Em procariotos, a principal forma de reprodução é a divisão binária, que permite à célula-mãe dar origem a duas outras células-filhas, com conteúdo genético idêntico ao da progenitora. Em Bacillus subtilis este processo acontece graças ao divisomo, um complexo formado por aproximadamente dezesseis proteínas, que leva à constrição da membrana e da parede, formando o septo de divisão. A montagem do divisomo é coordenada por FtsZ, um homólogo de tubulina, que polimeriza na região central da bactéria e serve de arcabouço para a montagem do divisomo. Partindo de um levantamento detalhado da distribuição dos genes envolvidos em divisão em genomas completos de procariotos detectamos que divIVA, um gene de divisão já bem caracterizado, apresentava um gene parálogo em B. subtilis, conhecido como ypsB. Para determinarmos se YpsB seria um novo componente do divisomo foi realizada uma caracterização citológica e funcional desta proteína. Utilizamos microscopia de fluorescência e fusões de YpsB a GFP para determinar a localização subcelular de YpsB. Estes experimentos revelaram que YpsB está presente no divisomo, apresentando um padrão de localização semelhante mas não idêntico ao de DivIVA. Medindo-se a taxa de co-localização entre o anel Z e YpsB ficou demonstrado que estas proteínas co-localizam em aproximadamente 50%, sugerindo que YpsB é recrutada depois que o anel Z é montado. Para determinar quando YpsB chega ao divisomo, usamos mutantes termo-sensíveis das proteínas de divisão que revelaram a dependência de YpsB pelo sub complexo DivIB-DivIC-FtsL-FtsW-PBP2B. Já na ausência de DivIVA, YpsB continua associado ao divisomo, indicando que não depende do seu parálogo para localizar. Além disso, análises de deleções de YpsB mostraram que a porção N-terminal da proteína é a mais importante para o seu recrutamento ao divisomo. Para determinarmos o papel de YpsB durante a divisão foi construído um mutante com deleção completa do gene. DivIVA é uma proteína responsável por localizar o sistema Min nos pólos da bactéria e assim contribui para a precisão espacial da divisão. Apesar de serem parálogos, a função de YpsB, no entanto, parece ser diferente da de DivIVA. Análise do mutante ypsB- mostrou que na sua ausência, o divisomo é montado e o seu posicionamento tanto em fase vegetativa como em esporulação não são afetados. Como a ausência de YpsB não afeta perceptivelmente a divisão, combinamos a mutação em ypsB com mutações em outros genes envolvidos em divisão. A análise destes duplos mutantes revelou que a ausência simultânea de YpsB e FtsA produz exacerbada lise celular e letalidade. Com base neste fenótipo e em evidências evolutivas, sugerimos que YpsB esteja envolvida na regulação da síntese de peptideoglicano do septo. Mais especificamente, YpsB seria responsável por modular a atividade de PBP1, uma enzima necessária para a síntese de peptideoglicano septal. / In prokaryotes, the main form of reproduction is binary fission, which allows the mother-cell to give origin the two daughter-cells, with identical genetic material. In Bacillus subtilis, this process is performed by the divisome, a complex formed for approximately sixteen proteins that leads to the constriction of the membrane and the wall, creating the division septum. The assembly of the divisome is coordinated by FtsZ, a homolog of tubulin, that polymerizes in the central region of the bacteria and serves as the base for the assembly of the divisome. From a detailed survey of the distribution of the genes involved in division in complete genomes of prokaryotes, we detected that divIVA, a well characterized division gene, showed a paralog in B. subtilis, known as YpsB. To determine if YpsB would be a new component of the divisome, a cytological and functional characterization of this protein was carried out. We used fluorescence microscopy and fusion of YpsB to GFP to determine the subcellular localization of YpsB. These experiments displayed that YpsB is present in the divisome, with similar but not identical localization as DivIVA. Measuring co-localization between the Z ring and YpsB demonstrated that this happened in approximately 50% of the cells, suggesting that YpsB go to the divisome after the Z ring is formed. To determine when YpsB goes to the divisome, we used temperature-sensitive mutants of the division proteins. This showed that YpsB depends on the DivIB-DivIC-FtsL-FtsW-PBP2B sub-complex to associate with the divisome. In the absence of DivIVA, YpsB is still present in the divisome, indicating that it does not depend on its paralog to localize. Moreover, deletion analyses of YpsB showed that the N-terminal portion of the protein is the most important for its recruitment to the divisome. To determine the role of YpsB during division, we constructed a ypsB- mutant. DivIVA is the protein responsible for localization of the Min system in polar regions of B. subtilis and, thus, contributes for the spatial precision of division. Our results showed that the function of YpsB must be different from that of DivIVA, since analysis of the ypsB- mutant showed that in the absence this protein the divisome is assembled and septum position in vegetatively growing or sporulating cells is not affected. Since the absence of YpsB does not affect division, we combined the ypsB- mutant with mutants involved in division. Analysis of these double mutants showed that the simultaneous absence of YpsB and FtsA caused cellular lysis and lethality. Based on this phenotype and evolutionary evidences, we suggest that YpsB is involved in the regulation of peptidoglycan synthesis in the septum. More specifically, YpsB would be responsible for modulating the activity of PBP1, a necessary enzyme for septum peptidoglycan synthesis.

Em procariotos, a principal forma de reprodução é a divisão binária, que permite à célula-mãe dar origem a duas outras células-filhas, com conteúdo genético idêntico ao da progenitora. Em Bacillus subtilis este processo acontece graças ao divisomo, um complexo formado por aproximadamente dezesseis proteínas, que leva à constrição da membrana e da parede, formando o septo de divisão. A montagem do divisomo é coordenada por FtsZ, um homólogo de tubulina, que polimeriza na região central da bactéria e serve de arcabouço para a montagem do divisomo. Partindo de um levantamento detalhado da distribuição dos genes envolvidos em divisão em genomas completos de procariotos detectamos que divIVA, um gene de divisão já bem caracterizado, apresentava um gene parálogo em B. subtilis, conhecido como ypsB. Para determinarmos se YpsB seria um novo componente do divisomo foi realizada uma caracterização citológica e funcional desta proteína. Utilizamos microscopia de fluorescência e fusões de YpsB a GFP para determinar a localização subcelular de YpsB. Estes experimentos revelaram que YpsB está presente no divisomo, apresentando um padrão de localização semelhante mas não idêntico ao de DivIVA. Medindo-se a taxa de co-localização entre o anel Z e YpsB ficou demonstrado que estas proteínas co-localizam em aproximadamente 50%, sugerindo que YpsB é recrutada depois que o anel Z é montado. Para determinar quando YpsB chega ao divisomo, usamos mutantes termo-sensíveis das proteínas de divisão que revelaram a dependência de YpsB pelo sub complexo DivIB-DivIC-FtsL-FtsW-PBP2B. Já na ausência de DivIVA, YpsB continua associado ao divisomo, indicando que não depende do seu parálogo para localizar. Além disso, análises de deleções de YpsB mostraram que a porção N-terminal da proteína é a mais importante para o seu recrutamento ao divisomo. Para determinarmos o papel de YpsB durante a divisão foi construído um mutante com deleção completa do gene. DivIVA é uma proteína responsável por localizar o sistema Min nos pólos da bactéria e assim contribui para a precisão espacial da divisão. Apesar de serem parálogos, a função de YpsB, no entanto, parece ser diferente da de DivIVA. Análise do mutante ypsB- mostrou que na sua ausência, o divisomo é montado e o seu posicionamento tanto em fase vegetativa como em esporulação não são afetados. Como a ausência de YpsB não afeta perceptivelmente a divisão, combinamos a mutação em ypsB com mutações em outros genes envolvidos em divisão. A análise destes duplos mutantes revelou que a ausência simultânea de YpsB e FtsA produz exacerbada lise celular e letalidade. Com base neste fenótipo e em evidências evolutivas, sugerimos que YpsB esteja envolvida na regulação da síntese de peptideoglicano do septo. Mais especificamente, YpsB seria responsável por modular a atividade de PBP1, uma enzima necessária para a síntese de peptideoglicano septal. / In prokaryotes, the main form of reproduction is binary fission, which allows the mother-cell to give origin the two daughter-cells, with identical genetic material. In Bacillus subtilis, this process is performed by the divisome, a complex formed for approximately sixteen proteins that leads to the constriction of the membrane and the wall, creating the division septum. The assembly of the divisome is coordinated by FtsZ, a homolog of tubulin, that polymerizes in the central region of the bacteria and serves as the base for the assembly of the divisome. From a detailed survey of the distribution of the genes involved in division in complete genomes of prokaryotes, we detected that divIVA, a well characterized division gene, showed a paralog in B. subtilis, known as YpsB. To determine if YpsB would be a new component of the divisome, a cytological and functional characterization of this protein was carried out. We used fluorescence microscopy and fusion of YpsB to GFP to determine the subcellular localization of YpsB. These experiments displayed that YpsB is present in the divisome, with similar but not identical localization as DivIVA. Measuring co-localization between the Z ring and YpsB demonstrated that this happened in approximately 50% of the cells, suggesting that YpsB go to the divisome after the Z ring is formed. To determine when YpsB goes to the divisome, we used temperature-sensitive mutants of the division proteins. This showed that YpsB depends on the DivIB-DivIC-FtsL-FtsW-PBP2B sub-complex to associate with the divisome. In the absence of DivIVA, YpsB is still present in the divisome, indicating that it does not depend on its paralog to localize. Moreover, deletion analyses of YpsB showed that the N-terminal portion of the protein is the most important for its recruitment to the divisome. To determine the role of YpsB during division, we constructed a ypsB- mutant. DivIVA is the protein responsible for localization of the Min system in polar regions of B. subtilis and, thus, contributes for the spatial precision of division. Our results showed that the function of YpsB must be different from that of DivIVA, since analysis of the ypsB- mutant showed that in the absence this protein the divisome is assembled and septum position in vegetatively growing or sporulating cells is not affected. Since the absence of YpsB does not affect division, we combined the ypsB- mutant with mutants involved in division. Analysis of these double mutants showed that the simultaneous absence of YpsB and FtsA caused cellular lysis and lethality. Based on this phenotype and evolutionary evidences, we suggest that YpsB is involved in the regulation of peptidoglycan synthesis in the septum. More specifically, YpsB would be responsible for modulating the activity of PBP1, a necessary enzyme for septum peptidoglycan synthesis.

Target of rapamycin est une large kinase conservée chez la plupart des eucaryotes. Elle est au centre d’une voie de signalisation régulant la croissance, le métabolisme en fonction de l’environnement et a été largement étudiée chez l’homme du fait de son implication dans des maladies telles que le cancer. Chez les plantes, son étude est moins avancée mais le développement d’inhibiteurs ATP compétitifs chez l’homme a offert de nouvelles possibilités pour la recherche en biologie végétale. En effet, l’utilisation d’un inhibiteur de TOR nous a permis de réaliser le criblage d’une banque de mutants ethyl méthansulfonate et de découvrir une nouvelle cible de TOR : YAK1. Cette dernière régule la croissance en inhibant la prolifération. Le criblage de mutants a également permis de découvrir des mutations dans TOR affectant sa sensibilité ou son affinité pour l’inhibiteur. Ceci offre un nouvel outil pour étudier la fonction de TOR de plantes. / Target of rapamycin is a large kinase existing in most eucaryots such as plants and animals. It is at the center of a signaling pathway regulating growth and metabolism in response to environmental changes, which has been the subject of many studies in humans because of its implication in diseases like cancer. However in plants, the exploration of this pathway is less advanced but the development of ATP competitive inhibitors in humans has offered new possibilities for plant research. Indeed, the use of a TOR inhibitor has allowed us to screen an ethyl methansulfonate mutant bank and discover a new target of TOR: YAK1. The latter regulates growth by inhibiting proliferation notably through cyclin-dependant kinase inhibitors. The screen also allowed us to uncover TOR mutations which potentially affect TOR activity and/or affinity to the inhibitor. This offers a new tool for the study of TOR function in plants.

Archaea is one of the three domains of life and studies of archaeal biology are important for understanding of life in extreme environments, fundamental biogeochemical processes, the origin of life, the eukaryotic cell and their own, unique biology. This thesis presents four studies of the archaeal cell, using the extremophilic Sulfolobus and ocean living Nitrosopumilus as model systems. Cell division in crenarchaea is shown to be carried out by a previously unknown system named Cdv (cell division). The system shares homology with the eukaryotic ESCRT-III system which is used for membrane reorganization during vesicle formation, viral release and cytokinesis. Organisms of the phylum Thaumarchaeota also use the Cdv system, despite also carrying genes for the euryarchaeal and bacterial cell division system FtsZ. The thaumarchaeal cell cycle is demonstrated to be dominated by the prereplicative and replicative stage, in contrasts to the crenarchaeal cell cycle where the cell at the majority of the time resides in the postreplicative stage. The replication rate is remarkably low and closer to what is measured for eukaryotes than other archaea. The gene organization of Sulfolobus is significantly associated with the three origins of replication. The surrounding regions are dense with genes of high importance for the organisms such as highly transcribed genes, genes with known function in fundamental cellular processes and conserved archaeal genes. The overall gene density is elevated and transposons are underrepresented. The archaeal virus SIRV2 displays a lytic life style where the host cell at the final stage of infection is disrupted for release of new virus particles. The remarkable pyramid-like structure VAP (virus associated pyramids), that is formed independently of the virus particle, is used for cell lysis. The research presented in this thesis describes unique features of the archaeal cell and influences our understanding of the entire tree of life.

Das stäbchenförmige Bakterium Escherichia coli teilt sich in zwei gleich große Tochterzellen. Dies ist nur möglich, wenn sich die Zelle in der Mitte teilt. Bei E. coli wird die Zellteilung durch den Zusammenschluss der FtsZ-Proteine an der Membran zum Z-Ring eingeleitet. Topologische Regulierung des Z-Ringes erfolgt durch räumlich-zeitliche Oszillationen von Min-Proteinen zwischen den beiden Zellpolen. MinC, MinD und MinE binden an und lösen sich von der Membran unter Hydrolyse von ATP und in antagonistischer Art und Weise, was zu einer alternierenden Ansammlung von MinC und MinD an den Zellpolen führt. Gemittelt über die Zeit ergibt sich somit ein MinD-Verteilungsprofil, das maximale Konzentration an den Zellpolen und ein Minimum in der Zellmitte aufweist. MinC bindet an MinD und folgt somit seiner Verteilung. Der Zusammenschluss von FtsZ-Proteinen wird durch MinC unterbunden, und somit kann sich der Z-ring nur an einer Position herausbilden, die ein Minimum an MinC aufweist - der Zellmitte. Das Min-system wurde in der Vergangenheit auch mit einem in-vitro-Ansatz untersucht, indem Min-Proteine in künstliche, aufliegende Lipiddoppelschichten (supported lipid bilayers, SLB) rekonstitutiert wurden. Dabei bildeten die Min-Proteine kein oszillierendes Muster aus, sondern organisierten sich vielmehr in parallelen und propagierenden Wellen (Loose, 2008, Science, 320). In diesen in-vitro-Experimenten war das Membransubstrat wesentlich größer als die Wellenlänge der Min-Proteinwellen. In vivo hingegen ist die Länge der Zelle in der gleichen Größenordnung wie die charakteristische Länge des Oszillationsmusters der Min-Proteine. Daher war es das Ziel dieser Arbeit, den Einfluß einer beschränkten Fläche und geometrischer Formgebung der künstlichen Lipiddoppelschichten auf die Wellenpropagation der Min-Protein zu untersuchen. Flächige Beschränkung künstlicher Membranen erfolgte durch Mikrostrukturtechnologie. Deckglässchen wurden mit einer Goldschicht und mikroskopischen Aussparungen unterschiedlicher geometrischer Formen strukturiert. Funktionale SLBs bildeten sich nur auf Glasflächen ohne Goldbeschichtung aus. Nach der Rekonstitution der Min-Proteine, organisierten sich diese auf den Membranstücken in parallele Wellen. Dabei bestimmte die flächige Beschränkung der künstlichen Membranen die Ausbreitungsrichtung der Min-Proteinwellen. Min-Proteinwellen konnten entlang gekrümmter Membranstreifen, in Ring- und sogar in Slalomstrukturen geleitet werden. In geraden, länglichen Strukturen richteten sich die Wellen entlang der längsten Achse aus. Kopplung von Proteinwellen auf räumlich getrennten Membranstücken in Abhängigkeit des Abstandes und des sogenannten Molecular Crowdings in der wässrigen Lösung konnte ebenfalls beobachtet werden. Diese Kopplung ist ein Indiz für inhomogene Proteinverteilungen in der Lösung oberhalb der Membran. Desweiteren konnten Min-Proteinwellen auch in diversen dreidimensionalen künstlichen Membranen rekonstitituiert werden. Im Wildtyp von E. coli ähneln die Min-Proteindynamiken der einer Oszillation mit einer charakteristischen Länge von 5 µm. Auf SLBs, bilden Min-Proteine Wellen mit einer Wellenlänge aus, die ca. zehnmal größer ist als in vivo. Dieser Unterschied zwischen der in-vivo- und der in-vitro-Welt wurde untersucht und diskutiert. In vitro konnte die Wellenlänge um 50 % durch Erhöhung des Molecular Crowding in der Lösung sowie um 33 % durch Temperaturerhöhung verkleinert werden. Das oszillierende Muster könnte dahingegen eine Folge der Kompartimentierung sein. Erste Versuche, das Min-System in geschlossene Membrankompartimente zu rekonstitutieren, wurden getestet. / Escherichia coli, a rod-like bacterium, divides by binary fission. Cell division into two daughter cells of equal size requires that fission takes place at a midcell position. In E. coli, cell division is initiated by assembly of the FtsZ-proteins at the inner membrane to the Z-ring. Topological regulation of the Z-ring is achieved by spatiotemporal pole-to-pole oscillations of Min-proteins. MinC, MinD and MinE bind to and detach from - under hydrolysis of ATP - the membrane in an antagonistic manner leading to an alternating accumulation of MinC and MinD at the cell poles. Averaged over time, the distribution profile of MinD exhibits maximal concentration at the cell poles and a minimum at the cell center. MinC binds to MinD and thus follows its distribution. FtsZ assembly is inhibited by MinC and therefore the Z-ring can only form at a cell position low in MinC - at the cell center. In the past, the Min-system was also investigated in an in vitro approach by reconstitution of Min-proteins into a supported lipid bilayer (SLB). Here, Min-proteins did not self-organize into an oscillatory pattern but into parallel and propagating waves (Loose, 2008, Science, 320). In this in vitro assay, the membrane substrate was infinitely large compared to the wavelength. However, in vivo, the cell length is on the same order of magnitude as the respective length scale of the oscillatory pattern of Min-proteins. Therefore, we wished to investigate the effect of lateral confinement and geometric structuring of artificial lipid bilayers on the Min-protein wave propagation. Lateral confinement of artificial membranes was achieved by microfabrication technology. Glass slides were patterned by a gold coating with microscopic windows of different geometries, and functional SLBs were only formed on uncoated areas. Upon reconstitution, Min-proteins organized into parallel waves on the geometric membrane patches. Confinement of the artificial membranes determined the direction of propagation of Min-protein waves. Min-protein waves could be guided along curved membrane stripes, in rings and even along slalom-geometries. In elongated membrane structures, the protein waves always propagate along the longest axis. Coupling of protein waves across spatially separated membrane patches was observed, dependent on gap size and level of molecular crowding of the aqueous media above the bilayer. This indicates the existence of an inhomogeneous and dynamic protein gradient in the solution above the membrane. Furthermore, reconstitution of Min-protein waves in various three-dimensional artificial membranes was achieved. In wild-type E. coli, Min-protein dynamics resemble that of an oscillation with a characteristic length scale of 5 µm. On supported lipid bilayers, Min-proteins self-organize into waves with a wavelength approximately 10-fold larger than in vivo. These discrepancies between the in vivo and in vitro world were investigated and discussed. In vitro, the wavelength could be decreased by a factor of 50 % by increase of the molecular crowding in solution and by 33 % through temperature increase. The oscillatory pattern is thought to be a consequence of compartmentalization and first attempts to encapsulate the Min-system in closed bilayer compartments are presented.

Symmetric cell division in gram-negative bacteria is essential for generating two equal-sized daughter cells, each containing cellular material crucial for growth and future replication. The Min system, comprised of proteins MinC, MinD and MinE, is particularly important for this process since its deletion leads to minicells incapable of further replication. This thesis focuses on the interactions involving MinE that are important for allowing cell division at the mid-cell and for directing the dynamic localization of MinD that is observed in vivo. Previous experiments have shown that the MinE protein contains an N-terminal region that is required to stimulate MinD-catalyzed ATP hydrolysis in the Min protein interaction cycle. However, MinD-binding residues in MinE identified by in vitro MinD ATPase assays were subsequently found to be buried in the hydrophobic dimeric interface in the MinE structure, raising the possibility that these residues are not directly involved in the interaction. To address this issue, the ability of N-terminal MinE peptides to stimulate MinD activity was studied to determine the role of these residues in MinD activation. Our results implied that MinE likely undergoes a change in conformation or oligomerization state before binding MinD. In addition we performed circular dichroism spectroscopy of MinE. The data suggest that direct interactions between MinE and the lipid membrane can lead to conformational changes in MinE. Using NMR spectroscopy in an attempt to observe this structure change, different membrane-mimetic environments were tested. However the results strongly suggest that structural studies on the membrane-bound state of MinE will pose significant challenges. Taken together, the results in this thesis open the door for further exploration of the interactions involving MinE in order to gain a better understanding of the dynamic localization patterns formed by these proteins in vivo.

Crumbs is a transmembrane protein and apical determinant in Drosophila epithelial cells. Its cytoplasmic tail contains a PDZ and a FERM domain-binding site through which Crumbs interacts with the FERM proteins Yurt, Moesin and Expanded. Recent evidence suggests that Crumbs can also interact with the uncharacterised FERM proteins CG34347 and Cdep. The main objective of my thesis was to generate mutations in CG34347 and Cdep to facilitate the functional analysis of these genes. I generated a mutation for Cdep that remains to be characterised and two mutant lines for CG34347; one lacking the first exon and one lacking the entire gene, using a FRT-based recombination strategy. Both CG34347 mutants cause severe ovarian defects. The most consistent defect is a multilayering of the interfollicular stalk. These defects are also observed when Notch, Hippo, Wingless and Hedgehog signalling pathways are overactive in ovaries suggesting that CG34347 participates in one of those pathways.

Crumbs is a transmembrane protein and apical determinant in Drosophila epithelial cells. Its cytoplasmic tail contains a PDZ and a FERM domain-binding site through which Crumbs interacts with the FERM proteins Yurt, Moesin and Expanded. Recent evidence suggests that Crumbs can also interact with the uncharacterised FERM proteins CG34347 and Cdep. The main objective of my thesis was to generate mutations in CG34347 and Cdep to facilitate the functional analysis of these genes. I generated a mutation for Cdep that remains to be characterised and two mutant lines for CG34347; one lacking the first exon and one lacking the entire gene, using a FRT-based recombination strategy. Both CG34347 mutants cause severe ovarian defects. The most consistent defect is a multilayering of the interfollicular stalk. These defects are also observed when Notch, Hippo, Wingless and Hedgehog signalling pathways are overactive in ovaries suggesting that CG34347 participates in one of those pathways.

No description available.

Advancement in Image Acquisition Equipment and progress in Image Processing Methods have brought the mathematicians and computer scientists into areas which are of huge importance for physicians and biologists. Early diagnosis of diseases like blindness, cancer and digestive problems have been areas of interest in medicine. Development of Laser Photon Microscopy and other advanced equipment already provides a good idea of very interesting characteristics of the object being viewed. Still certain images are not suitable to extract sufficient information out of that image. Image Processing methods have been providing good support to provide useful information about the objects of interest in these biological images. Fast computational methods allow complete analysis, in a very short time, of a series of images, providing a reasonably good idea about the desired characteristics. The thesis covers application of these methods in 3 series of images intended for 3 different types of diagnosis or inference. Firstly, Images of RP-mutated retina were treated for detection of rods, where there were no cones present. The software was able to detect and count the number of cones in each frame. Secondly, a gastrulation process in drosophila was studied to observe any mitosis and results were consistent with recent research. Finally, another series of images were treated where biological cells were observed to undergo mitosis. The source was a video from a photon laser microscope. In this video, objects of interest were biological cells. The idea was to track the cells if they undergo mitosis. Cell position, spacing and sometimes contour of the cell membrane are broadly the factors limiting the accuracy in this video. Appropriate method of image enhancement and segmentation were chosen to develop a computational method to observe this mitosis. Cases where human intervention may be required have been proposed to eliminate any false inference.