A biofilm is a complex community of cells enveloped in a self-produced polymeric matrix. Entry into a biofilm is exquisitely controlled at the level of transcription and in Bacillus subtilis it requires the concerted efforts of several major transcription factors including the repressor SinR and activator DegU. I initially identified that these transcriptional regulators control biofilm formation via parallel pathways. Through investigating the regulation of biofilm formation by SinR and DegU, I discovered that biofilm formation is also regulated at the post-translational level. This was achieved by identifying three key proteins which are needed for biofilm formation. These proteins are PtkA, a bacterial tyrosine kinase; TkmA, the cognate modulator of PtkA; and PtpZ, a bacterial tyrosine phosphatase. By introducing amino acid point mutations within the catalytic domains of PtkA and PtpZ it was identified that the kinase phosphatase activities, respectively, are essential function.In addition, PtkA contains a conserved C-tyrosine cluster that is the site autophosphorylation. Investigation of the role of the C-terminal tyrosine cluster tentatively suggests that this domain acts to block access to the active site of PtkA, thus affecting the ability of PtkA to phosphorylate its targets. Deletion of the gene coding for TkmA demonstrated that this modulator was also required for biofilm formation. It was also demonstrated that TkmA may interact with other protein partners, at least in the absence of PtkA, raising the question of how signal specificity is maintained. Finally, a systematic mutagenesis approach was used with the aim of identifying the target(s) of PtkA and PtpZ during biofilm formation but,despite extensive efforts, it remained elusive. The findings presented in this thesis highlight the complexity of biofilm formation by B. subtilis by revealing an additional level of regulation in the form of protein tyrosine phosphorylation.

Maize is an important food crop in most parts of the world including the United States. The plants growing in the field are constantly challenged with various biotic stresses like insect herbivores and fungal pathogens. The physical wounds produced on the growing crops by the insects render the plants more vulnerable to the fungal pathogens. Hence developing both insect and fungal resistant maize varieties is crucial to benefit more from the harvest. Several studies have been in advance in this direction and as a consequence insect, in particular lepidopteran larve resistant maize genotype Mp708 and Aspergillus flavus resistant genotype Mp313E were developed. This study particularly focuses on understanding the functional involvement of the major phytohormones in the signal transduction and expression of the unique defense protein, Maize insect resistance 1-cysteine protease (Mir1-CP) shown to accumulate in response to herbivory by lepidopteran larvae, Spodoptera frugiperda (Fall armyworm, FAW) as a defense mechanism. Using a pharmacological approach involving exogenous hormone and hormone inhibitor treatments and analyzing the expression and accumulation of Mir1-CP protein and mir1 transcript by immunoblot and qRT-PCR analysis respectively, both JA and ET were found to be involved in mediating Mir1-CP accumulation with JA acting upstream of ET. Results also indicate that Mir1-CP accumulation involves both transcriptional and post-transcriptional (or post-translational) regulations. A different part of the study involved in understanding and evaluating the performance of Aspergillus flavus on the resistant and susceptible maize genotypes during infection. As of part of this study I also analyzed and compared the defense response offered by the resistant maize genotype, Mp313E and the susceptible genotype, Va35 by looking at the expression levels of the various defense related genes. The potency of the resistant maize genotype in sustaining the fungal infection in the field was of particular focus. Resistant maize genotype Mp313E was found to potentially oppose A.flavus proliferation and colonization and also delay aflatoxin biosynthesis unlike Va35. The up regulation of the maize defense genes during the early time points of infection, in Mp313E, indicate the potential role of these genes in conferring resistance against fungal pathogens.

Du fondamental à la clinique, cette thèse a été construite autour d’un seul mot clefs : KCC2, grâce à plusieurs projets collaboratifs. Ce co-transporteur d’ion est une molécule à plusieurs facettes dont la multiplicité des rôles et ses implications dans diverses pathologies font d’elle un élément clef de l’organisme vivant. En plus des études phylogénétiques et thérapeutiques effectuées au cours de cette période, mon principal travail a été de déterminer le rôle physio-pathologiques in vitro et in vivo d’un mécanisme de régulation post-traductionnelle de KCC2. Nous avons dans un premier temps montré que la déphosphorylation des Thréonines (Thr) 906 et 1007 in vitro était un puissant activateur de la protéine. En effet, nous avons montré que l’état de phosphorylation des sites dicté par la voie Wnk-Spak/OSR1 était impliqué dans le niveau d’expression en surface de la protéine. Par la suite, nous avons pu révéler que les souris porteuses d’une mutation phospho-mimétique Glu906 et Glu1007 “(KCC2E/+)” sur un allèle de la protéine, présentaient un décalage de l’émergence de la force inhibitrice GABAergique, une altération de la balance excitation/inhibition, ainsi qu’une augmentation de la susceptibilité à générer des crises. De plus, ces même souris développent des troubles de la communication chez le jeune ainsi qu’un défaut de sociabilité chez l’adulte, deux symptômes clefs des TSA. Ces résultats suggèrent que la régulation post-traductionnelle est un mécanisme physio-pathologique clef de la protéine. / From basic to clinical aspects, this thesis comprises different collaborative projects focusing on KCC2. KCC2 is a complex protein with multiple roles and implications in various pathologies that makes this molecule a key element of living organisms. In addition to the phylogenetic and therapeutic studies performed during this period, my main work has been to determine the in vitro and in vivo physio-pathological role of a KCC2 post-translational regulatory mechanism. We first showed in vitro that dephosphorylation of Threonines (Thr) 906 and 1007 was a potent activator of the protein. We have shown that phosphorylation state by the Wnk-Spak/OSR1 pathway of these two residues is implicated in the level surface expression of KCC2. Subsequently we have revealed that mice carrying in one allele a phospho-mimetic mutations Glu906 and Glu1007 “(KCC2E/+)”, preventing the developmental dephosphorylation at these sites, exhibited a delayed onset of fast synaptic GABA inhibition, a decreased ratio of spontaneous GABA- to glutamate-driven post-synaptic responses, and a significantly reduced flurothyl-induced seizure threshold. Furthermore, KCC2E/+ pups and adult mice, respectively, exhibited impaired communication and sociability, classic ASD phenotypes. These results suggest that post-translational regulation is a key physio-pathological mechanism of KCC2.

Catharanthus roseus (Madagascar periwinkle) is the exclusive source of an array of terpenoid indole alkaloids (TIAs) that are used in the treatments of hypertension and certain types of cancer. TIA biosynthesis is under stringent spatiotemporal control and is induced by jasmonate (JA) and fungal elicitors. Tryptamine, derived from the indole branch, and secologanin from the iridoid branch are condensed to form the first TIA, strictosidine. Biosynthesis of TIA is regulated at the transcriptional level and several transcription factors (TFs) regulating the expression of genes encoding key enzymes in the pathway have been isolated and characterized. The JA-responsive APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF), ORCA3, and the basic helix-loop-helix (bHLH) factor, CrMYC2, are the key activators of the TIA biosynthesis. Recently, two other TFs, the bHLH IRIDOID SYNTHESIS 1 (BIS1) and BIS2 were also identified as regulators of TIA pathway. Analysis of C. roseus genome sequence has revealed that ORCA3 forms a physical cluster with two uncharacterized AP2/ERFs, ORCA4 and ORCA5. In plants, physically linked clusters of TFs are less characterized. Moreover, the regulation of TF clusters is relatively unexplored. My research uncovered that the ORCA gene cluster is differentially regulated. ORCA4 and ORCA5, while functionally overlapping with ORCA3, regulate an additional set of TIA pathway genes. ORCA4 or ORCA5 overexpression has resulted in significant increase of TIA accumulation in C. roseus hairy roots. In addition, ORCA5 directly regulates the expression of ORCA4 and indirectly regulates ORCA3, likely via unknown factor(s). Interestingly, ORCA5 also activates the expression of ZCT3, a negative regulator of the TIA pathway. In addition CrMYC2 is capable of activating ORCA3 and co-regulating pathway genes concomitantly with ORCA3. Several lines of evidence suggest that, in addition to the transcriptional control, biosynthesis of TIAs is also controlled at the posttranslational level, such as protein phosphorylation. Available literature indicates that a mitogen-activated protein kinase (MAPK) cascade is involved in this process. Analysis of C. roseus MAP kinome, identified two independent MAPK cascades regulating the indole and iridoid branches of the TIA pathway. We showed that the ORCA cluster and CrMYC2 act downstream of a MAP kinase cascade consisting of CrMAPKK1, CrMAPK3 and CrMAPK6. Overexpression of CrMAPKK1 in C. roseus hairy roots upregulates TIA pathway genes expressions and boosts TIA accumulation. The other cascade, consisting of CrMAPKK6 and CrMAPK13, mostly regulates the iridoid branch of the TIA pathway. Overexpression of CrMAPK13 in C. roseus hairy roots significantly upregulates iridoid pathway genes and boosts tabersonine accumulation. Moreover, we recently identified the third MAPK cascade, consisting of CrMAPKK1 and CrMAPK20, that negatively regulates the indole branch of the TIA pathway. Overexpression of CrMAPK20 in C. roseus hairy roots represses the genes regulated by CrMYC2-ORCAs and reduces catharanthine accumulation. These findings significantly advance our understanding of transcriptional and post-translational regulatory mechanisms that govern TIA biosynthesis in C. roseus.

Régulation post-traductionnelle des canaux potassiques par les CPKs (Protéines Kinases Dépendantes du Calcium) chez Arabidopsis thaliana : un rôle dans la réponse adaptative aux stress environnementaux ? Les canaux potassiques de la famille Shaker sont des voies majeures du transport de K+ à travers la membrane plasmique. Ces canaux sont impliqués dans l'absorption du potassium depuis le sol et dans sa redistribution dans les parties aériennes de la plante. Ils sont également impliqués dans les mouvements stomatiques et sont pour cela finement régulés. Ils peuvent subir des modifications post-traductionnelles telle que la phosphorylation par des protéines kinases. L'objectif principal de ce travail de thèse s'inscrit dans ce contexte et a pour but d'évaluer l'implication des CPKs dans la régulation post-traductionnelle des canaux Shaker. Les mécanismes d'action de deux CPKs (CPK13 et CPK6) sur la sous-unité entrante KAT2 sont plus spécifiquement étudiés. La première partie du travail de thèse avait pour but de mettre en place le matériel nécessaire pour l'étude en réalisant les clonages, la production des protéines recombinantes et leur caractérisation et testant les premiers effets des CPKs sur l'activité des canaux en expression hétérologue. La seconde partie concerne l'étude du rôle de CPK13 dans la régulation stomatique via la sous-unité KAT2. Nous montrons que la sur-expression de CPK13 dans les lignées transgéniques induit, à court terme, un défaut dans l'ouverture stomatique et également, à long terme, un défaut dans la croissance de la plante. L'existence d'une interaction physique à la membrane plasmique entre CPK13 et KAT2 est montrée à l'aide de la technique de FRET-FLIM. et la phosphorylation de la sous-unité KAT2 par la protéine recombinante CPK13 est montrée in vitro à l'aide de puces à peptides. Enfin, il est montré par voltage-clamp en ovocyte de xénope que CPK13 inhibe l'activité de KAT2 de plus de 60%. Dans la dernière partie, nous présentons un ensemble de résultats qui suggèrent un rôle de CPK6 dans la tolérance au stress salin via son action sur KAT2. Il est en effet connu qu'en cas de stress salin, l'activité des canaux responsables de l'influx de potassium est stimulée, ce qui contribue au maintien d'un faible ratio Na+/K+ dans les cellules. Or, nous montrons un effet activateur de la CPK6 sur l'activité de KAT2, à l'aide de la technique de voltage-clamp. Nous montrons que l'expression du gène CPK6 est très augmentée en réponse à un stress salin et que ceci est concomitant avec le déclenchement d'une vague calcique en réponse à ce même stress. L'utilisation de lignées GUS a permis de vérifier que les patrons d'expression des gènes CPK6 et KAT2 sont identiques chez Arabidopsis thaliana. Enfin, nous montrons une interaction physique entre le canal KAT2 et la protéine CPK6 (FRET-FLIM) et la phosphorylation de KAT2 par CPK6 (puces à peptides). / Post-translational regulation of potassium channels by CPKs (Calcium-dependent Protein Kinases) in Arabidopsis thaliana: a role in adaptive response to environmental stresses?Potassium Shaker channels are major pathways for K+ across plant cell plasma membrane. These channels are implicated in K+ absorption from soil and in its redistribution throughout the plant. They are more particularly implicated in stomatal movement and therefore are finely regulated. They can especially undergo post-translational modifications such as phosphorylation by protein kinases. The aim of this work is to determine the implication of CPKs (Ca2+-dependent Protein Kinases) in Shaker channel post-translational regulation. CPK13 and CPK6 molecular mechanisms of action on Shaker sub-unit KAT2 activity are specifically studied here. First part of this work consisted in cloning, producing and characterizing recombinant proteins and broad screening of CPK effects on Shaker channel activity, using heterologous expression. Second part focuses on the role of CPK13 in stomatal regulation through its effect on KAT2 activity. Over-expression of CPK13 in plant is shown to induce a defect of stomatal aperture and plant growth. KAT2 and CPK13 interaction at the plasma membrane is evidenced by using FRET-FLIM technique. KAT2 phosphorylation by CPK13 is checked on peptide arrays. Finally, a 60% decrease of KAT2 activity by CPK13 is shown using voltage-clamp on xenopus oocyte. Third and last part of this work suggests a role of CPK6 in salt stress resistance through KAT2 channel regulation. Inward potassium channels are indeed known to be activated upon salt stress to contribute keeping a low Na+/K+ ratio. Now, voltage-clamp technique demonstrates that KAT2 activity is increased by CPK6 and salt stress is shown to both increase CPK6 expression and elicit a calcium wave. Using GUS lines evidences KAT2 and CPK6 co-expression in Arabidopsis thaliana (in phloem and guard cells). Physical interaction between these two partners is shown by FRET-FLIM, and KAT2 phosphorylation by CPK13 gets strong support from peptide array assays.

Der erste Teil der Arbeit beschreibt die Etablierung einer modifizierten Form des klassichen SILAC-Verfahrens, das in der quantitativen Massenspektrometrie zur Bestimmung von relativen Änderungen in Proteinmengen benutzt wird. Im sog. „pulsed SILAC (pSILAC)“ Verfahren werden Zellen im Zuge einer differentiellen Behandlung in Kulturmedien transferiert, die unterschiedlich Isotop-markierte Aminosäuren enthalten. Da hier die Quantifizierung auf dem Verhältnis der neusynthetisierten Proteinmengen beruht, können gezielt Unterschiede in der Proteinproduktion bestimmt werden. Mit Hilfe von pSILAC konnte im zweiten Teil der Arbeit erstmals quantitativ erfasst werden, welchen Einfluss microRNAs auf die Proteinsynthese ausüben. So konnte gezeigt werden, dass sowohl die Überexpression als auch die Repression einzelner microRNAs die Produktion hunderter Proteine beeinflussen kann. Außerdem konnten Genprodukte identifiziert werden, die ausschließlich translational reguliert werden. Die Messung von Proteinneusynthese ermöglichte auch die Bestimmung von Proteinumsatzraten, dargestellt im dritten Teil der Arbeit. Zusammen mit mRNA-Umsatzraten sowie Protein- und mRNA-Mengen bilden sie die Grundlage für eine dynamische Beschreibung zelluärer Genexpression. Durch den gleichzeitigen Einsatz des Nukleosidanalogons 4-Thiouridin (4sU) und von schweren Aminosäuren (SILAC) konnte eine metabolische Markierung neusynthetiserter mRNAs und Proteine in murinen Fibroblasten erreicht und damit eine Berechnung von Protein- und mRNA-Halbwertszeiten und absoluten Mengen für ca. 5,000 Gene ermöglicht werden. Während mRNA- und Proteinenmengen deutlich korrelierten, war zwischen mRNA- und Proteinhalbwertszeiten nur eine äußerste schwache Korrelation zu erkennen. Dennoch stehen mRNA- und Proteinumsatzraten nicht einem willkürlichen Zusammhang zu einander, da bestimmte Kombinationen von mRNA- und Proteinhalbwertszeiten eine Optimierung von Genen hinsichtlich ihrer biologischen Funktionen erkennen ließen. / The first part of the thesis describes the establishment of a modified version of the classic SILAC approach routinely used in quantitative mass spectrometry (MS) to assay relative changes in protein levels. In the newly-devised approach termed pulsed SILAC (pSILAC) differentially treated cells are transferred to culture medium supplemented with different versions of stable-isotope labeled heavy amino acids. As MS-based relative quantification is exclusively based on the newly-synthesized heavy protein amounts the method enables the detection of differences in protein production resulting from the treatment. The second part of the thesis shows the use of pSILAC to globally quantify the impact of microRNAs onto the proteome. Ectopic over-expression or knock-down of a single microRNA both affected protein production of hundreds of proteins. pSILAC identified several target genes as exclusively translationally regulated as changes in corresponding transcript levels were virtually absent. Measuring newly-synthesized protein amounts with heavy amino acids in a pulsed-labeling fashion has also been used to determine turnover rates of individual proteins, described in the third part of the present work. Along with transcript turnover as well as mRNA and protein levels they are essential for a dynamic description of gene expression. Simultaneous application of the nucleoside analogue 4-thiouridine (4sU) and heavy amino acids (SILAC) to metabolically label newly-produced mRNAs and proteins in mouse fibroblasts resulted in the calculation of mRNA and protein lifetimes and absolute levels for approximately 5,000 genes. While mRNA and protein levels were overall well correlated, a correlation between mRNA and protein half-lives was virtually absent. Yet this seemingly chaotic distribution of mRNA and protein half-lives was highly instructive since specific gene subsets have obviously evolved distinct combinations of half-lives that relate to their biological functions.