Rozprawy doktorskie na temat „Cyclic guanosine 3',5'-monophosphate”

Cyclic guanosine 3', 5'-monophosphate (cGMP) has recently emerged as an endogenous regulator for controlling or reversing cardiac hypertrophy. Increased protein accumulation is a key feature of cardiac hypertrophy; thus, our study investigates the effects of a cGMP analog on protein accumulation in primary culture of adult rat cardiomyocytes and dissects out the mechanisms involved. We confirmed that a cGMP analog, 8-bromo-cGMP, inhibits phenylephrine (PE)-increased accumulation of newly synthesized proteins in cultured adult rat ventricular cardiomyocytes. Firstly, we have obtained data showing that 8-bromo-cGMP does not inhibit phosphorylation of S6K1 by PE during short time treatment (10 min to 2 h), but blocks phosphorylation of S6K1 by PE at 6 h; moreover this blocking effect is completely abolished by phosphatase inhibitor Tautomycin. Then, we have demonstrated that PE and cGMP induce sustained and transient increased phosphorylation of ERK, respectively. Moreover, cGMP inhibits PE-induced phosphorylation of ERK during long term treatment (3 and 6h). We have also shown that 8-bromo-cGMP inhibits ROS generation induced by PE. Other effects of PE that could be related to hypertrophy (i.e. increased concentration of upstream binding factor mRNA and decreased concentration of the mRNAs of Atrogin and muscle specific RING finger) were not abolished by 8-bromo-cGMP. We conclude that cGMP analog blocks protein accumulation by inhibiting the sustained phosphorylation of S6K1 via the activation of phosphatases.

A persistência bacteriana correlacionada à formação de biofilmes bacterianos é, há algum tempo, fonte de grande preocupação médica em virtude de sua ampla associação com a dificuldade de tratamento de infecções crônicas. Por outro lado, as perspectivas de utilização de biofilmes bacterianos em novas aplicações biotecnológicas e até mesmo para fins terapêuticos são promissoras. Há, portanto, grande interesse em compreender os mecanismos que levam as células bacterianas a deixar o estado planctônico, de vida livre, e associarem-se nesses conglomerados celulares altamente complexos. Ao longo das últimas décadas, o segundo mensageiro c-di-GMP – em conjunto com as moléculas que catalisam sua síntese (diguanilato ciclases) e sua degradação (fosfodiesterases) e seus receptores – estabeleceu-se como um elemento central de regulação de uma série de respostas celulares que determinam a formação ou a dispersão de biofilmes. Curiosamente, as proteínas que participam do metabolismo deste segundo mensageiro estão, frequentemente, codificadas múltiplas vezes em um mesmo genoma bacteriano. Em vista dessa observação, estudos mais recentes apontam que, para reger paralelamente uma variedade tão ampla de fenótipos, este sistema opera em modo de alta especificidade de sinalização e que, portanto, o sinal metabolizado por determinados conjuntos de diguanilato ciclases e fosfodiesterases tem alvos celulares específicos. Evidências robustas, porém isoladas até o momento, apontaram que um dos meios pelo qual ocorre a segregação entre sinal produzido e alvo específico é a interação direta entre as proteínas componentes das vias de sinalização. Mais, demonstrou-se que, em algumas vias, a transmissão de sinal ocorre exclusivamente via interação proteica, dispensando a intermediação do sinalizador em si. Para avaliar a validade e relevância global deste mecanismo, propôs-se, neste estudo, a investigação da rede total de interações entre as proteínas tipicamente associadas às vias de sinalização por c-di-GMP em Pseudomonas aeruginosa, utilizando ensaios de duplo-hibrido bacteriano. Para tanto, foram construídas duas bibliotecas de DNA direcionadas e foram feitos testes de interação de forma estratégica para possibilitar o esgotamento e averiguação de todas as possíveis interações entre as proteínas alvo identificadas. O resultado obtido, um mapa inicial, porém abrangente, da rede de interações proteicas em P. aeruginosa, indica uma grande probabilidade de que os mecanismos previamente descritos sejam realmente recorrentes e relevantes para o intermédio da sinalização nesse organismo. Algumas das interações mais robustas encontradas são bastante interessantes e serão, em estudos futuros, mais extensivamente estudadas.
Persister bacteria are correlated to biofilm formation and have been a source of great medical concern due to its close association with the impairment of traditional treatment in combating chronic infections. On the other hand, using bacterial biofilms to create original biotechnological applications or even as a means of therapeutic treatment in medical settings constitutes a promising prospect. There is, therefore, a great interest in understanding the mechanisms that allow bacteria to leave the free-living planktonic lifestyle and associate in these highly complex cellular aggregates. Over the last decades, the second messenger c-di-GMP – and also the molecules involved in its synthesis (diguanylate ciclases) and degradation (phosphodiesterases) along with its receptors – has been established as a key element implicated in regulation of a series of cellular responses that determine biofilm formation or dispersion. Curiously, the proteins that play a part in the metabolism of this second messenger are frequently coded multiple times in single bacterial genomes. Taking this into account, recent studies indicate that, in order to control such a wide range of phenotypes, this system operates via high specificity of signaling – which means that the signal metabolized by a certain set of diguanylate ciclases and phosphodiesterases has specific cellular targets. Robust but yet isolated evidence indicate that a means by which a signal is segregated with its correlated phenotypic response is through direct protein-protein interaction involving the components of these signaling pathways. Even more, there has been strikingly evidence that, in some of these pathways, signal transduction occurs exclusively through protein-protein interaction, entirely dismissing any mediation by the signal molecule. In order to validate and evaluate the global relevance of this type of mechanism, this study proposed the investigation of the entire network of interactions between proteins typically associated with c-di-GMP signaling pathways of Pseudomonas aeruginosa by employing bacterial two-hybrid system assays. To make that possible, two DNA libraries were constructed and interaction essays were performed in a strategic way so that all possibilities of interaction between target proteins were explored. The results obtained from these experiments allowed the construction of a broad map of interactions that, although still primitive, indicates that, chances are, the mechanisms previously described are both recurrent and relevant to signaling regulation in this organism. Some of the interaction partners found are particularly interesting and will be further investigated in future studies.

Streptomyces clavuligerus was grown in nutrient-limited defined media in laboratory scale fermenters using continuous and batch culture methods. Cephamycin C was produced in all fermentations. Clavulanic acid was produced in carbon- and nitrogenlimited continuous culture and in carbon- and phosphate-limited batch culture. Low levels of intracellular guanosine 5'-diphosphate 3'-diphosphate (ppGpp) were detected at D= 0.02 h' in continuous culture in all media. Low levels of intracellular guanosine 5 '-diphosphate 3 '-monophosphate (ppGp) were detected at D=0.02 if' in carbon- and nitrogen- limited media. ppop was not detected under phosphate limitation at any dilution rate. Increased production of cephamycin C was observed at D=0.02 If' under nitrogen limitation coinciding with the detection of elevated levels of ppGpp, ppGp and ATP. Increased production of clavulanic acid was observed at D=0.02 If' under carbon limitation coinciding with the detection of elevated levels of ppGpp and ppGp. There was no correlation between dilution rate and basal levels of either ppGpp or ppGp in any growth-limiting medium. ppGpp was produced at low levels in carbon- and nitrogen-limited batch fermentations prior to the detection of cephamycin C and clavulanic acid in the medium. High levels of ppGpp were detected under phosphate limitation immediately prior to the transcription of cas, the gene encoding clavaminate synthase. High levels of ppGp were detected in all batch fermentations following a downturn in nitrogen and carbon levels and immediately prior to the detection of isopenicillin N synthetase (IPNS). ppGp was detected following nutrient shifidown by amino acid depletion and was not produced via degradation of ppGpp. The results point to a possible role for ppGpp in the regulation of clavulanic acid synthesis under phosphate limitation only, and a potential role for ppGp in the regulation of cephamycin C production in Streptomyces clavuligerus.

Two enzymes capable of hydrolysing cytidine 3',5'-cyclic monophosphate have previously been reported, one (cCMP-specific PDE) with an absolute specificity for cCMP as substrate, and the other (multifunctional PDE) capable of hydrolysing a number of cyclic nucleotide substrates. This phosphodiesterase preparation was capable of hydrolysing different substrates (cyclic CMP > cyclic AMP > cyclic UMP > cyclic GMP) with the highest specific activity toward cyclic CMP as substrate. It was found to contain both the multifunctional and the cyclic CMP-specific phosphodiesterase, as shown by kinetic data, mass spectrometric analysis, and by utilizing isoelectric focusing and polyacrylamide gel electrophoresis. The PDE activity of the preparation was activated by cytidine and mercaptoethanol, inhibited by aspartate and arginine, but was insensitive to calmodulin. It was active in the absence of metal ions but inhibited by addition of Fe²⁺ and Ca²⁺ when cyclic CMP was substrate. Various types of inhibition were observed with different effectors. Cyclic CDP-deoxy cyclic CMP, glutamyl cyclic CMP and 3',5'-cyclic AMP produced competitive inhibition; theophylline produced noncompetitive inhibition; and cytidine 2'-monophosphate 3',5'-cyclic monophosphate, 5-CMP, 2',3'-cyclic CMP, 2',3'-cyclic AMP and 3',5'-cyclic UMP produced mixed type inhibition (either competitive-noncompetitive or uncompetitive-noncompetitive inhibition). Molecular modelling of the substrates and effectors was carried out, and it was deduced that the nitrogen atom bonded to carbon atom 4 (N4) and the oxygen atom bonded to carbon atom 5'(5'-O) with an interatomic distance of 8.92A° was crucial to the binding of ligands; good correlation was obtained between this distance and the potency of the effector. Mass spectrometric analysis suggested that both 5'- and 3'-CMP were products of the enzyme preparation's activity upon 3',5'-cCMP.

The objective of this thesis was to understand the regulation of islet Cl⁻ current by cAMP. This current, known as Icl,islet flew is the first Cl⁻ channel current characterized in pancreatic 𝛃 cells. Icl,islet has been hypothesized to modulate insulin secretion through changes in islet electrical activity. Both 5 𝛍M forskolin and 100 𝛍M IBMX (3-isobutyl-1-methylxanthine), agents that increase intracellular cAMP, were shown to activate an outwardly-rectifying ionic current in HIT cells that closely resembled Icl,islet. The current was blocked when iodide was substituted for external Cl⁻ or when the Cl⁻ channel blocker niflumic acid was applied to cells. In contrast, removal of [Na⁺]O did not inhibit the current. In many cells, Cl⁻ current activated and then spontaneously deactivated following cAMP stimulation, suggesting the possibility that the channel desensitizes to [cAMP]i. Exposing cells to multiple cAMP activators revealed that Cl⁻ current declined because it became refractory to increased [cAMP]i. The implication of these results to islet physiology is discussed.

The LNCaP cell line is a versatile and useful model that is suitable for the study of human prostate cancer in vitro. The elevation of LNCaP intracellular cAMP levels through the addition of membrane permeable cAMP analogues, phosphodiesterase inhibitors, adenylate cyclase activators, or components of the cAMP signal transduction pathway can induce reversible neuroendocrine differentiation. Elucidation of those genes that are differentially expressed between undifferentiated prostate cancer cells and prostate cancer cells that have been induced to differentiate may present new insights for the molecular mechanisms governing neuroendocrine differentiation, early detection of prostate cancer, and/or potential targets for gene therapy. In this study, differential display PCR was used to identify 226 differentially expressed PCR products. Twelve of the differential display PCR products were confirmed by Northern blot analysis and cloned. DNA sequencing and database comparisons were performed. Among the differentially expressed genes, the human ribosomal S3a gene was identified as down regulated in response to LNCaP differentiation. In order to better ascertain the mechanism by which HRS3a gene expression is decreased during differentiation, the promoter region for this gene was analyzed. Electrophoretic mobility shift assay, antibody supershift assays, site-directed mutagenesis, and luciferase reporter gene analysis were employed to authenticate the roles of several transcription factors in the regulation of the HRS3a gene. Two cyclic AMP response elements, a Sp1 element and a GA-binding protein element, were involved in the regulation of HRS3a gene expression. In order to ascertain the effect of HRS3a down regulation in LNCaP cells, antisense phosphorothioate oligonucleotides were designed to inhibit HRS3a gene expression. Treatment of LNCaP cells with antisense HRS3a oligonucleotides did not influence cAMP induced neuroendocrine differentiation but antisense treatment did result in a decrease in LNCaP cell growth. In addition, it was determined that morphological changes associated with cAMP induced differentiation of LNCaP cells from the epithelial to the neuroendocrine state may not require alterations in gene expression nor the expression of novel proteins.
Ph. D.

L'objet de ce travail a consiste en une etude biochimique du canal cationique active par la gmpc des batonnets retiniens de bovins. (1) des reactifs bloqueurs des fonctions thiol ou capables de former des ponts disulfure entre deux cysteines proches ont un double effet sur l'activite des canaux: a faible concentration ils provoquent une augmentation de l'affinite apparente du canal pour le nucleotide cyclique (activation) et une perte de la cooperativite de liaison du nucleotide. A de plus fortes concentrations, ils entrainent une reduction de l'amplitude et de la vitesse initiale maximales des efflux calciques induits par le nucleotide cyclique. Les resultats suggerent que le fait de bloquer au moins une des 3 cysteines cytoplasmiques, situees au voisinage ou dans le site de liaison du nucleotide cyclique, ou la formation d'un pont disulfure entre deux sous-unites adjacentes du canal entrainent l'activation. L'inhibition resulterait du blocage d'au moins une des deux autres cysteines (par les bloqueurs des -sh) ou des deux autres (formation d'un pont disulfure intramonomerique). La liaison du nucleotide cyclique engendrerait un changement conformationnel au niveau des sites nucleotidiques du canal. (2) le phenomene dit d'inactivation, qui se traduit par une liberation partielle du contenu ionique des vesicules membranaires a des concentrations non saturantes en nucleotide cyclique, ne peut s'expliquer par une desesibilisation du canal, ni par une inactivation consecutive a l'apparition d'un potentiel membranaire apres addition du nucleotide cyclique, ni par un blocage du canal par les ions ca#2#+ extracellulaires. Ce phenomene pourrait s'expliquer par la variation de la porportion de vesicules capables de decharger leur contenu ionique. (3) la sous-unite beta du canal peut etre phosphorylee dans les membranes natives

Thesis (Ph. D.)--Chemical and Biomolecular Engineering, Georgia Institute of Technology, 2006.
Dr. Peter A. Lane, Committee Member ; Dr. Larry V. McIntire, Committee Member ; Dr. Ronald W. Rousseau, Committee Member ; Dr. James R. Eckman, Committee Member ; Dr. Timothy M. Wick, Committee Chair.

Dopamine and 3',5'-cyclic adenosine monophosphate-regulated neuronal phosphoprotein (DARPP-32) is a critical mediator of neuroplasticity in striatal medium spiny neurons (MSNs). The work presented in this thesis used a global gene knockout (KO) construct to investigate the role of DARPP-32 in reward-based learning and performance. Global deletion of the DARPP-32 gene disturbed performance during the intertemporal (delay) discounting procedure. DARPP-32 KO mice were less sensitive than their wildtype (WT) littermates during long delays to reinforcement. In comparison to WT mice, DARPP-32 KO mice also developed a risk-sensitive pattern of choices during a probability discounting task. Unlike the effects of DARPP-32 deletion on reinforcement along dimensions of time and risk, DARPP-32 knockout did not affect the degree of effort that subjects were willing to invest during food-reinforced progressive ratio testing. DARPP-32 KO mice also failed to exhibit Pavlovian-to-instrumental transfer and this impairment could not be rescued by administering methylphenidate prior to test. Finally, DARPP-32 KO mice were indistinguishable from WT mice during an amphetamine psychomotor sensitisation study. Overall, the data in this thesis suggest DARPP-32 is involved in adaptive reward-based learning and performance.

Presently, the literature regarding vascular smooth muscle contraction is coloured with many contradictory observations and conclusions. However, like many physiological systems, the biochemical pathways and functional events of vascular smooth muscle contraction vary between individual species and/or tissues. Therefore, determination of a ubiquitous excitation-contraction coupling mechanism is unlikely; variations between receptor classes, receptor density, excitation-contraction coupling pathways and the efficiency of the receptor-pathway interaction contribute to the various observations and conclusions. The inositol 1,4,5-trisphosphate (IP₃) second messenger cascade regulates the mobilization of intracellular Ca²⁺, and subsequently contraction, in vascular smooth muscle. However, phospholipase G-mediated production of IP₃ appears to be controlled by tissue-specific regulatory factors. This study examines the effects of three such factors, the presence of extracellular Ca²⁺, the sensitivity of the associated G-protein and inhibition by 8-bromoguanosine 3':5'-cyclic monophosphate (8-brombcGMP), in isolated rat caudal artery. Concentration-response curves were constructed for phenylephrine and isometric contractions measured in isolated tissues. In addition, phosphatidylinositol turnover was assessed using anion exchange chromatography. The effects of 8-bromo-cGMP on phenylephrine-induced contractions and phosphatidylinositol hydrolysis were compared to those of felodipine, a dihydropyridine Ca²⁺-channel antagonist, and ryanodine, a putative depletor of intracellular Ca2* stores in rat caudal artery. Pertussis toxin was used to determine the identity of the G-protein regulating phenyiephrine-induced contraction. Further, the effects of felodipine and ryanodine on contraction were determined in rat thoracic aorta to compare the contribution of extracellular and intracellular Ca²⁺ to contraction between a large conduit vessel and a small conduit vessel. The results of this investigation suggest that phospholipase C-activated phosphatidylinositol hydrolysis in the rat caudal artery is dependent on extracellular Ca²⁺, mediated, in part, through dihydropyridine sensitive Ca²⁺ channels. Phospholipase C activity is not directly inhibited by 8-bromo-cGMP. However, the nucleotide may regulate vascular smooth muscle contraction by inhibition of Ca²⁺ release from IP₃-mediated intracellular stores, but it is unlikely that 8-bromo-cGMP affects ryanodine-sensitive stores. None of the G-proteins coupled to the ctiadrenoceptor mediated excitation-contraction pathway in rat caudal artery appear to be sensitive to pertussis toxin. Rat aortic tissue does not rely on intracellular Ca²⁺ to the same extent that rat caudal artery does, confirming the tissue specificity of ctiadrenoceptor agonist induced excitation-contraction in vascular smooth muscle.

Cyclic guanosine 3’,5’-monophosphate (cGMP) performs a wide range of functions in various cell types and tissues. The cellular levels of cGMP are maintained by the enzymatic conversion of guanosine 5’-triphosphate (GTP) to cGMP by guanylyl cyclases, which can also be membrane-associated receptors. Receptor guanylyl cyclase C (GC-C; gene GUCY2C) is predominantly expressed on the apical surface of the intestinal epithelial cells. GC-C is activated by peptide hormones guanylin and uroguanylin and the heat-stable enterotoxin (ST) produced by enterotoxigenic E.coli that causes traveller’s diarrhoea. Several disease-causing mutations in GUCY2C have been reported. Patients with gain-of-function mutations show diarrhoea and inflammatory bowel disease (IBD). Several cases of paediatric IBD have also been associated with mutations in GUCY2C. This study addresses the physiological implications of increased cGMP using a transgenic mouse model harbouring the first-identified hyperactive mutation in human patients leading to familial GUCY2C diarrhoea syndrome (FGDS). Mice with hyperactive GC-C showed increased levels of cGMP in intestinal epithelial cells, which led to activation of Cftr and inhibition of Nhe3, resulting in diarrhoea-like symptoms and increased luminal pH and faecal sodium levels. Global transcriptome analysis of the distal colon revealed activation of the interferon signalling pathway, and transgenic mice showed greater susceptibility to DSS-induced colitis. Histological analysis of the terminal ileum revealed a reduction in functional Paneth cells, goblet cells, and mucus barrier. The barrier integrity of the small intestine was compromised in these mice. Global transcriptome analysis of the terminal ileum revealed a Th1-type gene signature. Immune cell profiling across the gut-associated lymphoid tissue (GALT) showed reduced regulatory dendritic cells and an increased abundance of CD4+ Th cells. Increased levels of Stat1 were observed in the ileal epithelial cells of these mice, along with elevated expression of interferon-stimulated genes. Small intestinal organoids were prepared from wild type and transgenic mice. The organoids from transgenic mice showed greater swelling in the presence of ST and uroguanylin due to increased fluid secretion into the lumen. Administration of cGMP increased Stat1 phosphorylation in the intestinal organoids. Our observations suggest that high cGMP levels have epithelial cell-extrinsic and cell-intrinsic roles in inducing intestinal inflammation. Furthermore, the administration of zinc inhibited the activity of GC-C and reduced diarrhoea and intestinal inflammation in the transgenic mice. Thus, the similarities observed in these transgenic mice with that of chronic diarrhoea and IBD patients indicate that they can be used as a pre-clinical model to understand the effects of chronically elevated cGMP on intestinal pathophysiology and for identifying novel therapeutic strategies for patients with hyperactivating mutations in GUCY2C.

Evaluating aerodynamic noise from aircraft engines is a design stage process, so that it conform to regulations at airports. Aerodynamic noise is also a principal source of structural vibration and internal noise in short/vertical take off and landing and rocket launches. Acoustic loads may be critical for the proper functioning of electronic and mechanical components. It is imperative to have tools with capability to predict noise generation from turbulent flows. Understanding the mechanism of noise generation is essential in identifying methods for noise reduction. Lighthill (1952) and Lighthill (1954) provided the first explanation for the mechanism of aerodynamic noise generation and a procedure to estimate the radiated sound field. Many such procedures, known as acoustic analogies are used for estimating the radiated sound field in terms of the turbulent fluid flow properties. In these methods, the governing equations of the fluid flow are rearranged into two parts, the acoustic sources and the propagation terms. The noise source terms and propagation terms are different in different approaches. A good description of the turbulent flow field and the noise sources is required to understand the mechanism of noise generation. Computational aeroacoustics (CAA) tools are used to calculate the radiated far field noise. The inputs to the CAA tools are results from CFD simulations which provide details of the turbulent flow field and noise sources. Reynolds-Averaged Navier Stokes (RANS) solutions can be used as inputs to CAA tools which require only time-averaged mean quantities. The output of such tools will also be mean quantities. While complete unsteady turbulent flow details can be obtained from Direct Numerical Simulation (DNS), the computation is limited to low or moderate Reynolds number flows. Large eddy simulations (LES) provide accurate description for the dynamics of a range of large scales. Most of the kinetic energy in a turbulent flow is accounted by the large-scale structures. It is also the large-scale structures which accounts for the maximum contribution towards the radiated sound field. The results from LES can be used as an input to a suitable CAA tool to calculate the sound field. Numerical prediction of turbulent flow field, the acoustic sources and the radiated sound field is at the focus of this study. LES based on explicit filtering method is used for the simulations. The method uses a low-pass compact filter to account for the sub-grid scale effects. A one-parameter fourth-order compact filter scheme from Lele (1992) is used for this purpose. LES has been carried out for four different flow situations: (i) round jet (ii) plane jet (iii) impinging round jet and (iv) impinging plane jet. LES has been used to calculate the unsteady flow evolution of these cases and the Lighthill’s acoustic sources. A compact difference scheme proposed by Hixon & Turkel (1998) which involves only bi-diagonal matrices are used for evaluating spatial derivatives. The scheme provides similar spectral resolution as standard tridiagonal compact schemes for the first spatial derivatives. The scheme is computationally less intensive as it involves only bi-diagonal matrices. Also, the scheme employs only a two-point stencil. To calculate the radiated sound field, the Helmholtz equation is solved using the Green’s function approach, in the form of the Kirchhoff-Helmholtz integral. The integral is performed over a surface which is present entirely in the linear region and covers the volume where acoustic sources are present. The time series data of pressure and the normal component of the pressure gradient on the surface are obtained from the CFD results. The Fourier transforms of the time series of pressure and pressure gradient are then calculated and are used as input for the Kirchhoff-Helmholtz integral. The flow evolution for free jets is characterised by the growth of the instability waves in the shear layer which then rolls up into large vortices. These large vortical structures then break down into smaller ones in a cascade which are convected downstream with the flow. The rms values of the Lighthill’s acoustic sources showed that the sources are located mainly at regions immediately downstream of jet break down. This corresponds to the large scale structures at break down. The radiated sound field from free jets contains two components of noise from the large scales and from the small scales. The large structures are the dominant source for the radiated sound field. The contribution from the large structures is directional, mainly at small angles to the downstream direction. To account for the difference in jet core length, the far field SPL are calculated at points suitably shifted based on the jet core length. The peak value for the radiated sound field occurs between 30°and 35°as reported in literature. Convection of acoustic sources causes the radiated sound field to be altered due to Doppler effect. Lighthills sources along the shear layer were examined in the form of (x, t) plots and phase velocity pattern in (ω, k) plots to analyse for their convective speeds. These revealed that there is no unique convective speeds for the acoustic sources. The median convective velocity Uc of the acoustic sources in the shear layer is proportional to the jet velocity Uj at the center of the nozzle as Uc ≈ 0.6Uj. Simulations of the round jet at Mach number 0.9 were used for validating the LES approach. Five different cases of the round jet were used to understand the effect of Reynolds number and inflow perturbation on the flow, acoustic sources and the radiated sound field. Simulations were carried out for an Euler and LES at Reynolds number 3600 and 88000 at two different inflow perturbations. The LES results for the mean flow field, turbulence profiles and SPL directivity were compared with DNS of Freund (2001) and experimental data available in literature. The LES results showed that an increase in inflow forcing and higher Reynolds number caused the jet core length to reduce. The turbulent energy spectra showed that the energy content in smaller scale is higher for higher Reynolds number. LES of plane jets were carried out for two different cases, one with a co-flow and one without co-flow. LES of plane jets were carried out to understand the effect of co-flow on the sound field. The plane jets were of Mach number 0.5 and Reynolds number of 3000 based on center-line velocity excess at the nozzle. This is similar to the DNS by Stanley et al. (2002). It was identified that the co-flow leads to a reduction in turbulence levels. This was also corroborated by the turbulent energy spectrum plots. The far field radiation for the case without co-flow is higher over all angles. The contribution from the low frequencies is directional, mainly towards the downstream direction. The range of dominant convective velocities of the acoustic sources were different along shear layers and center-line. The plane jet results were also used to bring out a qualitative comparison of flow and the radiation characteristics with round jets. For the round jet, the center-line velocity decays linearly with the stream-wise distance. In the plane jet case, it is the square of the center-line velocity excess which decays linearly with the stream-wise distance. The turbulence levels at any section scales with the center-line stream-wise velocity. The decay of turbulence level is slower for the plane jet and hence the acoustic sources are present for longer distance along the downstream direction. Subsonic impinging jets are composed of four regions, the jet core, the fully developed jet, the impingement zone and the wall jet. The presence of the second region (fully developed free jet) depends on the distance of the wall from the nozzle and the length of the jet core. In impinging jets, reflection from the wall and the wall jet are additional sources of noise compared to the free jets. The results are analysed for the contribution of the different regions of the flow towards the radiated sound field. LES simulations of impinging round jets and impinging plane jet were carried out for this purpose. In addition, the results have been compared with equivalent free jets. The directivity plots showed that the SPL levels are significantly higher for the impinging jets at all angles. For free jets, a typical time scale for the acoustic sources is the ratio of the nozzle size to the jet velocity. This is ro/Uj for round jets and h/Uj for plane jets. For impinging jets, the non-dimensionlised rms of Lighthill’s source indicates that the time scale for acoustic sources is the ratio of the height of the nozzle from the wall to the jet velocity be L/Uj. LES of impinging round jets was carried out for two cases with different inflow perturbations. The jets were at Reynolds number of 88000 and Mach number of 0.9, same as the free jet cases. The impingement wall was at a distance L = 24ro from the nozzle exit. For impinging round jets, the SPL levels are found to be higher than the equivalent free jets. From the SPL levels and radiated noise spectra it was shown that the contribution from the large scale structures and its reflection from the wall is directional and at small angles to the wall normal. The difference in the range of angles where the radiation from the large scale structures were observed shows the significance of refraction of sound waves inside the flow. The rms values of the Lighthill’s sources indicate two dominant regions for the sources, just downstream of jet breakdown and in the impingement zone. The LES of impinging plane jet was done for a jet of Mach number 0.5 and Reynolds number of 6000. The impingement wall was at a distance L = 10h from the nozzle exit. The radiated sound field appears to emanate from this impingement zone. The directivity and the spectrum plots of the far field SPL indicate that there is no preferred direction of radiation from the impingement zone. The Lighthill’s sources are concentrated mainly in the impingement zone. The rms values of the sources indicate that the peak values occur in the impingement zone. The results from the different flow situations demonstrates the capability of LES with explicit filtering method in predicting the turbulent flow and radiated noise field. The method is robust and has been successfully used for moderate Reynolds number and an Euler simulation. An important feature is that LES can be used to identify acoustic sources and its convective speeds. It has been shown that the Lighthill source calculations, the calculated sound field and the observed radiation patterns agree well. An explanation for these based on the different turbulent flow structures has also been provided.

Evaluating aerodynamic noise from aircraft engines is a design stage process, so that it conform to regulations at airports. Aerodynamic noise is also a principal source of structural vibration and internal noise in short/vertical take off and landing and rocket launches. Acoustic loads may be critical for the proper functioning of electronic and mechanical components. It is imperative to have tools with capability to predict noise generation from turbulent flows. Understanding the mechanism of noise generation is essential in identifying methods for noise reduction. Lighthill (1952) and Lighthill (1954) provided the first explanation for the mechanism of aerodynamic noise generation and a procedure to estimate the radiated sound field. Many such procedures, known as acoustic analogies are used for estimating the radiated sound field in terms of the turbulent fluid flow properties. In these methods, the governing equations of the fluid flow are rearranged into two parts, the acoustic sources and the propagation terms. The noise source terms and propagation terms are different in different approaches. A good description of the turbulent flow field and the noise sources is required to understand the mechanism of noise generation. Computational aeroacoustics (CAA) tools are used to calculate the radiated far field noise. The inputs to the CAA tools are results from CFD simulations which provide details of the turbulent flow field and noise sources. Reynolds-Averaged Navier Stokes (RANS) solutions can be used as inputs to CAA tools which require only time-averaged mean quantities. The output of such tools will also be mean quantities. While complete unsteady turbulent flow details can be obtained from Direct Numerical Simulation (DNS), the computation is limited to low or moderate Reynolds number flows. Large eddy simulations (LES) provide accurate description for the dynamics of a range of large scales. Most of the kinetic energy in a turbulent flow is accounted by the large-scale structures. It is also the large-scale structures which accounts for the maximum contribution towards the radiated sound field. The results from LES can be used as an input to a suitable CAA tool to calculate the sound field. Numerical prediction of turbulent flow field, the acoustic sources and the radiated sound field is at the focus of this study. LES based on explicit filtering method is used for the simulations. The method uses a low-pass compact filter to account for the sub-grid scale effects. A one-parameter fourth-order compact filter scheme from Lele (1992) is used for this purpose. LES has been carried out for four different flow situations: (i) round jet (ii) plane jet (iii) impinging round jet and (iv) impinging plane jet. LES has been used to calculate the unsteady flow evolution of these cases and the Lighthill’s acoustic sources. A compact difference scheme proposed by Hixon & Turkel (1998) which involves only bi-diagonal matrices are used for evaluating spatial derivatives. The scheme provides similar spectral resolution as standard tridiagonal compact schemes for the first spatial derivatives. The scheme is computationally less intensive as it involves only bi-diagonal matrices. Also, the scheme employs only a two-point stencil. To calculate the radiated sound field, the Helmholtz equation is solved using the Green’s function approach, in the form of the Kirchhoff-Helmholtz integral. The integral is performed over a surface which is present entirely in the linear region and covers the volume where acoustic sources are present. The time series data of pressure and the normal component of the pressure gradient on the surface are obtained from the CFD results. The Fourier transforms of the time series of pressure and pressure gradient are then calculated and are used as input for the Kirchhoff-Helmholtz integral. The flow evolution for free jets is characterised by the growth of the instability waves in the shear layer which then rolls up into large vortices. These large vortical structures then break down into smaller ones in a cascade which are convected downstream with the flow. The rms values of the Lighthill’s acoustic sources showed that the sources are located mainly at regions immediately downstream of jet break down. This corresponds to the large scale structures at break down. The radiated sound field from free jets contains two components of noise from the large scales and from the small scales. The large structures are the dominant source for the radiated sound field. The contribution from the large structures is directional, mainly at small angles to the downstream direction. To account for the difference in jet core length, the far field SPL are calculated at points suitably shifted based on the jet core length. The peak value for the radiated sound field occurs between 30°and 35°as reported in literature. Convection of acoustic sources causes the radiated sound field to be altered due to Doppler effect. Lighthills sources along the shear layer were examined in the form of (x, t) plots and phase velocity pattern in (ω, k) plots to analyse for their convective speeds. These revealed that there is no unique convective speeds for the acoustic sources. The median convective velocity Uc of the acoustic sources in the shear layer is proportional to the jet velocity Uj at the center of the nozzle as Uc ≈ 0.6Uj. Simulations of the round jet at Mach number 0.9 were used for validating the LES approach. Five different cases of the round jet were used to understand the effect of Reynolds number and inflow perturbation on the flow, acoustic sources and the radiated sound field. Simulations were carried out for an Euler and LES at Reynolds number 3600 and 88000 at two different inflow perturbations. The LES results for the mean flow field, turbulence profiles and SPL directivity were compared with DNS of Freund (2001) and experimental data available in literature. The LES results showed that an increase in inflow forcing and higher Reynolds number caused the jet core length to reduce. The turbulent energy spectra showed that the energy content in smaller scale is higher for higher Reynolds number. LES of plane jets were carried out for two different cases, one with a co-flow and one without co-flow. LES of plane jets were carried out to understand the effect of co-flow on the sound field. The plane jets were of Mach number 0.5 and Reynolds number of 3000 based on center-line velocity excess at the nozzle. This is similar to the DNS by Stanley et al. (2002). It was identified that the co-flow leads to a reduction in turbulence levels. This was also corroborated by the turbulent energy spectrum plots. The far field radiation for the case without co-flow is higher over all angles. The contribution from the low frequencies is directional, mainly towards the downstream direction. The range of dominant convective velocities of the acoustic sources were different along shear layers and center-line. The plane jet results were also used to bring out a qualitative comparison of flow and the radiation characteristics with round jets. For the round jet, the center-line velocity decays linearly with the stream-wise distance. In the plane jet case, it is the square of the center-line velocity excess which decays linearly with the stream-wise distance. The turbulence levels at any section scales with the center-line stream-wise velocity. The decay of turbulence level is slower for the plane jet and hence the acoustic sources are present for longer distance along the downstream direction. Subsonic impinging jets are composed of four regions, the jet core, the fully developed jet, the impingement zone and the wall jet. The presence of the second region (fully developed free jet) depends on the distance of the wall from the nozzle and the length of the jet core. In impinging jets, reflection from the wall and the wall jet are additional sources of noise compared to the free jets. The results are analysed for the contribution of the different regions of the flow towards the radiated sound field. LES simulations of impinging round jets and impinging plane jet were carried out for this purpose. In addition, the results have been compared with equivalent free jets. The directivity plots showed that the SPL levels are significantly higher for the impinging jets at all angles. For free jets, a typical time scale for the acoustic sources is the ratio of the nozzle size to the jet velocity. This is ro/Uj for round jets and h/Uj for plane jets. For impinging jets, the non-dimensionlised rms of Lighthill’s source indicates that the time scale for acoustic sources is the ratio of the height of the nozzle from the wall to the jet velocity be L/Uj. LES of impinging round jets was carried out for two cases with different inflow perturbations. The jets were at Reynolds number of 88000 and Mach number of 0.9, same as the free jet cases. The impingement wall was at a distance L = 24ro from the nozzle exit. For impinging round jets, the SPL levels are found to be higher than the equivalent free jets. From the SPL levels and radiated noise spectra it was shown that the contribution from the large scale structures and its reflection from the wall is directional and at small angles to the wall normal. The difference in the range of angles where the radiation from the large scale structures were observed shows the significance of refraction of sound waves inside the flow. The rms values of the Lighthill’s sources indicate two dominant regions for the sources, just downstream of jet breakdown and in the impingement zone. The LES of impinging plane jet was done for a jet of Mach number 0.5 and Reynolds number of 6000. The impingement wall was at a distance L = 10h from the nozzle exit. The radiated sound field appears to emanate from this impingement zone. The directivity and the spectrum plots of the far field SPL indicate that there is no preferred direction of radiation from the impingement zone. The Lighthill’s sources are concentrated mainly in the impingement zone. The rms values of the sources indicate that the peak values occur in the impingement zone. The results from the different flow situations demonstrates the capability of LES with explicit filtering method in predicting the turbulent flow and radiated noise field. The method is robust and has been successfully used for moderate Reynolds number and an Euler simulation. An important feature is that LES can be used to identify acoustic sources and its convective speeds. It has been shown that the Lighthill source calculations, the calculated sound field and the observed radiation patterns agree well. An explanation for these based on the different turbulent flow structures has also been provided.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1994.
Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 195-235).

The discovery of cyclic AMP (cAMP), nearly 50 years ago by Sutherland radically altered the appreciation of metabolic regulation. Since then the presence of cAMP and its tremendous physiological impact has been demonstrated in many prokaryotic systems. In fact, virulence mechanisms of several pathogens known today exploit cAMP dependent pathways. Interestingly the genome of Mycobacterium tuberculosis H37Rv, the causative agent of tuberculosis, encodes as many as 16 adenylyl cyclases (enzymes that convert ATP to 3’, 5’-cAMP) and 10 cyclic-nucleotide binding proteins. Recent reports show that bacterial-derived cAMP manipulates host signaling for bacterial survival, suggesting an important role for cAMP in the pathogenesis of M. tuberculosis. A large number of non-pathogenic species of mycobacteria also share and conserve several of these cAMP metabolism genes, suggesting that cAMP is not only important for pathogenesis but also may play a critical physiological role in the genus. The work carried out in this thesis aims at a better understanding of the role of cAMP by studying the adenylyl cyclases and cyclic AMP receptor proteins (CRPs) from Mycobacterium smegmatis, a non-pathogenic member of the genus. Intracellular cAMP levels in a cell are precisely maintained by modulating the activities of the adenylyl cyclases (cAMP synthesising enzymes), the phosphodiesterases (cAMP hydrolysing enzymes) and the secretion machinery, if any. To assess the role of cAMP in mycobacteria, cAMP levels were measured in M. smegmatis during growth and under various stress conditions. The results show that cAMP levels peak at log phase of growth and decline thereafter. Under acidic conditions or on perturbing the cell-wall, cellular cAMP levels are altered, which indicate a possible role of cAMP in stress adaptation. Earlier work in our laboratory has led to the identification of multiple adenylyl cyclases in the mycobacterial genomes. These cyclases are similar in sequence to the mammalian enzymes and several of them have been shown to be active in vitro displaying a diverse range of biochemical properties. The M. smegmatis genome encodes 10 adenylyl cyclase-like genes. In order to understand the role of cAMP in M. smegmatis, individual cyclases were analysed for their biochemical properties and physiological functions. The work presented in this thesis is concerned with the functional characterization of MSMEG_3578 and MSMEG_3780, two of the several adenylyl cyclases from M. smegmatis. MSMEG_3578 encodes for a protein that comprises two transmembrane domains, an extracellular receptor-like domain, a membrane anchoring HAMP domain and an intracellular cyclase domain. The cyclase domain is closely related to mammalian cyclases but lacks the canonical residues that are critical for the catalysis of class III cyclases. Interestingly, the stop codon of this gene overlaps with the start codon of the downstream gene, MSMEG_3579 (a putative cyclic nucleotide gated mechanosensitive ion channel), suggesting a functional link between the two genes. The conservation of this gene pair across the mycobacterial genus indicates the importance of this putative receptor-effector pair in the physiology of mycobacteria. Additionally, microarray analysis by various groups have shown that this gene pair in Mycobacterium tuberculosis is differentially regulated in conditions that mimic stress the bacteria may experience during infection. In order to ascertain the physiological role of MSMEG_3578, a knock-out M. smegmatis strain was generated and tested for growth and cAMP defects. The knock-out strain showed growth and cAMP profiles similar to the wild-type strain. Over-expression of MSMEG_3578 in M. smegmatis resulted in a significant rise in cAMP levels. Interestingly, over-expression of the MSMEG_3578 adenylyl cyclase in E. coli did not lead to an elevation in cAMP levels indicating that other mycobacterial proteins may be required for the activity of MSMEG_3578 in vivo. In agreement with this, the purified adenylyl cyclase domain of MSMEG_3578 was found to be biochemically inactive in vitro. Additionally, the over-expressing strain has altered colony morphology as compared to the wild type strain. Perturbation of cAMP levels by over-expression of other cyclases also leads to a similar colony morphology phenotype, indicating the phenotype to be controlled by cAMP in general rather than by a specific cyclase in the cell. MSMEG_3780 is a highly conserved, biochemically active adenylyl cyclase, speculated to play a house-keeping function in M. smegmatis. Its orthologs from M. tuberculosis (Rv1647) and M. leprae (ML1399) have been biochemically characterized earlier in our laboratory. To unravel the role of this gene in vivo, the ∆MSMEG_3780 strain was tested for growth and cAMP defects under various conditions. The deletion strain did not show any difference in growth rate or morphology when compared to the wild-type strain. However it showed a reduction in intracellular cAMP levels at the log-phase of growth. Reintroduction of the MSMEG_3780 gene in the deletion strain restored cAMP to wild-type levels, thus indicating a crucial role for this adenylyl cyclase in the maintenance of intracellular cAMP levels during logarithmic growth. In order to investigate the regulation of the MSMEG_3780 gene, its promoter activity was tested under various stress-conditions. Acid-stress specifically resulted in the repression of the MSMEG_3780 promoter activity, a condition which also leads to a decrease in cAMP levels in the cells. Further evidence for the susceptibility of the MSMEG_3780 gene to acid-stress was obtained when the ∆MSMEG_3780 strain failed to reduce intracellular cAMP content upon sustained acid-stress conditions. Since Rv1647 shares similar biochemical properties with MSMEG_3780 and can also heterodimerize with the MSMEG_3780 protein in vitro, it was interesting to test whether the M. tuberculosis ortholog could functionally complement MSMEG_3780. To assess this, a complement strain was generated that contained the Rv1647 gene under the control of MSMEG_3780 promoter, integrated into the genome of ∆MSMEG_3780 strain. Rv1647 protein was able to restore the cAMP phenotype seen on acid stress as well as the cAMP levels in the mutant strain at the log phase of growth. This study indicated the role of cAMP and MSMEG_3780 in acid adaptation and also suggested a non-redundancy of adenylyl cyclases in mycobacteria, where different individual cyclases may have unique functions in the cells. Since Rv1647 could complement the cAMP defective phenotype in ∆MSMEG_3780, this suggests functional parallels between the proteins from the two species. Bacterial adaptation to environmental stress is brought about by a rapid change in its gene expression profile. Cyclic AMP plays an important role by binding to and activating a transcriptional factor, cAMP receptor protein or CRP. We have identified two CRPs from M. smegmatis, viz., MSMEG_0539 and MSMEG_6189 that possess high similarity at the amino acid level (78% overall sequence identity). The CRP ortholog from M. tuberculosis, Rv3676 has been characterized structurally, biochemically and functionally earlier. Western blot and RT-PCR analyses showed that CRPs in M. smegmatis were present during all phases of growth. Both the CRPs were cloned, expressed and shown to bind cAMP. Since the DNA binding domains of Rv3676 and the two M. smegmatis CRPs are nearly identical, the CRPs from M. smegmatis were predicted to bind similar target sequences. Interestingly, a CRP site was identified in the promoter of the MSMEG_3780 gene, suggesting a possible feed-forward or feed-back loop, where the enzymatic product of the adenylyl cyclase now governs its own gene expression. We performed Electrophoretic Mobility Gel Shift Assays (EMSAs) with M. smegmatis lysates to show that CRP binds to the MSMEG_3780 promoter at the CRP site. Subsequent Chromatin Immunoprecipitation (ChIP) assays confirmed that CRP binding to the MSMEG_3780 promoter occurred in vivo. To investigate the role of CRP in the regulation of the MSMEG_3780 gene, luciferase reporter assays with the wild-type and CRP site mutant promoters were carried out. Results suggest that CRP regulates the MSMEG_3780 gene under osmotic stress. However, CRP did not play any role in basal expression of MSMEG_3780 during growth. To assess which CRP of the two is functionally linked to the MSMEG_3780 promoter, we carried out a footprint assay with purified CRPs. It was intriguing to note that both the CRPs were in fact able to bind the promoter albeit under different conditions. Whereas MSMEG_6189 bound the promoter both in the presence and absence of cAMP, MSMEG_0539 bound the promoter only in the presence of cAMP. MSMEG_6189 thus deviates from the accepted CRP paradigm that seeks an absolute requirement of cAMP for specific DNA binding. The present study identifies cAMP as an important stress signal in M. smegmatis. Using MSMEG_3780 as a model gene, the role of cAMP in mycobacteria was studied. The two divergent CRPs that were characterized may function and dictate cAMP-mediated and perhaps independent functions in cells. Taken together, our results provide compelling evidence for the important role of cAMP in the general physiology and stress adaptation in M. smegmatis.

The discovery of cyclic AMP (cAMP), nearly 50 years ago by Sutherland radically altered the appreciation of metabolic regulation. Since then the presence of cAMP and its tremendous physiological impact has been demonstrated in many prokaryotic systems. In fact, virulence mechanisms of several pathogens known today exploit cAMP dependent pathways. Interestingly the genome of Mycobacterium tuberculosis H37Rv, the causative agent of tuberculosis, encodes as many as 16 adenylyl cyclases (enzymes that convert ATP to 3’, 5’-cAMP) and 10 cyclic-nucleotide binding proteins. Recent reports show that bacterial-derived cAMP manipulates host signaling for bacterial survival, suggesting an important role for cAMP in the pathogenesis of M. tuberculosis. A large number of non-pathogenic species of mycobacteria also share and conserve several of these cAMP metabolism genes, suggesting that cAMP is not only important for pathogenesis but also may play a critical physiological role in the genus. The work carried out in this thesis aims at a better understanding of the role of cAMP by studying the adenylyl cyclases and cyclic AMP receptor proteins (CRPs) from Mycobacterium smegmatis, a non-pathogenic member of the genus. Intracellular cAMP levels in a cell are precisely maintained by modulating the activities of the adenylyl cyclases (cAMP synthesising enzymes), the phosphodiesterases (cAMP hydrolysing enzymes) and the secretion machinery, if any. To assess the role of cAMP in mycobacteria, cAMP levels were measured in M. smegmatis during growth and under various stress conditions. The results show that cAMP levels peak at log phase of growth and decline thereafter. Under acidic conditions or on perturbing the cell-wall, cellular cAMP levels are altered, which indicate a possible role of cAMP in stress adaptation. Earlier work in our laboratory has led to the identification of multiple adenylyl cyclases in the mycobacterial genomes. These cyclases are similar in sequence to the mammalian enzymes and several of them have been shown to be active in vitro displaying a diverse range of biochemical properties. The M. smegmatis genome encodes 10 adenylyl cyclase-like genes. In order to understand the role of cAMP in M. smegmatis, individual cyclases were analysed for their biochemical properties and physiological functions. The work presented in this thesis is concerned with the functional characterization of MSMEG_3578 and MSMEG_3780, two of the several adenylyl cyclases from M. smegmatis. MSMEG_3578 encodes for a protein that comprises two transmembrane domains, an extracellular receptor-like domain, a membrane anchoring HAMP domain and an intracellular cyclase domain. The cyclase domain is closely related to mammalian cyclases but lacks the canonical residues that are critical for the catalysis of class III cyclases. Interestingly, the stop codon of this gene overlaps with the start codon of the downstream gene, MSMEG_3579 (a putative cyclic nucleotide gated mechanosensitive ion channel), suggesting a functional link between the two genes. The conservation of this gene pair across the mycobacterial genus indicates the importance of this putative receptor-effector pair in the physiology of mycobacteria. Additionally, microarray analysis by various groups have shown that this gene pair in Mycobacterium tuberculosis is differentially regulated in conditions that mimic stress the bacteria may experience during infection. In order to ascertain the physiological role of MSMEG_3578, a knock-out M. smegmatis strain was generated and tested for growth and cAMP defects. The knock-out strain showed growth and cAMP profiles similar to the wild-type strain. Over-expression of MSMEG_3578 in M. smegmatis resulted in a significant rise in cAMP levels. Interestingly, over-expression of the MSMEG_3578 adenylyl cyclase in E. coli did not lead to an elevation in cAMP levels indicating that other mycobacterial proteins may be required for the activity of MSMEG_3578 in vivo. In agreement with this, the purified adenylyl cyclase domain of MSMEG_3578 was found to be biochemically inactive in vitro. Additionally, the over-expressing strain has altered colony morphology as compared to the wild type strain. Perturbation of cAMP levels by over-expression of other cyclases also leads to a similar colony morphology phenotype, indicating the phenotype to be controlled by cAMP in general rather than by a specific cyclase in the cell. MSMEG_3780 is a highly conserved, biochemically active adenylyl cyclase, speculated to play a house-keeping function in M. smegmatis. Its orthologs from M. tuberculosis (Rv1647) and M. leprae (ML1399) have been biochemically characterized earlier in our laboratory. To unravel the role of this gene in vivo, the ∆MSMEG_3780 strain was tested for growth and cAMP defects under various conditions. The deletion strain did not show any difference in growth rate or morphology when compared to the wild-type strain. However it showed a reduction in intracellular cAMP levels at the log-phase of growth. Reintroduction of the MSMEG_3780 gene in the deletion strain restored cAMP to wild-type levels, thus indicating a crucial role for this adenylyl cyclase in the maintenance of intracellular cAMP levels during logarithmic growth. In order to investigate the regulation of the MSMEG_3780 gene, its promoter activity was tested under various stress-conditions. Acid-stress specifically resulted in the repression of the MSMEG_3780 promoter activity, a condition which also leads to a decrease in cAMP levels in the cells. Further evidence for the susceptibility of the MSMEG_3780 gene to acid-stress was obtained when the ∆MSMEG_3780 strain failed to reduce intracellular cAMP content upon sustained acid-stress conditions. Since Rv1647 shares similar biochemical properties with MSMEG_3780 and can also heterodimerize with the MSMEG_3780 protein in vitro, it was interesting to test whether the M. tuberculosis ortholog could functionally complement MSMEG_3780. To assess this, a complement strain was generated that contained the Rv1647 gene under the control of MSMEG_3780 promoter, integrated into the genome of ∆MSMEG_3780 strain. Rv1647 protein was able to restore the cAMP phenotype seen on acid stress as well as the cAMP levels in the mutant strain at the log phase of growth. This study indicated the role of cAMP and MSMEG_3780 in acid adaptation and also suggested a non-redundancy of adenylyl cyclases in mycobacteria, where different individual cyclases may have unique functions in the cells. Since Rv1647 could complement the cAMP defective phenotype in ∆MSMEG_3780, this suggests functional parallels between the proteins from the two species. Bacterial adaptation to environmental stress is brought about by a rapid change in its gene expression profile. Cyclic AMP plays an important role by binding to and activating a transcriptional factor, cAMP receptor protein or CRP. We have identified two CRPs from M. smegmatis, viz., MSMEG_0539 and MSMEG_6189 that possess high similarity at the amino acid level (78% overall sequence identity). The CRP ortholog from M. tuberculosis, Rv3676 has been characterized structurally, biochemically and functionally earlier. Western blot and RT-PCR analyses showed that CRPs in M. smegmatis were present during all phases of growth. Both the CRPs were cloned, expressed and shown to bind cAMP. Since the DNA binding domains of Rv3676 and the two M. smegmatis CRPs are nearly identical, the CRPs from M. smegmatis were predicted to bind similar target sequences. Interestingly, a CRP site was identified in the promoter of the MSMEG_3780 gene, suggesting a possible feed-forward or feed-back loop, where the enzymatic product of the adenylyl cyclase now governs its own gene expression. We performed Electrophoretic Mobility Gel Shift Assays (EMSAs) with M. smegmatis lysates to show that CRP binds to the MSMEG_3780 promoter at the CRP site. Subsequent Chromatin Immunoprecipitation (ChIP) assays confirmed that CRP binding to the MSMEG_3780 promoter occurred in vivo. To investigate the role of CRP in the regulation of the MSMEG_3780 gene, luciferase reporter assays with the wild-type and CRP site mutant promoters were carried out. Results suggest that CRP regulates the MSMEG_3780 gene under osmotic stress. However, CRP did not play any role in basal expression of MSMEG_3780 during growth. To assess which CRP of the two is functionally linked to the MSMEG_3780 promoter, we carried out a footprint assay with purified CRPs. It was intriguing to note that both the CRPs were in fact able to bind the promoter albeit under different conditions. Whereas MSMEG_6189 bound the promoter both in the presence and absence of cAMP, MSMEG_0539 bound the promoter only in the presence of cAMP. MSMEG_6189 thus deviates from the accepted CRP paradigm that seeks an absolute requirement of cAMP for specific DNA binding. The present study identifies cAMP as an important stress signal in M. smegmatis. Using MSMEG_3780 as a model gene, the role of cAMP in mycobacteria was studied. The two divergent CRPs that were characterized may function and dictate cAMP-mediated and perhaps independent functions in cells. Taken together, our results provide compelling evidence for the important role of cAMP in the general physiology and stress adaptation in M. smegmatis.

Improved sequencing technologies have created an explosion of sequence information that is analyzed and proteins are annotated automatically. Annotations are made based on similarity scores to previously annotated sequences, so one misannotation is propagated throughout databases and the number of misannotated proteins grows with the number of sequenced genomes. A systematic approach to correctly identify the function of proteins in the amidohydrolase superfamily is described in this work using Clusters of Orthologous Groups of proteins as defined by NCBI. The focus of this work is COG1816, which contains proteins annotated, often incorrectly, as adenosine deaminase enzymes. Sequence similarity networks were used to evaluate the relationship between proteins. Proteins previously annotated as adenosine deaminases: Pa0148 (Pseudomonas aeruginosa PAO1), AAur_1117 (Arthrobacter aurescens TC1), Sgx9403e and Sgx9403g, were purified and their substrate profiles revealed that adenine and not adenosine was a substrate for these enzymes. All of these proteins will deaminate adenine with values of kcat/Km that exceed 105 M-1s-1. A small group of enzymes similar to Pa0148 was discovered to catalyze the hydrolysis of N-6-substituted adenine derivatives, several of which are cytokinins, a common type of plant hormone. Patl2390, from Pseudoalteromonas atlantica T6c, was shown to hydrolytically deaminate N-6-isopentenyladenine to hypoxanthine and isopentenylamine with a kcat/Km of 1.2 x 107 M^-1 s^-1. This enzyme does not catalyze the deamination of adenine or adenosine. Two small groups of proteins from COG1816 were found to have 6-aminodeoxyfutalosine as their true substrate. This function is shared with 2 small groups of proteins closely related to guanine and cytosine deaminase from COG0402. The deamination of 6-aminofutalosine is part of the alternative menaquinone biosynthetic pathway that involves the formation of futalosine. 6-Aminofutalosine is deaminated with a catalytic effeciency of 105 M-1s-1 or greater, Km’s of 0.9 to 6.0 µM and kcat’s of 1.2 to 8.6 s-1. Another group of proteins was shown to deaminate cyclic- 3’, 5’ -adenosine monophosphate (cAMP) to produce cyclic-3’, 5’-inosine monophosphate, but will not deaminate adenosine, adenine or adenosine monophosphate. This protein was cloned from a human pathogen, Leptospira interrogans. Deamination may function in regulating the signaling activities of cAMP.