Despite the importance of molecular recognition in nearly all aspects of protein function, the determinants of specificity for enzyme-substrate and protein-protein interactions are poorly understood. The majority of these complexes involving bacterial luciferase from V. harveyi have yet to be fully characterized. Luciferase catalyzes the reaction of molecular oxygen, FMNH2 and a long-chain aliphatic aldehyde yielding FMN, the corresponding carboxylic acid and blue-green light. In vivo, luciferase is thought to obtain FMNH2 following transfer from a transiently associated oxidoreductase. To identify the oxidoreductase responsible for providing FMNH2 in E. coli, bioluminescence was compared using single gene deletion strains deficient in either a homolog to the endogenous V. harveyi oxidoreductase (Frp) or an oxidoreductase distantly related to luxG from V. fischeri (Fre). Fre is responsible for reducing flavin in vivo but does not physically interact with luciferase. The association between luciferase and the flavin product is also described. Luciferase was crystallized and subjected to soaking with high concentrations of FMN. A model was obtained for luciferase bound to FMN. Using molecular dynamics, models for the enzyme:aldehyde, enzyme:FMNH2, and luciferase bound to several reaction intermediates are presented. Finally, a conserved loop region adjacent to the active center was investigated for the ability to facilitate protein:protein interaction between luciferase and the endogenous Frp oxidoreductase. Following alanine mutagenesis of the charged residues throughout this loop, it appears that the residues targeted by this study are not components of a docking platform but facilitate a lid-gating mechanism of paramount importance for catalytic function.

Orientador: Vadim R. Viviani / Banca: Marcia Regina Brochetto Braga / Banca: Mauricio Bacci Junior / Banca: Etelvino José Henriques Bechara / Banca: Cleide Costa / Resumo: A partir dos coleópteros luminescentes, mais de 20 luciferases já foram clonadas e seqüenciadas. Dessas, a maioria é de lampirídeos das regiões Neártica e Paleártica, quatro de elaterídeos jamaicanos e uma de um fengodídeo asiático. Apenas outras cinco são oriundas da América do Sul, o continente mais rico em espécies de coleópteros luminescentes e o provável berço evolutivo de Lampyridae, a família com maior número de coleópteros luminescentes. Espécies desta região apresentam a maior variedade de cores de bioluminescência. No presente trabalho clonamos e seqüenciamos luciferases dos gêneros Brasilocerus sp., Phrixothrix sp. e Taximastinocerus sp., da família Phengodidae. Com base na análise filogenética dessas luciferases e outras já publicadas, concluímos que as luciferases das lanternas laterais e cefálicas são codificadas por genes parálogos, e propusemos um modelo para a evolução das cores da bioluminescência nessa família. Também determinamos o genoma mitocondrial de Pyrophorus divergens, membro da família Elateridae. A partir desse genoma e outros já publicados, analisamos a evolução da bioluminescência na superfamília Elateroidea sensu Lawrence e Newton (1995) e concluímos que essa pode ter surgido três vezes independentemente nesse grupo. / Abstract: From luminescent Coleopteran's, more than 20 luciferases have already been cloned and sequenced. Among them, most part is from lampyrids of Neartic and Paleartic regions, four are from Jamaican elaterids and one is from Asiatic phengodids. Just five are from South American species, the richest continent in luminescent Coleopteran's and, probably, the evolutionary cradle of Lampyridae. Species from this region display the greatest range of bioluminescence colors. At the present work, we cloned and sequenced luciferases from the genera Brasilocerus sp., Phrixothrix sp. and Taximastinocerus sp., from Phengodidae family. Based on the phylogenetic analysis of these genes and other already published, we concluded that head and lateral lantern luciferases are coded by paralogous genes, and we also proposed a model for bioluminescence color evolution in this family. We also sequenced the mitochondrial genome of Pyrophorus divergens, an Elateridae member. Based on this genome and other already published, we analysed the evolutionary history of bioluminescence in Elateroidea superfamily sensu Lawrence e Newton (1995) and concluded that it could have appeared three times independently in this group. / Doutor

Cattle are naturally colonized by enterohemorrhagic Escherichia coli within the gastrointestinal tract. The most notorious of the enterohemorrhagic E. coli is E. coli O157:H7, which can cause serious illness to humans if ingested. To ensure that the United States has a safe food supply, research is ongoing in pre-harvest food safety and pathogen intervention strategies. While advances in pre-harvest intervention strategies are encouraging, no method has proven to completely eliminate and/or control O157:H7. A key limitation to successful pathogen intervention strategies is the inability to track and monitor pathogens in a real-time fashion. Through the use of bioluminescent plasmids harboring the luxCDABE cassette, pathogen tracking could be a viable solution. Bioluminescent plasmids are capable of facilitating the tracking, pathogenesis and physical locations of pathogens, thus enabling researchers to have a better understanding of the pathogenic process.

Fireflies are some of the most captivating organisms on the planet. Because of this, they have a rich history of study, especially concerning their bioluminescent and visual behavior. Among insects, opsin copy number variation has been shown to be quite diverse. However, within the beetles, very little work on opsins has been conducted. Here we look at the visual system of fireflies (Coleoptera: Lampyridae), which offer an elegant system in which to study visual evolution as it relates to their behavior and broader ecology. They are the best-known case of a terrestrial organism that communicates through the use bioluminescence. The molecular basis for this communication is relatively simple: one gene-family (opsins) controls the detection of the signal, and one gene family (luciferase) controls the production of the signal. We use a transcriptomic approach to sample for and investigate opsin evolution in fireflies. We also present the first total evidence approach using both an extensive molecular matrix and a robust morphological matrix to reconstruct the lampyrid phylogeny. We then use this phylogeny to assess the hypothesis that adult use of bioluminescence occurred after the origin of Lampyridae. We find evidence for only two expressed opsin classes in each of the nine firefly species studied, one in the ultra-violet sensitive and one in the long-wavelength sensitive areas of the visible spectrum. Despite the need for most adult fireflies to respond to a clearly sexual and colorful visual signal (bioluminescence) to maximize fitness, their visual system is relatively simple, and does not match the trend for opsin duplication found in other insect groups. All subfamilies except for Lampyrinae are recovered as monophyletic; Pterotinae and Ototretinae are recovered within the Lampyridae. The ancestral state of adult bioluminescence is suggested to be non-bioluminescent, with at least three gains and at least three losses.

Dans la recherche de thérapie antitumorale de plus en plus innovante, nous avons évalué un traitement local basé sur l’utilisation de plasma froid. Le plasma froid (dans ce cas, <40°C) est un gaz ionisé par un apport d’énergie. Il contient des charges (électrons, ions), des radicaux libres et des molécules excitées. Il peut être généré à l’extrémité de cathéter permettant un traitement locorégional comme le traitement de dysplasie ou encore de tumeurs non résécables. Une activité antitumorale importante du plasma a été mise en évidence in vitro sur diverses lignées tumorales (colorectale, pulmonaire, pancréatique et cérébrale). Par ailleurs les cellules tumorales sont plus sensibles au plasma que les cellules normales. Les ROS générés sont à l’origine des principaux mécanismes d’action du plasma. Ils induisent de nombreux dommages à l’ADN, suivi d’un arrêt du cycle cellulaire conduisant à l’apoptose des cellules. Les études de tolérance ont mis en évidence l’innocuité de faibles doses de plasma sur le tissu traité permettant de définir les doses de plasmas utilisable dans le cadre de traitements antitumoraux. En utilisant des tumeurs xénogreffées en sous cutané et l’imagerie de bioluminescence, une activité antitumorale du plasma froid a été mise en évidence pour la première fois in vivo avec une augmentation de la survie des souris traitées d’environ 60%. Le traitement induit un arrêt de la prolifération tumoral avec une induction d’apoptose dans l’ensemble de la tumeur sans augmenter la surface de nécrose. L’effet antitumoral a également été démontré en utilisant le plasma gun sur un modèle de tumeurs colique et pancréatique en situation orthotopique chez la souris avec une augmentation de la survie (115%) accompagné d’une diminution de la métastasie. Ces résultats obtenues dans une démarche de recherche translationnelle montrent l’intérêt potentiel du plasma comme nouvel agent antitumoral. / In the context of new innovated antitumor treatment discovery, we evaluated the efficacy of a new local treatment based on non-thermal plasma (NTP). NTP is a cold (in this case, <40°C) ionized gas (a ir or noble gas) thanks to an electric discharge. It contains free charges (electrons, ions), free radicals and excited molecules. It can be generated at the end of a catheter allowing a local treatment that is compatible with usual endoscopes for dysplasia or non resecable tumors. We showed that NTP has a significant antitumor effect in vitro on various cell lines including colorectal, pancreatic, lung and brain tumor cells. The major action mechanisms of NTP was linked to a high rate generation of ROS in the vicinity of tumors cells and others plasma components have a minor implications. These ROS induce lethal DNA damages leading to a multiphase cell cycle arrest and finally to apoptosis. In vivo, a good tolerance of plasma treatment was highlighted and NTP treatment parameter was defined. Using subcutaneous xenografts and bioluminescence imaging, we showed a major antitumor effect of plasma in vivo with a 60% increase of mice life span. NTP treatments of tumor induce a tumor cell cycle arrest with a significant apoptosis induction in the whole tumor without increase of necrotic area. This in vivo antitumor effect was also observed with an in situ treatment using plasma gun of colorectal and pancreatic orthotopic tumor xenografts. A significant increase of mice lifespan (115%) was obtained together with a metastasis decrease. These results obtained in translational research showed the potential antitumor activity of NTP as a new type of treatment for cancer treatment.

Les maladies thrombotiques sont la cause majeure de décès dans les pays industrialisés. Les cellules souches dérivées de la moelle osseuse ont été impliqués dans la réparation vasculaire et contribuent à restaurer l'intégrité de l'endothélium. Les cellules progéniteurs CD34 positives ont été rapportées pour jouer un rôle important suite à une blessure de la paroi vasculaire en se liant aux plaquettes ou à la fibrine, modulant la formation du thrombus et participant à la ré-endothélialisation de la paroi vasculaire lésée. Parmi les cellules progéniteurs CD34 positives, les cellules endothéliales formant colonie (ECFC) ont été caractérisés comme présentant des propriétés endothéliale. La première partie de ce travail met en évidence un nouveau partenariat entre les neutrophiles et les ECFC. Par l'utilisation de la microscopie intravitale chez les souris, nous montrons que les neutrophiles recrutent les ECFC au site de lésion vasculaire induite par rayon laser. Ce recrutement est dépendant du PSGL-1 mais indépendant de l'expression de la P-sélectine. L'interaction avec les neutrophiles accroît le potentiel pro-angiogénique des ECFC in vitro. L'identification de ce nouveau partenariat entre les neutrophiles et les ECFC dans la formation de thrombus possède des implications potentiellement critiques dans le contrôle de l'angiogenèse.&#8232;La seconde partie de ce travail décrit une nouvelle méthode pour imager en temps réel le devenir des ECFCs in vivo. Nos résultats montrent que les ECFC s'accumule au site de lésion vasculaire.&#8232;En conclusion, ce travail démontre que les ECFC peuvent participer favoriser et réguler l'angiogenèse en interagissant avec les neutrophiles. / Thrombotic diseases are major cause of death in industrialized countries. Bone marrow derived progenitor cells have been implicated in vascular repair and contribute to restore the integrity of endothelium, thus constituting important partners for vascular wall restoration. CD34 positive progenitors cells were reported to play an important role following an injury of the vessel wall by binding to platelets or fibrin, modulating thrombus formation and participating in the re-endothelization of the injured vessel wall. Among CD34 positive progenitors cells, Endothelial Colony forming Cells (ECFCs) have been characterized as a unique subset displaying endothelial properties. The first part of this work described a new partnership between neutrophils and ECFCs. Using high- speed digital fluorescent intravital microscopy in living mice we show that neutrophils recruit ECFCs at the site of a laser-induced vessel injury via PSGL-1 axis independently of P-selectin. This interaction enhances the pro-angiogenic potential of ECFCs in vitro. The identification a new central partnership between neutrophils and ECFC in thrombus formation has critical potential implications to control angiogenesis.&#8232;The second part of this work, described a new method to image in real-time the homing and survival ECFCs in vivo. Our results show that ECFCs transducted with a gene coding for luciferase accumulates at site of vascular traumatism.&#8232;In conclusion, this work indicates that ECFCs may participate in the promotion and regulation of angiogenesis by interacting with neutrophils at a site of vascular traumatism.

Au cours de ce travail de thèse, les deux approches permettant la caractérisation de nouveaux agents antileishmaniens ont été suivies : d’une part identification de molécules de synthèse originales et actives, par des méthodes de criblage, et d’autre part recherche de nouvelles cibles thérapeutiques leishmaniennes, faisant appel à des outils de biologie moléculaire, et de protéomique.Dans une première partie consacrée à l’optimisation du criblage antileishmanien de molécules de synthèse, nous avons notamment mis au point et validé une nouvelle méthode applicable aux formes promastigotes. Cette méthode reposant sur le principe de la bioluminescence, s’est avérée précise, rapide, répétable, sensible, automatisable et applicable à des isolats cliniques. Nous nous sommes également intéressés à la recherche d’une nouvelle méthode de criblage sur les formes amastigotes intracellulaires remplissant ces mêmes critères.Dans une seconde partie consacrée au lien entre la mort cellulaire programmée et les cystéines peptidases (métacaspase et Raptor) chez Leishmania, nous avons mis en évidence un lien possible entre métacaspase et autophagie chez L. infantum. De plus, nous avons identifié, in vivo, plusieurs substrats protéiques potentiels de ces peptidases : HSP70, ARN-Hélicase ATP-Dépendante et Lmjf09.1010 pour la métacaspase ; NDPKb et la protéine associée à l’ADN du kinétoplaste pour Raptor. Ces différents résultats ont permis de proposer un modèle conciliant les rôles possibles des cystéine-Peptidases métacaspase et Raptor au cours de l’autophagie et de l’apoptose chez Leishmania, rôles potentiellement dus au clivage de substrats protéiques spécifiques. / During this thesis work, two approaches affording the characterization of new antileishmanial agents were followed: on the one hand, the identification of new original antileishmanial synthetic drugs, through screening assays and on the other hand, research of new parasitic therapeutic targets by using molecular biology and proteomic tools. In the first part, dedicated to the optimization of the antileishmanial screening of synthetic compounds, we set up and validated a new bioluminescence-Based screening method for studying anti-Promastigote compounds. This method appears accurate, rapid, repeatable, sensitive and is also transposable to automats and usable on clinical isolates. In parallel, we investigated new screening protocols aiming at improving the screening in intracellular amastigotes which could meet the same criteria. In the second part focusing on the link between programmed cell death and cystein peptidases (metacaspase and Raptor) in Leishmania, our study first highlighted a possible link between metacaspase and autophagy in L. infantum. Moreover, we identified in vivo several potential subtrates for both peptidases: HSP70, ATP-Dependent RNA-Helicase and Lmjf09.1010 for the metacaspase; NDPKb and kinetoplast-DNA-Associated-Protein for Raptor. These results allowed us to propose a model reconciling the possible roles of cystein peptidases metacaspase and Raptor during autophagy and apoptosis in Leishmania, roles potentially due to the cleavage of specific proteic subtrates.

Certaines observations suggèrent que les afférences méchano-sensorielles peuvent moduler l’activité des générateurs centraux du rythme locomoteur (ou Central Pattern Generators, CPGs). Cependant, il est impossible d’explorer les circuits neuronaux sous-jacents chez l’animal en mouvement à l’aide d’enregistrements électrophysiologiques lors d’expériences de locomotion dite « fictive ». Dans cette étude, nous avons enregistré de façon sélective et non-invasive les neurones moteurs et sensoriels dans la moelle épinière pendant la locomotion active en ciblant génétiquement le senseur bioluminescent GFP-Aequorin chez la larve de poisson zèbre. En utilisant l’imagerie calcique à l’échelle des neurones individuels, nous confirmons que les signaux de bioluminescence reflètent bien le recrutement différentiel des groupes de motoneurones spinaux durant la locomotion active. La diminution importante de ces signaux chez des animaux paralysés ou des mutants immobiles démontre que le retour méchano-sensoriel augmente le recrutement des motoneurones spinaux pendant la locomotion active. En accord avec cette observation, nous montrons que les neurones méchano-sensoriels spinaux sont en effet recrutés chez les animaux en mouvement, et que leur inhibition affecte les réflexes d’échappement chez des larves nageant librement. L’ensemble de ces résultats met en lumière la contribution du retour méchano-sensoriel sur la production locomotrice et les différences qui en résultent entre les locomotions active et fictive. / There is converging evidence that mechanosensory feedback modulates the activity of spinal central pattern generators underlying vertebrate locomotion. However, probing the underlying circuits in behaving animals is not possible in “fictive” locomotion electrophysiological recordings. Here, we achieve selective and non-invasive monitoring of spinal motor and sensory neurons during active locomotion by genetically targeting the bioluminescent sensor GFP-Aequorin in larval zebrafish. Using GCaMP imaging of individual neurons, we confirm that bioluminescence signals reflect the differential recruitment of motor pools during motion. Their significant reduction in paralyzed animals and immotile mutants demonstrates that mechanosensory feedback enhances the recruitment of spinal motor neurons during active locomotion. Accordingly, we show that spinal mechanosensory neurons are recruited in moving animals and that their silencing impairs escapes in freely behaving larvae. Altogether, these results shed light on the contribution of mechanosensory feedback to motor output and the resulting differences between active and fictive locomotion.

Le suivi des flux calciques dans le cerveau de l’animal en mouvement nécessite de nouvellessondes. Nous utilisons la bioluminescence observée chez la méduse Aequorea victoria etimpliquant la protéine aequorine. Une fusion entre l’aequorine et la protéine fluorescente GFP(GA) permet d’obtenir un senseur calcique bioluminescent dont la stabilité et les propriétésspectrales sont adéquates pour de nombreuses applications. L’émission de bioluminescencepermet de suivre la propagation de l’information nerveuse de cellule en cellule, en temps réeldans des réseaux de neurones.Nous avons tout d’abord montré au moyen de construction de lignées transgéniques murinesque la protéine chimère GA peut être exprimée dans des microdomaines cellulaires pouranalyser l’activité neuronale. Nos résultats montrent pour la première fois qu’il est possibled’enregistrer in vivo et de manière non invasive dans l’animal en mouvement deschangements dans la concentration de calcium mitochondrial. Nous avons ensuite réalisé unciblage post synaptique du senseur par fusion à la protéine PSD95. Ce ciblage permet dedétecter l'entrée de calcium au niveau du récepteur NMDA.Parallèlement, nous avons cherché à améliorer les propriétés du senseur GA pour détécterl’activité calcique dans l’animal in toto. Nous identifié un nouvel analogue de lacoelenterazine conduisant à un décalage du spectre de bioluminescence de l’aequorine vers lerouge. Et par ailleurs, nous avons testé l’activité de l’aequorine en fusion avec diversesprotéines fluorescentes. Nous disposons avec ce travail de nouveaux senseurs bioluminescentspour le suivi de l’activité cérébrales dans des études comportementales. / Monitoring calcium fluxes in the brain of freely moving animals requires the development ofnew probes. We use the bioluminescence of the protein aequorin observed in the jellyfishAequorea victoria. A fusion between aequorin and GFP fluorescent protein (GA) provides abioluminescent calcium sensor whose stability and spectral properties are adequate for manyapplications. The emission of bioluminescence is suitable to track in real-time the propagationof nervous impulses from cell to cell in neural networks.We first showed by transgenic murine lines construction that the chimeric protein GA can beexpressed in cell microdomains to analyze neuronal activity. Our results show for the firsttime it is possible to record in vivo and non-invasively in the moving animal, changes in theconcentration of mitochondrial calcium. We then performed a post synaptic targeting of thesensor by fusion with the protein PSD95. This permits to detect the entry of calcium next tothe NMDA receptor.Meanwhile, we tried to improve the properties of the GA sensor to detect calcium activity inthe animal in toto and mor specifically through the skull. We identified a new analogue ofcoelenterazine leading to a shift in the spectrum of aequorin bioluminescence to red. We thentested the activity of aequorin fused with different fluorescent proteins. This leads to newbioluminescent sensors for monitoring the brain activity in behavioral studies.

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Lactic acid bacteria (LAB) are common inhabitants of the human gastro-intestinal tract (GIT). Some LAB, especially lactobacilli, are well known for their application in fermented foods and probiotic properties. These microorganisms exert many beneficial effects on human health, such as digestion and assimilation of food and preventing pathogens colonising the GIT. Furthermore, some selected probiotic strains are believed to perform a critical role in the treatment of gastro-intestinal disorders, lactose intolerance and in the stimulation of the immune system. Despite the ever increasing consumer interest in probiotic LAB, the mechanisms by which they exert their beneficial effects and the activities of probiotics in the GIT often remain poorly understood. Understanding survival mechanisms of LAB in the GIT, especially the interaction between LAB and pathogens, would be facilitated by the direct in vivo monitoring of these processes. Using the mCherry fluorescence gene, we successfully constructed Lactobacillus plantarum 423 and Enterococcus mundtii ST4SA reporter strains. With this study we showed that fluorescence imaging can be used to detect Lb. plantarum 423 and Ent. mundtii ST4SA in the GIT of mice. The two species colonized the cecum and colon for at least 24 h after one oral administration. To our knowledge, this is the first report on fluorescence imaging of LAB expressing mCherry in a mouse model. Using a bioluminescence marker system, we evaluated the impact of Lb. plantarum 423 and Ent. mundtii ST4SA on orally acquired Listeria monocytogenes infection and the ability of the probiotics to compete with the pathogen in the GIT of mice. Challenging Lb. plantarum 423 and Ent. mundtii ST4SA that were already established in the GIT of mice with L. monocytogenes EGDe had no effect on the survival and persistence of the probiotic strains. We demonstrated that the colonization of mice with Lb. plantarum 423 and Ent. mundtii ST4SA, or a combination of the strains, protected the animals against colonization of the GIT by L. monocytogenes EGDe. Enterococcus mundtii proved more effective than Lb. plantarum 423 in reducing the number of L. monocytogenes EGDe in the mouse model. / AFRIKAANSE OPSOMMING: Melksuurbakterieë (MSB) kom algemeen in die mens se spysverteringkanaal (SVK) voor. Verskeie MSB, veral lactobacilli, is bekend vir hul gebruik in gefermenteerde voedsel en as probiotika. Die bakterieë het baie eienskappe wat die mens se gesondheid kan bevoordeel, insluitend vertering en assimilasie van voedsel en voorkoming van kolonisering van die SVK deur patogeniese bakterieë. Sekere probiotiese rasse speel ook ʼn belangrike rol in die behandeling van SVK versteurings, laktose intoleransie en die stimulering van die immuun stelsel. Alhoewel die belangstelling in probiotiese bakterieë toeneem, is daar min inligting bekend oor die meganismes wat MSB gebruik om hulle voordelige eienskappe in die SVK uit te voer. Die oorlewing van MSB in die SVK, veral die interaksies tussen MSB en patogene, kan met behulp van ʼn in vivo moniteringsisteem bestudeer word. Deur die mCherry fluorisensie geen in Lactobacillus plantarum 423 en Enterococcus mundtii ST4SA te kloneer, het ons daarin geslaag om ʼn effektiewe verklikker sisteem te ontwikkel en kon die voorkoms en migrasie van die twee spesies in die SVK van muise bestudeer word. Lactobacillus plantarum 423 en Ent. mundtii ST4SA het veral die blindederm en kolon gekoloniseer. Beide rasse het na ʼn enkele mondelingse toediening vir ten minste 24 h in die SVK oorleef. Sover ons kennis strek, is hierdie die eerste verslag van fluoriserende MSB wat met behulp van die mCherry geenproduk in die SVK bestudeer is. Deur gebruik te maak van ʼn bioliggewende verklikker sisteem, het ons die vermoë van Lb. plantarum 423 en Ent. mundtii ST4SA om met Listeria monocytogenes in die SVK te kompeteer, bestudeer. Listeria monocytogenes het geen invloed gehad op die kolonisering van Lb. plantarum 423 en Ent. mundtii ST4SA nie. Deur die muise vooraf met Lb. plantarum 423 en Ent. mundtii ST4SA te koloniseer (in kombinasie of met net een van die twee rasse), kon ons daarin slaag om kolonisering van die SVK met L. monocytogenes te voorkom. In die muis model wat in hierdie studie gebruik is, was Ent. mundtii ST4SA meer effektief as Lb. plantarum 423 in die verlaging van Listeria selgetalle.