Mycobacterium abscessus (Mabs) est un pathogène émergent entrainant de graves infections pulmonaires, notamment chez les patients mucoviscidosiques. L'expression différentielle des glycopeptidolipides (GPLs) permet de distinguer le morphotype rugueux (R), présentant un défaut de synthèse des GPLs, du morphotype lisse (S) exprimant les GPLs. Différents modèles ex vivo et in vivo rapportent que le variant R est impliqué dans des manifestations plus sévères associées à une réponse inflammatoire intense. Cependant, ces modèles d'étude restent particulièrement limités pour élucider les caractéristiques de cette infection. L'embryon de zebrafish (ZF) offre de nombreux avantages motivant et validant son utilisation pour une meilleure compréhension des maladies infectieuses. Ce travail de thèse a pour objectif de développer un modèle d'infection de Mabs dans l'embryon de ZF.Pour étudier la physiopathologie de l'infection de Mabs dans ce modèle, l'élaboration d'un protocole de microinjection des bactéries et des méthodes de suivi de la charge bactérienne ont été réalisés. Les techniques d'imagerie ont été employées pour déterminer la chronologie de l'infection au sein des embryons infectés. Les techniques de qRT-PCR, l'utilisation de lignées de ZF transgéniques et la technologie antisens (morpholinos) ont été utilisées pour déterminer le rôle du système immunitaire (Si) inné et de l'inflammation dans la physiopathologie infectieuse. Par ailleurs, le potentiel du ZF en tant qu'organisme modèle en pharmacologie a été mis à profit pour étudier l'activité in vivo d'antibiotiques (ATB) sur Mabs.Le variant R induit une infection létale plus robuste que le S, caractérisée par le développement d'abcès au niveau du système nerveux central (SNC) associés à une réponse inflammatoire intense et au recrutement de neutrophiles. Le suivi des infections a révélé que les bactéries étaient rapidement phagocytées par les macrophages au niveau du site d'injection. Une fois infectés, ces derniers traversent la barrière endothéliale et transportent les mycobactéries dans les tissus du SNC, soulignant leur rôle clé dans la dissémination du pathogène. Des expériences menées dans des embryons dépourvus de macrophages ont validé ces observations en montrant que les bactéries étaient incapables de rejoindre le SNC et restaient confinées dans le système vasculaire. Implanté au sein du tissu nerveux, le macrophage infecté entre en apoptose, libérant ainsi le pathogène dans le milieu extracellulaire. Une fois libéré, à la différence du variant S, la morphotype R forme des cordes augmentant rapidement de taille et capables d'initier le développement d'abcès volumineux. La taille démesurée de ces cordes par rapport à celle des phagocytes professionnels représenterait une stratégie permettant au variant R d'échapper à la phagocytose et donc de promouvoir sa multiplication extracellulaire et d'assurer la progression létale du processus infectieux. Enfin, ce modèle nous a permis de déterminer, en temps réel, l'efficacité thérapeutique de plusieurs ATBs sur les embryons infectés,qui s'accompagne d'une forte réduction de mortalité des embryons et d'une importante diminution des signes physiopathologiques au niveau du SNC. Ces résultats indiquent que l'embryon de ZF représente un modèle d'infection prometteur et pertinent pour 1) l'étude de la virulence de Mabs 2) l'évaluation de la contribution du SI innée au cours de l'infection et 3) le suivi directe de l'effet d'ATBs. Ce nouveau modèle, combiné aux outils déjà disponibles chez le ZF, devrait permettre de mieux caractériser la relation entre Mabs et mucoviscidose, notamment l'implication éventuelle de la protéine CFTR dans la résistance à cette bactérie. Par ailleurs, l'embryon étant particulièrement propice au criblage à haut débit, l'optimisation de ce système biologique pourrait être exploitée dans le cadre d'approches thérapeutiques innovantes pour identifier de nouveaux agents anti-infectieux contre Mabs. / The emerging pathogen Mycobacterium abscessus causes severe lung infections particularly in cystic fibrosis (CF) patients. The Smooth (S) morphotype displays surface expression of glycopeptidolipids (GPL) while the Rough (R) morphotype is characterized by the loss of surface-associated GPL. Previous studies suggested that the R variant is involved in more severe clinical forms, associated with a hyper-proinflammatory response. However, the molecular mechanisms responsible for the virulence and physiopathology associated to the Rvariant remain unknown. The zebrafish embryo offers many advantages that motivated and validated its use for a better understanding of infectious diseases. In this study, a zebrafish model of infection was developed toinvestigate and compare the pathogenesis of R and S variants.A microinjection protocol was first developed and the fate and progression of the infection was monitored at a spatiotemporal level by videomicroscopy. A transcriptomic approach by qRT-PCR, an antisense technology using morpholinos and transgenic zebrafish lines were used to evaluate the contribution of theinnate immune system and the role of inflammation during infection. In addition, the potential of the embryo has been used to study the in vivo pharmacological activity of antibiotics during M. abscessus infection. In contrast to the S variant, the R morphotype induced a more robust and lethal infection in zebrafish embryos, characterized by the rapid development of bacterial foci within the central nervous system (CNS). The use of a mpx:GFP zebrafish transgenic line, exhibiting green fluorescent granulocytes, indicated that neutrophils are actively recruited to CNS infection foci. An intense pro-inflammatory response with production of TNFα was measured by qRT-PCR. Next, the use of a mpeg1:mCherry transgenic zebrafish line, exhibiting red fluorescent macrophages, demonstrated the presence of isolated or small aggregated bacilli within macrophages during early infection. In contrast, later stages were characterized by the presence of large aggregates of extensively replicating extracellularly that enables mycobacteria to induce a strong inflammatoryresponse, leading to rapid tissue damage (abscess) and to larval death. In addition, the high propensity of the R variant to form cords in vivo may, represent a strategy evolved by the R (but not S) M. abscessus, to escape themacrophage or avoid being phagocytosed by macrophages or granulocytes. The role of macrophages in the diffusion of bacteria to the CNS was evaluated in macrophage-depleted embryos. Here, M. abscessus failed to disseminate from vasculature to CNS as shown by infections performed in KDR:GFP transgenic line, exhibiting green vascular endothelium. In addition, we also showed that the activity of antibiotics on infected-embryos is associated with a strong reduction of embryonic mortality, reduction in the bacterial burden and a significant decrease in physiopathological signs in the CNS, which could be imaged in real-time and at high resolution.These results propose the zebrafish embryo as a suitable model, particularly relevant to 1) the study of M. abscessus virulence, 2) the evaluation of role of innate immune system during infection process and to 3)monitor, at spatiotemporal level, the effects of antibiotics in an infected vertebrate. In addition, the antisense technology allowing knocking-down cftr expression can now be optimized to mimic a CF environment. This should greatly help to define the relationship between M. abscessus in CF patients. Moreover, the embryo isparticularly conducive to high-throughput screening, thus allowing this biological system to be exploited in the search for new therapeutic molecules against M. abscessus and other CF-associated patients

Tuberculosis remains one of the oldest diseases known to mankind but still persists as a very major risk. Discovery of several antimycobacterials was marked by a steady decline in the active cases of pulmonary tuberculosis. However, in the recent past there has been a surge in its clinical incidence. The reasons for this failure are the emergence of multi drug resistance and the ability of the organism to survive under extreme condition or for a very long period of time known as ‘persistence’. The latter one established itself as a major hindrance in the effective control of tuberculosis. The latent bacilli are confined for a very long period after the infection in caseous cavities, called granulomma, inside the host and gets reactivated any time when the host becomes immuno-compromised. Latency has been successfully simulated in vitro by various models which mimic the in vivo condition by depleting O2 (Wayne, 1977), nutrients (Nyka, 1974) or the carbon source (Ojha et al., 2000). Stationary phase is exemplary of a stage in bacterial growth where the organism is exposed to various stresses like nutrient starvation, accumulation of toxic metabolites, low temperature, high osmolarity and acidity to name a few. Some evidences suggest that cells survive in nutrient deprived stationary phase. The present investigation was pursued with an objective to further our understanding on the mechanism of adaptation that the persistent mycobacterium may undertake to survive during the stationary phase of growth. The fast growing M.smegmatis, a nonpathogenic member in the non-tuberculous genera, however, with a genetic and metabolic similarity to M.tuberculosis has been used as a model for this study. Chapter 1 introduces the challenges in tuberculosis therapy and discusses the reason for drug tolerance and persistence of M.tuberculosis and M.avium complexes that were uncovered recently. It focuses on the intricate lipid rich cell wall which forms the first barrier for drug delivery with an emphasis on the cell surface antigenic glycolipids, the glycopeptidolipids. A detail account of their structure, biosynthetic pathway, intracellular function and their implications on biofilm formation has been provided. The evolution of the genetic approaches currently used in mycobacterial research is highlighted. The transcription apparatus and the regulation of gene expression in mycobacteria at different environmental condition and stages of growth are also discussed. The need for a detail investigation of the stationary phase RNAP in mycobacteria is stressed. Chapter 2 observes the changes in the cell surface of M.smegmatis at different ambience of growth. It focuses on the composition of glycopeptidolipid, one of the non-covalently attached free lipids and the mycolic-acids which are covalently attached to the inner layer of the cell wall. Composition of the mycobacterial cell wall with respect to the glycopeptidolipids and mycolic acids during biofilm mode of growth is also addressed. This chapter examines the conditional synthesis of a novel class of polar glycopeptidolipid in carbon starved cultures of M.smegmatis and determines their molecular structure. Chapter 3 revisits the biosynthetic pathway of the glycopeptidolipids and justifies a need for a fresh perspective. It identifies a glycosyltransferase responsible for the transfer of an extra rhamnose to the existing rhamnose linked to the terminal alaninol in the new polar glycopeptidolipid. This chapter also identifies a conserved Polyketide synthase in the glycopeptidolipid biosynthetic cluster. Characterization of the domains present in its two distinct modules with a correlation to the structure of the fatty acylchain together with the formation of a hydroxy fatty acyl chain is delineated. Chapter 4 deals with the construction of a suicide vector which when recombines to the mc2155 genome, incorporates a hexa-histidine tag at the C’ of the β΄ subunit of the RNAP. It details the strategy for the construction of the strain and established the genetic exchange event both genotypically and phenotypically. A single step procedure for purification of the holo-RNAP is also described in this chapter. In chapter 5 the role of the mycobacterial principal likes sigma factor, SigB, at the stationary phase of growth is highlighted. An approach of expression proteomics involving differential display of the total protein was undertaken to investigate the genes that are under the SigB regular during the stationary phase of growth. This chapter also examines the stationary phase induced changes in the RNAP. Various proteins that interact with the assembly are identified and their role in conferring rifampicin resistance to the RNAP is described. Appendix 1 details the preparation of the partially methylated deoxy monosaccharide using the esoteric reactions of organic synthesis. They were used extensively for glycosyl linkage analysis of the glycopeptidolipids by mass spectrometry, where they acted as standards.

The stringent response is a highly conserved physiological response mounted by bacteria under stress (Ojha and Chatterji, 2001; Magnusson et al., 2005; Srivatsan and Wang, 2007; Potrykus and Cashel, 2008). Until recently, the only known players in this pathway were the (p)ppGpp synthesizing and hydrolyzing long RSH enzymes (Mittenhuber, 2001; Atkinson et al., 2011) - RelA and SpoT in Gram negative bacteria and the bifunctional Rel in Gram positive bacteria including mycobacteria. The existence of Short Alarmone Synthetases (SAS) (Lemos et al., 2007, Nanamiya et al., 2008; Das et al., 2009; Atkinson et al., 2011) and Short Alarmone Hydrolases (SAH) (Sun et al., 2010, Atkinson et al., 2011), small proteins possessing a single functional (p)ppGpp synthetase or hydrolase domain respectively, is a recent discovery that has modified this paradigm. Around the same time that the presence of the SAS proteins was reported, we chanced upon such small (p)ppGpp synthetases in the genus Mycobacterium. The stringent response in the soil saprophyte Mycobacterium smegmatis was first reported by Ojha and co-workers (Ojha et al., 2000), and the bifunctional RSH, RelMsm, responsible for mounting the stringent response in this bacterium, has been characterized in detail (Jain et al., 2006 and 2007). RelMsm was the only known RSH enzyme present in M. smegmatis, and consequently, a strain of M. smegmatis deleted for the relMsm gene (ΔrelMsm) (Mathew et al., 2004), was expected to show a null phenotype for (p)ppGpp production. In this body of work, we report the surprising observation that the M. smegmatis ΔrelMsm strain is capable of synthesizing (p)ppGpp in vivo. This unexpected turn of events led us to the discovery of a second (p)ppGpp synthetase in this bacterium. The novel protein was found to possess two functional domains – an RNase HII domain at the amino-terminus, and a (p)ppGpp synthetase or RSD domain at the carboxy-terminus. We have therefore named this protein ‘MS_RHII-RSD’, indicating the two activities present and identifying the organism from which it is isolated. Orthologs of this novel SAS protein occur in other species of mycobacteria, both pathogenic and non-pathogenic. In this study, we report the cloning, purification and in-depth functional characterization of MS_RHII-RSD, and speculate on its in vivo role in M. smegmatis. Chapter 1 reviews the available literature in the field of stringent response research and lays the background to this study. A historical perspective is provided, starting with the discovery of the stringent response in bacteria in the early 1960s, highlighting the development in this area till date. The roles played by the long and short RSH enzymes, ‘Magic Spot’ (p)ppGpp, the RNA polymerase enzyme complex, and a few other RNA and proteins are described, briefly outlining the inferences drawn from recent global gene expression and proteomics studies. The chapter concludes with a description of the motivation behind, and the scope of the present study. Chapter 2 discusses the in vivo and in silico identification of MS_RHII-RSD in M. smegmatis. Experiments performed for the genotypic and phenotypic revalidation of M. smegmatis ΔrelMsm strain are described. Detailed bioinformatics analyses are provided for the in silico characterization of MS_RHII-RSD in terms of its domain architecture, in vivo localization, and protein structure prediction. A comprehensive list of the mycobacterial orthologs of MS_RHII-RSD from a few representative species of infectious and non-infectious mycobacteria is included. Chapter 3 summarizes the materials and methods used in the cloning, purification, and the biophysical and biochemical characterization of full length MS_RHII-RSD and its two domain variants – RHII and RSD, respectively. A detailed description of the purification protocols highlighting the specific modifications and changes made is given. Peptide mass fingerprinting to confirm protein identity, as well as preliminary mass spectrometric, chromatographic, and circular dichroism-based characterization of the proteins under study is also provided. Chapter 4 deals in detail with the in vivo and in vitro functional characterization of the RNase HII and (p)ppGpp synthesis activities of full length MS_RHII-RSD and its two domain variants - RHII and RSD, respectively. The RNase HII activity is characterized in vivo on the basis of a complementation assay in an E. coli strain deleted for the RNase H genes; while in vitro characterization is done by performing a FRET-based assay to monitor the degradation of a RNA•DNA hybrid substrate in vitro. The (p)ppGpp synthesis activity is characterized in terms of the substrate specificity, magnesium ion utilization, and a detailed analysis of the kinetic parameters involved. A comparison of the (p)ppGpp synthesis activity of MS_RHII-RSD vis-à-vis that of the classical RSH protein, RelMsm, is also provided. Inferences drawn from (p)ppGpp hydrolysis assays and the in vivo expression profile of MS_RHII-RSD in M. smegmatis wild type and ΔrelMsm strains are discussed. Based on the results of these functional assays, a model is proposed suggesting the probable in vivo role played by MS_RHII-RSD in M. smegmatis. Chapter 5 describes the attempts at generating MS_RHII-RSD overexpression and knockout strains in M. smegmatis, using pJAM2-based mycobacterial expression system, and mycobacteriophage-based specialized transduction strategy, respectively. The detailed methodology and the principle behind the techniques used are explained. The results obtained so far, and the future work and strain characterization to be carried out in this respect are discussed. Chapter 6 takes a slightly different route and summarizes the work carried out in characterizing the glycopeptidolipids (GPLs) from M. smegmatis biofilm cultures. A general introduction about the mycobacterial cell wall components, with special emphasis on GPLs, is provided. The detailed protocols for chemical composition and chromatographic analyses are mentioned, and the future scope of this work is discussed. Appendix-1 briefly revisits the preliminary studies performed to determine the pppGpp binding site on M. smegmatis RNA polymerase using a mass spectrometry-based approach. Appendices-2, 3, 4 and 5 give a comprehensive list of the bacterial strains; PCR primers; antibiotics, buffers and media used; and the plasmid and phasmid maps, respectively.