Au laboratoire, une famille de tyrosine kinases propres aux bactéries et ne présentant aucune ressemblance structurale avec les protéine-kinases d’origine eucaryote a été identifiée. Ces enzymes, appelées BY-kinases, sont notamment impliquées dans la biosynthèse des polysaccharides extracellulaires, mais leurs rôles précis ainsi que leurs mécanismes catalytiques sont encore peu compris.Dans la première partie de ce travail, nous avons caractérisé le rôle physiologique de la phosphorylation sur la tyrosine de la protéine Ugd, une UDP-glucose déshydrogénase, par les BY-kinases Wzc et Etk d’E. coli. Nous avons démontré que la phosphorylation d’Ugd sur un site commun à Wzc et Etk augmente son activité. Nous avons également établi que la phosphorylation d’Ugd par Wzc participe à la régulation de la quantité d’acide colanique produit, tandis que la phosphorylation d’Ugd par Etk influence la résistance de la bactérie à la polymyxine.Nous avons également effectué une analyse structure-fonction du domaine cytoplasmique de deux BY-kinases, CapA1/CapB2 de S. aureus et Wzc d’E. coli. Nous avons montré que ces deux protéines s’associent en octamère, grâce au motif EX2RX2R et qu’elle s’autophosphoryle selon un mécanisme intermoléculaire. Nous avons, de plus, identifié le mécanisme d’activation de ces protéines et révélé l’importance d’un domaine particulier dans l’autophosphorylation de Wzc et la biosynthèse de l’acide colanique.La caractérisation structurale et fonctionnelle des BY-kinases représente une approche prometteuse et originale en vue de l’élaboration de molécules inhibant spécifiquement leur activité et pouvant affecter le pouvoir virulent des bactéries pathogènes. / A new class of bacterial enzymes, named BY-kinases, has been shown to catalyze protein-tyrosine phosphorylation. These enzymes share no structural and functional similarities with their eukaryotic counterparts. Evidence of their involvement in extracellular polysaccharide biosynthesis has been provided, but their accurate functions and their catalytic mechanism remain largely unknown.First, we characterized the physiological role of tyrosine phosphorylation of Ugd, a UDP-glucose dehydrogenase, by the BY-kinases Wzc and Etk of E. coli. We demonstrated that Ugd phosphorylation by Wzc or Etk occurs on the same site and increases its activity. We also established that Wzc-mediated phosphorylation of Ugd participates in the regulation of colanic acid production whereas Ugd phosphorylation by Etk influences resistance to polymyxin.In addition, we performed a structure-function analysis of the cytoplasmic domain of two BY-kinases, namely CapA1/CapB2 from S. aureus and Wzc from E. coli. We showed that these two proteins associate in a ring-shaped octamer in which the motif EX2RX2R plays a crucial role. In addition, we showed that BY-kinases autophosphorylate using an intermolecular mechanism. We also identified the activation mechanism of BY-kinases and we revealed the role of a particular domain, found specifically in BY-kinases from proteobacteria, in Wzc autophosphorylation and colanic acid biosynthesis.Structural and functional characterization of BY-kinases represents an original and promising approach in order to develop new molecules inhibiting specifically these enzymes and to affect the virulence of bacterial pathogens.

La voie de signalisation HH joue un rôle crucial dans le contrôle de la prolifération et la différenciation cellulaires. Le dérèglement de cette voie est responsable de nombreux cancers. J’ai ainsi mis en place les outils moléculaires nécessaires pour identifier des régions importantes dans les interactions protéines-protéines au sein du complexe intracellulaire de la voie qui vont permettre de mieux comprendre les mécanismes de régulation du facteur de transcription CI en fonction de l’état d’activation de la voie. Mes travaux ouvrent la voie à de nombreuses études structurales et fonctionnelles de ces protéines jusqu'ici peu étudiées. / The Hedgehog (Hh) signaling pathway is a highly conserved regulator of growth and differentiation that is essential for both vertebrate and invertebrate development. In Drosophila, the HH pathway is regulated by a high molecular weight intracellular protein complex called the Hedgehog Transducing Complex (HTC), whose composition is controlled by the activation of the pathway. My thesis project is to characterise the HTC complex that regulates the fate of the HH transcription factor, CI. I am using structural studies, biochemistry and enzymology to better understand the protein-protein interactions and function that govern the Hedgehog pathway. My work provide a high resolution view of the HTC and help to understand how those proteins work and interact with each other.

As quinases dependentes de ciclinas são proteínas que podem ser divididas de acordo com a sua atuação no ciclo celular ou no controle transcricional, elas se tornam ativas em determinadas etapas do ciclo celular dependendo do seu grau de fosforilação e de sua ligação com ciclinas e proteínas inibitórias, e exercem sua função fosforilando outras proteínas envolvidas no ciclo de divisão celular e transcrição influenciando suas atividades, garantindo que cada processo do ciclo ocorra em uma sequência ordenada. A CDK13 faz parte da família de proteínas quinases dependentes de ciclina, pode se ligar a ciclinas do tipo L ou K, regula os eventos de \"splicing\" alternativo, e interage com a proteína Tat do vírus HIV atuando como um possível fator de restrição, sendo que sua superexpressão diminui a produção de algumas proteínas virais suprimindo a produção do vírus. O DNA referente à CDK13 é replicado em células cancerosas, principalmente dos tipos hepático e cólon e reto, sendo um alvo para inibidores para tratamento de câncer. A fim de contribuir para o estudo dessa proteína, o projeto tem como objetivo expressá-la utilizando métodos de tecnologia de DNA recombinante. A sequência de DNA referente à CDK13 foi amplificada pela reação em cadeia da polimerase, após sua purificação, foi inserida no vetor pCR-Blunt e clonada em células de E. coli DH5α competentes. Porém, o DNA não foi liberado pela reação com as enzimas de restrição BamHI e NdeI. As bactérias Rosetta(DE3) transformadas com um plasmídeo sintético e crescidas em meio de auto-indução expressaram a CDK13. Após lise celular e purificação em coluna de Ni2+, a proteína foi detectada por Western Blot. Já as bactérias Rosetta(DE3) transformadas com o plasmídeo sintético modificado (o qual compreende a região do DNA que expressa o bolsão de ligação da CDK13), e induzidas em meio LB expressaram a CDK13, porém não foi possível purificá-la em coluna de afinidade ao Ni2+. / The cyclin-dependent kinases are proteins that can be classified by their function in the cell cycle or transcriptional control. They are activated in particular steps of the cell cycle depending on their phosphorylation degree, cyclin binding and inhibitory proteins. They act phosphorylating other proteins involved in the cell cycle and transcriptional control, influencing in their activities, ensuring that each step of the cell cycle occur in an ordered sequence. The CDK13 is one of the cyclin-dependent kinases family member, it can bind to L or K cyclins, regulates the alternative splicing and interact with HIV Tat protein, acting as a possible restriction factor, its overexpression decreases the production of some viral proteins, and suppresses the virus production. The DNA corresponding to CDK13 is replicated in cancer cells, mainly of hepatic and colon rectal types; therefore it is a target for inhibitors for cancer therapy. In order to contribute for the studies of this protein, the goal of the project is to express it using methods of recombinant DNA technology. The DNA sequence corresponding to CDK13 was amplified by polymerase chain reaction, after its purification, it was inserted to pCR-Blunt vector and cloned into E. coli DH5α competent cells. However, the DNA wasn\'t released by the BamHI and NdeI restriction enzymes. The Rosetta(DE3) cells transformed with a synthetic plasmid pET28a::CDK13 and grown in auto-induction media expressed the CDK13. After cell lysis and purification by Ni2+ affinity colum, the protein was identified by Western Blot. However, the Rosetta(DE3) cells transformed with the modified synthetic plasmid (that comprehends the DNA region which expresses the binding pocket region) induced in LB media, expressed the CDK13. Yet, it wasn\'t possible to purify the protein in the Ni2+ affinity column.

As proteínas fosfatases desempenham um papel fundamental na modificação pós-traducional reversível de proteínas por fosforilação, ao atuarem na remoção do grupo fosforil estável de resíduos de serina, treonina e tirosina. Embora predominem em eucariotos, as serina/treonina fosfatases (STPs) também existem em bactérias, nas quais atuam controlando diversos aspectos fisiológicos e de virulência. Neste trabalho investigamos o papel das STPs na virulência e fisiologia de Chromobacterium violaceum, uma ?-proteobactéria que atua como um patógeno ocasional de humanos e é amplamente encontrada em água e solos de regiões tropicais e subtropicais. Análises in silico revelaram a presença de quatro STPs no genoma de C. violaceum, sendo que duas possuem apenas o domínio de fosfatase (CV_0881 e CV_3848) e duas possuem um domínio adicional de regulador de resposta (CV_2644 e CV_3505). Mutantes nulos foram construídos para as quatro STPs e todas estas linhagens apresentaram crescimento semelhante ao da linhagem selvagem em meio rico e meio mínimo. As linhagens mutantes ?0881, ?2644 e ?3505 não apresentaram alteração de virulência em camundongos. Os mutantes ?2644 e ?3505 apresentaram menor formação de biofilme, o que sugere papel dessas fosfatases neste processo. Uma caracterização mais aprofundada da linhagem ?3848 por diferentes técnicas de microscopia revelou que este mutante apresenta células de tamanho diminuído, irregularidades no envelope celular e problemas na distribuição do DNA. Estes dados sugerem que CV_3848 tem papel em divisão celular, condensação do material genético e manutenção da parede celular. Nos ensaios de virulência o mutante ?3848 mostrou menor capacidade de causar morte e manter-se no fígado de camundongos, indicando que a STP CV_3848 é importante na patogenicidade de C. violaceum. / Protein phosphatases play a key role in reversible post-translational modification of proteins through phosphorylation since they act removing the stable phosphoryl group of serine, threonine and tyrosine residues. Although dominant in eukaryotes, the serine/threonine phosphatases (STPs) also exist in bacteria, in which they act by controlling various physiological and virulence traits. In this work we investigated the role of STPs on the virulence and physiology of Chromobacterium violaceum, a ?-proteobacterium that occasionally acts as a pathogen of humans and it is widely found in water and soil of tropical and subtropical regions. In silico analyzes revealed the presence of four STPs in the genome of C. violaceum, two of which have only the phosphatase domain (CV_0881 and CV_3848) and two that possess an additional domain of response regulator (CV_2644 and CV_3505). Null mutants were constructed for the four STPs and all of them showed similar growth to the wild type strain on rich and minimal medium. The mutant strains ?0881, ?2644 and ?3505 did not show any change in virulence in mice. The ?2644 and ?3505 mutants had lower biofilm formation, suggesting the role of these phosphatases in this process. Further characterization of ?3848 by different microscopy techniques revealed that this mutant presents cells of diminished size, irregularities in the cellular envelope and problem on the DNA distribution. These data suggest that CV_3848 has role in cell division, condensation of the genetic material and cell wall maintenance. In virulence assays the ?3848 mutant showed a lower ability to cause death and to remain in the liver of mice, indicating that the STP CV_3848 is important for the pathogenicity of C. violaceum.

αB-crystallin is a small heat-shock chaperone protein (sHSP) required for the homeostasis of multiple tissues including eye lens, retina, heart and brain. Correspondingly, mutation or altered levels of αB-crystallin are associated with multiple degenerative diseases including cataract, retinal degeneration, cardiomyopathy and Lewy body disease. Based on its wide-ranging importance understanding the protective and homeostatic properties of α B-crystallin is critical for understanding degenerative diseases and could lead to the development of therapies to treat these diseases. αB-crystallin is localized to the mitochondria suggesting a direct effect on mitochondrial function. My thesis work has examined those molecular pathways required for translocation of αB-crystallin to the mitochondria and to identify the downstream pathways controlled by mitochondrial translocation of αB-crystallin that could be important for cellular protection and differentiation. My results point to a novel role of αB-crystallin in regulation of key apoptotic pathways that mediate the balance between cell survival and differentiation. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

This research developed a biosensor for kinase drug discovery applications. In particular it combined electronic techniques with optical techniques to understand the phosphorylation of proteins. There are two major electronic characteristics of phosphorylation that aid in its detection and subsequently biosensor development: first is the release of a proton upon phosphorylation of a protein (change in pH) and second is the addition of negative charge to the protein upon its phosphorylation. The work in this thesis reports an electrolyte–insulator–semiconductor sensing structures to detect the pH changes associated with phosphorylation and metal–insulator–semiconductor structures to detect the charge change upon phosphorylation of proteins. Major application of the developed devices would be to screen inhibitors of kinase that mediate phosphorylation of proteins. Inhibitors of kinase act as drugs to prevent or cure diseases due to the phosphorylation of proteins. With the advancements in VLSI and microfluidics technology this method can be extended into arrays for high throughput screening for discovering drugs.

Chan Kam Leung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1999. / Includes bibliographical references (leaves 175-182). / Abstract also in Chinese. / Acknowledgements --- p.i / Abstract --- p.ii / Abbreviations --- p.v / Table of Contents --- p.vii / Chapter Chapter 1 --- General Introduction / Chapter 1.1 --- Drosophila as a model for studying development --- p.1 / Chapter 1.2 --- The formation of the body axis in Drosophila --- p.2 / Chapter 1.3 --- The maternal genes are essential for development --- p.9 / Chapter 1.4 --- Maternal gene bicoid is essential for formation of the anterior structures in the embryo --- p.11 / Chapter 1.5 --- The formation of the biocid protein gradient from anterior pole to posterior pole of the embryo --- p.13 / Chapter 1.6 --- The bed protein gradient controls the downstream zygotic target genes in a concentration-dependent manner --- p.15 / Chapter 1.7 --- The formation of the bed protein gradient in embryo --- p.17 / Chapter 1.8 --- Components required for bcd mRNA localization at anterior pole of oocyte --- p.21 / Chapter 1.8.1 --- Cis-acting elements --- p.21 / Chapter 1.8.2 --- Trans-acting elements --- p.21 / Chapter 1.9 --- The properties of exuperantia protein --- p.25 / Chapter 1.9.1 --- The function of exu protein --- p.25 / Chapter 1.9.2 --- Exuperantia is a phosphoprotein --- p.26 / Chapter 1.9.3 --- Phosphorylation pattern of exuperantia protein is stage-specific --- p.28 / Chapter 1.9.4 --- Reversible phosphorylation is one of the major mechanisms to control protein activity in all eukaryotic cells --- p.29 / Chapter 1.9.5 --- The relationship between the exu protein phosphorylation and the bcd mRNA localization --- p.30 / Chapter 1.10 --- Aim of project --- p.31 / Chapter CHAPTER 2 --- Preparation of the exuperantia genomic DNA and complement DNA (cDNA) mutant Constructs / Chapter 2.1 --- Introduction --- p.33 / Chapter 2.2 --- Materials and methods --- p.35 / Chapter 2.2.1 --- DNA preparation methods --- p.35 / Chapter 2.2.1.1 --- Preparation of double-stranded DNA by polyethylene glycol6000 --- p.35 / Chapter 2.2.1.2 --- Preparation of M13mp8 single-stranded DNA --- p.37 / Chapter 2.2.1.3 --- "Preparation of double-stranded DNA by Biol prep (Modified from Maniatis et al.,1989)" --- p.38 / Chapter 2.2.2 --- "Preparation of DH5α，JM109, TG1 competent cells" --- p.39 / Chapter 2.2.3 --- Bacteria transformation --- p.40 / Chapter 2.2.4 --- Restriction enzyme digestion --- p.40 / Chapter 2.2.5 --- Phenol/chloroform extraction --- p.41 / Chapter 2.2.6 --- Purification of DNA fragment by electro-elution --- p.42 / Chapter 2.2.7 --- DNA ligation --- p.43 / Chapter 2.2.8 --- DNA dephosphorylation --- p.43 / Chapter 2.2.9 --- In vitro site-directed mutagenesis --- p.44 / Chapter 2.2.9.1 --- The Sculptor´ёØ in vitro mutagenesis --- p.44 / Chapter 2.2.9.2 --- The GeneEditor´ёØ in vitro site-directed mutagenesis --- p.47 / Chapter 2.2.10 --- The double-stranded or single-stranded DNA sequencing by T7 DNA polymerase sequencing system --- p.50 / Chapter 2.2.11 --- Denatured polyacrylamide gel electorphoresis --- p.51 / Chapter 2.2.11 --- Nucleotide sequence of the sequencing primers and the mutageneic oligonucleotides --- p.54 / Chapter 2.3 --- Results --- p.55 / Chapter 2.3.1 --- Design exuperantia mutant constructs --- p.55 / Chapter 2.3.1.1 --- Comparison of exu protein amino acids sequence with different Drosophila species --- p.56 / Chapter 2.3.2 --- The exu genomic mutant constructs --- p.63 / Chapter 2.3.3 --- The exu cDNA mutant constructs --- p.63 / Chapter 2.4 --- Discussion --- p.76 / Chapter CHAPTER 3 --- Epitope tagging of exuperantia protein with c-myc eptiope / Chapter 3.1 --- Introduction --- p.79 / Chapter 3.2 --- Materials and methods --- p.84 / Chapter 3.2.1 --- Preparation of the c-myc eptiope DNA fragment --- p.84 / Chapter 3.2.2 --- End-filling of 5'overhang DNA fragment by Klenow fragment --- p.86 / Chapter 3.2.3 --- In vitro translation of protein by TNT® Quick coupled transcription and translation system --- p.86 / Chapter 3.2.4 --- Immunoprecipitation of recombinant exu protein --- p.87 / Chapter 3.2.5 --- Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) --- p.88 / Chapter 3.2.5.1 --- SDS-PAGE preparation --- p.88 / Chapter 3.2.5.2 --- SDS-PAGE electrophoresis --- p.90 / Chapter 3.2.6 --- Western blot analysis --- p.90 / Chapter 3.2.6.1 --- Transfer the protein to a nitro-cellulose membrane by semi-dried blotting --- p.90 / Chapter 3.2.6.2 --- Western blot blocking and antibody recognition --- p.91 / Chapter 3.3 --- Results --- p.92 / Chapter 3.3.1 --- Construction of the plasmid containing exu cDNA tagging with a c-myc epitope --- p.92 / Chapter 3.3.2 --- In vitro translation of c-myc epitope tagged exu protein --- p.102 / Chapter 3.3.3 --- Immunoprecipitation of c-myc labeled exu protein by a polyclonal rabbit anti-exu antibody and monoclonal mouse anti-myc antibody --- p.104 / Chapter 3.4 --- Discussion --- p.109 / Chapter CHAPTER 4 --- In vitro phosphorylation of exuperantia Protein / Chapter 4.1 --- Introduction --- p.111 / Chapter 4.2 --- Materials and methods --- p.113 / Chapter 4.2.1 --- Exogenous kinase phsophorylation reactions --- p.113 / Chapter 4.2.2 --- Separation of the phosphorylated exu protein variants by SDS- PAGE --- p.114 / Chapter 4.3 --- Results --- p.115 / Chapter 4.3.1 --- Western blot analysis of in vitro translated exu protein variants --- p.115 / Chapter 4.3.2 --- Phosphorylation of in vitro translated exu protein variants by exogenous cAMP-dependent protein kinase --- p.118 / Chapter 4.3.3 --- Phosphorylation of in vitro translated exu protein variants by exogenous cGMP-dependent protein kinase --- p.123 / Chapter 4.3.4 --- Phosphorylation of in vitro translated exu protein variants by exogenous protein kinase C --- p.128 / Chapter 4.4 --- Discussion --- p.133 / Chapter CHAPTER 5 --- Introduction of the exuperantia genomic constrcuts into the germline of Drosophila by P element-mediated transformation / Chapter 5.1 --- Introduction --- p.136 / Chapter 5.2 --- Materials and methods --- p.138 / Chapter 5.2.1 --- Construction of a genomic construct for production of transgenic flies --- p.138 / Chapter 5.2.2 --- Preparation of double-stranded DNA by ultra-centrifugation --- p.142 / Chapter 5.2.3 --- P-element mediated transformation --- p.143 / Chapter 5.2.3.1 --- Eggs collection --- p.143 / Chapter 5.2.3.2 --- Dechorionating the eggs --- p.143 / Chapter 5.2.3.3 --- Orientating the eggs --- p.144 / Chapter 5.2.3.4 --- Microinjection --- p.145 / Chapter 5.2.4 --- Collecting virgin female Drosophila --- p.146 / Chapter 5.2.5 --- Setup a crossing experiment --- p.146 / Chapter 5.2.6 --- Preparation of total ovaries and testes extracts exu protein from Female and male Drosophila --- p.147 / Chapter 5.2.7 --- Immunohistochemical distribution of exuperantia protein --- p.147 / Chapter 5.3 --- Results --- p.150 / Chapter 5.3.1 --- Insertion of the mutated exu fragments into the Drosophila Transformation vector (pCaSpeR) --- p.150 / Chapter 5.3.2 --- Introduction of the mutated exu gene into the genome of Drosophila by P-element mediated transformation --- p.153 / Chapter 5.3.3 --- Western blot analysis of the exu protein in the exu (ES2.1) transgenic fly --- p.160 / Chapter 5.3.4 --- Immunohistochemical distribution of exu protein in exuES21 mutants --- p.162 / Chapter 5.3.5 --- Rescue test of exuES2.1 trangenic flies --- p.165 / Chapter 5.4 --- Discussion --- p.168 / Chapter CHAPTER 6 --- General Discussion --- p.171 / References --- p.173 / Chapter Appendix I: --- List of reagents --- p.183 / Chapter Appendix II: --- Publication --- p.187

Phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3)-dependent RAC exchanger 2 (PREX2) is a guanine nucleotide exchange factor (GEF) for the Ras-related C3 botulinum toxin substrate 1 (RAC1) GTPase. As a GEF, PREX2 facilitates the exchange of GDP for GTP on RAC1. GTP bound RAC1 then activates its downstream effectors, including p21-activated kinases (PAK). PREX2, RAC1, and PAK kinases all have key roles within the insulin signaling pathway. The insulin receptor is a tyrosine kinase that phosphorylates the insulin receptor substrate (IRS) family of adaptor proteins, leading to the activation of phosphatidylinositide 3-kinase (PI3K) and the generation of PI(3,4,5)P3. PI(3,4,5)P3 then activates numerous downstream signaling proteins, including AKT and RAC1, to regulate several important cellular processes, such as glucose metabolism and cell proliferation. In addition to being a RAC1 GEF, PREX2 affects the insulin signaling pathway by inhibiting the lipid phosphatase activity of phosphatase and tensin homolog (PTEN), which dephosphorylates PI(3,4,5)P3 to antagonize PI3K. PREX2 is also important in cancer, which is likely a consequence of both its role as a RAC1 GEF and as a PTEN inhibitor. PREX2 GEF activity is activated by PI(3,4,5)P3 and by Gβγ, which is a heterodimer that is released after GPCR activation. However, PREX2 regulation within specific signaling pathways is poorly understood. This thesis aims to understand the regulation of PREX2 downstream of ligand binding to receptors on the cell surface, with a focus on insulin. This is achieved by studying the phosphorylation of PREX2 after insulin stimulation and by characterizing protein-protein interactions involving PREX2 and key proteins in the insulin signaling pathway. Herein, we identified PI(3,4,5)P3-dependent phosphorylation events on PREX2 that occur downstream of insulin stimulation. Phosphorylation of PREX2 also occurred downstream of Gβγ, suggesting that phosphorylation was associated with the activation of PREX2 GEF activity. Interestingly, phosphorylation of PREX2 reduced GEF activity towards RAC1 and a phospho-mimicking mutation of PREX2 at an insulin-mediated phosphorylation site reduced cancer cell invasion. Phosphorylation of PREX2 also decreased PREX2 binding to the cellular membrane, PI(3,4,5)P3, and Gβγ, providing a mechanism for reduced GEF activity. These data suggested that phosphorylation was part of a negative feedback circuit to decrease the RAC1 signal, which led to the identification of the PAK kinases as mediators of PREX2 phosphorylation. Importantly, insulin-induced phosphorylation of PREX2 was delayed compared to AKT, which is consistent with a model where PREX2 phosphorylation by PAK occurs after activation of PREX2 to attenuate its function. Altogether, we propose that second messengers activate the PREX2-RAC1 signal, which sets in motion a cascade whereby PAK kinases phosphorylate and negatively regulate PREX2 to decrease RAC1 activation. This type of regulation would allow for transient activation of the PREX2-RAC1 signal. We then asked whether PAK phosphorylation of PREX2 was altered in cancer. To do this, we analyzed four recurrent somatic PREX2 tumor mutations, R155W, R297C, R299Q, and R363Q. Interestingly, all four mutants had reduced insulin and PAK1 dependent phosphorylation, and R297C had lower levels of phosphorylation induced by PI3K activating tumor mutants. This suggests that tumors might be mutating PREX2 in order to avoid PAK mediated negative regulation of RAC1. Lastly, we characterized PREX2 interactions with proteins that are critical for insulin signaling, with a focus on the interaction between the PREX2 pleckstrin homology (PH) domain and PTEN. PREX2 inhibition of PTEN is mediated by the PH domain, and we discovered that the β3β4 loop of the PH domain was required for binding of the isolated PH domain to PTEN. We also found that PREX2 co-immunoprecipitates with other insulin related proteins, including the p85 regulatory subunit of PI3K, IRS4, and the insulin receptor. Taken together, the studies in this thesis solidify the role of PREX2 in insulin signaling by showing that PREX2 GEF activity is tightly regulated by insulin and PAK-induced phosphorylation and also by characterizing PREX2 interactions with critical insulin related proteins. Further, this PAK dependent negative regulatory circuit downstream of both PI(3,4,5)P3 and Gβγ activation of PREX2 could have impacts in many aspects of biology given the roles that PREX2 and RAC1 have in critical cellular functions such as cell motility and glucose metabolism, and in diseases such as cancer and diabetes.

Genomic stability is essential for maintaining cellular function and preventing oncogenic transformation. DNA double strand breaks (DSBs) are the most severe form of DNA damage. Classical non-homologous end joining (cNHEJ) is one of two major DSB repair pathways in mammalian cells. During lymphocyte development, NHEJ is required for the repair of programmed double strand breaks (DSBs) occurring during V(D)J recombination and Class Switch Recombination (CSR). Defects in cNHEJ cause severe combined immunodeficiency (SCID) in patients and animal models. Misrepair of physiological DSBs generated during normal lymphocyte development results in clonal translocations, which is characteristic of human lymphoid malignancy: it is the most common cancer type in children and the third leading cancer type in adults. Lymphoid malignancies are characterized by clonal translocations involving the antigen receptor loci, which often arise from the misrepair of programmed double strand breaks (DSBs). Furthermore, cNHEJ also plays a critical role in aging and therapeutic responses to genotoxic cancer therapy. My thesis study focuses on the function and regulation of DNA-dependent protein kinase catalytic subunit (DNA-PKcs). DNA-PKcs is a vertebrate specific NHEJ factor and one of most abundant proteins in human cells. Together with the DNA binding Ku70 and Ku80 heterodimer, DNA-PKcs forms the DNA dependent protein kinase (DNA-PK) holoenzyme. In addition to its important role in cNHEJ, DNA-PK also orchestrates the mammalian DNA damage response (DDR) together with the related ATM and ATR kinases by phosphorylating hundreds of partially overlapping substrates. My thesis goes deeper than the kinase and signaling function of DNA-PKcs during cNHEJ. We investigated the structural function of DNA-PKcs in cNHEJ (chapter 2) and A-EJ (chapter 3), using a mouse model with point mutations that lead to the expression of kinase dead (KD) DNA-PKcs. Second, we explored potential roles of DNA-PKcs outside of cNHEJ and A-EJ with a mouse model of DNA-PKcs lacking specific phosphorylation sites (chapter 4). Altogether, our results identified an unexpected structural function of DNA-PKcs in cNHEJ and the DNA damage response and expanded the purview of the function of DNA-PKcs into new areas, including hematopoiesis, alternative end-joining and potentially nucleoli stress.

In mammals, there are two isoforms of eukaryotic translation elongation factor 1A (eEF1A) called eEF1A1 and eEF1A2. They share 98% similarity at the amino acid level, and the main function of both is to facilitate the elongation process in protein translation. However, they have very different expression patterns. While eEF1A1 is universally expressed, eEF1A2 is strictly expressed in muscle, brain and heart. The over-expression of eEF1A2 has been found in cancers, such as ovarian and breast cancer. The factors influencing the different expression patterns of the two isoforms and the mechanisms by which eEF1A2 can act as an oncogene are not clear, therefore, the main aim of this study was to further investigate these two areas. The first aim was to find out whether the resveratrol induced down-regulation of eEF1A2 was mediated by miR-663. Western blotting in MCF7 cells showed that the level of endogenous eEF1A2 was decreased after resveratrol treatment while eEF1A1 remained stable. In contrast, NIH-3T3 stable cell lines which stably express the eEF1A2 coding sequence (CDS) only did not show this down-regulation, suggesting that the untranslated regions (UTRs) might play a role in this regulation. I then showed that miR-663 has ability to down-regulate a reporter linked to the UTRs of eEF1A2. The same reporter gene harbouring UTRs in which the binding sites of miR-663 had been deleted also showed down-regulation after resveratrol treatment, suggesting that the UTRs of EEF1A2 are key to the down-regulation of eEF1A2 by resveratrol but that miR-663 does not mediate this decrease. The second project aimed to address why eEF1A2 is an oncogene but eEF1A1 is not. The 3D structure of human eEF1A1 and eEF1A2 shows that the most of the highly conserved amino acids differences between the two isoforms are Ser and Thr residues, which are potential sites for phosphorylation. I mutated these three sites in eEF1A2 expression constructs to the equivalent amino acid from eEF1A1. Firstly, by transient transfection, all the mutant eEF1A2 were shown expressed and the sub-cellular locations of eEF1A2 remain unchanged after site-directed mutagenesis. Then, stable cell lines were generated. Anchorage independent growth (soft agar) and focus formation assays showed that the stable cell lines harbouring wild type eEF1A2 were significantly more transformed that those expressing the eEF1A2 mutants. However, there was no apparent difference in global protein synthesis between these cell lines. The results suggest that the potential phosphorylated sites in eEF1A2 play an important role in its oncogenicity and that this oncogenicity is not related to the canonical function of eEF1A2.