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.

A exposição das plantas a estresses bióticos e abióticos pode levar ao aumento dos níveis de espécies ativas de oxigênio (EAOs) nas células, gerando estresse oxidativo. Dentre os causadores de estresses abióticos mais estudados, estão a salinidade e o cádmio (Cd). A salinidade pode causar um desequilíbrio de íons nas células, resultando estresse osmótico. Já o Cd gera distúrbios nutricionais, estruturais e bioquímicos, levando ao aumento de EAOs. Para combater este excesso, as plantas desenvolveram um complexo sistema de defesa que inclui mecanismos enzimáticos e não enzimáticos de desintoxicação. Os hormônios vegetais, como o etileno, controlam importantes vias do metabolismo celular, fazendo com que as plantas respondam de diferentes maneiras às condições de estresse. Fatores de estresse distintos podem resultar em respostas diferenciadas por parte das células e dos diferentes tecidos das plantas. O presente trabalho utilizou o tomateiro cv. Micro-Tom e seu mutante hormonal para etileno Never ripe (Nr) cultivados em solução nutritiva e submetidos aos estresses por 100 mM de NaCl e 0,5 mM de CdCl2 em coletas distintas (sete, 20 e 36 dias). Neste trabalho, as respostas das enzimas superóxido dismutase (SOD), catalase (CAT), glutationa redutase (GR), ascorbato peroxidase (APX) e guaiacol peroxidase (GPOX) foram analisadas. Além disso, outros parâmetros importantes como quantificação de Cd e Na, peroxidação lipídica, peróxido de hidrogênio (H2O2), análise do perfil protéico por SDS-PAGE e teor de clorofila foram avaliados. De acordo com os resultados, o Cd acumulou-se mais nas raízes, e o Na foi absorvido pela plantas e transportado até as folhas e frutos. O estresse provocado pelo Cd foi mais prejudicial ao desenvolvimento do MT, aumentando os níveis de H2O2 e MDA, assim como a atividade das enzimas antioxidantes. Alterações nos perfis protéicos dos tecidos submetidos aos tratamentos com Cd e Na também foram observadas. A absorção de Na pelos frutos foi elevada, alterando a atividade das enzimas antioxidantes. A enzima que mais apresentou aumento de atividade foi a GR, tanto em folhas quanto em raízes, nos três períodos analisados, sugerindo que essa enzima pode estar associada à síntese de fitoquelatinas (PCs) nos tecidos. Isso mostra que as enzimas antioxidantes agem de maneira particular, conforme o período de estresse ao qual as plantas estão submetidas, de maneira que a resposta antioxidante é dinâmica e particular a cada tecido da planta. / Plant exposure to abiotic and biotic stresses can lead to enhanced production of Reactive Oxygen Species (ROS) in cells, causing oxidative stress. Cadmium (Cd) and salt (NaCl) are among the most studied abiotic stresses. Salinity can cause ion disturb in the cell, resulting in osmotic stress. In the case of Cd, it can induce nutritional, structural and biochemistry changes, leading to increased ROS levels. Plants have developed efficient antioxidant systems to act against ROS, including a series of enzymatic and non-enzymatic detoxification mechanisms. Plant hormones, such as ethylene, can control important pathways, which may result in different manners for the plant to respond to stressful conditions. Different stress factors can result in different responses depending of plant cells and tissues. This work used the miniature tomato Micro-Tom and its hormonal mutant to ethylene counterpart, Never ripe (Nr), which were maintained in nutritional solution and submitted to 100 mM of Na Cl and 0.5 mM of CdCl2 for 7, 20 and 36 days. Antioxidant enzymes responses mainly by changes in activities of superoxide dismutase (SOD), catalase (CAT), gluthathione reductase (GR), ascorbate peroxidase (APX) and guaiacol peroxidase (GPOX) were analyzed. Moreover, others important evaluation parameters such as Cd and Na quantification, lipid peroxidation, level of H2O2, SDS-PAGE and chlorophyll amount, were assessed. According to the results, Cd accumulated in roots while Na was uptaked and translocated to the leaves and fruits. The stress caused by Cd was the most damaging to MT plant development, increasing H2O2 and lipid peroxidation, as well as antioxidant enzymes activities. Alterations in SDS-PAGE protein profiles were also observed. The uptake of Na in fruits was high, modifying antioxidant enzymes activities. GR was the enzyme that exhibited the highest increase in activity in leaves and roots during all periods analyzed, suggesting that this enzyme can be related to phytochelatin synthesis (PCs) in tissues and/or increased glutathione synthesis. The results confirmed that the enzymes may respond differently depending on the tissue, organ, time length of exposure and concentrations of the stressful agent.

Evolution of enzymes with novel functional properties has gained much attention in recent years. Naturally evolved enzymes are adapted to work in living cells under physiological conditions, circumstances that are not always available for industrial processes calling for novel and better catalysts. Furthermore, altering enzyme function also affords insight into how enzymes work and how natural evolution operates. Previous investigations have explored catalytic properties in the directed evolution of mutant libraries with high sequence variation. Before this study was initiated, functional analysis of mutant libraries was, to a large extent, restricted to uni- or bivariate methods. Consequently, there was a need to apply multivariate data analysis (MVA) techniques in this context. Directed evolution was approached by DNA shuffling of glutathione transferases (GSTs) in this thesis. GSTs are multifarious enzymes that have detoxication of both exo- and endogenous compounds as their primary function. They catalyze the nucleophilic attack by the tripeptide glutathione on many different electrophilic substrates. Several multivariate analysis tools, e.g. principal component (PC), hierarchical cluster, and K-means cluster analyses, were applied to large mutant libraries assayed with a battery of GST substrates. By this approach, evolvable units (quasi-species) fit for further evolution were identified. It was clear that different substrates undergoing different kinds of chemical transformation can group together in a multi-dimensional substrate-activity space, thus being responsible for a certain quasi-species cluster. Furthermore, the importance of the chemical environment, or substrate matrix, in enzyme evolution was recognized. Diverging substrate selectivity profiles among homologous enzymes acting on substrates performing the same kind of chemistry were identified by MVA. Important structure-function activity relationships with the prodrug azathioprine were elucidated by segment analysis of a shuffled GST mutant library. Together, these results illustrate important methods applied to molecular enzyme evolution.

Human Immunodeficiency Virus (HIV) has become a global pandemic with at least 25 million deaths and no cure. One of the most important targets to inhibit this virus is HIV-1 protease (PR), which is required to cleave the viral proteins needed for maturation of the virus after it invades and replicates in the host cell. There are nine protease inhibitors that are used in AIDS treatment. The virus loses susceptibility to these inhibitors by drug resistance due to mutations. The goal of the project is to examine the highly drug resistant HIV PR P51 in its complex with inhibitors. In this experiment we expressed and purified HIV PR P51 protein. We performed protein crystallization with inhibitors Tipranavir, Amprenavir, Darunavir, and Saquinavir to obtain the structure of the protease and the inhibitors in their complexes. Future analysis of the crystal structures will help with the development of successful therapeutic inhibitors.

No description available.

Myocilin, expressed in the trabecular meshwork of the eye, has been linked to inherited primary open-angle glaucoma (POAG). The biological function of myocilin is unknown, but mutant myocilin exhibits a gain-of-function mechanism, aggregating within the endoplasmic reticulum of human trabecular meshwork cells, causing cell stress and eventually apoptosis. After apoptosis occurs, the trabecular meshwork is compromised, leading to an increase in intraocular pressure, a symptom of glaucoma. In this thesis, I have expressed and purified the wild-type olfactomedin (OLF) domain and 24 reported disease-causing variants. I developed a facile thermal stability assay using differential scanning fluorimetry, which follows the unfolding of a protein through the fluorescence of a dye sensitive to hydrophobic regions of a protein. Also in this thesis I have determined melting temperatures for the wild-type and for each of the disease-causing mutants. I have tested the stability of the mutants in the presence of seven osmolytes, with sarcosine and trimethylamine-N-oxide restoring the melting temperature closest to wild-type. Additionally, I expressed and purified three reported single nucleotide polymorphisms (SNPs) (E352Q, E396D, K398R), which are considered benign variants. Variants were also compared by circular dichroism, revealing high b-sheet content and wild-type structure. When compared to previous studies, there is a positive correlation between the melting temperature, and previously reported qualitative assays, which measure the mutant myocilin solubility in detergent, secretion from mammalian cells, and aggregation propensity. Taken together, these data give insight into the relationship between glaucoma genotypes and phenotypes.

The studies reported in this thesis address the aspects of initiator tRNA selection in Escherichia Coli. A summary of the relevant literature discussing the process of ptotein biosynthesis in general and initiator tRNA selection, in particular is presented in chapter 1. The next chapter (Chapter2) describes the ‘Materials and Methods’ used throughout the experimental work carried out in this thesis. It is followed by two chapters(Chapter 3 and Chapter 4) which describe the isolation and characterization of an E. coli mutant, to understand the mechanism of initiator tRNA selection. Chapter 5 comprises of some experimental work and future perspectives on the utility of the E.coli mutant. The last chapter (Chapter 6) summarizes the published work where I have contributed to besides the work described in Chapters 3 to 5. The summary of chapters 3-5 is as described below:- (i)Isolation and genetic mapping of extragenic suppressors of mutant initiator tRNA lacking the three consecutive G, C base pairs in the anticodon stem Initiator tRNA selection on the ribosomes is a result of several steps, some of which are unique to the prokaryotic world. Structure-function analyses of E.Coli tRNAfMet have revealed that the most important features of tRNAfMet, pertinent to its in vivo function as an initiator, are located in the acceptor stem and the anticodon arm regions. The three consecutive G-C base pairs in the anticodon stem of the tRNAfMet, conserved across all kingdoms of life, have been implicated in preferential binding to 30S ribosomal P-site. How the 3G-C base pairs are exploited by ribosomes in selecting the initiator tRNA, has been a long standing question. In the present work, a genetic screen was developed to isolate second site compensatory mutations of the mutant tRNAfMet, inactive in initiation because the 3G-C base pairs in it were changed to those found in the elongator tRNAMet(‘3G-C mutant’). Two extragenic suppressors were mapped to defined regions in the 12 min and 85 min locations in the E. Coli genome and three others were classified in these two broad groups. A super suppressor strain exhibiting synergistic suppression was generated. Further genetic mapping identified a G122D mutation in the folD gene encoding 5, 10 methylene tetrahydrofolate dehydrogenase/cyclohydrolase in one of the suppressor strains E. Coli A48. Complementation analysis using over expression of fold confirmed the results obtained by genetic mapping. (ii) Role of the intracellular S-adenosylmethionine flux in initiation with an initiator versus elongator tRNAs in Escherichia Coli How a defect in folD gene product (in E. Coli A48) leads to initiation with the ‘3G-C mutant’ initiator tRNA, has been addressed in this work. The FolD enzyme plays a key role in the one-carbon metabolism. The mutation in folD resulted in a lethal phenotype in minimal medium. The end-products of the pathway, 10 formyl-THF, methionine and S-adenosylmethionine(SAM) were analyzed for their possible role in initiation with the ‘3G-C mutant’ tRNAfMet, which revealed that lowering of the steady-state abundance of methionine and SAM had a direct role in initiation with the ‘3G-C mutant” tRNAfMet. Analysis of the 16S tRNA revealed that the methylations, as a result of reduced levels of SAM, were undetectable in the E.Coli A48. This prompted us to generate targeted mutations in the methyltransferase genes, which have highlighted the importance of methylations in initiator tRNA selection. Consistent with the growth retardation phenotype of methylase deficient strains at higher temperatures, the E. Coli A48 also displays temperature sensitivity. Further analysis of mycoplasma genomes, which do not follow the strong conservation of three G-C base pairs in the anicodon stem of initiator tRNA has uncovered an hitherto unknown evolutionary connection between methylations of 16S rRNA and initiator tRNA selection. We observed genetic interaction between infC(encoding IF3) and fold (encoding FolD). We also demonstrate initiation with tRNAfMet containing mutations in one, two or all the three G-C base pairs, as also with the elongator tRNA (tRNAGln). (iii) Utility of E. Coli A48 in investigation of biological processes: Some Preliminary studies and future perspectives. The availability of the E. Coli A48 strain is a valuable addition to the field of initiator tRNA selection and opens up further opportunities for its application. In this study, we have analyzed some of the properties of the E. Coli A48 strain viz. sensitivity to UV light and formylation independent initiation. E. Coli possess multiple copies of initiator tRNA, encoded by the metZVW operon and the metY gene. We reasoned that the abundance of cellular initiator tRNA might be a contributing factor in maintenance of specificity of initiation. Consistent with our prediction, we observed initiation with the ‘3G-C mutant’ tRNAfMet in E. Coli strains deficient in initiator tRNA genes. The various aspects of SAM limitation, biological functions of post-transcriptional modifications, incorporation of non-methionine amino acids in then-terminus of proteins and genetic approaches to system biology for the understanding of one-carbon metabolism are discussed.

RORα (Retinoic acid receptor related Orphan Receptor α) est un récepteur nucléaire<br />dont la perte de fonction entraîne chez la souris staggerer - entre autres phénotypes - une<br />sévère ataxie cérébelleuse. RORα a longtemps été considéré comme un récepteur nucléaire<br />orphelin, cependant, le cholestérol (ou un de ses dérivés) semble être un ligand physiologique<br />de ce récepteur.<br />Le mutant staggerer, identifié dès 1962 par Sidman, Lane et Dickie, présente une<br />hypoplasie cérébelleuse liée à l'absence de la grande majorité des cellules de Purkinje, ainsi<br />que des grains du cervelet. L'expression de la mutation staggerer dans les cellules de Purkinje<br />conduit à leur mort massive pendant le développement, et les cellules de Purkinje survivantes<br />chez l'adulte présentent d'importantes anomalies de différenciation. Par ailleurs, à l'état<br />hétérozygote, le mutant staggerer présente une diminution de la survie des cellules de<br />Purkinje ainsi que des anomalies de différenciation au cours du vieillissement.<br />Le phénotype cérébelleux des mutants homozygote et hétérozygote staggerer<br />suggère que RORα est impliqué dans la survie et/ou la différenciation des cellules de Purkinje<br />au cours du développement et du vieillissement. Au cours de cette thèse, nous avons donc<br />tenté de déterminer le rôle de RORα dans la survie et la différenciation dans des neurones<br />corticaux et/ou dans des cellules de Purkinje, en étudiant l'effet de sa surexpression dans ces<br />processus.<br />Afin de surexprimer RORα, nous avons construit un vecteur lentiviral exprimant<br />l'isoforme humaine RORα1. Ce vecteur nous a permis de transduire avec une très grande<br />efficacité des neurones corticaux en culture primaire ainsi que les cellules de Purkinje en<br />culture organotypique.<br />Dans une première étude, nous avons cherché à déterminer si RORα pouvait exercer<br />un rôle dans la survie neuronale. Dans ce but, nous avons évalué la survie de neurones<br />corticaux surexprimant ou non RORα et soumis à un stress oxydatif entraînant l'apoptose des<br />neurones. RORα protège les neurones en diminuant le stress oxydatif causé par ces inducteurs<br />pro-apoptotiques. L'expression des deux enzymes Glutathion peroxydase 1 et Peroxiredoxine<br />6 est augmentée dans les neurones qui surexpriment hRORα1, et semble partiellement médier<br />l'effet neuroprotecteur de RORα. Nous avons par ailleurs évalué et comparé la survie des<br />cellules de Purkinje en culture organotypique qui expriment RORα de façon endogène, ou qui<br />surexpriment hRORα1, et nos résultats suggèrent que la surexpression de RORα a également<br />un effet neuroprotecteur dans ces cellules.<br />Dans une seconde étude, afin de déterminer le rôle de RORα dans la différenciation<br />des cellules de Purkinje, nous avons analysé en culture la progression de la différenciation<br />dendritique précoce de cellules de Purkinje en fonction de l'expression de RORα. RORα est<br />crucial pour l'étape de régression des neurites des cellules de Purkinje au stade bipolaire<br />embryonnaire. Alors que l'absence de RORα chez les mutants homozygotes staggerer<br />entraîne un arrêt de la différenciation des cellules de Purkinje à ce stade (les cellules de<br />Purkinje ne parviennent pas à entamer la régression des neurites), la surexpression de<br />hRORα1 accélère l'étape de régression. Cette étape de régression est totalement dépendantede l'expression de protéines RORα fonctionnelles et cet effet est vraisemblablementintrinsèque. Nous montrons enfin que l'hormone thyroïdienne accélère la différenciationdendritique précoce des cellules de Purkinje, et que RORα semble contribuer à ce processus.<br />L'ensemble de ces résultats montre que RORα intervient de façon cruciale à la foisdans la survie et dans la différenciation des cellules de Purkinje dans une étape très précoce de<br />leur développement post-natal.

Dissertation (Ph.D.)--University of South Florida, 2007. / Includes vita. Includes bibliographical references. Also available online.

The study evaluated the Mutant Prevention Concentration (MPC) of Pradofloxacin on three Escherichia coli (E.coli) strains, 2 wildtypes and one first-step gyrA resistant mutant. We also measured the value of AUC (Under the Concentration)/MPC that prevents growth of resistant mutants. It is of importance to reach a concentration above MPC that prevent E.coli from developing resistance against the antibiotic. We used an in vitro kinetic model where we added bacteria? and antibiotic. The culture flask was attached to a pump with an adjustable pump-speed. This made it possible to dilute the antibiotics in a satisfying elimination half-life (t1/2= 7 hours) pace. Samples were removed with a syringe at different times in the study. The samples where then cultured on agar- plates to enable counting of the viable colonies after incubation. The optimal concentration to completely eradicate both E.coli wildtypes Nu14 and MG1655 with Pradofloxacin was Cmax ≥8 times MPC and AUC/MPC then became73. Additional experiments needs to be done on the resistant mutant LM378 before we can determine the optimal concentration. But results so far indicate that the concentration of Cmax would be about 8-12 timesMPC to completely eradicate that mutant.