Les levures Candida sont des pathogènes opportunistes responsables d’infections graves chez les patients immunodéprimés. Au cours de ce travail, nous avons développé un modèle cellulaire in vitro pour la caractérisation multiparamétrique des phénotypes d’interaction entre les levures Candida et les macrophages et les neutrophiles, principaux effecteurs de la défense anti-Candida. Il repose sur l’utilisation de marqueurs fluorescents pour le suivi quantitatif de l’interaction en cytométrie en flux et en fluorimétrie. Ce modèle a été validé par la comparaison de l’interaction de trois espèces de levures, C. albicans, C. glabrata et C. lusitaniae, avec des macrophages murins et des neutrophiles humains. Deux stratégies principales de survie des levures à la phagocytose ont été mises en évidence : par la résistance à la phagolyse et la multiplication des levures à l’intérieur des phagocytes jusqu’à leur éclatement, ou par l’évitement de la phagocytose et la multiplication des levures à l’extérieur des phagocytes. L’interprétation des données quantitatives a été confirmée par microscopie à fluorescence et vidéo-microscopie. Afin de mieux comprendre les interactions Candida-phagocytes, nous avons mis au point des outils pour l’analyse fonctionnelle de gènes chez C. lusitaniae. Une stratégie de PCR chevauchante a été développée pour l’obtention de mutants nuls de C. lusitaniae, sans étape de clonage. C’est ainsi que le gène OLE2, codant une Δ9 désaturase d’acides gras potentiellement impliquée dans la biosynthèse de la prostaglandine PGE2, a été invalidé. Le mutant ole2Δ présentait de très nets défauts de filamentation et de reproduction sexuée. Par rapport à une souche sauvage, le mutant ole2∆ était massivement phagocyté par les macrophages, et la survie des phagocytes était plus importante, ce qui suggère un rôle important des lipides insaturés et des oxylipides dans la signalisation cellulaire au cours de l’interaction Candida-phagocytes. Dans la dernière partie de notre travail, nous avons construit une banque de 10 000 mutants de C. lusitaniae par l’intégration aléatoire d’un marqueur dans le génome. Le criblage de cette banque à travers notre modèle cellulaire d’interaction permettra d’identifier de nouveaux gènes impliqués dans l’interaction avec les phagocytes afin de mieux comprendre la physiopathologie des candidoses et de trouver de nouvelles pistes thérapeutiques. / Candida species are opportunistic pathogens causing severe infectious diseases in immunocompromised patients. In this work, we developed a tool for a multi-parameter characterization of the cell interactions between the yeasts Candida and both macrophages and neutrophils, which constitute the main defense against candidiasis. It relies on the labelling of each population with specific fluorescent markers, and on the use of fluorimetry and flow cytometry to assess interactions. The tool has been validated by comparing the interactions of three yeast species C. albicans, C. glabrata and C. lusitaniae, with murine macrophages and human neutrophils. We found that yeasts use two main ways for escaping phagocytosis, which has been confirmed using video-microscopy: either (1) by surviving to phagolysis and dividing into the phagosome until phagocytes burst, or (2) by avoiding phagocytosis and dividing outside phagocytes. In order to better understand the cellular and molecular mechanisms involved in Candida-phagocytes interactions, we developed new molecular tools for the functional analysis of genes in C. lusitaniae, notably a two-step cloning-free PCR-based method for the deletion of genes. This method was successfully used for the deletion of OLE2, a gene encoding a Δ9-desaturase of fatty acids, possibly implicated in prostaglandin PGE2 biosynthesis. The ole2Δ mutant exhibited strong defects in both pseudofilamention and sexual mating. During macrophages infection, ole2Δ yeast cells were massively internalized and triggered less phagocytes cell death than the wild type strain, suggesting that unsaturated fatty acids and/or oxylipids could play a role during interaction with phagocytes. Lastly, a bank of 10,000 mutants was constructed in C. lusitaniae by the random integration of a genetic marker in the genome. The screening of this bank through our tool to analyse cellular interactions will be undertaken to gain insights into understanding of the early stages of the infectious process.

Le virus du syndrome reproducteur et respiratoire porcin (VSRRP) est un pathogène d’importance dans l’industrie porcine et est responsable d’importantes pertes économiques. Il n’existe pas d’antiviral efficace contre celui-ci. Il a récemment été mis en évidence que le surnageant de culture d’Actinobacillus pleuropneumoniae, l’agent étiologique de la pleuropneumonie porcine, possédait une activité antivirale in vitro contre le VSRRP dans la lignée cellulaire SJPL. Les objectifs de mon projet sont (i) d’étudier les mécanismes cellulaires menant à l’activité antivirale causée par le surnageant de culture d’A. pleuropneumoniae, et (ii) de caractériser les molécules actives présentes dans le surnageant de culture d’A. pleuropneumoniae. Dans un premier temps, des analyses de protéome ont été effectuées et ont permis d’observer que le surnageant de culture modulait la régulation du cycle cellulaire. Dans le but d’analyser le cycle cellulaire des cellules SJPL, la cytométrie en flux a été utilisée et a permis de démontrer que le surnageant de culture induisait un arrêt du cycle cellulaire en phase G2/M. Deux inhibiteurs de la phase G2/M ont alors été utilisé. Il s'est avéré que ces inhibiteurs avaient la capacité d’inhiber le VSRRP dans les cellules SJPL. Enfin, la spectrométrie de masse a été utilisée dans le but de caractériser les molécules actives présentes dans le surnageant de culture d’A. pleuropneumoniae et d’identifier deux molécules. Ce projet a permis de démontrer pour la première fois qu’A. pleuropneumoniae est capable de perturber le cycle cellulaire et que ce dernier était un élément important dans l’effet antiviral contre le VSRRP. / Porcine reproductive and respiratory syndrome virus (PRRSV) is the most important pathogen in the swine industry and causes important economic losses. No effective antiviral drugs against it exist. It was recently reported that the culture supernatant of Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, possesses an antiviral activity in vitro against PRRSV in SJPL cells. The objectives of this project were (i) to identify the mechanism behind the antiviral activity displayed by A. pleuropneumoniae, and (ii) to characterize the active molecules present in the culture supernatant. Proteomic analyses were first conducted and demonstrated the culture supernatant ability to induce modulations of the cell cycle regulation. In order to determine the SJPL cell cycle, flow cytometry analyses were performed and demonstrated that the culture supernatant induced a G2/M-phase cell cycle arrest. Two G2/M-phase cell cycle inhibitors were then used and their ability to inhibit PRRSV infection in SJPL cells was demonstrated. Finally, in order to characterize the active molecules present in the A. pleuropneumoniae culture supernatant, mass spectrometry was used and two molecules were identified. This is the first study demonstrating the A. pleuropneumoniae ability to disrupt cell cycle and the cell cycle importance to the inhibitory activity against PRRSV.

Mycoplasma hominis est une bactérie opportuniste qui peut être responsable d’infections du tractus urogénital, d’infections néonatales ou d’infections disséminées notamment chez les patients immunodéprimés. La membrane des mycoplasmes constitue l’interface d’interaction directe avec le milieu extérieur en raison de l’absence de paroi. Cette membrane contient de nombreuses lipoprotéines qui ont le pouvoir d’activer des cellules dendritiques humaines (hDCs), d’induire la production de cytokines et de polariser le système immunitaire adaptatif. Nous avons étudié l’interaction de M. hominis PG21 avec les hDCs en nous penchant d’une part sur la fraction du mycoplasme qui active les hDCs et d’autre part sur la réponse immunitaire innée des hDCs. Apres avoir déterminé les lipoprotéines contenues dans un extrait TX-114 de M. hominis PG21, nous avons enrichi en lipoprotéines bioactives une fraction de vésicules membranaires du mycoplasme par une double extraction utilisant deux détergents non dénaturants, le Sarkosyl puis le Triton X-114. Apres séparation par SDS-PAGE, nous avons identifié vingt lipoprotéines qui pourraient entrainer la sécrétion d’IL-23 par les hDCs, notamment la lipoprotéine MHO_4720. Un lipopeptide synthétique correspondant à la fraction N-terminale de MHO_4720 est capable de stimuler les hDCs. En analysant les variations transcriptionnelles des gènes codant pour les 48 lipoprotéines de M. hominis PG21 par qRT-PCR, nous avons également déterminé que 21 lipoprotéines sont surexprimées après 4h ou 24h de contact entre le mycoplasme et les hDCs. Enfin, la réponse cellulaire a été évaluée par PCR array et ELISA. Nous avons observé l’activation d’inflammasome(s) par la mise en évidence de la production d’IL-1β dépendant de la caspase 5. / Mycoplasma hominis is involved in urogenital tract infections, neonatal infections or disseminated infections particularly in immunocompromised patients. Mycoplasmas have no cell wall and their membrane is the main interface mediating the interaction between the mycoplasma and its environment. Lipoproteins that are anchored to the extracellular side of the plasma membrane are known to induce the maturation of human dendritic cells (hDCs), to stimulate the pro-inflammatory cytokine production by hDCs and to polarize the adaptive immune system. We studied the interaction of M. hominis PG21 with hDCs in order to assess the lipoproteins that can induce the stimulation of hDCs, to determine the lipoproteins that are regulated upon interaction of the mycoplasma with the host cell and to evaluate the innate host cell response. Using a double extraction strategy with two non-denaturing detergents, Sarkosyl then Triton X-114, and separation by SDS-PAGE, we found that 20 lipoproteins may induce the secretion of IL-23 by the hDCs, especially the MHO_4720 lipoprotein. We showed that a synthetic lipopeptide corresponding to the N-terminus part of the MHO_4720 lipoprotein can stimulate the hDCs in a dose-dependent manner. Using qRT-PCR for the evaluation of the transcriptional regulation of the 48 lipoprotein-coding genes of M. hominis PG21, we also determined that 21 lipoproteins were upregulated upon 4h and 24h of contact of M. hominis with hDCs. Finally, the hDC innate immune response was evaluated by PCR array and ELISA. We observed a caspase 5-dependent production of IL- 1β corresponding to the activation of an inflammasome.

Study of cell signalling pathways affected by pathogen entry comprises a fundamental aspect of understanding host-pathogen interactions. In this respect, the current study attempted to ascribe novel roles to Bone Morphogenesis Protein (BMP) signaling during infection. BMP pathway has been majorly studied in context of development where it plays an imperative role and its contribution to immunity has been poorly documented. Subsequent narrative talks about the perturbation of BMP signaling in context of specific signaling networks and its collaboration with other molecular players of host innate armamentarium. There is a pressing need to develop effective chemotherapy against Mycobacterium tuberculosis, the causative agent of tuberculosis, which has garnered the world’s attention as a leading cause of public health emergency. The tyrosine kinase, c-Abl was previously reported to be activated in murine bone marrow derived macrophages infected with mycobacteria. Yet, the identities of host signaling players and mechanisms exploited by mycobacteria in association with c-Abl lacked identification. Here, we deciphered an intricate signaling mechanism linking tyrosine kinase c-Abl, chromatin modifier, lysine acetyl transferase KAT5 and transcription factor, TWIST1 acting at Bmp2 and Bmp4 promoters. This molecular circuitry was observed to affect mycobacterial survival. Emerging studies suggest repurposing of c-Abl inhibitor, Imatinib, as an adjunct to existing anti-tuberculosis therapy. Through the use of Imatinib in an established model of tuberculosis, we demonstrated the ability of c-Abl inhibitors in potentiating innate immune responses. Distinctive instances report the cross regulation among Pattern Recognition Receptors (PRRs). Interestingly, TLR3 signaling cascade induced in response to its cognate ligand was dampened through c-Abl-BMP induced miR27a. TLR3 is known to activate immune surveillance upon viral infections; however, recent studies also suggest its role in tumour regression and induction of apoptosis. Our observation of mycobacteria elicited down regulation of TLR3 pathway corroborated with increased incidences of lung cancer among TB patients and mycobacterial evasion of a well characterized form of cell-death i.e. apoptosis. Further, we utilized a panel of such Mtb mutants associated with virulence and questioned their relevance in the activation of c-Abl-dependent BMP signaling. We found that nitric oxide, hypoxia and carbon monoxide-responsive mycobacterial WhiB3 and DosR, but not the sec-dependent protein secretion pathway, orchestrate mycobacteria driven c-Abl-BMP signaling. Continuing with the theme of exploring roles for BMP signaling during infection, we identified an important role for the C-type Lectin Receptor (CLR), Dectin-2, in activating Candida albicans-driven BMP signaling. Mounting evidences suggest BMP antagonists promote repair and regeneration in cells of varied lineages. We observed a role for BMP signaling in aggravating MMP2 and MMP9, factors that result in chronic non-healing wounds. Wounds are now increasingly recognized as being colonized with fungi along with bacteria. We propose a role for C. albicans orchestrated BMP signaling in contributing to enriched repressive methylation at Egf, Pdgf and Tissue Inhibitors of Matrix Metalloproteases (Timp2/3/4) promoters. Repressive H3K27me3 at these loci impedes the reparative tissue homeostasis, resulting in C. albicans endorsed impaired wound healing. Altogether, we uncovered hitherto unknown roles of BMP signaling during mycobacterial and fungal infections, enabling a better understanding of lesser studied pathways in mediating pathogenesis.

Mycobacterium tuberculosis (M.tb), the causative agent of tuberculosis (TB), has remained the largest killer among infectious diseases for over a century. The increasing emergence of drug resistant varieties such as the multidrug resistant (MDR) and extremely drug resistant (XDR) strains are only increasing the global burden of the disease. Available statistics indicate that nearly one-third of the world’s population is infected, where the bacteria remains in the latent state but can reactivate into an actively growing stage to cause disease when the individual is immunocompromised. It is thus immensely important to rethink newer strategies for containing and combating the spread of this disease. Extraction of iron from the host cell is one of the many factors that enable the bacterium to survive in the harsh environments of the host macrophages and promote tuberculosis. Host–pathogen interactions can be interpreted as the battle of two systems, each aiming to overcome the other. From the host’s perspective, iron is essential for diverse processes such as oxygen transport, repression, detoxification and DNA synthesis. Infact, during infection, both the host and the pathogen are known to fight for the available iron, thereby influencing the outcome of the infection. It is of no surprise therefore, that many studies have investigated several components of the iron regulatory machinery of M.tb and the host. However, very few attempts have been made to study the interactions between these components and how such interactions lead to a better adapted phenotype. Such studies require exploration at multiple levels of structural and functional complexity, thereby necessitating the use of a multiscale approach. Systems biology adopts an integrated approach to study and understand the function of biological systems. It involves building large scale models based on individual biochemical interactions, followed by model validation and predictions of the system’s response to perturbations, such as a gene knock-out or exposure to drug. In multiscale modeling, an approach employed in this thesis, a particular biological phenomenon is studied at different spatiotemporal levels. Studying responses at multiple scales provides a broader picture of the communications that occur between a host and pathogen. Moreover, such an analysis also provides valuable insights into how perturbation at a particular level can elicit responses at another level and help in the identification of crucial inter-level communications that can possibly be hindered or activated for a desired physiological outcome. The broad objectives of this thesis was to obtain a comprehensive in silico understanding of mycobacterial iron homeostasis and metabolism, the influence of iron on host-pathogen interactions, identification of key players that mediate such interactions, determination of the molecular consequences of inhibiting the key players and finally the global response of M.tb to altered iron concentration. Perturbation of iron homeostasis holds a strong therapeutic potential, given its essentiality in both the host and the pathogen. Understanding the workings of iron metabolism and regulation in M.tb has been a main objective, so as to ultimately obtain insights about specific therapeutic strategies that capitalize on the criticality of iron concentration. An in-depth study of iron metabolism and regulation is performed at different levels of temporal and spatial scales using diverse methods, each appropriate to investigate biological events associated with the different scales. The specific investigations carried out in the thesis are as follows, a) Reconstruction of a host-pathogen interaction (HPI) model, with focus on iron homeostasis. This study represented the inter-cellular level analysis and was crucial for the identification of key players that mediate communication between the host and pathogen. Additionally, the model also provided a mathematical framework to study the effect of perturbations and gene knock-outs. b) Understanding the influence of iron on IdeR, an iron-responsive transcription factor, also identified as a key player in the HPI model. The study was carried out at the molecular level to identify atomistic details of how IdeR senses iron and the resulting structural modifications, which finally enables IdeR-DNA interaction. The study enabled identification of residues for the functioning of IdeR. c) Genome scale identification of genes that are regulated by IdeR to obtain an overview of the various biological processes affected by changing iron concentrations and IdeR mutation in M.tb. d) To understand the direct and indirect influences of iron and IdeR on the M.tb proteome using large scale protein-protein interaction network. The study enabled identification of highest differentially regulated genes and altered activity of the different biological processes under differing iron concentrations and regulation. e) Systems level analysis of the M.tb metabolome to investigate the metabolic re-adjustments undertaken by M.tb to adapt to altered iron concentration and regulation. The conceptual details and the background of each of the methods used to study the specific aims are provided in the Methodology chapter (Chapter 2). Construction of the host-pathogen interaction (HPI) model and the insights obtained from this study are presented in Chapter 3. A rule based HPI model was built with a focus on the iron regulatory mechanisms in both the host and pathogen. The model consisted of 194 rules, of which 4 rules represented interactions between the host and pathogen. The model not only represented an overview of iron metabolism but also allowed prediction of critical interaction that had the potential to form bottleneck in the system so as to control bacterial proliferation. Infact, model simulation led to the identification of 5 bottlenecks or chokepoints in the system, which if perturbed, could successfully interfere with the host-pathogen dynamics in favour of the host. The model also provided a framework to test perturbation strategies based on the bottlenecks. The study also established the importance of an iron responsive transcription factor, IdeR for regulating iron concentration in the pathogen and mediating host-pathogen interactions. Additionally, the importance of mycobactin and transferrin as key molecular players, involved in host-pathogen dynamics was also determined. The model provided a mathematical framework to test TB pathogenesis and provided significant insights about key molecular players and perturbation strategies that can be used to enhance therapeutic strategies. Given the importance of IdeR in HPI, its molecular mechanism of activation and dimerization was explored in Chapter 4. The main objective of the study was to explore the structural details of IdeR and its iron sensing capacity at the molecular level. A combination of molecular dynamics and protein structure network (PSN) were used to analyse IdeR monomers and dimers in the presence and absence of iron. PSNs used in this thesis are based on non-covalent interactions between sidechain atoms and are quite efficient in identifying iron induced subtle conformational variations. The study distinctly indicated the role of iron in IdeR stability. Further, it was observed that IdeR monomers can take up two major conformations, the ‘open’ and ‘close’ conformation with the iron bound structure preferring the ‘close’ conformation. Major structural changes, such as the N-terminal folding and increased propensity for dimerization were observed upon iron binding. Interestingly, careful analysis of structure suggests a role of these structural modifications towards DNA binding and has been tested in the next chapter. Overall, the results clearly highlight the influence of iron on IdeR activation and dimerization. The predisposition of IdeR to bind to DNA in the presence of metal is clearly visible even when the simulations are performed solely on protein molecules. However, to confirm the conjectures proposed in this chapter and to obtain the atomistic details of IdeR-DNA interactions, the IdeR-DNA complex was investigated. Chapter 5 focuses on the mechanistic details of IdeR-DNA interactions and the influence of iron on the same. IdeR is known to bind to a specific stretch of DNA, known as the ‘iron-box’ motif to form a dimer-of-dimer complex. Molecular dynamics followed by protein-DNA bipartite network analysis was performed on a set of four IdeR-DNA complexes to obtain a molecular level understanding of IdeR-DNA interactions. A striking observation was the dissociation of IdeR-DNA complex in the absence of iron, undoubtedly establishing the importance of iron for IdeR-DNA binding. At the residue level, hydrogen bond and non-covalent interactions clearly established the importance of N-terminal residues for DNA binding, thereby confirming the conjecture put forth in the previous chapter. An important aspect studied in this chapter is the allosteric nature of IdeR-DNA binding. Recent years have witnessed a paradigm shift in the understanding of allostery. Unlike the classical definition of allostery that was based on static structures, the newer definition is based on the conformational ensemble as represented by the shift in the energy landscape of the protein. The allosteric nature of IdeR-DNA complex was probed using simulated trajectories and indeed they suggest iron to be an allosteric regulator of the protein. Finally, based on the known experimental data and observations presented in Chapters 4 and 5, a multi-step model of IdeR activation and DNA binding has been proposed. In chapter 6, a global perspective of IdeR regulation in M.tb was obtained. This was important to gain insights about the influences of iron and its regulation at the M.tb cellular level. A genome scale identification of all possible IdeR targets based on the presence of ‘iron-box’ motif in the promoter region of the genes was carried out. An interesting aspect of this study was the use of energetic information from previous molecular dynamics study as an input for generation of the motif. A total of 255 such IdeR targets were identified and converted into an IdeR target network (IdeRnet). Along with IdeRnet, an unbiased systems level protein-protein interaction network was also generated. To study the response of the pathogen to external perturbations, iron-specific gene expression data was integrated into the network as node weights and edge weights. Analysis of IdeRnet provides interesting associations between fatty acid metabolism and IdeR regulations. Specific genes such as fadD32, DesA3 or lppW have been found to be affected by IdeR mutation. While IdeRnet discusses the direct associations, the global level responses are monitored by analysing pathways for the flow of information in the protein-protein interaction network (PPInet). Comparisons of the PPInets under conditions such as altering iron concentrations and lack of iron homeostasis led to the identification of the ‘top-most’ active paths under the different conditions. The study clearly suggests a halt in the protein synthesis machinery and decreased energy consumption under iron scarcity and an uninhibited consumption of energy when iron homeostasis is perturbed. In the final chapter (Chapter 7), flux balance analyses has been used to investigate the influence of iron on M.tb metabolism. The importance of iron for metabolic enzymes has already been established in the previous chapter. Additionally, M.tb is known to produce siderophores, an important metabolite that requires amino acids as its precursors, for iron extraction. All this, together highlighted the importance of iron and its regulation of M.tb metabolism. Flux balance analysis has been used previously to study the metabolic alterations that occur in an organism under different conditions. For this study, iron specific gene expression data was also incorporated into the model as reaction bounds and the flux values so obtained were compared in different environmental conditions. The study provided valuable insights into the metabolic adjustments taken up by M.tb under iron stress conditions and correlates well with the responses observed from the interactome as well as experimental observations. Most significantly, changes were observed in the energy preferences of the cell. For instance, it was noted that while the wild type strain of M.tb prefers synthesis of ATP via glycolysis, the IdeR mutant strain preferred oxidative phosphorylation. The picture becomes clearer when one accounts for the uncontrolled utilization of energy and rapid activation of protein synthesis machinery in the IdeR mutant strain. Biological systems are inherently multiscale in nature and therefore for a successful drug target regime, analysis of the genome to the phenome, which captures interactions at multiple levels, is essential. In this thesis, a detailed understanding of iron homeostasis and regulation in M.tb at multiple levels has been attempted. More importantly, insights obtained from one level, formed questions in the next level. The study was initiated at the inter-cellular level, where the influence of iron on HPI was modeled and analysed. From this study, IdeR, an iron-responsive transcription factor was identified as a key player that had the potential to alter host-pathogen interactions in the favour of the host. For a complete understanding of how IdeR regulates iron homeostasis, it was imperative to obtain a molecular level insight of its mechanism of action. Finally, the various aspects of IdeR regulation were investigated at the cellular level by analysing direct and indirect influences of IdeR on M.tb proteome and metabolome. The study suggests certain therapeutic interventions, such as 1) reduction in the concentration of free transferrin various, 2) mutations at the N-terminal sites of IdeR, 3) regulation of proteins involved in production of mycolic acids by iron and 4) perturbation of altering energy sources, which capitalize on iron and should be investigated in detail. In summary, the consequences of iron on TB infection were studied by threading different levels. This is based on the belief that most biological functions involve multiple spatio-temporal levels with frequent cross talks between the different levels, thereby making such multiscale approaches very useful.

La leptospirose est une zoonose causée par les bactéries du genre Leptospira. Elle touche près de 1 million d'individus par an dans le monde entier et sévit à l'état endémique dans les pays au climat tropical tel que La Réunion. Les manifestations habituelles sont variables d'un individu à l'autre et englobent une simple fièvre jusqu'aux défaillances poly-viscérales avec mortalité dans 5 à 10% des cas. Sa physiopathologie est encore mal comprise, en particulier la part que joue une réponse immunitaire inappropriée dans la genèse des manifestations graves qui surviennent en quelques heures, et avant la mise en place d'une réponse immunitaire adaptative propre à éliminer le microorganisme. Si l'échappement de la bactérie au système du complément est bien documenté, le rôle des acteurs cellulaires du système immunitaire inné reste à étayer. Notre étude avait donc pour objectif d'explorer l'immunopathologie de la leptospirose humaine dans la phase initiale de l’infection. Notre méthodologie s'est appuyée principalement sur des analyses quantitatives et qualitatives des acteurs cellulaires du système immunitaire inné à partir de prélèvements sanguins en phase précoce de la maladie, et comparaison avec la phase de convalescence et des sujets contrôles. Dans un premier temps nous avons montré qu'une population particulière de lymphocytes T impliquée dans la réponse immune innée, les lymphocytes Tγδ, avaient un taux abaissé et que cette baisse était corrélée à la charge bactérienne ainsi qu'à l’intensité de l'atteinte hépatique classiquement retrouvée lors de la leptospirose. Dans un deuxième temps, nous avons analysé les polynucléaires neutrophiles circulants dont le taux augmente d’autant plus que la maladie est sévère, mais sans pour autant présenter de modification de certains marqueurs d’activation ou de recrutement tissulaire (CD15, CD11b, CD182). Une des principales chimiokines des neutrophiles, l'interleukine 8, était à taux peu élevés. Les derniers travaux concernent les principales formes solubles issues des molécules membranaires impliquées dans le processus de recrutement/diapédèse leucocytaire. Nous retrouvons de manière isolée une forte élévation des formes solubles d'E-sélectine et ICAM-1 qui sont notamment exprimées par les cellules endothéliales. Ces augmentations n'étaient pas corrélées aux marqueurs de gravité de la maladie. La signification biologique de cette élévation n’est pas encore connue lors de la leptospirose. L'ensemble de nos données permet d’apporter des informations nouvelles sur des acteurs du système immunitaire inné présents dans le compartiment vasculaire lors de la leptospirose humaine. Cette réponse immunitaire semble inadaptée pour permettre une clairance du pathogène au stade de dissémination hématogène. / Leptospirosis is a bacterial zoonosis caused by Leptospira and affecting 1 million people each year worldwide and mainly in tropical areas such as Reunion Island. Usual presentations encompass flu-like syndrome to multiorgan failure with mortality rate between 5 to 10%. To date, pathophysiology in humans is poorly understood, notably the capacity of innateimmunity to mount a robust response to clear pathogen or to induce tissue damages and contributing to disease severity. Our study aimed at assessing the role of innate immune cells and molecules within the first days of leptospiral infection.Using blood samples, we performed quantitative and qualitative assessment of circulating innate immune cells from leptospirosis cases and healthy controls. The first study explored the levels of gamma-delta T-cells (γδT-cells), a subset of unconventional T cells with innate immune functions. Gamma-delta T cells were found deeply decreased and levels wereinversely correlated to bacterial burden and liver damage. The second study focused on membrane bound receptors indicative of activation and tissue migration ability of neutrophil polymorphonuclear cells: CD15, CD11b, and CD182. Although neutrophil rates were high in leptospirosis cases, the levels of studied receptors were either lower (CD15) or identical to healthy controls (CD11b, CD182). In addition, only low levels of interleukin-8, a key chemokine for neutrophils, was detected in patients. Lastly, we ascertained the plasmatic levels of several shed cell adhesion molecules notably expressed by endothelial cells. The levels of soluble E-selectin and ICAM-1 were significantly increased compared to controls, while P-selectin level was lower. We did not find any correlation with disease severity or organ failure. This finding indicates that endothelial cell may be activated but further experiments are warranted to explain the functional impact of our findings. Altogether, our results add to the field of knowledge of leptospirosis pathophysiology, and in particular the implication of key innate immune cells at the stage of plasmatic bacterial dissemination. Our findings will support the view that there is an inappropriate immune response to Leptospira.

Legionella pneumophila est une bactérie opportuniste qui émerge de l'environnement après multiplication dans des amibes et peut infecter accidentellement les macrophages alvéolaires humains, provoquant une pneumonie sévère, la légionellose. La capacité de L. pneumophila à survivre dans ses cellules hôtes est strictement dépendante du système de sécrétion de type 4 Dot/Icm, qui sécrète un large répertoire d'effecteurs dans le cytosol de l'hôte. Identifier la contribution individuelle de chaque protéine bactérienne sécrétée par le système Dot/Icm, dans le cycle infectieux de L. pneumophila reste un enjeu majeur pour comprendre les bases moléculaires de la virulence des légionelles. Mes travaux de thèse participent à cet objectif en caractérisant la voie cellulaire ciblée par la protéine kinase LegK2. Des tests d'interaction et de phosphorylation ont identifié le complexe nucléateur d'actine ARP2/3 comme cible de LegK2. Suite à l'adressage de LegK2 à la surface de la vacuole après sa translocation dans le cytosol de l'hôte, l'interaction LegK2-ARP2/3 inhibe la polymérisation d'actine sur le phagosome. Cette inhibition permet à Legionella de diminuer le trafic des endosomes tardifs et/ou des lysosomes vers le phagosome et favorise ainsi l'évasion du phagosome à la voie de dégradation endocytique. L'interaction LegK2-ARP2/3 met en évidence un mécanisme original de virulence dans lequel le remodelage local du cytosquelette d'actine de la cellule hôte permet à la bactérie de manipuler le trafic vésiculaire pour échapper aux défenses de l'hôte / Legionella pneumophila is an opportunistic bacterium that emerges from the environment after multiplication in protozoans and can accidentally infect human alveolar macrophages leading to a severe pneumonia, the legionellosis. The L. pneumophila ability to survive within host-cells is strictly dependent on the Dot/Icm Type 4 Secretion System that translocates a large repertoire of effectors into the host cell cytosol. Deciphering the individual contribution of each bacterial protein translocated by the Dot/Icm system in the L. pneumophila infectious cycle remains a major challenge to understand the molecular basis of Legionella virulence. My works contribute to this objective by characterizing the cellular pathway targeted by the protein kinase LegK2. Interaction and phosphorylation assays identified the actin nucleator ARP2/3 complex as the target of LegK2. Following the LegK2 addressing to the vacuole surface after its translocation into host cytosol, LegK2- ARP2/3 interplay inhibits the actin polymerization on the phagosome. This inhibition allows Legionella to decrease the late endosome/lysosome trafficking towards the phagosome and promotes the phagosome evasion from endocytic degradation pathway. LegK2-ARP2/3 interplay highlights an original mechanism of virulence wherein the local actin cytoskeleton remodeling of host cell allows bacteria to hijack the vesicles trafficking in order to escape host-cell defenses

Le champignon Fusarium graminearum est l'un des principaux agents responsables de la fusariose des épis, une maladie nécrosante des céréales associée à une contamination des grains et des aliments par des mycotoxines. De récentes observations suggèrent une évolution de l’agressivité des populations de ce pathogène, questionnant l’efficacité et la durabilité des moyens de luttes actuels. Mieux anticiper cette évolution nécessite une meilleure caractérisation de la diversité phénotypique et génotypique existante entre souches. Six nouveaux génomes de F. graminearum ont été séquencés et ont permis l’identification et la caractérisation de 243 000 variations génétiques. La majorité de ces variants (77%) est concentrée dans des îlots de polymorphisme, représentant 32% du génome et enrichis en probables effecteurs liés à la pathogénicité de F. graminearum. La construction d’une population recombinante, et son génotypage avec 1 300 marqueurs moléculaires, ont permis le développement de la première carte génétique à haute-densité de l’espèce. La corrélation entre le taux de recombinaison et le polymorphisme a mis en évidence une organisation « à deux-vitesses » du génome de cette espèce. Finalement, l’intégration de ces données dans une approche de génétique quantitative a permis l’identification d’un locus polymorphe, affectant le gène FgVeA, et responsable de 90% de la variation d’agressivité et de la production de mycotoxine observée. Les différents résultats obtenus durant ces travaux font l’objet d’une discussion générale sur le potentiel adaptatif et d’évolution de ce pathogène. / F. graminearum is one of the main causal agents of the fusarium head-blight (FHB), a cereal disease leading to head necrosis, in addition to grain and food/feed contamination by stable and toxic metabolites. Recent observations refer to an increase of pathogenicity, questioning efficiency and durability of current management practices. In order to anticipate this evolution, we must bring a deeper characterization of the currently existing diversity. Six new genomes of F. graminearum were sequenced, and 243,000 genetic variations have been identified and characterized. Seventy seven percent of the total number of the variants was located within 32% of the genome, delineating highly polymorphic islands. These islands are enriched with probable effectors linked to Fusarium’s pathogenicity. The construction and the genotyping on 1,300 molecular markers of a recombinant population have enabled the development of the first high-density genetic map of the species. The remarkable correlation between polymorphism and recombination rate highlighted the 'two-speed' genome organization of this pathogen. Finally, the integration of these data through a quantitative genetic approach allowed the discovery of one quantitative trait locus, likely to affect the gene FgVeA, and responsible for 90% of the observed variation of aggressiveness and mycotoxin production. These results are discussed in the light of F. graminearum’s adaptive potential and evolution.

The Gram-negative aerobic coccobacillus Bordetella pertussis is one of the few exclusively human pathogens and the main causative agent of the respiratory infectious disease called pertussis, or whooping cough. Despite global vaccination programs, pertussis remains an important public-health burden and still accounts for over 100,000 infant deaths and over a dozen of millions of whooping cough cases every year. Substantial effort is devoted to studies on the mechanisms of action of virulence factors of B. pertussis, but the biology of interactions of B. pertussis with its human host remains largely underexplored. Evolution, genetics and adaptation of B. pertussis to the complex environment of human nasopharynx and the mechanisms enabling B. pertussis to overcome host innate and adaptive mucosal immune defenses, remain poorly understood. In such situations, unbiased exploratory omics approaches represent valuable tools for uncovering of unknown aspects of host-pathogen interactions and open the path to detailed analysis of virulence-underlying processes by mechanistic studies. In this thesis, I am presenting the results of three omics projects on B. pertussis biology that involved high-throughput proteomics. In the inital phosphoprotemics project, we analyzed the kinase signaling pathways hijacked...

Fusarium head blight (FHB), caused mainly by Fusarium graminearum (teleomorph: Gibberella zeae), is one of the most damaging diseases of wheat. A ‘Brio’/‘TC 67’ spring wheat population was used to map quantitative trait loci (QTLs) for resistance to FHB, and to study the association of morphological and developmental characteristics with FHB resistance. Interval mapping (IM) detected a major QTL on chromosome 5AL for resistance to disease severity (type II resistance) and Fusarium-damaged kernels (FDK) under greenhouse and field conditions, respectively. Inconsistent QTL(s) was also detected on chromosome 5BS for disease severity and index using field data. The associations of plant height and number of days to anthesis were negative with disease incidence, severity, index, and deoxynivalenol (DON) accumulation data under field conditions. However, number of days to anthesis was positively correlated with disease severity (greenhouse) and FDK (field). Awnedness had a negative effect on FHB, namely the presence of awns resulted in less disease in the population. Spike threshability also affected FHB so that the hard threshable genotypes represented lower disease. Phylogenetic relationships of putative F. graminearum isolates from different sources were characterized using Tri101 gene sequencing data. Canadian and Iranian isolates clustered in F. graminearum lineage 7 (=F. graminearum sensu stricto) within the F. graminearum clade while the isolates received from CIMMYT, Mexico were placed in F. graminearum lineage 3 (=Fusarium boothii) within the Fg clade or Fusarium cerealis. The PCR assay based on the Tri12 gene revealed the presence of the NIV, 3-ADON, and 15-ADON chemotypes with 15-ADON being the predominant chemotype. While we did not find the NIV chemotype among the Canadian isolates, it was the predominant chemotype among the Iranian isolates. High variation in aggressiveness was observed among and within Fusarium species tested, with the isolates of F. graminearum sensu stricto being the most aggressive and the NIV chemotype being the least aggressive. The interactions between Fusarium isolates and wheat genotypes from different sources were investigated by inoculating isolates of F. graminearum sensu stricto and F. boothii on wheat genotypes. Significant differences were observed among the genotypes inoculated by single isolates. Results also showed significant interactions between Fusarium isolates and wheat genotypes. The F. boothii isolates from CIMMYT produced low disease symptom and infection on wheat genotypes regardless of the origin of the genotypes while F. graminearum sensu stricto isolates from Canada and Iran resulted in higher FHB scores.