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O fungo filamentoso Trichoderma reesei é uma espécie de grande importância biotecnológica no que tange a degradação de biomassa lignocelulósica para a produção de bioetanol em larga escala. Seu sistema de enzimas celulolíticas é muito eficiente, apesar de ser possuir poucas celulases, sugerindo que o controle dessas enzimas vai além da regulação transcricional. Assim, neste trabalho nós obtivemos o perfil fosfoproteômico de T. reesei cultivado em glicose e bagaço de cana-de-açúcar a partir de análise fosfoproteômica LC-MS/MS por spectral counting. A comparação entre os perfis de fosfoproteínas obtidos das linhagens parental QM6a de T. reesei e dos mutantes knockout para TMK1 e TMK2 permitiu a demonstração de que essas MAPK agem de maneira interconectada com outras vias de transdução de sinal na célula, especialmente a via de TOR e de AMPc-PKA, para regulação da produção de celulases. Além disso, também demonstramos a regulação da resposta a estresse celular por TMK2, e o papel da fosforilação no controle direto de enzimas CAZy. Nossos resultados mostram que a fosforilação desempenha papel importante na regulação dessas enzimas e de outras funções celulares no fungo após a transcrição de seus respectivos genes. O agrupamento desses dados permite melhor entendimento da via de sinalização mediada pelas MAPK TMK1 e TMK2 de T. reesei, e como as modificações pós-traducionais promovidas por elas afetam no sensing de nutrientes celulares e, por consequência, na produção de enzimas celulolíticas, de forma direta ou indireta. / The filamentous fungus Trichoderma reesei has great biotechnological importance in regards to the lignocellulosic biomass degradation for large-scale production of bioethanol. Its cellulolytic system is very efficient, despite being composed by only a few cellulases, which suggests that the control of these enzymes goes beyond their transcriptional regulation. Thus, in this study, we performed a spectral counting LC-MS/MS analysis and achieved the phosphoproteomic profile of T. reesei grown either in glucose or sugarcane bagasse as sole carbon source. The comparison between the phosphoproteins profiles obtained from the parental strain QM6a and the knockout mutants for TMK1 and TMK2 allowed us to demonstrate that these MAPK act in an interconnected manner with other signaling transduction pathways, especially the TOR and cAMP-PKA pathways, in order to regulate the cellulases production. Furthermore, we were also able to determine the regulation of cellular stress response by TMK2, and the role of phosphorylation in the direct control of CAZymes. Our results show that phosphorylation plays an important role on the control of these enzymes and other cellular functions in T. reesei after the transcription of their respective genes. Taken together, this data allows better comprehension of the signaling pathways mediated by TMK1 and TMK2 in T. reesei, and how the post-translational modification promoted by these MAPK might affect the nutrient sensing and, therefore, the production of the cellulolytic enzymes, either directly or indirectly.

O fungo filamentoso Trichoderma reesei é uma espécie de grande importância biotecnológica no que tange a degradação de biomassa lignocelulósica para a produção de bioetanol em larga escala. Seu sistema de enzimas celulolíticas é muito eficiente, apesar de ser possuir poucas celulases, sugerindo que o controle dessas enzimas vai além da regulação transcricional. Assim, neste trabalho nós obtivemos o perfil fosfoproteômico de T. reesei cultivado em glicose e bagaço de cana-de-açúcar a partir de análise fosfoproteômica LC-MS/MS por spectral counting. A comparação entre os perfis de fosfoproteínas obtidos das linhagens parental QM6a de T. reesei e dos mutantes knockout para TMK1 e TMK2 permitiu a demonstração de que essas MAPK agem de maneira interconectada com outras vias de transdução de sinal na célula, especialmente a via de TOR e de AMPc-PKA, para regulação da produção de celulases. Além disso, também demonstramos a regulação da resposta a estresse celular por TMK2, e o papel da fosforilação no controle direto de enzimas CAZy. Nossos resultados mostram que a fosforilação desempenha papel importante na regulação dessas enzimas e de outras funções celulares no fungo após a transcrição de seus respectivos genes. O agrupamento desses dados permite melhor entendimento da via de sinalização mediada pelas MAPK TMK1 e TMK2 de T. reesei, e como as modificações pós-traducionais promovidas por elas afetam no sensing de nutrientes celulares e, por consequência, na produção de enzimas celulolíticas, de forma direta ou indireta. / The filamentous fungus Trichoderma reesei has great biotechnological importance in regards to the lignocellulosic biomass degradation for large-scale production of bioethanol. Its cellulolytic system is very efficient, despite being composed by only a few cellulases, which suggests that the control of these enzymes goes beyond their transcriptional regulation. Thus, in this study, we performed a spectral counting LC-MS/MS analysis and achieved the phosphoproteomic profile of T. reesei grown either in glucose or sugarcane bagasse as sole carbon source. The comparison between the phosphoproteins profiles obtained from the parental strain QM6a and the knockout mutants for TMK1 and TMK2 allowed us to demonstrate that these MAPK act in an interconnected manner with other signaling transduction pathways, especially the TOR and cAMP-PKA pathways, in order to regulate the cellulases production. Furthermore, we were also able to determine the regulation of cellular stress response by TMK2, and the role of phosphorylation in the direct control of CAZymes. Our results show that phosphorylation plays an important role on the control of these enzymes and other cellular functions in T. reesei after the transcription of their respective genes. Taken together, this data allows better comprehension of the signaling pathways mediated by TMK1 and TMK2 in T. reesei, and how the post-translational modification promoted by these MAPK might affect the nutrient sensing and, therefore, the production of the cellulolytic enzymes, either directly or indirectly.

Critical illness is an aetiologically and clinically heterogeneous syndrome that is characterised by organ failure and immune dysfunction. Mortality in critically ill patients is driven by inflammation-associated organ damage and a profound vulnerability to nosocomial infection. Both factors are influenced by the complement protein C5a, released by unbridled activation of the complement system during critical illness. C5a suppresses antimicrobial functions of key immune cells, in particular the neutrophil, and this suppression has been shown to be associated with poorer outcomes amongst critically ill adults. The intracellular signalling pathways which mediate C5a-induced neutrophil dysfunction are incompletely understood, and scalable tools with which to assess immune cell dysfunction in patients are lacking. This thesis aimed to develop tools with which to assess neutrophil function and delineate intracellular signalling pathways driving C5a-induced impairment. Neutrophils were isolated from healthy volunteer blood and functions (priming, phagocytosis and reactive oxygen species production) were assessed using light microscopy, confocal microscopy and flow cytometry. A new assay was developed using an Attune Nxt™ acoustic focusing cytometer (Life Technologies) which allowed the rapid assessment of multiple neutrophil functions in small samples of unlysed, minimally-manipulated human whole blood. Complete proteomes and phosphoproteomes of phagocytosing neutrophils were obtained from four healthy donors pre-treated with C5a or vehicle control. Several key insights were gained from this work and are summarised here. Firstly, C5a was found to induce a prolonged (greater than seven hours) impairment of neutrophil phagocytosis. This defect was found to be preventable by previous or concurrent phagocytosis, indicating common signalling mechanisms. Secondly, a novel assay was developed which allows the rapid assessment of multiple neutrophil functions in less than 2 mL of whole blood, and this assay can feasibly be applied in clinical settings. Thirdly, cell-surface expression of the C5a receptor was found to be markedly decreased during phagocytosis, and this decrease was not mediated by protease activity. Finally, unbiased proteomics quantified 4859 proteins and 2712 phosphoproteins respectively. This quantification is the deepest profile of the human neutrophil proteome published to date, and has revealed novel insights into the mechanisms of C5a-induced neutrophil dysfunction and phagocytosis.

In the last four years, seven new drugs have been FDA approved for the treatment of late stage melanoma, for the field of melanoma, this marks an incredibly exciting. Three of these new therapies, vemurafenib, dabrafenib and trametinib are small molecule kinase inhibitors that target the MAPK pathway and as such have been approved for the treatment of BRAFV600 mutant melanomas. Yet despite recent advances, mechanisms of intrinsic and acquired BRAF inhibitor resistance continue to undermine uniform and long-lasting therapeutic responses. Several studies have shown that the reactivation of MAPK signaling is a critical event leading to BRAF inhibitor resistance. These studies lead to the evaluation and subsequent FDA approval of frontline BRAF (dabrafenib) plus MEK (trametinib) inhibitors to delay drug resistance. Though this approach has meaningful clinical benefit, there are still a number of patients who do not respond to therapy or who, through unknown mechanisms, succumb to refractory disease. In an effort to identify drivers of MAPK inhibitor resistance, several studies have relied on traditional genomics methods. While gene-based approaches have guided precision medicine, they do not address the dynamics of the global signaling changes that occur following acquired resistance. The dissertation herein will describe our efforts to fill these gaps of knowledge and will expand upon the evolution and development of our understanding of intrinsic and acquired MAPK pathway inhibitor resistance. This work will elaborate on our early understanding of single agent BRAF inhibitor resistance, the use of genomic and proteomic approaches to further elucidate these mechanisms, and evidence based approaches to delay and overcome single agent BRAF inhibitor resistance. This work will describe global phosphoproteomic and bioinformatics methodologies to elucidate the underlying processes of both single (BRAF) and dual agent (BRAF plus MEK) inhibitor resistance as well as strategies to constrain dual agent BRAF plus MEK inhibitor resistance.

Acute myeloid leukemia (AML) is a clonal hematopoietic stem cell malignancy, marked by suppressed production of normal terminally differentiated and progenitor hematopoietic cells, and increased cellular proliferation, survival, invasion, and migration of poorly differentiated hematopoietic precursor cells called leukemic blasts. Clinical outcomes vary from good to very poor, and standard therapeutic regiments are only successful in inducing remission for approximately one half of patients. Through the use of phospho tyrosine mass spectrometry, we have identified putative candidate proteins which may be implicated in disease pathogenesis. Our in vitro data suggest a complex within the AML cell lines MOLM-14 and MV4-11 involving tyrosine phosphorylated DAP12, FCER1G, SYK, LYN, and CBL. In addition, we show the ability of high concentrations (µM) of SB203580, a p38α catalytic site inhibitor, to paradoxically sensitize cells to cytarabine while providing a modest proliferative advantage to cells treated with daunorubicin.

Acute myeloid leukemia (AML) is a clonal hematopoietic stem cell malignancy, marked by suppressed production of normal terminally differentiated and progenitor hematopoietic cells, and increased cellular proliferation, survival, invasion, and migration of poorly differentiated hematopoietic precursor cells called leukemic blasts. Clinical outcomes vary from good to very poor, and standard therapeutic regiments are only successful in inducing remission for approximately one half of patients. Through the use of phospho tyrosine mass spectrometry, we have identified putative candidate proteins which may be implicated in disease pathogenesis. Our in vitro data suggest a complex within the AML cell lines MOLM-14 and MV4-11 involving tyrosine phosphorylated DAP12, FCER1G, SYK, LYN, and CBL. In addition, we show the ability of high concentrations (µM) of SB203580, a p38α catalytic site inhibitor, to paradoxically sensitize cells to cytarabine while providing a modest proliferative advantage to cells treated with daunorubicin.

Les récepteurs 5-HT2A de la sérotonine et mGlu2 du glutamate suscitent un grand intérêt vu la dérégulation des deux récepteurs observée dans la schizophrénie et leur statut de cibles des antipsychotiques dits atypiques et de nouvelle génération, respectivement. Même si les antipsychotiques atypiques ciblant le récepteur 5-HT2A ont montré une efficacité contre les symptômes positifs, leur effet reste très limité contre les symptômes négatifs et cognitifs, et leurs effets secondaires nombreux. Depuis les années 1990, une nouvelle classe d’antipsychotiques ciblant le système glutamatergique, en particulier le récepteur mGlu2, est en développement. Les tests cliniques n’ont montré leur efficacité que pour les patients n’ayant pas été traités auparavant par des antipsychotiques atypiques. Ceci suggère une interaction fonctionnelle forte entre les récepteurs 5-HT2A et mGlu2 dans le mode d’action de ces deux classes d’antipsychotiques. De plus, plusieurs études ont démontré l’existence d’un hétéromère des deux récepteurs dans le cortex préfrontal qui semble important pour la réponse aux hallucinogènes et aux antipsychotiques ciblant l’un ou l’autre récepteur. Ainsi, étant donné l’impact du profil de phosphorylation adopté par les récepteurs couplés aux protéines G (RCPG) sur leur fonction, j’ai caractérisé au cours de ma thèse l’impact de la co-expression du récepteur 5-HT2A sur le profil de phosphorylation du récepteur mGlu2 en réponse à différentes stimulations. Parmi les 5 sites de phosphorylation identifiés, la phosphorylation de la Ser843 est potentialisée en réponse à la stimulation par un agoniste du récepteur mGlu2 uniquement lorsque le récepteur 5-HT2A est co-exprimé. Ces résultats ont été validés grâce à la génération d’un nouvel anticorps dirigé spécifiquement contre la forme phosphorylée de la Ser843 sur culture cellulaire HEK-293 et in vivo dans le cortex préfrontal de souris, région où les deux récepteurs sont co-exprimés. Des études fonctionnelles ont démontré que la phosphorylation de la Ser843 est nécessaire à la potentialisation de l’activité Gi/o du récepteur mGlu2 en réponse à ses agonistes et constitue un cross-talk fonctionnel entre les deux récepteurs puisque les agonistes du récepteur 5-HT2A stimulent également la phosphorylation de la Ser843 du récepteur mGlu2. Ainsi, mes résultats de thèse ont permis d’identifier la phosphorylation du récepteur mGlu2 sur la Ser843 comme un événement moléculaire clé du cross-talk fonctionnel avec le récepteur 5-HT2A et apporte un élément important dans la compréhension du mode d’action des antipsychotiques atypiques et de nouvelle génération. / The serotonin 5-HT2A and glutamate mGlu2 receptors keep on attracting particular attention given their implication in psychosis associated with schizophrenia and in the mechanism of action of atypical antipsychotics and of a new class of antipsychotics, respectively. Though atypical antipsychotics, targeting 5-HT2A receptor, are efficient against positive symptoms, these drugs do not act against negative, cognitive symptoms and display many side effects. Since the 90’s, new classes of antipsychotics triggering glutamatergic system, in particular mGlu2 receptor, have been developed. Their clinical trials have shown efficacy only in patients who have not been previously treated with atypical antipsychotics. This suggests a strong interaction between 5-HT2A and mGlu2 receptors in the mechanism of action of both classes of antipsychotics. Moreover, a large body of evidence indicates the presence, in prefontal cortex, of 5-HT2A/mGlu2 heteromer that is important for the response to hallucinogens and antipsychotics targeting one receptor or the other. Thus, in view of the importance of the phosphorylation profile adopted by G-protein coupled receptor (GPCR) on their activity, I characterized the impact of 5-HT2A receptor co-expression on the phosphorylation profile of mGlu2 receptor in response to various stimulations. Among the five identified phosphorylated residues, the phosphorylation of Ser843 increases upon mGlu2 receptor stimulation only when the 5-HT2A receptor is co-expressed. A new antibody against the phosphorylated form of Ser843 confirmed these results in HEK-293 cells and in mouse prefrontal cortex, area where both receptors are co-expressed. Functional studies demonstrated that Ser843 phosphorylation is necessary to enhance Gi/o signaling of mGlu2 receptor and constitutes a functional crosstalk between 5-HT2A and mGlu2 receptor since 5-HT2A receptor agonists also stimulate Ser843 phosphorylation. Collectively, my thesis findings identify mGlu2 receptor phosphorylation at Ser843 as a key molecular event of the functional crosstalk with 5-HT2A receptor that might be critical to understand the mechanism of action of atypical and potential future antipsychotics treatments.

L'entrée en mitose est initiée par le complexe cycline B – Cdk1. La phosphorylation de ses substrats déclenche des transformations incluant la condensation des chromosomes, le bris de l'enveloppe nucléaire et la formation d'un fuseau mitotique. Ces transformations permettent à la cellule de se diviser. La protéine phosphatase 2A (PP2A) en complexe avec sa sous-unité B55/Twins (Tws) reconnaît et déphosphoryle les substrats de cycline B – Cdk1. Pour éviter la déphosphorylation précoce des phosphoprotéines mitotiques, PP2A-B55/Tws est inhibée en entrée de mitose. Cette inhibition de la phosphatase est attribuable au module Greatwall (Gwl) – endosulfines. Activée en entrée de mitose, la kinase Gwl phosphoryle les endosulfines, qui inhibent alors de manière spécifique PP2A-B55/Tws. Gwl est exportée du noyau vers le cytoplasme en prophase, avant le bris de l’enveloppe nucléaire. Les mécanismes de régulation spatiotemporelle du module Gwl – endosulfines – PP2AB55/Tws ne sont pas entièrement élucidés. De plus, les substrats ciblés par PP2AB55/Tws en sortie mitose ne sont pas tous identifiés à ce jour. Dans mon travail de thèse, j’ai trouvé que Tws peut transiter par le noyau via un signal de localisation nucléaire (NLS), mais que ses fonctions essentielles sont au cytoplasme. De plus, j’ai trouvé que l’unique endosulfine présente chez Drosophila melanogaster, Endos, a une localisation cytoplasmique. Cette localisation est requise pour qu’Endos soit efficacement phosphorylée par la forme active et cytoplasmique de Gwl. Endos phosphorylée lie ensuite PP2A-Tws pour l’inhiber. Empêcher la localisation cytoplasmique d’Endos avant le bris de l’enveloppe nucléaire entraîne des défauts mitotiques dépendants de l’activité de PP2A-Tws. Les substrats mitotiques de PP2A-Tws ne sont pas tous connus. Par des cribles de phosphoprotéomique, j’ai identifié des substrats mitotiques potentiels de PP2A-Tws. L’un des candidats hyperphosphorylés suite à la déplétion de Tws, Otefin (Ote), est une protéine de l’enveloppe nucléaire. Les sites de phosphorylation d’Otefin identifiés dans mes cribles sont adjacents à son domaine d’interaction avec BAF, une protéine liant l’ADN et certaines protéines de l’enveloppe nucléaire. L’introduction de mutations phosphomimétiques à ces sites abolit l’association d’Otefin avec BAF, en plus de retarder le recrutement d’Otefin à l’enveloppe nucléaire en sortie de mitose. Par ailleurs, l’association Otefin – BAF dépend de l’activité de PP2A-Tws. Enfin, la perte d’Otefin dans l’embryon syncytial de mouche affecte le développement. En somme, mes travaux ont permis d’approfondir notre compréhension mécanistique de la régulation spatiotemporelle du module Gwl – endosulfines – PP2A et d’identifier de nouveaux substrats potentiels de PP2A-Tws. / Mitosis is triggered by the cyclin B – Cdk1 complex that phosphorylates multiple substrates to promote transformations such as chromosome condensation, nuclear envelope breakdown and mitotic spindle formation. These transformations are required for cell division. The protein phosphatase 2A (PP2A) in complex with its B55/Twins (Tws) subunit dephosphorylates cyclin B – Cdk1 substrates. To prevent premature dephosphorylation of the mitotic phosphoproteins, PP2A-B55/Tws is inhibited upon mitotic entry. The Greatwall (Gwl) – endosulfines pathway is responsible for PP2AB55/Tws inhibition. Activated upon mitotic entry, the Gwl kinase phosphorylates small proteins called endosulfines to turn them into specific inhibitors of PP2A-B55/Tws. Gwl is exported from the nucleus to the cytoplasm before nuclear envelope breakdown. However, the mechanisms of spatiotemporal regulation of the Gwl – endosulfines – PP2A module are not entirely elucidated. Moreover, the identity of the proteins targeted by PP2A-Tws during mitotic exit is still unclear. During my PhD training, I found that Tws can transit through the nucleus via a nuclear localization signal (NLS), but its essential functions are cytoplasmic. Moreover, the sole endosulfine present in Drosophila melanogaster, Endos, has a cytoplasmic localization. Such localization is required for efficient phosphorylation of Endos by active and cytoplasmic Gwl. Once phosphorylated, Endos binds PP2A-Tws to inhibit its activity. Preventing the cytoplasmic localization of Endos prior to nuclear envelope breakdown causes mitotic defects that are PP2A-Tws-dependent. The mitotic substrates of PP2A-Tws are not all identified. By phosphoproteomic screening, I identified potential novel PP2A-Tws substrates. Among the hits that are hyperphosphorylated following Tws depletion, there is the nuclear envelope protein Otefin (Ote). The identified phosphosites on Otefin are adjacent to its domain of interaction with BAF, a protein binding DNA and nuclear envelope proteins. Introducing phosphomimetic mutations at these sites abolishes the Otefin – BAF association and delays Otefin recruitment at the reforming nuclear envelope during mitotic exit. Moreover, the Otefin – BAF association is PP2A-Tws-dependent. Finally, loss of Otefin in the syncytial embryo of the fly impairs development. Altogether, my results deepen our understanding of the spatiotemporal coordination of the Gwl – endosulfines – PP2A module and provide potential novel PP2A-Tws substrates.

Plasmodium falciparum, the organism that causes the most prevalent and most virulent cases of malaria in humans, poses a major health burden on the developing world, especially in the tropical regions of Sub-Saharan Africa, Southeast Asia, and Latin America. The burden of the disease is intensified by the fact that the parasite has developed widespread resistance to all current antimalarial therapies, such as chloroquine. This drug resistance underscores the need to develop novel therapeutics that target the parasite, but show low toxicity in the human host. Protein kinases, because of their integral roles in cell signaling networks, are considered to be attractive drug targets. Cyclin dependent kinases, or CDKs, and Mitogen-Activated Protein kinases, or MAPKs, are common to eukaryotes and regulate cellular processes of growth and proliferation. Plasmodium falciparum Protein Kinase 6, or PfPK6, is an atypical protein kinase that shows similarities to both MAPKs and CDKs. PfPK6 is expected to have an important role in the intraerythrocytic cell cycle progression and growth in the malaria organism, as it has been found to be essential in the parasite. In order to better understand the function of PfPK6 within Plasmodium, we have identified serveral potential substrates and interactors of the kinase using co-immunoprecipitation with an HA epitope-tagged cell line of PfPK6, as well as phosphoproteomic analysis. These methods resulted identification of 15 novel protein interactors, with 4 being studied for further investigation, and 45 putative substrates after strict peptide filtering, five of which are used in this study. In order to verify putative substrates and interactors, both in vitro and in vivo methods were used. In vitro kinase assays using GST-PfPK6 with 5 recombinant substrates confirmed direct phosphorylation of two novel substrates: MAL7P1.38, a regulator of chromosome condensation, and PF10_0047, a putative RNA binding protein. After attempts to generate bacterial constructs of several putative interactors and a global failure of a usable amount of protein to express under IPTG induction conditions, an alternative form of expression using a cell free Transcription and Translation reaction (TNT) with Wheat Germ Extract was used to generate radiolabeled PF11_0154, PFF0625w, and PF11_0305. Pull down analysis using GST-PfPK6 showed the kinase's ability to "pull" the interactors out of solution, confirming the interactions defined by the initial epitope tagged Co-Immunoprecipitation. Additionally, for in vivo analysis, parasites were transfected with RFP- PFF_0695w, an uncharacterized Plasmodium protein, in order to cellular localization of this interactors. Immunofluorescence assays of transfected lines showed punctate forms of PFF_0695w in the host erythrocyte in the late trophozoite and schizont stages of the parasite development, suggesting this interactor is a previously undiscovered protein in the Plasmodium secretome. The research presented here is an initial step to defining the interactome of PfPK6.