Kinesins are molecular motors that transport intracellular cargos along microtubules (MTs) and influence the organization and dynamics of the MT cytoskeleton. Their force-generating functions arise from conformational changes in their motor domain as ATP is bound and hydrolyzed, and products are released. In the budding yeast Saccharomyces cerevisiae, the Kar3 kinesin forms heterodimers with one of two non-catalytic kinesin-like proteins, Cik1 and Vik1, which lack the ability to bind ATP, and yet they retain the capacity to bind MTs. Cik1 and Vik1 also influence and respond to the MT-binding and nucleotide states of Kar3, and differentially regulate the functions of Kar3 during yeast mating and mitosis. The mechanism by which Kar3/Cik1 and Kar3/Vik1 dimers operate remains unknown, but has important implications for understanding mechanical coordination between subunits of motor complexes that traverse cytoskeletal tracks. In this study, we show that the opportunistic human fungal pathogen Candida albicans (Ca) harbors a single version of this unique form of heterodimeric kinesin and we present the first in vitro characterization of this motor. Like its budding yeast counterpart, the Vik1-like subunit binds directly to MTs and strengthens the MT-binding affinity of the heterodimer. However, in contrast to ScKar3/Cik1 and ScKar3/Vik1, CaKar3/Vik1 exhibits weaker overall MT-binding affinity and lower ATPase activity. Preliminary investigations using a multiple motor motility assay indicate CaKar3/Vik1 may not be motile. Using a maltose binding protein tagging system, we determined the X-ray crystal structure of the CaKar3 motor domain and observed notable differences in its nucleotide-binding pocket relative to ScKar3 that appear to represent a previously unobserved state of the active site. Together, these studies broaden our knowledge of novel kinesin motor assemblies and shed new light on structurally dynamic regions of Kar3/Vik1-like motor complexes that help mediate mechanical coordination of its subunits. / Thesis (Master, Biochemistry) -- Queen's University, 2012-02-29 17:15:03.654

Diss. (sammanfattning) Umeå : Univ., 2009. / Härtill 4 uppsatser.

Genome wide association studies (GWAS) have identified the H1 microtubule associated protein tau (MAPT) haplotype single nucleotide polymorphisms as leading common risk variants for Parkinson's disease (PD), progressive supranuclear palsy (PSP) and corticobasal degeneration (CBD). Gene expression studies have demonstrated haplotype-specific increases in expression of MAPT exon 3-containing transcripts from the protective H2 allele compared to the H1. The difference in alternative splicing between the haplotypes likely contributes risk or protection in the absence of protein coding variants. Here, we investigate the regulation of MAPT exon 3 alternative splicing by common, risk-associated, non-coding, haplotype-specific single nucleotide polymorphisms (SNPs) through a combination of in silico analysis of the MAPT locus, in vitro gene expression and biochemistry studies. Comparative sequence analysis of whole-locus genomic H1 and H2 MAPT (143 kb) vectors showed they capture over 86% of the MAPT sequence diversity. We generated and expressed haplotype-hybrid H1 and H2 MAPT vectors in a human neuroblastoma cell culture model and demonstrated that a functional SNP rs17651213 near the exon 3 5' splice site regulates exon 3 inclusion in a haplotype-specific manner. Using RNA-electrophoretic mobility shift assays (RNA-EMSA), we showed differential RNA-protein complex formation at the H1 and H2 sequence variants of SNP rs17651213. We further identified candidate trans-acting splicing factors interacting with functional SNP rs17651213 sequences by RNA-protein pull-down experiment and mass spectrometry. Finally, gene knockdown of candidate splice factors identified by mass spectrometry demonstrated a role for hnRNP F and hnRNP Q in the haplotype-specific regulation of exon 3 inclusion. In this study, we have dissected the MAPT locus to identify sequences regulating the allele-specific alternative splicing of exon 3 and provided mechanistic insights into how common non-coding H1/H2 MAPT haplotype-specific SNPs may contribute to the risk/protection of neurodegeneration at a complex genetic locus.

Dynactin is a multi-subunit complex which was initially identified in 1991 as an activator of cytoplasmic dynein-driven microtubule-based organelle motility in vitro. Although genetic studies also supported the involvement of both complexes in the same functional pathways in yeast, filamentous fungi, and Drosophila, none of these findings yielded significant insights into dynactin's mechanism of action. The full range of cytoplasmic dynein functions in vertebrate cells has also remained poorly understood, due, in large part, to the lack of a specific method of inhibition. The present thesis work was designed to investigate these issues through a study of the 50 kDa subunit of dynactin. As a first step (Chapter 1), I cloned mammalian p50 and characterized its expression at the tissue and subcellular levels. Rat and human cDNA clones revealed p50 to be a novel α-helix-rich protein containing several highly-conserved structural features including one predicted coiled-coil domain. Immunofluorescence staining of p50, as well as other dynactin and cytoplasmic dynein components in cultured vertebrate cells showed that both complexes are recruited to kinetochores during prometaphase and concentrate near spindle poles thereafter. These findings represented the first evidence for dynactin and cytoplasmic dynein co-localization within cells, and for the presence of dynactin at kinetochores. The second major phase of the thesis (Chapter 2) was focused on investigating dynactin and cytoplasmic dynein function in cultured cells in vivo using a dominant negative inhibition approach based on transient transfections of p50 constructs. Overexpression of wild type human p50 in cultured cells resulted in a dramatic fragmentation and dispersal of the Golgi apparatus. Time-lapse fluorescence microscopy analysis of p50-overexpressing cells revealed that microtubule-based vesicle transport from the endoplasmic reticulum to the Golgi was inhibited. Also, the interphase microtubule organizing center was found to be less well-focused in some but not all transfected cells. Overexpression of p50 also disrupted mitosis, causing cells to accumulate in a prometaphase-like state. Chromosomes were condensed but unaligned, and spindles, while still generally bipolar, were dramatically distorted. Sedimentation analysis revealed the dynactin complex to be dissociated in the transfected cultures. Furthermore, both dynactin and cytoplasmic dynein staining at prometaphase kinetochores was markedly diminished in cells expressing high levels of p50. These findings provided the first in vivoevidence for the role of dynactin in cytoplasmic dynein function, i.e. mediating the motor's binding to at least one "cargo" organelle, the kinetochore, and probably also to others such as vesicles destined for the Golgi complex. These data also strongly implicated both dynactin and dynein in Golgi organization during interphase, and chromosome alignment and spindle organization during mitosis. Based on the remarkable disruptive phenotypic effects associated with overexpressing of p50, the name of dynamitin was proposed for this polypeptide. In the third and last phase of the thesis (Chapter 3), two issues were addressed: first, the dynamitin-induced mitotic arrest phenotype was studied in greater detail to better understand the exact sites of dynactin and cytoplasmic dynein activity throughout mitosis. Second, a domain analysis of dynamitin was performed to gain insight into its function within the dynactin complex. A time-lapse fluorescence microscopy study of mitosis in living dynamitin-overexpressing COS-7 cells strongly suggested specific defects in interactions of astral microtubules with the cell cortex, and in both spindle pole assembly and maintenance. Analysis of the mitotic arrest phenotype in a second cell line revealed a second arrest point at metaphase, and a clear effect of dynamitin overexpression on spindle axis orientation, again consistent with defects in interactions between microtubules and the cell cortex. Refined analyses of kinetochore and spindle pole components also confirmed specific defects in kinetochore function and spindle pole organization. Taken together, these findings support three main sites of dynactin and cytoplasmic dynein activity during vertebrate mitosis: prometaphase kinetochores, spindle poles, and the cell cortex. Finally, the domain analysis revealed dynamitin to be capable of self-association through at least two separate interaction domains, consistent with models of the mechanism underlying dynamitin-induced dynactin dissociation, and therefore, yielding important new insights into dynactin assembly. This study also indicated that a third region within dynamitin, residues 105 to 154, is essential for dynamitin and dynactin function. An independent study confirmed this finding, implicating this region in binding to ZW10, an upstream kinetochore protein. Dynamitin has therefore been revealed to be the kinetochore-targeting subunit of dynactin, and indirectly, cytoplasmic dynein. Through the body of this thesis work, dynamitin has also emerged as a powerful new tool for studying vertebrate dynactin and cytoplasmic dynein function in vivo and in vitro.

Trypanosoma brucei, un parasite flagellé unicellulaire, est responsable de la trypanosomiase humaine africaine aussi connue comme la maladie du sommeil.Les microtubules (MTs) sous-pelliculaires, le quartet de MTs (MTQ), le flagelle (F) et le collier de la poche flagellaire (CPF) sont les principaux composants du cytosquelette dutrypanosome. À ce jour, une seule protéine du CPF, BILBO1, a été identifiée et caractérisée.Dans cette étude, nous montrons in vivo que BILBO1 forme des polymères capables deconstruire un échafaudage qui permet l’ancrage de protéines partenaires. Ainsi, un crible en double hybride chez la levure a identifié plusieurs protéines partenaires de BILBO1,notamment une nouvelle protéine appelée FPC4. Nous démontrons que FPC4 est une protéine spécifique des kinétoplastides, localisée au CPF mais aussi au hook-complex, une structure proche du CPF. L’interaction FPC4 – BILBO1 est démontrée in vitro et in vivo, etles domaines d'interaction identifiés. En outre, nous démontrons in vivo et in vitro que FPC4est une protéine associée aux microtubules. Nos données suggèrent fortement que FPC4est impliquée dans le processus de séparation des CPFs au cours du cycle cellulaire. Nos résultats mettent en évidence un lien étroit entre le MtQ et le CPF et l'implication probable duhook-complex. Enfin, nous mettons en évidence une structure analogue au hook-complex chez les Leishmanies. L’interaction BILBO1 – FPC4 représente une nouvelle cible thérapeutique et sera caractérisée plus avant. / Trypanosoma brucei, a unicellular flagellated parasite, is responsible for the human African trypanosomiasis also known as sleeping sickness. Sub-pellicular microtubules (MT), the MT quartet (MtQ), the flagellum (F) and the Flagellar Pocket Collar (FPC) are the main components of the T. brucei cytoskeleton. To date, only a single FPC protein, BILBO1, has been identified and characterized. In this study we demonstrate in vivo that BILBO1 forms polymers able to build a scaffold structure that anchors partner proteins. As such, a yeast-2-hybrid screen identified several BILBO1 interacting protein partners. We demonstrate that FPC4 is a kinetoplastid-specific protein, which is localized at the FPC and at the hook complex. Its specific interaction with BILBO1 has been demonstrated in vitro and in vivo, and the interacting domains identified. Furthermore, we demonstrate that FPC4 is a microtubule binding protein. Our data strongly suggest that FPC4 is involved in the separation of the old and the newly formed FPC during the cell cycle. Altogether, our results demonstrate a tight connection and interplay between the MtQ and the FPC and the likely involvement of an adjacent third structure, the hook complex. Finally, we highlight a structure similar to the hook-complex in Leishmania. The BILBO1 – FPC4 interaction represents a new therapeutic target and will be characterized further.

The amino acid proline is unique – within a polypeptide chain, proline adopts either a cis or trans peptide bond conformation while all other amino acids are sterically bound primarily in the trans configuration. In proteins, the isomeric state of a single proline can have dramatic consequences on structure and function. Consequently, cis-trans interconversion confers both barrier and opportunity – on one hand, isomerization is a rate limiting step in de novo protein folding and on the other can be utilized as a post-translational regulatory switch. Peptidyl-prolyl isomerases (PPIs) are a ubiquitous superfamily that catalyzes the interconversion between conformers. Although pervasive, the functions and substrates of most PPIs are unknown. The two largest subfamilies, FKBPs and cyclophilins, are the intracellular receptors of clinically relevant immunosuppressant drugs that also show promise in the treatment of neurodegenerative disorders and cancer. Therefore, narrowing the knowledge gap has significant potential to benefit human health. FKBP25 is a high-affinity binder of the PPI inhibitor rapamycin and is one of few nuclear-localized isomerases. While it has been shown to bind DNA and associate with chromatin, its function has remained largely uncharacterized. I hypothesized that FKBP25 targets prolines in nuclear proteins to regulate chromatin-templated processes. To explore this, I performed high-throughput transcriptomic and proteomic studies followed by detailed molecular characterizations of FKBP25’s function. Here, I discover that FKBP25 is a multifunctional protein required for the maintenance of genomic stability. In Chapter 2, I characterize the unique N-terminal Basic Tilted Helical Bundle (BTHB) domain of FKBP25 as a novel dsRNA binding module that recruits FKBP25’s prolyl isomerase activity to pre-ribosomal particles in the nucleolus. In Chapter 3, I show for the first time that FKBP25 associates with the mitotic spindle apparatus and acts to stabilize the microtubule cytoskeleton. In this chapter, I also present evidence that this function influences the stress response, cell cycle, and chromosomal stability. Additionally, I characterize the regulation of FKBP25’s localization and nucleic acid binding activity throughout the cell cycle. Finally, in Chapter 4, I uncover a role for FKBP25 in the repair of DNA double-stranded breaks. Importantly, this function requires FKBP25’s catalytic activity, identifying for the first time a functional requirement for cis-trans prolyl isomerization by FKBP25. Collectively, this work identifies FBKP25 as a multifunctional protein that is required for the maintenance of genomic stability. The knowledge gained contributes to the exploration of PPIs as important drug targets. / Graduate

Abstract Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) are the two most common neurodegenerative diseases leading to early onset dementia (< 65 years). Mutations in the amyloid precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2) genes cause a proportion of familial early-onset AD (eoAD), while the microtubule-associated protein tau (MAPT) and progranulin (PGRN) mutations have been identified in FTLD patients. Only a few PSEN1 and APP mutations have previously been found in Finnish AD patients, and one MAPT mutation in a FTLD family, while the role of PGRN in Finnish FTLD patients is unknown. Increasing evidence suggests that mitochondrial dysfunction and oxidative stress also play an important role in neurodegenerative diseases. The aim here was to investigate the genetics of eoAD and FTLD in the population of the province of Northern Ostrobothnia, Finland. Sequencing analysis of the APP, PSEN1 and PSEN2 genes was performed to determine whether mutations in these genes could be detected. The MAPT and PGRN genes were analysed in the FTLD patients by sequencing and MAPT haplotypes were determined. The contributions of mtDNA and its maintenance enzymes to eoAD and FTLD were studied by comparing the frequencies of mtDNA haplogroups and their clusters between the patient groups and controls and by screening for the five common POLG1 mutations (T251I, A467T, P587L, W748S, Y955C), two common mtDNA mutations (m.3243A>G, m.8344A>G) and mutations in the PEO1 and ANT1 genes. This is the first report of a significant association between the mtDNA haplogroup cluster IWX and FTLD. The H2 MAPT haplotype was also associated with FTLD in our cohort. No significant differences in the frequencies of the mtDNA haplogroups were observed between the eoAD patients and controls, nor were there any pathogenic mutations detected in the genes analysed. The findings suggest that possession of the mtDNA haplogroup cluster IWX and the H2 MAPT haplotype may be possible risk factors for FTLD in our cohort. The absence of any pathogenic mutations in the MAPT, PGRN, APP or PSEN genes in our series, together with the previous reports of only a few mutations found in this region, supports a minor role for these genes in the aetiology of eoAD and FTLD in Northern Ostrobothnia and indicates that this population may have its own genetic features. There may be other, still unknown genetic factors to be discovered, that explain familial diseases in the region.

De nos jours, les agents anti-microtubules (MTA) sont administrés dans de nombreuses pathologiques cancéreuses reflétant ainsi leur grande efficacité anti-tumorale. Cependant, leur utilisation se voit limitée pour deux raisons : (i) l’apparition d’effets indésirables et, (ii) l’émergence de cellules tumorales résistantes. Pour palier ces problèmes, les MTA font l’objet de nombreux travaux de recherche faisant ainsi de ces composés des médicaments toujours dans l’ère du temps. L’objectif principal des travaux présentés dans ce manuscrit repose sur l’étude du mécanisme d’action des MTA afin d’optimiser, par la suite, leur administration. Dans une première partie s’inscrivant dans le domaine de la recherche fondamentale, nous avons caractérisé les mécanismes moléculaires à l’origine de l’efficacité anticancéreuse de ces agents. En effet, nous avons mis en lumière l’existence d’un pont signalétique entre les mitochondries et les microtubules avec un rôle crucial de la voie de signalisation Akt/GSK3β plaçant ainsi, de façon inattendue, la kinase Akt au cœur de l’efficacité des MTA. Ces résultats fournissant un rationnel mécanistique aux stratégies thérapeutiques associant les MTA aux thérapies ciblées anti-Akt, nous avons alors mené une étude oncopharmacologique démontrant que l’association MTA/anti-Akt est fortement synergique in vitro et in vivo.Mieux comprendre le mécanisme d’action des MTA, afin de proposer de nouvelles stratégies thérapeutiques aux cliniciens était l’objectif principal de cette thèse. Les résultats obtenus ici ouvrent ainsi la voie de l’association de ces agents avec les thérapies ciblées anti-Akt nouvelle génération. / Microtubule-Targeting Agents (MTA) are a broad group of anticancer drugs that are currently administered in a lot of cancers. Nevertheless, they can cause undesired side effects and can lose their effectiveness as a result of resistance development. The main objective of my PhD work was to characterize the MTA’s mechanism of action in order to optimize their administration in the future. In the first part, we demonstrated the important role of the kinase Akt in MTA effects. In the second part, we evaluated the interest to combine MTA with anti-Akt drugs. We observed that MTA efficacy is highly important with Akt targeting drugs, particularly in lung adenocarcinoma. These promising results will need further explorations in order to develop more convenient cancer therapy strategies.

La migration des cellules tumorales à travers la matrice extracellulaire dépend de l'activité d'une métalloprotéase matricielle, MT1-MMP, ancrée à la membrane plasmique. MT1-MMP accumule aux invadopodes, des protrusions membranaires à base d'actine responsables de la dégradation de la matrice. La petite protéine G ARF6 est impliquée dans la régulation du trafic membranaire et dans le remodelage du cytosquelette d'actine. Dans mon travail de thèse, j'ai montré qu'ARF6 et deux de ses protéines effectrices JIP3 et JIP4, sont nécessaires à l'exocytose de MT1-MMP au niveau des invadopodes et, par conséquent, à la capacité des cellules tumorales à remodeler la matrice extracellulaire et migrer à travers un environnement matriciel tridimensionnel. ARF6, à travers son interaction avec JIP3/4, contrôle négativement l'activité du complexe dynactine/dynéine, un moteur moléculaire qui se déplace en direction du bout (-) des microtubules, et donc la clairance des endosomes MT1-MMP à partir de la périphérie cellulaire. En plus dans des échantillons humaines ARF6 est accumulée au niveau de la membrane plasmique, avec MT1-MMP, dans un sous-groupe de carcinomes mammaires agressifs, en confirmant donc l'implication d'un axe ARF6-JIP3/JIP4-MT1-MMP dans le processus invasif du cancer du sein. Dans une deuxième étude, j'ai montré que l'hyperactivation d'ARF6 induit un réarrangement important du cytosquelette d'actine à la surface ventrale des cellules tumorales mammaires et contribue à l'activation et au ciblage de Rac1 au front cellulaire. Mon travail a permis d'identifier de nouveaux mécanismes moléculaires par lesquels ARF6 contribue au programme invasif des cellules tumorales mammaires. / The ability of cancer cells to traffic through the extracellular matrix relies on the action of the membrane-anchored matrix metalloprotease MT1-MMP. MT1-MMP is exocytosed to invadopodia, the actin-based membrane protrusions responsible for matrix degradation. The small GTP-binding protein ARF6 is known to coordinate post-endocytic recycling and actin cytoskeletal organization at the plasma membrane and was shown to be up-regulated in breast cancer cells. In my PhD work I showed that ARF6 and two of its effectors JIP3 and JIP4 are required for MT1-MMP endosomes intracellular positioning and exocytosis at invadopodia and consequently for tumor cells ability to remodel the matrix and invade through a three-dimensional matrix environment. ARF6, through the interaction with JIP3/4, negatively controls the activity of the minus-end-directed microtubule motor dynactin/dynein, thus negatively regulating the clearance and inward movement of MT1-MMP endosomes from the cell periphery. In human samples ARF6 is accumulated at the plasma membrane, together with MT1-MMP, in a subset of highly aggressive breast carcinomas, thus corroborating the ARF6-JIP3/JIP4-MT1-MMP axis in breast cancer invasion. In a second study I addressed the contribution of ARF6 activation on actin cytoskeleton remodeling in breast cancer cells. ARF6 links epidermal growth factor receptor signaling to Rac1 activation and targeting to the leading edge where it activates the SCAR/WAVE complex and regulates ventral actin polymerization during lamellipodia extension. Collectively my work identifies novel molecular mechanisms through which ARF6 contributes to the invasive program of breast tumor cells

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