The Epsilonproteobacteria Helicobacter pylori and Campylobacter jejuni are major human pathogens. Both bacteria encode only a small number of transcription factors, but employ small non-coding RNAs (sRNAs) to regulate gene expression at the post-transcriptional level. While these regulatory RNAs often need the help of a protein chaperone to fulfill their function in well-studied enterobacterial model organisms, H. pylori and C. jejuni, like half of all bacteria, lack homologs of this protein named Hfq. In all domains of life, RNA-binding proteins (RBPs) play diverse roles in post-transcriptional regulation beyond their function in supporting base-pairing RNA regulators, and can themselves also directly influence mRNA stability or translation. The global identification of RBPs in eukaryotes by oligo(dT)-capture methods has previously identified a number of interesting novel candidates, including metabolic enzymes, that play a role in post-transcriptional regulation. However, these approaches are not applicable to bacteria, which lack polyA-tails on their mRNAs, and the RBPome of prokaryotes remains incompletely studied. This thesis aimed to identify auxiliary protein factors that are involved in post-transcriptional regulation, especially by sRNAs, in Epsilonproteobacteria. First, the H. pylori sRNA NikS, which we characterize as a nickel-regulated and possibly phase-variable regulator of at least five virulence and colonization factors, served as a model sRNA for a number of biochemical and genetic approaches to capture a potential RBP. NikS was chosen as it regulates its targets at the post-transcriptional level by binding to the site of translation initiation, a mechanism common to Hfq-dependent sRNAs in other bacteria. For biochemical assays, a number of RNA fusions combining the MS2, S1, and D8 aptamers with the sRNAs NikS and RepG were constructed. Fusions that were still able to regulate their targets in vivo were used for affinity purification to identify proteins associated with the sRNAs. In addition to these approaches, H. pylori sRNAs were also fused to a 14nt-long bait sequence that was then used for purification using an antisense oligonucleotide. In addition to these biochemical approaches, a functional genetic screen based on transposon mutagenesis was also used. Fluorescent reporter fusions of NikS targets were combined with transposon mutant libraries to identify genes that are necessary for sRNA function. While these genetic and biochemical screens revealed proteins such as known nickel-associated factors that likely affect NikS transcription, and known RBPs such as RNA degradosome components, thereby validating the approaches, a promising sRNA chaperone candidate was not identified. I therefore aimed to develop two novel methods to identify RBPs. One approach is based on the CRISPR/Cas-system of C. jejuni. Here, the sRNA of interest is fused to either a single-guide RNA (sgRNA) or tracrRNA, two RNAs that are specifically bound by the Cas9 protein. Cas9 is immobilized on affinity resin, in principle allowing purification of the sRNA with associated protein factors from a lysate. In proof-of-principle experiments in E. coli with the Hfq-dependent sRNA MicA, sRNA fusions could be co-purified with Cas9, but Hfq was not detected. Therefore, a second novel method, termed CoCap (Co-purification of RNA-binding proteins with biotin-capped primary transcripts), was developed to investigate the protein interactome of primary transcripts. Here, primary transcripts (including many sRNAs) were selectively biotinylated and purified via Streptavidin, along with associated proteins including potential RBPs, which were identified by mass spectrometry. The method was first established in Salmonella as a model organism for a bacterium encoding the global RNA chaperones Hfq and ProQ, and then applied to C. jejuni. CoCap identified known and novel RBPs in both organisms. In Salmonella, a number of proteins that were previously not associated with RNA binding were validated and investigated independently via RIP-seq (RNA immunoprecipitation followed by deep sequencing), including the plasmid-encoded ProQ-like protein YafB, which turned out to be a global binder of mRNAs and sRNAs. The CoCap dataset for C. jejuni revealed a KH domain-containing protein as a novel RBP candidate. We show that this protein forms a complex with another KH domain-containing protein, and that both proteins can bind RNA and potentially interact with a number of cell envelope proteins. RNA binding of the H. pylori homologs of these proteins could also be verified, although these proteins bind different and smaller subsets of RNAs. While this thesis revealed these KH domain proteins as RNA binders and gives first insights into their potential functions, the roles of these proteins in vivo remain elusive. In summary, I applied diverse genetic and biochemical screens to search for auxiliary protein factors in RNA-based regulation in Epsilonproteobacteria. I further developed a novel approach to globally identify the primary RNA-binding proteome named CoCap and applied it to Salmonella and C. jejuni. This led to the identification of novel RBPs in both organisms and established CoCap as a method applicable to a large number of bacteria. / Die Epsilonproteobakterien Helicobacter pylori und Campylobacter jejuni sind wichtige Humanpathogene. Beide Bakterien kodieren nur eine begrenzte Anzahl an Transkriptionsfaktoren, nutzen jedoch kleine nicht-kodierende RNAs (sRNAs), um die Genexpression auf der posttranskriptionellen Ebene zu regulieren. In gut erforschten enterobakteriellen Modellorganismen benötigen diese regulatorischen RNAs häufig die Hilfe eines Proteins namens Hfq. In H. pylori und C. jejuni, wie in der Hälfte aller Bakterien, fehlt jedoch ein Hfq-Homolog. In allen Domänen des Lebens können RNA-Bindeproteine (RBP) verschiedene Funktionen in der posttranskriptionellen Regulation übernehmen. Sie können zum Beispiel die Basenpaarung von RNAs ermöglichen oder auch direkt die Stabilität oder Translation von mRNAs beeinflussen. Die globale Identifizierung von RBP in Eukaryoten mittels sogenannter „oligo(dT)-capture“-Methoden hat einige interessante Kandidaten zutage gebracht, einschließlich metabolischer Enzyme, die eine Rolle in der posttranskriptionellen Regulierung übernehmen. Diese Methoden können jedoch nicht in Bakterien angewandt werden, da deren mRNAs nicht polyadenyliert sind, weshalb es an einer vollständigen Liste der bakteriellen RBP mangelt. Ziel dieser Arbeit war es, Proteinfaktoren der posttranskriptionellen Regulierung, vor allem durch sRNAs, in Epsilonproteobakterien zu identifizieren. Zuerst wurde die sRNA NikS aus H. pylori, welche wir als einen nickelabhängigen, potenziell phasenvaribalen Regulator von mindestens fünf Virulenz- und Kolonisierungsfaktoren charakterisieren, als Modell-RNA in verschiedenen biochemischen und genetischen Ansätzen verwendet, um potenzielle RBP zu identifizieren. NikS wurde ausgewählt, da es seine Zielgene durch die Interaktion mit der Region der Translationsinitiations reguliert, was ein Mechanismus ist, den auch Hfq-abhängige sRNAs in anderen Bakterien verwenden. Für die biochemischen Ansätze wurden einige RNA-Fusionen aus MS2-, S1- und D8-Aptameren mit den sRNAs RepG und NikS konstruiert. Funktionale Fusionen wurden dann zur Affinitätsaufreinigung verwendet, um Proteine zu identifizieren, die mit den sRNAs interagieren. Zudem wurde eine Ködersequenz an die sRNAs fusioniert, welche dann in einem „Antisense-Oligo“-Ansatz zur Aufreinigung genutzt wurde. Neben diesen biochemischen Ansätzen wurde eine funktionelle Suche basierend auf einer Transposonmutantenbibliothek durchgeführt. Hier wurden Fusionen aus NikS-Zielen und fluoreszenten Proteinen mit der Bibliothek kombiniert, um Gene zu identifizieren, die für die sRNA-Funktion benötigt werden. Die genetischen und biochemischen Experimente konnten Proteine identifizierten, die durch ihre Verbindung zu Nickel vermutlich die NikS-Expression beeinflussen, oder die als Teil des Degradosoms bekannte RBP sind, was die Methoden validiert. Es konnte jedoch kein guter Kandidat für ein sRNA-Hilfsprotein ausgemacht werden. Daher wurden zwei neue Methoden entwickelt. Eine davon basiert auf dem CRISPR/Cas-System von C. jejuni. Hier wird die sRNA an eine “sg RNA” oder “tracrRNA” fusioniert. Diese beiden RNAs werden von Cas9 gebunden, wodurch eine Immobilisierung von Cas9 auch eine Aufreinigung der sRNA und gebundener Proteine erlauben sollte. Um die Machbarkeit zu überprüfen, wurden Fusionen der Hfq-abhängigen sRNA MicA mittels Cas9 aus E. coli aufgereinigt. Eine Anreicherung von Hfq konnte jedoch nicht nachgewiesen werden. Daher wurde eine zweite Methode namens CoCap (Co-purification of RNA-binding proteins with biotin-capped primary transcripts) entwickelt, um Proteine, die mit primären Transkripten, inklusive zahlreicher sRNAs, interagieren, zu identifizieren. Diese Transkripte werden biotinyliert und zusammen mit gebundenen Proteinen aufgereinigt, welche dann mittels Massenspektrometrie identifiziert werden können. Die Methode wurde in Salmonella, als Modell für ein Bakterium, das die globalen RBP Hfq und ProQ exprimiert, entwickelt und dann in C. jejuni angewandt. In beiden Organismen wurden bekannte und neue RBP identifiziert. Einige Proteine aus Salmonella konnten mittels einer unabhängigen Methode verifiziert wurden. So z.B. YafB, ein plasmidkodiertes ProQ-ähnliches Protein, das sich als globales mRNA- und sRNA-Bindeprotein herausstellte. In C. jejuni wurde mittels CoCap ein KH-Domänen-Protein als neues RBP identifiziert. Wir zeigen, dass dieses mit einem weiteren KH-Protein interagiert und dass beide Proteine RNA und wahrscheinlich auch Zellhüllenproteine binden können. Die Interaktion mit RNAs wurde auch für die homologen Proteine aus H. pylori verifiziert, wobei diese eine unterschiedliche und kleinere Gruppe von RNAs binden. Obwohl die KH-Proteine in dieser Arbeit als RBP validiert werden konnten, ist deren Funktion in der Zelle noch unklar. Zusammenfassend habe ich diverse genetische und biochemische Ansätze angewandt, um Hilfsproteine der RNA-basierten Regulierung in Epsilonproteobakterien zu identifizieren. Zudem habe ich eine neue Methode namens CoCap entwickelt, die das primärtranskriptbindende Proteom global ermittelt, und diese in Salmonella und C. jejuni angewandt. Dies führte zur Identifizierung neuer RBP in beiden Organismen und etablierte CoCap als Methode, die in zahlreichen Bakterien angewandt werden kann.

Les systèmes toxine-antitoxine (TA) sont de petits modules génétiques largement présents dans les génomes bactériens. Ils codent pour une petite protéine toxique et une antitoxine. Ils sont classés en six types en fonction de la nature et du mode d'action de l'antitoxine. Ce travail a porté sur l'étude du type I, pour lequel l'antitoxine est un ARN antisens qui cible l'ARNm de la toxine afin de réprimer son expression. Au cours de cette thèse, nous avons étudié le système aapA3/IsoA3, codé sur le chromosome du pathogène gastrique humain Helicobacter pylori. À ce jour, la plupart des systèmes TA ont été étudiés à l'aide de systèmes d'expression artificiels, qui ne permettent pas de caractériser la régulation transcriptionnelle ou post-transcriptionnelle. En utilisant la létalité induite par l’expression chromosomique de la toxine obtenue en absence d’antitoxine, nous avons développé une sélection génétique de mutants suppresseurs révélés par séquençage haut-débit. Cette approche, appelée FASTBAC-Seq, nous a permis de cartographier une myriade de déterminants de toxicité localisés dans les régions codantes et non codantes du gène de la toxine AapA3. En particulier, certaines de ces mutations ont révélé l'existence de tige-boucles ARN transitoires qui agissent de manière co-transcriptionnelle pour empêcher l'initiation de la traduction pendant la synthèse de l'ARNm codant pour la toxine. Ces structures ARN métastables fonctionnelles sont nécessaires pour découpler les processus de transcription et de traduction et permettent la présence de ces gènes toxiques sur le chromosome bactérien. Bien que les ARNm non traduits deviennent rapidement instables, nos travaux ont également révélé l'existence de deux tige-boucles protectrices situées aux deux extrémités de l'ARNm. Ces structures secondaires empêchent des activités exonucléolytiques agissant en 5' et 3'. Dans l’ensemble, notre travail met en évidence les conséquences de la forte pression de sélection pour limiter l'expression des toxines sous laquelle évoluent les systèmes TA. Cela nous a permis de mieux comprendre l’influence du repliement secondaire des ARNm, non seulement lors de la régulation posttranscriptionnelle, mais aussi co-transcriptionnelle de l’expression de cette famille particulière de gènes. Ces caractéristiques de régulation basées sur l'ARN peuvent être exploitées à l'avenir pour des applications biotechnologiques (p. ex., production accrue de protéines par stabilisation d'ARNm) ou biomédicales (p.ex., développement de stratégies antimicrobiennes alternatives pour l'activation de la synthèse de toxines). / Toxin-antitoxin (TA) systems are small genetic modules widely present in bacterial genomes. They usually code for a small toxic protein and its cognate antitoxin and can be classified into six types depending on the nature and mode of action of the antitoxin. This work focuses on the study of type I, for which the antitoxin is an antisense RNA that targets the toxin mRNA to inhibit its expression. We characterized the aapA3/IsoA3 system, encoded on the chromosome of the human gastric pathogen Helicobacter pylori. To date, most TAs have been studied using artificial expression systems, which do not allow the characterization of transcriptional or post-transcriptional regulation. Taking advantage of the lethality induced by the toxin chromosomal expression in the absence of antitoxin, we developed a high-throughput genetic selection of suppressor mutations revealed by Next-Generation Sequencing. This approach, named FASTBAC-Seq, allowed us to map a myriad of toxicity determinants located in both, coding and noncoding regions, of the aapA3 toxic gene. More precisely, some suppressor mutations revealed the existence of transient RNA hairpins that act co-transcriptionally to prevent translation initiation while the toxinencoding mRNA is being made. Such functional RNA metastable structures are essential to uncouple the transcription and translation processes and allow the presence of these toxic genes on bacterial chromosomes. Although untranslated mRNAs become rapidly unstable, our work also revealed the presence of two protective stem-loops located at both mRNA ends that prevent from both, 5’ and 3’ exonucleolytic activity. Altogether, our work evidenced the consequences of the strong selection pressure to silence toxin expression under which the TAs evolve, and highlighted the key role of mRNA folding in the co- and post-transcriptional regulation of this family of genes. These RNA-based regulatory mechanisms may be exploited in the future for biotechnological (e.g., increased protein production through mRNA stabilization) or biomedical (e.g., development of alternative antimicrobial strategies aiming at the activation of toxin synthesis) applications.

Submitted by JACIARA CRISTINA ALMEIDA DO AMARAL (jaciaramaral@ufpa.br) on 2018-03-14T18:08:28Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_PrevalenciaAssociacaoInfeccao.pdf: 914836 bytes, checksum: 230ad3b3857c71456bdb6ad0d9a3fde0 (MD5) / Approved for entry into archive by JACIARA CRISTINA ALMEIDA DO AMARAL (jaciaramaral@ufpa.br) on 2018-03-14T18:13:01Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_PrevalenciaAssociacaoInfeccao.pdf: 914836 bytes, checksum: 230ad3b3857c71456bdb6ad0d9a3fde0 (MD5) / Made available in DSpace on 2018-03-14T18:13:01Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_PrevalenciaAssociacaoInfeccao.pdf: 914836 bytes, checksum: 230ad3b3857c71456bdb6ad0d9a3fde0 (MD5) Previous issue date: 2017-11-03 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A epidemiologia da HP e do vírus Epstein-Barr (EBV) é mundial. A prevalência de ambos os agentes carcinogênicos na população humana mundial é de cerca de 45%. Um estudo recente sugere que coinfecção de EBV com HP cagA positiva, aumenta o potencial oncogênico desta bactéria. O objetivo deste trabalho foi identificar a prevalência da bactéria HP e do EBV e a associação desses patógenos e do gene cagA em pacientes com gastrite na população do Amapá. Foi realizado um estudo descritivo, do tipo transversal, onde foram analisadas 292 amostras de mucosa gástrica de pacientes com gastrite submetidos a endoscopia, com faixa etária entre 14 e 83 anos de idade. Para detecção da HP foi utilizado o teste da Urease e a Reação em Cadeia da Polimerase, esta metodologia também serviu para revelar as cepas cagA positivas da bactéria. Adicionalmente, foi utilizada a técnica de hibridação in situ para detecção do EBV e a análise microscópica que determinou as características histopatológicas da mucosa gástrica. Resultados: Nosso estudo mostrou alta prevalência de casos de HP em pacientes com gastrite com uma frequência relativa de 87,67% dos 292 casos analisados, sendo maior incidência, dos casos positivos para HP, no sexo feminino, 88,27%. A incidência do gene cagA em amostras de pacientes positivos para HP foi de 72,66%, com maior prevalência no sexo feminino, 75,32%. No presente estudo foram encontrados 8,59% dos pacientes com infecção viral causada por EBV em amostras positivas para HP com maior prevalência no sexo masculino, 9,18%. De acordo com a faixa etária nosso estudo mostrou maior prevalência do gene cagA e do EBV em pacientes positivos para HP no segmento entre 44 e 54 anos, com 23,12% e 36,37%, respectivamente. A maioria dos achados deste estudo assemelha-se aos relatos da literatura, contudo, evidenciou-se a necessidade de estudos com maior casuística a fim de melhor esclarecer se há ou não há correlação entre a infecção por HP e EBV no norte do Brasil. / The epidemiology of HP and of the Epstein-Barr virus (EBV) is worldwide. The prevalence of both carcinogenic agents, in the world human population is about 45%. A recent study suggests that EBV coinfection with HP cagA positive increases the oncogenic potential of this bacterium. The objective of this study was to identify the prevalence of the bacterium HP and of the virus EBV and the association of those pathogens and of the cagA gene in patients with gastritis in the population of Amapá. A descriptive study was accomplished, of the traversal type, where 292 samples of gastric mucous of the patients were analyzed with gastritis submitted to the endoscopy, age group between 14 and 83 years. For detection of HP, Urease test and Polymerase Chain reaction were used; this methodology was also useful to reveal the positive cagA of the bacterium. Additionally, the technique of in situ hybridization was used for detection of EBV and the microscopic analysis that determined the histopathological characteristics of the gastric mucous. Results: The study showed high prevalence of cases of HP in patients with gastritis with a relative frequency of 87,67% of the 292 analyzed cases, a higher incidence, of HP positive cases, in female, 88,27%. The incidence of the cagA gene in samples of positive patients for HP was 72,66%, higher prevalence in female, 75,32%. In the present study 8,59% of the patients were found with viral infection caused by EBV in positive samples for HP with bigger prevalence in male, 9,18%. According to the age group, the study showed higher prevalence of the gene cagA and of EBV in positive patient for HP in the age group between 44 and 54 years, with 23,12% and 36,37%, respectively. Conclusion: Most of the findings of this study are similar to the reports from the literature, however, it is necessary other studies in order to explain if there is or there is no correlation between the infection for HP and EBV in the north of Brazil.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / O carcinoma gÃstrico à a segunda causa de morte por cÃncer no mundo. No Cearà à o segundo mais freqÃente entre os homens e o terceiro entre as mulheres. Dos cÃnceres gÃstricos os adenocarcinomas representam em torno de 95%. A doenÃa tem sido associada a fatores genÃticos e ambientais sendo demonstrada Ãntima relaÃÃo com a infecÃÃo por Helicobacter pylori, principalmente associada à presenÃa do gene cagA e genÃtipos vacAs1m1. Entretanto, apesar dos mecanismos pelos quais a bactÃria promove a carcinogÃnese gÃstrica ainda nÃo estarem esclarecidos, uma das hipÃteses seria atravÃs da inativaÃÃo de supressores tumorais. O objetivo do presente trabalho foi verificar, em adenocarcinomas gÃstricos, se a presenÃa de H. pylori, e de seus genes cagA e vacA, està relacionada com a mutaÃÃo e/ou alteraÃÃo na expressÃo protÃica dos supressores tumorais p53 e p27. Neste estudo, 74 amostras de pacientes foram analisadas quanto à presenÃa de H. pylori, cagA+ e os genÃtipos de vacA, pela reaÃÃo em cadeia da polimerase (PCR). A anÃlise mutacional do gene p53 foi realizada por PCR-SSCP e a detecÃÃo da mutaÃÃo/superexpressÃo do p53 e expressÃo da proteÃna p27 pelo mÃtodo imunohistoquÃmico. A bactÃria foi detectada em 95% das amostras, das quais 63% eram cagA(+). Dentre os alelos de vacA, observou-se predomÃnio de s1 (74%) e m1 (82%), associados em 69% dos casos. Na anÃlise mutacional do p53 verificou-se que 72% dos casos exibiram alteraÃÃo no padrÃo de mobilidade eletroforÃtica, sendo esta associada significativamente à presenÃa do gene cagA. Por outro lado, apenas 29% dos casos apresentaram detecÃÃo pelo mÃtodo imunohistoquÃmico, nÃo sendo encontrada associaÃÃo com a H. pylori. A proteÃna p27 demonstrou acentuada reduÃÃo em sua expressÃo (detectada em apenas 19% dos casos), nÃo demonstrando atividade compensatÃria em relaÃÃo à proteÃna p53 mutada e sem associaÃÃo estatÃstica dos casos negativos com a presenÃa da H. pylori. Finalmente, os resultados sugerem que estes supressores simultaneamente inativados podem ser o ponto chave da desregulaÃÃo do ciclo celular que, associados a outros fatores, favoreÃam o desenvolvimento e progressÃo dos adenocarcinomas gÃstricos. Hà indÃcios de que a presenÃa bacteriana, e dos seus genes cagA(+) e vacA/s1m1, possam influenciar, de forma nÃo esclarecida, as alteraÃÃes moleculares ocorridas nos supressores tumorais p53 e p27. / Gastric carcinoma is the second cause of death by cancer in the world. On State of Ceara-Brazil is the second most frequent type of cancer in men and third in women. Adenocarcinomas account for approximately 95% of all malignant gastric neoplasms. It has been associated to genetic and environmental factors and a intimate relationship between the infection by the bacteria Helicobacter pylori and the gastric carcinoma have been related. The presence of the cagA gene and specific genotypes (s1m1) of the gene vacA have been detected in more pathogenic strains. Although the precise molecular mechanisms by which H. pylori could promote the process of gastric carcinogenesis are under investigation, one hypothesized mechanism involves the tumor supressor genes inactivation. The aim of the present study was to verify if the presence of Helicobacter pylori, cagA and vacA genes is related to mutations in the tumor supressor gene p53 and altered expression of p53 and p27 proteins in gastric adenocarcinomas. Seventy-four (74) samples were analyzed to detect the presence of H. pylori, cagA and genotypes of vacA by Polymerization Chain Reaction (PCR). The mutational analysis of p53 gene was performed by PCR-SSCP (Polymerization Chain Reaction for analysis of the Single-strand Conformation Polymorphism). Analysis of mutation or overexpression of p53 protein and p27 expression was detected by the immunohistochemical method. The bacteria was detected in 95% of the samples, 63% was cagA(+). Among the vacA allele it was observed prevalence of s1 (74%) and m1 (82%), associated in 69% of the cases. Mutation analysis of p53 demonstrated 72% of the cases with altered electrophoretic mobility; The alterations were significatively more frequent in the presence of the cagA gene. Immunohistochemical analysis detected only 29% of cases with the expression of p53 protein. The protein p27 showed accentuated reduction in its expression (detected in only 19% of the cases), it has not demonstrated compensatory activity in relation to the p53 altered protein, neither association to H. pylori presence. Finally, these data suggest that simultaneous inactivation of these tumor suppressors genes may be the key point of deregulation of the cellular cycle that, associated to the other factors, favor the development and progression of the gastric cancer. There is some evidence that the bacterial presence, cagA and vacA/s1m1 genes, may influence, in a not understood way, the alterations observed in the tumor suppressors p53 and p27.

Atualmente, muitas são as diretrizes na literatura quanto à influência do Helicobacter pylori na Doença do Refluxo Gastroesofágico. Alguns autores acreditam que o H. pylori poderia ter um efeito protetor para o desenvolvimento na DRGE e outros até mesmo concluem que o agente possa ser um fator agravante na doença. Muitas publicações nos alertam para o desenvolvimento de sintomas da DRGE, ou mesmo da esofagite, em uma porcentagem razoável de pacientes erradicados pelo esquema tríplice para tratar o H. pylori, sendo que aproximadamente 10% teriam DRGE. Na verdade, por essas dúvidas, ainda não foi estabelecido um consenso quanto à importância do H. pylori na etiopatogenia da DRGE e suas complicações. Fato também discutido, seria a importância das cepas para a formação da esofagite em pacientes submetidos à erradicação. Talvez as mais virulentas, assim como a presença da “ilha de patogenicidade"(cagA) ou algumas cepas vacuolizantes (vacA), teriam uma maior relação com a prevenção da esofagite. Outro mecanismo importante, apontado por muitos, para a formação da esofagite em pacientes erradicados seria a elevação do índice de Massa Corpórea nesse grupo de pacientes erradicados associados ou não à presença da hérnia hiatal e justificados pela melhor qualidade de vida após melhora dos sintomas depois da erradicação. Em nosso estudo, 148 pacientes com úlcera péptica ativa ou cicatrizada receberam esquema tríplice de erradicação para o Helicobacter pylori e foram submetidos a exame endoscópico e ao teste histopatológico das amostras colhidas por biópsias de corpo e antro, teste respiratório com Carbono 14 e urease, antes e após o tratamento. Realizamos a genotipagem do agente, através do PCR, separando amostras de corpo e de antro, para determinar as cepas do agente. Os pacientes foram seguidos ambulatorialmente por um ano e avaliados quanto à melhora ou piora dos sintomas relacionados a DRGE (pirose) e sintomas considerados inespecíficos como a dor epigástrica; também procuramos quantificar o ganho ou perda do IMC. Encontramos 28 pacientes (18,9%) com esofagite erosiva (24 grau A e 4 grau B de Los Angeles) endoscópica após o tratamento do agente. Deste grupo, somente 3 pacientes que não tinham sintomas desenvolveram pirose (2%). A grande maioria dos pacientes se beneficiou com o tratamento, mostrando que 69 46,6%) melhoraram da pirose e outra grande maioria melhorou dos sintomas inespecíficos. Em 18 pacientes ulcerosos com esofagite, a análise de fragmentos de corpo foi cagA positiva (64,3%) e em amostras de antro 21 eram cagA positivos (75%). Assim como no grupo geral, as cepas vacuolizantes s1b/m1 e s1b foram, respectivamente, as mais encontradas no grupo da esofagite endoscópica. Houve ligeiro aumento nos Índices de Massa Corpórea em pacientes com e sem esofagite, sendo estatisticamente mais significativo nos 120 pacientes sem esofagite. Apesar do aparecimento da esofagite erosiva endoscópica em número razoável de pacientes, a sintomatologia não foi fator determinante, pois muitos melhoraram dos sintomas após o tratamento, e a erradicação não foi importante para determinar o grau de esofagite erosiva. Não foi encontrada nenhuma relação entre a genotipagem do agente e o desenvolvimento de esofagite endoscópica. O aumento de IMC, também não justifica, em nosso estudo a esofagite em pacientes ulcerosos tratados contra o H. pylori. / Nowadays, there are many directrixes in literature as to the influence of Helicobacter pylori, in the Disease of Gastroesophagic reflux. Some authors believe that H. pylori could have a protective effect to the development of GERD, and others even conclude that the agent may be an aggravating factor in the disease. Many publications allert us to the development of symptoms of GERD, or even the esophagitis,in a reasonable percentage of erradicated patients by the triplicit scheme to treat H. pylori, and 10%, approximately, would have GERD. In fact, due to these doubts, a consensus has not been established yet to the importance of H. pylori in the GERD’s etiopathogenic and its complications. The strains importance to the formation of esophagitis in patients submitted to erradication is another fact that has also been discussed. Maybe the most virulent ones, as the presence of “pathogenical island"(cagA) or some other vacuolating cytotoxin (vacA), would have a larger relation in the esophagitis prevention. Another important mechanism, pointed by many, to the formation of esophagitis in erradicated patients would be the elevation of Body Mass Index in this group of eradicated patients associated or not to the presence of hiatal hernia and justified by a better quality of life due to symptoms’ improvement after erradication. In our studies, 148 patients with active or healed peptic ulcer received triplicit scheme of erradication to the Helicobacter pylori and were submitted to endoscopic exams and histopathologic test of gathered samples by body and antro biopsies, respiratory test with carbon 14 and ureasis, before and after treatment. We have done the agent genotyping, through the PCR, separating samples of body and antro, to determine the agent Cepas. The patients have been followed ambulatorially for a year and evaluated as to the improvement or worsening of the symptoms related to GERD (pyrosis) and symptoms considered non-specific as epigastric pain; we have also tried to quantify the gain or loss of Body Mass Index. We found 28 patients(18.9%) with endoscopic erosive esophagitis (24 degree A and 4 degree B of Los Angeles) after agent’s treatment. In this group, only three patients who had no symptoms developed pyrosis (2%). Most of the patients benefitted from treatment showing that 69 (46.6%) presented improvement in pyrosis and another great majority improved non-specific symptoms. In 18 ulcered patients with esophagitis, the body analysis fragments was positive cagA (64.3%)and in antro samples of 21 were positive cagA (75%). As in the general group, the vacuolizing cepas slb/ml and slb were, respectivelly, the most found in the endoscopic esophagitis group. There was a slight raise in the BMI in patients with and without esophagitis, and it is, statistically more meaningful in the 120 patients without esophagitis. Even though there was the appearance of endoscopic erosive esophagitis in a reasonable number of patients, the symptmology was not a determining factor, because many have got better after the treatment, and erradication was not important to determine the erosive esophagitis. It was not found any relation between the agent genotyping and the development of endoscopic esophagitis. The raise of BMI does not justify in our study the esophagitis in ulcered patients treated against H. pylori.

Les acyl stéryl glycosides (ASGs) appartiennent à une famille de glycolipides qui possèdent un caractère amphiphile particulier dû à la présence de deux parties hydrophobes, un stéroïde et une chaine grasse. Dans le cadre de nos études des propriétés d’auto-organisation des glycoamphiphiles, ce travail est dédié à l’étude de deux ASGs, α-CAG et BbGL 1, composés naturels présents respectivement dans les membranes des bactéries Helicobacter pylori et Borrelia burgdorferi., présentant des structures similaires mais des activités biologiques différentes. Notre travail a consisté à déterminer les paramètres structuraux qui gouvernent leurs propriétés d’auto-assemblage. Deux séries de 6-O-acyl cholestéryl glycosides (glucosides et galactosides) variant dans leur configuration anomérique et la longueur et le niveau d’insaturation de leur chaine grasse ont été synthétisées et leur capacité à former des cristaux liquides et à promouvoir une ségrégation lipidique dans des monocouches de Langmuir modèles de membrane ont été étudiées. Les relations structure-propriétés établies montrent que la longueur de la chaine grasse est le paramètre le plus discriminant dans le comportement d’auto-assemblage dans les deux types d’expériences. Pour les cristaux liquides thermotropes, l’autre facteur discriminant est la configuration anomérique, deux phases colonnaires successives rectangulaires puis hexagonales étant observées pour les séries α alors qu’une seule a été observée en séries β Changer de sucre n’induit pas de différence significative dans le comportement LC. Concernant la formation de domaines lipidiques, les modifications de la configuration (α/β) et du sucre influencent significativement leur temps d’apparition, apportant pour la première fois une définition claire des paramètres structuraux et physicochimiques qui gouvernent le comportement de l’α-CAG et ses analogues, en lien avec les données commues sur l’augmentation de pathogénicité d’Helicobacter pylori. Ce travail de thèse donne une illustration de l’importance de la structure des carbohydrates dans les processus biologiques et du concept de glycoamphiphilie. / Acyl steryl glycosides (ASGs) are a family of glycolipids which exhibit a peculiar amphiphilic character based on the presence of two hydrophobic appendages, one steroid moiety and one fatty alkyl chain, attached on a polar carbohydrate backbone. In the frame of our studies on the self-organisation properties of carbohydrate-based amphiphiles, this thesis is an investigation of the behavior of ASGs, in particular α-CAG and BbGL 1, two natural compounds found in bacterial membranes, Helicobacter pylori, Borrelia burgdorferi repectively, who exhibit close structures but different bioactivity. Our work has aimed at determining the key structural parameters governing their self-organization behavior. Two series of acyl cholesteryl glycosides (glucosides or galactosides) have been synthesized, with variations in the anomeric configuration, the 6-O-acyl chain length and level of unsaturation, and investigated with respect to their ability to form liquid crystalline mesophases, and to drive lipid domain segregation in Langmuir monolayers as model membranes. Structure-properties relationships have been established, indicating that the fatty chain length showed the most remarkable influence on the self-organization behavior, in LC and model membrane experiments. For the LC mesophases, the other important parameter is the anomeric configuration, two successive columnar phases, rectangular then hexagonal, being observed for the α-anomers, whereas only one was found for the β-anomers. No significant changes were observed when comparing glucosides and galactosides. With respect the formation of domains, configuration modifications at both C-1 (α or β) and C-4 (gluco or galacto) influenced significantly the domains appearance time, giving the first, clear physicochemical proof of the structural influential factors in the behavior of α-CAG and analogues, in the context of the known increased pathogenicity of Helicobacter pylori. Overall, this thesis provides a nice illustration of the subtlety and the importance of carbohydrate structure in biological processes, and of the concept of glycoamphiphilicity.

Made available in DSpace on 2015-02-24T17:42:52Z (GMT). No. of bitstreams: 1 ThalesRFP_DISSERT.pdf: 5363462 bytes, checksum: 16f2d3a123870a2d8c63de00ac4bf689 (MD5) Previous issue date: 2014-02-24 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Helicobacter pylori is the main cause of gastritis, gastroduodenal ulcer disease and gastric cancer. The most recommended treatment for eradication of this bacteria often leads to side effects and patient poor compliance, which induce treatment failure. Magnetic drug targeting is a very efficient method that overcomes these drawbacks through association of the drug with a magnetic compound. Such approach may allow such systems to be placed slowed down to a specific target area by an external magnetic field. This work reports a study of the synthesis and characterization of polymeric magnetic particles loaded with the currently used antimicrobial agents for the treatment of Helicobacter pylori infections, aiming the production of magnetic drug delivery system by oral route. Optical microscopy, scanning electron microscopy, transmission electron microscopy, x-ray powder diffraction, nitrogen adsorption/desorption isotherms and vibrating sample magnetometry revealed that the magnetite particles, produced by the co-precipitation method, consisted of a large number of aggregated nanometer-size crystallites (about 6 nm), creating superparamagnetic micrometer with high magnetic susceptibility particles with an average diameter of 6.8 ? 0.2 μm. Also, the polymeric magnetic particles produced by spray drying had a core-shell structure based on magnetite microparticles, amoxicillin and clarithromycin and coated with Eudragit? S100. The system presented an average diameter of 14.2 ? 0.2 μm. The amount of magnetite present in the system may be tailored by suitably controlling the suspension used to feed the spray dryer. In the present work it was 2.9% (w/w). The magnetic system produced may prove to be very promising for eradication of Helicobacter pylori infections / A Helicobacter pylori ? a principal causa de gastrites, ?lceras gastroduodenais e c?ncer g?strico. O esquema terap?utico de primeira escolha para a erradica??o desse pat?geno leva muitas vezes a elevado n?mero de rea??es adversas, baixa ades?o do paciente e consequentemente falha na terap?utica. A vetoriza??o magn?tica ? uma t?cnica bastante difundida na literatura que visa minimizar esses problemas, atrav?s da associa??o de f?rmacos a n?cleos magn?ticos direcionando para o local de a??o por interm?dio de campo magn?tico externo. O presente trabalho relata o estudo da s?ntese e caracteriza??o de part?culas polim?ricas magn?ticas contendo os mais frequentes antimicrobianos (amoxicilina e claritromicina) usados no tratamento de infec??es por Helicobacter pylori, objetivando a produ??o de um sistema para vetoriza??o magn?tica por via oral. Granulometria baseada no di?metro de Feret, microscopia eletr?nica de varredura e transmiss?o, difratometria de raio-x, isotermas de adsor??o/dessor??o de nitrog?nio e magnetometria de amostra vibrante revelaram que as part?culas de magnetita, produzidas pelo m?todo da coprecipita??o, consistem em grande n?mero de agregados de cristalitos de tamanhos nanom?tricos (da ordem de 6 nm) os quais formam part?culas microm?tricas superparamagn?ticas de alta susceptibilidade magn?tica, tendo formato irregular com di?metro m?dio de 6,8 ? 0,2 μm. Os n?cleos magn?ticos foram revestidos por pol?mero (Eudragit? S100) em conjunto com amoxicilina e claritromicina (forma polim?rfica II) sendo obtido micropart?culas n?cleo-camada de formato irregular, pela t?cnica de secagem por aspers?o (spray dryer), com um di?metro m?dio de 14,2 ? 0,2 μm. A quantidade de magnetita presente no sistema pode ser adaptada pelo controle da suspens?o inicial usada na alimenta??o do spray dryer. No presente trabalho o conte?do magn?tico final foi estimado em 2,9 % (p/p). Com base nos resultados obtidos, o sistema magn?tico produzido pode se tornar bastante promissor na erradica??o de infec??es por Helicobacter pylori

Atualmente, muitas são as diretrizes na literatura quanto à influência do Helicobacter pylori na Doença do Refluxo Gastroesofágico. Alguns autores acreditam que o H. pylori poderia ter um efeito protetor para o desenvolvimento na DRGE e outros até mesmo concluem que o agente possa ser um fator agravante na doença. Muitas publicações nos alertam para o desenvolvimento de sintomas da DRGE, ou mesmo da esofagite, em uma porcentagem razoável de pacientes erradicados pelo esquema tríplice para tratar o H. pylori, sendo que aproximadamente 10% teriam DRGE. Na verdade, por essas dúvidas, ainda não foi estabelecido um consenso quanto à importância do H. pylori na etiopatogenia da DRGE e suas complicações. Fato também discutido, seria a importância das cepas para a formação da esofagite em pacientes submetidos à erradicação. Talvez as mais virulentas, assim como a presença da “ilha de patogenicidade”(cagA) ou algumas cepas vacuolizantes (vacA), teriam uma maior relação com a prevenção da esofagite. Outro mecanismo importante, apontado por muitos, para a formação da esofagite em pacientes erradicados seria a elevação do índice de Massa Corpórea nesse grupo de pacientes erradicados associados ou não à presença da hérnia hiatal e justificados pela melhor qualidade de vida após melhora dos sintomas depois da erradicação. Em nosso estudo, 148 pacientes com úlcera péptica ativa ou cicatrizada receberam esquema tríplice de erradicação para o Helicobacter pylori e foram submetidos a exame endoscópico e ao teste histopatológico das amostras colhidas por biópsias de corpo e antro, teste respiratório com Carbono 14 e urease, antes e após o tratamento. Realizamos a genotipagem do agente, através do PCR, separando amostras de corpo e de antro, para determinar as cepas do agente. Os pacientes foram seguidos ambulatorialmente por um ano e avaliados quanto à melhora ou piora dos sintomas relacionados a DRGE (pirose) e sintomas considerados inespecíficos como a dor epigástrica; também procuramos quantificar o ganho ou perda do IMC. Encontramos 28 pacientes (18,9%) com esofagite erosiva (24 grau A e 4 grau B de Los Angeles) endoscópica após o tratamento do agente. Deste grupo, somente 3 pacientes que não tinham sintomas desenvolveram pirose (2%). A grande maioria dos pacientes se beneficiou com o tratamento, mostrando que 69 46,6%) melhoraram da pirose e outra grande maioria melhorou dos sintomas inespecíficos. Em 18 pacientes ulcerosos com esofagite, a análise de fragmentos de corpo foi cagA positiva (64,3%) e em amostras de antro 21 eram cagA positivos (75%). Assim como no grupo geral, as cepas vacuolizantes s1b/m1 e s1b foram, respectivamente, as mais encontradas no grupo da esofagite endoscópica. Houve ligeiro aumento nos Índices de Massa Corpórea em pacientes com e sem esofagite, sendo estatisticamente mais significativo nos 120 pacientes sem esofagite. Apesar do aparecimento da esofagite erosiva endoscópica em número razoável de pacientes, a sintomatologia não foi fator determinante, pois muitos melhoraram dos sintomas após o tratamento, e a erradicação não foi importante para determinar o grau de esofagite erosiva. Não foi encontrada nenhuma relação entre a genotipagem do agente e o desenvolvimento de esofagite endoscópica. O aumento de IMC, também não justifica, em nosso estudo a esofagite em pacientes ulcerosos tratados contra o H. pylori. / Nowadays, there are many directrixes in literature as to the influence of Helicobacter pylori, in the Disease of Gastroesophagic reflux. Some authors believe that H. pylori could have a protective effect to the development of GERD, and others even conclude that the agent may be an aggravating factor in the disease. Many publications allert us to the development of symptoms of GERD, or even the esophagitis,in a reasonable percentage of erradicated patients by the triplicit scheme to treat H. pylori, and 10%, approximately, would have GERD. In fact, due to these doubts, a consensus has not been established yet to the importance of H. pylori in the GERD’s etiopathogenic and its complications. The strains importance to the formation of esophagitis in patients submitted to erradication is another fact that has also been discussed. Maybe the most virulent ones, as the presence of “pathogenical island”(cagA) or some other vacuolating cytotoxin (vacA), would have a larger relation in the esophagitis prevention. Another important mechanism, pointed by many, to the formation of esophagitis in erradicated patients would be the elevation of Body Mass Index in this group of eradicated patients associated or not to the presence of hiatal hernia and justified by a better quality of life due to symptoms’ improvement after erradication. In our studies, 148 patients with active or healed peptic ulcer received triplicit scheme of erradication to the Helicobacter pylori and were submitted to endoscopic exams and histopathologic test of gathered samples by body and antro biopsies, respiratory test with carbon 14 and ureasis, before and after treatment. We have done the agent genotyping, through the PCR, separating samples of body and antro, to determine the agent Cepas. The patients have been followed ambulatorially for a year and evaluated as to the improvement or worsening of the symptoms related to GERD (pyrosis) and symptoms considered non-specific as epigastric pain; we have also tried to quantify the gain or loss of Body Mass Index. We found 28 patients(18.9%) with endoscopic erosive esophagitis (24 degree A and 4 degree B of Los Angeles) after agent’s treatment. In this group, only three patients who had no symptoms developed pyrosis (2%). Most of the patients benefitted from treatment showing that 69 (46.6%) presented improvement in pyrosis and another great majority improved non-specific symptoms. In 18 ulcered patients with esophagitis, the body analysis fragments was positive cagA (64.3%)and in antro samples of 21 were positive cagA (75%). As in the general group, the vacuolizing cepas slb/ml and slb were, respectivelly, the most found in the endoscopic esophagitis group. There was a slight raise in the BMI in patients with and without esophagitis, and it is, statistically more meaningful in the 120 patients without esophagitis. Even though there was the appearance of endoscopic erosive esophagitis in a reasonable number of patients, the symptmology was not a determining factor, because many have got better after the treatment, and erradication was not important to determine the erosive esophagitis. It was not found any relation between the agent genotyping and the development of endoscopic esophagitis. The raise of BMI does not justify in our study the esophagitis in ulcered patients treated against H. pylori.

H. pylori has a panmictic population structure due to high genetic diversity. The homoplasy index for H. pylori is 0.85 (where 0 represents a completely clonal organism and 1.0 indicates a freely recombining organism) which is much higher than homoplasy index for E. coli (0.26) or naturally competent Neisseria meningitides (0.34). It undergoes both inter as well as intra strain transformation. Intergenomic recombination is subject to strain specific restriction in H. pylori. Hence, a high homoplasy index means that competence predominates over restriction in H. pylori. Annotation of the genomes of H. pylori strains 26695 and J99 show the presence of nearly two dozen R-M systems out of which 16 were postulated to be Type II for J99. H. pylori has been described to be an ideal model system for understanding the equilibrium between competing tension of genomic integrity and diversity (42). R-M systems allow some degree of sexual isolation in a population of competent cells by acting as a barrier to transformation. The mixed colonizing population of H. pylori has a polyploidy nature where each H. pylori strain adds to ‘ploidy’ of the colonizing population. Maintenance of polyploidy nature of mixed colonizing population in a selective niche of stomach needs a barrier to free gene flow. Restriction barrier maintains a polyploidy nature of H. pylori population which is considered as yet another form of genetic diversity helping in persistence of infection. Thus, according to the model proposed by Kang and Blaser, where H. pylori are considered as perfect gases like bacterial population, transformation and restriction both add to genetic diversity of the organism. Again, restriction barriers are not completely effective, which could be due to cellular regulation of restriction system. Thus, a perfect balance between restriction and transformation in turn regulates the gene flow to equilibrate competition and cooperation between various H. pylori strains in a mixed population. RecA, DprA and DprB have been shown to be involved in the presynaptic pathway for recombination substrates brought in through the Com system. Biochemical characterization of HpDprA, during this study revealed its ability to bind to ssDNA and dsDNA. Binding of HpDprA to both ssDNA as well as dsDNA results in large nucleoprotein complex that does not enter the native PAGE. However, DNA trapped in the wells could be released by the addition of excess of competitor DNA, illustrating that the complex are formed reversibly and do not represent dead-end reaction products. Transmission electron microscopy for SpDprA interaction with ssDNA established that a large nucleoprotein complex consisting of a network of several DNA molecules bridged by DprA is formed which is retained in the well. A large DNA-protein complex that sits in the well has also been observed with other DNA binding proteins like RecA. It has been observed for ssDNA binding protein (SSB) that they bind non-specifically to dsDNA under low salt condition (20 mM NaCl) in the absence of Mg2+. The non specific binding of SSB to dsDNA was prevented under high salt conditions (200 mM NaCl) or in the presence of Mg2+. HpDprA interaction with both ssDNA and dsDNA was stable under high salt condition (200 mM NaCl) and in the presence of Mg2+ indicating that these interactions are specific. The interaction of HpDprA with dsDNA is significant since dsDNA plays an important role in natural transformation of H. pylori. The pathway of transformation by dsDNA is highly facilitated (nearly 1000 fold) as compared to ssDNA. However, dsDNA is a preferred substrate for REases which are a barrier to horizontal gene transfer. This implies that the decision of ‘restriction’ or ‘facilitation for recombination’ of incoming DNA might be taken before the conversion of dsDNA into ssDNA. The incoming DNA has been shown to be in the double-stranded form in periplasm and in single-stranded form in cytoplasm. Hence, the temporal and spatial events surrounding endonuclease cleavage remain to be understood. Taken together, these results suggest a very important role of dsDNA in natural transformation in H. pylori. Hence, binding and protection of dsDNA by HpDprA is possibly of crucial importance in the success of natural transformation process of the organism. DprA is characterized by presence of a conserved DNA binding domain. The DNA binding domain adopts a Rossman fold like topology spanning most region of the protein. Rossman fold consists of alternating alpha helix and beta strands in the topological order of β-α-β-α-β. It generally binds to a dinucleotide in a pair as a single Rossman fold can bind to a mononucleotide only. All homologous DprA proteins characterized till date show that in addition of the prominent Rossman fold domain they consist one or more smaller domains. RpDprA consists two more domains other than the Rossman fold domain i.e., N- terminal SAM (sterile alpha motif) domain and a C-terminal DML-1 like domain. SpDprA consist of an N-terminal SAM domain other than Rossman fold domain. While the main function of Rossman fold is to bind DNA, the supplementary domains are highly variable in sequences and functions. For example, the SAM domain in S. pneumoniae plays a key role in shut-off of competence by directly interacting with ComE~P. HpDprA consist of an N-terminal Rossman fold domain and a C-terminal DML-1 like domain. Both these domains are found to be prominently α-helical in nature. Amino acid sequence analysis of the protein suggests that NTD is basic and CTD is acidic in nature. NTD is sufficient for binding with ssDNA and dsDNA, while CTD plays an important role in formation of higher order polymeric complex with DNA. For HpDprA and SpDprA, dimerization site was mapped in Rossman fold domain. Gel filtration data revealed an important observation that HpDprA can exist as a monomer (dominant species at lower concentration) as well as a dimer (dominant species at higher concentration) in solution. However, the exchange between these two forms is very fast resulting in a single peak of elution. Since, HpDprA binds to DNA in dimeric form, the dimer species will be favoured in presence of DNA. Hence, even at lower concentrations HpDprA will be mainly a dimer in presence of DNA. Interestingly, both domains of HpDprA i.e., NTD and CTD were able to form dimers but no higher oligomeric form. On the other hand, HpDprA was seen to form oligomeric forms higher than dimer in gluteraldehyde cross linking assay. The strength of CTD dimer was much lower that NTD dimer, therefore it could be proposed that there are two sites of interaction present in HpDprA - a primary interaction site (N-N interaction) and a secondary interaction site (C-C interaction). The N-N interaction is responsible for dimer formation but further oligomerization of HpDprA necessitates the interaction of two dimers using C-C interaction site. It was shown that NTD binds to ssDNA but forms lower molecular weight complex. SPR analysis of DprA and NTD – DNA interaction pointed out that deletion of CTD leads to faster dissociation of the protein from DNA. Concomitantly, reduction in binding affinity was observed for both ss and ds DNA upon deletion of CTD from full length protein. These results suggest that CTD does play an important role in interaction of full length HpDprA with DNA. Two possible roles of CTD were proposed by Wang et al (2014) group to explain their observation of formation of lower molecular weight complex in absence of CTD. (i) CTD possesses a second DNA binding site but much weaker than site present in NTD. (ii) CTD is not involved in DNA binding but mediates nucleoprotein complex formation through protein – protein interaction. EMSA and SPR analysis with purified CTD protein confirmed that there is no secondary DNA binding site present in CTD. As discussed above, it was observed that CTD can mediate interaction between two HpDprA through C-C interaction. Since the interaction is weaker it is lesser likely to be responsible for dimer formation but in trimer or higher oligomeric form of HpDprA, the presence of N-N interaction will facilitate and stabilize C-C interaction. These observations together bring forward an interesting model for HpDprA – DNA interaction. HpDprA forms dimer through N-N interaction (favourably in presence of DNA) and many HpDprA dimers bind to DNA owing to their high affinity and sequence independent nature of binding. These dimers interact with each other through C-C interaction resulting in higher molecular weight nucleoprotein complex. HpDprA - DNA complex formation is slower than NTD – DNA complex but the former one is more stable (Fig. 2). According to the above proposed model there are two binding events (DNA – protein and protein – protein) in case of HpDprA – DNA complex formation and hence it would take longer time than NTD-DNA complex formation which involves only one binding event. But the resulting higher order complex with HpDprA – DNA would be much more stable. NTD is able to offer equally efficient protection from nuclease to ssDNA and dsDNA (Fig. 7). This shows that NTD alone is sufficient to completely coat single molecule DNA. AFM images confirm the difference in binding pattern of HpDprA full length protein and NTD. As can be seen in Fig. 8F, NTD binds a DNA molecule by entirely occupying all the available space but forms nucleoprotein filaments isolated from each other. In contrast to full length HpDprA, which forms tightly packed, condensed, extensively cross linked polynucleoprotein complexes, NTD forms much thinner complexes with DNA. In the electron micrographs of SpDprA – DNA complex, extensive cross filament interaction was observed resulting in a dense molecular aggregate. Similar kinds of complexes with DNA were also observed for Bacillus subtilis DprA in atomic force microscope images. Thus, it could be proposed that HpDprA binds to a single DNA molecule (single strand or double strand) mainly as a dimer formed through N-N interaction. Such multiple individual nucleoprotein filaments come together and interact with each other through C- C interaction resulting in dense and intricate poly – nucleoprotein complex. HpDprA is proposed to undergo conformational changes from closed state to open state in presence of ssDNA. In agreement with this, structural transition (resulting in reduction of α-helicity of the protein) was observed in presence of ssDNA. Similar structural transitions were observed for dsDNA indicating possibly a common mode of interaction for both forms of DNA. Further, mutation of the residues shown to be involved in binding ssDNA from crystallographic data, resulted in decrease of binding affinity with dsDNA as well. The fold reduction in binding affinity of dsDNA was lower than that for ssDNA despite that it is obvious that the same positively charged pocket which is primarily involved in ssDNA interaction is also responsible (atleast partially) for binding with dsDNA. However, the residues crucial for interaction with these two forms of DNA may be different. Both DprA and R-M systems have been shown to have presynaptic role in natural transformation process. While DprA has a protective role, R-M systems have an inhibitory role for incoming DNA suggesting a functional interaction between them. Results of this study show that HpDprA interacts with dsDNA, inhibits Type II restriction enzymes from acting on it and at the same time stimulates the activity of MTases resulting in increased methylation of bound DNA. This observation is of significance from the view of genetic diversity as the only way a bacterial cell discriminates between self and nonself DNA is through the pattern of methylation. Binding of HpDprA to incoming DNA inhibits its access to restriction endonucleases but not to methyltransferases. As a result DNA will be methylated with the same pattern as that of the host cell. Hence, it no longer remains a substrate for restriction enzymes. HpDprA thus, effectively alleviates the restriction barrier. However, it remains to be understood as to how DNA in complex with HpDprA, while not accessible to REases or other cellular nucleases, is accessible to a MTase? A possible explanation could be that HpDprA interacts with MTase and recruits it on DNA. It has been shown that there is a overlap between DprA dimerization and RecA interaction interfaces and in presence of RecA, DprA-DprA homodimer is replaced with DprA-RecA heterodimer allowing RecA nucleation and polymerization on DNA followed by homology search and synapsis with the chromosome. A similar scenario can be thought for interaction of HpDprA with the MTase. R-M systems play an important role in protection of genomic DNA from bacteriophage DNA. Hence, downregulation of restriction barrier by HpDprA may not be desirable by host during the entire life cycle. Therefore, the expression of HpDprA, which is ComK dependent and that which takes place only when competence is achieved is noteworthy. In H. pylori, DNA damage induces genetic exchange via natural competence. Direct DNA damage leads to significant increase in intergenomic recombination. Taken together it can be proposed that when genetic competence is induced, R-M systems are down regulated to allow increased genetic exchange and thus, increasing adaptive capacity in a selective environment of stomach. There is an evolutionary arms race between bacterial genomes and invading DNA molecules. R-M systems and anti-restriction systems have co-evolved to maintain an evolutionary balance between prey and predator. Phages and plasmids employ anti-restriction strategies to avoid restriction barrier by a) DNA sequence alteration, b) transient occlusion of restriction sites and c) subversion of restriction-modification activities. DNA binding proteins have been shown to bind and occlude restriction sites. On the other hand, λ Ral protein alleviates restriction by stimulating the activity of Type IA MTases. The observations of MTase stimulation and site occlusion of restriction sites by HpDprA appears to be analogous to anti restriction strategies, otherwise employed by bacteriophages. Thus, DprA could be a unique bacterial anti-restriction protein used by H. pylori for downregulating its own R-M systems to maintain the balance between fidelity and diversity. In conclusion, HpDprA has unique ability to bind to dsDNA in addition ssDNA but displays higher affinity towards ssDNA. Binding of HpDprA to DNA results in a compact complex that is inert to the activity of nucleases. A novel site of oligomerization for HpDprA was observed which suggests the role of C-C interaction in inter-nucleoprotein filament interaction. It would be interesting to further study the effects of CTD deletion on the transformation efficiency of H. pylori, to understand these mechanisms better. It has been well demonstrated that R-M systems offer a barrier to incoming DNA, but our understanding of the regulation of R-M systems has been poor. While other factors like regulation of cellular concentration of restriction enzymes and conversion of dsDNA into ssDNA might play crucial roles in striking the perfect balance between genome diversity and integrity, one of the factors that regulate R-M systems could be DprA.

Helicobacter pylori causes chronic gastritis, peptic ulceration and gastric cancer. This bacterium is one of the most prevalent in the world, but affects mostly the populations with a lower socioeconomical status. While it causes gastric and duodenal ulcers in only 20% of infected patients, less then 1% will develop gastric adenocarcinoma. In fact, H. pylori is the most important risk factor in developing gastric cancer. Epidemiological studies have shown that 80% of gastric cancer patients are H. pylori positive. The outcome of the infection with this bacterium depends on bacterial factors, diet, genetic background of the host, and coinfection with other microorganisms. The most important cofactor in H. pylori induced disease is the host immune response, even though the exact mechanism of how the bacterium is causing disease is unknown. The structural complexity of Helicobacter bacteria makes us believe that different bacterial factors interact with different components of the innate immunity. However, as a whole bacterium it may need mainly the TLR2 receptor to trigger an immune response. The type of adaptive immunity developed in response to Helicobacter is crucial in determining the consequences of infection. It is now known for decades that a susceptible host will follow the infection with a strong Th1 immune response. IFNγ, IL-12, IL-1β and TNF-α are the key components of a strong adaptive Th1 response. This is further supported by our work, where deficient T-bet (a master regulator for Th1 response) mice were protected against gastric cancer, despite maintaining an infection at similar levels to wild type mice. On the other hand, a host that is resistant to Helicobacter develops an infection that is followed by a Th2 response sparing the mucosa from severe inflammation. Human studies looking at single nucleotide polymorphism of cytokines, like IL-1β, IL-10 and TNF-α have clearly demonstrated how genotypes that result in high levels of IL-1β and TNF-α, but low IL-10 expression may confer a 50-fold higher risk in developing gastric cancer. The outcome of Helicobacter infection clearly relies on the immune response and genetic background, however the coinfection of the host with other pathogens should not be ignored as this may result in modulation of the adaptive immunity. In studying this, we took advantage of the Balb/C mice that are known to be protected against Helicobacter induced inflammation by mounting a strong Th2 polarization. We were able to switch their adaptive immunity to Th1 by coinfected them with a T. gondii infection (a well known Th1 infection in mice). The dual infected mice developed severe gastritis, parietal cell loss and metaplastic changes. These experiments have clearly shown how unrelated pathogens may interact and result in different clinical outcomes of the infected host. A strong immune response that results in severe inflammation will also cause a cascade of apoptotic changes in the mucosa. A strict balance between proliferation and apoptosis is needed, as its disruption may result in uncontrolled proliferation, transformation and metaplasia. The Fas Ag pathway is the leading cause of apoptosis in the Helicobacter-induced inflammation. One mechanism for escaping Fas mediating apoptosis is upregulation of MHCII receptor. Fas Ag and MHCII receptor interaction inhibits Fas mediated apoptosis by an impairment of the Fas Ag receptor aggregation when stimulated by Fas ligand. Because H. pylori infection is associated with an upregulation of the MHCII levels on gastric epithelial cells, this indeed may be one mechanism by which cells escape apoptosis. The link between chronic inflammation and cancer is well known since the past century. Helicobacter infection is a prime example how a chronic inflammatory state is causing uncontrolled cell proliferation that results in cancer. The cell biology of “cancer” is regarded not as an accumulation of cells that divide without any control, but rather as an organ formed of cancer stem cells, tumor stromal support cells, myofibroblasts and endothelial cells, which function as a group. The properties of the cancer stem cells are to self-renew and differentiate into tumor cells thus maintaining the tumor grow, emphasizing that a striking similarity exists between cancer stem cells and tissue stem cells. We looked into what role would BMDCs play in chronic inflammation that causes cancer. Using the mouse model of Helicobacter induced adenocarcinoma we discovered that gastric cancer originates from a mesenchymal stem cell coming from bone marrow. We believe that chronic inflammation, in our case of the stomach, sets up the perfect stage for bone marrow stem cells to migrate to the stomach where they are exposed to inflammatory stimuli and transform into cancer stem cells. One of the mechanism by which the MSC migrate to the inflammation site is the CXCR4/SDF-1 axis. Our work sheds new light on Helicobacter induced gastric cancer pathogenesis. I hope that our findings will promote the development of new therapies in the fight against this deadly disease.