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La morphologie des cellules et leurs interactions avec l’environnement découlent de divers procédés mécaniques qui contribuent à la richesse et à la diversité de la vie qui nous entoure. À titre d’exemple, les cellules mammifères se conforment à différentes géométries en fonction de l’architecture de leur cytosquelette tandis que les bactéries et les levures adoptent une forme circulaire par turgescence. Je présente, dans cette thèse, la découverte d’un mécanisme de morphogénèse supplémentaire, soit la déformation de surface cellulaire via l’assemblage de protéines par démixtion de phases aqueuses non miscibles et l’adhésion entre les matériaux biologiques. J’expose de façon spécifique comment ce mécanisme régule le recrutement et le mouvement dynamique des protéines qui induisent l’invagination de la membrane plasmique lors de l’endocytose clathrine-dépendante (CME). Le phénomène de démixtion des protéines dans le cytoplasme est analogue à la séparation de phase de l’huile en solution aqueuse. Il constitue un mécanisme cellulaire important et conservé, où les protéines s’agglomèrent grâce aux interactions intermoléculaires qui supplantent la tendance du système à former un mélange homogène. Plusieurs exemples de compartiments cellulaires dépourvus de membrane se forment par démixtion de phase, tels que le nucléole et les granules de traitement de l’ARN [1-6]. Ces organes ou compartiments dénommés NMO, du terme anglais « non-membranous organelles », occupent des fonctions de stockage, de traitement et de modification chimique des molécules dans la cellule. J’explore ici les questions suivantes : est-ce que les NMO occupent d’autres fonctions à caractère morphologique ? Quels signaux cellulaires régulent la démixtion de phase des protéines dans la formation des NMO ? Fondée sur la physique mécanique du contact entre les matériaux, j’émets l’hypothèse que des compartiments cellulaires nanoscopiques, formés par démixtion de phase, génèrent des forces mécaniques par adhésion interfaciale. Le travail mécanique ainsi obtenu déforme le milieu cellulaire et les surfaces membranaires adjacents au NMO nouvellement créé. Le but de mon doctorat est de comprendre comment les cellules orchestrent, dans le temps et l’espace, la formation des NMO associés au CME et comment ceux-ci génèrent des forces mécaniques. Mes travaux se concentrent sur les mécanismes de démixtion de phase et d’adhésion de contact dans le processus d’endocytose chez la levure Saccharomyces cerevisiae. Pour enquêter sur le rôle des modifications post-traductionnelles dans ces mécanismes, nous avons premièrement analysé la cinétique de phosphorylation des protéines en conditions de stress. Mes résultats démontrent que le recrutement et la fonction de certaines protéines impliquées dans le CME se régulent via des mécanismes de phosphorylation. Outre les processus de contrôle post-traductionnel, nous avons élucidé le rôle des domaines de faible complexité dans l’assemblage de plusieurs protéines associées avec le CME. De concert avec les modifications de phosphorylation, des domaines d’interaction protéine-protéine de type PrD (du terme « prion-like domains ») modulent directement le recrutement des protéines au sein des NMO associés au CME. La nature intrinsèquement désordonnée de ces PrD favorise un mécanisme d’assemblage des protéines par démixtion de phase tel que postulé. Finalement, mes travaux confirment que la formation de ces NMO spécifiques génère des forces mécaniques qui déforment la membrane plasmique et assurent le processus de CME. D’un point de vue fondamental, mes recherches permettent de mieux comprendre l’évolution d’une stratégie cellulaire pour assembler des compartiments cellulaires sans membrane et pour fixer les dimensions biologiques associées au CME. De manière plus appliquée, cette étude a le potentiel de générer des retombées importantes dans la compréhension et le traitement de maladies neurodégénératives souvent associées à une séparation de phase aberrante et à la formation d’agrégats protéiques liés à la pathologie. / Evolution has resulted in distinct mechanical processes that determine the shapes of living cells and their interactions with each other and with the environment. These molecular mechanisms have contributed to the wide variety of life we observe today. For example, mammalian cells rely on a complex cytoskeleton to adapt specific shapes whereas bacteria, yeast and plants use a combination of turgor pressure and cell walls to have their characteristic bloated form. In this dissertation, I describe my discovery of an unforeseen additional mechanism of morphogenesis: protein aqueous-aqueous phase separation and adhesive contact between biomaterials as a simple and efficient ways for cells to organize internal matter and accomplish work to shape internal structures and surfaces. I specifically describe how a fundamental process of phospholipid membrane and membrane-embedded protein recycling, clathrin-mediated endocytosis (CME), is driven by this mechanism. Analogous to water and oil emulsions, proteins, and biopolymers in general, can phase separate from single to a binary aqueous phase. For proteins that de-mix from the bulk environment, the intermolecular interactions (or cohesive energy) that favors protein condensation only needs to overcome the low mixing entropy of the system and represents a conserved and energy efficient cellular strategy [2, 3, 7, 8]. So far, various examples of phase separated cellular compartments, termed non-membranous organelles (NMOs), have been discovered. These include the nucleoli, germ line P granules and P bodies, to name a few [1-6]. NMOs are involved in many conserved biological processes and can function as storage, bioreactor or signaling bodies. Cells use phase separation as a scheme to organize internal matter, but do NMOs occupy other complex functions, such as morphogenesis? What specific signals trigger protein phase separation? Based on mechanical contact theory, I proposed that hundreds of nanometer- to micron-scale phase separated bodies can deform the cellular environment, both cytoplasm and membranes, through interfacial adhesion. I studied how mechanical contact between a phase-separated protein fluid droplet and CME nucleation sites on membranes drive endocytosis in the model organism budding yeast, Saccharomyces cerevisiae. Specifically, this dissertation describes first, my investigations of post-translational modifications (phosphorylation) of several CME-mediating proteins and the implications of these modifications in regulating CME. I then describe how my efforts to understand what was distinct about the proteins that are phosphorylated led me to propose their phase separation into droplets capable of driving invagination and vesicle formation from plasma membrane. I used fluorescence microscopy, mass spectrometry and micro rheology techniques to respectively determine the spatiotemporal dynamics, phosphorylation modifications and material properties of coalesced CME-mediating proteins. I further investigated how phase separation of these proteins might generate mechanical force. I demonstrate that changes in the phosphorylation of some endocytic proteins regulates their recruitment to CME nucleation sites. We achieved reliable predictions of functional phosphosites by combining information on the conservation of the post-translational modifications with analysis of the proportion of a protein that is dynamically phosphorylated with time. The same dynamically phosphorylated proteins were enriched for low amino acid compositional complexity “prion-like domains”, which we demonstrated were essential to these proteins undergoing aqueous-aqueous phase separation on CME nucleation sites. I then demonstrate how phase separated droplet can produce mechanical work to invaginate membranes and drive CME to completion. In summary, I have discovered a fundamental molecular mechanism by which phase separated biopolymers and membranes could apply work to shape each other. This mechanism determines the natural selection of spatial scale and material properties of CME. Finally, I discuss broader implications of this dissertation to mechanistic understandings of the origins of neurodegenerative diseases, which likely involve pathological forms of protein phase separation and/or aggregation.

+ssRNA viruses after entering the cell develop platforms for RNA replication called replication organelles. Due to the activity of phosphatidylinositol 4-kinases is in these areas a higher concentration of PI4P, which establishes suitable binding environment for the viral polymerase 3DPOL . One of these kinases is PI4KB, which is recruited to the membrane by the ACBD3 protein, which is itself recruited by giantin. Some kobuviruses and enteroviruses from the Picornaviridae family use their 3A protein to displace ACBD3 protein from the complex with giantin and transfer it from Golgi aparathus to the replication organelles. Here, PI4KB binds to ACBD3 protein and synthesizes PI4P. Recently, two proteins - TBC1D22A and TBC1D22B - were discovered to bind to the same area of ACBD3 protein as PI4KB. The goal of this project was verification of this interaction and its subsequent characterization (e.g. dissociation constant measurements). My goal was to crystallize complexes of these interaction partners and to solve three-dimensional structure. Our results suggest, that interaction of ACBD3 protein with peptides derived from TBC1D22A and TBC1D22B proteins is much lower compared to interaction between ACBD3 protein and PI4KB. I successfully prepared crystals, however, they diffracted poorly, not allowing us to solve...

In der vorliegenden Arbeit wurde der spezifische Einfluss verschiedener kernkodierter phagentypischer RNA Polymerasen auf die organelläre Genexpression in Physcomitrella und die mitochondrial Genexpression in Arabidopsis untersucht. Während das Fehlen von AtRpoTm in Arabidopsis und PpRpoTmp1 in P. patens lethal ist, wurden Insertionsmutanten für PpRpoTmp2 und AtRpoTmp einer detailierten Untersuchung unterzogen. Sowohl PprpoTmp2, als auch AtrpoTmp Pflanzen zeigten Abweichungen im Phänotyp charakteristisch für mitochondriale Dysfunktion. Identifizierte organelläre Promotoren in P. patens wurden zum Nachweis der Transkriptionsaktivität von PpRpoTmp1 und PpRpoTmp2 in vitro herangezogen. Beide Proteine besitzen die inhärente Fähigkeit zur Promotorerkennung ohne zusätzliche Kofaktoren. Die hier vorgestellten Studien unterstreichen die essentielle Bedeutung von AtRpoTm und PpRpoTmp1 für die Transkription mitochondrialer bzw organellärer Gene in Arabidopsis und P. patens. Im Gegensatz dazu können die Funktionen von AtRpoTmp und PpRpoTmp2 partiell durch andere organelläre RNAPs ersetzt werden. Phänotypische Abweichungen belegen jedoch, das AtRpoTmp und PpRpoTmp2 für die normale Entwicklung von Arabidosis bzw. P. patens essentiell sind. Veränderte Transkriptmengen in AtrpoTmp Pflanzen korrelierten mit genspezifischen Änderungen in der mitochondrialen Transkription. AtRpoTmp muss daher als essentiel für die normale Expression eines spezifischen Sets mitochondrialer Gene angesehen werden. Jedoch konnten für diese mitochondrialer Gene keine AtRpoTmp spezifischen Promotormotive mit reduzierter Aktivität identifiziert werden. Initiationsraten an allen Promotoren stromaufwärts von mitochondrialen Genen mit geringeren Transkriptmengen sind jedoch reduziert. Es erscheint daher wahrscheinlich, daß für einen Teil der mitochondrialen Gene genspezifische Elemente existieren, welche die Transkription durch AtRpoTmp dirigieren. / This study aimed to elucidate how the different transcriptional activities are facilitated in mitochondria of Arabidopsis thaliana and in both organelles of Physcomitrella patens. Insertional mutants for PprpoTmp2 and AtrpoTmp were analysed in detail. As for Arabidopsis RpoTm, knock-out of Physcomitrella RpoTmp1 was found to be lethal. Null mutant plants PprpoTmp2 and AtrpoTmp show surprisingly similar but clearly convergent phenotypical aberrations reminiscent of phenotypes reported for other mitochondrial mutants. Evidence is provided that PpRpoTmp1 and PpRpoTmp2 are functional RNA polymerases, which both posses the inherent ability to recognize organellar promoters in a minimal in vitro transcription system without the aid of additional cofactors. The data suggest that coding for two RpoT proteins one representing an enzyme with a high portion of non-specific transcriptional activity, as seen for AtRpoTmp and PpRpoTmp1 and one that can act as a single-polypeptide enzyme and recognize numerous mitochondrial promoters in vitro as AtRpoTm and PpRpoTmp2 echo convergent inventions but reflect complementing roles of these RNA polymerases in plant mitochondrial transcription. Phenotypical aberrations of rpoTmp2 plants suggest RpoTmp2 is important for normal growth and development. Altered transcript levels in AtrpoTmp were found to result from gene-specific transcriptional changes, establishing that AtRpoTmp functions in distinct transcriptional processes within mitochondria. Decreased transcription of a specific set of mitochondrial genes in AtrpoTmp was not associated with changes in the utilisation of specific promoters. Therefore AtRpoTmp function is not promoter-specific but gene-specific. This indicates that additional gene-specific elements direct the transcription of a subset of mitochondrial genes by RpoTmp.

The mechanisms by which altered processing, distribution and secretion of proteolytic enzymes occur, facilitating degradation of the extracellular matrix in invasive and metastatic cells, are not fully understood. Studies on the MCF-10 A breast epithelial cell line and its premalignant, c-Ha-ras-transfected MCF-10AneoT counterpart have shown that the ras-transfected cell line has a more alkaline pH. The objective of this study was to determine which organelles of the endosome-lysosome route were alkalinized and shifted to the cell periphery after ras-transfection. Antibodies to the hapten 2,4-dinitrophenyl (DNP), required for pH studies, were raised in rabbits and chickens using DNP-ovalbumin (DNP-OVA) as immunogen. Cationised DNP-OVA (DNP-catOVA) was also inoculated to increase antibody titres. Anti-hapten and carrier antibody titres were assessed. In rabbits, cationisation seems useful to increase anti-DNP titres if a non-self carrier protein (OVA) is used. In chickens, cationisation of DNP-OVA seems necessary to produce a sustained anti-OVA (anti-self) response (implying a potential strategy for cancer immunotherapy). Oregon Green® 488 dextran pulse-chase uptake and fluorescent microscopy, and (2,4-dinitroanilino)-3'-amino-N-methyldipropylamine (DAMP) uptake, immunolabelling for DNP (a component of DAMP) and unique markers for the early endosome (early endosome antigen-I, EEAI), the late endosome (cation-independent mannose-6-phosphate receptor, CI-MPR) and the lysosome (small electron dense morphology and lysosome-associated membrane protein-2, LAMP-2) and electron mlcroscopy was performed. The pH of late endosomes and lysosomes in the ras-transfected MCF-10AneoT cell line were found to be relatively alkalinised and Iysosomes shifted toward the cell periphery. The acidic pH of late endosomes is required to release precursor cysteine and aspartic proteases from their receptors (e.g. CI-MPR), process the precursors to active proteases and to allow receptor recycling. The more alkaline pH observed potentially explains the altered processing of proteases in rastransfected cells. Alkalinisation ofthe cytosol may affect the cytoskeleton responsible for, among other things, the positioning and trafficking of various organelles, causing relocation of Iysosomes toward the cell periphery and actin depolymerisation. This may enable fusion of Iysosomes with the plasma membrane and the release of proteolytic enzymes, facilitating the observed invasive phenotype. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2005.

Diss. (sammanfattning) Linköping : Univ., 2001. / Härtill 4 uppsatser.

A la différence des mammifères, les plantes ne possèdent pas de cellules spécialisées dans la défense face aux pathogènes. Chaque cellule végétale peut déclencher une réponse immunitaire. Pour interagir avec succès avec la plante, les pathogènes doivent alors supprimer ou contourner les défenses de l’hôte. Afin d’y parvenir, les bactéries pathogènes disposent des effecteurs, des protéines qui peuvent être injectées dans la cellule végétale. De nombreux effecteurs sont connus pour cibler les organites lors de l’infection, confirmant l’importance du chloroplaste et de la mitochondrie dans les mécanismes de défense des cellules végétales. Dans ces conditions, il demeure vital pour la plante de garder la main sur l’expression des gènes des organites afin d’assurer une réponse proportionnée au risque encouru sans pénaliser la croissance de façon disproportionnée. A la différence de l’expression des gènes nucléaires, la régulation de l’expression des gènes des organites se fait principalement lors d’étapes très complexes de maturation post-transcriptionnelle. Parmi les protéines impliquées dans ces étapes de maturation, on trouve les protéines pentatricopeptide repeat (PPR). Les protéines PPR sont impliquées dans de nombreuses étapes de maturation des ARN des organites, comme l’édition C vers U ou l’épissage. Elles sont également présentes chez d’autres eucaryotes, mais n’ont jamais été étudiées chez les bactéries. L’hypothèse testée dans le cadre de la thèse est que ces protéines PPR, qu’elles soient d’origine exogène ou endogène, sont impliquées dans des modifications de l’expression des gènes des organites en condition de stress biotique. Afin de tester notre hypothèse, nous nous sommes intéressés à PGN (Pentatricopeptide repeat protein for Germination on NaCl) chez la plante modèle A. thaliana. Caractérisée par Laluk et al. (2011), le mutant KO montre une sensibilité accrue au nécrotrophe Botrytis cinerea, et l’expression du gène codant pour cette protéine est induite après infection. Nous avons mis en évidence des défauts d’édition dans la séquence non codante en amont de nad6 et dans cox2, deux gènes mitochondriaux. Leur édition ne varie cependant pas en condition d’infection par Botrytis cinerea. Dans la même optique, à la suite d’un crible bio-informatique, nous nous sommes intéressés à deux protéines PPR bactériennes que nous avons trouvées chez les phytopathogènes Erwinia amylovora et Ralstonia solanacearum. Probablement obtenues par les bactéries par transfert horizontal de gènes, il s’agit de la première caractérisation de PPR bactériennes à notre connaissance. Ces protéines possèdent des caractéristiques d’effecteurs, c’est—dire des protéines injectées par la bactérie dans la plante durant l’infection. Si nous n’avons pas vu de modification du transcriptome des organites de la plante provoqué par la surexpression de ces protéines PPR exogènes, nous avons cependant mis en évidence une baisse significative du taux d’incidence de la maladie provoquée par E. amylovora en l’absence d’un gène fonctionnel codant pour sa PPR chez la plante hôte Malus domestica « Golden delicious ». Pour la PPR d’E. amylovora comme celle de R. solanacearum, nous avons également trouvés plusieurs interactants en double hybride levure chez A. thaliana, représentant de nombreuses cibles putatives à étudier. Afin de réaliser ces expérimentations et d’obtenir ces résultats, nous avons eu besoins d’outils particuliers. Nous avons donc développé un pipeline spécifique d’analyse de données de séquençage d’ARN ainsi qu’une méthode améliorée de prédiction des zones de fixation des protéines PPR, ouvrant la voie à une caractérisation simplifiée de nombreuses protéines. / Compared to mammals, plants do not have highly specialized cells involved in defense against pathogens. Each plant cell is able to start an immune response. To interact successfully with plants, pathogens have to block or bypass host defenses. To do so, phytopathogenic bacteria can use effectors, which are basically bacterial proteins injected in the plant cell during infection. Several effectors are known to target organelles during infection, supporting the idea that chloroplasts and mitochondria are key players in plant cell defense. As a reason, it remains necessary for the plant to keep organellar gene expression under control in order to ensure a response in proportion to the risk, without penalizing growth. Unlike nuclear gene expression, organellar gene expression regulation goes through highly complex post-transcriptional maturation steps. Among proteins involved in these events, PPR proteins (for pentatricopeptide repeat) are known to be very important. PPR proteins are involved in several RNA maturation steps in organelles, like C to U editing or splicing. They are studied in several eukaryotes, but not in bacteria. During my PhD studies, the hypothesis is exogenous or endogenous PPR proteins are involved in organellar gene expression modifications during biotic stress. To test our hypothesis, we work on PGN (Pentatricopeptide repeat protein for Germination on NaCl) in plant model A. thaliana. Characterized by Laluk et al. (2011), the KO mutant displays an enhanced sensitivity to the necrotrophic pathogen Botrytis cinerea, and PGN gene expression is induced after infection. We find two editing defects for the KO mutant, in nad6 5’ non coding sequence and in cox2 coding sequence. However, editing at these two sites does not vary in wild type plants during Botrytis cinerea infection.Using a bioinformatic screen, we find several bacterial PPR proteins. Two of them are encoded by bacterial plant pathogens: Erwinia amylovora and Ralstonia solanacearum. To our knowledge, these proteins, putatively obtained through horizontal gene transfer, are the first bacterial PPR proteins to be characterized. They also share similarities with bacterial effectors. If overexpression of these bacterial PPR proteins in A. thaliana does not unveil organellar transcriptome modifications, we show a decrease of the incidence rate of the disease caused by E. amylovora in the host plant Malus domestica “Golden delicious” without a functional gene coding for the PPR protein. For both Erwinia and Ralstonia PPR, we find several interactants in A. thaliana using Yeast Two Hybrid, each of them representing a potential target that could be studied. In order to perform these experiments and obtain these results, we needed very specific tools. During the PhD studies, we develop an RNAseq analysis pipeline and an enhanced method to predict PPR binding sites, opening the way to an easier characterization of several PPR proteins.

A procedure was developed for dealing with two problems that have impeded the use of quantal parameters in studies of transmitter release. The first, involving temporal and spatial biasing in the estimates for the number of functional release sites (n̄) and probability of release (p̄), was addressed by reducing temporal variance experimentally and calculating the bias produced by spatial variance in p (var(s)p). The second, involving inaccuracies in the use of nerve-evoked endplate potentials (EPPs), was circumvented by using only miniature EPPs (MEPPs). Intracellular recordings were made from isolated frog cutaneous pectoris, after decapitation and pithing of the animals, and the concentration of K+ ([K+]) was raised to 10 mM to increase the level of transmitter release. The number of quanta released (m̄) by the EPP was replaced by the number of MEPPs in a fixed time interval (bin), and 500 sequential bins used for each quantal estimate. With the use of 50-ms bins, estimates for var(s)p were consistently negative. This was due to too large a bin (and introduction of undetected temporal variance) because the use of smaller bins (5 ms) produced positive estimates of var(s)p. Increases in m, n, and p but not var(s)p were found in response to increases in [K+] or [Ca2+]/[Co2+]. La3+ (20 μM) produced increases in m and n, which peaked after 20 min and declined toward zero. There were also large increases in p and var(s)p, which peaked and declined only to initial control values. The increase in var(s)p was presumed to reflect La3+-induced release of Ca2+ from intracellular organelles. The results suggest that this approach may be used to obtain unbiased estimates of n̄ and p̄ and that the estimates of var(s)p may be useful for studying Ca2+ release from intraterminal organelles.

Plants maintain organelle genomes that are descended from ancient microbes. Ages ago, these ancient microbes were engulfed by larger cells, beginning a process of co-evolution we now call the endo-symbiotic theory. Over time, DNA from the engulfed microbe was transferred to the genome of the larger engulfing cell, eventually losing the ability to be free-living, and establishing a permanent residency in the larger cell. Similarly, the larger cell came to rely so much on the microbe it had engulfed, that it too lost its ability to survive without it. Thus, mitochondria and plastids were born. Nearly all multicellular eukaryotes possess mitochondria; however, different evolutionary pressures have created drastically different genomes in plants versus animals. For one, animals have very compact, efficient mitochondrial genomes, with about 97% of the DNA coding for genes. These genomes are very consistent in size across different animal species. Plants, on the other hand, have mitochondrial genomes 10 to more than 100 times as large as animal mitochondrial genomes. Plants also use a variety of mechanisms to replicate and maintain their DNA. Central to these mechanisms are nuclear-encoded, organelle targeted replication proteins. To date, there are two DNA polymerases that have been identified in plant mitochondria and chloroplasts, Pol1A and Pol1B. There is also a DNA helicase-primase that localizes to mitochondria and chloroplasts called Twinkle, which has similarities to the gp4 protein from T7 phage. In this dissertation, we discuss the roles of the polymerases and the effects of mutating the Pol1A and Pol1B genes respectively. We show that organelle genome copy number decreases slightly and over time but with little effect on plant development. We also detail the interactions between Twinkle and Pol1A or Pol1B. Plants possess the same organellar proteins found in animal mitochondria, which are homologs to T7 phage DNA replication proteins. We show that similar to animals and some phage, plants utilize the same proteins in similar interactions to form the basis of a DNA replisome. However, we also show that plants mutated for Twinkle protein show no discernable growth defects, suggesting there are alternative replication mechanisms available to plant mitochondria that are not accessible in animals.

Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of a self-labeling protein to insulin allows for the quantification of age-distinct insulin granule pools in pancreatic beta cells by a combination of super resolution and transmission electron microscopy on Tokuyasu cryosections. In contrast to fluorescent proteins like GFP organic dyes covalently bound to self-labeling proteins retain their fluorescence also in epoxy resin following high pressure freezing and freeze substitution, or remarkably even after strong chemical fixation. This enables for the assessment of age-defined granule morphology and degradation. Finally, we demonstrate that this CLEM protocol is highly versatile, being suitable for single and dual fluorescent labeling and detection of different proteins with optimal ultrastructure preservation and contrast.