Orientador: Marcelo Lancellotti / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-22T23:59:18Z (GMT). No. of bitstreams: 1 Andrade_AliceTavaresReis_M.pdf: 3292132 bytes, checksum: ee5318f5b87992964c9d97bedc343f00 (MD5) Previous issue date: 2013 / Resumo: Em 1998, foi relatada a transferência lateral do gene sodC do gênero Haemophilus para a espécie Neisseria meningitidis. Sabe-se que, nestes dois grupos a dinâmica deste gene é bastante distinta. Este trabalho tem por objetivo estimar árvores filogenéticas que possam apontar qual a espécie do gênero Haemophilus compartilhou o gene sodC com a espécie N. meningitidis. Testes de seleção positiva foram empregados no intuito de avaliar quais forças evolutivas estão subjacentes ao processo de diversificação molecular do gene nestas espécies ao longo do tempo. Além disso, foi realizada uma modelagem protéica computacional por homogia para avaliar quais substituições de aminoácidos tinham impacto no processo adaptativo da enzima nas espécies consideradas. Ao se reconstruir uma filogenia para o gene sodC, foi constatado que a origem deste gene na espécie H. influenzae é distinta. Um grupo de linhagens recebeu o gene, provavelmente por transferência lateral, da espécie H. haemolyticus, enquanto o outro grupo recebeu o gene da espécie H. parainfluenzae. Neste grupo, o gene sofreu pseudogeneização. Foi observado também que as sequências de N. meningitidis agrupam com as sequências que compartilham um ancestral comum com a espécie H. haemolyticus, porém as sequências do meningococo formam um ramo distinto dentro deste clado. Dada à alta clonalidade das sequências de N. meningitidis, foi constatado que o evento de transferência lateral de genes foi muito recente na escala do tempo. O teste de seleção positiva demonstrou que seleção positiva está atuando especificamente no ramo da árvore que compartilha um ancestral comum com a espécie H. haemolyticus, através da modificação de uma alanina por uma serina na posição 72, embora a nota geral da árvore tenha sido menor que 1. Sabe-se que pseudogenes, por não codificarem uma proteína ativa e, portanto, por não estarem sob nenhum tipo de restrição funcional, estão sob uma ação maior da deriva genética. Portanto, diferentes forças evolutivas estão governando a evolução deste gene nas espécies consideradas. A modelagem protéica concluiu que tal modificação contribuiu para o aumento do potencial redox do sítio ativo. Desta forma, a ação da seleção positiva sob um único resíduo de aminoácido foi benéfica para a função da enzima como um todo / Abstract: In 1998, it was reported the lateral transfer of the sodC gene from the genus Haemophilus to Neisseria meningitidis. It is known that this two groups show a quite distinct dynamics of this gene. This study aims to estimate phylogenetic trees that might point to which species of the genus Haemophilus shared the sodC gene with N. meningitidis. In addition, tests of positive selection were employed in order to assess which evolutionary forces are governing the process of molecular diversification of the gene in these species through time. Moreover, we performed a computational protein modeling by homology to asses which amino acids substitutions had an impact on the adaptative process of the enzyme in the species considered. A phylogeny of the sodC gene was reconstructed and it was found that this gene in H. influenzae has two different origins. A group of lineages has received the gene, probably by lateral transfer, from H. haemolyticus, whereas the other group has received the gene from H. parainfluenzae. In the latter, the gene has become a pseudogene. It was also observed that the sequences from N. meningitides group together with those sequences that share a common ancestor with H. haemolyticus, but they form a distinct branch within this clade. Given the high clonality of the sequences from N. meningitidis, it was found that the lateral gene transfer event is very recent in the time scale. A test of positive selection showed that positive selection is acting specifically in the branch that shares a common ancestor with H. haemolyticus through the substitution of an alanine to a serine at position 72, though the overall score of the tree is less than one. It is known that pseudogenes do not encode active proteins and therefore they are not under any kind of functional constraints, so they are under greater influence of genetic drift. Thus, it was concluded that different forces are driving the evolution of this gene in the species considered here. Protein modeling concluded that this modification contributed to the increase in the redox potencial of the active site. Thus the action of positive selection under a single amino acid residue was beneficial to the function of the enzyme as whole / Mestrado / Bioquimica / Mestra em Biologia Funcional e Molecular

DNA repair processes are crucial for mutation avoidance and the maintenance of genetic integrity in all organisms. Organisms rely on repair processes to combat genotoxic stress imposed by hostile host environment, and sometimes by therapeutic agents. Most pathogens rapidly generate genetic variability to acquire increased virulence and evade host immune response. Therefore, there needs to exist a fine balance between mutation avoidance and fixation, which is perhaps regulated by repair processes. Haemophilus influenzae and Helicobacter pylori contribute significantly to morbidity and mortality caused by bacteria worldwide. H. influenzae is an obligate commensal of upper respiratory tract with the potential to cause a variety of diseases in humans like meningitis and respiratory infections. H. pylori, which inhabits the human stomach, is associated with gastric and duodenal ulcers and cancerous gastric lesions. One of the striking differences between these two genetically diverse bacterial species is the absence of recognized DNA mismatch repair (MMR) pathway homologs in H. pylori. MMR is a highly conserved post-replicative process, which corrects base pairing mismatches and small loops arising during DNA replication and recombination due to misincorporated nucleotides, insertions, and deletions. Defective MMR results in increased mutation frequency that can alter the pathogenic potential and antibiotic resistance of pathogens. MMR has been extensively studied in Escherichia coli, and requires an orchestrated function of different proteins like MutS, MutL, MutH, UvrD, SSB, RecJ, ExoVII, ExoI, ExoX, beta-clamp, DNA polymerase III and DNA ligase. A growing body of evidence suggests that bacteria other than the well-characterized E. coli paradigm differ in basic DNA repair machinery. MMR proteins involved in mismatch recognition and strand discrimination like MutS, MutL and MutH from H. influenzae have been characterized, but other downstream repair genes like UvrD helicase and exonucleases like RecJ have not been studied functionally in detail. H. pylori harbors a UvrD homolog, which shares limited homology with other UvrD proteins (29% identity with E. coli UvrD and 31 % with H. influenzae UvrD) and its cellular functions are not clear. Moreover, it is not well-understood how the activities of UvrD and RecJ proteins are regulated within these pathogens. It was, therefore, envisaged that biochemical characterization of UvrD and RecJ would lead to a better understanding of the mechanistic aspects of repair processes within these pathogens. The following sections summarize the results presented in this investigation. Functional characterization of UvrD from H. influenzae UvrD or DNA helicase II is a member of superfamily I of DNA helicases with well-documented roles in nucleotide excision repair (NER) and MMR, in addition to roles in replication and recombination. The 727-amino acid H. influenzae Rd KW20 UvrD (HiUvrD) protein was purified as an N-terminal (His)6-tagged protein to near homogeneity, and its authenticity was confirmed by peptide mass fingerprint analysis. HiUvrD displayed robust binding with single-stranded (ss) DNA as compared to double-stranded (ds) DNA. HiUvrD was found exhibit ~ 1000-fold higher affinity for ssDNA as compared to dsDNA as determined by surface plasmon resonance (SPR). In addition, to gain insights into the role of HiUvrD in replication, repair, recombination and transcription, the ability of HiUvrD to bind different DNA structures resembling intermediates of these processes was investigated using electrophoretic mobility shift assays. HiUvrD exhibited relatively high affinities for a number of branched DNA substrates and the order of affinity observed was; splayed-duplex ≥3’-flap ≥ ssDNA > 3’-overhang > four-way junction > three-way junction > nicked duplex > looped duplex ≥ duplex. Concurrent with its high affinity for ssDNA, HiUvrD exhibited a robust ssDNA-specific and Mg2+ - dependent ATPase activity. HiUvrD was able to unwind different DNA structures with varying efficiencies (3’ flap ≥ 3’-overhang > three-way junction > splayed-duplex > four-way junction > nicked > loop = duplex >>> 5’-overhang) and with a 3’-5’ polarity, which underpins its role in replication fork reversal, recombination and different DNA repair pathways. Multiple sequence alignment of HiUvrD with other helicases showed the presence highly conserved helicase motifs of which motif I and II are essential for ATP binding and hydrolysis. Mutation of an invariant glutamate residue (E226Q) in motif II of HiUvrD resulted in a dominant negative growth phenotype since, it was not possible to recover transformants when wild-type E. coli expression strains BL21(DE3)plysS or BL21(DE3)plysE were transformed with expression vector carrying hiuvrDE226Q. Mutation of a conserved arginine residue to alanine (R288A) in motif IV resulted in approximately 80 % reduction in ATP hydrolysis, and abrogation of helicase activity as compared to the wild-type protein. This can be attributed to ~ 70 % reduced ATP binding by HiUvrDR288A as determined by UV-crosslinking of radioactive ATP without change in affinity for ssDNA. HiUvrD was found to exist predominantly as a monomer with small amounts (~ 2-3 %) of higher oligomers like dimers and tetramers in solution. Deletion of 48 amino acid residues from distal C-terminus of HiUvrD resulted in abrogation of the oligomeric species implicating C-terminus to be involved in protein oligomerization. Interplay of UvrD with MutL and MutS in H. influenzae, and its modulation by ATP To investigate the effects of H. influenzae MutS (HiMutS) and MutL (HiMutL) on the helicase activity of HiUvrD, two different nicked DNA substrates were generated- a homoduplex and a heteroduplex DNA with a GT mismatch. HiMutL and HiMutS did not exhibit any helicase activity on either homoduplex or heteroduplex DNA, and unwinding of these substrates was observed only in presence of HiUvrD. In the presence of HiMutL the helicase activity of HiUvrD was stimulated on both homoduplex and heteroduplex nicked substrates whereas no significant modulation of HiUvrD ATPase activity in presence of HiMutL was observed. A much higher stimulation of unwinding of heteroduplex DNA was obtained, in presence of increasing concentrations of HiMutS. With increasing concentrations of HiMutL a progressive increase in HiUvrD mediated unwinding of the radiolabeled DNA strand was observed, which was ~ 15-fold higher than unwinding by HiUvrD alone. To investigate the effect of ATP in the stimulation of HiUvrD by HiMutL, two mutants of HiMutL–E29A (E29 is involved in ATP hydrolysis in E. coli UvrD), and D58A (D58 is essential for ATP binding in E. coli UvrD) were generated. HiMutLE29A retained only ~ 30 % of the wild-type ATPase activity, which was completely abolished in HiMutLD58A. Similar to wild-type protein, HiMutLE29A was able to stimulate HiUvrD helicase activity whereas HiMutLD58A failed to stimulate this activity. This indicated that ATP-bound form of MutL was essential for stimulation and perhaps interaction with UvrD. SPR analysis was carried out to validate and quantitate the direct protein-protein interaction between HiUvrD and HiMutL in absence or in presence of ATP, AMPPNP, and ADP. In the presence of ATP as well as AMPPNP, almost ~ 10,000-fold increase in the affinity between HiMutL and HiUvrD was observed but the same was not the case in presence of ADP. This clearly suggested that ATP binding rather than its hydrolysis promotes the interaction of MutL with UvrD. The effect of HiMutS on MutL-stimulated DNA unwinding by HiUvrD was determined using a heteroduplex nicked DNA with a GT mismatch. Interestingly, in the presence of HiMutS ~ 20-fold activation of DNA unwinding was observed, which is higher than the stimulation by HiMutL alone. The role of ATP-hydrolysis by MutS in regulation of UvrD helicase was studied by replacing wild-type protein with HiMutSE696A in the helicase assays. HiMutSE696A failed to hydrolyze ATP but was able to bind ATP with the same affinity as the wild-type protein and interacted with heteroduplex DNA with ~ 8-fold reduced affinity as compared to wild-type MutS. Intriguingly, increasing concentrations of HiMutSE696A failed to stimulate HiUvrD helicase activity in presence of HiMutL indicating that ATP hydrolysis by HiMutS is essential for stimulation of HiUvrD helicase activity post MutH-nicking during MMR. SSB, an essential component of all DNA metabolism pathways, possibly functions to stabilize the ssDNA tract generated by UvrD and exonucleases during MMR. ATPase and helicase activities of HiUvrD were inhibited by the cognate SSB protein. This inhibition could be overcome by increasing the concentration of HiUvrD helicases thus, pointing out the fact that SSB and UvrD perhaps compete with each other for ssDNA substrate. Noticeably, MutL and MutS proteins could alleviate the inhibition of HiUvrD by HiSSB. Functional characterization of UvrD from H. pylori In H. pylori, UvrD has been reported to limit homologous recombination and DNA-damage induced genomic recombinations but the protein has not been functionally studied. UvrD from H. pylori strain 26695 (HpUvrD) was over-expressed and purified as an N-terminal (His)6-tagged protein, and its authenticity was confirmed by peptide mass fingerprint analysis. HpUvrD exhibited high affinity for ssDNA as compared to dsDNA as determined by electrophoretic mobility shift assays and SPR. In addition, HpUvrD was able to bind a number of branched DNA structures (splayed duplex > ssDNA > 3’-flap > 3’overhang > three-way junction = four-way junction > loop >>> nicked ≥ duplex) suggesting its role in different DNA processing pathways. HpUvrD exhibited a Mg2+ - dependent ssDNA-specific ATPase activity, and a 3’-5’ helicase activity. HpUvrD was able to unwind different branched DNA structures with 3’-ssDNA regions like splayed duplex, 3’-overhang and 3’-flap. Blunt-ended duplex, duplexes with nick and loop as well as three-way and four-way junctions were unwound with less efficiency. Interestingly, the helicase activity of HpUvrD was supported by GTP and dGTP to almost the same level as ATP and dATP, which is in stark contrast to other characterized UvrD proteins. Moreover, HpUvrD was able to hydrolyze GTP albeit with ~ 1.5-fold reduced rate as compared to ATP. However, motifs associated with GTP binding and hydrolysis were not found in HpUvrD and it is possible that GTP binds in the same site as ATP. To investigate this possibility, helicase assay was done in the presence of ATP together with different concentrations of GMP-PNP, which is a non-hydrolysable analog of GTP, and did not support HpUvrD helicase activity. With increasing concentrations of GMP-PNP, a progressive inhibition of DNA unwinding by HpUvrD was observed suggesting that GMP-PNP could compete with ATP for a common binding site within HpUvrD. Replacement of a highly conserved glutamate residue with gluatamine (E206Q) in Walker B motif of HpUvrD resulted in ~17-fold reduced ATPase activity, and abrogation of helicase activity as compared to the wild-type protein. HpUvrDE206Q was able to bind ssDNA and ATP with comparable affinities as the wild-type protein suggesting the role of E206 in ATP hydrolysis. Like HiUvrD, HpUvrD was found to exist predominantly as a monomer in solution together with the presence of small amounts of higher oligomeric species. However, unlike HiUvrD, deletion of distal C-terminal 63 amino acids in HpUvD did not abrogate the oligomeric species suggesting that additional regions of the protein may be involved in protein oligomerization. The ATPase and helicase activities of HpUvrD were inhibited by the cognate SSB protein, and this inhibition could be overcome by increasing HpUvrD concentrations again suggesting that both UvrD and SSB proteins compete for ssDNA substrate. To investigate the role of UvrD in the physiology of H. pylori, a knock-out of hpuvrD was constructed in H. pylori strain 26695 by insertion of chloramphenicol cassette in its open reading frame. The mutant H. pylori strain 26695 obtained after disruption of hpuvrD was extremely slow growing under the normal microaerophilic conditions compared to the wild-type strain. Growth defect of H. pylori strain 26695ΔhpuvrD highlights the importance of UvrD in H. pylori cellular processes and in vitro fitness. Characterization of H. influenzae RecJ and its interaction with SSB Among the four exonucleases involved in MMR pathway, RecJ is the only known nuclease that degrades single-stranded DNA with 5’ to 3’ polarity. RecJ exonuclease plays additional important roles in base-excision repair, repair of stalled replication forks, and recombination. RecJ exonuclease from H. influenzae (HiRecJ) is a 575 amino acid protein, which harbors the characteristic motifs conserved among RecJ homologs. Due to limited solubility of HiRecJ, the protein was purified as a fusion protein with maltose binding protein (MBP). The purified protein exhibited a Mg2+ or Mn2+- dependent, and a highly processive 5’ to 3’ exonuclease activity, which is specific for ssDNA. MBP did not affect the exonuclease activity of HiRecJ. The processivity of HiRecJ was determined as ~ 700 nucleotides per binding event, using a ssDNA substrate labelled internally with 3H and at its 5’-terminus with 32P. Cd2+ inhibited the Mg2+ - dependent exonuclease activity of RecJ, which could not be overcome by increasing Mg2+ concentration. Site-directed mutagenesis of highly conserved residues in HiRecJ- D77A, D156A and H157A abolished the enzymatic activity. Interestingly, HiRecJD77A was found to interact with ssDNA with a 10-fold higher affinity than wild-type protein suggesting that this conserved aspartate residue may function to coordinate the binding of metal ion or DNA to hydrolysis of DNA. E. coli HU protein inhibited the HiRecJ exonuclease activity in a concentration-dependent manner possibly due to sequestration of ssDNA, thus making it unavailable for HiRecJ. During MMR, ssDNA tracts generated by UvrD helicase activity are most probably stabilized by SSB and hence, the in vivo substrate for RecJ would be SSB-ssDNA complex. The exonuclease activity of HiRecJ was stimulated approximately 3-fold by H. influenzae SSB (HiSSB) protein. HiSSB was able to stimulate HiRecJ exonuclease activity on a ssDNA substrate, which formed either a very strong secondary structure or on a homopolymeric ssDNA substrate, which did not form any secondary structure, suggesting that HiRecJ exonuclease was stimulated independent of the ability to HiSSB to melt secondary structures and stabilize ssDNA. Significantly, steady-state-kinetic analysis clearly showed that HiSSB increases the affinity of HiRecJ for ssDNA. H. influenzae SSBΔC and T4 gene 32 protein, a SSB homolog from bacteriophage T4, failed to enhance the HiRecJ exonuclease activity suggesting a specific functional interaction between HiSSB and HiRecJ mediated by C-terminus tail of HiSSB. More importantly, HiRecJ was found to directly associate with its cognate SSB. The C-terminus of HiSSB protein was found to be essential for this interaction. To delineate the regions of HiRecJ that interact with HiSSB, different truncated forms of HiRecJ were generated in which regions external to conserved motifs required for exonuclease activity were deleted. Different deletion mutants of HiRecJ- RecJ∆N34, RecJ∆C76 and the core catalytic domain (which contains amino acid residues 35-498) were purified as fusion proteins with MBP. HiSSB was found to interact with all the truncated forms of HiRecJ suggesting that its core-catalytic domain harbors a site for interaction with SSB. Taken together, the results presented in this study lead to a better understanding of the structure-function relationships of the UvrD helicase and RecJ exonuclease. Importantly, they provide insights into the interplay between various proteins in DNA MMR pathway. Characterization of repair proteins that are involved in multiple genome fidelity pathways is of fundamental importance to understand repair processes, more so in pathogenic bacteria wherein they regulate mutation rates, which can alter the fitness and virulence of the pathogens. Publication Sharma R., and Rao, D.N. (2009). Orchestration of Haemophilus influenzae RecJ exonuclease by interaction with single-stranded DNA-binding protein. J. Mol. Biol., 385, 1375-1396.

La Broncho-Pneumopathie Chronique Obstructive (BPCO) est une maladie pulmonaire inflammatoire consécutive à l'exposition chronique à la pollution atmosphérique et surtout au tabagisme dans environ 90% des cas. Cette maladie se caractérise par une obstruction des bronches due à une hypersécrétion de mucus, une hypertrophie des muscles lisses, ainsi qu’une destruction de la paroi des alvéoles respiratoires amenant le patient à l’emphysème. Le stress induit par la fumée de cigarette provoque une activation de la barrière épithéliale pulmonaire associée à une altération de la réponse immunitaire responsable d’une susceptibilité accrue aux infections pulmonaires. De ce fait, les patients atteints de cette maladie développent des exacerbations principalement liées à ces infections bactériennes en particulier à Non-Typable Haemophilus influenza (NTHi) et Streptoccocus pneumoniae (Sp).La cytokine IL-22 est un acteur très important des défenses antibactériennes et du maintien de la barrière épithéliale. Cette cytokine appartient à la grande famille de l’IL-10, et à la sous-famille des cytokines IL-20 composée de l’IL-19, l’IL-20 et l’IL-24. L’IL-22 se lie au récepteur formé par les sous-unités IL-10Rb et IL-22Ra, tandis que les cytokines IL-19, IL-20 et IL-24 utilisent deux récepteurs associant l’IL-20Rb avec l’IL-20Ra ou l’IL-22Ra. Il a été démontré que les cytokines de la famille IL-20 (IL-19, IL-20, IL-24) agissent sur la clairance bactérienne au cours d’une infection cutanée par Staphylococcus aureus (Myles et al., 2013), en inhibant la production des cytokines IL-17 et IL-22. De plus, des précédents travaux au laboratoire, ont montré un défaut de l’expression des cytokines IL-17 et IL-22 qui participaient à la susceptibilité à l’infection chez les souris atteintes de BPCO (Pichavant et al., 2015). Enfin, nos données actuelles montrent que l'exposition à la fumée de cigarette augmente l'expression des cytokines de la famille IL-20 et que l'inhibition de cette voie permet de bloquer le développement d'épisodes d'exacerbation chez des souris BPCO.L'objectif de cette thèse est de préciser le rôle des cytokines IL-20 dans la réponse à l'infection bactérienne (Sp, NTHi) tant dans un contexte physiologique qu'au cours d’un contexte mimant la BPCO. Pour cela, nous nous focaliserons sur le rôle de l’épithélium pulmonaire tant dans la production que dans la fonction de ces cytokines en contexte infectieux.Pour répondre à ces questions, nous avons analysé l’expression des cytokines IL-20 par l’épithélium pulmonaire in vitro et ex vivo dans un modèle murin mimant l’exacerbation de la BPCO ainsi que dans des biopsies pulmonaires de patients fumeurs atteints ou non de BPCO. Dans un second temps nous avons évalué la modulation par un anticorps bloquant le récepteur des cytokines IL-20 (anti-IL-20Rb) au cours de la réponse anti-infectieuse de l'épithélium dans nos modèles in vivo (souris infectées par Sp) et in vitro (cellules épithéliales de trachées murines). Nous avons en parallèle évalué l'implication des cytokines IL-20 dans la réparation épithéliale.L’ensemble des résultats acquis au cours de la thèse nous a permis de démontrer l'implication des cytokines IL-20 et de préciser leur rôle sur l’épithélium pulmonaire au cours de l'infection bactérienne ainsi que dans la pathologie de la BPCO. De plus, les résultats obtenus avec l’anticorps neutralisant anti-IL-20Rb dans ces contextes d’infections et de BPCO, font de celui-ci une potentielle piste thérapeutique pour le traitement des lésions dues à l’infection. / Chronic Obstructive Pulmonary Disease (COPD) is an inflammatory lung disease due to chronic exposure to air pollution and especially to cigarette smoke exposure in approximately 90% of the cases. This disease is characterized by obstruction of the bronchi due to hypersecretion of mucus, hypertrophy of the smooth muscles, and destruction of the alveolar wall leading the patient to emphysema. The stress induced by cigarette smoke exposure causes activation of resident cells including pulmonary epithelial cells and an alteration of the immune system responsible for an increased susceptibility to pulmonary infections. As a result, patients with this disease develop exacerbations especially du to Non-Typable Haemophilus influenza (NTHi) and Streptoccocus pneumoniae (Sp).The IL-22 cytokine plays a key role in antibacterial defenses and maintenance of the epithelial barrier. This cytokine belongs to the large IL-10 family, and to the IL-20 cytokine subfamily also including IL-19, IL-20 and IL-24. IL-22 binds to the receptor formed by the IL-10Rb and IL-22Ra subunits, while the IL-19, IL-20 and IL-24 cytokines binds to IL-20Rb associated with either IL-20Ra or IL-22Ra subunits. IL-20 cytokines (IL-19, IL-20, IL-24) have been shown to impair bacterial clearance during cutaneous infection with Staphylococcus aureus (Myles et al., 2013), by inhibiting the production of IL-17 and IL-22 cytokines. In addition, previous work in the laboratory showed a defect in the expression of IL-17 and IL-22 cytokines contributing to the susceptibility to infection in COPD mice (Pichavant et al., 2015). In fact, our current data show that exposure to cigarette smoke increases cytokine expression of the IL-20 family and that inhibition of this pathway blocks the development of exacerbation episodes in COPD mice.The aim of this thesis is to clarify the role of IL-20 cytokines in the response to bacterial infections (Sp, NTHi) both in a physiological context and in a context mimicking COPD. To do so, we will focus on the role of pulmonary epithelium both in the production and function of these cytokines in infectious context.To answer these questions, we analyzed the expression of IL-20 cytokines by pulmonary epithelium in vitro and ex vivo in a mouse model mimicking the COPD exacerbation as well as in pulmonary biopsies of smokers and non-smokers patients and of COPD patients. In a second step we evaluated the modulation by an IL-20 receptor blocking antibody (anti-IL-20Rb) of the anti-infectious response in our in vitro (murine tracheal epithelial cells) and in vivo models (Sp-infected mice). In parallel, we evaluated the involvement of IL-20 cytokines in the epithelial repair.All the results acquired during the thesis allowed us to demonstrate the expression of IL-20 cytokines and to demonstrate their role on the pulmonary epithelium during bacterial infection as well as in COPD. In addition, the results obtained with the anti-IL-20Rb neutralizing antibody in these contexts of infections and COPD, suggests a potential therapeutic application for respiratory infection.

La BPCO se traduit rapidement par l'apparition d'une susceptibilité aux infections liées aux atteintes des mécanismes de défense du poumon. Les travaux antérieurs de l’équipe montrent qu'une altération de la réponse IL-17/IL-22 et de la fonction des cellules dendritiques (DC) participe au développement de l’exacerbation de la BPCO par les bactéries. Les mécanismes responsables de ce défaut de réponse ne sont pas élucidés. Au cours de cette thèse, nous nous sommes intéressés aux points suivants :1-Mécanismes cellulaires responsables du défaut de production d'IL-17 et d'IL-22 au cours de l'infection.Les cellules présentatrices d'antigène (APC) et en particulier, les DC jouent un rôle essentiel dans la réponse antimicrobienne, par leur fonction de phagocytes et par l’activation et la polarisation de cellules immunitaires innées et adaptatives. Sur des modèles murins d’exacerbation de la BPCO par Streptococcus pneumoniae ou Haemophilus influenzae non typable (NTHi), nous avons réalisé des tris de macrophages, DC et monocytes inflammatoires du poumon par cytométrie en flux. Ces analyses montrent que les cellules APC pulmonaires présentent des altérations fonctionnelles aboutissant à une limitation de leur capacité à polariser la réponse Th17 de Lymphocytes T CD4+. Une analyse transcriptomique est également effectuée sur les ARN des APC triées afin de préciser les altérations fonctionnelles de ces cellules par rapport aux souris contrôles.2-Rôle des cytokines IL-20 dans la susceptibilité à l'infection et l'exacerbation de la BPCO Myles et al ont montré en 2013 que les cytokines IL-20 (IL-19, IL-20 et IL-24) jouent un rôle délétère dans la réponse immunitaire cutanée contre Staphylococcus aureus par un mécanisme impliquant une inhibition indirecte d’IL-17 produite par les cellules T. La fonction des DC peut être affecté par l'environnement cytokinique. Comme les cytokines IL-20 sont surexprimées chez les souris BPCO, notre objectif a été de définir leur rôle au cours de l'exacerbation de la BPCO et l'impact de ces cytokines sur les DC dans ce contexte.Dans notre modèle d’exacerbation de la BPCO, nous avons bloqué cette voie en neutralisant l'IL-20RB qui est commune aux 2 récepteurs de ces cytokines afin d’étudier leur impact sur l'exacerbation et sur la réponse immune associée, notamment la réponse IL-17/IL-22. En parallèle, nous avons analysé la modulation de la fonction des DC humaines par ces cytokines dans un contexte d'infection bactérienne. Nos résultats montrent que le traitement avec l'anticorps bloquant anti-IL-20RB permet de bloquer le développement de l'exacerbation de la BPCO en diminuant la charge bactérienne et l'inflammation associée. Cet effet est associé à une diminution importante de la mobilisation des DC dans le poumon mais sans affecter sur la réponse IL-17/IL-22. In vitro, les cytokines IL-20 sont produites par les DC dans un contexte infectieux. De plus, ces cytokines sont capables de diminuer l'activation des ces cellules par les bactéries et de réduire leur capacité à activer les Lymphocytes T dans ce contexte.3-Capacité d'un immunostimulant à restaurer la réponse IL-17/IL-22, et à limiter le développement de l'exacerbation.L’utilisation d’immunostimulant dont la flagelline (agoniste du TLR-5, principale composante du flagelle bactérien) est souvent proposé comment pouvant promouvoir la réponse immunitaire des muqueuses et en particulier la réponse IL-17/IL-22. Nous avons analysé la capacité de cet agoniste du TLR-5 à améliorer la réponse à S. pneumoniae et NTHi dans notre modèle d’exacerbation de la BPCO.Le traitement par la flagelline permet de limiter les conséquences de l'infection bactérienne chez les souris BPCO en diminuant l'inflammation et les lésions pulmonaires associées. L'effet de ce ligand de TLR est au moins en partie dépendant de la production d'IL-22._A terme, ces données permettent d'envisager de nouvelles options thérapeutiques pour le traitement des exacerbations de la BPCO. / Patients with COPD often presented a susceptibility to respiratory infections. Previous works in our lab have showed that a defect of IL-17/IL-22 response and an altered dendritic cell (DC) function is involved in COPD exacerbation with bacteria. However, the mechanism responsible for this defect is not elucidated yet. In order to better define these mechanisms and to develop new therapeutic approaches against COPD exacerbation, we focused on the following points during this PhD project:1-Cellular mechanisms responsible of the defect of IL-17 and IL-22 production during infection in COPD.Antigen presenting cells (APC) particularly, DC are essential in antimicrobial immune response since they are professional phagocytes able to engulf and kill bacteria, but also by their essential role in the polarization of innate and adaptive immune responses. We worked on COPD exacerbation mice model infected with Streptococcus pneumoniae or Nontypeable Haemophilus influenzae (NTHi). APC including macrophages, DC and inflammatory monocytes were sorted by flow cytometry for phenotype and functional analysis. We found an altered function of these lung APC showing limited capacity of Th17 polarization. Transcriptional analysis on total RNA from sorted APC is performed to decipher the mechanisms involved in this functional alteration regarding to control mice.2-The role of IL-20 cytokines in the susceptibility to infection during COPD exacerbation.Myles et al showed in 2013 that IL-20 cytokines (IL-19, IL-20 and IL-24) are deleterious in skin immune response against Staphylococcus aureus. Indeed, these IL-20 cytokines indirectly inhibited IL-17 produced by T cells. The function of DC is also controlled by the presence of cytokines in the microenvironment. Because IL-20 cytokines are overexpressed in COPD, we aimed to determine their role during COPD exacerbation and the impact on DC.We used IL-20RB (common subunits of the 2 receptors) neutralizing antibodies to blocked IL-20 cytokines in COPD exacerbation mice model. We analyzed the impact of this treatment on the immune response, more particularly IL-17/IL-22 response. In addition, we analyzed the modulation of human monocyte derived DC (MDDC) function by IL-20 cytokines in the context of bacterial infection.Our results shows that treatment with IL-20 RB neutralizing antibodies limited COPD exacerbation by reducing the bacterial burden and the associated inflammatory response. This process was associated to reduced number of DC in the lung without impacting IL-17 and IL-22 production. In vitro, MDDC produced IL-20 cytokines upon bacterial infection. Additionally, these cytokines impaired MDDC activation following bacterial infection, which was associated to a reduced capacity of MDDC to activate T lymphocytes.3-The possibility to restore IL-17 and IL-22 response with immuno-stimulants in order to limit the development of COPD exacerbation.Flagellin (a TLR-5 agonist, the main component of bacterial flagellum) is an immuno-stimulant often used to promote mucosal immune response. This activity is related to its ability to promote IL-17 and IL-22 production. In this PhD work, we analyzed the capacity of this TLR-5 agonist to improve the immune response during S. pneumoniae and NTHi infection in COPD exacerbation mice model.Flagellin treatment reduced the bacterial burden and limited the consequences of bacterial infection in COPD mice, by lowering the inflammation and the associated lung remodeling. We also found that the immunomodulatory effect of flagellin was at least partially IL-22 dependent.Finally, these data allow to identify new therapeutic tools potentially useful for the treatment of COPD exacerbations.

Made available in DSpace on 2016-08-17T18:39:34Z (GMT). No. of bitstreams: 1 3277.pdf: 7015864 bytes, checksum: 9834075e819d2bb62213cf25d21ce5e5 (MD5) Previous issue date: 2010-08-27 / Haemophilus influenzae type b (Hib) is a Gram negative bacterium responsible for causing meningitis worldwide. The capsular polysaccharide b, a polymer composed by repeating units of ribosyl-ribitol phosphate (PRP), is the major virulence factor and it is used in the formulation of the vaccine against this microorganism. Despite their high efficiency, the conjugated vaccine against Hib is a product of high production cost, which involves fermentation, purification and conjugation processes to obtain a final product within the specifications of the World Health Organization (WHO). The improvement of the culture medium and cultivation conditions can contribute to reduce the cost of this vaccine in order to facilitate its dissemination in developing countries. The main objective of this work was to identify culture conditions that result in higher production of capsular polysaccharide, helping to reduce costs in the steps of purification and conjugation. The experiments were carried out in shake flasks or in bioreactors with 7-13 liters of capacity. The temperature was maintained at 37 °C, pH controlled at 7.5 by adding NaOH 5M and the concentration of dissolved oxygen (CDO) maintained at 30% of air saturation. The specific flow rate of air ranged between 0.2 and 1 VVM. Samples were collected at regular time intervals to measure optical density (DO540nm), biomass concentration, capsular polysaccharide (PRP) production and concentrations of glucose and metabolites. Two possibilities for increasing polysaccharide production were studied: 1) different strategies of fed-batch cultivation consisting of: a) intermittent addition of glucose (FBIG), b) constant feeding (FBCF), c) exponential feeding (FBEF), e d) exponential feeding with cell recycle and perfusion (FBER + P); 2) improvement of culture media composition regarding the carbon/nitrogen ratio through the use of central composite rotational design (CCRD) methodology, having as independent variables: Soy Peptone (S), Yeast Extract (YE) and Glucose (G). Quality parameters were also evaluated to assess the molecular weight profile of the product (PRP) as well as morphological aspects of the microorganism. Economic analysis of different cultivation strategies was used to identify the more economically viable process. The results of the different cultivation strategies together with the outputs of the studied processes cost analysis showed that FBCF, with a cost of U.S.$ 425.50/g PRP and productivity of 88 mg/L.h, showed to be the best alternative among PRP production processes due to its lower cost with a good productivity. In the study of the culture media composition through the statistical analysis of the CCRD results showed that the best culture media composition (BCM) consisted of S 5 g/L; YE 5.5g /L and G of 15.25 g/L. DO540nm and PRP volumetric production values of 8.4 and 410 mg/L, respectively, were attained in validation experiments carried out in shake flasks at the BCM condition. For the bioreactor BCM validation experiment, biomass concentration of 3 g DW/L and polysaccharide production of 600 mg PRP/L were observed. Similar values were reached at validation runs performed in shake flasks and bioreactor for the central point CP condition, showing that both BCM and CP conditions belong to the optimum region. The analysis of quality parameters showed that the cultivation time influences strongly the size of the polysaccharide molecule. The longer the cultivation time, the lower molecular weight was found. The analysis by transmission electron microscopy (TEM) of H. influenzae cells revealed a predominance of round cells in the sixth hour of cultivation, whereas in the twelfth hour of cultivation the cells exhibited a more elongated morphology with the presence of cytoplasmic inclusions in the shape of granules, possibly due to the accumulation of some reserve material. Based on these results, the new composition of the culture medium resulted in an increased of cell growth and capsular polysaccharide production with half of the sources nitrogen (soybean peptone and yeast extract) concentrations, which reduces the production cost. The cultivations that resulted in higher production and productivity of polysaccharide were FBCF (1600 mg PRP/L and 88 mg PRP/(L.h)) and FBER+ P (1800 mg PRP/L and 129 mg PRP/(L.h)). The FBER+P reached 30% higher productivity of polysaccharide than the best result described in the literature (90 mg PRP/(L.h)). However, the FBCF cultivation was economically more viable. / Haemophilus influenzae tipo b (Hib) é uma bactéria Gram negativa responsável por causar meningite em todo o mundo. O polissacarídeo capsular b, um polímero composto por unidades repetidas de ribosil-ribitol-fosfato (PRP) e o principal fator de virulência, sendo utilizado na formulação da vacina contra este microrganismo. Apesar de sua elevada eficiência, a vacina conjugada contra Hib é um produto de alto custo de produção por envolver processos de fermentação, purificação e conjugação para obtenção de um produto final dentro das especificações da Organização Mundial da Saúde (OMS). O melhoramento do meio de cultura e das condições de cultivo pode contribuir para redução do custo desta vacina de forma a facilitar sua difusão nos países subdesenvolvidos. Assim, o principal objetivo deste trabalho foi identificar condições de cultivo que resultem em maior produção de polissacarídeo capsular, contribuindo para reduzir os custos nas etapas de purificação e conjugação. Os ensaios foram conduzidos em frascos agitados ou em biorreatores com 7 a 13 litros de capacidade nominal. A temperatura foi mantida em 37oC, o pH controlado em 7,5 através da adição de NaOH 5M e a concentração de oxigênio dissolvido (COD) mantida em 30 % da saturação do ar. A vazão especifica de ar variou entre 0,2 e 1 VVM. Amostras foram coletadas em intervalos regulares de tempo para mensurar densidade óptica (DO540nm), concentração celular, produção de polissacarídeo capsular (PRP) e concentrações de glicose e metabolitos. Duas possibilidades para aumentar a produção de polissacarídeo foram estudadas: 1) diferentes estratégias de cultivo descontinuo alimentado consistindo por: a) adição intermitente de glicose (CDAIG), b) vazão constante (CDAVC), c) vazão exponencial (CDAVE), e d) reciclo de células seguido de perfusão (CDAVE+P)); e 2) o melhoramento da composição do meio de cultura quanto à relação carbono/nitrogênio através do uso da metodologia de delineamento composto central rotacional (DCCR), tendo como variáveis independentes: Peptona de Soja (S), Extrato de Levedura (EL) e Glicose (G). Parâmetros de qualidade também foram avaliados para verificar o perfil da massa molecular do produto (PRP) e os aspectos morfológicos do microrganismo. Os resultados das diferentes estratégias de cultivo juntamente com os resultados da analise econômica do custo dos processos estudados mostraram que o CDAVC, com custo de US$ 425.50/g PRP por ano e produtividade de 88 mg/(L.h), demonstrou ser a melhor alternativa para o processo de produção de PRP por apresentar menor custo com boa produtividade. Já o estudo da composição do meio de cultura através da analise estatística dos resultados do DCCR mostraram que a melhor composição do meio de cultivo (MMC) consistia em S de 5 g/L, EL de 5,5 g/L e G de 15,25 g/L. Valores de DO540nm de 8,4 e de produção volumétrica de polissacarídeo de 410 mg PRP/L foram alcançados em experimentos de validação na condição MMC realizados em shaker. Para o ensaio de validação da condição MMC em reator, a concentração de biomassa de 3,0 g MS/L e a produção de polissacarídeo capsular de 600 mg PRP/L foram observadas. Valores semelhantes foram obtidos em experimentos de validação realizados em shaker e biorreator na condição CPC, mostrando que tanto a condição CPC como a MMC pertencem a região de ótimo. A analise dos parâmetros de qualidade mostrou que o tempo de cultivo influencia fortemente no tamanho da molécula do polissacarídeo, sendo que quanto maior o tempo de cultivo, menor a sua massa molecular. A analise por microscopia eletrônica de transmissão (MET) das células de H. influenzae mostrou a predominância de células com morfologia arredondada na sexta hora de cultivo, enquanto que, na décima segunda hora de cultivo, as células apresentaram morfologia mais alongada e exibiram a presença de inclusões citoplasmáticas na forma de grânulos, possivelmente devido ao acumulo de algum material de reserva. Diante dos resultados obtidos, a nova composição de meio resultou em maior crescimento celular e produção de polissacarídeo capsular, com metade das concentrações das fontes de nitrogênio (peptona de soja e extrato de levedura), o que reduz o custo de produção. Os cultivos que resultaram em maior produção e produtividade foram o CDAVC (1600 mg PRP/L e 88 mg PRP/L.h) e o CDAVE+P (1800 mg PRP/L e 129 mg PRP/L.h), sendo que este ultimo (CDAVE+P) atingiu produtividade 30 % maior que o melhor resultado ate então descrito na literatura (90 mg PRP/L.h). No entanto, o cultivo CDAVC apresentou maior viabilidade do ponto de vista econômico e de execução e passível de escalonamento.