Das SurA-Protein ist ein wichtiger Bestandteil der periplasmatischen Faltungsmaschinerie aus Escherichia coli. Trotz zahlreicher Erkenntnisse sind die Mechanismen der Substraterkennung und -bindung noch nicht abschließend geklärt. Das SurA-Protein ist aus einem Chaperonmodul und zwei PPIase-Domänen aufgebaut. Die Bindestelle eines artifiziellen Peptides wurde zu Beginn der Arbeit in der PPIase-inaktiven Parvulin-Domäne I publiziert. Im Rahmen dieser Arbeit wurde untersucht, ob auch biologisch relevante, natürliche Peptide an dieser Bindestelle interagieren und ob es noch weitere Substratbindestellen innerhalb von SurA gibt. In ESR-spektroskopischen Versuchen wurde die Interaktion der isolierten Parvulin-Domäne I von SurA mit Peptiden aus einer LamB-Peptid-Bibliothek, sowie mit dem artifiziellen Peptid analysiert. Die Bindung des artifiziellen Peptides und eines Peptides aus der LamB-Peptid-Bibliothek an die isolierte Parvulin-Domäne I konnte nachgewiesen werden. Für weitere an SurA-bindende Peptide konnte an dieser Position keine Interaktion nachgewiesen werden. Mittels des genetischen Indikatorsystems ToxR wurden gezielt Kontaktpunkte zwischen dimerisierten SurA-Untereinheiten bzw. zwischen SurA und Peptid unterbunden, um deren Einfluss auf die wechselseitige Interaktion zu untersuchen. Hierbei wurden einzelne Positionen in isolierten SurA-Domänen identifiziert, die an einer Interaktion beteiligt sind. Die Mutation dieser Interaktionsstellen führten zu keinem signifikanten Verlust der in vivo-Funktion, welche mittels der Fähigkeit der SurA-Varianten zur Komplementation des synthetisch letalen Phänotypen einer surA skp-Doppelmutante untersucht wurde. Die Grundlagen für die Methodik der photoaktivierbaren, ortsspezifischen Quervernetzung von OMP-Polypeptiden an SurA- bzw. SurAI-Proteine wurden etabliert. / The SurA protein is an important part of the periplasmic folding machinery in Escherichia coli. Despite numerous findings are the mechanisms of substrate recognition and folding not yet completely resolved. The SurA protein consists of a chaperone module and two parvulin domains. In the beginning of this work a peptide binding site was published which was located in the PPIase inactive parvulin domain I. It was investigated in this thesis whether biological relevant, natural peptides would also bind with this binding site and if additional substrate binding sites exist within the SurA protein. In ESR-spectroscopy experiments both the interaction of the isolated parvulin domain I of SurA with peptides of a LamB peptide library and with the artificial peptide were examined. Binding of the artificial peptide and one peptide of the LamB peptide library to the isolated parvulin domain I could be detected. For the remaining tested peptides, which are confirmed to be SurA binders, no interaction could be verified at this position. By use of the genetic indicator system ToxR the contact points between dimerized SurA subunits respectively between SurA and peptide were prevented site-specifically to examine their influence on the mutual interaction. Here single positions in isolated SurA-domains were identified, which are part of an interaction. The mutation of these interaction sites lead to no significant loss of the in vivo function, which was analyzed by the capability of the SurA variants to complement the synthetic lethal phenotype of a surA skp double mutant. The fundamentals for the method of photoactivated site-specific crosslinking of OMP polypeptides to SurA respectively SurAI were established.

La régulation de l’expression des gènes est critique pour l’adaptation des cellules à leur environnement et pour leur homéostasie. La transcription, qui représente une étape essentielle de l’expression des gènes, est contrôlée par plusieurs facteurs et cofacteurs. L’un de ces cofacteurs, TRRAP, correspond à la plus grosse sous-unité de deux complexes de remodelage de la chromatine, SAGA et TIP60. TRRAP interagit avec divers facteurs de transcription, tels que c-MYC et E2Fs et permet ainsi le recrutement de SAGA et TIP60 aux promoteurs des gènes. TRRAP est un membre d’une famille de kinases atypiques, les PIKKs. Des études antérieures ont défini la co-chaperonne TTT comme régulateur essentiel de la stabilité et l’activité des PIKKs. Contrairement aux autres PIKKs, TRRAP ne possède pas les résidus requis à son activité catalytique et représente donc la seule pseudo-kinase parmi les PIKKs. Bien que TTT interagit et stabilise TRRAP, son rôle sur l’activité de ce dernier reste inconnu. En utilisant un système de dégron inductible qui permet la dégradation rapide de protéines endogènes, nous avons démontré que TTT est requis pour l’assemblage de TRRAP dans ses complexes fonctionnels précédent son import nucléaire. De plus, à travers des analyses transcriptomiques, nous avons pu déterminer que TTT régule la transcription de plusieurs gènes TRRAP-dépendants dans des cellules de cancer colorectal. L’analyse du profile de fixation de TRRAP à l’échelle du génome grâce à la technique du CUT&RUN suivie d’un séquençage à haut débit (CUT&RUN-seq), a permis d’identifier les cibles directes de TRRAP, parmi lesquelles seule une fraction restreinte correspond à des cibles directes de MYC. Nous avons également découvert que TRRAP possède un rôle de répresseur direct sur la transcription d’une partie des gènes stimulés par l’interféron (ISGs) qui interviennent dans la réponse à l’interféron du système immunitaire innée. En outre, nos résultats suggèrent que TRRAP et sa co-chaperonne TTT participent à la tumorigenèse notamment en maintenant et régulant un programme transcriptionnel spécifique. / Gene expression regulation is critical for cells to adapt to external changes and maintain their homeostasis. Transcription is an essential step in gene expression and is controlled by numerous factors and cofactors. One such cofactor is TRRAP, the largest subunit of two distinct chromatin-modifying complexes, SAGA and TIP60. TRRAP interacts with a diverse range of transcription factors including c-MYC and E2Fs, and mediates the recruitment of SAGA and TIP60 to gene promoters. TRRAP is a member of the PIKK family of atypical kinases. Prior studies defined the TTT co-chaperone as an essential regulator of PIKK stability and activity. In contrast to its cognate kinases, TRRAP lacks catalytic residues and is the sole pseudokinase among PIKKs. Although TTT has been shown to stabilize and interact with TRRAP, the role of TTT on TRRAP function remains unknown. Using an inducible degron system that allows the rapid and acute depletion of endogenous proteins, we demonstrated that TTT is required to assemble TRRAP within its functional complexes prior its nuclear import. Additionally, through transcriptomic analyses we determined that TTT regulates a large number of TRRAP-dependent genes in colorectal cancer cells. Profiling of the genome-wide binding of TRRAP via CUT&RUN-seq identified the direct targets of TRRAP, of which only a small fraction overlaps with MYC targets. We also uncovered a direct inhibitory role of TRRAP on a subset of the interferon-stimulated genes, which mediate the interferon response in the innate immune system. Altogether, our data suggest that TRRAP and its chaperone TTT are involved in tumorigenesis through the maintenance of a specific transcriptional program.

Le lupus érythémateux disséminé est une maladie autoimmune systémique provoquant des lésions tissulaires graves. Notre laboratoire a découvert un peptide phosphorylé, appelé P140, présentant des propriétés thérapeutiques pour le traitement du lupus. Le mode d’action du peptide P140 dans le traitement du lupus repose sur son interaction avec la protéine de choc thermique HSPA8/HSC70 et l’objectif de mon projet de thèse a été de consolider et compléter ce mécanisme. Nous avons démontré qu’après internalisation par endocytose dépendante des clathrines, le peptide P140 se localise rapidement au sein du lysosome des lymphocytes B. Dans cet organelle, il réduit l’import de substrat cytosolique par autophagie dépendante des chaperonnes en ciblant et réduisant l’activité de HSPA8 intralysosomale. Nous avons également entrepris une analyse comparative du répertoire des lymphocytes T et B des souris lupiques par rapport aux souris saines. Nos résultats révèlent un changement dans la fréquence de certains réarrangements du TCR entre les souris lupiques et les souris saines et un effet bénéfique du peptide P140 sur certains réarrangements associés au lupus. / Systemic lupus erythematosus is a multi-organ autoimmune disease provoking tissue damages. Our laboratory has discovered a phosphorylated peptide, named P140, with therapeutic activities in lupus. The mode of action used by P140 peptide relies on its interaction with the heat shock protein HSPA8/HSC70. The aim of my thesis project was to consolidate and complete this HSPA8-dependent mechanism. We have demonstrated that, upon internalization by clathrin-mediated endocytosis, P140 peptide homes rapidly into B cell lysosome. In this organelle, the peptide reduces chaperone-mediated autophagy by interacting and inhibiting intralysosomal HSPA8 activity. We also performed a comparative analysis of T cell and B cell repertoire on lupic mice compared to healthy mice Our results show a modification in the frequency of certain TCR rearrangements between lupus-prone mice and healthy mice and a beneficial effect of P140 peptide on certain lupus-associated rearrangements.

<p>In order to establish colonisation of a human host, pathogenic <i>Yersinia</i> use a type III protein secretion system to directly intoxicate host immune cells. Activation of this system requires target cell contact and is a highly regulated process. Both the intoxication and regulation events depend on the <i>lcrGVHyopBD </i>transloco<i>n</i> operon, which is highly conserved in many bacterial pathogens. In this study, the role of individual operon members was analysed and functional domains identified by using the highly homologous <i>pcrGVHpopBD</i> operon of <i>P. aeruginosa</i> as a comparative tool. </p><p><i>Yersinia</i> spp. and<i> P. aeruginosa </i>were shown to form translocation pores of a similar size that promoted equally efficient protein delivery. A strong dependency on interactions between native translocator(s) in protein delivery was revealed, suggesting that each pathogen has delicately fine-tuned this process to suit its own infection niche. In particular, the C-terminus of YopD was shown to possess functional specificity for effector delivery in <i>Yersinia</i> that could not be conferred by the comparable region in homologous PopD. Moreover, a role for LcrV and PcrV in substrate recognition during the protein delivery process was excluded. </p><p>The N-terminus of LcrH was recognized as a unique regulatory domain, mediating formation of LcrH-YscY regulatory complexes in <i>Yersinia</i>, while equivalent complexes with analogous proteins were not formed in <i>P. aeruginosa</i>. These results compliment the idea that a negative regulatory pathway involving LcrH, YopD, LcrQ and YscY is unique to <i>Yersinia</i>. </p><p>Finally, PcrH was identified as a new member of the translocator class of chaperones, being essential for assembly of a functional PopB/PopD mediated translocon in <i>P. aeruginosa</i>. However, in contrast to the other members of this family, PcrH was dispensable for type III regulation. Moreover, both LcrH and PcrH were shown to possess tetratricopeptide repeats crucial for their chaperone function. One tetratricopeptide repeat mutant in LcrH was even isolated that failed to secrete both YopB and YopD substrates, even though stability was maintained. This demonstrates for the first time that LcrH has a role in substrate secretion in addition to its critical role in promoting substrate stability.</p>

<p>Nerve injury induces up-regulation of the chaperone protein clusterin in affected neurons and adjacent astrocytes but the functional significance of this response is unclear. We find that motor neuron survival is significantly greater in clusterin(+/+) compared to (-/-) mice. These results suggest that endogenous expression of clusterin is neuroprotective after nerve injury. However, motor neuron survival in clusterin overexpressing mice was not different from that in wildtype mice. In contrast, treatment of neuronal cultures with clusterin-TAT recombinant protein is neuroprotective, including a positive effect on neuronal network complexity.</p><p>Since extracellular clusterin complexes are endocytosed after binding to various receptors, we examined the expression of known clusterin binding receptors in the spinal cord. We find that megalin is expressed in the nuclei of two cell populations in the mouse spinal cord: i) oligodendrocytes in late postnatal and adult spinal cord white matter, and ii) transiently (E11-15) in a population of immature astrocytes in the dorsal spinal cord. We find no correlation between clusterin and megalin in the intact or injured spinal cord. However, intranuclear localization of megalin, suggesting signalling properties, is supported by the co-localization with γ-secretase, the enzyme responsible for endodomain cleavage of megalin. Megalin deficient mice display a pronounced deformation of the dorsal part of spinal cord, an almost complete absence of oligodendroglial progenitor cells, and a marked reduction in the population of mature astrocytes at later prenatal developmental stages.</p><p>Taken together, our findings indicate that megalin is a novel signalling molecule for distinct populations of glial cells in the pre- and postnatal spinal cord. The functional role(s) of megalin is unknown. However, its expression patterns and cellular localization suggest that megalin regulates differentiation of oligodendrocytes and astrocytes in the prenatal spinal cord, as well as the function of myelinating oligodendrocytes in the postnatal spinal cord.</p>

In order to establish colonisation of a human host, pathogenic Yersinia use a type III protein secretion system to directly intoxicate host immune cells. Activation of this system requires target cell contact and is a highly regulated process. Both the intoxication and regulation events depend on the lcrGVHyopBD translocon operon, which is highly conserved in many bacterial pathogens. In this study, the role of individual operon members was analysed and functional domains identified by using the highly homologous pcrGVHpopBD operon of P. aeruginosa as a comparative tool. Yersinia spp. and P. aeruginosa were shown to form translocation pores of a similar size that promoted equally efficient protein delivery. A strong dependency on interactions between native translocator(s) in protein delivery was revealed, suggesting that each pathogen has delicately fine-tuned this process to suit its own infection niche. In particular, the C-terminus of YopD was shown to possess functional specificity for effector delivery in Yersinia that could not be conferred by the comparable region in homologous PopD. Moreover, a role for LcrV and PcrV in substrate recognition during the protein delivery process was excluded. The N-terminus of LcrH was recognized as a unique regulatory domain, mediating formation of LcrH-YscY regulatory complexes in Yersinia, while equivalent complexes with analogous proteins were not formed in P. aeruginosa. These results compliment the idea that a negative regulatory pathway involving LcrH, YopD, LcrQ and YscY is unique to Yersinia. Finally, PcrH was identified as a new member of the translocator class of chaperones, being essential for assembly of a functional PopB/PopD mediated translocon in P. aeruginosa. However, in contrast to the other members of this family, PcrH was dispensable for type III regulation. Moreover, both LcrH and PcrH were shown to possess tetratricopeptide repeats crucial for their chaperone function. One tetratricopeptide repeat mutant in LcrH was even isolated that failed to secrete both YopB and YopD substrates, even though stability was maintained. This demonstrates for the first time that LcrH has a role in substrate secretion in addition to its critical role in promoting substrate stability.

The type III secretion system (T3SS) is a highly conserved secretion system among Gram negative bacteria that translocates anti-host proteins directly into the infected cells to overcome the host immune system and establish a bacterial infection. Yersinia pseudotuberculosis is one of three pathogenic Yersinia spp. that use a plasmid encoded T3SS to establish an infection. This complex multi-component Ysc-Yop system is tightly regulated in time and space. The T3SS is induced upon target cell contact and by growth in the absence of calcium. There are two kinds of substrates for the secretion apparatus, the translocator proteins that make up the pore in the eukaryotic target cell membrane, and the translocated effector proteins, that presumably pass through this pore en route to the eukaryotic cell interior. The essential YopD translocator protein is involved in several important steps during effector translocation, such as pore formation, effector translocation. Moreover, in complex with its cognate chaperone LcrH, it maintains regulatory control of yop gene expression. To understand the molecular mechanism of YopD function, we made sequential in-frame deletions throughout the entire protein and identified discrete functional domains that made it possible to separate the role of YopD in translocation from its role in pore formation and regulation, really supporting translocation to be a multi-step process. Further site-directed mutagenesis of the YopD C-terminus, a region important for these functions, revealed no function for amino acids in the coiled-coil domain, while hydrophobic residues within the alpha-helical amphipathic domain are functionally significant for regulation, pore formation and translocation of effectors. Unique to the T3SSs are the chaperones which are required for efficient type III protein secretion. The translocator-class chaperone LcrH binds two translocator proteins, YopB and YopD, which is necessary for their pre-secretory stabilization and their efficient secretion. We have shown that LcrH interacts with each translocator at a unique binding-site established by the folding of its three tandem tetratricopeptide repeats (TPRs). Beside the regulatory LcrH-YopD complex, LcrH complexes with YscY, a component of the Ysc-Yop T3SS, that is also essential for regulatory control. Interestingly the roles for LcrH do not end here, because it also appears to function in fine tuning the amount of effector translocation into target cells upon cell contact. Moreover, LcrH’s role in pre-secretory stability appears to be an in vitro phenomenon, since upon bacteria-host cell contact we found accumulated levels of YopB and YopD inside the bacteria in absence of a LcrH chaperone. This suggests the true function of LcrH is seen during target cell contact. In addition, these stable YopB and YopD are secreted in a Ysc-Yop independent manner in absence of a functional LcrH. We propose a role for LcrH in conferring substrate secretion pathway specificity, guiding its substrate to the cognate Ysc-Yop T3SS to secure subsequent effector translocation. Together, this work has sought to better understand the key functions of LcrH and YopD in Yersinia pathogenicity. Using an approach based heavily on recombinant DNA technology and tissue culture infections, the complex molecular cross-talk between chaperone and its substrate, and the effect this has on the Yersinia lifestyle, are now being discovered.

Nerve injury induces up-regulation of the chaperone protein clusterin in affected neurons and adjacent astrocytes but the functional significance of this response is unclear. We find that motor neuron survival is significantly greater in clusterin(+/+) compared to (-/-) mice. These results suggest that endogenous expression of clusterin is neuroprotective after nerve injury. However, motor neuron survival in clusterin overexpressing mice was not different from that in wildtype mice. In contrast, treatment of neuronal cultures with clusterin-TAT recombinant protein is neuroprotective, including a positive effect on neuronal network complexity. Since extracellular clusterin complexes are endocytosed after binding to various receptors, we examined the expression of known clusterin binding receptors in the spinal cord. We find that megalin is expressed in the nuclei of two cell populations in the mouse spinal cord: i) oligodendrocytes in late postnatal and adult spinal cord white matter, and ii) transiently (E11-15) in a population of immature astrocytes in the dorsal spinal cord. We find no correlation between clusterin and megalin in the intact or injured spinal cord. However, intranuclear localization of megalin, suggesting signalling properties, is supported by the co-localization with γ-secretase, the enzyme responsible for endodomain cleavage of megalin. Megalin deficient mice display a pronounced deformation of the dorsal part of spinal cord, an almost complete absence of oligodendroglial progenitor cells, and a marked reduction in the population of mature astrocytes at later prenatal developmental stages. Taken together, our findings indicate that megalin is a novel signalling molecule for distinct populations of glial cells in the pre- and postnatal spinal cord. The functional role(s) of megalin is unknown. However, its expression patterns and cellular localization suggest that megalin regulates differentiation of oligodendrocytes and astrocytes in the prenatal spinal cord, as well as the function of myelinating oligodendrocytes in the postnatal spinal cord.

The trimorphic fungus Candida albicans is the leading cause of systemic candidiasis, a disease with poor prognosis affecting immunocompromised patients. The capacity to switch between growth morphologies is tightly coupled to its ability to cause life-threatening infection. Recently, the molecular chaperone Heat Shock Protein 90 (Hsp90) has been implicated as a major regulator of C. albicans morphogenesis via the Ras1-PKA pathway. In model organisms from plant, animal and fungal kingdoms, Hsp90 stabilizes regulators of cell signaling and participates in many important cellular processes. Hsp90’s roles in C. albicans are beginning to be dissected. This thesis represents a comprehensive overview of the morphological response of C. albicans to compromised Hsp90 function, illuminating previously unidentified roles for this chaperone in cell cycle progression, cytokinesis and vacuole maintenance. This work sheds light on the importance of Hsp90 in fungal development and the therapeutic potential of Hsp90 inhibitors in the treatment of fungal infections.

The trimorphic fungus Candida albicans is the leading cause of systemic candidiasis, a disease with poor prognosis affecting immunocompromised patients. The capacity to switch between growth morphologies is tightly coupled to its ability to cause life-threatening infection. Recently, the molecular chaperone Heat Shock Protein 90 (Hsp90) has been implicated as a major regulator of C. albicans morphogenesis via the Ras1-PKA pathway. In model organisms from plant, animal and fungal kingdoms, Hsp90 stabilizes regulators of cell signaling and participates in many important cellular processes. Hsp90’s roles in C. albicans are beginning to be dissected. This thesis represents a comprehensive overview of the morphological response of C. albicans to compromised Hsp90 function, illuminating previously unidentified roles for this chaperone in cell cycle progression, cytokinesis and vacuole maintenance. This work sheds light on the importance of Hsp90 in fungal development and the therapeutic potential of Hsp90 inhibitors in the treatment of fungal infections.