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Soybean mosaic virus (SMV), has been the cause of numerous and often devastating disease epidemics, causing reduction in both the quality and quantity of soybeans worldwide. Two important genes for resistance to SMV are Rsv1 and Rsv4. Alleles at the Rsv1 locus have been shown to control resistance to all but the most virulent strain of SMV. This locus has been mapped previously to the soybean F linkage group. Rsv4 is an SMV resistance locus independent of Rsv1 and confers resistance to all strains of SMV. This locus has not been mapped previously. The purpose of this study is to investigate the two genomic regions that contain these vitally important resistance genes. A population of 281 F2 individuals that had previously been genotyped for reaction to SMV was evaluated in a mapping study which combined bulk segregant analysis with Amplified Fragment Length Polymorphism (AFLP). A Rsv4-linked marker, R4-1, was identified that mapped to soybean linkage group D1b using a reference mapping population. More than 40 markers were mapped in the Rsv4 segregating population including eleven markers surrounding Rsv4. This will provide the necessary framework for the fine mapping of this important genetic locus. Previous work has located Rsv1 to a genomic region containing several important resistance genes including Rps3, Rpg1, and Rpv. An RFLP probe, NBS5, whose sequence closely resembles that of several cloned plant disease resistance genes has been mapped to this chromosomal region. The efficacy of using this sequence to identify potential disease resistance genes was assessed by screening a cDNA library to uncover a candidate disease resistance gene which corresponds to this NBS5 sequence. Two related sequence classes were identified that correspond to NBS5. Interestingly, one class corresponds to a full length gene closely resembling other previously cloned disease resistance genes offering evidence that this NBS5-derived clone is a candidate disease resistance gene. A new marker technique was developed by combining the speed and efficiency of AFLP with DNA sequence information from cloned disease resistance genes. Using this strategy, three new markers tightly linked to Rsv1 were identified. One of these markers, which maps 0.6 cM away from Rsv1, has motifs consistent with other cloned disease resistance genes, providing evidence that this approach is an efficient method for targeting genomic regions where disease resistance genes are located. / Ph. D.

Le cancer papillaire de la thyroïde (CPT) est la tumeur endocrine la plus fréquente. Des anomalies moléculaires activant la voie des MAPK (Mitogen-Activated Protein Kinases) sont identifiées, de façon mutuellement exclusive, dans environ 70% des cas. Il s’agit de réarrangements chromosomiques, le plus souvent de type RET/PTC (10%), de mutations ponctuelles activatrices des trois isoformes de l’oncogène RAS (H, N et K-RAS) (10%), ou de l’oncogène B-RAF (50%). La mutation « hot spot » B-RAFV600E est la plus fréquemment identifiée, elle est associée à une plus grande agressivité clinique (diagnostic à un stade tardif, risque de récidives et de décès accru). Ces évènements moléculaires ont pour conséquence commune l’activation de la voie des MAPK, se traduisant en aval par la phosphorylation de MEK (Mitogen-activated Extracellular signal-Regulated Kinase) puis de ERK (Extracellular signal-Regulated Kinase). Cette dernière est régulée négativement par des phosphatases, appartenant à la famille des Dual Specificity Phosphatases (DUSPs), d’expression ubiquitaire, et en particulier de deux phosphatases spécifiques de ERK, l’une cytoplasmique (DUSP6) et l’autre nucléaire (DUSP5). Nous avons fait l’hypothèse que ces phosphatases pouvaient être soit des gènes suppresseurs de tumeurs (leur perte d’expression conduisant à une augmentation de phosphorylation de ERK et une prolifération accrue), soit des marqueurs du degré d’activation de la voie MAPK dans le cadre d’une boucle de rétrocontrôle négatif. Ceci nous a conduits à analyser la régulation et l’expression de ces phosphatases dans trois modèles : la lignée cellulaire PCCL3 (thyroïde de rat), exprimant l’un des trois principaux oncogènes mutés dans les CPT (RET/PTC3 ou H-RASV12 ou B-RAFV600E) sous le contrôle d’un promoteur inductible par la doxycycline, des lignées cellulaires humaines dérivant de CPT et des CPT humains. (...) / Papillary thyroid cancer (PTC) is the most common endocrine malignancy. Mutually exclusive and activating alterations of the MAPK pathway (Mitogen-Activated Protein Kinases) are identified in 70% of cases. Common mutations found in PTCs are point mutation of the B-RAF (50%) and RAS genes (10%) as well as RET/PTC chromosomal rearrangements (10%). The hot spot B-RAFV600E mutation is the most frequently alteration identified and is connected with agressive clinical characteristics (high stage at diagnosis, high recurrence risk and death). These molecular events lead to constitutive activation of the MAPK pathway, resulting in MEK (Mitogen-activated Extracellular signal-Regulated Kinase) and ERK (Extracellular signal-Regulated Kinase) phosphorylation. ERK is negatively regulated by phosphatases and among them, Dual Specificity Phosphatases (DUSPs), ubiquitary expressed, in particular two ERK-specific phosphatases DUSP5 (nuclear) and DUSP6 (cytosolic). We hypothesized that these phosphatases could have tumor supressor properties (i.e. their loss would be associated with an increase in MAPK pathway activation) or may serve as a surrogate marker of MAPK pathway activation in the context of a negative feedback loop. We analysed regulation and expression of both phosphatases in 3 models: three PCCL3 cell lines (rat thyroid cells) expressing one of the most common oncogene identified in PTCs (RET/PTC3 or H-RASV12 or B-RAFV600E) under the control of a doxycycline-inducible promoter, human PTC-derived cell lines and human PTC. We demonstrated that MAPK pathway activation was correlated with induction of DUSP5 and DUSP6. These phosphatases are involved in a negative feedback loop that contributes to a tight regulation of phospho-ERK levels. DUSP5 and DUSP6 mRNA are overexpressed in human PTCs, especially in B-RAF mutated tumors suggesting a higher MAPK signaling output in these agressive PTCs. Silencing of DUSP5 and/or DUSP6 by small interfering RNA does not affect proliferation of human B-RAFV600E thyroid carcinoma-derived cell lines, suggesting the lack of tumor suppressor gene role. Compensatory changes in expression of DUSPs when a specific one is inactivated may explain this lack of effect. On the opposite, a DUSP6 pharmacological inhibitor induced a concentration dependent decrease in proliferation of human B-RAFV600E cells, suggesting « off-target » effect of this inhibitor. In a second part, we analysed the regulation of DUSP5 expression, which is a target of the MAPK pathway activation. We demonstrated, using pharmacological inhibitors, that DUSP5 is an early response gene, regulated mostly by the MAPK pathway, at the transcriptional level. Two contiguous CArG boxes that bind serum response factor (SRF) were found in a 1Kb promoter region, as well as several E twenty-six transcription factor family binding sites (EBS). These sites potentially bind Elk-1, a transcription factor activated by ERK1/2. Using wild type or mutated DUSP5 promoter reporters, we demonstrated that SRF plays a crucial role in serum induction of DUSP5 promoter activity, the proximal CArG box being important for SRF binding in vitro and in living cells. Moreover Elk-1 was bound in vitro to a promoter region containing the proximal CArG box and a putative EBS. Its specific binding to SRF was necessary to elicit promoter response to dominant positive Elk-VP16 and to enhance the response to serum stimulation. Altogether our results suggest that the MAPK pathway is more active in B-RAFV600E PTC than in PTC with other genetic alteration and could explain their clinical agressivity. DUSP5 and DUSP6, as well as phosphorylated MEK, are markers of activation of the MAPK pathway. Neither phosphatase has tumor suppressor properties in our thyroid cancer cell models. Our results suggest redundancy and functional compensation among DUSPs. (...)

The chloride/proton antiporter ClC-5 is primarily expressed in the kidney where it aids in re-absorption of proteins from the glomerular filtrate. Functional disruption of ClC-5 causes Dent’s Disease – a renal condition characterized by proteinuria and kidney failure in a third of all cases. The majority of disease-causing mutations translate into premature truncations of the carboxy-terminal (Ct) region of ClC-5 and are predicted to disrupt the protein-protein interactions mediated by this domain. In this thesis, direct ATP binding to the two cystathionine β-synthase (CBS) domains of ClC-5 was demonstrated. ATP binding enhanced the global compactness of the ClC-5 Ct region likely through a clamping motion of the CBS domains around the nucleotide. Along with ATP, the sodium proton exchange regulatory factor 2 (NHERF2) also binds ClC-5; however, the molecular mechanism behind this interaction was unknown as ClC-5 lacked the PDZ binding motif traditionally localized at the Ct end of bait proteins. Here, we also identified a class I PDZ binding motif (657-660; TSII) within the internal sequence of ClC-5. Despite the buried position of this motif in the Ct peptide’s X-ray crystal structure (PDB: 2J9L), the high propensity of this region for dynamic flexibility prompted us to test whether it could mediate NHERF2 interactions. In support of this hypothesis, we demonstrated that the motif is transiently available to interact directly with NHERF2 in vivo and to enable an enhancement in receptor-mediated endocytosis in mammalian cells. Collectively, these results gave further evidence that the intracellular Ct region of ClC-5 serves as a hub to mediate interactions essential for its maturation, stability, and trafficking in renal epithelium, as well as providing further insights into the molecular basis of Dent’s Disease.

Das SurA-Protein ist ein wichtiger Bestandteil der periplasmatischen Faltungsmaschinerie aus Escherichia coli. Trotz zahlreicher Erkenntnisse sind die Mechanismen der Substraterkennung und -bindung noch nicht abschließend geklärt. Das SurA-Protein ist aus einem Chaperonmodul und zwei PPIase-Domänen aufgebaut. Die Bindestelle eines artifiziellen Peptides wurde zu Beginn der Arbeit in der PPIase-inaktiven Parvulin-Domäne I publiziert. Im Rahmen dieser Arbeit wurde untersucht, ob auch biologisch relevante, natürliche Peptide an dieser Bindestelle interagieren und ob es noch weitere Substratbindestellen innerhalb von SurA gibt. In ESR-spektroskopischen Versuchen wurde die Interaktion der isolierten Parvulin-Domäne I von SurA mit Peptiden aus einer LamB-Peptid-Bibliothek, sowie mit dem artifiziellen Peptid analysiert. Die Bindung des artifiziellen Peptides und eines Peptides aus der LamB-Peptid-Bibliothek an die isolierte Parvulin-Domäne I konnte nachgewiesen werden. Für weitere an SurA-bindende Peptide konnte an dieser Position keine Interaktion nachgewiesen werden. Mittels des genetischen Indikatorsystems ToxR wurden gezielt Kontaktpunkte zwischen dimerisierten SurA-Untereinheiten bzw. zwischen SurA und Peptid unterbunden, um deren Einfluss auf die wechselseitige Interaktion zu untersuchen. Hierbei wurden einzelne Positionen in isolierten SurA-Domänen identifiziert, die an einer Interaktion beteiligt sind. Die Mutation dieser Interaktionsstellen führten zu keinem signifikanten Verlust der in vivo-Funktion, welche mittels der Fähigkeit der SurA-Varianten zur Komplementation des synthetisch letalen Phänotypen einer surA skp-Doppelmutante untersucht wurde. Die Grundlagen für die Methodik der photoaktivierbaren, ortsspezifischen Quervernetzung von OMP-Polypeptiden an SurA- bzw. SurAI-Proteine wurden etabliert. / The SurA protein is an important part of the periplasmic folding machinery in Escherichia coli. Despite numerous findings are the mechanisms of substrate recognition and folding not yet completely resolved. The SurA protein consists of a chaperone module and two parvulin domains. In the beginning of this work a peptide binding site was published which was located in the PPIase inactive parvulin domain I. It was investigated in this thesis whether biological relevant, natural peptides would also bind with this binding site and if additional substrate binding sites exist within the SurA protein. In ESR-spectroscopy experiments both the interaction of the isolated parvulin domain I of SurA with peptides of a LamB peptide library and with the artificial peptide were examined. Binding of the artificial peptide and one peptide of the LamB peptide library to the isolated parvulin domain I could be detected. For the remaining tested peptides, which are confirmed to be SurA binders, no interaction could be verified at this position. By use of the genetic indicator system ToxR the contact points between dimerized SurA subunits respectively between SurA and peptide were prevented site-specifically to examine their influence on the mutual interaction. Here single positions in isolated SurA-domains were identified, which are part of an interaction. The mutation of these interaction sites lead to no significant loss of the in vivo function, which was analyzed by the capability of the SurA variants to complement the synthetic lethal phenotype of a surA skp double mutant. The fundamentals for the method of photoactivated site-specific crosslinking of OMP polypeptides to SurA respectively SurAI were established.

<p>OVARIAN cancer research focuses on answering important questions related to the disease, determining whether new approaches are feasible to contribute towards improving current treatments or discovering new ones. This study focused on the transcriptional regulation of genes that have been implicated in ovarian cancer, based on the occurrences of single nucleotide polymorphisms (SNPs) within transcription factor binding sites (TFBSs). Through the application of several in silico tools, databases and custom programs, this research aimed to contribute toward the identification of potentially bio-medically important genes or SNPs for pre-diagnosis and subsequent treatment planning of ovarian cancer. A total of 379 candidate genes that have been experimentally associated with ovarian cancer were analyzed. This led to the identification of 121 SNPs that were found to coincide with putative TFBSs potentially influencing a total of 57 transcription factors that would normally bind to these TFBSs. These SNPs with potential phenotypic effect were then evaluated among several population groups, defined by the International HapMap consortium resulting in the identification of three SNPs present in five or more of the eleven population groups that have been sampled.</p>

Protein-protein and protein-ligand interactions are fundamental as many proteins mediate their biological function through these interactions. Many important applications follow directly from the identification of residues in the interfaces between protein-protein and protein-ligand interactions, such as drug design, protein mimetic engineering, elucidation of molecular pathways, and understanding of disease mechanisms. The identification of interface residues can also guide the docking process to build the structural model of protein-protein complexes. This dissertation focuses on developing computational approaches for protein-ligand and protein-protein binding site prediction and applying these predictions to improve protein-protein docking. First, we develop an automated approach LIGSITEcs to predict protein-ligand binding site, based on the notion of surface-solvent-surface events and the degree of conservation of the involved surface residues. We compare our algorithm to four other approaches, LIGSITE, CAST, PASS, and SURFNET, and evaluate all on a dataset of 48 unbound/bound structures and 210 bound-structures. LIGSITEcs performs slightly better than the other tools and achieves a success rate of 71% and 75%, respectively. Second, for protein-protein binding site, we develop metaPPI, a meta server for interface prediction. MetaPPI combines results from a number of tools, such as PPI_Pred, PPISP, PINUP, Promate, and SPPIDER, which predict enzyme-inhibitor interfaces with success rates of 23% to 55% and other interfaces with 10% to 28% on a benchmark dataset of 62 complexes. After refinement, metaPPI significantly improves prediction success rates to 70% for enzyme-inhibitor and 44% for other interfaces. Third, for protein-protein docking, we develop a FFT-based docking algorithm and system BDOCK, which includes specific scoring functions for specific types of complexes. BDOCK uses family-based residue interface propensities as a scoring function and obtains improvement factors of 4-30 for enzyme-inhibitor and 4-11 for antibody-antigen complexes in two specific SCOP families. Furthermore, the degrees of buriedness of surface residues are integrated into BDOCK, which improves the shape discriminator for enzyme-inhibitor complexes. The predicted interfaces from metaPPI are integrated as well, either during docking or after docking. The evaluation results show that reliable interface predictions improve the discrimination between near-native solutions and false positive. Finally, we propose an implicit method to deal with the flexibility of proteins by softening the surface, to improve docking for non enzyme-inhibitor complexes.

<p>OVARIAN cancer research focuses on answering important questions related to the disease, determining whether new approaches are feasible to contribute towards improving current treatments or discovering new ones. This study focused on the transcriptional regulation of genes that have been implicated in ovarian cancer, based on the occurrences of single nucleotide polymorphisms (SNPs) within transcription factor binding sites (TFBSs). Through the application of several in silico tools, databases and custom programs, this research aimed to contribute toward the identification of potentially bio-medically important genes or SNPs for pre-diagnosis and subsequent treatment planning of ovarian cancer. A total of 379 candidate genes that have been experimentally associated with ovarian cancer were analyzed. This led to the identification of 121 SNPs that were found to coincide with putative TFBSs potentially influencing a total of 57 transcription factors that would normally bind to these TFBSs. These SNPs with potential phenotypic effect were then evaluated among several population groups, defined by the International HapMap consortium resulting in the identification of three SNPs present in five or more of the eleven population groups that have been sampled.</p>