Le cytosquelette représente un élément crucial dans les processus cellulaires essentiels des cellules lymphoïdes. Les différents filaments du cytosquelette et leurs modes de régulation représentent donc des cibles thérapeutiques majeures pour le développement de nouveaux composés pharmacologiques. Au cours de ce travail de thèse, nous avons mis au point une nouvelle méthode d’analyse par cytométrie en flux (CytoFRET) permettant de visualiser simultanément la dynamique de polymérisation des filaments d’actine, des microtubules et des filaments intermédiaires de vimentine dans la lignée leucémique T Jurkat. Cette méthode a été utilisée pour le criblage d’une mini-chimiothèque composée d’inhibiteurs d’enzymes impliquées dans les modifications post-traductionnelles des protéines. Nous avons ainsi identifié deux composés, le WP1130 et le b-AP15, des inhibiteurs d’enzymes de déubiquitination (DUBs), comme puissants inducteurs de la polymérisation/nucléation de l’actine. Nous avons montré que l’effet de ces inhibiteurs sur les microfilaments d’actine est consécutif à une poly-ubiquitination de la Destrine, une protéine de liaison à l’actine. Nous avons également identifié des inhibiteurs des déacétylases HDAC6 et SIRT2 comme inducteurs de la polymérisation des microtubules et de l’assemblage de la vimentine. L’effet de ces inhibiteurs a été corrélé à une acétylation directe de la tubuline mais pas de la vimentine. Ces résultats ouvrent ainsi de nouvelles perspectives à la fois fondamentale et thérapeutique sur la physiopathologie du cytosquelette des cellules lymphoïdes. / Actin, microtubules, and intermediate filaments compose three major cytoskeletal structures of vertebrate cells that are characterized by highly dynamic balances between assembly and de-assembly, underlying critical cellular processes such as mitosis, architecture and movement. Consequently, cytoskeleton dysfunctions have been implicated in several pathological situations including cell transformation and metastasis. Thus, cytoskeletal networks represent major targets for the development of novel anti-cancer and anti-metastatic therapies. However, drug development is currently limited by the availability of high-throughput screening systems allowing the simultaneous monitoring of actin, microtubules and intermediate filaments dynamics in living cells. In this work, we have developed a novel screening assay of cytoskeleton dynamics based on the simultaneous recording by flow cytometry of FRET signals produced by the variation of actin, tubulin and vimentin filaments dynamics in living cells. Our novel method was employed to screen a mini-library of drugs known for their ability to interfere with post-translationnal modifications of proteins. Interestingly, our approach revealed that compounds interfering with lysine acetylation have a dramatic impact on vimentin filaments assembly and microtubules polymerization. In addition, two inhibitors (WP1130 and b-AP15) of deubiquitinating enzymes showed increase of actin polymerization. This effect was attributed to poly-ubiquitnation of Destrin, an actin binding protein. In conclusion, our FRET multiplex flow cytometry assay represents a novel effective method for the future development of new anti-cancer therapies.

Posttranslational modification (PTM) of proteins is essential to creating a diverse proteome with the complex functions necessary to regulate key cellular processes. Redox-based PTMs exhibit many desirable characteristics to finely modulate transcriptional regulators; they occur rapidly and can alter protein conformation, localisation and activity. The plant immune system offers an excellent model in which to study redox-based modifications due to the rapid accumulation of oxidising agents that occurs during immune invasion. This so-called “oxidative burst” causes spontaneous oxidation of cysteine residues that are present in many regulatory proteins. These modifications fine-tune the activities of proteins that harbour them, enabling them to act in a concerted effort to reprogram the transcriptome, prioritising the expression of immune-related genes over housekeeping genes. Disulphide bonds (S-S) and S-nitrosothiols (SNO, i.e. the addition of an NO group to a cysteine moiety) have been shown to play particularly important roles in plant immunity. However, what still remains unclear is how these redox-based PTMs are rendered reversible, enabling them to act as molecular signalling switches. The work presented in this thesis explores a class of enzymes that are responsible for controlling the cellular levels of protein oxidation: the Thioredoxins. In addition to their well-established role in reducing disulphide bonds, I demonstrate in Chapter 3 that Thioredoxins are able to reverse protein S-nitrosylation during plant immune signalling. Immune-inducible Thioredoxin-h5 (TRXh5) was shown to be unable to restore immunity in gsnor1 mutants that display excessive accumulation of the NO donor S-nitrosoglutathione, but rescued impaired immunity and defence gene expression in nox1-mutants that exhibit elevated levels of free NO. This data indicates that TRXh5 discriminates between protein-SNO substrates to provide previously unrecognized specificity and reversibility to protein-SNO signalling in plant immunity. Furthermore, data is presented to show that TRXh5 reversed the effects of S.nitrosylation on many immune-related transcriptional regulators in vitro, forming the initial stages of an investigation into which proteins and pathways might be controlled by reversible S-nitrosylation in plant immunity (Chapters 3 & 4). Although the majority of transcriptional regulators are likely modified at their site of action, the nucleus, very little is currently known about nuclear redox signalling in plants. Therefore, in Chapter 5 a subclass of theThioredoxin superfamily was studied, the Nucleoredoxins, which have previously been shown to display disulphide reduction activity and localise in part to the nucleus. Here it is revealed that the activity and nuclear accumulation of Nucleoredoxin 1 (NRX1) is induced by the plant leaf pathogen Pseudomonas syringae, suggesting a key role for this protein in immune signalling. Target-capture experiments and subsequent mass spectrometry analysis identified the first in vitro targets of NRX1 and revealed many proteins with roles in oxidative stress, including the hydrogen peroxide scavenger Catalase 2 (CAT2). Moreover, overexpression of NRX1 was shown to be able to rescue the enhanced cell death phenotype of cat2 knockout mutants in response to the oxidative stressor, methyl viologen. Accordingly, nrx1 knockout mutants also exhibited an enhanced cell death phenotype in response to methyl viologen treatment. Together, these data indicate that NRX1 plays a key role in the control of oxidative stress-mediated cell death, potentially through direct regulation of Catalase proteins. Taken together, the work in this thesis implicates members of the Thioredoxin family as key regulators of transcriptional reprogramming during plant immunity and uncovers a novel role for Thioredoxin superfamily member, NRX1, in the control of oxidative stress.

Inorganic contaminants, including potentially toxic metals (PTMs), originating from un-reclaimed abandoned mine areas may accumulate in soils and present significant distress to environmental and public health. The ability to generate realistic spatial distribution models of such contamination is important for risk assessment and remedial planning of sites where this has oc-curred. This study evaluated the prediction accuracy of optimized ordinary kriging compared to spatial regression-informed cokriging for PTMs (Zn, Mn, Cu, Pb, and Cd) in soils near abandoned mines in Bumpus Cove, Tennessee, USA. Cokriging variables and neighborhood sizes were system-atically selected from prior statistical analyses based on the association with PTM transport and soil physico-chemical properties (soil texture, moisture content, bulk density, pH, cation exchange capacity (CEC), and total organic carbon (TOC)). A log transform was applied to fit the frequency histograms to a normal distribution. Superior models were chosen based on six diagnostics (ME, RMS, MES, RMSS, ASE, and ASE-RMS), which produced mixed results. Cokriging models were preferred for Mn, Zn, Cu, and Cd, whereas ordinary kriging yielded better model results for Pb. This study determined that the preliminary process of developing spatial regression models, thus enabling the selection of contributing soil properties, can improve the interpolation accuracy of PTMs in abandoned mine sites.

No description available.

La voie de réparation NER implique une cascade de complexes protéiques dont le senseur des dommages de l’ADN (XPC/HR23B). Des mutations dans les gènes de la NER (TTD-A, XPA-G, XPV, CSA et CSB), sont associées à des maladies génétiques humaines dont le Xeroderma Pigmentosum (XP), la Trichothiodystrophie (TTD) et le syndrome de Cockayne (CS). L’ensemble des symptômes des patients ne peut être expliqué seulement par un défaut de la réparation de l’ADN. Or depuis quelques années, il a été prouvé que les facteurs de la NER sont aussi impliqués lors de la transcription. Dans le cadre de ma thèse, je me suis particulièrement intéressé à la protéines XPC en déterminant son rôle transcriptionnel à l’échelle génomique afin de mieux comprendre les conséquences de sa dérégulation dans un contexte pathologique. En ce sens, mon second objectif a été de caractériser au niveau moléculaire l’étiologie de nouveaux patients XP en analysant de manière combinée les évènements moléculaires de la NER et la transcription associés à XPC. Nos différentes approches expérimentales ont permis d’identifier au niveau génomique un ensemble de gènes sont les promoteurs sont régulés aussi bien positivement que négativement par XPC dans un contexte RAR dépendant. De plus, nous montrons que XPC interagit avec KAT2A contenu dans le complexe ATAC, ainsi que qu’avec le facteur de transcription E2F1, le facteur de remodelage de la chromatine BRD2 et le variant d’histone H2A.Z. Via KAT2A, ce complexe va acétyler non seulement H2A.Z mais également H3K9 au niveau des promoteurs ciblés par E2F1. / NER involves a cascade of protein complexes including the DNA damage sensor (XPC/HR23B). Mutations in NER genes (TTD-A, XPA-G, XPV, CSA and CSB) are associated with human genetic diseases including Xeroderma pigmentosum (XP), Trichothiodystrophy (TTD) and Cockayne Syndrome (CS). All the symptoms can only be explained by a defect of the DNA repair. However all the symptoms can only be explained by a defect of the DNA repair. However, it has been proven that NER factors are also involved in transcription. As the genomic scale to better understand the consequences of its deregulation in a pathological context. In this sense, my second goal has been to characterize at the molecular level the etiology of new XP patients by analyzing in a combined way the molecular events of the NER and the transcription associated with XPC. Our different experimental approaches have made it possible to identify at genomic level a set of gene whose promoters are regulated both positively and negatively by XPC in a dependent RAR context. In addition, we show that XPC interacts with KAT2A contained in the ATAC complex, as well as with the transcription factor E2F1, the chromatin remodeling factor BRD2, and the histone variant H2A.Z. Via KAT2A, this complex will acetylate not only H2A.Z but also H3K9 at promoters targeted by E2F1.

Eukaryotische DNA ist in Chromatin verpackt, einem Komplex aus DNA und Proteinen. Das ermöglicht Transkriptionsregulation von Genen durch Modulation ihrer Zugänglichkeit. Histone sind evolutionär konservierte Chromatinproteine, die durch posttranslationale Modifikationen (PTMs) modifiziert sind. Das legt nahe, dass deren Primärstruktur und ihre PTMs funktionellen Beschränkungen unterliegen. Genetische Ansätze zur Entschlüsselung von Struktur-Funktions-Beziehungen für Histone waren auf Einzeller und D. melanogaster beschränkt. Das Histon-Ersatz-System in D. melanogaster, bei dem Histontransgene verwendet werden, um endogene Histone zu ersetzen, war nicht für systematische Untersuchung dieser Beziehungen ausgelegt. In meiner Arbeit habe ich die Funktion von Threonin 11 in Histon H3 (H3T11) untersucht, das phosphoryliert werden kann. Ich analysierte zwei Mutationen in H3T11 (H3T11A und H3T11E) und stellte fest, dass beide zur Derepression von Transposons führen. H3T11E hat in Gegenwart von Wildtyp-Histon H3 einen dominanten Phänotyp mit transkriptomweiten Folgen. Dazu gehören Induktion von Immun-Genen und Unterdrückung von mit DNA-Stoffwechsel in Verbindung stehenden Genen. Die Mutationen wurden unter der Prämisse charakterisiert, ein Analyse-Schema für eine große Anzahl von Histon-Ersatz-Stämmen zu entwickeln und Probleme zu identifizieren, die die Analyse beeinträchtigen. Dabei habe ich das Verfahren zur Erzeugung von Histon-Ersatz-Stämmen optimiert. Dazu gehören die optionale Verwendung größerer Histon-Transgene und zuverlässigere Produktion und optimierte Rekombinations-Strategie dieser. Ich habe das Klonierungsverfahren gestrafft und eine Plasmid-Bibliothek erstellt, die es erlaubt, 178 verschiedene mutierte Histon-H3-Transgene zu erzeugen. Mit den Änderungen am Produktionsschema, ist diese Bibliothek eine wertvolle Ressource und wird dazu beitragen, die Funktion von Histon H3 und seiner PTMs während der Entwicklung eines Vielzellers besser zu verstehen. / Eukaryotic DNA is packaged into chromatin, a complex composed of DNA and proteins. This enables transcriptional regulation of genes through modulation of their accessibility. Histones are chromatin proteins, modified by post-translational modifications (PTMs) and their sequences are conserved in evolution. This suggests functional constraints for the primary structure of histones and their PTMs. Genetic approaches to decipher structure-function relationships for histone proteins were restricted to unicellular organisms and D. melanogaster. The histone replacement system in D. melanogaster, which uses histone transgenes to replace endogenous histones, was not adapted for systematic interrogation of such relationships. Here, I investigated the function of threonine 11 in histone H3 (H3T11), which can be phosphorylated. I analyzed two mutations in H3T11 (H3T11A and H3T11E) and found that both lead to de-repression of transposable elements. I also found that H3T11E, has a dominant phenotype in the presence of wildtype histone H3 with transcriptome-wide consequences. These include induction of immune-related genes and repression of genes associated with DNA metabolism. I characterized both mutations under the premise of establishing an analysis scheme suitable for a large set of histone replacement strains and identifying problems that interfere with this analysis. As a consequence, I optimized the procedure to generate histone replacement strains. These include an option to incorporate larger histone transgenes, a more reliable production of transgenes and an optimized strategy to recombine them. I streamlined the cloning procedure and created a plasmid library allowing for the generation of 178 distinct mutant histone H3 transgenes. Together with my amendments to the production scheme, this library provides a valuable resource to the field and will help to better understand the function of histone H3 and its PTMs during the development of a multicellular organism.

No description available.

Kovalente posttranslationale Modifikationen (PTMs) beeinflussen die Struktur und Funktion von Proteinen. Zu den bedeutendsten PTMs zählt die Proteinphosphorylierung. Labile Phosphorylierungen an Cystein- und Lysinresten, sowie Pyrophosphorylierungen an Serin- und Threoninbausteinen sind vermehrt in den Fokus der Wissenschaft gerückt. Trotz großer Fortschritte auf dem Gebiet der Massenspektrometrie (MS) bleibt die Analyse dieser empfindlichen Modifikationen mittels Tandem-MS eine große Herausforderung. In der vorliegenden Arbeit wird gezeigt, dass Elektronentransferdissoziation (ETD) in Kombination mit zusätzlicher HCD Aktivierung (EThcD) in der Lage ist, Peptide mit labilen Phosphorylierungen in der Seitenkette unter Erhalt der Modifikation zu fragmentieren. In verschiedenen proteomischen Ansätzen wird demonstriert, dass EThcD eine zweifelsfreie Identifizierung natürlich vorkommender Cysteinphosphorylierungen ermöglicht. Darüber hinaus wurde unter dem Gesichtspunkt der Labilität von Lysinphosphorylierungen ein bottom-up-Phosphoproteomikansatz etabliert. Das MS-Verfahren beruht auf der Generierung eines diagnostischen Phospholysinimmoniumions, welches im zweiten Schritt die Erfassung eines zusätzlichen EThcD-Spektrums desselben Precursorions veranlässt (triggert). Darüber hinaus wird im Zuge dieser Arbeit gezeigt, dass sich pyrophosphorylierte Peptide unter CID-Bedingungen in ihrem Neutralverlustmuster von isobaren diphosphorylierten Peptiden unterscheiden. Dieses Verhalten stellt einen Schlüsselschritt in einer neutralverlustgetriggerten EThcD Methode dar, welche die zweifelsfreie Identifizierung von Pyrophosphorylierungen ermöglicht. Darauf basierend konnten in Hefezellen und humanen embryonalen Nierenzellen die ersten Proteinpyrophosphorylierungen, einer neuen endogenen posttranslationalen Modifikation, nachgewiesen werden. / Covalent posttranslational modifications (PTMs) influence the structure and function of proteins. Protein phosphorylations belong to the most important PTMs. Rarely characterized labile phosphorylations, for instance phosphorylations of cysteine and lysine and pyrophosphorylations of serine and threonine residues got into the focus of science. However, the analysis of those delicate modifications via tandem mass spectrometry remains a challenge. In the present work, it is shown that electron-transfer dissociation (ETD) combined with HCD supplemental activation (EThcD) is able to fragment peptides with labile phosphorylations at the side chains without losing the modification. In several bottom-up proteomic approaches, EThcD allowed the reliable identification of a naturally occurring cysteine phosphorylation. Moreover, methods for identification of lysine phosphorylations were developed. For the proteome wide analysis of lysine phosphorylations, considering the lability, a bottom-up phosphoproteomic approach with a highly selective mass spectrometry method was established. The MS-method relies on the generation of diagnostic phospholysine immonium ions during HCD, which trigger in a second step an additional EThcD spectrum of the same precursor ion. This strategy ensures the confident identification of lysine phosphorylated peptides. Furthermore, the present work shows that isobaric pyro- and diphosphorylated peptides differ in their neutral loss pattern during CID. This behavior was a key step in a specific neutral loss triggered EThcD method, which enabled the reliable identification of pyrophosphorylations. This method allowed the identification of the first protein pyrophosphorylations, a new endogenous PTM, in yeast and human embryonic kidney cells.

Apoptosis is a programmed cell death mechanism that is evolutionary conserved from worms to humans. Apoptosis is mediated by initiator and effector caspases. The initiator caspases carry long pro-domains for their interaction with scaffolding proteins to form a cell-death platform, which is essential for their activation. Activated initiator caspases then cleave effector caspases that execute cell death through cleaving downstream targets. In addition to their apoptotic function, caspases also participate in events where caspase activity is not required for cell killing, but for regulating other functions, so-called non-apoptotic functions of caspases. The Drosophila initiator caspase Dronc, the ortholog of mammalian caspase-2 and caspase-9 has a CARD domain that is essential for its interaction with the scaffolding protein Dark to form the apoptosome. Apoptosome formation is crucial for activation of Dronc. Activity of both initiator and effector caspases are further kept in control by the ubiquitin system to avoid inappropriate caspase activity. However, mechanistic details of how the ubiquitin system regulates activation of Dronc are not clear. Therefore, I investigated the ubiquitylation status of Dronc and its function in Drosophila. I found that Dronc is mono-ubiquitylated at Lys78 (K78) in its CARD domain, which blocks its interaction with Dark and formation of the apoptosome. Furthermore, I demonstrated that K78 mono-ubiquitylation plays an inhibitory role in Dronc’s non-apoptotic functions, which may not require its catalytic activity but may be important for the survival of the fly. This thesis study unveils the link between the ubiquitin system and caspases through a regulatory mechanism where a single mono-ubiquitylation event could inhibit both apoptotic and non-apoptotic functions of a caspase.

In recent years, Generative Language Models have exploded into the mainstream with household names like BERT and ChatGPT, proving that text generation could have the potential to solve a variety of tasks. As the number of students enrolled into programming classes has increased significantly, providing adequate feedback for everyone has become a pressing logistical issue. In this work, we evaluate the ability of near state-of-the-art Generative Language Models to provide said feedback on an automated basis. Our results show that the latest publicly available model GPT-3.5 has a significant aptitude for finding errors in code while the older GPT-3 is noticeably more uneven in its analysis. It is our hope that future, potentially fine-tuned models could help fill the role of providing early feedback for beginners, thus significantly alleviating the pressure put upon instructors.