La NADPH oxydase, Nox4, appartient à la famille des Nox qui génèrent les espèces radicalaires de l'oxygène, ROS, en transférant un électron à l'oxygène moléculaire. Malgré sa large distribution dans les tissus, Nox4 est encore mal comprise. Contrairement aux autres Nox, Nox4 est unique par son activité constitutive et sa capacité à former H2O2. Les ROS sont des espèces bactéricides dans les phagocytes et des outils de signalisation dans les cellules non phagocytaires en étant associés à de nombreuses pathologies inflammatoires et du vieillissement. Une étude de la structure en lien avec la fonction de Nox4 permettra de mettre l'accent sur un mécanisme de fonctionnement et sur de nouvelles cibles thérapeutiques. 5 nouveaux anticorps monoclonaux ont été générés contre une construction recombinante tronquée (AA: 206-578) de Nox4. La spécificité de 3 anticorps monoclonaux (8E9, 5F9, 6B11) a été confirmée par western blot dans les cellules HEK293 transfectées et le cortex de rein humain. L'anticorps 8E9 est le seul à permettre un marquage des cellules TRex-Nox4 sans perméabilisation par FACS. L'immunofluorescence confocale a montré que Nox4 est localisée dans la zone périnucléaire et le réticulum endoplasmique. La microscopie TIRF a confirmé sa présence dans la membrane plasmique. Un phénomène intéressant est que 5F9 ne détecte pas Nox4 à la membrane plasmique. L'épitope de 8E9 reconnaît une région sur la dernière boucle E extracellulaire de Nox4 (222H-E241), tandis que les anticorps monoclonaux, 6B11 et 5F9 marquent respectivement les régions 6B11 (389S-P416) et 5F9 (392D-F398). Par ailleurs, seuls 5F9 et 6B11 inhibent l'activité de Nox4, ce qui suggère que les deux régions marquées par ces ACm sont impliquées dans le transfert d'électrons. Une étude ciblée sur la boucle E de Nox4 a permis de montrer que le changement de 2 cystéines modifie la nature des ROS générés par Nox4 avec la production de O2- au lieu de H2O2. O2- est mis en évidence par la formation de peroxynitrite en présence de NO. Par ailleurs l'ACm 8E9 diminue la production de H2O2 dans les cellules COS7 qui expriment Nox4 à la membrane plasmique alors que celle de O2- est augmentée. Des constructions recombinantes de Nox4 (native ou tronquée) ont été générées par induction bactérienne, E.Coli, et par un système de transcription/traduction (RTS). Les protéines correspondantes, solubles, ont été produites à grande échelle et l'activité diaphorase mesurée; cette activité est constitutive. L'étude de la topologie membranaire de Nox4 et p22phox a été abordée en préparant des protéines de fusion avec l'ubiquitine marquée à la GFP. Cette méthode, TDUFA, particulièrement originale, devrait permettre d'appréhender la topologie de l'hétérodimère Nox4/p22phox, actif. / NADPH oxidase, Nox4, belongs to the Nox family which could generate reactive oxygen species by transferring an electron to molecular oxygen. Despite its wide distribution in tissues, Nox4 is still poorly understood. Unlike the other Noxes, Nox4 shows some unique characters: the constitutive activity, H2O2 formation. Nox4 involved ROS has been proposed to be implicated in several pathologies. Thus, to study the structure/function and the regulation of the activity of Nox4 will provide new ideas and new drug targets for the effective prevention and treatment of clinical diseases related with ROS. To know more about Nox4, in this study, 5 novel monoclonal antibodies were raised against a truncated recombinant protein (AA: 206-578) of Nox4. The specificity of 3 mAbs (8E9, 5F9, 6B11) was confirmed by western blot analysis in HEK293 transfected cells and human kidney cortex. In FACS studies, only mAb 8E9 could react with intact tet-induced T-RExTM Nox4 cells. Immunofluorescence confocal microscopy showed that Nox4 localized not only in the perinuclear and endoplasmic reticulum regions but also at the plasma membrane of the cells which was further confirmed by TIRF-microscopy. An interesting phenomena is that mAb 5F9 failed to detect Nox4 at the plasma membrane. Epitope determination showed that mAb 8E9 recognizes a region on the last extracellular loop of Nox4 (222H-E241), while mAb 6B11 (389S-P416) and 5F9 (392D-F398) are directed to its cytosolic tail. Cell-free oxidase assays showed a moderate but significant inhibition of constitutive Nox4 activity by mAb 5F9 and 6B11. To study the protein region which is responsible for the unique ability of Nox4 of releasing H2O2 rather than O2-, chimeric proteins and mutants were used. E-loop of Nox4 is 28 amino acid longer than that of Nox1 or Nox2. Deletion of E-loop amino acids only present in Nox4 or change of the two cysteines in the E-loop switch Nox4 from H2O2 to O2- generation. In the presence of a NO donor, the O2--producing Nox4 mutants, but not widetype Nox4, generated peroxynitrite, excluding artifacts of the detection systems as the apparent origin of O2-. A second approach was used to confirm the responsibility of E-loop for the H2O2 formation. In Cos7 cells, which exhibit some plasma membrane expression of Nox4, addition of the mAb 8E9 decreased H2O2 production but increased O2- formation. Unlike Nox1 or Nox2, the E-loop of Nox4 contains a highly conserved histidine H222. Mutation of H222 also switched Nox4 from H2O2 to O2- formation. The structure of the E-loop might hinder O2- egress and/or provide a source for protons to accelerate dismutation to form H2O2. Two bacterial protein expression approaches (in vitro RTS and bacterial induction) were used to produce Nox4 cytosolic tail for characterizing the electronic transfer property of Nox4. The presence of rare codons (1363AGA AGA CUA1371) and high level of hydrophobicity affects the production of soluble and active recombinant Nox4Aqc and Nox4Bqc. After optimization of the conditions, soluble and active recombinant proteins were obtained by RTS or by bacteria induction. The soluble proteins were produced in large scale, purified onto affinity chromatography and were tested for the diaphorase activity (INT and cytochrome c). Results showed that electronic acceptor cytochrome c gives a higher rate than INT. Nox4Aqc produced a lower specific activity by a cell-based system compared to the protein synthesized in cell-free technology. This activity is not stimulated by the addition of cytosolic factors. A new method, topological determination by ubiquitin fusion assay (TDUFA), was used to investigate the topology of Nox4 and p22phox. ubGFP fusion proteins are used as tools to obtain details of membrane protein topology. This method was first validated by using two membrane proteins with known topology and then should get more topology information of Nox4 and p22phox further.

Since a proper balance between anabolic and catabolic reactions is essential for all eukaryotes, the basic mechanisms for regulation of the energy and carbon metabolism have been conserved throughout evolution. The moss Physcomitrella patens, which belongs to one of the basal clades among land plants, has many unique properties that make it an excellent plant model system. We have used a yeast two-hybrid system to identify novel possible regulators or targets of the moss Snf1-related kinases, previously shown to regulate energy homeostasis. The function of the identified interactors PpSki1 and PpSki2 was analyzed in order to better understand the biological role of plant Snf1-related kinases. The recently completed genome sequence of Physcomitrella was used in a comparative approach to study to what extent key enzyme and gene families involved in transport and metabolism of sugars and in regulation of the energy and carbon metabolism are conserved between mosses and vascular plants. It has long been known that transformed DNA can replicate episomally in Physcomitrella. We have now shown that such DNA can be rescued back into E. coli. Surprisingly, we found that the original plasmid can be recovered from moss transformants obtained with circular DNA. Plasmids rescued from transformants obtained with linearized DNA had been repaired either by homologous recombination or by cohesive end re-ligation. These findings suggest that methods using shuttle plasmids are feasible in Physcomitrella. Hexokinase, a key enzyme in the carbon metabolism, catalyzes the first step in hexose metabolism, but is also involved in sugar sensing and signaling. We have now made an initial characterization of the complete hexokinase family in Physcomitrella which is encoded by 11 genes. Two new types of plant hexokinases, types C and D, were found in addition to the previously described types A and B.

Until recently, the main mechanism of argininosuccinate synthase (AS) regulation was described to exist mainly at the level of transcription. Transcriptional regulation of AS has been shown to be coordinate with eNOS in response to shear stress, hypoxia, tumor necrosis factor á (TNF-á), and PPAR ã agonist troglitizone. However, it is now understood that one level of NO regulation is cellular control of arginine availability to eNOS via post-translational modifications of AS such as phosphorylation. The purpose of this investigation was to determine under what conditions AS is phosphorylated at S328, identify the pathway that AS phosphorylation at S328 plays a role, and how phosphorylation affects AS function in endothelial cells. We developed a phospho-specific antibody directed against pS328 AS and assayed for increases or decreases in phosphorylation relative to physiological factors. We found that AS phosphorylation at S328 occurred when endothelial cells were stimulated with physiological factors that stimulate nitric oxide production through calcium-dependent stimulation of eNOS. Furthermore, by utilizing kinase inhibitors and kinase knockdown experiments, we showed that phosphorylation at S328 significantly decreased when PKCá was knocked down, suggesting that S328 phosphorylation of AS is involved in PKCá signaling. In addition, by confocal microscopy, immunoprecipitation, and membrane fractionation, we showed that phosphorylation at S328 of AS promotes its co-localization with eNOS in the perinuclear region. These findings describe a novel pathway involving AS regulation of nitric oxide production, and may serve as a novel drug target in the restoration of vascular nitric oxide homeostasis.

The fundamental goal of proteomics is to gain an understanding of the expression and function of the proteome on the level of individual proteins, on the level of defined cell types and on the level of the entire organism. In this thesis, the human proteome is explored using membrane protein topology prediction methods to define the human membrane proteome and by global protein expression profiling, which relies on a complex study of the location and expression levels of proteins in tissues and cells. A whole-proteome analysis was performed based on the predicted protein-coding genes of humans using a selection of membrane protein topology prediction methods. The study used a majority decision-based method, which estimated that approximately 26% of the human genes encode for a membrane protein. The prediction results are displayed in a visualization tool to facilitate the selection of antigens to be used for antibody generation. Global protein expression profiles in a large number of cells and tissues in the human body were analyzed for more than 4000 protein targets, based on data from the antibody-based immunohistochemistry and immunofluorescence methods within the framework of the Human Protein Atlas project. The results revealed few cell-type specific proteins and a high fraction of human proteins expressed in most cells, suggesting that cell and tissue specificity is attained by a fine-tuned regulation of protein levels. The expression profiles were also used to analyze the relationship between 45 cell lines by hierarchical clustering and principal component analysis. The global protein expression patterns overall reflected the tumor origin of the cells, and also allowed for identification of proteins of importance for distinguishing different categories of cell lines, as defined by phenotype of progenitor cell. In addition, the protein distribution in 16 subcellular compartments in three of the human cell lines was mapped. A large fraction of proteins were localized in two or more compartments and, in line with previous results, a majority of proteins were detected in all three cell lines. Finally, mass spectrometry-based protein expression levels were compared to RNA-seq-based transcript expression levels in three cell lines. Highly ubiquitous mRNA expression was found and the changes of expression levels between the cell lines showed high correlations between proteins and transcripts. Large general differences in abundance of proteins from various functional classes were observed. A comparison between categories based on expression levels revealed that, in general, genes with varying expression levels between the cell lines or only expressed in one cell line were highly enriched for cell-surface proteins. These studies show a path for a systematic analysis to characterize the proteome in human cells, tissues and organs. / QC 20110317 / The Human Protein Atlas project

Machine learning techniques have been widely used for classification problems in computational biology. They require that the input must be a collection of fixedlength feature vectors. Since proteins are of varying lengths, there is a need for a means of representing protein sequences by a fixed-number of features. This thesis introduces three novel methods for this purpose: n-peptide compositions with reduced alphabets, pairwise similarity scores by maximal unique matches, and pairwise similarity scores by probabilistic suffix trees. New sequence representations described in the thesis are applied on three challenging problems of computational biology: remote homology detection, subcellular localization prediction, and solvent accessibility prediction, with some problem-specific modifications. Rigorous experiments are conducted on common benchmarking datasets, and a comparative analysis is performed between the new methods and the existing ones for each problem. On remote homology detection tests, all three methods achieve competitive accuracies with the state-of-the-art methods, while being much more efficient. A combination of new representations are used to devise a hybrid system, called PredLOC, for predicting subcellular localization of proteins and it is tested on two distinct eukaryotic datasets. To the best of author&rsquo / s knowledge, the accuracy achieved by PredLOC is the highest one ever reported on those datasets. The maximal unique match method is resulted with only a slight improvement in solvent accessibility predictions.

En tant qu’acteurs moléculaires impliqués dans le transport d’eau au travers des membranes biologiques, les aquaporines (AQP) jouent un rôle et sont régulées en réponse à des stress. Ils sont soumis à d’intenses recherches, en particulier chez le riz. En utilisant une approche de génomique fonctionnelle, nous avons généré 5 lignées transgéniques de riz dans le fond génétique Nipponbare, en sur-exprimant des AQP uniques fusionnées à un marqueur fluorescent ; parmi celles-là, figurent trois AQP de la membrane plasmique (OsPIP1;1, OsPIP2;4, OsPIP2;5) fusionnées à la GFP et deux AQP de la membrane tonoplastique (OsTIP1;1 and OsTIP2;2) fusionnées à la mCherry. Leurs localisations subcellulaires en condition contrôle ont été observées. Chez le riz, les isoformes OsPIP présentaient un marquage homogène typique de la membrane plasmique, tandis que les isoformes OsTIP ont été trouvées avec un marquage des invaginations intracellulaires qui entourent le noyau, typique du tonoplaste. Le comportement des AQP de la membrane plasmique a été testé en conditions de stress salin et osmotique. Les stress abiotiques ont provoqué une relocalisation des AQP et le stress salin a augmenté l’endocytose de l’isoforme OsPIP2;5 dans les cellules de la racine. Par ailleurs, la sur-expression de tels transgènes ne semblait pas affecter la morphologie des plantes et ne conférait pas un effet bénéfique sur la production de graines, aussi bien en condition contrôle que stressée. Enfin, nous nous sommes focalisés sur la contribution des AQP dans la racine de riz en relation avec la morphologie racinaire. Nous avons trouvé que les AQP contribuaient à un pourcentage relativement important dans le transport de l’eau dans la racine entière (44-58%) et que cette contribution semblait plus importante dans les racines primaires que latérales. / As molecular players involved into the water transport through biological membranes, aquaporins (AQPs) have a role and are regulated in stress response. They were deeply investigated in plants and particularly in rice. Using functional genetic approach, we generated 5 transgenic rice lines based on Nipponbare cultivar, by overexpressing a single AQP in fusion with a fluorescent marker; among them, 3 plasma membrane AQPs (OsPIP1;1, OsPIP2;4, OsPIP2;5) fused with GFP and 2 tonoplast AQPs (OsTIP1;1 and OsTIP2;2) fused with mCherry. Their subcellular localizations in resting condition were investigated. In rice, OsPIP isoforms showed typical homogeneous labelling of the plasma membrane, whereas OsTIP isoforms were observed localized in the tonoplast with a typical labelling of intracellular invaginations that skirted the nucleus. The behaviors of plasma membrane AQPs were tested in salt and drought stress-mimicked-conditions. Abiotic stresses triggered a re-localization of plasma membrane AQPs and salt stress enhanced endocytosis process of OsPIP2;5 in rice root cells. Overexpressing such transgenes did not seem to affect the plant morphology and showed no beneficial effects for grain yield in both non-stress and stress conditions. We took more focus on the contribution of AQPs in rice root water transport in link with root morphology. AQPs contributed a relative high percentage of water transport in whole root system (44-58%) and seemed to contribute more in primary roots rather than in lateral roots.

No description available.

SABP2-interacting protein 470 (SIP470), a non-specific lipid transfer protein (nsLTP), was discovered in a yeast two-hybrid screening using SABP2 as bait and tobacco leaf proteins as prey. SABP2 is an important enzyme in systemic acquired resistance that converts salicylic acid to methyl salicylate. Localization studies are an important aspect to understanding the biological function of proteins. nsLTPs are generally considered apoplastic proteins and has been localized intracellularly and extracellularly. Transient expression shows highest expression of SIP470-eGFP at 2 days post infiltration into Nicotiana benthamiana. Confocal microscopy showed localization near the periphery of the cell. Subcellular localization using differential centrifugation showed that SIP470 is localized in the mitochondria. Mitochondria membranes are rich in lipids and have shown lipid exchange with the endoplasmic reticulum in mammalian systems. Co-localization of SIP470-eGFP+mCherry did not express complete co-localization in the targeted organelles. Co-localization pattern suggests possible localization in the endoplasmic reticulum.

Anthracene was attached to light activated, ruthenium-based DNA disruptors to probe their distribution in cancer cells. The objective of this research is to understand the photophysical properties (Chapter 2), photoreactivity toward DNA and proteins (Chapter 3), and localization within cancer cells (Chapter 4) of ruthenium complexes that demonstrate promise as photodynamic therapy (PDT) agents. [(AnthbpyMe)(bpy)Ru(dpp)]2+ (1) and [(AnthbpyMe)2Ru(dpp)]2+ (2) absorb visible light with metal-to-ligand charge transfer (MLCT) transitions at 459 nm (16,000 M-1 cm-1 ) and 461 nm (21,000 M-1 cm-1 ), respectively. These species exhibit 3 MLCT emissions at λem = 661 nm and λem = 663 nm for 1 and 2, respectively, while the anthracene show emissions at 450 – 560 nm. The anthracene unit(s) quench the 3 MLCT to give quantum yields (lifetime) of Φem = 0.0059 [398(1) ns] and Φem = 0.0011 [414(1) ns] for 1 and 2, respectively. Voltammetry shows an irreversible anthracene oxidation at 1.23 – 1.28 V, RuIII/II oxidation at 1.53 – 1.55 V, and quasi-reversible reduction couples attributed to dpp0/-1 at 0.98 V. DNA gel shift assays demonstrate that complexes 1 and 2 modify DNA in the presence and absence of 3 O2 upon light activation to convert supercoiled DNA to a mixture of open circular (OC) DNA and a species that exhibit sa distinctly different migration rate than either OC and linear DNA. Binding constants, Kb, for complexes 1 and 2, toward DNA are 3.50 × 105 (3.50 × 104 ) and 4.50 × 103 (4.50 × 102 ) respectively. SDS-PAGE assays show that the complexes 1 and 2 modify bovine serum albumin (BSA) through an 3 O2-dependent mechanism upon light iii activation. The localization and PDT potency of the anthracene-Ru-dpp complexes are tested against F98 cells, which are rat glioma cells that simulate the infiltrative patterns of growth in cancer. Confocal microscopy demonstrates that complexes 1 and 2 internalize and localize primarily along the cell membrane and associate with dot-like vesicles within the cytoplasm. Complexes 1 and 2 show IC50 values of 107 µM and 85 µM, respectively, after 15 min of drug exposure and 1 h of PDT-treatment (λPDT = 455 nm). / Ph. D.

Chez les eucaryotes, la voie de protéolyse Ub/ protéasome 26S est responsable de la dégradation sélective de la plupart des protéines intracellulaires. Cette dégradation par le protéasome 26S est initiée par une polyubiquitination de la protéine réalisée grâce à l’action d’une cascade enzymatique impliquant 3 types d'enzymes nommées « ubiquitin-activating enzyme » (E1), « ubiquitin-conjugating enzyme » (E2) et « ubiquitin-protein ligase » (E3). Il existe différentes classes d’ubiquitines ligases (E3), parmi lesquelles la plus connue est le complexe SCF (Skp1-Cullin-F-box). La protéine SKP1 fixe à la fois la Culline et la F-box qui va reconnaitre spécifiquement la protéine cible. Contrairement aux protistes, les champignons et certains vertébrés qui possèdent un unique gène SKP1 fonctionnel, de nombreux animaux et espèces de plantes présentent plusieurs SKP1 homologues. Vingt et un et trente deux gènes SKP1 ont été décrits respectivement chez Arabidopsis thaliana et Oryza sativa. En dépit de l’importance du complexe SCF, chez le riz, peu de travaux décrivent les interactions entre les dizaines de protéines « SKP1-like » et les centaines de protéines F-box. Dans un premier temps, nous avons collecté et analysé les séquences de 288 gènes « SKP1-like » appartenant à 17 espèces, dont la mousse Physcomitrella patens, cinq monocotylédones et 11 eudicotylédones. Les analyses structurales et phylogénétiques de ces gènes indiquent qu’ils peuvent être divisés en différentes sous-familles. Nos analyses ont montré qu’OSK1 et OSK20 chez le riz constituent une classe de gènes SKP1 à intron unique conservé. Dans un deuxième temps, nous avons étudié le profil d’expression des gènes « SKP1-like » chez le riz. Notre investigation sur le nombre d’EST a montré que les gènes OSK1 et OSK20 sont les plus largement représentés dans les bases de données EST publiques. La méta-analyse de l’expression des gènes « SKP1-like » chez le riz, indique que les gènes OSK présentent des profils d'expression hétérogènes selon les tissus et les conditions physiologiques. Les résultats des intearctions protéine-protéine en double hybride ont révélé que les protéines OSK présentent différentes capacités d’interactions avec les protéines F-box. Cependant, OSK1 et OSK20 semblent interagir avec la plupart des protéines F-box testées. Les études de localisation subcellulaire ont indiqué que OSK1 et OSK20 sont des protéines nucléaires et cytosoliques. En se basant sur les divers résultats obtenus dans ce travail, nous pouvons suggérer que chez le riz, les gènes OSK1 et OSK20 sont fonctionnellement équivalents aux gènes ASK1 et ASK2 chez Arabidopsis thaliana. Nous pouvons également proposer les équivalents de ces gènes chez les autres espèces végétales dont le génome a été séquencé. / In eukaryotes, the ubiquitin Ub/26S proteasome pathway is responsible for the selective degradation of most intracellular proteins. This cellular process is initiated by protein polyubiquitination mediated by a three-step cascade involving: an ubiquitin-activating enzyme (E1), an ubiquitin-conjugating enzyme (E2) and an ubiquitin-protein ligase (E3). The E3 ubiquitin ligases contain several classes, among which the best-known are Skp1-Cullin-F-box (SCF) complexes. The SKP1 protein binds both Cullin and F-box which recognizes specifically the target proteins. Whereas protists, fungi and some vertebrates have a single functional SKP1 gene, many animal and plant species possess multiple SKP1 homologues. Twenty one and thirty-two SKP1-related genes have been described respectively in the Arabidopsis and Oryza sativa genome. Despite the importance of the SCF complex, there have been a few reports of systematic surveys of interactions between the dozens of SKP1-like proteins and the hundreds of F-box proteins in rice. In a first step, we retrieved and analyzed 288 SKP1-like genes belonging to 17 species including the moss Physcomitrella patens, five monocots and 11 eudicots. Structural and phylogenetic analysis of rice OSK genes and other plant SKP1-like genes have indicated that the different members of the plant SKP1 can be split into different subfamily. Our analyses indicated that OSK1 and OSK20 belong to a class of SKP1 genes that contain one intron at a conserved position. In a second step, we studied expression profiles of the rice Skp1-like genes. Our EST survey indicated that OSK1 and OSK20 are the most widely represented genes in public EST databases. Meta-analysis of the expression of rice SKP1-like genes indicated that OSK genes exhibit an expression profile that was heterogeneous in terms of tissues, conditions and overall intensity. Yeast two-hybrid results revealed that OSK proteins display a differing ability to interact with F-box proteins. However, OSK1 and OSK20 seemed to interact with most F-box proteins tested. Subcellular localization studies indicated that OSK1 and OSK20 are nuclear and cytosolic proteins. Based on the results obtained in this study, we can suggest that rice OSK1 and OSK20 are likely to have similar functions as do the Arabidopsis ASK1 and ASK2 genes. Similarly, we suggest a list of functional equivalent in the other sequenced plant genomes.