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All organisms must sense and respond to their environment in order to survive. The processes that allow a living cell to sense changes in its environment, and respond appropriately are collectively referred to as ‘signal transduction’. Cyclic AMP is a ubiquitously used second messenger molecule that plays diverse roles from hormone signalling in mammalian cells to catabolite repression in enteric bacteria. In several bacterial pathogens such as Pseudomonas aeruginosa, cAMP has also been found to mediate pathogenesis, usually by regulating the production of several virulence factors aiding in colonisation of the host. Cyclic AMP signalling has been suggested to regulate the virulence of the obligate intracellular Mycobacterium tuberculosis. Mycobacteria, including M. tuberculosis, code for a large number of adenylyl cyclases, enzymes that synthesise cAMP. Of the 16 putative adenylyl cyclases encoded by M. tuberculosis H37Rv, 10 have received extensive biochemical attention. A knockout of one of these cyclases, Rv0386, resulted in compromised virulence of M. tuberculosis. Ten proteins predicted to bind cAMP and mediate its cellular roles have also been identified in M. tuberculosis. Among these are the cAMP-regulated transcription factor, CRPMt, and cAMP-regulated protein acetyl transferase, KATmt. Comparatively little information is available, however, regarding the roles of cAMP-degrading machinery in mycobacteria. Two phosphodiesterases, with modest activity against cAMP in vitro, have been identified from M. tuberculosis, and are encoded by the Rv0805 and Rv2795c loci. Of these, Rv2795c has orthologs in all sequenced mycobacterial genomes. However, Rv0805-like proteins are coded only by slow growing mycobacteria such as the M. tuberculosis-complex, M. marinum and M. leprae, several of which are human or animal pathogens. Rv0805 belongs to the metallophosphoesterase superfamily of proteins, consisting of metal-dependent phosphoesterases with substrates ranging from large polymers like nucleic acids to small molecules like cAMP and glycerophospholipids. Like other metallophosphoesterases, Rv0805 displays promiscuous substrate utilisation and efficient hydrolysis of 2’3’-cAMP in vitro. Rv0805 also hydrolyses 3’5’-cAMP in vitro. Overexpression of Rv0805 is reported to lead to reduction in intracellular cAMP levels in M. smegmatis and M. tuberculosis, suggesting that it is capable of hydrolysing cAMP in the bacterial cell as well. The structure of Rv0805 revealed a sandwich-like α/β fold, typical of metallophosphoesterases, along with a relatively flexible C-terminal domain of unknown function. Despite extensive biochemical and structural information on Rv0805 however, its roles in mycobacteria remain unknown. In this study, the cellular roles of Rv0805 are explored and using information from biochemical and structural analyses, novel activities and interactions of Rv0805 have been identified. Rv0805, when expressed in M. smegmatis, led to a reduction in intracellular cAMP, as previously reported. However, the extent of reduction was modest (~30 %) and limited to the exponential phase of growth when both Rv0805 and intracellular cAMP are at their highest levels. Overexpression of Rv0805 also resulted in hypersensitivity to cell wall perturbants like crystal violet and sodium dodecyl sulphate (SDS) indicative of a change in the properties of the cell envelope of M. smegmatis. Importantly, these effects were independent of cAMP-hydrolysis by Rv0805, as overexpression of catalytically inactive Rv0805N97A also elicited similar changes. Unexpectedly, Rv0805 was localised to the cell envelope, both in M. tuberculosis as well as in M. smegmatis. The ability of Rv0805 to localise to the cell envelope was dependent on it C-terminus, as truncation of Rv0805 in this region (Rv0805Δ10, Rv0805Δ20 and Rv0805Δ40) resulted in progressively greater enrichment in the cytosol of M. smegmatis. Overexpression of Rv0805Δ40, which was localised almost completely to the cytosol, did not result in hypersensitivity to SDS, suggesting that cell envelope localisation, rather than cAMP-hydrolysis, was crucial for the cell envelope modifying roles of Rv0805. A possible mechanism behind the cell envelope-related effects of Rv0805 overexpression was the ability of the protein to interact with the cell wall of mycobacteria in a C-terminus-dependent manner. Purified Rv0805, but not Rv0805Δ40, could associate with crude mycobacterial cell wall as well as purified cell wall core polymer (mycolyl-arabinogalactan-peptidoglycan complex) in vitro. In addition to the C-terminus, the architecture of the active site was also crucial for this interaction as mutations in the active site that compromised metal-binding also resulted in poor interaction with the cell wall. Most significant among these residues was His207, which when mutated to Ala almost completely abrogated interaction with the cell wall in vitro. Further, Rv0805H207A was unable to localise to the cell envelope when expressed in M. smegmatis, even in the presence of the C-terminus, highlighting the importance of this residue in maintaining the structural integrity of Rv0805, and demonstrating that the structure of the C-terminus, rather than its sequence alone, played a role in cell envelope localisation and interaction. In order to verify that the observed sensitivity of Rv0805-overexpressing M. smegmatis to cell wall perturbants was due to a change in cell envelope properties atomic force microscopy was employed. Two distinct modes of operation were used to analyse surface and bulk properties of the mycobacterial cell envelope. These were tapping mode phase imaging, and contact mode force spectroscopy. Using tapping mode phase imaging, it was found that the cell surface of M. smegmatis was inherently heterogeneous in its mechanical properties. Further, contact mode force-spectroscopy revealed that the cell envelope of M. smegmatis in cross-section had at least three layers of varying stiffness. Typically, a middle layer of high stiffness was observed, sandwiched between two lower stiffness layers. This organisation is reminiscent of the current model of the mycobacterial cell envelope, possessing a central polysaccharide rich layer and outer and inner lipid rich layers. Treatment of wild type M. smegmatis with cell wall-perturbing antibiotics isoniazid and ethambutol resulted in markedly altered phase images, as well as significantly lower stiffness of the bacterial cell envelopes, validating that the methodology employed could indeed be used to assess cell wall perturbation in mycobacteria. Further, M. smegmatis harbouring deletions in cell envelope biosynthesis related genes, MSMEG_4722 and aftC, showed significantly lower cell wall stiffness than wild type M. smegmatis, providing evidence that genetic perturbation of the cell wall of mycobacteria could also be studied using atomic force microscopy. While phase imaging revealed similar surface properties of Rv0805-overexpressing and control M. smegmatis, force spectroscopy revealed significantly lower cell envelope stiffness, particularly of the middle layer, of the former. Cell envelope stiffness was, however, unaffected by expression of Rv0805Δ40 in M. smegmatis, providing direct evidence for C-terminus-dependent cell envelope perturbation upon Rv0805 overexpression. Additionally, overexpression of Rv0805N97A, but not Rv0805H207A led to reduced stiffness of the cell envelope of M. smegmatis, demonstrating that the cell wall remodelling activity of Rv0805 was independent of cAMP-hydrolysis, but dependent on cellular localisation and cell wall interaction. Like in M. smegmatis, overexpression of Rv0805 also led to lower cAMP levels in M. tuberculosis. Using a microarray-based transcriptomics approach, pathways affected by Rv0805 overexpression were identified. Rv0805 overexpression elicited a transcriptional response, leading to the down-regulation of a number of virulence associated genes such as whiB7, eis, prpC and prpD. Importantly, Rv0805-overexpression associated gene expression changes did not include genes regulated by CRPMt, the primary cAMP-regulated transcription factor in M. tuberculosis. Further, Rv0805N97A overexpression in M. tuberculosis led to similar changes in gene expression as overexpression of the wild type protein. These observations reiterated that, at least upon overexpression, the effects of Rv0805 were largely independent of cAMP-hydrolysis. Using overexpression in M. smegmatis and M. tuberculosis, cAMP-hydrolysis independent roles of Rv0805 in mycobacteria were identified. To further validate these observations, a knockout strain of the Rv0805 gene was generated in M. bovis BCG, a well-established model to study M. tuberculosis. Curiously, deletion of Rv0805 did not lead to a change in intracellular cAMP levels, demonstrating that cAMP-hydrolysis by Rv0805 may not contribute to the modulation of mycobacterial cAMP levels under standard laboratory growth conditions. Rv0805 deletion led to altered colony morphology and possible reduction in cell wall thickness, reaffirming the roles of this phosphodiesterase in regulating cell envelope physiology of mycobacteria. Additionally, Rv0805 deletion also resulted in compromised growth of M. bovis BCG in fatty acid-deficient media, implicating Rv0805 as a possible regulator of carbon metabolism. In summary, this thesis explores novel links between Rv0805 and the mycobacterial cell wall and elucidates the critical importance of the C-terminus domain of this metallophosphodiesterase in modulating its cellular localisation to, and interaction with, the mycobacterial cell envelope. En route to understanding the effects of Rv0805 overexpression on the cell wall of M. smegmatis, an atomic force microscopy-based methodology to assess perturbation of the cell envelope of mycobacteria was also developed. Finally, using a combination of biochemical and genetic analyses, cellular roles of Rv0805, independent of cAMP-hydrolysis, were identified in slow-growing mycobacteria. This study therefore provides direct evidence against the sole role of this mycobacterial phosphodiesterase as a regulator of intracellular cAMP levels, and opens up new avenues to understanding the cellular functions of Rv0805 and indeed other members of the metallophosphoesterase superfamily.

Mycobacteria are multifaceted pathogens capable of causing both acute disease as well as an asymptomatic latent infection. Protective immunity against pathogenic mycobacteria depends principally on cell-mediated immunity executed by efficient anti-infectious functions of type 1 T helper (Th1) subset of CD4+ T cells. The polarization of Th1 responses is orchestrated by IL-12 secreted by antigen presenting cells (APCs) such as macrophages and dendritic cells (DCs). A hallmark of Th1 type CD4+ T cells is the production of IFN-γ that activates plethora of innate cell-mediated immunity. It is well known that cytokines such as IFN-γ, IL-12 and TNF-α are required for control of mycobacterial infection in humans as well as in mice. However, it remains unclear that why the immune response controls mycobacteria, but does not eradicate infection suggesting critical roles for series of survival strategies employed by pathogenic mycobacteria. In general, these evasion strategies include blockade of phagosome-lysosome fusion, secretion of ROI antagonistic proteins like superoxide dismutase & catalase, inhibition of processing of its antigens for presentation to T cells, induced secretion of immunosuppressive cytokines like IL-10 and TGF-β etc. that ultimately suppress the secretion of IL-12 and IFN-γ from APCs and T cells respectively, culminating in a skewed Th1/Th2 balance towards unprotective Th2 responses. Th2 cells secrete IL-4, IL-5, IL-9, IL-10 and IL-13 but are deficient in clearing intracellular infections including pathogenic mycobacteria. This eventually leads to inhibition of host’s immuno-protective responses with concomitant increase in the vulnerability to chronic mycobacterial infection. In this intricate process, modulation of cyclooxygenase-2 (COX-2) levels, a key enzyme catalyzing the rate-limiting step in the inducible production of prostaglandin E2 (PGE2), by mycobacteria like Mycobacterium bovis BCG assumes critical importance in influencing the overall host immune response. PGE2, an immunosuppressive member of prostaglandin family, is known to restrain production of IL-12, as well as reactive oxygen intermediates. PGE2-mediated inhibition of IL-12R, diminishes IL-12 responsiveness of macrophages and dendritic cells. PGE2 also inhibits the secretion of IFN-γ, which is important in activating T cells and macrophages. In contrast, PGE2 promotes IL-10 production by macrophages, dendritic cells and Th1-to-Th2 shift of acquired immune responses by inhibiting IL-2 and enhancing IL-4 production. Albeit, mitogen-activated protein kinase (MAPK) and nuclear factor-kappa B (NF-κB) signaling pathways are generally believed to be involved, little is known about the signaling molecules playing significant roles upstream of MAPK and NF-κB pathways during mycobacteria triggered COX-2 expression. Further, information on early receptor proximal signaling mechanisms essential during mycobacteria mediated induction of COX-2 remains scanty. In this regard, signaling cascade triggered upon recognition of mycobacterial components by pattern recognition receptors (PRR) signify as critical event in overall regulation of cell fate decisions. PRR like Toll like receptor (TLR2) and nucleotide-binding oligomerization domain 2 (NOD2) are two nonredundant recognition mechanisms of pathogenic mycobacteria. Several components of mycobacteria have been identified as being responsible for TLR2-dependent activation including 19-kDa lipoprotein, lipomannan etc.; while NOD2 recognizes mycobacterial peptidoglycans through its interaction with muramyl dipeptide (MDP). Interestingly, although mycobacteria reside within phagolysosomes of the infected macrophages, many cell wall antigens like lipoarabinomannan (LAM), phosphatidyl-myo-inositol mannosides (PIM), trehalose 6,6′-dimycolate (TDM; cord factor), PE/PPE family proteins etc., are released and traffic out of the mycobacterial phagosome platform into endocytic compartments. Importantly, these antigens could gain access to the extracellular environment in the form of exocytosed vesicles. In this perspective, PIM represents a variety of phosphatidyl-myo-inositol mannosides (PIM) 1-6 containing molecules and are integral component of the mycobacterial envelope. Further, PIM2 is a known TLR2 agonist and reported to activate NF-κB, AP-1, and MAPK suggesting that mycobacterial envelope antigen PIM2 could modulate the inflammatory responses similar to mycobacteria bacilli. In this context, we explored the signaling events modulated by M. bovis BCG, and role for TLR2 and NOD2 in this intricate process, to trigger the expression of COX-2 in macrophages. Our studies demonstrated that M. bovis BCG triggered TLR2-dependent signaling leads to COX-2 expression and PGE2 secretion in vitro in macrophages and in vivo in mice. Further, the presence of PGE2 could be demonstrated in sera or CSF of tuberculosis patients. Similarly, mycobacterial TLR2 agonist PIM2 and NOD2 ligand MDP triggered COX-2 expression in macrophages. The induced COX-2 expression in macrophages either by M. bovis BCG or PIM2 or MDP was dependent on NF-κB activation, which was in turn mediated by iNOS/NO and Wnt-β-Catenin dependent participation of the members of Notch1-PI3K signaling cascade. Importantly, loss of iNOS activity either in iNOS null macrophages or by pharmacological intervention in wild type macrophages severely abrogated M. bovis BCG ability to trigger the generation of Notch1 intracellular domain (NICD) as well as activation of PI3K signaling cascade. On contrary, treatment of macrophages with SIN-1, an NO donor, resulted in a rapid increase in generation of NICD, activation of PI3K pathway as well as the expression of COX-2. Interestingly, pharmacological inhibition as well as siRNA mediated knockdown of Wnt-β-Catenin signaling compromised ability of M. bovis BCG to induce activation of Notch1-PI3K signaling and drive COX-2 expression. Concomitantly, activation of Wnt-β-Catenin signaling by LiCl triggered activation of Notch1 and PI3K pathway as well as COX-2 expression. Stable expression of NICD in RAW 264.7 macrophages resulted in augmented expression of COX-2. Further, signaling perturbation experiments suggested involvement of the cross-talk of Notch1 with PI3K signaling cascade. In this perspective, we propose TLR2 and NOD2 as two major receptors involved in mycobacteria mediated activation of Notch1PI3K signaling, and the activation of iNOS/NO and Wnt-β-Catenin signaling axis as obligatory early receptor proximal signaling events during mycobacteria induced COX-2 expression in macrophages. Functional characterization of mycobacterial antigens that are potent modulators of host immune responses to pathogens by virtue of induced expression of COX-2 assumes critical importance for deciphering pathogenesis of mycobacterial diseases as well as to identify novel therapeutic targets to combat the disease. In this context, a group of novel antigens carried by M. tuberculosis that are expressed upon infection of macrophages belong to PE and PPE family of proteins. Ten percent of the coding capacity of M. tuberculosis genome is devoted to the PE and PPE gene family members, exemplified by the presence of Pro-Glu (PE) and Pro-Pro-Glu (PPE) motifs near the N-terminus of their gene products. Many members of the PE family exhibit multiple copies of polymorphic guanine-cytosine– rich sequences (PGRS) at the C-terminal end, which are designated as the PE_PGRS family of proteins. A number of PE/PPE proteins associate with the cell wall and are known to induce strong T & B cell responses in humans. However information related to effects of PE/PPE antigens on the maturation and functions of human dendritic cells and eventual modulation of T cell responses as well as underlying signaling events remains obscure. Our results demonstrated that two cell wall associated/secretory PE_PGRS proteins PE_PGRS 17, PE_PGRS 11 and PPE family protein PPE 34 recognize TLR2, induce maturation and activation of human dendritic cells and enhance the ability of dendritic cells to stimulate CD4+ T cells. In addition, tuberculosis patients were found to have a high frequency of T cells specific to PE_PGRS and PPE antigens. We further found that PE/PPE proteins-mediated activation of dendritic cells involves participation of ERK1/2, p38 MAPK and NF-κB signaling pathways. While, PE_PGRS antigens-matured dendritic cells secreted high amounts of inflammatory cytokine IL-12, PPE 34 triggered maturation of dendritic cells was associated with secretion of high amounts of anti-inflammatory cytokine IL-10 but not the Th1-polarizing cytokine IL-12. Consistent with these results, PPE 34-matured dendritic cells favored secretion of IL-4, IL-5 and IL-10 from CD4+ T cells and contributed to Th2 skewed cytokine balance ex vivo in healthy individuals and in patients with pulmonary tuberculosis. Interestingly, PPE 34-skewed Th2 immune response involved induced expression of COX-2 in dendritic cells. Our results suggest that by inducing differential maturation and activation of human dendritic cells, PE/PPE proteins could potentially modulate the initiation of host immune responses against mycobacteria. Taken together, our observations clearly signify the potential role for TLR2 and NOD2 triggering by M. bovis BCG in activating receptor proximal Notch1-PI3K signaling during induced COX-2/PGE2 expression which represents a crucial immune subversion mechanism employed by mycobacteria in order to suppress or attenuate host immune responses. Further, differential maturation of human dendritic cells by PE_PGRS and PPE antigens as well as their ability to stimulate CD4+ T cells towards Th1 and Th2 phenotype respectively, improves our understanding about host-mycobacteria interactions and clearly paves a way towards the development of novel combinatorial therapeutics.

Tuberculosis continues to be one of the major causes of morbidity and mortality worldwide. Several mycobacterial species such as M. tuberculosis and M. africanum are responsible for causing this disease in humans. Reports of high cAMP levels in mycobacterial species (as compared to other bacteria such as E. coli) suggested that this second messenger may play an important role in the biology of mycobacteria. Further, it was reported that infection with mycobacteria led to an increase in the cAMP levels within the host macrophage. More recent studies have shown that this cAMP increase may be due to bacterially derived cAMP, hinting at a role for cAMP in mycobacterial pathogenesis. Given this background, the study of cAMP in mycobacteria proves to be an interesting field of research. Signalling through cAMP involves an interaction of this cyclic nucleotide with a cAMP-binding protein. These proteins typically contain a cyclic nucleotide-binding domain (CNB domain) linked to another (effector) domain. The CNB domain is thought to allosterically control the activity of the effector domain, thus mediating cellular responses to altered cAMP levels. For example, in the case of eukaryotic protein kinase A (PKA), binding of cAMP to the CNB domain results in relieving the inhibitory effects of the regulatory subunit on the catalytic subunit. The catalytic subunit then phosphorylates its target substrates, eliciting a variety of cellular responses. This work involves the characterisation of novel cAMP-binding proteins from mycobacteria, in an attempt to better understand cAMP signalling mechanisms in these organisms. The genome of M .tuberculosis H37Rv is predicted to code for ten CNB domain-containing proteins. One of these genes is Rv0998 (KATmt). KATmt was found to contain a GCN5 related N-acetyltransferase (GNAT) domain linked to a CNB domain. KATmt finds orthologues throughout the genus Mycobacterium, thereby suggesting its role in the basic physiology of these organisms. In addition, such a domain fusion is unique to mycobacteria and hence promises to deliver insights into the biology of this medically important genus. Presented here are the biochemical and functional characterisation of KATmt and its orthologue from M. smegmatis, MSMEG_5458 (KATms). Recombinant KATms bound cAMP with high affinity, validating the functionality of its CNB domain. Mutational and analogue-binding studies showed that the biochemical properties of the CNB domain were similar to mammalian protein kinase A and G-like CNB domains. The substrate for the GNAT acetyltransferase domain was identified to be a universal stress protein from M. smegmatis (MSMEG_4207). MSMEG_4207 was acetylated at a single lysine residue (Lys 104) by KATms in vitro. Further, cAMP binding to KATms increased the initial rate of acetylation of MSMEG_4207 by 2.5-fold, suggesting allosteric control of acetyltransferase activity by the CNB domain. To ascertain that KATms acetylated MEMEG_4207 in vivo, an in-frame deletion of the KATms gene was generated in M. smegmatis (ΔKATms). MSMEG_4207 was immunoprecipitated from wild-type M. smegmatis and the ΔKATms strains, followed by mass spectrometric analysis. Acetylated MSMEG_4207 was only present in the wild-type strain, confirming that KATms and MSMEG_4207 is an in vivo enzyme-substrate pair. Key biochemical differences were observed between KATms and KATmt. KATmt had an affinity for cAMP in the micromolar range, close to three log orders lower than that of KATms. In addition, KATmt showed strictly cAMP-dependent acetylation of MSMEG_4207. This demonstrates that orthologous proteins often evolve under varied selective pressures, resulting in divergent properties. Using a combination of bioluminescence resonance energy transfer (BRET) and amide hydrogen/deuterium exchange mass spectrometry (HDXMS), the conformational changes that occur upon cAMP binding to the CNB domain of KATms were monitored. A BRET-based conformation sensor was constructed for KATms by inserting KATms between GFP2 (green fluorescent protein) and Rluc (Renilla luciferase). An increase in BRET upon cAMP binding to the sensor was observed. HDXMS analysis revealed that besides the CNB domain, the only other region that showed conformational changes in KATms upon cAMP-binding was the linker region. To confirm that the linker region was important in propagating the effects of cAMP-binding to the acetyltransferase domain, an additional construct for BRET analysis encompassing the CNB domain and the linker region was generated. The magnitude of the increase in BRET was similar to the full length BRET-based sensor, validating the crucial role of the linker region in propagating cAMP-mediated conformational changes. A ‘PXXP’ motif found in the linker region, showed maximum exchange in HDXMS analysis. Mutation of both these proline residues to alanine in KATms, as well as KATmt, resulted in decoupling of cAMP-binding and allosteric potentiation of acetyltransferase activity. In contrast to the intricate parallel allosteric relays observed in other CNB domain-containing proteins, the CNB domain in KATms functions as a simpler cyclic nucleotide binding-induced switch involving stabilization of the CNB and linker domain alone. Therefore, KATms is an example of a primordial CNB domain where conformational changes are a consequence of binding-induced ordering alone. Using a computational approach, putative substrate proteins of KATmt from M. tuberculosis were identified. The substrate specificity of lysine acetyltransferases is determined loosely by a consensus sequence around the lysine residue which is acetylated. Using this property of protein acetyltransferases, the genome of M. tuberculosis H37Rv was mined for proteins harboring lysine residues in a similar sequence context as seen in MSMEG_4207. In vitro biochemical analysis of some of the predicted substrates helped confirm a subset of enzymes belonging to the fatty acyl CoA synthetase (FadD) class as substrates of KATmt. The acetylation of FadDs by KATmt was cAMP-dependent. In each of the four proteins tested, acetylation was found to occur at a single conserved lysine residue. To confirm that FadDs were acetylated by KATmt in vivo, BCG_1055, the orthologue of KATmt in M. bovis BCG, was deleted using the specialised transduction method. FadD13, one of the FadDs acetylated by KATmt in vitro, was immunoprecipitated from wild-type M. bovis and the ΔBCG_1055 strains using a FadD13-specific polyclonal antibody. Acetylated FadD13 was almost completely absent in ΔBCG_1055 but substantial amounts of acetylated FadD13 were present in the wild-type strain, indicating that FadD13 was indeed an in vivo substrate of KATmt. The functional consequences of acetylation of FadDs were analysed using an in vitro fatty acyl CoA synthetase assay. The activities of FadD2 and FadD13 were inhibited on acetylation with KATmt, while acetylation of FadD5 resulted in the formation of a novel product. Therefore, modification of the highly conserved lysine residue in these enzymes by acetylation led to loss or alteration of their enzymatic activity, suggesting that acetylation may be used as a regulatory mechanism to modulate the activities of some of the FadDs by KATmt in a cAMP-dependent manner. Given the extensive role of FadDs in cell wall biosynthesis and lipid degradation in mycobacteria, it seems possible that post-translational control by KATmt in a cAMP-dependent manner constitutes a novel mechanism utilised by these bacteria to regulate these pathways. This direct regulation of protein lysine acetylation by cAMP appears to be unique to mycobacteria, as orthologues of KATmt are not found outside this genus. In addition, the biochemical differences between KATmt and its orthologue from M. smegmatis KATms, indicate species specific variation, on a common theme. This study is the first report of protein lysine acetylation in mycobacteria. In addition to the identification of several proteins subject to this post-translational modification, the effect of acetylation on the enzymatic activities of some of them has been elucidated.

Thesis (MScMedSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Background Individuals who are latently infected with Mycobacterium tuberculosis (M.tb) are able to quell the infection by balancing the innate and adaptive immune responses. Glucocorticoids (GCs) can affect this balance and can increase the risk of reactivation of TB. The three month injectable contraceptive medroxyprogesterone acetate (MPA) is widely used by women in developing countries, where TB is rife. MPA, unlike the two monthly contraceptive norethisterone enanthate (NET), possesses selective glucocorticoid activity, and could therefore alter immune responses to TB. Aims The aim of my investigation was to elucidate the immune modulatory effects of the synthetic progestins, MPA and NET, compared to the endogenous hormones, cortisol and progesterone, in Mycobacterium bovis Bacillus Calmette–Guérin (BCG) or anti-CD3 stimulated peripheral blood mononuclear cells (PBMC). I aim to determine the effects of MPA, NET, cortisol and progesterone on the receptor expression of glucocorticoid and various progesterone receptors. I investigate the effect of the above mentioned hormones on the downstream signalling cascades in the presence or absence of either BCG or anti-CD3. The overall immune modulation will be determined with regard to the cytokine production in PBMCs. Methods The presence of receptors for these steroid hormones in PBMCs was verified and BCG, anti-CD3 and hormone induced changes in receptor expression determined through RT-PCR. The impact of cortisol, MPA, NET and progesterone on BCG or anti-CD3 mediated activation of downstream signalling molecules were determined by Western blot as well as Luminex analysis. Results and Conclusion My results show that BCG and anti-CD3 mediated activation of the T cell receptor associated signalling molecules, Lck, ZAP-70, LAT was inhibited by the steroid hormones. Similarly several kinases including JNK, ERK and p38 and transcription factors including STAT3, STAT5 and CREB were differentially affected by the hormones. The inhibition of phosphorylation seen in the different signalling molecules indicated an inhibition of activation of downstream signalling cascades. To investigate the impact of the hormone induced changes in the signalling cascades on the expression of inflammatory and anti-inflammatory cytokines Luminex analysis was performed on the supernatant of the BCG and anti-CD3 stimulated PBMC cultures. Cortisol and MPA, but not NET and progesterone, significantly inhibited the secretion of IL-1α, IL-1β, IL-6, IL-10, TNF-α, IL-12 and IL-13. These results suggest that the immune suppressive effects of MPA are likely mediated through a combination of direct genomic GR action as well as through direct or indirect inhibition of several signalling molecules. The inhibition of the IFN-γ, IL-12, IL-1and IL-6 secretion by MPA could potentially increase the risk of susceptibility to TB in women using this contraceptive. Therefore the absence of glucocorticoid activity seen with NET could make this contraceptive a better choice for women in TB endemic areas. / AFRIKAANSE OPSOMMING: Agtergrond Individue wat latent met Mikobakterium tuberkulose (M.tb) geïnfekteer is, is in staat om die infeksie te onderdruk deur die ingebore en aanpasbare immuunrespons te balanseer. Glukokortikoïede (GCs) kan hierdie balans beïnvloed en kan die risiko van heraktivering van tuberkulose (TB) verhoog. Die drie maande inspuitbare voorbehoedmiddel medroksiprogestroon-asetaat (MPA) word algemeen gebruik deur vroue in ontwikkelende lande, waar TB volop is. MPA, in teenstelling met die twee maandelikse voorbehoedmiddel noretisteroon enantaat (NET), beskik selektiewe glukokortikoïed aktiwiteit, en kan dus die immuunrespons teenoor TB verander. Doelwitte Die doel van my studie was om die immuunregulerende effekte van die sintetiese progestiene, MPA en NET, toe te lig , in vergelyking met die endogene hormone, kortisol en progesteroon, in Mycobacterium bovis Bacillus Calmette - Guerin (BCG) of anti- CD3 gestimuleerde perifere bloed mononukleêre selle (PBMSe). Ek het beoog om die gevolge van MPA, NET, kortisol en progesteroon op die reseptor uitdrukking van glukokortikoïede en verskeie progesteroon reseptore te bepaal. Ek het ondersoek ingestel op die effek van die bogenoemde hormone op die sein transduksie in die teenwoordigheid of afwesigheid van óf BCG of anti-CD3. Die algehele immuun -modulasie sal bepaal word met betrekking tot die produksie van sitokiene in PBMSe . Metodes Die teenwoordigheid van reseptore vir die steroïedhormone in PBMSe is geverifieer en BCG en anti-CD3 en die veranderinge deurdie hormone in verband met die reseptor uitdrukking bepaal deur RT -PCR. Die impak van kortisol, MPA, NET en progesteroon op BCG of anti- CD3 aktivering van sein transduksie molekules is bepaal deur ‘Western blot’ asook Luminex analise. Resultate en gevolgtrekking My resultate toon dat BCG en anti-CD3 die aktivering van die T-sel reseptor wat verband hou met sein molekules , LCK , ZAP -70 , en LAT word geïnhibeer deur die steroïedhormone . Van die kinases insluitend JNK , ERK en p38 en transkripsie faktore, insluitend STAT3 , STAT5 en CREB is beïnvloed deur die hormone. Die inhibisie van fosforilering gesien in die verskillende sein molekules dui daarop aan dat 'n inhibisie van aktivering van sein transduksie. Die impak van die hormoon veroorsaak veranderinge in die sein transduksie met betrekking tot die uitdrukking van inflammatoriese en anti -inflammatoriese sitokiene Luminex analise is uitgevoer op die supernatant van die BCG en anti-CD3 gestimuleerde PBMS kulture. Kortisol en MPA, maar nie NET en progesteroon , het aansienlik die produksie van IL-1α , IL-1β , IL-6 , IL-10 , TNF-α , IL-12 en IL-13 geïnhibeer. Hierdie resultate dui daarop dat die immuunstelsel se onderdrukkende effekte van MPA is waarskynlik bemiddel deur 'n kombinasie van direkte genomiese GR interaksie sowel as deur direkte of indirekte inhibisie van verskeie sein molekules . Die inhibisie van die IFN-γ, IL-12, IL-1 en IL-6 sekresie deur MPA kan potensieel die risiko verhoog van vatbaarheid vir TB in vroue wat hierdie voorbehoedmiddel gebruik. Daarom oor die afwesigheid van glukokortikoïede aktiwiteit wat gesien is met NET, kan maak laat hierdie voorbehoedmiddel 'n beter keuse vir vroue in TB endemiese gebiede.

MSc., Faculty of Science, University of the Witwatersrand, 2011 / The increasing emergence of drug-resistant pathogens poses a major threat to public health. Although influenced by multiple factors, resistance is often associated with mutations in drug target-encoding or associated genes. The potential fitness cost of such resistance mutations is, in turn, a key determinant of the spread of drug-resistant strains. Rifampicin (RIF) is a frontline anti-tuberculosis agent that targets the rpoB-encoded β-subunit of the DNA-dependent RNA polymerase (RNAP). RIF resistance (RIFR) maps primarily to mutations in rpoB that might be expected to affect transcription and so the ability of the organism to cause disease. Accordingly, numerous studies have assessed the impact of RIFR on key fitness indicators in pathogens including Mycobacterium tuberculosis (MTB). In contrast, the specific consequences of RIFR for bacterial physiology remain poorly understood. Notably, previous studies of the effects of RIFR-associated rpoB mutations on mycobacterial physiology have been conducted using strains generated by RIF exposure, without accounting for the potential impact of second-site mutations that may compensate for fitness costs or contribute to drug resistance. In this study, site-directed mutagenesis and allelic exchange were employed to generate a panel of M. smegmatis (MSM) strains containing clinically-relevant RIFR-associated point mutations. Importantly, this methodology enables the introduction of rpoB mutations into defined strain backgrounds in the complete absence of RIF. Using this approach, we constructed “RIF naive” MSM rpoB mutant strains carrying either an S531L or H526Y mutation. The resulting mutants were 100-fold less susceptible to RIF than the isogenic, parental strain. Notably, the inclusion of selected efflux inhibitors in susceptibility assays had little impact on mutant susceptibility to RIF. In contrast, restoration of the wild-type allele returned the observed susceptibility to parental levels, thereby providing strong evidence of the sufficiency of a single rpoB mutation for clinical RIFR in mycobacteria. Competitive growth assays utilizing the S531L mutant and the parental strain exposed a growth defect for the S531L mutant. However, discriminating between wild-type and mutant rpoB strains proved a significant technical challenge, again highlighting the difficulties associated with inferring in vivo fitness from in vitro assays conducted under a limited number of different conditions. In summary, our results suggest the benefit of a deeper exploration of the physiological and fitness implications of RIFR-associated mutations. In addition, in coupling a system which enables an evaluation of the physiological consequences of drug resistance-associated mutations with evolutionary analyses, we provide preliminary evidence of the benefits of a multipronged approach to elucidating the physiological implications of drug resistance in MTB.

Les mycobactéries, dont les plus connues sont Mycobacterium tuberculosis et Mycobacterium leprae, agents étiologiques de la tuberculose et de la lèpre respectivement, présentent une enveloppe complexe et atypique faisant l'objet de nombreuses études dans le cadre de la lutte contre ces pathologies. Cette enveloppe est composée d'une couche externe aussi appelée capsule dans le cas de bactéries pathogènes, d'une paroi (mycomembrane - arabinogalactane (AG) - peptidoglycane (PG)) et d'une membrane plasmique. La membrane externe des mycobactéries, appelée mycomembrane est composée de protéines et majoritairement d'acides mycoliques, acides gras à très longues chaînes a-ramifiés et ß-hydroxylés. Ces derniers sont retrouvés covalemment liés, d'une part au complexe AG-PG dans le feuillet interne de la mycomembrane, et d'autre part au tréhalose au niveau du feuillet externe de la mycomembrane. On trouve également en fonction des mycobactéries des lipides complexes dont la localisation exacte dans l'enveloppe n'est à ce jour pas clairement connue et reste sujette à débats. Ce travail a permis de mettre au point un protocole, en deux étapes majeures, permettant le fractionnement cellulaire de deux espèces mycobactériennes, M. aurum et M. smegmatis. Le but étant d'isoler les deux membranes mycobactériennes afin de déterminer leur composition en terme de lipides mais aussi de protéines. Tout d'abord, des culots enrichis en mycomembranes (liées à l'AG-PG) ou en membranes plasmiques sont obtenus par ultracentrifugations différentielles puis purifiés sur gradients de densité discontinus de saccharose. L'absence de contaminations des membranes entre elles est vérifiée grâce à des marqueurs spécifiques. Il a été montré que les phospholipides qui sont les composants majoritaires de la membrane plasmique sont également présents dans la mycomembrane à côté des mycolates de tréhalose. De plus ce travail a permis de montrer que les lipoglycanes, lipoarabinomannanes et lipomannanes, lipides possédant des propriétés antigéniques, sont retrouvés dans les deux fractions membranaires. Ce travail de fractionnement a été le point de départ d'une étude de protéomique afin d'identifier les protéines retrouvées spécifiquement au niveau de la mycomembrane-AG-PG mais également les protéines de la membrane plasmique, les protéines sécrétées et les protéines solubles, provenant des cytosol et périplasme. Une étude de dynamique par RMN sur les fractions membranaires natives menée conjointement avec l'étude protéomique, devrait permettre de mieux comprendre l'organisation de l'enveloppe cellulaire des mycobactéries ainsi que certains des mécanismes impliqués dans la pathogénicité. / Mycobacteria, including Mycobacterium tuberculosis and Mycobacterium leprae, etiological agents of tuberculosis and leprosy respectively, are composed of a complex and atypical cell wall, which is the focus of numerous studies in the context of the fight against these pathologies. This cell envelope, to which many biological properties have been attributed, is composed of three entities: an outer layer also called capsule in the case of pathogenic species, a cell wall and a plasma membrane. Within the mycobacterial cell wall, the outer membrane, called mycomembrane, is mainly composed of proteins and mycolic acids, very long chain a-branched and ß-hydroxylated fatty acids. These mycolic acids are found in the inner leaflet of the mycomembrane, covalently linked to the arabinogalactan-peptidoglycan complex (AG-PG), and in the outer leaflet where they are linked to trehaloses. Complex lipids are also known in mycobacteria, and may vary depending on the species, however their exact localization within the cell envelope is not yet clearly known and remains open to debate. In order to better delineate the composition of the two mycobacterial membranes, mycomembrane and plasma membrane, a two-step protocol was developed for cell fractionation of two mycobacterial species, M. aurum and M. smegmatis. Firstly, pellets enriched in mycomembranes (linked to AG-PG) or plasma membranes are obtained by differential ultracentrifugations. Then, these membrane pellets are purified using a sucrose step density gradient. To ensure the absence of cross-contaminations of the membranes, specific markers of each membranes are used. Phospholipids, which are the major components of the plasma membrane, are also found in the mycomembrane with trehalose mycolates. Moreover, this study allowed us to demonstrate that immunogenic lipoglycans, lipoarabinomannans and lipomannans, are found in the two mycobacterial membranes. Once the fractionation successfully achieved, it was possible to initiate proteomic studies in order to identify proteins that are specific of the mycomembrane-AG-PG but also those secreted or present in the soluble fraction, derived from the cytosol and periplasm compartments. Future NMR dynamic studies, to be performed on the native membranes, combined with the proteomic studies will help deciphering the organization of the mycobacterial cell envelope as well as the mechanisms involved in pathogenicity.

Whole genome sequencing (WGS) is an attractive approach for mycobacteria diagnosis and epidemiological studies. It provides the potential for a rapid method that produces detailed information and could theoretically be used as a routine tool in clinical settings. This thesis focuses on the benefits and challenges involved in transforming molecular approaches into practical clinical mycobacteriology in general, and in particular WGS, as well as examining how it might be implemented. We first set out to improve the quantification of viable mycobacteria cells in vitro and make the molecular bacterial load assay (MBLA) sensitive enough to use in future clinical trials that monitor treatment response. The results showed the assay is rapid and accurate in its detection and count of viable bacteria. WGS was tested with different types of mycobacteria species to address different epidemiological questions. WGS not only provides a higher resolution result than traditional epidemiological methods but it can rapidly identify an outbreak, thus simplifying the investigation and reducing the cost. WGS accurately identified the sources of TB recurrence and could therefore have a potential role in determining the endpoints for clinical trials. Rapid genotyping of species in this way has been demonstrated in our studies. In addition, WGS has the ability to, in most circumstances, predict TB drug resistance. This could also prove very beneficial from a clinical standpoint. We used different approaches in our studies; for example, single nucleotide polymorphism threshold methods and the creation of a putative outbreak reference genome, which can be used in future outbreak investigations. WGS is a cost-effective, high-resolution method with a short turnaround. This makes it potentially usable as a routine tool in clinical settings and reference laboratories. Future studies are needed to improve the mycobacterial genome sequencing procedure, analysis and bioinformatics in order to implement WGS in clinical practice.

TB remains a major health issue worldwide causing around 1.5 deaths each year. The recent phase III clinical trials of shortened TB treatment failed to show superiority compared to the current regimen and this mainly because of relapse. Relapse is thought to be caused by dormant bacteria. Dormancy in Mycobacterium species has been shown to be associated with the accumulation of intracellular lipids, defining two phenotypes: the lipid rich (LR) cells (associated with dormancy) and the lipid poor (LP) cells (non-dormant). LR cells were shown to have a higher phenotypic antibiotic resistance compared to LP cells. Studying these two phenotypes is therefore central in tuberculosis research to understand better the disease and also potentially start to reveal the bacteriology of relapse. We investigated the power of Raman spectroscopy, a label-free and non-destructive technique, to discriminate LR and LP bacteria both in-vitro and ex-vivo. This represents the first Raman spectroscopy study that tries to discriminate the phenotypes of M. tuberculosis and investigate them directly at the site of the disease. Using total lipid extract of M. tuberculosis, we showed the location of the main lipid bands in the Raman spectrum. The two major lipid peaks were located around 1300 cm⁻¹ and 1450 cm⁻¹. Raman spectroscopy can discriminate LR and LP cells with high sensitivity and specificity. The main differences between the two groups are located in the two major Raman lipid peaks, the lipid band A (1300 cm⁻¹) and lipid band B (1440 to 1450 cm⁻¹). The two phenotypes were successfully discriminated in TB infected guinea pig lung tissue sections also from in-vitro culture using wavelength modulated Raman (WMR) spectroscopy combined with fluorescence imaging. We developed a protocol to perform both Raman spectroscopy and immunohistochemistry on the same tissue sample. We studied the evolution of LR and LP proportion in mycobacterial population as the growth conditions changed and showed that LR cells could rapidly convert to LP cells as they face favourable growth conditions. The results presented in this thesis showed that LR M. tuberculosis cells could be predominant at the site of infection. This would suggest that drug sensitivity testing should be performed on culture presenting both LR and LP cells in high proportion.

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No. of bitstreams: 2 Dissertação - Viviane Lopes Rocha - 2014.pdf: 3025545 bytes, checksum: 8144fc57a9ecf1ebc51b1286fa161d44 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-05-21 / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / Mycobacterium massiliense (MM) has been associated as the causative agent of many nosocomial outbreaks related to laparoscopy, arthroscopic and wound infections. Several outbreaks have been reported in Brazil. The cities of Goiânia, Rio de Janeiro and Belem reported a high number of cases in 2006 and 2007. The iron ion (Fe) is extremely important for many biochemical processes in all organisms and, in the case of microorganisms, the success of the infection. Microorganisms synthesize molecules called siderophores (SD) to aid Fe uptake. Micobactin and carboximicobactin are the SDs that has been described in mycobacteria. One of the genes responsible for the assembly of these SD in M. tuberculosis is the mbtb. A MM strain, which belongs to the outbreak that happened in Goiânia (MM GO06) had its genome sequenced and the analysis revealed that the species has a putative gene with high similarity to M. tuberculosismbtb, which could be an indication that MM also synthesizes a siderophore molecule and that this can be helping this mycobacteria to install the infection in the host. It is known that in the absence of mbtb gene M. tuberculosis do not synthesize their SD. To estimate whether a gene similar to mbtb and with the same function is present in MM (smbtb) will assist in the understanding of the infection mechanisms of MM and discover new drug targets for treating infections with this microorganism. Total RNA was obtained from cultures grown at different concentrations of Fe. Real time PCR was performed targeting the smbtb to evaluate the expression of this gene during bacterial growth in each condition. The expression of smbtb was higher with the increase of the availability of iron. In vivo studies with mice supplemented with or chelated fromiron showed expression profile of smbtb different from those obtained in in vitro studies. In mice, M. massiliense smbtb expressed at higher levels when the animal were treated for iron depletion. Thus, we have evidence that smbtb is involved in iron uptake both for subsequent storage, when this ion is available, and for prompt use in the metabolism of the bacteria when it is not in an environment where there is availability of this ion. / Mycobacterium massiliense (MM) tem sido associado como agente causador de vários surtos nosocomiais relacionados à laparoscopia, artroscopia e infecções de feridas. Inúmeros surtos têm sido reportados no Brasil. As cidades de Goiânia, Rio de Janeiro e Belém apresentaram um alto número de casos em 2006 e 2007. O íon ferro é extremamente importante para vários processos bioquímicos em todos os organismos e, no caso dos microrganismos, para o sucesso da infecção. Para auxiliar a captação de Fe durante este processo, os microrganismos sintetizam moléculas chamadas sideróforos, que desempenham esta função. Micobactina e carboximicobactina são os sideróforos que já foram descritos em micobactérias. Um dos genes responsáveis pela síntese dos sideróforos em M. tuberculosis é o mbtb. Um isolado de MM, com origem no surto que aconteceu em Goiânia (MM GO06) teve seu genoma sequenciado e sua análise revelou que esta espécie possui um gene putativo com alta similaridade com o mbtb de M. tuberculosis, o que poderia indicar que MM também sintetiza sideróforos e que está molécula poderia estar auxiliando esta micobactéria a instalar a infecção no hospedeiro. Sabemos que a ausência do gene mbtb em M. uberculosis torna esta micobactéria incapaz de sintetizar sideróforos. Avaliar se um gene similar ao mbtb e com a mesma função está presente em MM (smbtb) irá auxiliar o entendimento dos mecanismos de infecção de MM e a descoberta de novos alvos para drogas para o tratamento de infecções causadas por MM. RNA total foi obtido de culturas onde MM foi crescido em diferentes concentrações de ferro. Realizou-se Real Time PCR para o gene smbtb a fim de avaliar a expressão deste gene durante o crescimento bacteriano em cada condição. A expressão do sbmtb aumentou com o aumento da disponibilidade de ferro. Estudos in vivo com camundongos suplementados ou privados do íon ferro apresentaram um perfil de expressão diferente daquele obtido nos estudos in vitro. Em camundongos, MM expressou smbtb em altos níveis nos animais que foram tratados com quelante para o íon ferro. Evidenciamos então, que smbtb pode estar envolvido na captação de ferro tanto para armazenamento deste íon, quando o mesmo está isponível, quanto para a utilização imediata no metabolismo da bactéria, quando há uma baixa disponibilidade de ferro no ambiente que MM se encontra.