Abstract Acinetobacter baumannii is a prevalent nosocomial where infections are typically secondary infections to patients that already have an infection or other source of being immunocompromised. Like many other infectious bacteria, A. baumannii is increasingly considered a multi-drug resistant pathogen. This eliminates the ability to treat A. baumannii infections with traditional antibiotics, hence the need for another method of treating A. baumannii. This research study was designed to find a way to affect the survival of A. baumannii such that it can be applied to a hospital setting to prevent further infections to immunocompromised patients. One mechanism potentially used by A. baumannii to persist on hospital surfaces is through the use of the bacterial second messenger cyclic-di-GMP (c-di-GMP). This nucleotide signal is regulated in response to environmental conditions, and then activates c-di-GMP-binding proteins that induce phenotypic changes. I hypothesized that by deleting these c-di-GMP-binding proteins that it will produce measurable differences in phenotype like biofilm formation, motility, and desiccation survival. Reducing phenotypes such as these may alter A. baumannii’s ability to persist on hospital surfaces, and potentially lead to future surface eradication. A. baumannii encodes two potential c-di-GMP-binding proteins of particular interest, one that contains a sole PilZ domain and another that pairs a PilZ domain with a hydrolase domain. PilZ domains bind c-di-GMP within a conserved binding site, regulating the conformational structure of the protein, and are named for the first studied PilZ domain within the pilus-associated PilZ protein. Pili are used in pilus-mediated motility and surface attachment, and they are A. baumannii’s primary method of motility due to not having flagellum. I hypothesized that by removing these c-di-GMP-binding proteins, I would interrupt the c-di-GMP signaling that might regulate motility. I am testing two A. baumannii strains: 5075, a recent military hospital isolate and 17978, an older lab strain. A notable difference between these two strains is that 5075 demonstrates twitching motility where it utilizes type IV pili, but 17978 demonstrates swarming motility that has unknown mechanisms. Both c-di-GMP-binding proteins were tested for their role in twitching or swarming motility of the respective strains. I found that swarming motility of 17978 is regulated by both c-di-GMP-binding proteins. While I am still generating the deletion strain for the c-di-GMP-binding hydrolase enzyme, the sole PilZ domain protein is also required for twitching motility in the 5075 strain. These results suggest c-di-GMP regulates both forms of motility in A. baumannii. Future plans include determining the role of the c-di-GMP-binding hydrolase enzyme in twitching motility and identifying the role that these proteins play through binding of c-di-GMP.

Acinetobacter baumannii is an increasingly multidrug-resistant Gram-negative bacterial pathogen and contributes to many hospital-acquired infections. Discovering new treatments against Acinetobacter baumannii infections is necessary as the pathogen adapts to the antimicrobials prescribed by physicians. Cyclic di-GMP (c-di-GMP), a bacterial second messenger, can regulate various phenotypes including biofilm formation, desiccation tolerance, motility, etc.; many of these phenotypes may help A. baumannii better survive a hospital environment, such as dryness on hospital surfaces. Up to twelve c-di-GMP modulating enzymes (CMEs) and two c-di-GMP binding proteins are predicted to be encoded by this pathogen. Diguanylate cyclases (DGCs) produce c-di-GMP, whereas phosphodiesterases (PDEs) degrade c-di-GMP. More c-di-GMP that can bind to its binding proteins means more biofilm formation and less motility. Of the eleven CMEs, 7 are DGCs, 2 are PDEs, and 3 encode both domains (DGCs/PDEs). I hypothesized that biofilm formation, desiccation tolerance, and motility were controlled by c-di-GMP and that we could target these parts of the c-di-GMP signaling network for new treatments. If we disrupt these genes, then we should see a reduction in the regulatory effects of these phenotypes. In this investigation, we generated mutants with a single gene knockout or transposon mutagenesis in two different A. baumannii strains: 17978, a historical laboratory strain that exhibits swarming motility and AB5075, a recent clinical isolate that exhibits twitching motility. To test biofilm formation, we let the mutants grow to their maximum concentration in 96-well plates, stained the plates with crystal violet, and quantified the crystal violet that stained the biofilm. To test for motility, a LB agar plate was stabbed to the plastic surface or dropped on the agar surface with diluted culture to determine the presence of twitching or swarming motility, respectively. To test for desiccation tolerance, we washed the cultures in distilled water to rid the sample of any salt, serially diluted the samples in solution, and plated them out onto LB agar plates. Bacterial counts were quantified before and after desiccation to determine survival of each mutant. From these experiments, 6 DGCs, 1 PDE, and 2 DGCs/PDEs were shown to regulate biofilm formation in AB5075. Furthermore, a PDE and a DGC/PDE were shown to regulate twitching motility in AB5075, while a single DGC was required for tolerating dryness. In strain 17978, we have found a PDE and 4 DGCs that are necessary for swarming motility and are currently conducting biofilm and desiccation tolerance assays. So far, we’ve identified a role for c-di-GMP in A. baumannii biofilm formation, motility, and desiccation survival. Inhibiting the regulation of these pathways could produce novel mechanisms to combat this pathogen in the hospital environment.

Gärningsmannaprofilering (GMP) är en polisiär metod som används vid svårlösta utredningar. I Sverige praktiseras metoden av en central grupp vid Rikskriminalpolisen, den såkallade GMP-gruppen. Studiens övergripande syfte är att förstå och förklara GMP som polisiär metod, samt undersöka metodens effektivitet, korrekthet och vetenskaplighet. Ett särskilt syfte är att testa inlärningsteorin och rutinaktivitetsteorin gentemot GMP-metoden för diskutera eventuella samband. Studien är kvalitativt orienterad och bygger på den hermeneutiska teorin om tolkning av källor. Studien bygger på en omfattande systematisk litteraturstudie i kombination med två intervjuer. Sammanfattningsvis kan man säga att de slutsatser som analysen har är att GMP är en metod som i många fall tycks vara effektiv och som ofta genererar korrekta gärningsmannaprofiler. Dock behövs det mer kunskap om GMPs vetenskapliga förankring. Det har även visat sig att det finns ett samband mellan GMP och både rutinaktvitetsteorin och inlärningsteorin. Sambandet med inlärningsteorin är dock marginellt.

Cyclic di-GMP is a second messenger used by bacteria to regulate motility, extracellular polysaccharide production, and the cell cycle. Recent advances in the measurement of real time cyclic di-GMP levels in single cells have uncovered significant dynamic heterogeneity of second messenger concentrations within bacterial populations. This heterogeneity results in a wide range of phenotypic outcomes within a single population, providing the potential for population survival and adaptability in response to rapidly changing environments. In this chapter, we discuss some of the measurement technologies available for single-cell measurement of cyclic di-GMP concentrations, the resulting discovery of heterogeneous cyclic di-GMP populations, the mechanisms bacteria use to generate this heterogeneity, and the biochemical and functional consequences of heterogeneity on cyclic di-GMP effector binding and the bacterial population.

O diguanilato cíclico (c-di-GMP) é uma molécula de sinalização intracelular que atua na regulação de importantes processos bacterianos como motilidade, formação de biofilme e virulência. As diguanilato ciclases (DGCs), contendo um domínio GGDEF ativo, catalisam a formação de c-di-GMP a partir de duas moléculas de GTP. A bactéria Xanthomonas citri subsp. citri (Xanthomonas axonopodis pv citri; Xac) é o agente causal do cancro cítrico, uma doença que ataca todas as variedades e espécies de citros. O genoma de Xac codifica 31 proteínas contendo domínios GGDEF. Treze destas proteínas possuem também domínios PAS e/ou GAF, que são ubíquos domínios sensores e de sinalização. Para tentar entender melhor o papel na sinalização por c-di-GMP das interações entre domínios GGDEF e domínios PAS e/ou GAF, estudos bioquímicos e funcionais foram realizados com as proteínas XAC0610 e XAC2446. XAC0610 contém um domínio GAF, quatro domínios PAS e um domínio GGDEF conservado. Análises fenotípicas com a linhagem nocaute XacΔ0610 mostraram que XAC0610 atua na regulação da motilidade e sobrevivência de Xac ao tratamento com H2O2. Ensaios de atividade enzimática demonstraram que XAC0610 é uma DGC cataliticamente ativa, e que a mutação sítio-dirigida de um resíduo conservado de lisina (Lys759) provoca uma grande redução na atividade de DGC. Os domínios GAF e PAS de XAC0610 aparentemente não atuam como domínios sensores, entretanto são importantes para a dimerização da proteína, necessária para a obtenção de altos níveis de atividade de DGC. Além disso, várias observações sugerem que XAC0610 não é submetida à inibição alostérica pelo produto, um mecanismo regulatório comumente utilizado para o controle da atividade de DGC. Por outro lado, os dados de cinética enzimática de XAC0610HIS-35-880 revelaram um efeito de cooperatividade positiva para a ligação dos substratos, com uma constante de dissociação para a ligação da primeira molécula de GTP (K1) cerca de 3-5 vezes maior que a constante de dissociação para a ligação da segunda molécula de GTP (K2). A partir deste estudo, nós apresentamos um esquema cinético geral mais apropriado para as análises dos dados cinéticos de enzimas DGCs e propomos que a ligação cooperativa do substrato talvez possa desempenhar um importante papel na regulação in vivo da atividade de algumas DGCs, aumentando sua sensibilidade a pequenas variações nos níveis celulares de GTP. Outra proteína caracterizada neste trabalho, XAC2446 possui um domínio GAF e um domínio GGDEF que, ao contrário do domínio GGDEF de XAC0610, não deve apresentar atividade de DGC. Mesmo assim, análises funcionais mostraram que XAC2446 regula negativamente a formação de biofilme e positivamente a motilidade de Xac. Ensaios de duplo híbrido em leveduras identificaram que XAC2446 interage com XAC2897, contendo um domínio GGDEF potencialmente ativo, e XAC1185, contendo um domínio HD fosfohidrolase de (p)ppGpp. Alguns estudos indicam que altos níveis celulares de c-di-GMP e baixos níveis de (p)ppGpp podem ser necessários durante a formação de biofilme. XAC2446 talvez possa atuar como um inibidor da atividade enzimática de XAC2897 e XAC1185 e influenciar, indiretamente e antagonicamente, tanto os níveis celulares de c-di-GMP quanto de (p)ppGpp. / Cyclic di-GMP is a bacterial second messenger that regulates a range of functions, including cellular motility, biofilm formation and virulence. This molecule is produced from two GTP substrates by the activity of diguanylate cyclases (DGCs) containing a GGDEF domain. The phytopathogenic bacteria Xanthomonas citri subsp. citri (Xanthomonas axonopodis pv citri; Xac) causes citrus canker in a wide variety of citrus species. The Xac genome codes for 31 proteins with GGDEF domains. Thirteen of the 31 Xac GGDEF domain-containing proteins also possess PAS (Per-Arnt-Sim) or GAF (cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA) domains that are ubiquitous signaling and sensory domains. In order to better understand the relationship between these commonly associated domains, biochemical and functional studies were carried out with the XAC0610 and XAC2446 proteins. XAC0610 is a large multi-domain protein containing one GAF domain, four PAS domains and one GGDEF domain. This protein has a demonstrable in vivo and in vitro diguanylate cyclase (DGC) activity. Analysis of a XacΔ0610 knockout strain revealed that XAC0610 plays a role in the regulation of Xac motility and resistance to H2O2. Site-directed mutagenesis of a conserved DGC lysine residue (Lys759 in XAC0610) resulted in a severe reduction in XAC0610 DGC activity. XAC0610 DGC activity was also impaired by removal of the N-terminal GAF and PAS domains, which are probably needed for proper protein dimerization. Furthermore, experimental and in silico analysis suggest that XAC0610 is not subject to allosteric product inhibition, a common regulatory mechanism for DGC activity control. Instead, steady-state kinetics of XAC0610 DGC activity revealed a positive cooperative effect of the GTP substrate with a dissociation constant for the binding of the first GTP molecule (K1) approximately three to five times greater than the dissociation constant for the binding of the second GTP molecule (K2). We present a general kinetics scheme that should be used when analyzing DGC kinetics data and propose that cooperative GTP binding could be a common, though up to now overlooked, feature of these enzymes that may in some cases offer a physiologically relevant mechanism for regulation of DGC activity in vivo. The other characterized protein, XAC2446, has a GAF domain and a degenerated GGDEF domain. Unlike XAC0610, XAC2446 should not present DGC activity. Nevertheless, functional analysis of XAC2446 demonstrated that it plays a role in the regulation of Xac motility and biofilm formation. A yeast two-hybrid screen identifies XAC2897 (a potentially active GGDEF domain-containing protein) and XAC1185 (a (p)ppGpp hydrolase) as specific binding partners of the XAC2446 protein. As indicated by studies in other bacteria, high cellular levels of c-di-GMP and low levels of (p)ppGpp may be both required for biofilm formation. It is possible that XAC2446 might have a role in the antagonistic regulation of c-di-GMP and (p)ppGpp cellular levels by acting as an inhibitor of both XAC2897 and XAC1185 enzymatic activities.

O diguanilato cíclico (c-di-GMP) é uma molécula de sinalização intracelular que atua na regulação de importantes processos bacterianos como motilidade, formação de biofilme e virulência. As diguanilato ciclases (DGCs), contendo um domínio GGDEF ativo, catalisam a formação de c-di-GMP a partir de duas moléculas de GTP. A bactéria Xanthomonas citri subsp. citri (Xanthomonas axonopodis pv citri; Xac) é o agente causal do cancro cítrico, uma doença que ataca todas as variedades e espécies de citros. O genoma de Xac codifica 31 proteínas contendo domínios GGDEF. Treze destas proteínas possuem também domínios PAS e/ou GAF, que são ubíquos domínios sensores e de sinalização. Para tentar entender melhor o papel na sinalização por c-di-GMP das interações entre domínios GGDEF e domínios PAS e/ou GAF, estudos bioquímicos e funcionais foram realizados com as proteínas XAC0610 e XAC2446. XAC0610 contém um domínio GAF, quatro domínios PAS e um domínio GGDEF conservado. Análises fenotípicas com a linhagem nocaute XacΔ0610 mostraram que XAC0610 atua na regulação da motilidade e sobrevivência de Xac ao tratamento com H2O2. Ensaios de atividade enzimática demonstraram que XAC0610 é uma DGC cataliticamente ativa, e que a mutação sítio-dirigida de um resíduo conservado de lisina (Lys759) provoca uma grande redução na atividade de DGC. Os domínios GAF e PAS de XAC0610 aparentemente não atuam como domínios sensores, entretanto são importantes para a dimerização da proteína, necessária para a obtenção de altos níveis de atividade de DGC. Além disso, várias observações sugerem que XAC0610 não é submetida à inibição alostérica pelo produto, um mecanismo regulatório comumente utilizado para o controle da atividade de DGC. Por outro lado, os dados de cinética enzimática de XAC0610HIS-35-880 revelaram um efeito de cooperatividade positiva para a ligação dos substratos, com uma constante de dissociação para a ligação da primeira molécula de GTP (K1) cerca de 3-5 vezes maior que a constante de dissociação para a ligação da segunda molécula de GTP (K2). A partir deste estudo, nós apresentamos um esquema cinético geral mais apropriado para as análises dos dados cinéticos de enzimas DGCs e propomos que a ligação cooperativa do substrato talvez possa desempenhar um importante papel na regulação in vivo da atividade de algumas DGCs, aumentando sua sensibilidade a pequenas variações nos níveis celulares de GTP. Outra proteína caracterizada neste trabalho, XAC2446 possui um domínio GAF e um domínio GGDEF que, ao contrário do domínio GGDEF de XAC0610, não deve apresentar atividade de DGC. Mesmo assim, análises funcionais mostraram que XAC2446 regula negativamente a formação de biofilme e positivamente a motilidade de Xac. Ensaios de duplo híbrido em leveduras identificaram que XAC2446 interage com XAC2897, contendo um domínio GGDEF potencialmente ativo, e XAC1185, contendo um domínio HD fosfohidrolase de (p)ppGpp. Alguns estudos indicam que altos níveis celulares de c-di-GMP e baixos níveis de (p)ppGpp podem ser necessários durante a formação de biofilme. XAC2446 talvez possa atuar como um inibidor da atividade enzimática de XAC2897 e XAC1185 e influenciar, indiretamente e antagonicamente, tanto os níveis celulares de c-di-GMP quanto de (p)ppGpp. / Cyclic di-GMP is a bacterial second messenger that regulates a range of functions, including cellular motility, biofilm formation and virulence. This molecule is produced from two GTP substrates by the activity of diguanylate cyclases (DGCs) containing a GGDEF domain. The phytopathogenic bacteria Xanthomonas citri subsp. citri (Xanthomonas axonopodis pv citri; Xac) causes citrus canker in a wide variety of citrus species. The Xac genome codes for 31 proteins with GGDEF domains. Thirteen of the 31 Xac GGDEF domain-containing proteins also possess PAS (Per-Arnt-Sim) or GAF (cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA) domains that are ubiquitous signaling and sensory domains. In order to better understand the relationship between these commonly associated domains, biochemical and functional studies were carried out with the XAC0610 and XAC2446 proteins. XAC0610 is a large multi-domain protein containing one GAF domain, four PAS domains and one GGDEF domain. This protein has a demonstrable in vivo and in vitro diguanylate cyclase (DGC) activity. Analysis of a XacΔ0610 knockout strain revealed that XAC0610 plays a role in the regulation of Xac motility and resistance to H2O2. Site-directed mutagenesis of a conserved DGC lysine residue (Lys759 in XAC0610) resulted in a severe reduction in XAC0610 DGC activity. XAC0610 DGC activity was also impaired by removal of the N-terminal GAF and PAS domains, which are probably needed for proper protein dimerization. Furthermore, experimental and in silico analysis suggest that XAC0610 is not subject to allosteric product inhibition, a common regulatory mechanism for DGC activity control. Instead, steady-state kinetics of XAC0610 DGC activity revealed a positive cooperative effect of the GTP substrate with a dissociation constant for the binding of the first GTP molecule (K1) approximately three to five times greater than the dissociation constant for the binding of the second GTP molecule (K2). We present a general kinetics scheme that should be used when analyzing DGC kinetics data and propose that cooperative GTP binding could be a common, though up to now overlooked, feature of these enzymes that may in some cases offer a physiologically relevant mechanism for regulation of DGC activity in vivo. The other characterized protein, XAC2446, has a GAF domain and a degenerated GGDEF domain. Unlike XAC0610, XAC2446 should not present DGC activity. Nevertheless, functional analysis of XAC2446 demonstrated that it plays a role in the regulation of Xac motility and biofilm formation. A yeast two-hybrid screen identifies XAC2897 (a potentially active GGDEF domain-containing protein) and XAC1185 (a (p)ppGpp hydrolase) as specific binding partners of the XAC2446 protein. As indicated by studies in other bacteria, high cellular levels of c-di-GMP and low levels of (p)ppGpp may be both required for biofilm formation. It is possible that XAC2446 might have a role in the antagonistic regulation of c-di-GMP and (p)ppGpp cellular levels by acting as an inhibitor of both XAC2897 and XAC1185 enzymatic activities.

Orientador: Edson Antunes / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-21T23:29:22Z (GMT). No. of bitstreams: 1 Monteiro_PriscilaFukumura_M.pdf: 903494 bytes, checksum: 9d17a9657d72fedec2f6efc40cc3b082 (MD5) Previous issue date: 2013 / Resumo: As plaquetas desempenham uma função fisiológica importante no sistema hemostático, em resposta a lesão vascular através da prevenção da hemorragia. A adesão ou agregação plaquetária são eficazes na contribuição sinérgica de várias interações de múltiplos receptores, que transmitem sinais de ativação que iniciam uma série de respostas bioquímicas e morfológicas, associadas à remodelação do citoesqueleto, a secreção granular e a geração e liberação de agonistas endógenos solúveis, tais como ADP e tromboxano A2 (TXA2). O NO derivado da célula endotelial exerce um efeito inibitório na função da plaquetaria através da ativação de cGMP / PKG, a qual, por sua vez leva a uma redução na concentração de Ca2 + prevenindo assim a adesão e agregação de plaquetas à parede vascular. No entanto, a disfunção endotelial, presente em certas condições patológicas é caracterizada por uma diminuição da biodisponibilidade de NO que leva a ativação anormal das plaquetas conduzindo a trombose vascular À disfunção plaquetária é considerada uma fase final de complicações cardiovasculares no diabetes mellitus tipo II, obesidade, aterosclerose, levando ao resultado clínico, tais como enfarte do miocárdio, acidente vascular cerebral e doença arterial periférica. A obesidade é um importante problema de saúde pública, atingindo todas as idades e grupos socioeconômicos elevando a incidência de doenças cardiovasculares e endócrino-metabólica. Um estado crônico de stress oxidativo e inflamação são a marcados pela adiposidade que desempenha um papel crucial nos eventos fisiopatológicos desta desordem. Estes efeitos pró-inflamatórios e pró-oxidante estão associados com o aumento de ERO com diminuição da biodisponibilidade, o que aumenta o risco de eventos trombóticos aterosclerose. No entanto, os mecanismos pelos quais a adiposidade induz disfunção plaquetária são pouco esclarecidos. Além disso, a maioria dos eventos cardiovasculares fatais como consequência de complicação trombótica não estão associadas à estenose vascular completa, mas sim com as alterações de biomarcadores pró-inflamatórios e pró-oxidantes, o que pode prever futuros eventos cardiovasculares. Nossa hipótese é que a produção de ERO intraplaquetário causada pela adiposidade contribui para eventos trombóticos e distúrbios endocrinometabólico. Assim, investigou-se a reatividade plaquetária ex-vivo em resposta ao ADP e trombina, em ratos alimentados com dieta hiperlipídica, e o envolvimento de ERO e via do NO-cGMP na modulação da reatividade de plaquetária / Abstract: Platelets play an important physiological function in haemostasis system in response to vascular injury by preventing hemorrhage. Effective platelet adhesion and aggregation require the synergistic contribution of multiple receptor-ligand interactions that transmit activating signals initiating a range of platelet biochemical and morphological responses, linked to cytoskeleton remodeling, granule secretion and the generation and release of endogenous soluble agonists, such as ADP and thromboxane A2 (TXA2). Endothelial cell-derived nitric oxide (NO) exerts an inhibitory effect in the platelet function by activation of cGMP/PKG pathway, which in turn leads to reduction in concentration of Ca2+, thus preventing adhesion and aggregation of platelets to the vascular wall. Nonetheless, endothelium dysfunction, present in certain pathological conditions is characterized by a decreased NO bioavailability which incites abnormal platelet activation leading to vascular thrombosis. Platelet dysfunction is considered an end stage of cardiovascular complications in type II diabetes mellitus, obesity and atherosclerosis that results in clinical outcomes such as myocardial infarction, stroke and peripheral artery disease. Obesity is an important public health problem affecting all ages and socioeconomic groups greatly elevating the incidence of cardiovascular and endocrine-metabolic disorders. A chronic state of oxidative stress and inflammation are the hallmark of adiposity that plays a pivotal role in the physiopathological events in this disorder. These proinflammatory and pro-oxidant effects are associated with increased reactive-oxygen species (ROS) production and decreased NO bioavailability, which increases the risk of athero thrombotic events. Nonetheless, the exact mechanisms by which adiposity induces platelet dysfunction remain poorly investigated. In addition, most of fatal cardiovascular events as consequence of thrombotic complication are not associated with complete vascular stenosis, but rather with alterations of pro-inflammatory and pro-oxidant biomarkers, which can predict future cardiovascular events. We hypothesized that intraplatelet ROS production in adiposity contributes to thrombotic events in endocrinemetabolic disorders. Therefore, we have investigated the ex-vivo platelet reactivity in response to ADP and thrombin in high fat-fed rats, and the involvement of platelet-derived ROS and NO-cGMP pathway in modulating the platelet reactivity / Mestrado / Farmacologia / Mestra em Farmacologia

Des conditions de carence entrainent une mort cellulaire développementale chez le protiste Dictyostelium discoideum. Dans un système in vitro, des cellules de Dictyostelium sont mises en conditions de carence, puis l'addition des inducteurs DIF-1 ou c-di-GMP conduit à une mort cellulaire vacuolaire. DIF-1 est un polyketide produit par Dictyostelium et induisant la différenciation des cellules pré-tiges. Le dinucléotide cyclique c-di-GMP était connu comme un second messager chez les procaryotes, et comme un déclencheur de l'immunité innée dans des cellules de mammifères. Il a été montré par d'autres que des cellules de Dictyostelium peurent produire et détecter c-di-GMP.Pour analyser la signalisation par c-di-GMP chez Dictyostelium, nous avons utilisé la mutagénèse aléatoire et la mutagénèse ciblée. En utilisant des mutants inactivant stlB ou dmtA, nous avons démontré que DIF-1 endogène ou exogène est nécessaire pour la signalisation par c-di-GMP dans Dictyostelium. En conséquence, nous avons amélioré l'étape de sélection dans une mutagenèse aléatoire en utilisant c-di-GMP et un peu de DIF-1 comme inducteurs, ce qui a produit plusieurs mutants. Par ailleurs j’ai testé par mutagenèse ciblée des hypothèses basées sur les informations connues dans Dictyostelium ou d'autres types de mort cellulaire. Trois molécules ont été essayées, DDX41 comme récepteur putatif de c-di-GMP, l' uniport mitochondrial pour le Ca2+(MCU) et la Na+/K+ATPase (IonA).En résumé, au cours de ma thèse, nous avons démontré une relation entre la signalisation c-di-GMP et a signalisation DIF-1 dans Dictyostelium et identifié plusieurs nouvelles molécules de la mort cellulaire par mutagenèse aléatoire. / The protist Dictyostelium discoideum undergoes development cell death when under starvation. To investigate the molecular mechanism of Dictyostelium cell death, an in vitro system has been used. Dictyostelium cells were starved and then cell death was induced by DIF-1 or c-di-GMP. About 40h after induction, cells underwent vacuolar cell death. DIF-1 is a polyketide, produced by Dictyostelium prespore cells, which induces prestalk cell differentiation. c-di-GMP was well known not only as a second messenger produced and sensed by bacteria but also as a trigger of innate immunity in mammalian cells. Dictyostelium was recently found by another laboratory to produce and sense c-di-GMP. To analyze c-di-GMP signaling in Dictyostelium cell death, we used random mutagenesis and targeted mutagenesis. By using the knockout mutants stlB- and dmtA-, we demonstrated that endogenous or exogenous DIF-1 is required for c-di-GMP signaling in Dictyostelium. In contrast, endogenous c-di-GMP is not necessary for exogenous DIF-1 signaling. As a consequence, we improved the selection step in random mutagenesis by using c-di-GMP and a little DIF-1 as inducers, which produced several mutants. Another part of my project was to test by targeted mutagenesis some hypotheses, based on known information in Dictyostelium or other similar cell death types. Three molecules have been tested, the c-di-GMP putative receptor DDX41, the mitochondrial Ca2+ uniporter (MCU) and the Na+/K+-ATPase (IonA).In summary, during my thesis, we have demonstrated a relation between c-di-GMP signaling and DIF-1 signaling in Dictyostelium and identified several new cell death molecules by random mutagenesis.

T cells modified for expression of Chimeric Antigen Receptors (CARs) were the first genemodified cell products approved for use in cancer immunotherapy. CAR-T cells engineered with gammaretroviral or lentiviral vectors (RVs/LVs) targeting B-cell lymphomas and leukemias have shown excellent clinical efficacy and no malignant transformation due to insertional mutagenesis to date. Large-scale production of RVs/ LVs under good-manufacturing practices for CAR-T cell manufacturing has soared in recent years. However, manufacturing of RVs/LVs remains complex and costly, representing a logistical bottleneck for CAR-T cell production. Emerging gene-editing technologies are fostering a new paradigm in synthetic biology for the engineering and production of CAR-T cells. Firstly, the generation of the modular reagents utilized for gene editing with the CRISPR-Cas systems can be scaled-up with high precision under good manufacturing practices, are interchangeable and can be more sustainable in the long-run through the lower material costs. Secondly, gene editing exploits the precise insertion of CARs into defined genomic loci and allows combinatorial gene knock-ins and knock-outs with exciting and dynamic perspectives for T cell engineering to improve their therapeutic efficacy. Thirdly, allogeneic edited CAR-effector cells could eventually become available as “off-the-shelf” products. This review addresses important points to consider regarding the status quo, pending needs and perspectives for the forthright evolution from the viral towards gene editing developments for CAR-T cells.

Die Biofilmbildung von E. coli K-12 Makrokolonien wird durch eine komplexe Signalkaskade gesteuert, die den Wechsel von einer planktonischen, motilen und wachstums-orientierten hin zu einer mulitzellulären Lebensweise reguliert. Der sekundäre Botenstoff c-di-GMP spielt bei diesem Prozess eine Schlüsselrolle, indem er die Expression des Masterregulators CsgD kontrolliert. Die Ergebnisse dieser Arbeit führten zu einem besseren Verständnis der Signaltransduktion des RdcA-RdcB-DgcE-Komplexes. Der Sensor RdcA-RdcB nimmt das Gleichgewicht zwischen GTP und (p)ppGpp wahr, was eine präzise und schnelle Anpassung an Veränderungen ihrer Konzentrationen ermöglicht. Damit misst und kontrolliert das Sensor-Transduktionssystem ein komplexes Zusammenspiel der drei Nukleotide GTP, (p)ppGpp und c-di-GMP zur Regulation der ECM-Synthese in Makrokolonien. Darüber hinaus ermöglicht diese Arbeit Einblicke in die Biofilm-hemmende Wirkung von extrazellulären Signalen Kretischer Pflanzen. Während die Hauptstrategie darin zu bestehen scheint, die Polymerisation von Curli-Fasern zu verhindern, hemmen einige Pflanzen auch die Synthese der Matrix durch eine Störung das Gleichgewicht zwischen Wachstum/Proliferation und Überleben/Stressreaktion auf Transkriptionsebene. Des Weiteren zeigte diese Arbeit, dass c-di-GMP ein wirksamer globaler Regulator ist, der die Genexpression vieler stress- und metabolischer Gene moduliert. C-di-GMP hat einen Effekt auf die generelle Stressantwort durch differenzielle Regulierung einiger RpoS-abhängiger Gene. Eine Kombination aus spezifischen und globalen c-di-GMP-Effekten auf der Ebene der Transkription, des mRNA-Umsatzes und der Proteinacetylierung vermittelt dies. Insgesamt deuten die Ergebnisse darauf hin, dass sehr hohe globale c-di-GMP-Spiegel zu einer präzisen Anpassung der allgemeinen Stressantwort in Zellen der stationären Phase in der oberen Biofilmschicht führen, welche aufgrund ihrer Position in der exponiertesten Schicht des Biofilms erforderlich ist. / The macrocolony biofilm formation of E. coli K-12 is controlled by a complex network that regulates the switch from a planktonic and flagellated, growth-orientated to a multicellular lifestyle characterized by increased stress resistance and survival strategies. The second messenger c-di-GMP plays a key role in this process by controlling the expression of the master regulator CsgD. The results of this work led to a better understanding of the signaling mechanism of the RdcA-RdcB-DgcE complex. RdcA-RdcB senses the balance between GTP and (p)ppGpp which enables precise and fast adaptation to small changes in their concentrations. With this, the sensor-transduction system senses and/or controls a complex interplay of the three guanosine-based nucleotides GTP, (p)ppGpp, and c-di-GMP to regulate the ECM synthesis of a macrocolony. In addition, this work allows further insights into the anti-biofilm activity of extracellular stimuli by Cretan plants. While the major strategy seems to be preventing the polymerization of curli fibers, some plants also inhibit the synthesis of the matrix by modulating the master regulator CsgD caused by a disturbance of the growth/proliferation vs. survival/stress response balance. Furthermore, this work revealed that c-di-GMP is a potent global regulator that modulates gene expression and many stress-related and metabolic genes. C-di-GMP modulates the stationary phase response by differentially regulating a subset of RpoS-dependent genes. A combination of specific and global c-di-GMP effects on the level of transcription, mRNA turnover and protein acetylation mediate this regulation. Overall, the findings indicate that very high global c-di-GMP levels - found only in biofilms but not in liquid cultures of E. coli K-12 - result in a precise adjustment of the general stress response in stationary phase cells of the upper biofilm layer needed due to their position in the most exposed layer of the biofilm.