Le réseau de protéines chaperons est hautement conservé dans l'ensemble du vivant. Il régule l'homéostasie des protéines au sein de la cellule en condition de croissance normale ainsi qu'en réponse à des stress environnementaux. Les chaperons membres de la famille HSP70 (Heat Shock Protein 70 kDa), famille particulièrement conservée, agissent tout au long de la biogénèse des protéines et orchestrent une pléthore de processus cellulaires liés au repliement et/ou au remodelage de protéines. Le cycle ATP-dépendant du chaperon HSP70 repose sur une étroite collaboration avec ses partenaires co-chaperons. Parmi ces co-chaperons, on distingue les membres de la famille DnaJ/HSP40 qui transfèrent les substrats vers HSP70 et stimulent son activité ATPasique, et les facteurs d'échange de nucléotides qui assurent la réinitialisation du cycle d'HSP70 permettant ainsi la libération du substrat. Au sein de la bactérie E. coli, la protéine HSP70 est appelée DnaK. Elle agit de concert avec les deux co-chaperons DnaJ et GrpE (ensemble nommés DnaKJE) afin d'assister les protéines dans leur repliement au cours de la synthèse de novo, de désagréger des protéines mal repliées, de faciliter l'adressage et le passage de protéines à travers les membranes biologiques, et de remodeler certains complexes protéiques impliqués dans des processus cellulaires variés. DnaKJE coopère efficacement avec d'autres systèmes chaperons majeurs, tels que la protéine Trigger Factor (TF) associée aux ribosomes et le complexe chaperonine GroESL, notamment pour le repliement de protéines nouvellement synthétisées dans le cytosol. De plus, une des fonctions cellulaires majeure du système DnaKJE est son implication dans la réponse au stress thermique (Heat Shock Response - HSR). DnaKJE contrôle la HSR en interagissant directement avec le facteur de transcription s32, sous-unité de l'ARN polymérase. Cette interaction facilite la dégradation de s32 par la protéase FtsH. En condition de stress, l'accumulation de protéines mal repliées au sein de la cellule entraine le recrutement de DnaKJE et par conséquent, la stabilisation de s32. Suite à cette stabilisation, une induction de la transcription de plus d'une centaine de gènes codant entre autres, pour des protéines chaperons et des protéases se met en place dans la cellule pour lutter contre le stress environnant. De ce fait, DnaK et ses co-chaperons sont considérés comme des éléments clés de la réponse cellulaire contre le collapse de l'homéostasie protéique par action directe sur des protéines mal repliées et indirecte en modulant la synthèse de nombreuses HSPs, via s32. L'étude récente de l'intéractome de DnaK révèle qu'au moins 50% des enzymes impliquées au sein du métabolisme central (MC) de la cellule interagissent avec DnaK à température physiologique. A travers l'analyse d'une banque de suppresseurs multi-copie, nous avons identifié six gènes associés au MC : ackA, ldhA, lpd, pykF, talB et csrC qui lorsqu'ils sont surexprimés, permettent de restaurer partiellement le défaut de croissance d'une souche mutante n'exprimant pas les chaperons DnaK et Trigger Factor (deltatig deltadnaKJ). Remarquablement, la surexpression d'ackA, talB et csrC supprime également le défaut de croissance d'un mutant dnaK à haute température, ce qui suggère une implication importante de DnaK au niveau du MC. Dans ce projet, l'implication de DnaK dans le fonctionnement du métabolisme carboné a été établi par une analyse métabolique combinant analyses macro-cinétiques (suivi de croissance, analyse de la consommation des substrats et de la production de produits du métabolisme) sur différentes sources de carbones seules ou en mélange et analyses micro-cinétiques (flux métaboliques par marquage 13C). Finalement, ces travaux apportent différentes hypothèses quant au rôle de DnaK dans le contrôle du MC, directement ou indirectement via la régulation de la HSR, en réponse à une défaillance de l'homéostasie protéique ou d'une carence nutritionnelle. / Intricate networks of highly conserved molecular chaperone machines govern cellular protein homeostasis, both under lenient and more stressful growth conditions. Members of the highly conserved HSP70 family of molecular chaperones are key players in this process, acting at nearly every step in protein biogenesis. The ATP-dependent chaperone cycle of HSP70 chaperones relies upon the cooperation with a cohort of essential cochaperones, including DnaJ/HSP40 family members that recruit the chaperone to specific substrate and/or cellular localization and stimulate its ATPase activity, and nucleotide exchange factors, which insure proper resetting of the chaperone cycle and the resulting substrate release. In the bacterium Escherichia coli, the multifunctional HSP70 chaperone, named DnaK, acts in concert with its cochaperones DnaJ and GrpE (all together referred as DnaKJE) to efficiently, assist de novo protein folding, protein disaggregation, protein targeting and translocation through biological membranes, and protein complexes remodeling leading to multiple cellular activities. Remarkably, previous works also showed that DnaKJE can efficiently cooperate with other major cytosolic chaperones, including the ribosome-bound Trigger Factor (TF) and the chaperonin GroESL, especially during the folding of newly-synthesized cytosolic proteins. In addition, one of the key cellular functions of DnaKJE in E. coli is the regulation of the heat shock response (HSR). In this case, DnaKJE controls the HSR by interacting directly with the heat shock sigma factor s32 subunit of the RNA polymerase to facilitate it degradation by the FtsH protease. Under stress condition, DnaKJE is recruited to accumulating misfolded proteins, leading to an increased stability of s32 and the subsequent induction of more than hundred heat shock proteins. Therefore, DnaK, and its cochaperones are central components of the cellular response to proteostasis collapse, both by acting directly on misfolded proteins and by modulating the synthesis a plethora of heat shock chaperones and proteases. The recently described in vivo interactome of DnaK in E. coli revealed that at least 50% of the central metabolism enzymes interact with DnaK at physiological temperature. Remarkably, through a multicopy suppression analysis we have now identified six genes of the central metabolism (CM), namely ackA, ldhA, lpd, pykF, talB and csrC, which when overexpressed partially suppress the growth defect of the sensitive double mutant lacking DnaK and Trigger Factor (deltatig deltadnaKJ ), with half of them, namely ackA, talB and csrC, additionally suppressing the growth defect of the single ?dnaKJ mutation at high temperature, thus strongly suggesting a major role of DnaK in this process. Using a combination of growth assays on specific carbon sources entering the CM at various metabolic nodes with NMR analyses for characterizing the carbon source assimilation, identifying and quantifying the metabolism by-products and determining metabolic flux rearrangements, we show that DnaKJE impacts the responsiveness of the central metabolism by acting either directly at the level of the CM or along the first step of substrate assimilation. How does the multifunctional DnaK chaperone modulate the CM, either directly or indirectly via the control of the HSR, in response to proteostasis failure or nutrient starvation is discussed.

Aptamers are nucleic acid ligands that bind to a specific target molecule. They are discovered by in-vitro selection, whereby binding sequences are selected from a large library of random sequences through iterative affinity steps. Aptamers are used as molecular recognition elements in aptamer-based, as such, creating aptamers with high affinity and specificity to their targets is important to the field. Ligands with two binding sites have been reported to have enhanced binding affinity than ligands with one binding site. To improve the quality of aptamers for downstream applications, multidomain selection is proposed as a new method for selecting aptamers compatible with dimerization. Here, we applied the multidomain selection approach to Fusobacterium nucleatum DnaK and produced aptamers that target the N-terminal domain (NTD) and the C-terminal domain (CTD) of DnaK. The top aptamer for DnaK-NTD had a Kd of 59.7 nM, and for DnaK-CTD had a Kd of 202.0 nM. However, the aptamers did not bind to the full-length DnaK and could not be dimerized. Multiple-site binding offers greater flexibility in the design of detection systems, which could provide higher selectivity and sensitivity than aptamers found through standard approaches. Validation of a method to discover aptamers compatible with dimerization would result in the development of a targeted approach to discover high-quality aptamers for bacterial proteins that can be used in bacteria-detection techniques. / Thesis / Master of Science (MSc)

Type IV pili (T4P) systems are widely utilized among bacteria to power and direct surface motility. The production and secretion of a viscous polysaccharide to provide friction and resistance to the extended pilus structure is seen in several species of cyanobacteria including Nostoc punctiforme. The complex coregulation of polysaccharide secretion and T4P motor activity is not fully understood, although studies indicate a consistent relationship between functional motility and intact pathways of polysaccharide secretion and pilus extension in cyanobacteria. Using a combination of protein-protein interaction analysis, cytological studies, and comparative genomics this study proposes a theoretical mechanism for T4P motor influenced regulation of hormogonium polysaccharide secretion by a heat-shock protein (HSP) DnaK-type chaperone system in N. punctiforme. The results of this study indicate a tripartite HSP system consisting of DnaK1, DnaJ3, and coregulator GrpE is influenced by the activation of certain motor proteins in the T4P complex and are required for the production and secretion of hormogonium polysaccharide. Conservation of this system in Synechocystis sp. also implies a potential system that is conserved among all motile cyanobacteria for regulation of T4P.

Neisseria gonorrhoeae, the causative agent of the STI gonorrhea, is not preventable by vaccination and is rapidly developing resistance to antibiotics. One important strategy for gonococcal survival in the host is iron acquisition in the face of nutritional immunity. To overcome iron limitation, the gonococcus expresses TonB dependent transporters (TdTs), outer membrane proteins that facilitate nutrient acquisition. Of the TdTs, the transferrin (Tf), lactoferrin (Lf), and hemoglobin (Hb) receptors hijack iron directly from host proteins, and studies have already shown that the Tf receptor is essential for the initiation of human infection. Given that the TdTs are virulence factors, they are widely conserved across strains, and are not subject to antigenic variation, they are ideal targets for novel therapeutics and vaccine development. As such, studies exploring these proteins and their potential as vaccine candidates and antimicrobial targets are needed. In this study we report that loops of the Tf receptor protein TbpA are not strongly immunogenic, and the antibodies raised against them are incapable of inhibiting TbpA-Tf interactions on the gonococcal cell surface. We also report that the loop 3 helix motif of TbpA is a critical functional domain for Tf-binding and iron uptake; however, no single residue was identified that was essential for these functions. In addition, we report the development of a platform for the structure-function analysis of HpuA, a member of the poorly studied Hb receptor. We also present evidence that novel small molecules may be able to inhibit TbpA-Tf interaction, presenting the Tf receptor as a novel, species-specific antimicrobial target. Finally, we demonstrated that a novel drug, OSU-03012, has antimicrobial activity against the gonococcus through down-regulation of DnaK, a protein chaperone. These findings suggest that DnaK, a widely conserved protein, may be a universal target for antimicrobial development. These studies provide insight into the structure function relationship of TbpA, the drug potential of DnaK, and lay the framework for future investigations of the TdTs for use in a multi-antigen vaccine.

Hsp70 molecular chaperones protect proteins from aggregation, assist in their native structure formation, and regulate stress responses in the cell. A mechanistic understanding of Hsp70 function will be necessary to explain its physiological roles and guide the therapeutic modulation of various disease states. To this end, several fundamental features of the Hsp70 structure-function relationship are investigated. The central component of Hsp70 chaperone function is its capacity for allosteric signaling between structural domains and tunable binding of misfolded protein substrates. In order to identify a cooperative network of sites that mediates interdomain allostery within Hsp70, a mutational correlation analysis is performed using genetic data. Evolutionarily correlations that describe an allosteric network are validated by examining roles for implicated sites in cellular fitness and molecular function. In a second component of the Hsp70 molecular mechanism, a novel function is discovered for the disordered C-terminal tail. This region of the protein enhances the refolding efficiency of substrate proteins independently of interdomain allostery and is required in the cell upon depletion of compensatory chaperones, suggesting a previously undescribed mode of chaperone action. Finally, experiments are initiated to assess the dynamic assembly of Hsp70 domains in various allosteric states and how domain orientations may be guided through interaction with partner co-chaperone proteins.

Rhodococcus equi is an important pathogen in foals between one to six months of age and is a major cause of death in in these animals. In addition, R. equi has recently emerged as a significant opportunistic pathogen in immunosuppressed humans, especially those infected with HIV. Despite the ability of the organism to survive stressful growth conditions, for example, exposure to elevated temperature and oxygen radicals, the role of heat shock proteins in the pathogenesis of R. equi has not been well documented. In this project we developed and optimised methods to purify the heat shock protein DnaK from R. equi, using a combination of ion-exchange and affinity chromatography. The effectiveness of the purification protocols were assessed using SDS-PAGE and Western-blotting with anti-DnaK antibodies, and the enzymic activity of the purified DnaK was verified with an ATPase assay. ATPase assays were also used to investigate the roles of other heat shock proteins in enhancing the activity of DnaK.

Clostridium difficile, the causative agent of C. difficile infection (CDI), causes hundreds of thousands of hospital-acquired infections in the United States and Canada annually. Furthermore, the prevalence and severity of CDI has been on the rise in developed countries, especially with the appearance of “hypervirulent” strains. Detection of CDI is thus of great importance. Traditional detection methods can be time consuming or lack the desired sensitivity. On the other hand, aptamers pose great prospects as diagnostic and therapeutic agents. Aptamers are nucleic acid ligands with molecular recognition capabilities rivaling those of antibodies. They are obtained by a process of in vitro selection known as systematic evolution of ligands by exponential enrichment (SELEX). However, the current approach may result in aptamers that experience non-specific binding in complex or biological samples. Here, we propose a multiple domain selection (MDS) method for aptamer isolation. This method utilizes independent selections on separate components of a single target in order to obtain uniquely specific aptamers. The aptamers can then be unified into a heterobivalent construct able to recognize two sites on one target. We hypothesize the combined aptamer would result in greater affinity and specificity for the target, resulting in greatly increased aptamer utility in current and future applications. In the current study, we have cloned and purified full length C. difficile DnaK as well as the N-terminal domain (NTD) and C-terminal domain (CTD) of the protein. MDS was performed on each target and the resulting aptamers were combined into a heterobivalent construct. The construct resulted in an approximately 100-fold affinity increase relative to the single aptamer for DnaK, and could detect much smaller quantities of target. Although it experienced low level recognition of high concentrations of purified E. coli DnaK, there was no detectable non-specific binding in several biological samples. / Thesis / Master of Science (MSc)

En 1977, Carl Woese sépare les procaryotes en deux grands groupes en proposant une nouvelle classification basée sur des critères phylogénétiques. Les Archaea deviennent ainsi un domaine à part entière aux cotés des Bacteria et des Eucarya. Depuis, la compréhension de ce nouveau groupe et de ses relations avec les deux autres domaines, essentielles pour comprendre l’évolution ancienne du vivant, est largement passée par l’étude de leur phylogénie. Presque 40 ans de recherche sur les archées ont permis de faire évoluer leur image : de bactéries vivant dans des milieux spécialisés, souvent extrêmes, on est passé à un domaine indépendant, très diversifié aussi bien génétiquement, métaboliquement ou encore écologiquement. Ces dernières années la barre symbolique de cent génomes complets d’archées séquencés a été franchie et, parallèlement, les projets génomiques et métagénomiques sur des groupes peu caractérisés ou de nouvelles lignées de haut rang taxonomique (e.g. Nanohaloarchaea, Thaumarchaeota, ARMAN, Aigarchaeota, groupe MGC, groupe II des Euryarchaeota, etc.) se sont multipliés. Tout ceci apporte un matériel sans précédent pour l’étude de l’histoire évolutive et de la diversité des Archaea. Les protéines ribosomiques ont été utilisées de façon courante pour inférer la position phylogénétique des nouvelles lignées d’Archaea. Néanmoins, les phylogénies résultantes ne sont pas complètement résolues, laissant des interrogations concernant d’importantes relations de parenté. La recherche de nouveaux marqueurs est donc cruciale et c’est dans ce contexte que mon projet de thèse s’inscrit. À partir de l’analyse des génomes de deux Thaumarchaeota et d’une Aigarchaeota, nous avons identifié 200 protéines conservées et bien représentées dans les différents phyla d’archées. Ces protéines sont impliquées dans de nombreux processus cellulaires, ce qui peut apporter un signal phylogénétique complémentaire à celui des marqueurs de type informationnel utilisés par le passé. En plus de confirmer la plupart des relations phylogénétiques inférées à partir de ces derniers (i.e., protéines ribosomiques et sous unités de l’ARN polymérase), l’analyse phylogénétique de ces nouveaux marqueurs apporte un signal permettant une meilleure résolution de la phylogénie des archées et la clarification de certaines relations jusqu’ici confuses. Un certain nombre de ces nouveaux marqueurs sont aussi présents chez les bactéries. Les relations entre les grands phyla d’archées restant encore non résolues, nous avons utilisé ces protéines pour essayer de placer la racine de l’arbre des Archaea en utilisant comme groupe extérieur les bactéries. Nous avons ainsi pu identifier 38 protéines, parmi les 200 sélectionnées précédemment, ayant un signal phylogénétique suffisamment fiable pour cette étude, auxquelles nous avons ajouté 32 protéines ribosomiques universelles. L’utilisation conjointe de ces données nous a permis de placer la racine entre les Euryarchaeota, d’une part, et un groupe rassemblant les Thaumarchaeota, les Aigarchaeota, les Korarchaeota et les Crenarchaeota, d’autre part. Ce nouvel éclairage sur l’évolution ancienne des archées nous a amené à proposer une révision de leur taxonomie avec, principalement, la création du nouveau phylum "Proteoarchaeota" contenant les quatre phyla actuels que nous proposons de rétrograder en classes : Thaumarchaea, Aigarchaea, Korarchaea et Crenarchaea.Finalement, l’analyse des protéines codées dans les trois génomes qui ont servi de point de départ de ma thèse nous a permis de générer une masse considérable de données qui ont révélé des traits particuliers ou encore des histoires évolutives inattendues. Un exemple est l’histoire du complexe formé par la chaperonne DnaK et de ses co-chaperonnes GrpE, DnaJ, et DnaJ-Fer chez les Thaumarchaeota, impliquant plusieurs transferts horizontaux entre les trois domaines du vivant. / In 1977, Carl Woese proposed a new classification of organisms based on phylogenetic criteria where he divided prokaryotes into two major groups. Thus, Archaea were defined as a new domain, together with Bacteria and Eucarya. Since then, the study of this group and its relationships with the two other domains, essential to understand the early evolution of Life, has been largely done through the investigation of its phylogeny. Almost 40 years of research on the archaea have led to a significant evolution of the knowledge on this group: from considering them as bacteria living in specialized environments, most often extreme ones, to defining them as an independent domain, highly diversified in genetic, metabolic and ecological terms. During the last years, the symbolic barrier of 100 complete archaeal genome sequences has been reached and, simultaneously, many genome projects from poorly-known groups or new high-rank lineages (e.g., Nanohaloarchaea, Thaumarchaeota, ARMAN, Aigarchaeota, MGC, group II Euryarchaeota, etc.) have been launched. All this provides unprecedented information to study the evolutionary history of Archaea. Ribosomal proteins have been used recurrently to infer the phylogenetic position of new archaeal lineages. Nevertheless, the resulting phylogenies are not fully resolved and several important nodes remain uncertain. The identification of new phylogenetic markers is therefore crucial. This represents the framework of my PhD thesis project. On the basis of the analysis of the genome sequences of two Thaumarchaeota and one Aigarchaeota, we have identified 200 conserved proteins well represented among the different archaeal phyla. These proteins are involved in a number of cellular functions, thus providing a phylogenetic signal complementary to the one obtained from the informational proteins (i.e., ribosomal proteins and RNA polymerase subunits). The phylogenetic analysis of these new markers has led to a better resolution of the archaeal phylogeny, including several relationships that remained unclear. Several of the new markers are also present in bacteria. Since the relationships among the different archaeal phyla are not yet resolved, we have used those markers to try to place the root of the archaeal phylogeny using the bacterial sequences as outgroup. We have identified 38 proteins among the 200 detected before containing a phylogenetic signal useful for that purpose, to which we have added 32 universal ribosomal proteins. The use of this complete dataset allowed us locating the root between the Euryarchaeota and a large group joining the Thaumarchaeota, Aigarchaeota, Korarchaeota and Crenarchaeota. This new result on the ancient evolutionary history of Archaea has led us to propose a taxonomic revision for this domain, in particular the erection of a new phylum "Proteoarchaeota", containing the current four phyla that we propose to retrograde into classes (Thaumarchaeales, Aigarchaeales, Korarchaeales and Crenarchaeales). Finally, the analysis of the proteins encoded by the three reference genomes at the origin of this work has generated a large amount of data, which reveals particular traits in certain organisms or unexpected evolutionary histories. One example concerns the evolution in Thaumarchaeota of the protein complex composed of the DnaK chaperon and its co-chaperons GrpE, DnaJ, and DnaJ-Fer, which involves several horizontal gene transfer events among the three domains of Life.

Bacteria have developed specialized responses that involve the expression of particular genes present in a given regulon. Sigma factors provide regulatory mechanisms to respond to stress by acting as transcriptional initiation factors. This work focuses on σ32 during oxidative stress in Escherichia coli. The differential response of key heat shock (HS) genes was investigated during HS and oxidative stress using qPCR techniques. While groEL and dnaJ experienced increases in transcriptional response to H2O2 (10 mM), HS (42°C), and paraquat (50 mM) exposure, the abundance of dnaK over the co-chaperones was apparent. It was hypothesized that DnaK undergoes oxidative modification by reactive carbonyls at its Lys-rich C-terminus, accounting for the differential response during oxidative stress. A σ32-mediated β-galactosidase reporter was devised to detect the activity of wild-type DnaK and DnaKV634X modified to lack the Lys-rich C-terminus. Under unstressed conditions and HS, σ32 was bound at the same rate in both strains. When subjected to H2O2, the WT DnaK strain produced significantly higher β-galactosidase than DnaKV634X (one-tailed Student’s t test p=0.000002, α=0.05) and approached the same level of output as the lacZ positive control. The β-galactosidase assay indicates that DnaK undergoes Lys modification in the WT strain, preventing the protein from binding σ32, increasing the activity of σ32, and resulting in higher β-galactosidase activity than the DnaKV634X strain. In the DnaKV634X strain DnaK continues to bind σ32 so that σ32 could not promote the production of β-galactosidase. These findings demonstrate how DnaK is oxidatively modified, hindering the interaction with σ32 in manner distinct from HS.

No description available.