Mit der Entwicklung und der Anwendung moderner Genomsequenzierungstechnologien können weitere Genmutationen identifiziert werden. Nach jetzigem Stand sind etwa 20% dieser Mutationen in Bereichen von Proteinen vorzufinden, die keine eindeutige 3D-Struktur haben. Diese werden intrinsisch ungeordnete Regionen genannt (intrinsic disordered regions, IDRs). Die IDRs sind für die Steuerung biologischer Prozesse wichtig. Sie enthalten kurze, lineare Abschnitte (SLiMs), die bei der Interaktion von Proteinen eine Rolle spielen und mittels Phosphorylierung reguliert werden können. Um Krankheiten besser zu verstehen, ist es entscheidend zu erforschen, wie diese IDR-Mutationen die Interaktionen von Proteinen beeinflussen. In dieser Doktorarbeit wird eine Methode verwendet, bei der synthetische Peptide, die den mutierten Proteinsequenzregionen entsprechen, auf eine Membran aufgebracht werden, um die Wechselwirkungen dieser Peptidsequenzen mit zellulären Proteinen systematisch zu untersuchen. Zusätzlich werden Änderungen dieser Interaktionen zwischen normalen, phosphorylierten oder zusätzlich sequenzveränderten Peptidvarianten untersucht, um die Auswirkungen der Genmutationen besser zu verstehen. Diese Arbeit zeigt deutliche Unterschiede in den Wechselwirkungen zwischen phosphorylierten und nicht-phosphorylierten Peptiden auf. Sie sind größtenteils auf die Störung der phosphorylierungsabhängigen SLiMs zurückzuführen. Unter den Proteinen sticht insbesondere die S102P Mutation im Transkriptionsfaktor GATAD1 heraus, die mit einer Herzmuskelerkrankung in Verbindung steht. Wir haben festgestellt, dass diese Mutation eine Phosphorylierungsstelle stört, die für die Bindung an 14-3-3-Proteine verantwortlich ist. Wir haben weitere Untersuchungen durchgeführt, um diese Interaktion besser nachvollziehen zu können. Diese Arbeit trägt dazu bei, die molekularen Mechanismen von Krankheiten besser zu verstehen und bietet Möglichkeiten für weiterführende Untersuchungen und Therapieansätze auf. / Approximately 20% of disease-linked point mutations are situated within protein regions devoid of 3D structure, known as intrinsically disordered regions (IDRs). IDRs harbour short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), often through post-translational modifications such as phosphorylation. Investigating the impact of these IDR mutations on protein-protein interactions is essential to comprehend human diseases. In this doctoral thesis, I present a comprehensive exploration of a peptide-based proteomics screen, employed to study 36 disease-associated mutations that impair phosphorylation sites within IDRs. This approach, uses immobilized synthetic peptides, corresponding to the mutated regions, to capture interacting proteins from cellular extracts. This method facilitated the simultaneous comparison of interaction partners among wild-type, phosphorylated, and mutated peptide forms, enabling the functional assessment of individual mutations. Our analysis uncovered significant disparities between the interactomes of phosphorylated and non-phosphorylated peptides. Building on our findings, we placed particular emphasis on the S102P mutation within the transcription factor GATAD1, a mutation associated with dilated cardiomyopathy. Our screening demonstrated that this mutation disrupts a phosphorylation site responsible for 14-3-3 protein binding. To delve deeper into this interaction, we conducted a thorough investigation, employing techniques such as isothermal titration calorimetry, X-ray crystallography, and alanine scanning coupled with mass spectrometry. Our analyses hinted at the regulatory role of 14-3-3 binding in GATAD1's nucleocytoplasmic transport, achieved by masking its nuclear localization signal. The insights from our research shed fresh light on potential molecular mechanisms underpinning the development of various human diseases, offering a promising avenue for further investigation and therapeutic exploration.

Alzheimer's disease (AD) accounts for around two thirds of all dementia cases and an increase in life expectancy of the population has resulted in a substantial increase in dementia cases and with that a rise in AD. AD is a debilitating and ultimately fatal neurodegenerative disorder of the elderly, and despite being identified over a century ago, the current treatments do not treat the underlying causes behind the disease, instead they help to mask the symptoms of the disease and prolong the brain's remaining function. It is therefore vital that an effective, disease modifying treatment for this disease is established as soon as possible. Soluble intracellular forms of amyloid β (peptide Aβ), a hallmark of AD have been identified and intracellular targets of Aβ are being investigated as potential drug targets for the disease. Two key intracellular, mitochondrial proteins investigated as potential drug targets: amyloid binding alcohol dehydrogenase (ABAD) and cyclophilin D (CypD) are the focus of the work reported in this thesis. To begin identifying potential inhibitors of the ABAD-Aβ interaction, a two-pronged approach was taken. Firstly, a series of analogues based on a known inhibitor of the interaction were tested using a variety of biophysical assays, for their therapeutic affect on the interaction, and secondly a fragment based screening approach was used to identify new small molecule binding partners of ABAD which could potentially be modified to produced inhibitors of the ABAD-Aβ interaction. Three different CypD constructs have been successfully expressed and purified, and taken into crystal trials. It is hoped that these constructs can be used to significantly aid the progress of identifying any potential inhibitors and binding partners of CypD that may produce therapeutic effects, and in the future could lead to the identification of an effective disease modifying drug in the treatment of AD. The work reported in this thesis has built upon previously reported findings and the groundwork has also been established for several in vitro biophysical assays, these include for example: measuring ABAD enzyme activity, and the novel morphology specific Aβ aggregation assay, which can be used as screening tools to help identify potential inhibitors of these interactions. Both the ABAD-Aβ interaction, and the blockade of CypD are known to be drug targets in the treatment of AD, and by elucidating the molecular mechanisms behind these interactions, through implementing biophysical assays, this will help in the identification and design of potential new therapeutic agents for the treatment of AD.

PhD / The overall objective of this thesis is to provide additional data to assist clinicians and experimental neurologists alike in the quest for better understanding, more accurately diagnosing and more successfully treating patients suffering from Parkinson’s disease (PD). The general theme of the thesis is the interaction between certain environmental stimuli, including the exposure to adverse events during early central nervous system (CNS) development and the manifestation of elements of neurodegeneration, whether by means of neurochemical changes or expressed as a dysfunctional voluntary motor system. The first chapter provides a general introduction to the research theme of the thesis. This includes, in particular, a discussion on current understanding concerning the etiology and clinical profile of PD, the relative contribution made by genetic factors compared to environmental ones, and current treatment strategies for treating the disease. Mention is also made of the failure of these therapeutic applications for reversing or protecting against the disease, due to the side-effects associated with them. The material covered in chapter 1 provides the basis for the more complete discussion concerning these various aspects, contained in the chapters to follow. The overall aim was also to characterise the effects of commonly used toxin-induced animal models of PD, and the extent of vulnerability that the CNS displays towards them. The destruction of dopaminergic neurons following the administration of 6-OHDA at targeted points along the nigrostriatal tract is used extensively to model PD pathology in rats and is an established animal model of the disease. However, mature or even aged animals are mainly used in these studies, while the effects that the toxin might have on the developing CNS remain unclear. The study reported in chapter 4 aimed to elucidate some of 6-OHDA’s actions on the young adolescent (35 days-old) CNS by comparing the motor and biochemical effects of a unilateral infusion of the toxin into two anatomically distinct basal ganglia loci: The medial forebrain bundle (MFB) and the striatum. Animals were randomly assigned to receive either a direct delivery of 6-OHDA (12μg/4μl) into the MFB or an indirect injection, into the striatum. Although both lesion types were used, the MFB model is considered a more accurate portrayal of end-stage PD, while the striatum-model better reflects the long-term progressive pathology of the disease. The different lesions’ effects on motor function were determined by observing animal’s asymmetrical forelimb use to correct for weigh shifting during the vertical exploration of a cylindrical enclosure. Following the final behavioral assessment, the concentration of dopamine (DA) and DA metabolites remaining in the post-mortem brains were determined using 4 HPLC electrochemistry (HPLC-EC) and the levels compared between the two groups. The HPLC-EC results revealed a compensatory effect for DA production and DA turnover on the lesioned hemisphere side of the toxin-infused animal group. Thus, following 6-OHDA treatment, there appears to be extensive adaptive mechanisms in place within the remaining dopaminergic terminals that may be sufficient for maintaining relatively high extracellular and synaptic concentrations of DA. However, since substantial changes in motor-function were observed, it is suggested that the capacity of the remaining dopaminergic neurons to respond to increased functional demands may be limited. In addition, the behavioral results indicate that the distinct indices relating to different functional deficits depend on the lesioning of anatomically distinct structures along the nigrostrial tract. It has long been known that far fewer women are diagnosed with PD than men are. This seeming protection offered to females against degenerative disease of the CNS may relate to estrogen, although the hormone’s mechanism of action on the dopaminergic system is poorly defined. With an estimated 10-15 million women using oral contraceptives (OCs) in the United States alone, the aim of chapter 2 was to examine the evidence for a possible relationship between PD and the female reproductive hormone estrogen. A review of the current literature available on the topic was performed by consulting Medline, and by performing a search of the case-reports contained within the World Health Organization’s (WHO) International Drug Monitoring database, for possible PD-related symptoms that may arise from estrogen replacement therapy (ERT). The results, whilst conflicting, seem to suggest that estrogen protects women from obtaining the disease, or at least some features of it. Intensive research efforts are called for, with sufficient power to establish the relationship between ERT and the onset and development of parkinsonism. Chapter 3 reports on the results obtained from an experiment that subjected young Sprague-Dawley rats, 35 days of age, to a lower and a higher dose of 6-OHDA delivered to the MFB. Control rats received equivalent saline infusions. At 14 days post-surgery, the rats were evaluated for forelimb akinesia. For the higher dose of 6- OHDA the female rats were less impaired than males in making adjustment steps in response to a weight shift and in the vibrissae-evoked forelimb placing test. In addition, Tyrosine hydroxylase (TH) immunoreactivity was significantly higher for the female rats. Early gender differences in cell survival factors and/or other promoters of neuroplasticity may have contributed to the beneficial outcome seen in the females. For example, nerve growth factor (NGF) was found to be higher in the female rats following administration of the DA neurotoxin. It is unclear whether gonadal steroids are involved, and, if so, whether female hormones are protective or whether male hormones are prodegenerative. Determining the mechanisms for the improved outcome seen in the young female rats may lead to potential treatment strategies against PD. 5 Many studies have shown that early life stress may lead to impaired brain development, and may be a risk factor for developing psychiatric diseases, including clinical depression. However, few studies have investigated the impact that early stress may have on the onset and development of neurodegenerative disorders such as PD. The study reported on in chapter 5 conjointly subjected rat pups to a maternal separation (MS) paradigm that is a well characterised model of adverse early life events, and a unilateral, intrastriatal injection of 6- OHDA. The combined effects of these models on motor deficits and brain protein levels were investigated. Specifically, the animals were assessed for behavioral changes at 28 days postlesion with a battery of tests that are sensitive to the degree of DA loss sustained. The results show that animals that had been subjected to MS display poorer performance in the vibrissae and single-limb akinesia test compared to non-MS control animals (that had also been subjected to the toxin exposure). In addition, there was a significant increase in the loss of TH staining in MS rats compared to non-MS ones. The results from this study therefore suggest that exposure to adverse experiences during the early stages of life may contribute towards making dopaminergic neurons more susceptible to subsequent insults to the CNS occurring during mature stages of life. Therefore, taken together, early exposure to stress may predispose an individual towards the onset and development of neurodegenerative disease, which especially becomes a threat during the later stages of adult life. Moreover, within the framework of these characteristics, the capacity of a widely-used pharmacological agent (statins) was tested for possible future therapeutic application in PD (chapter 7). Although the precise cause of sporadic PD remains an enigma, evidence suggests that it may associate with defective activity of complex I of the mitochondrial electron transport chain. Mitochondrial DNA transmit and express this defect in host cells, resulting in increased oxygen free radical production, depressed antioxidant enzyme activities, and greater susceptibility to apoptotic cell death. Simvastatin is a member of the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors (statins) group of drugs that are widely used for lowering cholesterol levels in patients who display elevated concentrations of low-density lipoprotein cholesterol. The study aimed to investigate the effects that statin-treatment have on motor-function and at the mitochondrial-protein level, using rotenone, a mitochondrial complex I inhibitor, as a rat-model of PD. Adult male Sprague-Dawley rats were treated either with simvastatin (6mg/day for 14 days) or with a placebo. Two different tests to assess motor function were used: The apomorphine-rotation test, and the vibrissae-elicited forelimb placement test. Following the drug administration protocol, the nigrostriatal tract was unilaterally lesioned with either rotenone (3 μg/4 μl) or, for the controls, were sham-operated by infusing the vehicle (DMSO:PEG) only. Five days later the rats were killed and a highly purified concentration of isolated mitochondria was prepared from the substantia nigra (SN) sections. 2- 6 Dimensional electrophoresis (2-DE) with subsequent identification of the spots using electronspray ionization quadruple time-of-flight mass spectrometrical (ESI-Q-TOF MS) was performed and the results BLAST-searched using bio-informatics tools for naming the identified peptides. The motor test results indicate that while unilateral rotenone causes behavioral asymmetries, treatment with simvastatin improved motor function relative to the rotenoneinduced ones. Mass Spectroscopy identified 23 mitochondrial proteins that differ significantly in protein expression (p < 0.05) following simvastatin treatment. The altered proteins were broadly classified according to their cellular function into 6 categories, with the majority involved in energy metabolism. This study effectively illustrated how neuroproteomics, with its sophisticated techniques and non-biased ability to quantify proteins, provides a methodology with which to study the changes in neurons associated with neurodegeneration. As an emerging tool for establishing disease-associated protein profiles, it also generates a greater understanding as to how these proteins interact and undergo post-translational modifications. Furthermore, due to the advances made in bioInformatics, insight is created concerning their functional characteristics. Chapter 4 summarises the most prominent proteomics techniques and discuss major advances made in the fast-growing field of neuroproteomics in PD. Ultimately, it is hoped that the application of this technology will lead towards a presymptomatic diagnosis of PD, and the identification of risk factors and new therapeutic targets at which pharmacological intervention can be aimed. The final chapter (chapter 8) provides a retrospective look at the academic work that had been performed for the purpose of this thesis, recaps on the main findings, and also highlights certain aspects of the project and provides relevant suggestions for future research. Lastly, the appendix provides a detailed overview of the methods followed for the experiments described in this thesis. It provides not only a comprehensive description of the techniques that had been followed, but provides information concerning the care taken with the animals (i.e. post-surgery) in order to control for the potential influence of experimental variables on the results.

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: The causative agent of human tuberculosis, Mycobacterium tuberculosis, is an intracellular pathogen that secretes virulence factors, namely ESAT-6 and CFP-10, as substrates of the ESX-1 secretion system. It is hypothesised that these substrates interact with host proteins in a targeted manner in order to elicit a required immune response, and they have been shown to be involved in processes related to pro-inflammatory responses, necrosis, apoptosis, membrane lysis and cytolysis. However, the biological function of ESX-1 substrates during host-pathogen interactions remains poorly and incompletely understood. Therefore, the present study was designed to gain insight into the role of the ESX-1 secretion system substrates in host-pathogen interactions and to identify how M. tuberculosis mediates the response of the human host. In this study, a cDNA yeast two-hybrid library was constructed from human lung mRNA, to identify mycobacterial-host protein-protein interactions that occur within the lung alveoli. The ESX-1 secretion system substrates, ESAT-6 and CFP-10, were cloned in-frame into the pGBKT7 vector, which was used in the yeast two-hybrid system to screen the lung cDNA library in Saccharomyces cerevisiae. The ESAT-6 and CFP-10 screens identified 79 and 19 positive colonies, respectively. Of the total number of clones characterised, only two in-frame inserts were identified with the ESAT-6 screen, corresponding to the human proteins filamin A and complement component 1, q subcomponent, A chain (C1QA). In addition, the screen with CFP-10 also identified C1QA as binding partner. Subsequent in vitro and in vivo experiments were unable to confirm the putative interactions of C1QA with ESAT-6 and CFP-10. However, the interaction between filamin A and ESAT-6 was demonstrated and confirmed by both in vivo co-localisation and co-immunoprecipitation. Furthermore, the degradation of filamin A in the presence of ESAT-6 was shown to be reflective of cytoskeleton remodelling and the induction of cell death. The work presented here suggests that as ESAT-6 gains access to the cytosol, it initiates cell death by inducing destabilisation of the cytoskeleton cell structure. This may possibly be driven by the interaction of ESAT-6 and filamin A. Finally, we also initiated an investigation of the identified putative binding partners (filamin A and C1QA) as possible genetic markers for genetic susceptibility studies to tuberculosis. A case-control analysis was performed involving 604 cases, of which 109 were Tuberculous Meningitis (TBM), and 486 were controls from the South African Coloured (SAC) population within the Ravensmead-Uitsig catchment area. The results of this analysis demonstrated a novel association of a regulatory variant (rs587585) located upstream of the C1QA gene and demonstrated an increasing trend towards increased values in tuberculosis patients with the associated genotype. This study has contributed significantly to our understanding of human-mycobacterial hostpathogen protein-protein interactions and has opened the way for future studies further exploring the consequences and function of the identified ESAT-6-filamin A interaction. It has also led to the identification of a novel genetic association with tuberculosis. Finally, it demonstrates the usefulness of the yeast two-hybrid system to identify potential proteinprotein (host-pathogen) interactions that can lead to additional important and exciting research. / AFRIKAANSE OPSOMMING: Die organisme wat tuberkulose veroorsaak, Mycobacterium tuberculosis, is `n intrasellulȇre patogeen wat virulensie faktore afskei, naamlik ESAT-6 en CFP-10, as substrate van die ESX-1 sekresiesisteem. Daar word vermoed dat hierdie substrate met gasheerproteïene in „n teiken wyse interaksie het om `n vereiste immuunreaksie voort te bring. Hierdie substrate is betrokke by prosesse soos pro-inflammatoriese reaksies, nekrose, apoptose, membraanlise en sitolise. Die biologiese funksie van die ESX-1 substrate tydens gasheer-patogeen interaksies word egter tans swak en onvolledig verstaan. Daarom was die huidige studie ontwerp om insig te bekom oor die rol hiervan in gasheer-patogeen interaksies en om te identifiseer hoe M. tuberculosis die reaksie teenoor die gasheer bemiddel. In hierdie studie was `n komplementȇre deoksiribonukleïensuur (kDNS) gis twee-hibried biblioteek gemaak vanaf long boodskapper ribonukleïensuur (bRNS) om proteïen-proteïen interaksies wat in die long plaasvind, te identifiseer. Die substrate van die ESX-1 sekresiesisteem, ESAT-6 en CFP-10, is in volgorde gekloneer in die pGBKT7 vektor en is gebruik om die long kDNS biblioteek in Saccharomyces cerevisiae te ondersoek. In die soeke na interaksies met ESAT-6 and CFP-10, was 79 en 19 positiewe kolonies onderskeidelik geïdentifiseer. Van die aantal klone, was slegs twee volgordes in-leesraam geïdentifiseer met ESAT-6. Hierdie proteïene het ooreengestem met filamin A en “complement component 1, q subcomponent, A chain” (C1QA). Bykomend hiertoe, is C1QA ook geïdentifiseer as „n bindende vennoot met CFP-10. Daaropvolgende in vitro and in vivo eksperimente kon nie die vermeende interaksie van C1QA met ESAT-6 en CFP-10 bevestig nie. Maar die interaksie tussen filamin A en ESAT-6 kon wel gedemonstreer word deur die gebruik van mede-lokalisering en medeimunopresipitasie. Die afbreek van filamin A in die teenwoordigheid van ESAT-6 is ook aangetoon en blyk „n weerspieëling te wees van sitoskelet hermodellering en die induksie van seldood. Die werk wat hier aangebied word, dui daarop dat soos ESAT-6 toegang kry tot die sitosol, inisieër dit seldood deur die destabilisaisie van die sitoskelet selstruktuur. Dit word moontlik aangedryf deur die interaksie van ESAT-6 met filamin A. Laastens het ons `n ondersoek van die geïdentifiseerde bindingsvennote (filamin A and C1QA) as moontlike genetiese merkers vir genetiese vatbaarheidsstudies vir tuberkulose uitgevoer. `n Pasiënt-kontrole studie is gedoen waarby 604 individue ingesluit is, waarvan 109 gediagnoseer is met Tuberculosis Meningitis (TBM), en die ander 486 kontrole individue was van die Suid Afrikaanse Kleurling (SAC) bevolking binne die Ravenmead-Uitsig opvanggebied. Die resultate het „n nuwe assosiasie van „n regulerende variant (rs587585) wat stroomop van die C1QA geen gelokaliseer is, getoon. Hierdie variant het `n verhoogde neiging in tuberkulose pasiënte met die geassosieërde genotipe getoon. Hierdie studie het `n beduidende bydrae gemaak tot ons begrip van menslike-mikobakteriese gasheer-patogeen proteïen-proteïen interaksies. Hierdie resultate het die weg oopgemaak om die gevolge en funksie van die geïdentifiseerde ESAT-6-filamin A interaksie verder te ondersoek. Dit het ook aanleiding gegee tot die identifikasie van `n genetiese assosiasie met tuberkulose. Om saam te vat, hierdie werk bewys die bruikbaarheid van die gis twee-hibriede sisteem, om potensiële proteïen-proteïen interaksies te ontdek wat die moontlikheid het om aanleiding te gee tot addisionele navorsingsvrae. / The National Research Foundation, / Harry Crossley Foundation / Medical Research Council of South Africa / Stellenbosch University Postgraduate bursary / Prof. Paul van Helden

Les interactions protéine-protéine jouent un rôle primordial dans de nombreux processus biologiques. L’importance de ces interactions a suscité le développement de nouvelles approches thérapeutiques qui ciblent ces complexes protéiques. Nous nous proposons d’inhiber ces interactions en élaborant une stratégie de reconnaissance de surfaces de protéines par des molécules synthétiques de taille intermédiaire, les foldamères d’oligoquinoline. Ces composés se replient en des structures hélicoïdales stables dont chaque élément constitutif peut être fonctionnalisé pour permettre des propriétés de reconnaissance de surface de protéine.Afin de valider ce concept, l’interaction entre l’anhydrase carbonique humaine de type II (HCAII) et son inhibiteur N-benzyl-4-sulphamoylbenzamide (SBB) a été sélectionnée comme système modèle. Plusieurs étapes de synthèse ont permis de concevoir de nouveaux foldamères capables de former un complexe avec l’enzyme par l’intermédiaire de l’inhibiteur SBB et d’un espaceur approprié. Chaque complexe protéine-foldamère a été co-cristallisé et l’affinité des interactions a été caractérisée par dichroïsme circulaire induit et par résonance plasmonique de surface. Ce concept a ensuite été appliqué à une interaction protéine-protéine d’intérêt thérapeutique, le complexe IL-4/IL-4R, dans le cadre du programme européenFOLDAPPI (FP7-PEOPLE-IAPP-2008). / Protein-protein interactions play key roles in many biological processes as well as in many diseases. The importance of these interactions has led to the development of new therapeutic approaches that target protein interfaces. We have developed a protein surface recognition strategy to inhibit protein-protein interactions by using intermediate size organicmolecules called oligoquino line foldamers, that result in very stable and well defined helical structures. These helical backbones are used as templates within each building block can be modulated to allow protein surface recognition.In order to validate this concept, the well-characterized interaction between the enzyme human carbonic anhydrase II (HCAII) and its N-benzyl-4-sulphamoylbenzamide (SBB) inhibitor was selected as a model system. Multi-steps synthesis allowed functionalization of new foldamers able to bind to the enzyme through the SBB inhibitor attached by a spacer.Each foldamer–protein complex was cocrystallized and the affinity of the interactions was assayed using both induced circular dichroïsm and surface plasmon resonance. The concept of using a foldamer against protein-protein interaction was then applied to a protein complex of therapeutic interest, IL-4/IL-4R, within the European FOLDAPPI program (FP7-PEOPLEIAPP- 2008).

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Les biomolécules exercent leurs fonctions en interagissant avec d'autres molécules. Le recensement de l'ensemble des biomolécules et leurs interactions permet de construire leurs réseaux d'interactions et de les analyser sur le plan structural et fonctionnel par des outils bioinformatiques (BiNGO, DAVID). Cela permet d'identifier les biomolécules clés, de prédire de nouvelles fonctions des protéines et de comprendre et modéliser les mécanismes moléculaires d'un processus biologique ou pathologique donné. Les protéines ou régions intrinsèquement désordonnées, qui possèdent une grande plasticité structurale, sont susceptibles d'interagir avec de nombreux partenaires et d'être importantes dans les réseaux d'interactions. A l'aide du prédicteur IUPred, nous avons dans un premier temps cartographié le désordre intrinsèque des protéines dans le réseau d'interactions de la matrice extracellulaire et dans le réseau extracellulaire des protéoglycanes construits à partir de la base de données MatrixDB développée dans l'équipe. Nous avons montré que les protéines très connectées de ces deux réseaux ne sont pas enrichies en désordre. Les fonctions moléculaires surreprésentées dans le jeu de protéines extracellulaires contenant au moins 50% de désordre intrinsèque sont les interactions avec les facteurs de croissance ou les glycosaminoglycanes. Nous avons étudié un jeu de données d'interactions protéine-héparine comportant 118 valeurs de cinétique et nous avons montré une relation positive entre la vitesse d'association des protéines à l'héparine et le pourcentage de désordre de leurs sites de fixation à l'héparine. Nous avons également étudié les interactions de la matrice extracellulaire avec un pathogène, le parasite Leishmania. Nous avons montré que les protéines sécrétées par les Leishmania ne sont pas enrichies en désordre par rapport au protéome. Nous avons établi une liste de onze protéines parasitaires sécrétées possédant au moins trois motifs d'interaction et susceptibles d'interagir avec l'hôte / Biomolecules perform their functions by interacting with other molecules. The identification of all biomolecules and their interactions is required to build their interaction networks. Their structural and functional analysis with bioinformatics tools (BiNGO, DAVID) allow us to identify the key biomolecules, to predict new protein functions and to understand and model the molecular mechanisms of biological or pathological process. Intrinsically disordered proteins or regions, which are characterized by structural plasticity, may interact with many partners and may play a role in the interaction networks. Using the predictor IUPred we mapped the intrinsic disorder in protein interaction networks of the extracellular matrix and of the proteoglycans constructed from the MatrixDB database developed in the laboratory. We have shown that the highest connected proteins of these two networks are not enriched in disorder. The molecular functions overrepresented in the set of extracellular proteins containing at least 50% of intrinsically disordered residues are interactions with growth factors or glycosaminoglycans. We studied a dataset of heparin-protein interactions including 118 kinetic values and we have shown that the association rate of proteins with heparin is related to the intrinsic disorder of heparin-binding sites. We also studied the interactions of the extracellular matrix with a pathogen, the parasite Leishmania. We have shown that proteins secreted by Leishmania are not enriched in disorder compared to their proteome. We have selected eleven parasite proteins containing at least three interaction motifs, which may interact with the host

Au fil du temps, la vie a évolué pour produire des organismes remarquablement complexes. Pour faire face à cette complexité, les organismes ont développé une pléthore de mécanismes régulateurs. Par exemple, les mammifères transcrivent des milliers d'ARN longs non codants (ARNlnc), accroissant ainsi la capacité régulatrice de leurs cellules. Un concept émergent est que les ARNlnc peuvent servir d'échafaudages aux complexes protéiques, mais la prévalence de ce mécanisme n'a pas encore été démontrée. De plus, pour chaque ARN messager, plusieurs régions 3’ non traduites (3’UTRs) sont souvent présentes. Ces 3’UTRs pourraient réguler la fonction de la protéine en cours de traduction, en participant à la formation des complexes protéiques dans lesquels elle est impliquée. Néanmoins, la fréquence et l’importance ce mécanisme reste à aborder.Cette thèse a pour objectif de découvrir et comprendre systématiquement ces deux mécanismes de régulation méconnus. Concrètement, l'assemblage de complexes protéiques promus par les ARNlnc et les 3'UTRs est étudié avec des données d’interactions protéines-protéines et protéines-ARN à grande échelle. Ceci a permis (i) de prédire le rôle de plusieurs centaines d'ARNlnc comme molécules d'échafaudage pour plus de la moitié des complexes protéiques connus, ainsi que (ii) d’inférer plus d’un millier de complexes 3'UTR-protéines, dont certains cas pourraient réguler post-traductionnellement des protéines moonlighting aux fonctions multiples et distinctes. Ces résultats indiquent qu'une proportion élevée d'ARNlnc et de 3'UTRs pourrait réguler la fonction des protéines en augmentant ainsi la complexité du vivant. / Over time, life has evolved to produce remarkably complex organisms. To cope with this complexity, organisms have evolved a plethora of regulatory mechanisms. For instance, thousands of long non-coding RNAs (lncRNAs) are transcribed by mammalian genomes, presumably expanding their regulatory capacity. An emerging concept is that lncRNAs can serve as protein scaffolds, bringing proteins in proximity, but the prevalence of this mechanism is yet to be demonstrated. In addition, for every messenger RNA encoding a protein, regulatory 3’ untranslated regions (3’UTRs) are also present. Recently, 3’UTRs were shown to form protein complexes during translation, affecting the function of the protein under synthesis. However, the extent and importance of these 3’UTR-protein complexes in cells remains to be assessed.This thesis aims to systematically discover and provide insights into two ill-known regulatory mechanisms involving the non-coding portion of the human transcriptome. Concretely, the assembly of protein complexes promoted by lncRNAs and 3’UTRs is investigated using large-scale datasets of protein-protein and protein-RNA interactions. This enabled to (i) predict hundreds of lncRNAs as possible scaffolding molecules for more than half of the known protein complexes, as well as (ii) infer more than a thousand distinct 3’UTR-protein complexes, including cases likely to post-translationally regulate moonlighting proteins, proteins that perform multiple unrelated functions. These results indicate that a high proportion of lncRNAs and 3’UTRs may be employed in regulating protein function, potentially playing a role both as regulators and as components of complexity.

Nos eucariotos, a evolução dos sistemas de transporte molecular foi essencial pois seu alto grau de compartimentalização requer mecanismos com maior especificidade para a localização de proteínas. Com o estabelecimento das mitocôndrias e plastídeos como organelas da célula eucariota, grande parte dos genes específicos para sua atividade e manutenção foram transferidos ao núcleo. Após a transferência gênica, a maioria das proteínas passaram a ser codificadas pelo núcleo, sintetizadas no citosol e direcionadas às organelas por uma maquinaria complexa que envolve receptores nas membranas das organelas, sequências de direcionamento nas proteínas e proteínas citossólicas que auxiliam o transporte. A importação depende em grande parte de uma sequência na região N-terminal das proteínas que contém sinais reconhecidos pelas membranas organelares. No entanto, muito ainda não é compreendido sobre o transporte de proteínas organelares e fatores ainda desconhecidos podem influenciar o direcionamento sub-celular. O objetivo deste trabalho foi a caracterização da General Regulatory Factor 9 (GRF9), uma proteína da família 14-3-3 de Arabidopsis thaliana potencialmente envolvida no direcionamento de proteínas organelares, e a geração de um genótipo para ser utilizado na obtenção de uma população mutante para genes que afetam o direcionamento da proteína Tiamina Monofosfato Sintetase (TH-1). Após experimentos in vivo e in planta, foi observado que GRF9 interage com as proteínas duplo-direcionadas Mercaptopyruvate Sulfurtransferase1 (MST1) e a Thiazole Biosynthetic Enzyme (THI1), e com a proteína direcionada aos cloroplastos TH-1. Experimentos de deleção e interação in vivo mostraram que a região Box1 de GRF9 é essencial para a interação com THI1 e MST1. Com a finalidade de dar continuidade a caracterização da GRF9 e para realização de testes com relação a sua função no direcionamento de proteínas organelares foi gerada uma linhagem homozigota que superexpressa GRF9. Plantas expressando o transgene TH-1 fusionado a Green Fluorescent Protein (GFP) em genótipo deficiente na TH-1 (CS3469/TH-1-GFP) foram obtidas para a geração de população mutante que possibilitará a descoberta de componentes genéticos ainda desconhecidos e responsáveis pelo direcionamento de proteínas aos cloroplastos. / In Eukaryotes, the evolution of molecular transport in the cell was essential due to their increase in compartmentalization, which requires more specific mechanisms for the correct localization of proteins. With the establishment of mitochondria and plastids as organelles, a great number of their genes, either specific for their metabolic functions or maintenance of their own transcription/translation processes, were transferred to the nucleus of the cell. These transfers caused most of the organellar proteins to be coded by the nucleus, then synthesized in the cytosol and targeted to the organelles by a complex machinery which involves membrane receptors in the organelles, targeting sequences in the proteins, and cytosolic proteins which assist them with the transport. Protein import depends greatly on an N-terminal sequence in proteins which has recognizable signals for the organellar membrane receptors. However, much is still not understood about the transport of organellar proteins, and unknown factors may still influence subcellular targeting. The goal of this work was the characterization of General Regulatory Factor 9 (GRF9), a protein of the 14-3-3 family in Arabidopsis thaliana potentially involved in the targeting of organellar proteins, and generating a genotype to be used in obtaining a mutant population for genes affecting the targeting of the protein Thiamine Requiring 1 (TH-1). After in vivo and in planta experiments it was observed that GRF9 interacts with the dual-targeted proteins Mercaptopyruvate Sulfurtransferase1 (MST1) and Thiazole Biosynthetic Enzyme (THI1), and with the chloroplast targeted protein TH-1. Deletion experiments followed by in vivo interaction assays showed that Box 1 region of GRF9 is essential for the interaction with THI1 and MST1. For the continuing characterization of GRF9 and for following tests of its function in the targeting of organellar proteins, a homozygous line was generated overexpressing GRF9. Plants expressing the transgene TH-1 fused to the Green Fluorescent Protein (GFP) in a TH-1 deficient genotype (CS3469/TH-1-GFP) were obtained for the generation of a mutant population which will allow the discovery of genetic components still unknown responsible for targeting proteins to the chloroplasts.

Veränderungen in phosphorylierungsabhängigen Signalwegen, Akkumulation von Proteinaggregaten im Gehirn und neuronaler Zelltod sind Neurodegenerationskennzeichen und Indikatoren für überlappende molekulare Mechanismen. Um Einblicke in die involvierten Signalwege zu erhalten, wurde mit Hilfe eines modifizierten Hefe-Zwei-Hybrid (Y2H)-Systems für 71 Proteine, die mit neurologischen Erkrankungen assoziiert sind, proteomweit nach Protein-Protein Interaktionen (PPIs) gesucht. Für 21 dieser Proteine wurden PPIs identifiziert. Das Gesamtnetzwerk besteht aus 79 Proteinen und 90 PPIs von denen 5 phosphorylierungsabhängig sind. Ein Teil dieser PPIs wurde in unabhängigen Interaktionsassays mit einer Validierungsrate von 66 % getestet. Der netzwerkbasierte Versuch verbindet erfolgreich neurologische Erkrankungen untereinander aber auch mit zellulären Prozessen. Ser/Thr-Kinase abhängige PPIs verknüpfen zum Beispiel das Parkinson Protein 7 (PARK7, DJ1) mit den E3 Ligase Komponenten ASB3 und RNF31 (HOIP). Die Funktion dieser Proteine bekräftigt den Zusammenhang zwischen dem Ubiquitin-Proteasom-System und der Parkinson Krankheit (PD). Neurofibromin 2 (NF2, merlin) Isoformen und PARK7 interagieren mit der regulatorischen PI3K Untereinheit p55-gamma (PIK3R3). Diese PPIs basieren auf Tyr-Kinase Aktivität im modifizierten Y2H System und funktionellen PIK3R3 pTyr-Erkennungsmodulen (SH2 Domänen) in co-IP und Venus PCA Versuchen. Dies verknüpft den PI3K/AKT Überlebenssignalweg mit zwei unterschiedlichen neurologischen Erkrankungsphenotypen: dem PD assoziierten neuronalen Zelltod und der Neurofibromatose Typ 2-assoziierten Tumorentstehung. Die vergleichende Beobachtung von PIK3R3, AOF2 (KDM1A, LSD1) Interaktionen auf NF2 Isoformlevel offenbart eine Bevorzugung von Isoform 7 bei zytoplasmatischer Lokalisation, wohingegen Isoform 1 PPIs an der Membran lokalisiert sind. Das modifizierungsabhängige und isoformspezifische PPI Netzwerk ermöglichte neue Hypothesen zu molekularen Pathomechanismen. / Alterations in phosphorylation-dependent signalling pathways, accumulation of aggregated proteins in the brain and neuronal apoptosis are common to neurodegeneration and implicate overlapping molecular mechanism. To gain insight into involved pathways, a modified yeast-two hybrid (Y2H) system was applied to screen 71 proteins associated with neurological disorders in a proteome-wide manner. For 21 of these proteins interactions were identified including 5 phosphorylation-dependent ones. In total, the network connected 79 proteins through 90 protein-protein interactions (PPIs). A fraction of these Y2H PPIs was tested in secondary interaction assays with a validation rate of 66 %. The described network-based approach successfully identified proteins associated with more than one disorder and cellular functions connected to specific disorders. In particular, the network revealed Ser/Thr kinase-dependent PPIs between the Parkinson protein 7 (PARK7, DJ1) and the E3 ligase components ASB3 and RNF31 (HOIP). The function of these proteins further substantiates the established connection between Parkinson’s disease (PD) and ubiquitination-mediated proteasome (dis)functions. Neurofibromin 2 (NF2, merlin) isoforms and PARK7 were identified as PI3K regulatory subunit p55-gamma (PIK3R3) interactors. These PPIs required Tyr kinase coexpression in the modified Y2H system and functional PIK3R3 pTyr-recognition modules (SH2 domains) in co-IP and Venus PCA experiments. This finding implicates the PI3K/AKT survival pathway in PD-associated neuronal apoptosis and Neurofibromatosis type 2-associated tumour formation. Investigation of PIK3R3, AOF2 (KDM1A, LSD1) and EMILIN1 PPIs on NF2 isoform level revealed preferential isoform 7 binding and cytoplasmic or membrane localisation of these PPIs for isoform 7 or 1, respectively. The generated modification-dependent and isoform-specific PPI network triggered many hypotheses on the molecular mechanisms implicated in neurological disorders.