escuro. A NR foi avaliada pelo método in vitro. O estímulo positivo na atividade da NR pelo frio ocorreu principalmente após 6 horas no claro, para as folhas, e após 6 horas no escuro, para as raízes. Novas plantas foram submetidas às mesmas condições para o fracionamento celular, mostrando que, tanto em folhas como em raízes, o incremento de atividade da NR observado a 10ºC foi associado à NR citossólica (NRc). Em ambos os casos, o estímulo ocorreu utilizando-se o NADPH como doador de elétrons, sugerindo o possível envolvimento de uma isoforma NAD(P)H biespecífica. A quantificação do NO foi realizada por leitura em espectrofluorímetro, apontando uma maior emissão induzida pelo frio para as folhas tanto na presença da luz (após 1 e 3 horas) como em sua ausência (1 e 9 horas) e em raízes apenas no escuro (9 horas), sugerindo o envolvimento do NO na sinalização da baixa temperatura. Para verificar a influência do frio em diferentes fases do dia, 4 horários foram selecionados (início da fase clara, meio da fase clara, início da fase escura, meio da fase escura) para início de cada experimento. A NR foi medida logo após a exposição ao frio (6 horas a 10ºC), pelo método in vitro e durante 24 horas em reaquecimento (25ºC), quantificada a cada 3 horas pelo método in vivo. As raízes apresentaram aumento da atividade da NR apenas quando o estímulo da baixa temperatura foi aplicado na fase escura, enquanto as folhas sofreram incremento da atividade da NR independente da condição luminosa. Em reaquecimento, a NR das folhas teve seu ritmo atrasado em todas as situações, com exceção quando o frio foi aplicado no início da fase escura, na qual houve perda quase completa de variação ao longo do dia. As raízes não mostraram grandes alterações no ritmo diário da NR. Este trabalho mostrou que a temperatura de 10ºC tem efeitos diferentes sobre folhas e raízes, sendo que as modificações na atividade da NR, em curto prazo, parecem ocorrer por alterações na NRc. O NO parece estar envolvido na sinalização do frio, mas não se determinou sua origem biossintética. As raízes tiveram um aumento da atividade da NR pela baixa temperatura, que foi dependente do escuro, enquanto as respostas das folhas dependeram da fase do ciclo na qual foram submetidas a 10ºC / Nitrate is the main nitrogen source available to plants, and nitrate reductase (NR) is the enzyme responsible for its reduction to nitrite. Because of its toxicity in high concentrations, nitrite production by NR has a complex regulation, especially at transcriptional and post-translational level. A previous work from our group, using pineapple plants cultivated in vitro, showed that, under thermoperiod of 28ºC day/15ºC night, NR activity increased in roots during absence of light compared to activity in plants grown under constant temperature of 28ºC. Based on these results it was questioned what would be the effect of cold stimulus application with or without light on NR activity in leaves and roots of pineapple plants. This study aimed to investigate the effects of low temperature on NR activity in leaves and roots of pineapple plants at different exposure times in the presence or absence of light and at different phases of a 24 hour cycle (light/darkness). We also investigated which NR was involved in these responses: cytosolic (cNR) or plasma membrane NR (PMNR), as well as verifying the role of nitric oxide (NO) signaling at low temperature. Furthermore, the NR daily rhythm activity was measured after cold exposure, in different phases of the light/dark cycle. Plants were exposed to 10ºC or 25ºC (control group) during 1, 3, 6 or 9 hours. NR was quantified by in vitro method. In the leaves, the increase of NR activity by low temperature (10ºC) occurred mainly after 6 hours in the presence of light, while in the roots the highest NR activity occurred after 6 hours at 10ºC in darkness. Based on these results, other groups of plants were subjected to the same conditions for cell partitioning, showing that in both leaves and roots the increase of NR activity by cold was associated with cytosolic NR (NRc). In both cases, the positive stimulation occurred with NADPH as the electron donor, suggesting the possible involvement of a NAD(P)H bispecific isoform. NO quantification, measured by spectrofluorimetry, indicated a greater emission induced by cold in the leaves both in the presence (after 1 and 3 hours) and absence (1 and 9 hours) of light and in roots only in darkness (9 hours), suggesting an involvement of NO in low temperature signaling. To evaluate the influence of cold at different day phases, we performed 4 experiments beginning at different times of the 24-hour cycle (beginning of light phase, middle of light phase, beginning of dark phase, middle of dark phase). NR activity was measured immediately after cold exposure (6 hours at 10°C) by in vitro method and after rewarming at 25°C during 24 hours, quantified by in vivo method every 3 hours. In roots, NR activity showed an increase only when the cold stimulus was applied at dark phase, while in leaves, NR was independent of the light condition. Upon rewarming, leaves presented a delay in NR daily behavior in all situations, except when low temperature was applied at the beginning of dark phase, showing almost no variation throughout the day. This study demonstrated that the temperature of 10ºC affected leaves and roots differently, and the changes in NR activity after short exposure time could be associated with NRc. NO seemed to be involved in cold signaling, but its biosynthetic origin has not been determined yet. Roots showed an increment of NR activity by low temperature dependent of the dark condition, while the responses of leaves depended on the phase of the 24-hour cycle in which they were subjected to 10ºC

Chiral amine motifs are found in many bioactive compounds and therefore strategies for their direct asymmetric synthesis are of great interest. Alongside traditional chemical methods, biocatalysis serves as an important tool for the formation of these compounds that can confer the benefits of sustainable catalyst supply and mild reaction conditions. This thesis describes the application of imine reductase (IRED) biocatalysts for the asymmetric reduction of pre-formed imines and the reductive amination of carbonyl compounds to produce chiral amines. These enzymes are relatively recent additions to the toolbox of biocatalysts for chiral amine synthesis and therefore their scope and application is still very much being explored. The research carried out as part of this PhD is presented as a series of manuscripts that have either been published or are planned for submission to peer-reviewed journals. The choice of presenting this thesis in journal format was made because a considerable body of the candidate's PhD research has been published, with the rest planned for publication in the near future. Furthermore, the compiled review articles and research papers lend themselves to a clear thesis narrative and, combined, have taken considerable time and effort to prepare, equal to that of a traditional thesis format. The contents are organised as follows: Chapter 1: an introduction to biocatalysis and its impact on sustainable chemical manufacturing; Chapter 2: a review assessing the current state of the art in imine reductase biocatalysts; Chapter 3: a perspective on the design and implementation of biocatalytic cascades; Chapter 4: a research article on the application of IREDs in a biocatalytic cascade for the synthesis of chiral piperidine and pyrrolidine frameworks; Chapter 5: aims of the PhD project; Chapter 6: a research article on the discovery and investigation of a reductive aminase (RedAm) found within the IRED family; Chapter 7: a research article on the screening of a diverse set of novel IREDs for their ability to facilitate reductive amination; Chapter 8: a research article on the synthesis of complex bulky dibenz[c,e]azepine compounds using IRED and transaminase biocatalysts; Chapter 9: a summary and outlook; Chapter 10: manuscript supporting information further detailing experimental work; Appendix: list of other publications resulting from this doctoral research.

Sufficient and balanced pools of deoxyribonucleotide triphophates (dNTPs) is crucial for high-fidelity DNA replication as well as correct DNA repair. The enzyme RiboNucleotide Reductase (RNR) catalyses NDP to dNDP and is therefore an essential enzyme by providing the “building blocks” to the cells. dNTPs production needs to be tightly regulated in order to minimize mutation frequencies and prevent genome instability. RNR in S. pombe is composed of two proteins, Cdc22R1 and Suc22R2, and has been described as a heterotetramer with a dimer of each subunit: the big subunit Cdc22R1 and the small subunit Suc22R2. S. pombe also posseses an RNR inhibitor: Spd1, as well as a second RNR regulator Spd2 which has been newly discovered. Spd1 has been demonstrated to inhibit RNR and to regulate its activity throughout the cell cycle. The detailed mechanism of the RNR regulation during the cell cycle or after DNA damage is not entirely clear, as are the means of inhibition by Spd1. In order to shed some light on the RNR complex and its regulation, we used various microscopybased methods to study RNR in vivo as well as in vitro. The data of this thesis suggest there are different forms of active RNR heterocomplexes, found throughout the cell cycle in the cytoplasm as well as in the nucleus. We propose that the precise stoichiometry of subunits in the complexes may vary, or that the complex conformation may be modified in an Spd1-dependent manner. In addition, treatment of the cells with a UV mimetic agent, 4NQO, seems to promote RNR regulation in an Spd1-dependent manner. On the contrary, inhibition of RNR by HydroxyUrea (HU) affects the RNR in a possible structure-related manner, independently of Spd1 or Spd2. The in vivo observations correlate with structural and/or oligomerization modifications of the RNR, representing a novel RNR regulation in S. pombe.

No ambiente aquático a maior fonte de nitrogênio encontra-se na forma de nitrato que necessita sofrer uma redução para formação de compostos biologicamente aproveitáveis, tais como aminoácidos, bases nitrogenadas e compostos nitrogenados. A assimilação de nitrogênio é um processo que ocorre em duas etapas catalisadas seqüencialmente pelas enzimas nitrato redutase (NR) e nitrito redutase (NiR). A NR catalisa a redução do nitrato a nitrito (etapa considerada limitante na assimilação de nitrogênio), sendo este posteriormente reduzido a amônio pela NiR. NR está amplamente distribuída e encontrada em diferentes organismos, incluíndo bactérias, fungos, cianobactérias, plantas terrestres e algas. Neste trabalho estudamos a NR de Microcystis aeruginosa que é uma cianobactéria tóxica de água doce encontrada principalmente em reservatórios de água. A toxina microcistina quando liberada por esta microalga está associada com problemas de saúde em humanos e animais. Foi mostrado que a NR de M. aeruginosa pertence a classe das NRs biespecíficas para NADH e NADPH. Apresenta constante de Michaelis-Menten aparente (Km) de 1,5 e 1,6 mM para NADPH e NADH, respectivamente. Ainda, Km aparente para nitrato foi estimado em 0,6 mM. As condições ótimas de ensaio encontradas foram em pH 10,0 e temperatura em 40ºC. A exposição da M. aeruginosa ao herbicida oxifluorfeno (10 &#181;g/L) promoveu a inibição de NiR, possibilitando a quantificação de &#8226;NO formado via NR, enzima que teve sua atividade 6 vezes maior durante a exposição a este agente. O estudo da enzima NR é de fundamental importância para a compreensão da regulação da expressão de enzimas assimiladoras de nitrogênio bem como dos mecanismos de nutrição e crescimento desta microalga. / Nitrate is the major source of nitrogen in the aquatic environment, which must be reduced before incorporation into biological compounds, such as amino acids, nitrogen bases and nitrogen compounds. The nitrogen assimilation process occurs in a two-step reaction catalyzed by 2 enzymes working sequentially, nitrate reductase (NR) and nitrite reductase (NiR). The NR catalyzes the reduction of nitrate to nitrite (is considered the limiting step in the nitrogen assimilation) being this later reduced to ammonium by NiR. NR is widely distributed and found in different organisms, including bacterium, fungus, cyanobacterium, plants and algae. In this work we study the NR of Microcystis aeruginosa, a toxic microalga, mainly found in water reservoirs. The microcystin toxin released by M. aeruginosa is associated with problems of health in humans and animals. We report that NR of M. aeruginosa belongs to a biespecific group of NRs for NADH and NADPH. It presents Michaelis-Menten\'s constant (Km) as 1.5 and 1.6 mM for NADPH and NADH, respectively. The apparent Km for nitrate was estimated as 0.6 mM. The optimum conditions of assay found were at pH 10.0 and temperature of 40ºC. The exposition of M. aeruginosa to the herbicide oxyfluorfen (10 &#181;g/L) promotes the inhibition of NiR, and it makes possible to quantify the &#8226;NO produced by NR, whose has it activity 6 hold higher during the agent exposition. In order to understand the regulation of nitrogen assimilation enzymes, as well as, the mechanisms of nutrition and growth of this algae, the study of the NR enzyme is of crucial importance.

Die Zahl der Tuberkuloseerkrankungen ist in den letzten Jahrzehnten weltweit gestiegen. Da es an innovativen Antituberkulotika mangelt, werden nach wie vor Medikamente der ersten Generation eingesetzt. Das wachsende Problem sind multi-resistente und extrem-resistente Bakterienstämme, die kaum oder gar nicht auf die medikamentöse Therapie ansprechen. Charakteristisch für M. tuberculosis ist eine dicke Zellwand. Der Aufbau der Zellwand ermöglicht es dem Bakterium in den Makrophagen zu persistieren und sich dort zu vermehren. Die Zellwand ist reich an Mykolsäuren und so wenig durchlässig für Fremdstoffe. Das mykobakterielle Zellwandskelett kann man in zwei Teile unterteilen, den Zellwandkern und die äußere Lipidhülle. Die freien Lipide der äußeren Lipidhülle dienen als Signalmoleküle im Krankheitsverlauf und interkalieren mit den Mykolsäuren des Zellwandkerns. M. tuberculosis besitzt für die Fettsäurebiosynthese zwei Enzymkomplexe: Die Typ-I-Fettsäuresynthase, die auch in Säugetieren zu finden ist, produziert Fettsäuren von C16- bis C26-Kettenlänge, die dann in der Typ-II-Fettsäuresynthase (FAS-II) zu Meromykolsäuren verlängert werden. Im Synthesezyklus des FAS-II sind mehrere monofunktionale Enzyme hintereinander geschaltet. Wird eines dieser Enzyme in seiner Funktion gestört, kumulieren Zwischenprodukte und benötigte Zellwandlipide können nicht synthetisiert werden. In der Folge wird die Zellwand instabil und das Bakterium stirbt. Die mykobakterielle Lipidbiosynthese ist somit ein ideales Target für die Entwicklung neuer Antituberkulotika. Ziel dieser Arbeit war es, eine neue Inhibitorklasse des FAS-II Enzyms InhA des M. tuberculosis mittels virtuellem Screening zu finden. Für das virtuelle Screening wurden drei aufeinander aufbauende Pharmakophorhypothesen entwickelt und mit diesen zwei unabhängige Datenbanken durchsucht. Als Grundlage für die Berechnungen des virtuellen Screenings diente die PDB Röntgenkristallstruktur 2h7m mit dem Liganden 1-Cyclohexyl-N-(3,5-dichlorophenyl)-5-oxopyrrolidin-3-carboxamid. Für die Erstellung der Pharmakophorhypothesen wurden zuerst die Strukturen des Enzyms mit und ohne Ligand bezüglich ihrer Konformationsunterschiede vor allem im Bereich der Bindetasche analysiert. Als nächstes wurden die Wechselwirkungen des Liganden mit den Aminosäuren der Bindetasche und dem Cofaktor näher analysiert und die verschiedenen Wechselwirkungsarten hinsichtlich ihrer Relevanz für eine inhibitorische Aktivität beurteilt. Schließlich wurde eine Bindetaschenanalyse durchgeführt und Hotspots für unterschiedliche chemische Funktionalitäten berechnet. Für das Datenbankenscreening wurden das ZINC 'drug-like' Subset (2005) und CCGs MOE 2006 Vendor Compound 3D Collection verwendet, beides Datenbanken exklusiv kommerziell erhältlicher Verbindungen. Das ZINC 'drug-like' Subset wurde über einen für InhA individuell angepassten hierarchischen Filter numerisch reduziert. Von den verbleibenden Verbindungen wurde eine Konformerendatenbank berechnet. Die MOE 2006 Vendor Compound 3D Collection lag bereits als Konformerendatenbank vor und wurde für das Screening 'as-is' verwendet. Mit den Pharmakophorhypothesen I und II wurde das reduzierte ZINC 'drug-like' Subset gescreent. Für die Treffer wurden Fingerprints berechnet, sie danach mithilfe des Tanimotokoeffizienten nach ihrer Ähnlichkeit in Cluster eingeteilt und visuell analysiert; 149 Verbindungen wurden für die Dockingsimulationen ausgewählt. Die MOE Konformerendatenbank wurde ebenso über einen für InhA individuell angepassten hierarchischen Filter numerisch reduziert und mit der Pharmakophorhypothese III gescreent, 28 Verbindungen wurden für die Dockingsimulationen ausgewählt. Die Dockingsimulationen wurden mit den Programmen MOE Dock und Autodock durchgeführt. Die Ergebnisse wurden numerisch ausgewertet und innerhalb der Bindetasche relativ zur jeweiligen zugrunde liegenden Pharmakophorhypothese visuell analysiert; 27 Substanzen wurden schließlich für die Testungen ausgewählt. Die Testungen erfolgten mit einem enzymatischen Assay und einem Assay an attenuierten M. tuberculosis Für die Etablierung des enzymatischen Assays wurde das Enzym InhA mittels Vektortransformation in E. coli überexprimiert und säulenchromatographisch aufgereinigt. Das Substrat 2-trans-Octenoyl-Coenzym A wurde synthetisiert. Von den 27 ausgewählten Substanzen waren 9 im Handel erhältlich und wurden schließlich auf ihre inhibitorische Aktivität getestet. Es wurden ein Thiazolidin-2,4-dion, ein 2-Thioxoimidazolidin-4-on und ein Sulfonamid als aktive Substanzen gefunden. / Worldwide the number of tuberculosis cases has increased in the decades. Since there is a lack of innovative anti-tuberculosis drugs, the first-generation drugs are still used as gold standard. Therefore, strains of mycobacteria, that respond only little or not at all to drug therapy, picture a growing problem. Characteristic of M. tuberculosis is its thick cell wall. The structure of the cell wall allows the bacterium to persist in the macrophages and to multiply there. The cell wall is rich in mycolic acids and, in this, little permeable to xenobiotics. The mycobacterial cell wall skeleton can be divided into two parts, the cell wall core and the outer lipid envelope. The free lipids of the outer lipid envelope serve as signalling molecules in course of the disease, and intercalate with the mycolic acids of the cell wall core. For fatty acid biosynthesis M. tuberculosis has two enzyme complexes: the type I fatty acid synthase, which is also found in mammals, produces fatty acids of C16 to C26 chain length; subsequently, these are extended to meromycolic acids in the type II fatty acid synthase (FAS II). The synthesis cycle of FAS-II consists of mono-functional enzymes that build up on each other. If one of these enzymes is disturbed in its functionality, intermediates accumulate and required cell wall lipids can not be synthesized. As a result, the cell wall turns unstable and the bacterium dies. Therefore, the mycobacterial lipid biosynthesis is an ideal target for developing new antituberculous drugs. The aim of this study was to develop a new inhibitor class of the mycobacterial FAS-II enzyme InhA by means of virtual screening. For the virtual screening three consecutive pharmacophore hypotheses were developed, and with these two independent databases were screened. As a basis for the calculations of the virtual screening the PDB X-ray crystal structure 2h7m with the ligand 1-cyclohexyl-N-(3,5-dichlorophenyl)-5-oxopyrrolidine-3-carboxamide was used. In order to construct the pharmacophore hypotheses, first, the structures of the enzyme with and without a ligand were analyzed for their conformational differences, in particular with respect to the geometry of the binding pocket. Next, the interactions of the ligand with the amino acids of the binding pocket and with the cofactor were analyzed in detail; thereby, the different types of interactions were assessed in terms of their relevance for the inhibitory activity. Finally, a hot spot analysis of the active site was carried out for different chemical functionalities. The ZINC 'drug-like' subset (2005) and CCG's 2006 Vendor MOE 3D compound collection were used for the database screening, both being databases of commercially available compounds. The ZINC 'drug-like' subset was numerically reduced by a hierarchical filter customized for InhA; of the remaining compounds a database of conformers was calculated. The MOE 2006 Vendor 3D Compound Collection was already available as a conformer database. The reduced ZINC 'drug-like' subset was screened with the pharmacophore hypotheses I and II. After calculating fingerprints the hits were clustered according to their similarity using the Tanimoto coefficient and visually analyzed; 149 compunds were selected for the docking simulations. The MOE conformers database also was numerically reduced by a hierarchical filter customized for InhA, and then screened with the pharmacophore hypothesis III, 28 compounds were chosen for the docking simulations. The docking simulations were performed with the programs MOE Dock and Autodock. The results were evaluated numerically, and analyzed visually within the binding pocket relative to the respective underlying pharmacophore hypothesis. Finally, 27 substances were selected for testing. The tests were carried out using an enzymatic assay and an assay on attenuated M. tuberculosis. For establishing the enzymatic assay, the enzyme InhA was overexpressed using vector transformation into E. coli and purified by column chromatography. The substrate 2-trans-octenoyl-coenzyme A was synthesized. Of the 27 selected compounds 9 substances were commercially available and were tested for their inhibitory activity. A thiazolidine-2,4-dione, a 2-thioxoimidazolidine-4-one and a sulfonamide were found to be active.

Les formes réactives de l'oxygène (FRO) ont été analysées dans différents compartiments cellulaires en utilisant des méthodes spectroscopiques (UV/VIS, fluorescence, infrarouge, résonance paramagnétique électronique). L'identité et les mécanismes catalytiques des enzymes qui produisent les FRO dans les membranes plasmiques (MP) et les mitochondries ont été étudiés, ainsi que le rôle protectif de l'oxydase terminale plastidiale (PTOX) des chloroplastes. Cd2+ s'est révélé être un inhibiteur de la NADPH oxydase des MP. In vivo Cd2+ inhibait la production extracellulaire de O2•- mais stimulait l'accumulation de H2O2. Dans des mitochondries isolées, Cd2+ a augmenté la production de FRO. Antimycin A a entraîné une élévation du H2O2 extracellulaire, confirmant que la mitochondrie est le site principal de production de l'H2O2 extracellulaire induite par Cd2+ in vivo. Une quinone réductase (QR) génératrice de FRO a été isolée des MP. La déprotonation pH-dépendante du quinole a produit des formes intermédiaires instables qui génèrent des FRO par réaction avec O2. Des espèces quinoniques ont été détectées dans la MP et pourraient servir de substrat aux QR in vivo. La protection de la chaine photosynthétique de transfert d'électron par la plastoquinol:O2 oxydoréductase a été étudiée chez des plantes PTOX+ surexprimant PTOX. En raison de leur réponse altérée en conditions de faible et forte intensité lumineuse, il a été proposé que pour fonctionner comme enzyme protectrice, PTOX est couplée à une SOD. Chez les lignées PTOX+, le niveau de SOD chloroplastique n'était pas plus élevé, limitant probablement leur capacité à détoxifier les taux élevés de O2•- généré.

<p>Homing endonuclease genes (HEGs) are selfish genetic elements that mediate their own super-Mendelian inheritance. This is mediated by the homing endonuclease cleavage of a HEG^-allele followed by recombination-repair with a HEG⁺ allele.</p><p>The majority of the HEGs are encoded in intervening sequences (IVSs). The insertion of the IVS interrupts the endonuclease recognition site, making the genome with the IVS resistant to further cleavage by homing endonucleases with specificity for that particular sequence, but susceptible for homing endonucleases with a target not affected by the IVS insert. In 39 studied strains of the <i>Bacillus cereus</i> group, 28 IVSs were found in the <i>nrdIEF</i> operon. Phylogenetic studies of these sequences showed a scattered distribution of the IVSs, indicating a frequent horizontal gene transfer and that there might be competition between the different IVSs in the <i>nrdIEF</i> operon in the <i>Bacillaceae</i> family. One novel group I intron was shown to encode a functional homing endonuclease with a GIY-(X)₈-YIG motif, expanding the family motif to GIY-(X)₈-₁₁-YIG. Interestingly, by studying the known insertion sites for IVSs in the ribonuclotide reductase genes, we show that the majority of the insertions are at conserved motifs, indicating that conservation is important for IVS survival.</p><p>Most freestanding HEGs in bacteriophage T4 cleave both HEG⁺ and HEG^- alleles, possibly providing a competitive advantage for the host organism when two phages infect the same bacterium. Two novel freestanding HEGs replace two putative HEGs in T4 in some T-even-like phages. The characterisation of these HEGs showed that both cleave double stranded DNA. SegH was shown to promote homing of its gene. Hef showed no homing, possibly due to general exclusion of other phages. The <i>mobE</i> putative HEG was shown to be homing proficient and showed strong general DNA degradation when expressed in <i>Escherichia coli.</i></p>

Thesis (M. Phil.)--University of Hong Kong, 2006. / Title proper from title frame. Also available in printed format.

Homing endonuclease genes (HEGs) are selfish genetic elements that mediate their own super-Mendelian inheritance. This is mediated by the homing endonuclease cleavage of a HEG- allele followed by recombination-repair with a HEG+ allele. The majority of the HEGs are encoded in intervening sequences (IVSs). The insertion of the IVS interrupts the endonuclease recognition site, making the genome with the IVS resistant to further cleavage by homing endonucleases with specificity for that particular sequence, but susceptible for homing endonucleases with a target not affected by the IVS insert. In 39 studied strains of the Bacillus cereus group, 28 IVSs were found in the nrdIEF operon. Phylogenetic studies of these sequences showed a scattered distribution of the IVSs, indicating a frequent horizontal gene transfer and that there might be competition between the different IVSs in the nrdIEF operon in the Bacillaceae family. One novel group I intron was shown to encode a functional homing endonuclease with a GIY-(X)8-YIG motif, expanding the family motif to GIY-(X)8-11-YIG. Interestingly, by studying the known insertion sites for IVSs in the ribonuclotide reductase genes, we show that the majority of the insertions are at conserved motifs, indicating that conservation is important for IVS survival. Most freestanding HEGs in bacteriophage T4 cleave both HEG+ and HEG- alleles, possibly providing a competitive advantage for the host organism when two phages infect the same bacterium. Two novel freestanding HEGs replace two putative HEGs in T4 in some T-even-like phages. The characterisation of these HEGs showed that both cleave double stranded DNA. SegH was shown to promote homing of its gene. Hef showed no homing, possibly due to general exclusion of other phages. The mobE putative HEG was shown to be homing proficient and showed strong general DNA degradation when expressed in Escherichia coli.