Deregulation of protein kinases is associated with many diseases making them important targets for therapeutic intervention. Kinases can switch between active and inactive conformations that can be targeted by type 1 or type 2 inhibitors respectively. One of the most relevant conformational switches is the ‘in’ and ‘out’ movement of the ATP/Mg2+ binding motif DFG. Factors modulating the conformational equilibria such as the residue environment of regulatory motifs remain poorly understood despite their importance for drug discovery. In this thesis, the first model system tested the hypothesis that accessibility of the DFG-out conformation is restricted by the energetic cost of transition between the in and out states. CDK2 was chosen as a target that was thought to have an inaccessible DFG-out conformation, and several point mutations were introduced to promote this conformational transition. Detailed biochemical and biophysical characterisation illustrated that the mutants bound type 2 inhibitors more potently than the wild type. In addition, the wild-type CDK2 was shown to bind type 2 inhibitors in the absence, but not in the presence, of cyclin. The first known CDK2 co-crystal structure in the DFG-out conformation was solved, opening the door to a new class of CDK2 inhibitors. In the second project, site-directed mutagenesis was used to explore the residues determining inhibitor selectivity between PIM1 and PIM2. Evaluation of ligand binding to the variants and comparison of PIM1 and PIM2 crystal structures showed that flexibility of the phosphate-binding loop was the dominant factor determining the differences in their affinities for ATP and small molecule inhibitors. These studies illustrate that residues contributing to kinase conformational equilibria can be just as important for inhibitor binding as contact residues formed in the ligand complex.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Orientador: Ângelo Berchieri Junior / Banca: Manoel Victor Franco Lemos / Banca: Gerson Nakazato / Resumo: Salmonella enterica sorotipo Typhimurium sintetiza cobalamina (Vitamina B12) apenas sobre condições anaeróbicas. Dois porcento do genoma da S. Typhimurium é dedicado a reações dependentes de vitamina B12 como cofator, sua síntese e absorção. Neste estudo nós preparamos mutantes de Salmonella sorotipos Enteritidis, Gallinarum e Pullorum duplo defectivos na biossintese de cobalamina, cepas ΔcobSΔcbiA. A virulência destes mutantes foi comparada com as respectivas cepas selvagens e, nenhuma deficiência na capacidade de causar doença foi observada para as cepas de S. Enteritidis ΔcobSΔcbiA e S. Pullorum ΔcobSΔcbiA. S. Gallinarum ΔcobSΔcbiA por sua vez, mostrou atenuação total. Posteriormente nós testamos a produção de B12 pelas cepas mutantes e selvagens já descritas, e incluímos neste estudo a cepa de S. Typhimurium ΔcobSΔcbiA, e sua respectiva cepa selvagem. Todas as cepas mutantes não tiveram produção de B12 detectada. As cepas selvagens mostraram produção de vitamina B12 em ambos os ensaios utilizados, com exceção da S. Gallinarum que não apresentou produção de cobalamina in vitro. Como conclusão, a produção de vitamina B12 in vitro diferiu entre os sorotipos de Salmonella testados, a deleção dos genes cbiA e cobS produziu alteração na relação parasita hospedeiro em diferentes níveis entre os sorotipos de Salmonella estudados, sendo que esta foi muito maior entre o sorotipo Gallinarum e as aves. / Abstract: Salmonella enterica serovar Typhimurium only synthesizes cobalamin (Vitamin B12) during anaerobiosis. Two-percent of the S. Typhimurium genome is devoted to the synthesis and uptake of Vitamin B12 and to B12-dependent reactions. In order to understand the requirement from cobalamin synthesis better, we constructed Salmonella serovar Gallinarum, Salmonella serovar Enteritidis and Salmonella serovar Pullorum mutants that are double-defective in cobalamin biosynthesis (ΔcobSΔcbiA). We compared the virulence of these mutants to that of their respective wild type strains and found no impairment in S. Enteritidis ΔcobSΔcbiA and S. Pullorum ΔcobSΔcbiA ability to cause disease in chickens. S. Gallinarum ΔcobSΔcbiA mutant showed attenuated for chickens. We then assessed B12 production by these mutants and their respective wild type strains, as well as S. Typhimurium ΔcobSΔcbiA, and their respective wild type strain. All mutants were unable to produce detectable B12. B12 was detectable in wild type strains, but, S. Gallinarum demonstrated no in vitro cobalamin production. In conclusion, the production of vitamin B12 in vitro differed across the Salmonella serotypes that were tested. Furthermore, the deletion of the cbiA and cobS genes resulted in an alteration in the relationship between the serotype Gallinarum and the birds more stronger than did to the others serotypes. / Mestre

The tumour suppressor p53 is often disrupted by missense mutations that can result in p53 protein accumulation and acquisition of novel oncogenic activities. Various studies have demonstrated that DNA-damaging drugs currently used in the clinic aimed at activating wild type p53, can also stabilise and activate mutant p53 oncogenic functions and thereby paradoxically enhance tumour progression, resulting in poor response to the treatment. In this study we aimed to investigate whether, like in wt p53, post-translational modifications (PTMs) drive such drug-induced mutant p53 accumulation and activation. For this purpose, we generated plasmids expressing non-phosphorylatable and phospho-mimic versions of R175H mutant p53 and tested them in different cell line models. We demonstrated that in response to DNA damage mutant p53 is accumulated and phosphorylated and these phenomena appeared to be mediated by ATM and ATR kinases. DNA-damage induced acetylation was also observed and occurred in a S15 phosphorylation-dependent manner. This suggested a role of the HAT p300, which is recruited by phosphorylated S15. Of note, other works have shown that p300 is required to trigger some oncogenic functions of mutant p53. We then aimed at developing systems to explore mutant p53 functions and their dependence on PTMs. Although we showed that cell growth is compromised upon endogenous mutant p53 depletion, exogenous expression of mutant p53 or its phosphorylation-site forms did not result in a successful rescue in our experimental conditions, thus we were unable to use this strategy to test the effect of PTMs. Ectopic expression of R175H mutant p53 or its phosphorylayion-site versions did not interfere with the growth rate and response to chemotherapy of the p53-null cell line H1299. We also found that mutant p53 phosphorylation does not affect subcellular localisation of mutant p53 and mutant p53-mediated inhibition of p63. Interestingly, ectopically expressed mutant p53 enhanced cell migration in H1299 cells. Notably, our results suggested an apparent threshold effect of mutant p53 levels required to induce migration. Due to the difficulty of obtaining cell lines expressing similar levels of the different phosphorylation-site mutants, the determination of the role of phosphorylation in mutant p53-induced migration was not conclusive. Remarkably, we found that, while S15 and S20 phosphorylation decreased MDM2-dependent degradation, only phosphorylated S20 interfered with CHIP-induced turnover in H1299 cells. Overall our data suggest that, despite exhibiting opposite biological effects, mutant and wt p53 can share upstream regulatory mechanisms and thus present phosphorylation as a promising target to prevent mutant p53 stabilisation and activation and improve response to therapy. Our results also highlight the challenge of developing a good system for determining the effects of the mutant p53 protein and its regulation by PTMs.

L'acide abscissique (ABA) est une hormone cruciale pour la tolérance des plantes au déficit hydrique. Son accumulation induit rapidement à la fois la fermeture stomatique qui limite les pertes en eau et l'expression de gènes qui participent à des processus de protection et détoxification des cellules. La thermographie infrarouge permet d'observer en temps réel la différence de température entre des plantes « froides » aux stomates ouverts et des plantes « chaudes » aux stomates fermés. Afin d'identifier de nouveaux gènes impliqués dans la réponse au déficit hydrique, cette technique a été utilisée pour rechercher des suppresseurs « chauds » de la mutation de déficience en ABA aba3-1 chez Arabidopsis thaliana. Quatre mutants suppresseurs « chauds » récessifs, nommés has aba3-1 (hot ABA-deficient suppressors), plus résistants qu'aba3-1 à une déshydratation progressive ont été isolés et étudiés. Leur meilleure tolérance au stress hydrique n'est pas due à une accumulation accrue d'ABA. Des analyses phénotypiques et transcriptomiques ont été effectuées, notamment pour étudier leur réponse à différents types de stress hydrique, à un stress biotique et leur sensibilité à l'ABA dans plusieurs tissus. Les mutations has ont été sélectionnées en l'absence de la mutation aba3-1 et certains phénotypes ont été étudiés dans ce fond sauvage. La mutation has1 semble complexe, entraînant la disruption d'un gène codant pour une hélicase à ARN putative dont la mutation n'est pas seule responsable de tous les phénotypes de has1 aba3-1. La mutation has2 diminue la perte en eau pendant une déshydratation rapide ou progressive, en contexte aba3-1 ou sauvage. Son analyse transcriptomique a montré que le niveau d'expression de l'ensemble des gènes était proche du sauvage en accord avec la suppression de la sensibilité au déficit hydrique. La mutation has3 semble induire une hypersensibilité à l'ABA au niveau des stomates et de la graine. Enfin, le suppresseur has4 aba3-1 est affecté dans la sensibilité à l'ABA pour tous les tissus testés et montre les phénotypes stomatiques les plus marqués des quatre suppresseurs, qui semblent conservés chez has4. Ces observations ont conduit à cartographier en priorité ce locus. L'étude des 32 gènes de son intervalle de cartographie est bien avancée et devrait prochainement permettre d'identifier lequel est muté. La cartographie des loci has2 et has3 a réduit la région contenant ces mutations à des zones d'environ 0,5 et 1 Mb respectivement. Les quatre loci has sont distincts et leurs régions de cartographie ne contiennent pas de gènes déjà étudiés dont la mutation correspondrait à leur phénotype. Ce projet devrait donc conduire à l'identification d'au moins trois nouveaux gènes intervenant dans la tolérance au dèficit hydrique.

The har1-1 mutant of Lotus japonicus line Gifu is characterised by increased nodulation and significantly inhibited root growth in the presence of its microsymbiont Mesorhizoboium loti (for example strain NZP2235). A sexual cross between the mutant and another L. japonicus genotype Funakura (with wild-type root and nodule morphology) demonstrated Mendelian recessive segregation of both phenotypes (for root and nodule) in 242 F2 individuals. No separation of phenotypes was observed, suggesting a single mutation with pleiotropic effects. Reciprocal grafting showed that the har1-1 controlled phenotype is governed by the shoot. Using a skeletal genetic map of arbitrary molecular markers produced from a Gifu x Funakura cross, the har1-1 locus was positioned between two markers at about 7 and 13 cM distance. Single nucleotide polymorphisms (SNPs) and transgene sequences were detected by allele-specific PCR in DNA isolated from small (1 mg mass) individual seeds and half-cotyledon of the model legume Lotus japonicus, allowing fast determination of a seedling’s genomic status. This permitted a shortening of the breeding cycle for multi-trait seed lines. Fast neutron mutagenesis of Lotus japonicus wild-type genotype Gifu resulted in the first time isolation of a stable mutant (FNN5-2) unable to form nitrogen-fixing nodules in symbiosis with Mesorhizobium loti, though being infected by mycorrhizal fungi. The mutation behaves as a loss-of-function recessive, and has no other apparent phenotypic effects. Molecular characterization indicates a partial loss of the LjNFR1 LysM type receptor kinase gene. Additionally part of the LjNIN gene (encoding a putative transcription factor needed for nodulation) is also missing. Transcript levels for both genes are severely reduced. As LjNIN and LjNFR1 are in the same chromosomal region we tested whether this terminal portion is lacking. PCR analysis confirms that genes within the relevant interval (such as LjPAL1 (encoding phenylalanine ammonia lyase) and LjEIL2 (encoding an ethylene insensitive-like response regulator)) are present, suggesting that the mutational event induced by the fast neutrons was either a double hit coincidently involving two nodulation-related genes, a major genome rearrangement, or a major segmental inversion. To develop an integrated nodule developmental model based on gene interactions in autoregulation, nodulation and plant hormone response deficient lines, HE double mutants have been built using the har1-1 mutant (hypernodulation and aberrant root) and the ethylene insensitive transgenic line Etr1-1. The homozygous loss-of-function mutant har1-1 has increased nodulation and decreased root growth. Ethylene insensitivity mediated by the transgene 35S::AtETR1-1 restores the normal root growth. The HE double mutants were confirmed by triple response test and allele- or gene-specific PCR. The current results in this study indicate that a) HE double mutants shown the same nodulation pattern as har1-1 and normal root formation as Etr1-1, suggesting that nodule and root control diverge at some stage with root control being ethylene-mediated and the Har1 gene, the orthologue of GmNARK is involved in nodulation. b) Grafting demonstrated that the shoot is the source of ethylene suppression of the har1-1 induced inhibition of root growth. c) The mutated Etr1-1 gene was able to replace AVG in BAP root inhibition; d) IPT-dependent cytokinin overproduction led to aberrant root architecture in har1-1; e) Crosstalk between ethylene and cytokinin in HE double mutant by qRT-PCR.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2007. / Härtill 4 uppsatser.

Thesis (M.S.); Submitted to Iowa State Univ., Ames, IA (US); 12 Dec 2003. / Published through the Information Bridge: DOE Scientific and Technical Information. "IS-T 2547" Elizabeth M. Lenihan. 12/12/2003. Report is also available in paper and microfiche from NTIS.

Thesis (Ph.D). / Written for the Dept. of Human Genetics. Title from title page of PDF (viewed 2009/06/08). Includes bibliographical references.

Resumo: O cancro cítrico é uma doença de importância mundial para o cultivo de laranjas e seu agente causador é a bactéria Xanthomonas axonopodis pv. citri. Embora todos os genes presentes nessa bactéria já tenham sido sequenciados, grande parte destas sequências não apresenta qualquer informação experimental sobre a contribuição para o sucesso da instalação do patógeno na planta hospedeira. Por outro lado, torna-se cada vez mais evidente que várias bactérias fitopatogênicas utilizam mecanismos de adaptação de origem genética que podem induzir efeitos fisiológicos na planta e adequar o ambiente de tal forma que permita a ocorrência da doença. Dentre estes mecanismos, está a possibilidade da bactéria produzir substâncias que se assemelhem a hormônios vegetais, como a auxina (AIA). O objetivo deste trabalho foi desenvolver metodologia genômica de busca para investigar se há genes que codificam para a produção de compostos iguais ou semelhantes a este hormônio em X. axonopodis pv. citri e se a sua participação no processo de patogênese é fundamental para o sucesso da infecção. Para tal, foi produzida coleção de mutantes genéticos funcionais aleatoriamente em X. axonopodis pv. citri, com posterior submissão desta mesma coleção a teste de produção de auxina utilizando o reagente Salkowski. Após produção e análise de grupo de mutantes dirigidos e coleção de aproximadamente 14200 mutantes aleatórios não foi detectada linhagem defectiva para a produção de AIA ou composto semelhante. Os resultados obtidos neste estudo, no entanto, mostram que a biossíntese do composto em X. axonopodis pv. citri é dependente do triptofano e que existe uma concentração ótima deste aminoácido a ser adicionado no meio de cultura para que a bactéria realize a biossíntese. Este é o primeiro estudo... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The citrus canker is a disease of global significance for the cultivation of oranges and its causative agent is the bacterium Xanthomonas axonopodis pv. citri. Although all the genes present in this bacterium have been sequenced, most of these sequences have no experimental information regarding the contribution to the successful installation of the pathogen on the host plant. On the other hand, it has been clearly demonstrated that several pathogenic bacteria use adaptative mechanisms that can induce physiological effects in plants and adjust the environment in a way that allows the occurrence of the disease. Among these mechanisms there is the possibility the bacteria produce substances that are similar to plant hormones such as auxin (IAA). The objective of this study was to develop a screening methodology to investigate the presence of genes that code for a compound identical or similar to auxins in X. axonopodis pv. citri as well as if it plays a role during the pathogenesis process. The main goal of this study was to produce a collection of random and directed genetic mutant strains of X. axonopodis pv. citri for the screening of auxin production by using the Salkowski reagent. After production and analysis of the group of mutants, including a collection of approximately 14,200 random mutant strains, defective production of IAA or similar compound was not detected. On the other hand, the results of this study show that such compound mimics effects of hormonal properties in X. axonopodis pv. citri and is dependent of tryptophan. In addition, it is shown that there is an optimum concentration of this amino acid to be added in the culture medium for the bacteria to carry out biosynthesis. To our knowledge, this is the first study to investigate systematically the production of auxin-like compounds in Xanthomonas axonopodis pv. citri. / Orientador: Alexandre Morais do Amaral / Coorientador: Henrique Ferreira / Banca: Nelson Wulff / Banca: Dario Abel Palmieri / Mestre