Thesis (Ph. D.)--University of Missouri-Columbia, 2002. / Typescript. Vita. Includes bibliographical references (leaves 177-189). Also available on the Internet.

Ribosome biogenesis is a crucial yet poorly understood and complex process in all cells. To date, most studies on eukaryotic ribosome biogenesis have relied on yeast genetics and whole cell analysis of ribosomal RNA processing. An early and critical step in ribosome biogenesis is the post-transcriptional modification of rRNA. Pseudouridylation is the most frequently occurring modification. Pseudouridylation is catalyzed by H/ACA small nucleolar ribonucleoproteins (snoRNPs) which are one of the two major classes of snoRNPs found within eukaryotes and archaea. H/ACA snoRNPs consist of four conserved core proteins Cbf5, Gar1, Nop10, and Nhp2 (eukaryotes), and a substrate specific H/ACA snoRNA. Mutations causing the rare inherited disease Dyskeratosis congenita are found in CBF5, NOP10, and NHP2. Here I report the purification of H/ACA protein Cbf5 in the presence of detergents. Additionally, I report initial in vitro RNA binding studies using Nhp2 and the snoRNA snR34 as well as the effects of Dyskeratosis congenita substitutions within Nhp2 on this interaction. / vii, 83 leaves : ill. ; 29 cm

Tandem mass spectrometry (MS/MS) has been routinely used to identify peptides from protein mixtures in the field of proteomics. However, only about 30% to 40% of current MS/MS spectra can be identified, while many of them remain unassigned, even though they are of reasonable quality. The ubiquitous presence of post-translational modifications (PTMs) is one of the reasons for current low spectral identification rate. In order to identify post-translationally modified peptides, most existing software requires the specification of a few possible modifications. However, such knowledge of possible modifications is not always available. In this thesis, we describe a new algorithm for identifying modified peptides without requiring users to specify the possible modifications before the search routine; instead, all modifications from the Unimod database are considered. Meanwhile, several new techniques are employed to avoid the exponential growth of the search space, as well as to control the false discoveries due to this unrestricted search approach. A software tool, PeaksPTM, has been developed and it has already achieved a stronger performance than competitive tools for unrestricted identification of post-translationally modified peptides. Another important reason for the failure of the search tools is the inaccurate mass or charge state measurement of the precursor peptide ion. In this thesis, we study the precursor mono-isotopic mass and charge determination problem, and propose an algorithm to correct precursor ion mass error by assessing the isotopic features in its parent MS spectrum. The algorithm has been tested on two annotated data sets and achieved almost 100 percent accuracy. Furthermore, we have studied a more complicated problem, the MS/MS preprocessing problem, and propose a spectrum deconvolution algorithm. Experiments were provided to compare its performance with other existing software.

A complete proteome analysis of the chloroplast stroma, using 2D-PAGE, from spinach and Arabidopsis was performed. To improve the identification of proteins a computer program named SPECLUST was used. In SPECLUST, peak masses that are similar in many spots cluster together because they originate from the same protein with different locations on the gel. Within this program peaks in a cluster can be investigated in detail by peaks-in-common, and the unidentified masses that differ between spots in a cluster could be caused by protein modifications, which was analysed further by MS/MS. The thylakoid is an internal membrane system in the chloroplast where protein complexes involved in photosynthesis are housed. Enclosed in the thylakoid membrane is the chloroplast lumen, with a proteome estimated to contain 80-200 different proteins. Because the chloroplast lumen is close to the photosynthesis machinery in the plant, one can expect that the lumen proteome will change depending on if the plant is dark or light adapted. DIGE analysis of lumen proteins found that 15 lumen proteins show increased relative abundance in light-adapted plants. In addition co-expression analysis of lumen protein genes suggests that the lumen protein genes are uniformly transcriptionally regulated, not only by light but in a general manner. Plastocyanin is one of the proteins involved in the electron transfer in photosynthesis. Two homologous plastocyanin isoforms are encoded by the genes PETE1 and PETE2 in the nuclear genome of Arabidopsis, where PETE2 is the more abundant isoform. Knockout mutants of each of the plastocyanin isoforms shows that a 90% reduction of plastocyanin levels affects rates of photosynthesis and growth only slightly. A corresponding over-expression of plastocyanin in each of the two knockout mutants results in essentially wild-type photosynthetic performance. Reduced plastocyanin levels make the plant sensitive to Cu stress and therefore plastocyanin plays a major role as a Cu sink. A by-product of photosynthesis is hydrogen peroxide, which may be harmful for the plant. The discovery that an abundant protein found in the chloroplast lumen, TL29, shared sequence homology to Ascorbate Peroxidase (APX) was therefore of interest. We have evidence that TL29 is not an APX protein; it lacks the heme-binding active site and shows no activity. TL29 is located in the grana region and is electrostaticaly attached to the thylakoid membrane. It has four isoforms, with different pIs, both in the native and denatured form. It has no interaction with ascorbate, when compared to raAPX1. TL29 has two cysteine residues and one of them seems to have redox-regulated function, proposing that it may interact with other proteins close to PSII.

High quality reagents are preconditions for high performance protein analyses. But despite progress in some techniques, e.g. mass spectrometry, there is still a lack of affinity-based detection techniques with enhanced precision, specificity, and sensitivity. Building on the concept of multiple affinity recognition reactions and signal amplification, a proximity ligation assay (PLA) was developed as a molecular tool for analyzing proteins and their post-translational modification and interactions. PLA enhanced the analysis of protein expression levels and post-translational modifications in western blotting (Paper I), which had elevated sensitivity and specificity, and an ability to investigate protein phosphorylation. A general and straightforward method was established for the functionalization of affinity reagents through adding DNA strands to protein domains for protein analysis in medicine (Paper II). A method for protein domain-mediated conjugation was developed to simplify the use of recombinant affinity reagents, such as designed ankyrin repeat protein (DARPin), in DNA-mediated protein analyses. Alzheimer’s disease (AD) is characterized by progressive cognitive decline and memory impairment, and amyloid-beta plaques and neurofibrillary tangles (NFT) in the brain are clinical hallmarks of the disease. In order to understand the mechanisms underlying the formation of NFT, in situ PLA was used to explore the role of microtubule affinity related kinase 2 (MARK2) in phosphorylating tau protein during the pathological progress of AD (Paper III). The analyses of roles of MARK proteins 1-4 in phosphorylating tau protein in cells and in post-mortem human brains were performed in Paper IV. The focus of this thesis was the study of post-translational modifications and interactions of proteins in medicine. Procedures for high performance protein analysis in western blotting via proximity ligation were developed, and a functionalization method for recombinant affinity reagents in DNA-mediated protein analysis was established. These and other techniques were used to investigate the roles of tau-phosphorylating MARK family proteins in AD.

Thesis (Ph. D.)--Ohio State University, 2006. / Full text release at OhioLINK's ETD Center delayed at author's request

La sumoylation représente, après l’ubiquitination, l’exemple le plus étudié de modification post-traductionnelle impliquant la liaison d’une protéine à une autre. Cependant, alors que l’ubiquitination est impliquée principalement dans la dégradation des protéines par le protéasome, la sumoylation semble réguler les propriétés biochimiques de ses substrats (localisation cellulaire, interaction protéique, activité, …). Pour venir lier une protéine appelée Sumo (Small Ubiquitin-like Modifier) sur un substrat, la sumoylation emprunte une voie enzymatique analogue à celle de l’ubiquitination mais utilise des enzymes différentes. A ce jour, bien que plusieurs centaines de substrats de la sumoylation aient été identifiés, seules 5 structures de protéines sumoylées ont été résolues. Elles ne sont vraisemblablement pas représentatives de l’ensemble des substrats de la sumoylation et mon travail de thèse vise à élargir les connaissances structurales sur la sumoylation pour permettre de dégager des concepts généraux. <p>Les études sur la sumoylation se heurtent généralement à la difficulté d’obtenir les substrats sumoylés. Ce projet a donc nécessité, au niveau technique, la mise au point d’un système de sumoylation in vivo en bactérie permettant de modifier des quantités importantes de protéines et de les purifier efficacement. <p>Des analyses bioinformatiques nous ont permis d’identifier des substrats de la sumoylation propices à une étude structurale de leur forme sumoylée. Au terme de ces analyses, nous avons retenu 3 protéines :DJ-1, PPARγ et IκBα. Bien que la complexité du sujet nous ait ensuite amené à écarter DJ-1 et PPARγ, nous sommes parvenus à purifier la forme sumoylée d’IκBα. Ce résultat nous a permis d’entreprendre une campagne de cristallogenèse d’IκBα complexé au facteur de transcription NF-κB. L’obtention d’IκBα sumoylé permettra également d’aborder des études fonctionnelles pour améliorer la compréhension du rôle de la sumoylation de ce substrat. <p>Nos analyses bioinformatiques ont également révélé que dans plus de 60% des cas, les sites de sumoylation des substrats se trouvent dans des zones prédites intrinsèquement désordonnées. L’importance du désordre dans le processus de sumoylation était jusqu’alors largement sous-estimée. A titre d’exemple, nous avons étudié par diffusion des rayons X aux petits angles la structure du domaine transactivateur du facteur de transcription ERM sous forme non modifiée et sous forme sumoylée. Cette étude indique que la sumoylation d’ERM n’induit pas le repliement de ce domaine transactivateur. De même, il apparait peu probable, au vu de la flexibilité de cette région, que la sumoylation empêche des interactions avec certains partenaires cellulaires. Dans ce contexte, la sumoylation semble servir de plateforme de recrutement de partenaires, reconnaissant de manière spécifique le Sumo. Ce mécanisme pourrait se généraliser à l’ensemble des sites de sumoylation prédits dans des zones intrinsèquement désordonnées. <p>Le système de sumoylation que nous avons développé permet de produire des protéines sumoylées pures en grande quantité et pourra également servir à identifier des protéines reconnaissant spécifiquement les substrats modifiés. Tous ces éléments devraient permettre de progresser dans la compréhension de cette modification post-traductionnelle impliquée dans de nombreux processus cellulaires fondamentaux. <p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

L’obésité est un problème de santé publique, de par son incidence et son association avec d’autres pathologies. La leptine est une hormone clé pour l’homéostasie énergétique et glucidique, en activant son récepteur OBR, exprimé majoritairement dans l’hypothalamus. L’obésité est fréquemment associée à une résistance à la leptine, caractérisée par une diminution de la sensibilité à l’hormone. Comprendre les mécanismes moléculaires à l’origine de cette résistance, afin de la prévenir ou de la corriger, constitue un enjeu thérapeutique majeur. L’objectif de mes travaux de thèse a été d’étudier deux nouveaux mécanismes de la régulation de la fonction d’OBR, suspectés être à l'origine de la résistance à la leptine associée à l’obésité.Concernant le premier mécanisme, notre laboratoire a découvert la protéine Endo1, qui interagit avec OBR, et le retient dans des compartiments intracellulaires, limitant ainsi la sensibilité de la cellule à l’hormone. Mon travail a contribué à montrer que l'extinction d'Endo1, dans le noyau arqué de l’hypothalamus, associée au retour à un régime classique, permet de corriger l’installation de la résistance à la leptine et de l’obésité de souris rendues obèses par régime gras. En revanche, l'extinction d'Endo1 n’arrive pas à corriger l’altération de l’homéostasie glucidique de ces animaux sous régime gras, montrant ainsi une dissociation entre obésité et diabète de type II. Sur le plan moléculaire, nous montrons qu'Endo1 régule de façon différentielle les voies de signalisation d’OBR. Endo1 inhibe, comme attendu, l'activation de la voie anorexigène STAT3 ; mais de façon plus surprenante, Endo1, en interagissant avec la sous-unité régulatrice de la PI3K (p85), semble nécessaire à l'activation de la voie PI3K/AKT, voie impliquée dans le métabolisme du glucose. Ces résultats suggèrent le rôle crucial d’Endo1 comme (i) régulateur de la sensibilité neuronale à la leptine, (ii) et médiateur de la signalisation de la leptine.Le second projet, mené en collaboration avec l'équipe du Dr Prévot, a permis d’identifier une nouvelle modification post-traductionnelle (PTM) affectant OBR. Nous avons étudié les conséquences de cette PTM sur l’activation d’OBR, sa signalisation et sur le développement de la résistance à la leptine et l'obésité. Des résultats in vivo ont montré que l’enzyme responsable de la PTM voit son activité augmentée dans l’hypothalamus de souris rendues obèses par régime gras. L’inactivation génétique ou pharmacologique de cette enzyme prévient la mise en place d’une résistance à la leptine, de façon dépendante d’OBR. Au niveau moléculaire, nous avons identifié certains résidus d’OBR comme cibles de cette PTM. La modification de ces résidus cruciaux altère l’état d’activation moléculaire d’OBR et abolie l’activation des voies de signalisation induites par la leptine. En outre, cette enzyme interagit avec OBR dans des cellules hypothalamiques ; sa suractivation au niveau cellulaire, après traitement au palmitate mimant le régime gras, abolit l’activation de la voie PI3K/AKT induite par la leptine. Aussi, ces résultats démontrent que cette PTM affectant OBR est un nouveau mécanisme à l’origine de la résistance à la leptine et ouvre donc de nouvelles perspectives thérapeutiques. / Obesity is a major issue of public health because of its incidence and association with other pathologies. Leptin is a key hormone involved in the regulation of energy and glucose homeostasis, through the activation of its receptor OBR, mainly expressed in the hypothalamus. Obesity is frequently associated with leptin resistance, characterized by a decreased sensitivity to the hormone. Understanding the molecular mechanisms related to leptin resistance, in order to prevent or reverse it, represents major therapeutic concerns. The objective of my PhD work was to explore two new mechanisms involved in the regulation of OBR function, suspected to be related to leptin resistance associated with obesity.Regarding the first mechanism, the laboratory described a new protein namely Endo1, which interacts with OBR and retains the receptor in intracellular compartments, leading to decreased cellular leptin sensitivity. We showed that Endo1 silencing, specifically in the arcuate nucleus of hypothalamus, combined with a switch to chow diet, reverses the establishment of leptin resistance and obesity of obese mice fed a high fat diet (HFD). However, Endo1 silencing cannot reverse the alteration of glucose homeostasis upon HFD feeding, underlying a disassociation between obesity and type II diabetes. At the molecular level, we showed that leptin-induced signaling pathways are differentially regulated by Endo1. Endo1 inhibits, as expected, the anorectic STAT3 pathway; but surprisingly, by interacting with the PI3K regulatory subunit (p85), Endo1 seems to be necessary for the activation of PI3K/AKT pathway, which is involved in glucose homeostasis. These results indicate a crucial role for Endo1 as (i) a regulator of neuronal leptin sensitivity, (ii) a scaffolding protein involved in leptin signaling transduction.The second mechanism, investigated in collaboration with Dr. Prevot’s team, is based on the discovery of a new post-translational modification (PTM) on OBR. We studied the functional consequences of this PTM on OBR activation state, its signaling and the development of leptin resistance and obesity. In vivo results showed that the enzyme responsible for the PTM has an increased activity in the hypothalamus of obese mice fed a HFD. Genetic or pharmacological inactivation of this enzyme prevents the establishment of leptin resistance, in an OBR dependent manner. At the molecular level, we identified some OBR residues that can undergo this PTM. Modifications of those crucial residues by the PTM impair the molecular activation state of OBR and subsequently abolish the activation of leptin-induced signaling pathways. Likewise, this enzyme interacts with OBR in hypothalamic cell; and its overactivation at the cellular level after palmitate treatment (mimicking HFD), abolishes the leptin-induced PI3K/AKT activation. These results demonstrate that the PTM targeting OBR is a new mechanism underlying leptin resistance and thus open new therapeutic perspectives against obesity.

La SUMOylation est une modification post-traductionnelle essentielle pour toutes les cellules eucaryotes. C’est un processus enzymatique qui permet la liaison covalente du polypeptide SUMO sur des résidus lysine de protéines cibles. La SUMOylation est un processus réversible sous l’action de désumoylases appelées SENP. Il est critique de maintenir un équilibre entre forme modifiée et non modifiée d’un substrat donné. En effet, la dérégulation de la balance SUMOylation/déSUMOylation a été mise en évidence dans plusieurs pathologies cérébrales. La synapse est le point de contact entre les neurones où s’effectue la communication synaptique. Ce sont des structures très denses où le processus de SUMOylation régule l’interaction et la fonction de multiples protéines. Durant ma thèse, j'ai combiné l’utilisation de l'imagerie en temps réel sur cellules vivantes avec des approches biochimiques et pharmacologiques pour identifier les mécanismes de régulation du transport de SENP1. J'ai ainsi démontré que l'activation neuronale augmente les niveaux synaptiques de SENP1. Cette augmentation synaptique résulte de la modification de la vitesse de diffusion de l’enzyme SENP1 entre les dendrites et les synapses d’une part, et d’autre part, de l’augmentation importante du temps de rétention synaptique de l’enzyme. Je rapporte également que ce mécanisme de régulation dynamique de SENP1 implique l'activation des récepteurs métabotropiques du glutamate. De plus, je suggère la participation du processus de phosphorylation dans cette régulation synapto-dendritique de SENP1 mettant ainsi en lumière un nouveau mécanisme de régulation de la balance neuronale entre SUMOylation et déSUMOylation. / Sumoylation is a vital eukaryotic posttranslational modification. Sumoylation occurs as an enzymatic cycle that conjugates SUMO proteins to target proteins. SUMO proteases (SENP) deconjugate SUMO from modified proteins and thus maintain balanced levels of SUMOylated and un-SUMOylated proteins required for physiological homeostasis. Neuronal synapses are protein-rich structures that underlie synaptic transmission and plasticity. Strong evidence exists that sumoylation occurs in synapses and regulates the function of synaptic proteins. Indeed, distortion of the SUMO balance has been linked to several pathologies of the synapse. Gaining a deeper understanding into the molecular mechanisms regulating the SUMO balance is a prerequisite to envisaging the development of novel therapies. In my PhD work, I used a combination of live-cell confocal imaging, protein biochemistry and pharmacological approaches to identify SENP1 regulatory mechanisms at synapses. I provided evidence that synaptic activation increases SENP1 protein levels at synapses. I showed that the increase in synaptic SENP1 upon synaptic activation is a result of two processes: Although (a) fewer SENP1 proteins enter into spines at low diffusion speed (b) a significant proportion of SENP1 becomes immobile and is retained in spines. I demonstrate that the regulatory mechanisms of SENP1 dynamics involve a direct activation of mGlu1/5 receptors. Moreover, I suggest that phosphorylation may play an important regulatory role in SENP1 synapto-dendritic diffusion. Altogether, I propose a novel mechanism driving for the SUMO balance at synapses.

The Bordetellae are aerobic Gram-negative coccobacilli colonizing the upper respiratory tract of mammals and thereby causing diseases with similar symptoms but different host specificity. The bacteria produce a variety of adhesins and toxins that facilitate their ability to promote infection and evade the innate immune system. Among them, the filamentous hemagglutinin (FHA) and the adenylate cyclase toxin (CyaA) are the major virulence factors providing the adherence to the host epithelial cells and the protection against bactericidal activity of phagocytic cells, respectively. Moreover, CyaA along with the Escherichia coli α-hemolysin (HlyA) and the Kingella kingae cytotoxin (RtxA) represent a prominent group of Repeats in ToXin (RTX) cytotoxins/hemolysins that undergo post-translational acylation on conserved lysine residues. Here, different mass spectrometry approaches were employed to analyze the structural features of FHA and to characterize the acylation status of the RTX toxins and their various hybrid molecules. First, the differential 16O/18O labeling revealed that the mature FHA proteins of B. pertussis (Bp-FHA) and the B. bronchiseptica (Bb-FHA) are processed at different sites, after Ala2348 and Lys2479 of the FhaB precursor, respectively. Second, the bottom-up proteomics of the...