Campylobacter jejuni is the main cause of bacterial diarrhoeal illness in developed countries, with ~7000 cases being reported each year in Sweden. C. jejuni has received growing attention since it’s recognition as a human pathogen in the 1970s, but its epidemiology is complex and much still remains unknown. There are several potential reservoirs for C. jejuni, including environmental sources as water and soil, wild and domesticated animals, particularly poultry, but also other livestock and pets. In this study 348 Swedish C. jejuni isolates from the year 2000 from humans (n = 164) and broilers (n = 184) were characterized with multilocus sequence typing (MLST) with the aim of comparing the population structures and diversity of C. jejuni between isolates from the two hosts. MLST is a method for characterization of bacterial isolates that indexes the variation in DNA sequence of multiple protein encoding housekeeping genes. A secondary aim in this study was to compare populations of C. jejuni from 11 subgroups of isolates based on location of the sampling. The overlap between the populations was analyzed numerically based on genotypes detected and with analysis of phylogeny, gene flow and molecular variation. It was shown that the population structure of C. jejuni isolates from broilers and humans show a high degree of similarity, supporting broilers as an important source of human infection. However, even though the population structure of human and broiler C. jejuni were almost genetically indistinguishable other sources of C. jejuni infections in humans cannot be ruled out since the same genotypes can be found in other sources as well. Analysis of the 11 subgroups suggested that there may be a difference in populations infecting humans in different Swedish regions, and between populations of C. jejuni in broilers from different slaughterhouses. But this could be a result of chance since most of the subgroups were small. Future studies to improve the understanding of C. jejuni epidemiology, for which MLST has proven itself as a valid method, is important to develop control strategies to prevent infection with this common cause of diarrhoeal illness.

Memoria para optar al Titulo Profesional de Médico Veterinario / El objetivo del presente estudio fue aislar, cuantificar y caracterizar molecularmente a Campylobacter jejuni (C. jejuni) proveniente de muestras de canales obtenidas en la etapa de eviscerado y enfriado en dos plantas faenadoras de pollos broiler de la Región Metropolitana. Además se obtuvo los datos del enfriador de agua de las canales (“chiller”) en ambas plantas para establecer las diferencias. Las cepas de C. jejuni fueron aisladas en medios de cultivo selectivos, posteriormente identificadas por pruebas bioquímicas y caracterizadas a través de “Electroforesis en Gel de Campo Pulsado” (PFGE) usando dos enzimas de restricción, SmaI y KpnI. Los resultados mostraron que, C. jejuni se aisló en 166 de las 259 muestras analizadas (64%). En la planta A se obtuvo un total de 82% (107/130) muestras positivas y en la planta B 46% (59/129). Al analizar la contaminación por etapa de proceso se observó mayor porcentaje de ocurrencia en la etapa de eviscerado 71% (97/136) que enfriado 56% (69/123), mientras que al analizar los datos por planta y etapa se obtuvo que en la planta A la etapa de eviscerado tuvo un 89% y la etapa de enfriado un 74% de ocurrencia para C. jejuni. Comparativamente, la contaminación con Campylobacter en la planta B fue menor en ambas etapas con un 53% de ocurrencia en el eviscerado y un 37% en el enfriado. Los resultados de la caracterización molecular de C. jejuni mostraron 13 patrones distintos de macrorrestricción al usar la enzima SmaI y 12 al aplicar KpnI. En ambos casos se obtuvo 6 patrones comunes, siendo los restantes patrones únicos (6 y 7 respectivamente). Los mismos patrones se observaron tanto en la etapa de eviscerado como de enfriado. Los controles de temperatura en el “chiller” de las plantas A y B fueron en promedio de 1,56ºC y 0,59ºC respectivamente. La planta B presenta temperaturas significativamente menores (p=0,0024). La concentración de cloro del agua del “chiller” medida en la planta A fue de 0,58 ppm y en la planta B de 0,53 ppm. Las diferencias observadas no fueron significativas (p=0,4315). Solo ocurrió una disminución estadísticamente significativa de los porcentajes de ocurrencia desde la etapa de eviscerado a enfriado por parte de la Planta A. Sin embargo, la ocurrencia en la planta A siempre fue mayor que la planta B. Los patrones de macrorrestricción observados fueron específicos para cada una de las plantas y según el día de muestreo, no así para las etapas. Estos resultados, inducen a pensar, que la mayor contaminación de las canales con C. jejuni corresponde a la proveniente de la crianza y no se genera al interior de la planta faenadora de aves

Memoria para optar al Título Profesional de Médico Veterinario / La resistencia a los antibióticos es un problema de salud pública mundial, ya que complica y encarece el tratamiento de las enfermedades infecciosas. En el caso de Campylobacter spp., este es un problema emergente, dado que en los últimos años se ha observado un incremento en la resistencia a antibióticos principalmente a las fluoroquinolonas y macrólidos. Esto es de gran importancia dado que estos fármacos son utilizados como primera elección para el tratamiento de campilobacteriosis. El uso indiscriminado, no solo en producción animal, sino también en medicina humana se describe como unas de las principales causas de este fenómeno. En Chile, existen muy pocos estudios sobre la susceptibilidad antimicrobiana en cepas de Campylobacter spp. El objetivo de este trabajo fue evaluar la susceptibilidad a los antibióticos en 120 cepas de Campylobacter spp., provenientes de cerdos y 60 cepas aisladas de bovinos de carne. Los antibióticos analizados fueron ciprofloxacino, tetraciclina, eritromicina y gentamicina. Se utilizaron dos métodos, primero se realizó un screening con la técnica de Kirby Bauer y todas aquellas cepas que resultaron resistentes, fueron sometidas a determinación de concentración mínima inhibitoria en placa mediante el Método Etest. Se analizaron 180 cepas y se observó que el 10,5% de ellas fueron resistentes a gentamicina, el 57,9% a eritromicina, el 82,6% a ciprofloxacino y el 91,4% lo fue a tetraciclina, mientras que el 87,1% de las cepas fueron clasificadas como multiresistentes. Nuestros resultados indican que los niveles de resistencia a los antimicrobianos en las cepas de Campylobacter spp., son elevados especialmente para ciprofloxacino y tetraciclina. Esto hace necesario proponer y establecer sistemas de vigilancia de la resistencia en este patógeno, con un enfoque integral entre Medicina Veterinaria, Medicina Humana y en producción de alimentos, con el fin de resguardar la salud pública. / Antibiotic resistance is a public health problem, because it complicates and increases the cost of treatment of infectious diseases. As for Campylobacter spp., this is a relevant emerging problem, since in recent years it has seen an increase in antibiotic resistance mainly to fluoroquinolones and macrolides. This is of great importance since drugs are used as the first choice for the treatment of campylobacteriosis. Their indiscriminate use not only animal production but also in human medicine, is described as one of the main causes of this phenomenon. In Chile, there are only a few studies on the antimicrobial susceptibility of Campylobacter spp strains. This study was meant to evaluate the susceptibility to antibiotics in 120 strains of Campylobacter spp isolated from pigs and 60 strains isolated from beef cattle. The antibiotics analyzed were: ciprofloxacin, tetracycline, erythromycin and gentamicin. Two methods were used, the first, the Kirby Bauer screening technique and all of those strains that performed resistant on this test, were subjected to determination of minimum inhibitory concentration MIC`s through Etest Method. A total of 180 strains were evaluated, and of these 10.5% strains were resistant to gentamicin, 57.9% to erythromycin, 82.6% to ciprofloxacin and 94.1% to tetracycline. Also, a total of 87.1% from the tested strains were multiresistant. Our results indicate that levels of antimicrobial resistance in strains of Campylobacter spp., they are higher especially for ciprofloxacin and tetracycline. Making it necessary to propose and establish systems for monitoring and reporting of resistance in this pathogen, an integrated approach between Veterinary Medicine, Food production and Human Medicine, in order to protect public health. / Financiamiento: Proyecto Fondecyt no. 11110200.

The major outer membrane protein, MOMP, is the main protein in the outer membrane of pathogenic Campylobacter bacteria. Infection with Campylobacter is the principle cause of severe enteritis and untreated may result in non-trauma related paralysis. Studies have shown, that MOMP can act as antigen and thus has the potential to provide protection by induced humoral immunity. In our study, we expressed recombinant MOMP in Escherichia1coli, developed an alternative method to extract the outer membrane protein from its lipid environment and solved and characterised its crystal structure. The information acquired through these structural studies sheds new light on the structural characteristics of this important membrane protein. The West-African Lassa virus can cause deadly haemorrhagic fever. Lassa virus only possesses five proteins, which are synergistically responsible for the virus' life cycle, and virulence. The way in which the individual proteins act with one another and with host cell proteins is not fully understood. The polymerase L is the largest of the five proteins and has multiple functions. In this study, we first divided the L protein into different domains and tested their recombinant expression in Escherichia1coli. For first time, we solved the crystal structure of the putative endonuclease domain of Lassa virus and validated its endonucleolytic function by means of RNA digestion assays and alanine point mutations.

Campylobacter jejuni is a major cause of bacterial gastroenteritis in the developed world; however, many aspects of its biology remain poorly understood, including its colonization of the mucus layer lining the gastrointestinal tract. In this study, we utilized microarray transposon tracking to compile a list of 195 genes essential for the growth of C. jejuni in vitro under microaerophilic conditions. Then we characterized C. jejuni growing in an extracted intestinal mucus medium. We found that C. jejuni will grow efficiently in a medium comprised of either chick and piglet intestinal mucus, and that these media have a dramatic impact on its transcriptome. Within the genes identified as differentially expressed during growth in a mucus medium, we identified a single operon, (cj0481-cj0490), which we have subsequently characterized as being responsible for both the uptake and metabolism of L-fucose. This represents the first observation of carbohydrate metabolism by the otherwise asaccharolytic C. jejuni. We further found that the inability to utilize L-fucose puts C. jejuni at a competitive disadvantage when colonizing the piglet intestine, but not the chick cecum. Finally, we examined C. jejuni’s ability to utilize mucins as a carbon source while growing within the mucus layer. We found that despite mucins being a major source of L-fucose and amino acids within the intestine, C. jejuni has a minimal ability to degrade and utilize mucins on its own. However, close proximity to mucolytic bacteria within the microbiota of the intestine, allows for increased C. jejuni growth. Together, this paints the picture of an organism that is well adapted to survival within the mucus lining of the intestine and establishing itself as part of the intestinal microbiota.

Membros termofílicos do gênero Campylobacter são reconhecidos como importantes enteropatógenos para o ser humano e animais. A grande diversidade ecológica destes microorganismos em diferentes habitats tais como: água, animais e alimentos predispõem ao aparecimento de novos fatores de virulência. Este trabalho teve por objetivo detectar os genes codificantes da Toxina Distensiva Citoletal (CDT) por meio da técnica de PCR, pesquisar a atividade de hemolisinas e a influência de soluções quelantes e de íons nesta atividade. Foram utilizadas 45 amostras de C. jejuni de origem avícolas para pesquisa de atividade hemolítica, cultivadas em Caldo Triptona de Soja (TSB). Após o crescimento bacteriano, as amostras foram semeadas em Ágar tríptico de soja (TSA) contendo 5% de sangue de ovino, equino e bovino, sendo cada sangue testado isoladamente. Para verificar a influência de agentes quelantes e solução de íons na atividade hemolítica, as amostras de C. jejuni foram cultivadas em TSB contendo separadamente os quelantes EDTA, ácido acético, soluções de íons CaCl2 , MgCl2 e FeCl3, em atmosfera de microaerofilia. Quanto à atividade de hemolisina de Campylobacter jejuni em placas de TSA – sangue, foi possível observar que houve hemólises em 48,89% das amostras quando utilizado sangue eqüino, em 40% em sangue de bovino e em 31,11% quando de ovino. Quanto à influência de agentes quelantes e íons em caldo TSB na atividade de hemolisinas em amostras de Campylobacter jejuni semeadas em placas de TSA – sangue ovino, foi observada atividade hemolítica em 26,67% quando utilizado CaCl2, 15,55% (FeCl3), 22,22% (EDTA), 11,11% (MgCl2) e apenas 2,22% (ácido acético). No tocante à atividade hemolítica, o TSA - sangue bovino apresentou 15,55% (CaCl2), 24,44% (FeCl3), 26,26% (EDTA), 20% (MgCl2) e 11,11% (ácido acético). A atividade hemolítica para o sangue equino foi de 24,44% (CaCl2), 22,22% (FeCl3), 28,89% (EDTA), 28,89% (MgCl2) e 8,89% (ácido acético). Para detecção dos genes cdtA, cdtB e cdtC através da técnica da Reação da Polimerase em Cadeia (PCR), foram utilizadas 119 amostras de C. jejuni de origem avícolas. Foi possível observar que 38% possuíam os três genes, e foram identificados somente os genes cdtA e cdtC em 19% do total de amostras, sendo que o gene cdtB foi encontrado em 14%, o gene cdtC foi observado em 12%, os genes cdtA e cdtB em somente 1%, os genes cdtB e cdtC em 1% e para cdtA em 1%. Observou-se que os resultados são dignos de atenção, pois demonstraram em amostras avícolas a presença de estirpes de C. jejuni com potencial virulento. A atividade hemolítica apresentou significativo aumento quando utilizado sangue de origem equina. A mesma foi diminuída quando utilizados agentes quelantes ou íons, nos três tipos de sangue. / Thermophilic members of the Campylobacter genus are recognized as important enteropathogenics for humans and also for other animals. The great diversity of ecological habitats in different organisms such as water, food, and animals may promote new virulence factors. This study aimed at detecting the distending cytolethal toxin (CDT) encoding genes by PCR, studying the activity of hemolysin and also the influence of chelation solutions and ions. A total of 45 samples of C. jejuni from poultry origin, grown in Tryptone Soy Broth (TSB) were used for investigating hemolytic activity. After bacterial growth, samples were plated on Tryptic Soy Agar (TSA) containing 5% sheep, equine or bovine blood, being each blood tested individually. In order to check the influence of chelation agents and ions solution on the hemolytic activity, samples of C. jejuni strains were grown in TSB containing chelation agents individually: EDTA, acetic acid, CaCl2 ion, MgCl2 and FeCl3 solutions, all in microaerophilic atmosphere. Regarding the detection of Campylobacter jejuni hemolysin activity on TSA plates, blood hemolysis were observed in 48.89 % of samples when equine blood was used; in 40% of samples when bovine blood was used and in 31.11 % when the blood used was of sheep origin. The influence of ions and chelation agents in hemolysin activity in TSB when Campylobacter jejuni was plated on TSA with sheep blood can be described as: hemolytic activity was observed at 26.67% of samples when CaCl2 was used, at 15.55 % for FeCl3, 22 22 % for EDTA, 11.11 % for MgCl2 and only 2.22% when acetic acid was used. The hemolytic activity detected when bovine blood - TSA was used indicated 15.55% for CaCl2, 24.44% for FeCl3, 26.26 % for EDTA, 20 % for MgCl2 and 11.11% for acetic acid. In terms of the hemolytic activity when equine blood was used, the results indicated 24.44% for CaCl2, 22.22 % for FeCl3, 28.89 % for EDTA, 28.89 % for MgCl2 and 8.89% for acetic acid. Finally, regarding the detection of cdtA, cdtB and cdtC through PCR, 119 samples of C. jejuni from poultry origin were used. The results indicated that all three genes were present in 38 % of the samples, whereas only two genes were identified in 19 % of samples, while the cdtB gene was singly found in 14%, the cdtC gene was independently observed in 12%, cdtA and cdtB genes together were found in 1% of the samples; the cdtB and cdtC genes associated were detected in 1%, while cdtA alone answered for 1% of detections. The results also showed the presence of C. jejuni strains with virulence potential. The hemolytic activity increased significantly when blood of equine origin was used, and that this activity was reduced when ions or chelating agents were used in combination with the three types of blood cells.

Antibiotic resistance is a worldwide threat to human health yet fewer new antibiotics are being approved. New antimicrobial drugs are urgently required. 3 Deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS) is a target for antimicrobial drug design. KDO8PS catalyzes the condensation of D-arabinose-5 phosphate (A5P) with phosphoenolpyruvate (PEP) to produce KDO8P. KDO8PS catalyzes the first committed step in the lipopolysaccharides (LPS) biosynthesis pathway in Gram-negative bacteria and is critical for bacterial pathogenicity/virulence. We have characterized KDO8PS from Campylobacter jejuni (cjKDO8PS), a new metal-dependent KDO8P synthase (KDO8PS). cjKDO8PS is a tetramer in solution and optimally active at pH 7.5 and 60 °C. We have kinetically established that cjKDO8PS follows a rapid equilibrium sequential ordered ter ter kinetic mechanism, where Mn2+ binds first, followed by PEP, then A5P. Pi dissociates first, before KDO8P, then Mn2+. cjKDO8PS was inhibited by KDO8P oxime, a novel slow tight-binding inhibitor. KDO8P oxime is a competitive inhibitor with respect to PEP and A5P, but uncompetitive with respect to Mn2+, with Ki = 10 ± 1 μM and an ultimate Ki* = 0.28 ± 0.10 μM. KDO8P oxime has a residence time (tR) of 5 days on the enzyme, a parameter that is highly correlated to in vivo efficacy. Crystallization conditions for the cjKDO8PS‧Mn2+‧KDO8P oxime complex have been found and can be optimized to obtain a crystal structure that shows how KDO8P oxime interacts with the active sites. / Thesis / Doctor of Science (PhD) / The relentless increase in global antibiotic resistance is, regrettably, not matched with an increase in new effective antibiotics. New antimicrobial drug discovery strategies are desperately needed. Enzymes are key targets for drug design because they catalyze the majority of biological processes. In this project we sought to study and inhibit the activity of KDO8P synthase (KDO8PS) from Campylobacter jejuni, a common cause of food poisoning. KDO8P synthase is a critical enzyme involved in the lipopolysaccharide (LPS) biosynthesis in Gram-negative bacteria. The LPS acts as a permeability barrier and is crucial for bacterial pathogenicity/virulence. We found that C. jejuni KDO8PS is potently inhibited by KDO8P oxime, a novel inhibitor of KDO8PS. This inhibitor presents a unique opportunity to study these enzymes and a platform from which antibiotics against Gram-negative bacteria can be developed.

This study was conducted to determine the extent in which Campylobacter jejuni colonized live birds would survive evisceration and contaminate the processed carcasses. Birds were infected with a marker strain of Campylobacter jejuni and allowed to grow to market age. Cloacal and fecal samples were analyzed to determine the level of Campylobacter jejuni present in the live bird. Prior to slaughter, birds were selectively subjected to two different temperatures (21 and 32°C) and three different times of feed withdrawal for chickens (3, 6,and 9 hours and turkeys 0, 4, and 8 hours). Birds were then slaughtered and the carcasses were sampled to determine the level of Campylobacter jejuni that survived. Results indicated a difference between chickens and turkeys, especially regarding the infective dose and bacterial survival rates. No significant differences in carcass contamination due to feed withdrawal times at either temperature were noted. The correlation of fecal samples with cloacal samples was significant for year 2 with r = .53 (p .04). For turkeys, the correlations were not significant. A longitudinal study of turkeys showed that the percentage of birds infected with Campylobacter jejuni peaked when the birds were 5-7 weeks old. The amount of Campylobacter contamination in each turkey peaked when the birds were 5 weeks old and then dropped off quickly. / Master of Science

Having a comprehensive view of the entire gene complement and coding capacity of bacterial pathogens, and how their gene expression is regulated, is crucial for understanding their strategy for survival, stress adaptation as well as host colonization and infection. In pathogens like Campylobacter jejuni, where homologs of key virulence factors used by other enteric pathogens are absent, it is important to gain a complete census of genes to understand how it causes disease. Deep sequencing approaches have expanded our knowledge on global gene expression profiles and aided in a better understanding of the coding complexity in bacteria. For example, they revealed small regulatory RNAs (sRNAs) involved in, e.g., stress response and adaptation or highlighted the concept of genes within genes, including dual-function sRNAs or alternative open reading frames (ORFs) within or antisense to known genes. Techniques like ribosome profiling (Ribo-seq) spotlighted a major gap in bacterial genome annotations, as it revealed that the so-called small proteome/sORFome (census of small proteins and small ORFs) is largely underrepresented. Small proteins, here defined as independently translated proteins ≤ 70 amino acids (aa), were overlooked or even discarded from genome annotations, and challenges in the biochemical detection further hindered their characterisation. Nevertheless, recently characterised examples of small proteins were identified as important players in physiological processes such as virulence and stress response. In C. jejuni, the leading cause of bacterial gastroenteritis, a recent differential RNA-seq (dRNA-seq) analysis revealed several sRNAs, some of which were shown to be relevant for infection. However, the small proteome of C. jejuni has not been systematically explored, leaving it unclear how many small open reading frames (sORFs) are encoded in the C. jejuni genome and expressed in vivo. Consequently, their function in C. jejuni physiology remains largely elusive, which is further hampering the understanding of how this major foodborne pathogen causes disease in humans. The focus of this thesis was to globally catalogue sORFs in C. jejuni, validate their translation status in vivo and functionally characterise infection-relevant candidates. Therefore, classical Ribo-seq, translation initiation site (TIS) profiling and a novel translation termination site (TTS) profiling method were combined to systematically investigate sORFs of C. jejuni. In addition, mass spectrometry and epitope tagging followed by western blotting were used to validate sORF translation. Collectively, these methodologies revealed novel and hidden sORFs encoded in diverse genomic contexts, as well as further annotation refinements. Hence, the C. jejuni small proteome was expanded almost two-fold by adding 42 novel sORFs to the annotation, and translation of 47 out of 54 already annotated sORFs was validated. Among these, the novel small protein CioY (34 aa), previously missed in the C. jejuni strain NCTC11168 genome annotation, was found to be adjacently encoded to the CioAB terminal oxidase. Further analysis showed that CioY is part of this terminal oxidase with potentially similar functions as the 37 aa-long CydX in E. coli. To aid further characterisation of novel sORFs and to allow for broad access to the translatomics data and our updated annotation, the online resource CampyBrowse was established. To gain insights into the potential functions of small proteins, available functional genetics datasets were inspected to identify candidates that might affect C. jejuni virulence. A transposon sequencing (Tn-seq) screen of C. jejuni infections of human Caco-2 cells in our lab identified the small protein Cj0978c (Mot2, 57 aa) required for motility and colonization. This thesis revealed that the small lipoprotein is necessary for flagellar disk and stator assembly, as it is required for stability and localisation of the basal disk protein FlgP. In addition, to allow for identification of potential interaction partners of small proteins, gradient profiling by sequencing (Grad-seq) as well as thermal proteome profiling (TPP) were successfully established for C. jejuni. While TPP is a sensitive method that is able to detect even slight changes in complex compositions, e.g., due to the absence of a small protein-binding partner, Grad-seq will be a valuable resource to study the C. jejuni complexome, the entire set of protein and RNA complexes. Overall, this thesis expands the genome map of C. jejuni NCTC11168 with novel high-confidence sORFs by using diverse Ribo-seq approaches combined with extensive validation. This integrative translatomic approach will promote the general understanding of the coding complexity in bacteria and allow for future characterisation of diverse small protein/sORF candidates in C. jejuni. Moreover, functional characterisation of Mot2 revealed the importance of a small protein for the functionality of the complex flagella machinery – a crucial virulence-determining process of C. jejuni. / Das gesamte Genkomplement bakterieller Pathogene sowie ihre Kodierungskapazität und Regulierung zu kennen, ist für das Verstehen von Überlebensstrategien, Stressanpassung sowie Wirtskolonisierung und Infektionen entscheidend. Dies ist besonders bei Krankheitserregern wie Campylobacter jejuni wichtig, denen homologe Gene von relevanten Virulenzfaktoren anderer Darmpathogenen fehlen, um zu verstehen, wie sie Krankheiten verursachen. Hochdurchsatz-Sequenziermethoden haben unser Wissen über globale Genexpressionsprofile erweitert und zu einem besseren Verständnis der Komplexität von Bakteriengenomen beigetragen. So wurden beispielsweise kleine regulatorische RNAs (sRNAs) entdeckt, die unter anderem an der bakteriellen Stressanpassung beteiligt sind, oder das Konzept von Genen innerhalb beschriebener Gene enthüllt. Beispiele dafür sind sogenannte dual-function sRNAs, oder alternative offene Leserahmen (ORFs) innerhalb von oder antisense zu bereits bekannten Genen. Techniken wie ribosome profiling (Ribo-seq) haben eine große Lücke in bakteriellen Genomannotationen aufgedeckt, und aufgezeigt, dass das sogenannte kleine Proteom/sORFom (Gesamtheit kleiner Proteine und kleiner ORFs) weitgehend unterrepräsentiert ist. Kleine Proteine, hier als unabhängig translatierte Proteine mit einer Länge von bis zu 70 Aminosäuren (aa) definiert, wurden in Genomannotationen übersehen, oder sogar aussortiert, und Schwierigkeiten beim biochemischen Nachweis beeinträchtigten zusätzlich ihre Charakterisierung. Dennoch haben jüngste Studien gezeigt, dass kleine Proteine wichtige Akteure bei physiologischen Prozessen wie der bakteriellen Virulenz und Stressreaktion sind. Bei C. jejuni, dem Hauptverursacher bakterieller Gastroenteritis, bestätigte eine differential RNA-seq-Analyse (dRNA-seq) die Existenz mehrerer sRNAs, von denen sich einige als infektionsrelevant erwiesen. Das kleine Proteom von C. jejuni wurde jedoch nicht systematisch untersucht, so dass unklar ist, wie viele kleine ORFs (sORFs) im Genom von C. jejuni kodiert und in vivo exprimiert werden. Folglich ist ihre Funktion in der Physiologie des Bakteriums nach wie vor weitgehend unbekannt und erschwert dadurch unser Verständnis darüber, wie dieser wichtige Lebensmittelkeim Krankheiten beim Menschen verursacht. Der Fokus dieser Dissertation lag auf der globalen Katalogisierung von sORFs in C. jejuni, der Validierung ihrer Translation in vivo und der funktionellen Charakterisierung von infektionsrelevanten Kandidaten. Daher wurden Ribo-seq, Translationsinitiationsstellen (TIS)-Profiling und das neue Translationsterminationsstellen (TTS)-Profiling kombiniert, um die Gesamtheit der sORFs von C. jejuni zu untersuchen. Darüber hinaus wurden Massenspektrometrie, Epitopmarkierung und Western Blot Analysen zur Validierung der Translation von sORFs eingesetzt. Insgesamt enthüllte eine Kombination dieser Methoden neue sORFs in den verschiedensten genomischen Kontexten, sowie weitere Nachbesserungen der Annotation. So konnten 42 neue kleine Proteine in die Annotation aufgenommen und damit das kleine Proteom von C. jejuni um nahezu das Zweifache vergrößert werden. Außerdem wurde die Translation von 47 der 54 bereits annotierten sORFs validiert. Das neuartige kleine Protein CioY (34 aa), das zuvor in der Genomannotation von C. jejuni NCTC11168 übersehen wurde, ist in unmittelbarer Nähe der terminalen Oxidase CioAB kodiert. Diese Doktorarbeit hat gezeigt, dass CioY eine Untereinheit dieser terminalen Oxidase ist, und möglicherweise ähnliche Funktionen wie das 37 aa-lange CydX in E. coli hat. Um die weitere Charakterisierung neuer sORFs zu unterstützen und einen breiten Zugang zu den Datensätzen und unserer aktualisierten Annotation zu ermöglichen, wurde die Online-Ressource CampyBrowse eingerichtet. Um kleine Proteine zu identifizieren, welche möglicherweise die Virulenz von C. jejuni beeinflussen könnten, wurden verfügbare funktionelle Datensätze untersucht. Ein vorheriger Tn-seq-Screen aus unserem Labor von C. jejuni infizierten menschlichen Caco-2-Zellen, identifizierte das für die Motilität und Kolonisierung erforderliche kleine Protein Cj0978c (Mot2, 57 aa). Diese Dissertation hat gezeigt, dass das kleine Lipoprotein für den Zusammenbau von funktionellen flagellaren Motoren notwendig ist, da es für die Stabilität und Lokalisierung des basalen flagellaren Disk-Proteins FlgP erforderlich ist. Zur Identifizierung potenzieller Interaktionspartner kleiner Proteine wurden gradient profiling by sequencing (Grad-seq) und thermal proteome profiling (TPP) für C. jejuni erfolgreich etabliert. Während TPP eine sensitive Methode ist, mit der selbst geringfügige Veränderungen in der Komplexzusammensetzung, z. B. durch das Fehlen eines kleinen Proteinbindungspartners, erkannt werden können, dient Grad-seq als wertvolle Ressource zur Untersuchung des C. jejuni-Komplexoms, der Gesamtheit an Protein- und RNA-Komplexen. Insgesamt erweitert diese Doktorarbeit die Genomannotierung von C. jejuni NCTC11168 durch die Kombination verschiedener Ribo-seq-Ansätze und einer umfassenden Validierung um neue sORFs. Dieser integrative Ansatz fördert das allgemeine Verständnis über die Komplexität von bakteriellen Genomannotationen und ermöglicht die künftige Charakterisierung verschiedener kleiner Proteine/sORFs in C. jejuni. Darüber hinaus hebt die funktionelle Charakterisierung von Mot2 die Bedeutung eines kleinen Proteins für die Funktionalität der komplexen Flagellenmaschinerie hervor – ein entscheidender Virulenzmechanismus von C. jejuni.

Enteric infections are widespread throughout the world and continue to pose a serious health threat, especially to younger children. Bacterial pathogens apply a plethora of distinct virulence mechanisms to efficiently infect and establish host colonization, consequently leading to various diseases. Campylobacter jejuni is currently the leading cause of bacterial foodborne diarrheal disease worldwide. However, in comparison to other enteric pathogens, relatively little is known about how this bacterium establishes infections and mediates virulence in humans. Its genome lacks classical virulence factors or toxins known from other enteric pathogens and only encodes three known sigma factors, suggesting additional layers of gene regulation. Recent transcriptome studies in C. jejuni confirmed the existence of several small regulatory RNAs (sRNAs). However, their function remains largely elusive. This thesis aimed to uncover novel regulators of C. jejuni virulence and physiology. Therefore, a dual RNA sequencing (dual RNA-seq) experiment was performed upon infection of Caco-2 cells in a recently advanced human intestinal three-dimensional (3D) infection model, in parallel to standard two-dimensional (2D) infection of monolayers. This deep-sequencing approach allows for the simultaneous quantification of host and pathogen transcriptomes on a global scale and was intended to unravel new bacterial host-adaptation and virulence-associated factors, as well as to assess host measures in response to C. jejuni infection. While only a small number of human genes were differentially regulated upon infection with C. jejuni NCTC11168 wild-type (WT) bacteria, a large proportion of bacterial genes were found to be differentially expressed. A closer look at the bacterial transcriptome post infection revealed little overlap between up- or downregulated genes in the 3D tissue model compared to 2D cell culture. In addition, different functional classes were enriched in adhered and internalized bacteria within these two different infection environments. Strikingly, several sRNAs were found to be upregulated during infection, highlighting their potential importance for host-pathogen interactions. In many bacterial species, sRNAs are involved in post-transcriptional regulation and fine-tuning of diverse fundamental processes including pathogenesis. Since their role in C. jejuni physiology was largely unexplored, candidates from the dual RNA-seq experiment were selected to uncover their putative targets and characterize their function in C. jejuni NCTC11168. Therefore, sRNA mutant strains were generated and tested for distinct phenotypic traits such as growth defects, protein expression, and motility in comparison to WT bacteria. Furthermore, growth-dependent differences in sRNA expression were determined and total RNA sequencing (RNA-seq) experiments with sRNA deletion mutants were performed to unravel their targetome, in combination with in-silico predictions. Since flagellar motility is a crucial virulence factor that allows Campylobacter to navigate through the viscous mucus of the human intestine, sRNA involvement in this process was explored in more detail. In contrast to transcriptional control of the hierarchically expressed flagellar components, little is known about post-transcriptional regulation of the flagellar biosynthesis cascade in C. jejuni. To this end, one sRNA (CJnc230), encoded downstream of the flagellar hook structural gene flgE and strongly upregulated after infection of the 3D tissue model, was selected to investigate a potential functional link to bacterial motility. CJnc230 is dependent on the flagellar sigma-54 factor (RpoN) and was found to be co-transcribed with the upstream gene flgE, requiring three distinct ribonucleases (RNases) for its processing and maturation. Termination site sequencing (term-seq) and differential RNA sequencing (dRNA-seq) techniques were used to further dissect CJnc230 biogenesis, revealing the boundaries of the most abundant CJnc230 fragment and the presence of an alternative transcriptional start site (TSS) originating from an independent promoter. RNA-seq was performed with an overexpression mutant of CJnc230 to decipher its biological function. In-vitro and in-vivo approaches confirmed direct interaction of the CJnc230 single-stranded region with the ribosome binding site (RBS) of Cj1387c (putative transcriptional regulator) and flgM (anti-sigma-28 factor) mRNAs, thereby repressing their translation. Phenotypic characterization further demonstrated that the CJnc230 overexpression mutant exhibits increased motility and flagellar filament length. The latter is most likely due to increased expression of the major flagellin flaA after repression of FlgM and indirect transcriptional activation of late flagellar genes, dependent on the flagellar sigma-28 factor (FliA). In contrast to CJnc230, the FliA-dependent sRNA CJnc170 was shown to decrease filament length and motility when overexpressed with a heterologous promoter. These observations suggest renaming CJnc230 and CJnc170 to FlmE and FlmR (flagellar length and motility enhancer/repressor), respectively, and that sRNA-mediated post-transcriptional regulation fine-tunes C. jejuni flagellar biosynthesis through balancing of the hierarchically expressed components. In summary, this thesis reveals the importance of C. jejuni sRNAs during infection and dissects the molecular targetome of selected candidates. Moreover, validation of target interactions and downstream functions uncovered a previously uncharacterized role for the CJnc230 sRNA in flagellar biogenesis and its effect on motility, a key determinant of C. jejuni virulence. / Infektionen des Gastrointestinaltrakts sind weltweit verbreitet und stellen nach wie vor eine Gesundheitsbedrohung, insbesondere für Kleinkinder, dar. Bakterielle Krankheitserreger nutzen eine Vielzahl unterschiedlicher Virulenzmechanismen, um den Wirt effizient zu infizieren und zu besiedeln, was zu verschiedenen Krankheiten führen kann. Campylobacter jejuni ist momentan die häufigste Ursache für über die Nahrung übertragene, bakterielle Durchfallerkrankungen weltweit. Im Vergleich zu anderen Darmpathogenen ist jedoch relativ wenig darüber bekannt, wie dieses Bakterium eine Infektion auslöst und welche Virulenzmechanismen diese beim Menschen vermitteln. Dem Genom von C. jejuni fehlen klassische Virulenzfaktoren oder Toxine, die von anderen Darmpathogenen bekannt sind, und es enthält nur drei bekannte Sigmafaktoren, was auf zusätzliche Ebenen der Genregulation schließen lässt. Jüngste Transkriptomstudien an C. jejuni bestätigten die Existenz mehrerer kleiner regulatorischer RNAs (sRNAs). Deren Funktion ist jedoch noch weitgehend ungeklärt. Ziel dieser Doktorarbeit war es, neue Regulatoren der Virulenz und Physiologie von C. jejuni aufzudecken. Dazu wurde ein duales RNA-Sequenzierungsverfahren (dual RNA-seq) nach Infektion von Caco-2-Zellen in einem kürzlich entwickelten dreidimensionalen (3D) Infektionsmodell des menschlichen Darms angewendet, parallel zu herkömmlichen Infektionen in zweidimensionaler (2D) Zellkultur. Diese Hochdurchsatz-Sequenziermethode ermöglicht die globale Quantifizierung des Transkriptoms von Wirt und Erreger in derselben Probe und sollte neue bakterielle Anpassungs- und Virulenzfaktoren aufdecken, sowie die Reaktion des Wirts auf die Infektion mit C. jejuni erfassen. Während nach der Infektion mit C. jejuni NCTC11168 Wildtyp (WT)-Bakterien nur wenige menschliche Gene dereguliert waren, wurde bei einem großen Teil des bakteriellen Transkriptoms eine veränderte Genexpression festgestellt. Ein genauerer Blick verriet, dass es nur wenige Überschneidungen zwischen hoch- und herunterregulierten bakteriellen Genen im 3D-Gewebemodell im Vergleich zu 2D-Zellkultur gab. Darüber hinaus waren, je nach Infektionsumgebung, verschiedene funktionelle Klassen von Genen unterschiedlich stark in adhärenten und internalisierten Bakterien repräsentiert. Auffallend war außerdem, dass mehrere sRNAs während der Infektion hochreguliert waren, was deren mögliche Bedeutung für die Interaktion zwischen Wirt und Erreger unterstreicht. In vielen Bakterienarten sind sRNAs an der post-transkriptionellen Regulierung und Feinabstimmung verschiedener grundlegender Prozesse beteiligt, unter anderem auch an der Pathogenese. Da ihre Rolle in der Physiologie von C. jejuni aber weitgehend unerforscht ist, wurden Kandidaten aus dem dualen RNA-seq Experiment ausgewählt, um mögliche Zielgene aufzudecken und ihre Funktion in C. jejuni NCTC11168 zu charakterisieren. Dazu wurden sRNA-Mutantenstämme erzeugt und auf unterschiedliche phänotypische Merkmale, wie Wachstumsdefekte, Proteinexpression und Motilität, im Vergleich zu WT-Bakterien getestet. Darüber hinaus wurden wachstumsabhängige Unterschiede in der sRNA-Expression bestimmt und RNA-Sequenzierungsexperimente (RNA-seq) mit den Deletionsmutanten durchgeführt, um deren Zielgen-Repertoire in Kombination mit in-silico Vorhersagen zu entschlüsseln. Da flagellare Motilität ein wichtiger Virulenzfaktor ist, der es Campylobacter ermöglicht, durch die zähflüssige Mukusschicht des menschlichen Darms zu navigieren, wurde die Beteiligung von sRNAs an diesem Prozess genauer untersucht. Im Gegensatz zur hierarchisch geordneten Transkription der einzelnen Komponenten der bakteriellen Geißel, ist über die post-transkriptionelle Regulation der Flagellen-Biosynthese in C. jejuni nur wenig bekannt. Daher wurde eine sRNA (CJnc230) ausgewählt, die hinter dem Strukturgen flgE (flagellarer Haken) liegt und nach Infektion des 3D-Gewebemodells stark hochreguliert war, um eine mögliche funktionelle Verbindung zur bakteriellen Motilität zu untersuchen. CJnc230 ist abhängig vom alternativen Sigmafaktor RpoN (Sigma 54) und wird zusammen mit dem vorgelagerten Gen flgE transkribiert, wobei drei verschiedene Ribonukleasen (RNasen) für die Prozessierung und Reifung erforderlich sind. Mit Hilfe von termination site sequencing (term-seq) und differential RNA sequencing (dRNA-seq) wurde die Biogenese von CJnc230 weiter aufgeschlüsselt. Dabei wurden die Enden des am häufigsten vorkommenden CJnc230-Fragments und die Existenz einer alternativen Transkriptionsstartstelle (TSS), die von einem unabhängigen Promotor stammt, aufgedeckt. Um die biologische Funktion von CJnc230 zu entschlüsseln, wurde RNA-seq mit einer Überexpressionsmutante der sRNA durchgeführt. In-vitro und in-vivo Ansätze bestätigten die direkte Interaktion der einzelsträngigen Region von CJnc230 mit der Ribosomenbindestelle (RBS) der mRNAs von Cj1387c (potenzieller Transkriptionsfaktor) und flgM (anti-Sigma-28-Faktor), wodurch die Translation unterdrückt wird. Die phänotypische Charakterisierung zeigte außerdem, dass die CJnc230-Überexpressionsmutante eine erhöhte Motilität und Länge des Geißelfilaments aufweist. Letzteres ist höchstwahrscheinlich auf eine verstärkte Expression des Hauptflagellins flaA nach Repression von FlgM und eine indirekte transkriptionelle Aktivierung von späten flagellaren Genen, die vom alternativen Sigmafaktor FliA (Sigma 28) abhängig sind, zurückzuführen. Im Kontrast zu CJnc230 wurde gezeigt, dass die FliA-abhängige sRNA CJnc170 die Filamentlänge und Motilität verringert, wenn sie mit einem heterologen Promotor überexprimiert wird. Diese Beobachtungen legen eine Umbenennung von CJnc230 und CJnc170 in FlmE bzw. FlmR (flagellar length and motility enhancer/repressor) nahe und zeigen, dass die Flagellen-Biosynthese in C. jejuni zusätzlich durch sRNA-vermittelte, post-transkriptionelle Feinabstimmung der hierarchisch exprimierten Komponenten im Gleichgewicht gehalten wird. Zusammenfassend zeigt diese Doktorarbeit die Bedeutung von C. jejuni sRNAs während der Infektion auf und entschlüsselt die Zielgene ausgewählter Kandidaten. Darüber hinaus wurde durch die Validierung von sRNA-mRNA Interaktionen und nachgeschalteten Funktionen eine bisher nicht charakterisierte Rolle für die CJnc230 sRNA in der Flagellen-Biogenese und ihre Auswirkung auf die Motilität, ein Hauptmerkmal der Virulenz von C. jejuni, aufgedeckt.