Two-component signal systems serve as basic stimulus-response coupling mechanism to allow organisms (predominantly bacteria) to sense and respond to changes in many environmental conditions. The prototypical system consists of two proteins, namely a histidine kinase, containing a sensor domain and catalytic kinase core, and a response regulator protein (RR protein). Extracellular stimuli are sensed by a histidine kinase sensor domain. Then ATP is bound to the catalytic kinase core and the γ-phosphoryl group is transferred to the conserved histidine residue. This phosphoryl group is subsequently transferred to a conserved aspartate residue within the RR protein. Phosphotransfer to the RR protein results in activation of a downstream effector domain that elicits the specific response (usually it is transcription activity, but a few RR proteins function as enzymes). The histidine kinase sensor domain is designed for specific ligand interactions. This master thesis focused on the unique histidine kinase containing a sensor domain with a globine structure, which coordinates a heme molecule, namely globin-coupled histidine kinase from Anaeromyxobacter sp. Fw 109-5 (AfGcHK) and its appropriate RR protein. The aim of this thesis was to study and characterize the phosphorylation activity of AfGcHK and RR...

La pourriture grise, causée par le champignon Botrytis cinerea, est l'une des principales maladies aériennes fongiques sur diverses cultures d'importance agronomique. La diversité génétique de B. cinerea est très forte et la capacité rapide d'adaptation de ce champignon à une pression sélective est également avérée. Ce champignon est ainsi capable de développer des résistances à une grande variété de composés fongicides de synthèse ou d'origine naturelle. Des méthodes alternatives de lutte ont de ce fait été développées ces dernières années : divers agents de lutte biologique (ALB) présentant différents modes d'actions ont été identifiés et pour certains d'entre eux commercialisés pour contrôler B. cinerea. Cependant la durabilité de la lutte biologique est un domaine encore très peu étudié. La perte d'efficacité d'un ALB pourrait résulter de la préexistence d'isolats moins sensibles de pathogènes dans les populations naturelles et/ou de la capacité de l'agent pathogène à produire, sous une pression de sélection continue exercée par l'ALB, des mutants ayant une sensibilité réduite. L'objectif global de la présente étude est d'évaluer le risque potentiel de perte d'efficacité de la lutte biologique vis-à-vis de B. cinerea. Dans cette étude, les efforts ont été concentrés sur la pyrrolnitrine, un antibiotique produit par divers ALBs, dont certains sont efficaces contre B. cinerea. Les objectifs spécifiques de l'étude étaient (i) d'évaluer la diversité de la sensibilité à la pyrrolnitrine au sein de la population naturelle de B. cinerea, (ii) d'estimer le risque de perte d'efficacité des ALBs produisant la pyrrolnitrine due à la pression de sélection exercée par la pyrrolnitrine et (iii) d'étudier le mécanisme de résistance à la pyrrolnitrine chez B. cinerea. Parmi 204 isolats de B. cinerea, une gamme importante de sensibilité à la pyrrolnitrine a été observée, avec un facteur de résistance de 8,4 entre l'isolat le plus sensible et l'isolat le moins sensible. La production de 20 générations successives pour 4 isolats de B. cinerea, sur des doses croissantes de pyrrolnitrine, a abouti au développement de mutants avec des niveaux élevés de résistance à l'antibiotique, et à une réduction in vitro de la sensibilité à la bactérie productrice de pyrrolnitrine Pseudomonas chlororaphis PhZ24. La comparaison entre les mutants résistants à la pyrrolnitrine et leurs parents sensibles pour la croissance mycélienne, la sporulation et l'agressivité sur plantes a révélé que la résistance à la pyrrolnitrine est associée à un fort coût adaptatif. Des observations cytohistologiques sur tomates ont confirmé que l'isolat sensible à la pyrrolnitrine attaque le pétiole rapidement et envahit la tige, alors que le mutant résistant à la pyrrolnitrine ne s'étend pas au-delà du pétiole. De plus, ce dernier mutant forme un mycélium anormal et des cellules ressemblant à des chlamydospores. Les résultats ont d'autre part révélé que les mutants de B. cinerea résistants à la pyrrolnitrine sont résistants au fongicide iprodione, suggérant ainsi qu'une pression exercée par la pyrrolnitrine sur le champignon conduit à une résistance au fongicide. Réciproquement, la production de générations successives sur iprodione conduit à une résistance à l'antibiotique. Afin d'étudier les déterminants moléculaires de la résistance de B. cinerea à la pyrrolnitrine, le gène histidine kinase Bos1, impliqué entre autres dans la résistance aux fongicides chez B. cinerea a été séquencé chez les souches sensibles et les mutants résistants. La comparaison des séquences a mis en évidence des mutations ponctuelles différentes chez les mutants de B. cinerea obtenus sur la pyrrolnitrine et ceux obtenus sur l'iprodione. De plus, les résistances à la pyrrolnitrine et à l'iprodione ne sont pas systématiquement associées à une mutation ponctuelle dans le gène Bos1. Enfin, aucune modification n'a été détectée dans la taille des allèles de neuf locus microsatellites quelle que soit la pression sélective exercée et quelle que soit le phénotype du mutant produit. Cette étude montre qu'un champignon pathogène des plantes est capable de développer progressivement une moindre sensibilité à un agent de lutte biologique mais que cette moindre sensibilité est associée à une forte perte de fitness

Made available in DSpace on 2015-03-26T13:51:47Z (GMT). No. of bitstreams: 1 texto completo.pdf: 1830082 bytes, checksum: ec907521bfa48f79975e5fe22c20d972 (MD5) Previous issue date: 2009-10-01 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / The filamentous fungus Colletotrichum lindemuthianum (Sacc & Magnus) Briosi & Cav., causal agent of anthracnose, is an important pathogen of common bean (Phaseolus vulgaris L.). This fungus is an excellent model organism for understanding the infection process of pathogenic fungi. A C. lindemuthianum non-pathogenic mutant (LVSa1) with partial deficiency in the production of melanin was obtained through plasmid insertional mutagenesis. The aim of this study was to isolate and characterize the interrupted gene in theLVSa1 mutant and demonstrate its importance in the plant infection process. The mutated gene was isolated from a C. lindemuthianum genomic bank and named slnCl1. The sequence analysis revealed that slnCl1 encodes a histidine kinase. The sequence presents an ORF of 3555 base pairs, interrupted by three putative introns, containing 51, 87 and 89 bp. The multiple alignment of the deduced sequence of the protein, including sequences of all histidine kinases classes available in the databases, grouped SlnCl1 in class VI; possessing highly conserved regions characteristic of histidine kinase, and related to its function. A mutant with partial deficiency for the production of melanin was obtained through site-directed insertional mutagenesis using a gene fragment. This mutant showed a significant reduction in the ability to infect bean leaves, demonstrating that SlnCl1 is important to the pathogenicity process of this fungus. As many histidines kinases already described in fungi, SlnCl1 is involved in osmoregulation and adaptation to different osmotic concentrations in C. lindemuthianum. Furthermore, through this sensor protein, the fungus can distinguish the osmotic stress caused by high concentrations of sugars and salts. The mutant was sensitive to fungicides that target a MAPK signaling pathway, probably regulated by slnCl1. The results suggest that C. lindemuthianum must have other histidines kinases involved in the osmoregulation process. The study of the signaling cascade regulated by slnCl1 may represent a major advance in understanding the pathogenicity and developing new methods to combat this disease. / O fungo filamentoso Colletotrichum lindemuthianum (Sacc & Magnus) Briosi & Cav., agente causal da antracnose, é um importante patógeno do feijoeiro comum (Phaseolus vulgaris L.). Esse fungo é um excelente modelo de estudo para o entendimento do processo de infecção de fungos fitopatogênicos. Por meio de mutagênese por inserção de plasmídeo foi obtido um mutante (LVSa1) não patogênico de C. lindemuthianum com deficiência parcial na produção de melanina. O objetivo desse trabalho foi isolar e caracterizar o gene interrompido no mutante LVSa1 e comprovar a sua importância no processo de infecção da planta. O gene mutado foi isolado de um banco genômico de C. lindemuthianum e denominado slnCl1. A análise da sequência revelou que slnCl1 codifica uma histidina quinase. A sequência apresenta uma ORF de 3555 pares de bases, interrompida por três íntrons putativos, contendo 51, 87 e 89 pb. O alinhamento múltiplo da sequência deduzida da proteína, com sequências de todas as classes de histidinas quinases disponíveis nos bancos de dados agrupou SlnCl1 na classe VI, possuindo regiões extremamente conservadas características de histidina quinases e relacionadas a sua função. Por meio de mutagênese insercional sítio dirigida utilizando um fragmento do gene, foi obtido um mutante que apresentou deficiência parcial na produção de melanina. Esse mutante apresentou uma redução significativa na capacidade de infectar folhas de feijoeiro, demonstrando que SlnCl1 é importante no processo de patogenicidade desse fungo. Como muitas histidinas quinases já descritas em fungos, SlnCl1 apresenta envolvimento no processo de osmorregulação e adaptação a diferentes concentrações osmóticas em C. lindemuthianum. Além disso, por meio dessa proteína sensora, o fungo pode distinguir o estresse osmótico causado por altas concentrações de açúcares e de sais. O mutante mostrou-se sensível a fungicidas que tem como alvo uma via de sinalização MAPK, provavelmente regulada por slnCl1. Os resultados obtidos sugerem que C. lindemuthianum deve possuir outras histidinas quinases envolvidas no processo de osmorregulação. O estudo da cascata de sinalização regulada por slnCl1 pode representar um grande avanço no entendimento do processo de patogenicidade e na elaboração de novos métodos de combate a doença.

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Sensorische Photorezeptorproteine vermitteln vielfältige Lichtreaktionen in allen Domänen des Lebens. Oftmals dienen verschiedene, durch helikale ‚Linker’ gekoppelte, Module der Lichtperzeption (Sensor) und der Umwandlung in ein biologisches Aktivität (Effektor). Der Zusammenbau chimärer Photorezeptoren aus unterschiedlichen Sensoren und Effektoren ermöglicht die präzise und minimalinvasive Regulation zellulärer Signalwege mit Hilfe von Licht, zu therapeutischen oder analytischen Zwecken. Eine große Herausforderung stellt dabei die korrekte Fusion der Linker beider Module dar, die Kommunikation zwischen Sensor und Effektor erlaubt. Die vorliegende Arbeit nimmt sich diesem Problem an und untersucht Strategien zum effizienten Bau chimärer Photorezeptorproteine. Ein rationaler, auf Sequenz- und Strukturhomologie der parentalen Proteine basierender Ansatz wurde maßgeblich durch unzureichendes Verständnis der funktionellen Mechanismen dieser modularen Proteinen erschwert. Die neuentwickelte und PATCHY-Methode umgeht dieses Hindernis, indem sie eine Bibliothek von Chimären aller Kombinationen der parentalen Linker generiert, welche anschließend mittels bakterieller Testsysteme nach funktionalen Varianten durchsucht wird. Angewendet auf die Fusion eines LOV-Blaulichtsensors und eines Histidinkinase-Effektors fanden sich sowohl lichtaktivierte, als auch zu lichtreprimierte Chimären, deren Linkerlängen jeweils einer Heptadenperiodizität folgten. Dass weniger als 5% aller Linkerkombinationen zu lichtregulierten Chimären führten, deutet zudem auf eine feine Abstimmung von Linkersequenz und Proteinfunktion hin. Die systematische Analyse von Fusionsvarianten mit PATCHY dient daher nicht nur der Entwicklung chimärer Rezeptorproteine zur Manipulation zellulärer Prozesse. Sondern sie zeigt darüber hinaus, komplementär zum rationalen Ansatz, molekulare Faktoren auf, die zur Modulkompatibilität und Signaltransduktion modularer Rezeptorproteine beitragen. / Sensory photoreceptor proteins mediate diverse responses to ambient light in all domains of life. Often distinct modules coupled by helical linkers enable light perception (sensor) and biological output function (effector). Rewiring different sensor and effector modules into photoreceptor chimeras allows using light to control target cellular processes with high spatiotemporal accuracy and minimal invasiveness for therapeutic or analytical purposes. Thereby, a major design challenge is fusing the linkers from both modules in a way that preserves signal transduction within the chimera. The present study tackles this issue and explores strategies for engineering photoreceptor chimeras. An initial rational-design approach guided by sequence and structure homology of the parent proteins was greatly hampered by insufficient knowledge of signaling mechanisms within these modular proteins. A novel and easy-to-use brute-force strategy, termed PATCHY (primer-aided truncation for the creation of hybrid enzymes) circumvents this problem by generating a complete library of fusion variants between target modules harboring all combinations of the parent linkers. Screening fusion libraries of a LOV (light-oxygen-voltage) blue-light sensor coupled to a histidine-kinase effector yielded light-induced and light-repressed chimeras, each group complying with a heptad periodicity of linker lengths. With less than 5% of all possible variants exhibiting light regulation, a delicate fine-tuning of linker sequence and protein function became evident. Thus, systematic testing of fusion variants with PATCHY not only facilitates the development of photoreceptor chimeras for manipulating cellular processes. Complementary to rational design, it also reveals molecular cues determining module compatibility and signal transduction in modular signal receptors.

EN Heme containing gas sensor proteins play important role in bacterial physiology in regulating many processes such as cell differentiation, virulence, biofilm formation or intercellular communication. For their structure, typical modular architecture is characteristic where various sensor domains (usually at the N-terminus) regulate the activity of the catalytic or functional domains (usually at the C-terminus). In this dissertation thesis, we focused on three representatives from the group of oxygen sensing proteins, namely histidine kinase AfGcHK, diguanylate cyclase YddV, phosphodiesterase EcDOS and also on protein RR, which is the interaction partner of AfGcHK. The main aim of the thesis was to study intra-protein/inter-domain signal transduction in two representatives of heme sensor proteins with a globin fold of the sensor domain (AfGcHK, YddV) and in one representative with PAS fold of the sensor domain (EcDOS). Another objective was to describe inter-protein signal transduction in the two component signaling system AfGcHK-RR and structurally characterize these two interacting partners. Emphasis was also placed on the study of the interaction between model sensor domains and different signaling molecules and also on function of individual amino acids involved in the binding of these...

Mycobacterium tuberculosis, the causative organism of the disease tuberculosis (TB) in humans, leads to nearly two million deaths each year. This versatile pathogen can exist in highly distinct physiological states such as asymptomatic latent TB infection where bacilli lie dormant or as active TB disease in which the bacilli replicate in macrophages. The pathogenic lifestyle requires the tubercle bacillus to sense and respond to multiple environmental cues to ensure its survival. Such stimuli include hypoxia, nutrient limitation, presence of reactive oxygen and reactive nitrogen intermediates, pH alterations, and cell wall/ membrane stress. Two component systems (TCSs) form the primary apparatus for sensing and responding to environmental cues in bacteria. A prototypical TCS is composed of a sensory protein called sensor kinase (SK) and a response generating protein called response regulator (RR). M. tuberculosis encodes 11 genetically paired TCSs, 2 orphan sensor kinases and six orphan response regulator proteins. Studies of the TB bacilli using transcriptional profiling and gene knockouts have revealed that TCSs play an important role in facilitating successful adaptation to diverse environmental conditions encountered within the host. The mtrAB and prrAB genes encoding corresponding TCSs have been shown to be essential for survival, mprAB for persistence and devRS for hypoxic adaptation. Further, inactivation of the TCSs regX3-senX3, tcrXY, trcRS, phoPR or kdpDE was shown to affect the growth and/or virulence of M. tuberculosis in animal infection models. The SK and RR proteins of TCSs are modular and contain variable input and output domains coupled to conserved ‘transmitter’ and ‘receiver’ domains. Despite the modular nature and extensive homology of SK and RR proteins across TCSs, which may allow non-cognate interactions, it is believed that crosstalk across different TCSs is not favored and that individual pathways are generally well insulated. The existing profiling studies have been performed on the TCSs of bacterial species containing a relatively large number of TCSs. In those studies, specificity and insulation have been the norm and thus become the prevalent paradigm of TCS signaling. In vitro genome wide phosphotransfer profiling has revealed only a few cross- communication nodes in the TCSs of Escherichia coli (~3%), while none in Caulobacter crescentus (in 352 interactions tested, in short time duration) and Myxococcus xanthus (in 250 interactions tested). Yet, many instances of cross talk have been reported in literature. For example, E. coli TCSs PmrAB and EnvZ-OmpR show cross-communication with QseBC and ArcBA, and many more. In M. tuberculosis, indirect evidence of the existence of such cross regulation has originated from studies where mutations in phoPR have been shown to affect the expression of the TCS devRS and its regulon. It is thus interesting to examine the extent of crosstalk in the TCSs of M. tuberculosis, which has an exceptionally small number of TCS proteins compared to E. coli. As mentioned earlier, M. tuberculosis H37Rv has 11 cognate pairs of TCSs, 2 orphan sensor kinases and 6 orphan response regulators. To study the entire landscape, we aimed to study all 221 connections between SK and RR proteins including 12 cognate interactions. While 10 of the cognate TCS interactions were established in the literature, two putative systems KdpDE and NarSL and 5 orphan response regulators were still uncharacterized, therefore we initiated our work with the characterization of these TCSs. At the biochemical level, the KdpDE two component system of M. tuberculosis is not well studied, though one report showed interaction of the C-terminal domain of KdpD SK and KdpE RR using yeast two hybrid assay and another reported the interaction of the SK with LRP protein. Besides these associations, there is no evidence for the functionality of KdpDE system. Similarly, NarSL system also has not been characterized and it not known whether these putative two component proteins are functional. The initial part of the study includes the characterization of these two TCSs, NarS-NarL and KdpD-KdpE, at biochemical and physiological levels. In our studies we demonstrated that KdpDE system is a bonafide two component system of M. tuberculosis, and KdpD SK undergoes autophosphorylation at His642 residue in presence of Mg+2 ions and then it transfers phosphoryl group to a conserved Asp52 residue on the KdpE RR protein. The acid-base stability analysis revealed the nature of chemical bonds present in the KdpD and KdpE proteins, and further confirmed that KdpD and KdpE are typical SK and RR respectively. SPR analysis demonstrated that KdpD and KdpE proteins interact under basal non-phosphorylated conditions and the interaction affinity reduced when SK was phosphorylated. The reduction in the interaction affinity indicated towards a possible dissociation of SK and RR protein during phosphotransfer, which allows RRs to exert their regulatory effect. On the similar line, the phosphorylation defective SK (KdpDH642Q) had least affinity with KdpE suggesting that perhaps this mutant SK, fails to interact with the RR. We have also shown that both the kdpD and kdpE genes are in the same operon and are up regulated in potassium ions limitation and osmotic stress conditions. Overall, using the biochemical approaches, we have established that Rv1027c–Rv1028c operon of M. tuberculosis encodes a functional and a typical KdpDE two component signal transduction system. Using the similar biochemical and biophysical approaches, we have demonstrated that NarS-NarL proteins constitute a functional TCS and His241 and Asp61 are the phosphorylatable residues. In contrast to KdpDE which shows typical behaviour of TCS, NarSL TCS showed atypical behaviour. Malhotra and group’s work on NarSL suggested that there is cross-regulation between NarS/NarL and DevS/DosT/DevR systems. We addressed this possibility on three separate levels, by examining (i) the cross-phosphorylation of DevR and NarL RRs by non-cognate sensor kinases NarS and DevS/DosT respectively, (ii) the interaction between DevR and NarL RR proteins, and (iii) examining the effect of DevR-NarL interactions on their DNA binding properties. Our studies ruled out the presence of any physiologically relevant phosphorylation mediated cross-talk between NarS/NarL and DevS/DosT/DevR. We identified that the cross talk between these TCSs could be explained on the basis of interaction between NarL and DevR RRs and their subsequent binding to the target gene promoter regions for concerted regulation of gene expression. We also identified that DevR activation is critical for cooperative action with NarL. This process comes out as a novel mechanism of gene regulation via heteromerization of RRs. We hypothesized that formation of NarL-DevR heteromers may arise because of high sequence similarities. Conclusively, our study provides insights into the functionality of M. tuberculosis NarL/NarS TCS and regulatory function of NarL protein which acts in concert with another RR, DevR. Overall, NarS-NarL system showed an atypical, novel mode of gene regulation involving RR heteromerization. Subsequent to the basic biochemical characterization of NarSL and KdpDE system, the genome wide phosphotransfer profiling was done to identify the cross-connections between TCSs. Remarkably, we found that specificity was the exception rather than the rule. While only three of the TCS pairs were completely specific, all the other nine TCS pairs exhibited crosstalk, including a few that were highly promiscuous. We classified the interactions as specific, one-to-many, and many-to-one signaling circuits. We also profiled all the RRs including the orphans for their ability to accept phosphoryl group from a low molecular weight donor, acetyl phosphate, and interestingly found that only two RRs DevR and NarL were capable of accepting phosphoryl group from such a donor. Interestingly, none of the orphan RRs accepted phosphoryl group from any donor, neither SKs nor low molecular weight phospho donors, warranting further analysis of their roles and presence in the M. tuberculosis genome. Our exhaustive map of the crosstalk between the TCSs of M. tuberculosis sets the stage for a renewed view of TCS signaling and proposes a dispersive-integrative landscape for TCS signaling rather than one of insulation. As an extension of our basic characterization work of NarSL TCS, we also attempted to understand the localization pattern of NarS sensor kinase in M. smegmatis cells using fluorescence approaches. It is known that many bacterial receptors including sensor kinases form clusters or show specific localization patterns inside the cell. We found that NarS shows distinct cellular localization pattern. However, the functional significance of this localization pattern is not obvious yet and warrants further investigations. We also developed a few non-radioactive methods to study interaction between two component systems to overcome the limitations associated with radioactive experiments in studying TCSs. We developed fluorescence resonance energy transfer (FRET) to study in vitro interaction between two component proteins which was sensitive to the phosphorylation status of the proteins. Using fluorescently tagged SKs and RRs, we determined a change in FRET for KdpDE and NarSL TCS pairs in vitro. Our study thus also provides an alternative approach to study TCS signaling, using an easier, non-radioactive and high throughput approach. In summary, our study presents the evidence of an alternative paradigm of bacterial signaling, where significant crosstalk between the underlying TCSs prevails. The new paradigm is expected to have important implications in our understanding of the virulence and pathogenesis of bacterial infections. Overall, our studies (i) allowed the establishment of functionality of all paired TCSs encoded in the genome of M. tuberculosis including NarSL and KdpDE TCSs, (ii) identified the novel mechanism of gene regulation by NarL RR and DevR, (iii) demonstrated the existence of TCS signaling which is contrary to the existing notion of specificity (iv) showed the distinct localization pattern of NarS and (v) developed non-radioactive approaches to study two component interactions.

Greater understanding of how we can use protein simulations and statistical characteristics of biomolecular interfaces as proxies for biological function will make manifest major advances in protein engineering. Here we show how to use calculated change in binding affinity and coevolutionary scores to predict the functional effect of mutations in the interface between a Histidine Kinase and a Response Regulator. These proteins participate in the Two-Component Regulatory system, a system for intracellular signalling found in bacteria. We find that both scores work as proxies for functional mutants and demonstrate a ~30 fold improvement in initial positive predictive value compared with choosing randomly from a sequence space of 160 000 variants in the top 20 mutants. We also demonstrate qualitative differences in the predictions of the two scores, primarily a tendency for the coevolutionary score to miss out on one class of functional mutants with enriched frequency of the amino acid threonine in one position.