Diss. (sammanfattning) Göteborg : Göteborgs universitet, 2006. / Härtill 3 uppsatser.

Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [90]-105).

Thesis (Ph. D.)--University of Chicago, Dept. of Molecular Genetics and Cell Biology. / Includes bibliographical references. Also available on the Internet.

Thesis (doctoral)--Université de Lausanne, 1905. / Original thesis title: Recherches sur l'origine des sphères directrices. Bibliography: p. 41-44.

Thesis (Ph. D.)--University of California, Riverside, 2010. / Includes abstract. Available via ProQuest Digital Dissertations. Title from first page of PDF file (viewed May 18, 2010). Includes bibliographical references. Also issued in print.

Cytoplasmic dynein is a highly conserved multi-subunit motor protein that transports a variety of cellular cargoes, including proteins and organelles, towards minus ends of microtubules. Dynein is recruited to specific subclasses of cellular organelles via a specialized class of adaptor proteins, that serve as physical scaffolds for dynein recruitment to cargoes. Recent work shows that these adaptor proteins are also capable of altering biophysical properties of dynein in vitro and in vivo. This work now finds that a dynein adaptor protein, RILP, through multiple interactors, coordinates the progression of a complex biological pathway. Autophagy is a multi-step, highly conserved pathway that involves de novo formation of a double-membraned autophagosome around ubiquitinated cellular cargoes including long-lived proteins and damaged organelles for subsequent degradation by the lysosome. My work finds a dynein adaptor protein, RILP, to control not only retrograde microtubule-based autophagosome transport but their formation as well. RILP achieves these functions by sequentially interacting with the isolation membrane protein, ATG5, and the autophagosome membrane protein, LC3. During autophagosome formation, ATG5 competes with dynein to bind to a common site within the RILP N-terminus to prevent premature initiation of autophagosome motility. Depletion or LC3-interacting site mutations in RILP prevent formation of autophagosomes as well as impede their retrograde transport. This in turn results in an accumulation of ubiquitinated cargoes, including p62/ Sequestosome-1 in cells, showing that RILP is essential for autophagic clearance in cells, a finding that has broad implications for aggregate-prone neurodegenerative diseases. Finally, this work characterizes the molecular composition of the RILP-dynein supercomplex, and identifies Lis1 (implicated in lissencephaly) as an obligate component of the RILP supercomplex. Interestingly, another dynein regulator, NudE (implicated in microcephaly) is absent. Lis1 depletion results in RILP vesicle dispersion, suggesting that it is needed for RILP-mediated dynein driven transport. Altogether, these findings show for the first time that dynein adaptor RILP controls a complex multi-step biological pathway. The unique composition of RILP supercomplex holds new possibilities for dynein regulation in vivo.

Charles University in Prague, Faculty of Pharmacy in Hradec Králové Department of Pharmacognosy Diploma thesis Author: Dana Kettnerová Supervisor: PharmDr. Jan Martin, Ph.D. Title of diploma thesis: Isolation of plant organelles and study of transport mechanisms Key words: isolation, chloroplast, protoplast, vacuole, cell wall Isolation of plant organelles and other cellular components is essential for the study of physiological and pathological processes within the plant cell. It is possible to analyze cell structures, detect accumulation of certain metabolites, ions, enzymes and other substances thanks to the isolation. The goal of this diploma thesis was to provide an overview of isolation methods used for the isolation of cell wall, protoplasts, chloroplasts and vacuoles of plant cells. Isolation processes used for individual types of cell structures, the pros and cons of the various isolation methods, components of used media and their functions, as well as the structure and function of individual plant structures were described.

Dans les organites des plantes, l’édition de l’ARN consiste majoritairement en une désamination de cytidines à des sites spécifiques de l’ARNm. Trente-quatre sites d’édition ont été découverts dans les transcrits chloroplastiques d’Arabidopsis thaliana et plus de 500 dans les transcrits mitochondriaux. Depuis 2005, beaucoup de facteurs d’édition ont été trouvés. La majorité de ces protéines appartiennent à la famille des «PentatricoPeptide Repeat» (PPR). Parmi ces PPR, certaines contiennent un domaine DYW possédant de faibles similarités avec les cytidines désaminases (CDA), alors que d’autres en sont dénuées, générant un doute sur le fait qu’il ait une activité CDA. Le gène At1g47580 (DYW1) code une protéine unique chez Arabidopsis thaliana contenant «seulement» un domaine DYW. Il a été proposé que DYW1 puisse interagir avec les PPR ne contenant pas de domaine DYW, pour former un hétérodimère, capable d’éditer spécifiquement un site. En accord avec cette hypothèse, nous avons montré que DYW1 agissait sur le même site d’édition que CRR4, une PPR sans domaine DYW, et que ces protéines interagissaient in vivo. De plus, nous avons montré que DYW1 remplaçait les parties manquantes de CRR4 pour l’édition. Pour obtenir plus d’informations sur la fonction du domaine DYW, des mutations ont été introduites dans DYW1. Nous avons montré que la signature CDA dans les protéines DYW était essentielle à l’édition de l’ARN ainsi qu’à l’interaction avec les ions zinc. Les données sont en accord avec l’hypothèse d’une activité CDA dans le domaine DYW. Cependant, aucune activité CDA n’a pu être mise à jour in vitro. Il est vraisemblable qu’au moins un cofacteur doive encore être identifié. / In plant organelles, RNA editing mostly takes the form of conversions of cytidines to uridines at specific sites in mRNAs. Thirty-four editing sites have been found in Arabidopsis thaliana chloroplast transcripts and more than 500 sites in mitochondrial transcripts. Since 2005, lots of proteins have been found to act as RNA editing factors. Most of these proteins belong to the PentatricoPeptide Repeat (PPR) family. Amongst these PPR, some contain a DYW domain with weak similarity to cytidine deaminases (CDA), whilst others lack such a domain, creating doubts about whether this domain is required for editing. The gene At1g47580 (named DYW1) encodes a protein in Arabidopsis thaliana that contains “only” a DYW domain. Our initial hypothesis was that DYW1 might interact with PPR proteins that lack a DYW domain, in order to form a heterodimer, able to perform site-specific editing. In accordance with this hypothesis, we discovered that DYW1 is involved in editing the same site as CRR4, a PPR lacking a DYW domain, and that these two proteins interact together in vivo. Moreover, we showed that DYW1 replaces all the missing parts of CRR4 for editing. So, other partners need to be hypothesized for other DYW-lacking editing factors if this hypothesis is to be generalized. The highly conserved residues making up the CDA signature in DYW proteins were found to be essential for RNA editing and are also required for zinc binding, which is a known characteristic of CDAs. All the data so far are consistent with the DYW domain being (part of) a CDA activity; nevertheless, no CDA activity could be detected in vitro. It is likely that at least one required cofactor remains to be identified.

Les mitochondries sont des organites semi autonomes, capables d’autoréplication, qui varient en nombre, en taille et en forme dans le cytoplasme de presque toutes les cellules eucaryotes. Elles sont notamment connues pour être les fournisseurs d’énergie de la cellule. Afin de mener à bien ce rôle, les mitochondries sont capables de fusionner et de se diviser, ce qui permet un contrôle de la forme du réseau mitochondrial. Le contrôle de ces évènements et la forme du réseau qui en résulte sont connus sous le nom de dynamique mitochondriale. Cette dynamique répond à de nombreux stimuli cellulaires et est très régulée. Récemment, il a été montré que le système ubiquitine-protéasome régule la fusion des mitochondries et qu’une des sous unités du protéasome contrôlait la fission des mitochondries. Le système ubiquitine-protéasome est un mécanisme qui repose sur plusieurs acteurs : les enzymes qui vont reconnaître les protéines cibles de ce système, une protéine appelée ubiquitine qui sert pour le marquage des protéines cibles et un complexe multi-protéique appelé protéasome effecteur de la dégradation des protéines cibles. Connu uniquement à l’origine pour son rôle dans la dégradation des protéines cibles, il est apparu dans les dernières années que le rôle de ce système ou de ses composants en dehors de ce système était bien plus vaste. Les études effectuées au laboratoire avaient déjà montré que Rpn11, une sous-unité du protéasome, régulait la fission des mitochondries indépendamment de l’activité protéolytique du protéasome. Le travail présenté ici porte sur le mécanisme d’action du domaine C-terminal de Rpn11 sur divers processus cellulaires tels que l’assemblage du protéasome, la régulation de la fission des mitochondries et des peroxysomes, la longévité cellulaire ou la formation de « Proteasome Storage Granule ». Ce manuscrit présente aussi le travail effectué pour trouver les partenaires qui permettent la régulation de la fission des mitochondries avec le domaine C-terminal de Rpn11 ainsi que l’étude de la localisation in vivo de Rpn11. / Mitochondria are semi-autonomous organelles, which size, shape and number vary in a wide range in almost every eukaryotic cell. They are famous to be the energy producer of the cells. For this purpose, mitochondria are able to fuse and divide. These events of fusion and fission are also known as the mitochondrial dynamic. This phenomenon is highly controlled and answers to many stimuli. Lately, it has been shown that the ubiquitin proteasome system controls the fusion of mitochondria and that a proteasome subunit controls the mitochondrial fission. The ubiquitin proteasome system is a mechanism that relies on many actors: enzymes recognizing the targets of this system, a protein called ubiquitin and a complex called proteasome in charge of the degradation of the targets. Primarily known for the protein degradation, many investigations suggest that this system has other roles. Our previous studies had already shown that the proteasome subunit named Rpn11 controls the fission of mitochondria independently of the proteolytic activities of the proteasome system. The work shown in this manuscript is focused on the mechanism of action of the C-terminus domain of Rpn11 on various cellular processes, including proteasome assembly, control of mitochondrial and peroxisomal fission, yeast lifespan and also the “Proteasome Storage Granule” formation. The in vivo localisation of Rpn11 and the elucidation of its partners on the mitochondrial fission regulation were also investigated.

The primary cilium is an organelle that serves as a signaling center of the cell and is involved in the hedgehog signaling, cAMP pathway, Wnt pathways, etc. Ciliary function relies on the transportation of molecules between the primary cilium and the cell, which is facilitated by intraflagellar transport (IFT). IFT88, one of the important IFT proteins in complex B, is known to play a role in the formation and maintenance of cilia in various types of organisms. The ciliary transition zone (TZ), which is part of the gating apparatus at the ciliary base, is home to a large number of ciliopathy molecules. Recent studies have identified important regulating elements for TZ gating in cilia. However, the architecture of the TZ region and its arrangement relative to intraflagellar transport (IFT) proteins remain largely unknown, hindering the mechanistic understanding of the regulation processes. One of the major challenges comes from the tiny volume at the ciliary base packed with numerous proteins, with the diameter of the TZ close to the diffraction limit of conventional microscopes. Using a series of stimulated emission depletion (STED) superresolution images mapped to electron microscopy images, we analyzed the structural organization of the ciliary base. Subdiffraction imaging of TZ components defines novel geometric distributions of RPGRIP1L, MKS1, CEP290, TCTN2 and TMEM67, shedding light on their roles in TZ structure, assembly, and function. We found TCTN2 at the outmost periphery of the TZ close to the ciliary membrane, with a 227±18 nm diameter. TMEM67 was adjacent to TCTN2, with a 205±20 nm diameter. RPGRIP1L was localized toward the axoneme at the same axial level as TCTN2 and TMEM67, with a 165±8 nm diameter. MKS1 was situated between TMEM67 and RPGRIP1L, with an 186±21 nm diameter. Surprisingly, CEP290 was localized at the proximal side of the TZ close to the distal end of the centrin-labeled basal body. The lateral width was unexpectedly close to the width of the basal body, distant from the potential Y-links region of the TZ. Moreover, IFT88 was intriguingly distributed in two distinct patterns, forming three puncta or a Y shape at the ciliary base found in human retinal pigment epithelial cells (RPE), human fibroblasts (HFF), mouse inner medullary collecting duct (IMCD) cells and mouse embryonic fibroblasts (MEFs). We hypothesize that the two distribution states of IFT88 correspond to the open and closed gating states of the TZ, where IFT particles aggregate to form three puncta when the gate is closed, and move to form the branches of the Y-shape pattern when the gate is open. Two reservoirs of IFT particles, correlating with phases of ciliary growth, were localized relative to the internal structure of the TZ. These subdiffraction images reveal unprecedented architectural details of the TZ, providing a basic structural framework for future functional studies. To visualize the dynamic movement of IFT particles within primary cilia, we further conducted superresolution live-cell imaging of IFT88 fused to EYFP in IMCD cells. Our findings, in particular, show IFT88 particles pass through the TZ at a reduced speed by approximately 50%, implying the gating mechanism is involved at this region to slow down IFT trafficking. Finally, we report the distinct transport pathways of IFT88 and Smo (Smoothened), an essential player to hedgehog signaling, to support our hypothesis that two proteins are transported in different mechanisms at the ciliary base, based on dual-color superresolution imaging.