Doctor of Philosophy / Department of Biology / Lynn Hancock / Enterococci are the third leading cause of nosocomial infections including urinary tract infections (UTI), surgical site infections (SSI) and blood stream infections. Enterococci are also found in the gastrointestinal tracts of humans, and other mammals. We elucidated the influence of the transcriptional regulator RpoN on enterococcal biofilm formation, virulence potential and cell wall architecture and proposed a potential involvement for carbohydrate metabolism in these processes. Biofilms are held together by matrix (BM) components such as extracellular DNA (eDNA) released by cell death from a sub-population of cells. The rpoN mutant (ΔrpoN) was resistant to autolysis as well as fratricide-mediated cell death and eDNA was not detected in planktonic as well as biofilm cultures. Unlike the parental strain V583, the ΔrpoN mutant formed proteinase K sensitive biofilms, suggesting that protein as well as eDNA serves as an important matrix component. The rabbit model of endocarditis was used to assess the effect of rpoN deletion on enterococcal virulence. Rabbits infected with ΔrpoN had reduced bacterial burden in heart, blood, liver, kidney and vegetation in comparison to the parental strain. The growth defect of ΔrpoN in physiologically relevant glucose levels (5 mM) partially explains the reduced bacterial burdens observed in the virulence study. Microarray analysis of ΔrpoN showed that 10% of the genome is differentially regulated by RpoN. Deletion of rpoN also protects Enterococcus faecalis from lysis in the absence of known modulators of cellular lytic events such as O-acetylation and D-alanylation. Of the four identified enhancer binding proteins in E. faecalis, MptR regulates the RpoN-dependent mannose/glucose uptake system (MptABCD) and the ΔmptR mutant phenocopied the ΔrpoN mutant in the eDNA release and growth assays. Because MptC and MptD have been shown to be the cellular receptors for class IIa and IIc bacteriocins, we are presently testing the hypothesis that these receptors may serve as a global receptor for bacteriocins. In conclusion, our data demonstrates that alterations in the metabolic state of the bacterium, as observed in the ΔrpoN mutant could be responsible for the switch in biofilm matrix composition, and this switch in turn likely influences the virulence potential of the bacterium.

Gram-positive pathogenic bacteria utilize cell-surface anchored proteins to bind and transport heme into the cell. These bacteria acquire iron from host proteins containing heme e.g., hemoglobin. Proteins like HmuT from Corynebacterium diphtheriae bind and help transport heme into the cell. Residues His136 and Tyr235 are utilized as the axial ligands, with a conserved Arg237 residue acting as the hydrogen bonding partner to the axial Tyr235. Similarly, Streptococcus pyogenes utilizes the cell anchored protein Shr to transfer heme into the cell. Shr-NEAT2 is hexacoordinated by two axial methionines and is prone to autoreduction where lysines are the most likely source of electrons. Lastly, PefR of Group A Streptococcus is a DNA transcription factor which regulates protein expression. Preliminary studies indicate a cysteine may coordinate the heme. A combination of UV-visible, resonance Raman, and magnetic circular dichroism spectroscopies shows these proteins play a crucial role heme transport and regulation.

Pour croître et proliférer, les cellules cancéreuses de la prostate activent des voies de signalisation dépendantes des androgènes. L'intervention thérapeutique en première ligne du cancer de la prostate (CaP) s'appuie donc d’abord sur le blocage de l'axe androgènes-récepteur aux androgènes (RA) mais rapidement, les patients développent des tumeurs résistantes (CRPC, Castration Resistant Prostate Cancer).Les récepteurs à activité tyrosine kinase de la famille ErbB semblent jouer un rôle dans cette résistance, en particulier le récepteur ErbB3. En effet, l'inactivation des voies en aval d'ErbB1 et ErbB2, en association avec les anti-androgéniques n'empêche pas la progression vers l'hormono-indépendance, et une accumulation nucléaire d'ErbB3 est observée dans les CRPC en même temps que la voie PI3K-Akt est réactivée.Dans ce contexte, nous avons validé l'expression d'une isoforme nucléaire ErbB380kDa chez les patients et dans des lignées hormono-sensible (LNCaP) et hormono-résistante (PC3). Par ChIP-on-chip, nous avons isolé 353 promoteurs cibles communs aux deux lignées, 245 spécifiques à la lignée LNCaP et 925 à la lignée PC3, et montré qu'ErbB380kDa est un co-régulateur transcriptionnel des gènes étudiés, parmi lesquels GATA2. L'analyse in silico de ces promoteurs révèle des sites de liaison pour les facteurs de transcription GATA2 et MZF1 au niveau des régions liant ErbB380kDa. Un complexe nucléaire GATA2-MZF1-ErbB380kDa est retrouvé dans les cellules LNCaP et PC3.Des travaux récents montrent que GATA2 s'associe au RA pour réguler l'expression de gènes et qu'il pourrait être participer à la dissémination métastatique dans le CaP.Nos résultats suggèrent qu'ErbB380kDa pourrait jouer un rôle régulateur, en amont de GATA2, dans les processus de résistance et l'apparition de métastases. Cette isoforme nucléaire insensible aux traitements actuels apparaît donc comme une cible privilégiée pour le ciblage thérapeutique. / Prostate cancer (PCa) is dependent on androgens and functional androgen-receptor (AR) for growth and proliferation. Androgen-directed therapy is used at the first stages of the disease but cancer cells frequently become resistant (CRPC) by inappropriate reactivation of AR activity. As ErbB receptors are expressed in PCa cells, therapies aiming at inactivate the pathways downstream have been tested in advanced prostate cancers alongside hormone-based therapy. Still, a significant proportion of CRPC treated by ErbB1/2 inhibitors resist to treatment. ErbB3 could be responsible for this failure through both its unexpected nuclear localization and the reactivation of the PI3K-Akt pathway in those advanced tumors.We have described a nuclear ErbB380kDa isoform, expressed in hormone-sensitive (LNCaP) and hormone-resistant (PC3) PCa cell lines that accumulates in the nucleus of tumor cells during cancer progression. ChIP-on-chip experiments led us to characterize 353 target promoters binding ErbB380kDa in both cell lines; 245 promoters specific to LNCaP and 925 specific to PC3 cells, among which the promoter of GATA2. We show that ErbB380kDa functions as a transcriptional co-regulator for the studied genes, potentially through its interaction with transcription factors. In silico analysis revealed binding sites for GATA2 and MZF1 transcription factors on the target promoters, and a complex GATA2-MZF1-ErbB380kDa has been found in LNCaP and PC3 cells. Recent publications have reported a role for GATA2 in the regulation of RA responsive-genes and in metastatic spreading. We propose that ErbB380kDa could act, upstream of GATA2, to induce resistance mechanisms and facilitate cancer progression. Thus, ErbB380kDa emerges as a putative target for the development of new therapies in prostate cancer.

<p>Prokaryotes are continually exposed to variations in their environment. Survival in unstable milieu requires a wide range of transcriptional regulators (TRs) that respond to specific environmental and cellular signals by modulating gene expression and provide an appropriate physiological response to external stimuli. These adaptive responses to environmental signals are mostly mediated by TRs from one of two families: the single or the two component signal transduction systems (1CSTS; 2CSTS). In this thesis the structural analysis of two 1CSTS – DntR and NikR − are presented. One study was carried out to try to develop a bacterial biosensor for synthetic dinitrotulenes compounds, the other to characterise the Ni-sensing mechanism that contributes to the acid adaptation of the human pathogen<i> Helicobacter pylori.</i> DntR belongs to the LysR family and the crystal structures obtained have allowed the proposal a model of the interaction of DntR with salicylate inducer as well as giving insights into the signal propagation mechanism in LysR-type transcription factors (<b>paper I</b>). DntR mutant crystal structures combined with the modelling of DntR-2,4-dnt interactions led to the design of a DntR mutant that has a limited response to 2,4-dnt in a whole cell biosensor system (<b>paper 2</b>). Crystal structures of apo-NikR from <i>H. pylori </i>(HpNikR) and of Ni-bound intermediary states of the protein were obtained. The latter have helped in unravelling the Ni incorporation and selectivity mechanisms of NikRs and have shown a strong cooperativity between conformational changes in the Ni binding domain with movements of the DNA binding domain (<b>paper 3</b>). Biochemical studies and comparisons of the HpNikR crystal structures with those of NikR homologues strongly suggest that HpNikR has evolved different surface properties (<b>paper 4</b>) and a new mode of DNA binding. </p>

Prokaryotes are continually exposed to variations in their environment. Survival in unstable milieu requires a wide range of transcriptional regulators (TRs) that respond to specific environmental and cellular signals by modulating gene expression and provide an appropriate physiological response to external stimuli. These adaptive responses to environmental signals are mostly mediated by TRs from one of two families: the single or the two component signal transduction systems (1CSTS; 2CSTS). In this thesis the structural analysis of two 1CSTS – DntR and NikR − are presented. One study was carried out to try to develop a bacterial biosensor for synthetic dinitrotulenes compounds, the other to characterise the Ni-sensing mechanism that contributes to the acid adaptation of the human pathogen Helicobacter pylori. DntR belongs to the LysR family and the crystal structures obtained have allowed the proposal a model of the interaction of DntR with salicylate inducer as well as giving insights into the signal propagation mechanism in LysR-type transcription factors (<b>paper I</b>). DntR mutant crystal structures combined with the modelling of DntR-2,4-dnt interactions led to the design of a DntR mutant that has a limited response to 2,4-dnt in a whole cell biosensor system (<b>paper 2</b>). Crystal structures of apo-NikR from H. pylori (HpNikR) and of Ni-bound intermediary states of the protein were obtained. The latter have helped in unravelling the Ni incorporation and selectivity mechanisms of NikRs and have shown a strong cooperativity between conformational changes in the Ni binding domain with movements of the DNA binding domain (<b>paper 3</b>). Biochemical studies and comparisons of the HpNikR crystal structures with those of NikR homologues strongly suggest that HpNikR has evolved different surface properties (<b>paper 4</b>) and a new mode of DNA binding.

Le cancer colorectal est la première pathologie cancéreuse de la sphère digestive, tant en terme de fréquence que de mortalité par an. Chaque année, 41 000 nouveaux cas sont diagnostiqués et 17 000 décès sont dus à ce cancer en France. Deux paramètres cliniques expliquent la mortalité de ce cancer; d'une part le fait qu'un patient sur deux est diagnostiqué au stade métastatique ou va présenter des lésions métastatiques durant l'histoire de sa pathologie, d'autre part le fait que les patients après traitement vont fréquemment présenter une récidive de leur pathologie. L'utilisation de régimes de chimiothérapies avant et après résection métastatique améliore la survie sans récidive à court terme, mais à 2 ans post chirurgie l'avantage apporté est perdu. Ainsi, la compréhension des mécanismes d'échappement à la chimiothérapie et régissant la croissance tumorale est d'intérêt pour tenter de limiter la récidive tumorale. L'objectif de ce travail de thèse a consisté en l'analyse de sous-populations obtenues sous pression de chimiothérapie au 5-Fluorouracile (5FU) dérivées de la lignée cancéreuse colique HT29, ainsi que les mécanismes moléculaires associés. Notre clone le plus chimiorésistant isolé, le modèle cellulaire 5F31, quitte le compartiment prolifératif sous traitement à fortes doses de 5FU, ceci étant associé à une perturbation de la voie de signalisation de la Src kinase c-Yes et de son partenaire, le co-activateur transcriptionnel YAP. Sous traitement, les cellules chimiorésistantes entrent en quiescence, le complexe protéique entre c-Yes et YAP est perdu et la quantité totale et nucléaire de YAP diminue de manière significative (Igoudjil, Touil, Corvaisier et al. 2014 Clinical Cancer Research). Dès lors, la suite des travaux a consisté en l'étude du rôle potentiel de YAP sur la balance quiescence/prolifération sous 5FU. L'inhibition pharmacologique ou l'inhibition transitoire de l'expression de YAP et de son paralogue, la protéine TAZ, dans plusieurs lignées cancéreuses coliques induit l'augmentation de la fraction de cellules quiescentes, associée au ralentissement significatif de la croissance tumorale. A l'inverse, la surexpression d'une forme constitutivement active de YAP demeurant nucléaire sous 5FU maintient les cellules 5F31 en prolifération et sensibilise les cellules à la chimiothérapie. Au niveau des effecteurs protéiques, l'induction de quiescence (par traitement à la chimiothérapie ou inhibition de YAP/TAZ) est associée à la perte d'expression de la Cycline E1 et du facteur de transcription c-Myc. A l'inverse, la surexpression du dominant constitutivement actif de YAP dans les cellules 5F31 conduit à l'expression soutenue de la Cycline E1 sous 5FU, expression nécessitant l'activation du facteur de transcription CREB. L'inhibition de la Cycline E1 permet d'induire la quiescence cellulaire, proposant cette protéine comme l'un des effecteurs des protéines YAP/TAZ dans la régulation entre la quiescence et la prolifération cellulaire (Corvaisier et al, Oncotarget, 2016). En conclusion, nos données montrent l'importance du rôle des protéines YAP/TAZ dans le maintien des cellules en prolifération via l'expression notamment de la Cycline E1. Nos résultats sur cohorte de patients atteints de métastases hépatiques de cancers colorectaux montrent que l'expression des co-activateurs YAP/TAZ est liée à un index prolifératif plus important, confortant nos données sur le rôle de ces protéines dans la croissance tumorale. De plus, l'expression élevée de YAP et TAZ est associée en analyses multivariées à une récidive plus précoce et à une survie globale plus faible. Ainsi, l'étude de l'expression et du niveau d'activation de ces acteurs serait un marqueur pronostic intéressant dans l'anticipation de la récidive métastatique ; ainsi que des cibles thérapeutiques intéressantes pour tenter de limiter la rechute tumorale. / Colorectal cancer is the most frequent and lethal cancerous pathology from the digestive system. Each year in France, 41 000 new cases are diagnosed and 17 000 patients die due to this pathology. This high mortality is mainly due to the rate of patients with liver metastatic lesions and the early relapse of those metastases after treatment. The use of chemotherapy prior to surgery induces a decrease of early relapse, however 2 years after resection this advantage is lost. Thus, understanding the mechanisms underlying escape to treatment is required to try to delay or prevent tumor recurrence.The aim of this doctoral work was to analyze clonal chemoresistant subpopulations derived from the colorectal cancer cell line HT29 after chronic exposure to 5-Fluorouracil (5FU) and molecular mechanisms associated with chemoresistance. The most chemoresistant clonal subpopulation, 5F31, stops its proliferation after treatment with high dose of 5FU, this behavior being associated with the modulation of the c-Yes/YAP axis. After treatment, 5F31 cells enter quiescence, interaction between c-Yes and YAP is lost and total and nuclear YAP protein expression reduces significantly (Igoudjil, Touil, Corvaisier et al. 2014, Clinical Cancer Research). The next step was to study functions of YAP protein in this chemotherapy- induced quiescence.Pharmacological or transient inhibition of YAP and its homolog TAZ, induces quiescence and reduces cellular growth in several colorectal cancer cell lines. On the other hand, overexpression of a constitutively active form of YAP in 5F31 cells forces cells to remain proliferative under 5FU treatment, enhancing 5F31 cell chemosensitivity to 5FU.Regarding proteic effectors, quiescence (either induced by 5FU or YAP/TAZ inhibition) is associated with loss of expression of the transcription factor c-Myc and Cyclin E1. In 5F31 cells expressing the active mutant form of YAP, Cyclin E1 expression is sustained after 5FU treatment through the activation of the transcription factor CREB. Cyclin E1 inhibition is sufficient to induce quiescence, therefore introducing this protein as one of the final effectors of YAP/TAZ co-activators in the regulation of the proliferation/quiescence switch in colorectal cancer cells (Corvaisier et al. 2016, Oncotarget).To conclude, our work reveals the importance of YAP/TAZ proteins for the maintenance of colorectal cancer cells proliferation through Cyclin E1 expression. Our work on liver metastases from patients with colorectal cancer shows that high expression of YAP/TAZ is connected to a higher proliferative index in metastatic lesions. Moreover, high YAP/TAZ expression is associated with shorter patient progression-free survival and shorter overall survival. Studying the expression and level of YAP/TAZ activation could be an interesting prognosis marker to anticipate metastatic relapse and potent druggable target to delay tumoral recurrence.

La bactérie Deinococcus radiodurans se distingue par sa résistance exceptionnelle aux rayonnements γ, UV, à la dessiccation et au stress oxydant. La radiorésistance de D.radiodurans résulte de l’association de plusieurs mécanismes, dont des systèmes efficaces de réparation de l’ADN et de détoxification des ROS, la protection des protéines contre l’oxydation, une structure compacte du nucléoïde et des protéines spécifiques aux Deinococcaceae, qui sont fortement induites après l’exposition des cellules au rayonnement γ. Le gène ddrI (DNA damage response) est fortement induit après exposition des cellules au rayonnement γ et code un régulateur transcriptionnel appartenant à la sous-famille CRP (cAMP receptor protein). Comparée à la souche sauvage, la souche privée de DdrI présente des défauts de division cellulaire et/ou de ségrégation de l’ADN, et est sensible aux agents génotoxiques, au stress oxydant et au choc thermique. La prédiction in silico des cibles potentielles de DdrI suggère que cette protéine régule l’expression d’une centaine de gènes impliqués dans la réplication, la réparation de l’ADN, la transduction de signal, la réponse au stress oxydant et au choc thermique. La séquence consensus 5’TGTGA(N6)TCACA3’, extrapolée à partir des 115 séquences cibles potentielles de DdrI, est spécifiquement fixée par DdrI uniquement en présence d’AMPc. Après un choc thermique, DdrI induit directement ou indirectement l’expression de nombreux gènes codant des protéases, des protéines du métabolisme de l’ADN, des lipides, des carbohydrates ainsi qu’un inhibiteur de la traduction. PprA, une protéine spécifique aux Deinococcaceae, joue un rôle crucial dans la radiorésistance et est impliquée dans la ségrégation des chromosomes et/ou la division cellulaire après réparation de l’ADN. De manière intéressante, l’absence de RecN, une protéine de la famille SMC, supprime la sensibilité du mutant ΔpprA aux agents génotoxiques, aux inhibiteurs de l’ADN gyrase et les défauts de ségrégation observés dans le mutant ΔpprA après irradiation des cellules. Après exposition des cellules au rayonnement γ, l’absence de RecN réduit la fréquence de recombinaison entre ADN chromosomique et plasmidique, suggérant que RecN intervienne dans la réparation de l’ADN par recombinaison homologue. Nous proposons un modèle, dans lequel RecN, en favorisant la réparation de l’ADN par recombinaison homologue, nécessite la présence de PprA pour favoriser le recrutement des ADN topoisomérases et la résolution des contraintes topologiques engendrées par ce mécanisme de réparation d’ADN. / The Deinococcus radiodurans bacterium exhibits resistance to γ and UV radiation, desiccation and oxidative stress. The molecular mechanisms contributing to the radioresistance of D. radiodurans include very efficient DNA repair mechanisms and ROS detoxification systems, protein protection against oxidation, a compact nucleoid structure and a subset of Deinococcus specific genes which are strongly induced after γ radiation. The ddrI (DNA damage response) gene is highly up-regulated after exposure to γ radiation and encodes a transcription factor belonging to the CRP (cAMP receptor protein) family. Compared to wild type cells, cells devoid of DdrI display defects in cell division and/or DNA segregation and is sensitive to DNA damaging agents, oxidative stress and heat shock treatment. In silico predictions of putative DdrI targets suggest that hundreds of genes,belonging to various cellular processes (DNA replication and repair, oxidative stress and heat shock responses, regulation of transcription and signal transduction) may be regulated by DdrI. The pseudopalindromic 5’TGTGA(N6)TCACA3’ consensus sequence, extrapolated from 115 potential DdrI binding sites, is specifically bound by DdrI only in presence of cAMP. After heat shock treatment, DdrI is involved directly or indirectly, in the induction of heat shock response genes coding proteases, proteins involved in DNA, lipid, carbohydrate metabolism and a translation inhibitor. Among the Deinococcus specific proteins required for radioresistance, the PprA protein was shown to play a major role for accurate chromosome segregation and cell division after completion of DNA repair. Here, we analyzed the cellular role of the RecN protein belonging to the SMC family and, surprisingly, observed that the absence of the RecN protein suppressed the sensitivity of cells devoid of the PprA protein to γ- and UV-irradiation and to treatment with mitomycin C or DNA gyrase inhibitors. The absence of RecN also alleviated the DNA segregation defects displayed by the ΔpprA cells recovering from irradiation. After irradiation, the absence of RecN reduced recombination between chromosomal and plasmid DNA, indicating that the RecN protein is important for recombinational repair of DNA lesions. Here, we propose a model in which RecN, by favoring recombinational repair of DNA double strand breaks, requires the PprA protein to facilitate the recruitment of the DNA topoisomerases to resolve the topological constraints generated by DNA double strand break repair through homologous recombination.

No description available.