Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Identifica Salmonella Typhimurium y Enteritidis aislada de cuyes mediante la técnica de PCR múltiple. Con ese fin, evalúa un total de 25 cepas obtenidas a partir de órganos de cuyes muertos con signos clínicos y lesiones anatomopatológicas sugerentes de salmonelosis además de pruebas bioquímicas que identifican las cepas como pertenecientes al género Salmonella spp. Analiza dichas cepas mediante la técnica de PCR múltiple con cebadores específicos para los genes invA, fliC y Prot6E correspondientes al género Salmonella, Salmonella Typhimurium y Salmonella Enteritidis, respectivamente. Las 25 cepas evaluadas son identificadas como Salmonella Typhimurium, evidenciando bandas de peso molecular correspondientes a los genes invA (284 pb) y el gen fliC (559 pb). La técnica de PCR es útil para identificar el género Salmonella y el serovar Typhimurium a partir de cuyes aislados con signos clínicos sugerentes de salmonelosis.

Tesis entregada a la Universidad de Chile en cumplimiento parcial de los requisitos para optar al grado de Doctor en Ciencias con Mención Microbiología. / Salmonella Typhimurium is an enteric pathogen able to infect different animal hosts, including humans. In immunocompetent humans, S. Typhimurium mainly causes gastroenteritis, a disease characterized by an inflammatory diarrhoea with massive neutrophil infiltration in the ileum and colon. The infective cycle of Salmonella starts with the ingestion of bacteria that reach the small intestine and invade epithelial cells by its apical face. After crossing the epithelial barrier, bacteria are captured by phagocytic cells of the immune system present in the sub-epithelium, such as macrophages, neutrophils and dendritic cells, being contained within a membrane bound compartment. Here, Salmonella subverts the endocytic route, avoiding the fusion of this compartment with the lysosomes and generating the Salmonella-containing vacuole (SCV). In this compartment, Salmonella is able to survive and replicate. The ability to modify this intracellular niche explains the ability of this pathogen to survive intracellularly. To carry out this process, Salmonella employs two Type Three Secretion Systems (T3SS) and an arsenal of secreted effector proteins in order to take control over the eukaryotic cell. An important aspect of Salmonella’s life cycle that has not been studied in detail is its survival in the environment, where bacteria are exposed to predation by protozoa, and specially by amoebae. These organisms are specialized phagocytes that feed on bacteria and fungi. To address this interaction, we and other groups use amoeba models to characterise the molecular processes involved in the survival of intracellular pathogens within environmental protozoa. Among these model organisms, the social amoeba Dictyostelium discoideum is amenable for molecular analyses in laboratory settings and several tools have been developed in this organism for the study of different aspects of its interaction with bacterial pathogens. Recently, our group described that S. Typhimurium is able to survive intracellularly in the social amoeba Dictyostelium discoideum, and that mutants in genes required for virulence in other infection models present survival defects in this host. Despite of this, the mechanisms that allow the intracellular survival of this pathogen in this kind of organism have not been studied in detail. This Thesis proposed the characterization at the cellular level of this interaction, with a focus on two secreted effector proteins of S. Typhimurium that are directly related to SCV generation and modification in other cell models: SopB and SifA. Our results show that these effectors are needed for intracellular survival of S. Typhimurium in D. discoideum. Furthermore, by means of a combination of microscopy and proteomic analyses we were able to characterise the protein composition of the vacuolar compartment containing Salmonella in this host. Our results show that known markers linked to this compartment in other cell types and the autophagy machinery play a role in the biogenesis of this intracellular niche in D. discoideum. / Salmonella Typhimurium es un patogeno enterico que tiene la capacidad de infectar diversos hospederos animals, incluyendo el ser humano. En individuos inmunocompetentes, S. Typhimurium provoca gastroenteriris, una enfermedad diarreica inflamatoria caracterizada por la masiva infiltracion de neutrofilos en el ileon y el colon. El ciclo infectivo de Salmonella comienza con la ingestion de las bacterias que al llegar al intestino delgado invaden las celulas epiteliales por la cara apical. Luego de cruzar la barrera epitelial, las bacterias son capturadas por las celulas fagociticas del sistema inmune que residen en el sub-epitelio, como macrofagos, neutrofilos y celulas dendriticas, quedando contenida en un compartimento membranoso. En esta etapa, Salmonella interviene la ruta endocitica, evitando la fusion de este compartimento con el lisosoma y generando la vacuola contenedora de Salmonella (Salmonella-containing vacuole: SCV). En este compartimento, Salmonella es capaz de sobrevivir y replicarse. La habilidad de modificar este nicho intracelular explica la habilidad de este patogeno de sobrevivir intracelularmente. Para esto, Salmonella utiliza dos Sistemas de Secrecion Tipo Tres (Type Three Secretion Systems: T3SS) y un arsenal de proteinas efectoras secretadas para tomar control sobre la celula eucarionte. Por otra parte, un importante aspecto del ciclo de vida de Salmonella que no ha sido estudiado en detalle es su supervivencia en el ambiente, donde las bacterias se encuentran expuestas a la depredacion por protozoos y en particular, amebas. Estos organismos son fagocitos profesionales que se alimentan de bacteria y hongos. Recientemente, nuestro grupo describio que S. Typhimurium es capaz de sobrevivir intracelularmente en la ameba social Dictyostelium discoideum y que mutantes en genes requeridos para la virulencia en numerosos modelos de infeccion tambien presentan defectos de supervivencia en este hospedero. A pesar de esto, los mecanismos que le permiten a este patogeno en este tipo de organismo no han sido estudiado en detalle. Para entender esta interaccion, nosotros y otros grupos usamos modelos de ameba a fin de caracterizar los procesos moleculares involucrados en la supervivencia de patogenos intracelulares en el interior de protozoos ambientales. Dentro de estos organismos modelo, la ameba social Dictyostelium discoideum es sencilla para el analisis molecular en condiciones de laboratorio. Por otra parte, numerosas herramientas se han desarrollado en este organismo para el estudio de diversos aspectos de su interaccion con patogenos bacterianos. Esta Tesis propuso caracterizar a nivel cellular esta interaccion, enfocandonos en dos proteinas efectoras secretadas de S. Typhimurium que estan directamente relacionadas a la formacion y modificacion de la SCV en otros modelos celulares: SopB y SifA. Nuestros resultados muestran que estos efectores son necesarios para que S. Typhimurium sobreviva intracelularmente en D. discoideum. Adicionalmente, mediante una combinacion de tecnicas de microscopia y analisis proteomicos pudimos caracterizar la composicion proteica de este compartimento vacuolar que contiene a Salmonella en este hospedero. Nuestros resultados muestran que marcadores asociados a la SCV en otras lineas celulares se encuentran en elcompartimento que se genera en D. discoideum y que la maquinaria de autofagia juega un rol importante en la biogenesis de este nicho intracelular en D. discoideum. / FONDECYT grants 1140754 y 1171844, CONICYT Doctoral Fellowship 21140615. / Enero 2020.

Die in dieser Arbeit etablierte Insertions-Duplikations-Mutagenese IDM ermöglicht es, das Genom von pathogenen Bakterien zu mutagenisieren und die so generierte Mutantenbank im high-throughput-Format auf Gene zu untersuchen, die unter bestimmten Bedingungen für das infektiöse Potential oder für das Überleben dieser Keime von Bedeutung sind. Die Grundlage von IDM bildet ein konditional replizierender Vektor, in den eine Genbank des Wirtsorganismus kloniert wird und der unter nicht-permissiven Replikationsbedingungen mittels homologer Rekombination ins Chromosom integriert und dadurch einen Gen-Knockout bedingt. Das IDM-Verfahren weist gegenüber der Transposon-Mutagenese den Vorteil auf, dass das Genom nach dem Zufallsprinzip saturierend mutagenisiert werden kann und dass keine hot spots für die Insertion auftreten. Darüber hinaus kann der mutierte Genlocus nach Screening der Mutanten schnell per PCR identifiziert werden, indem die Exzision des Vektors induziert und das klonierte, homologe Fragment sequenziert wird. Die Insertion des Vektors ins Chromosom und damit der Gen-Knockout ist selbst ohne Selektionsdruck sehr stabil, so dass die Mutanten im Zellkultur- oder Tier-System untersucht werden können. IDM wurde im Rahmen dieser Arbeit erfolgreich auf Salmonella enterica Serovar typhimurium und Listeria monocytogenes angewandt. Die Applikation von IDM auf S. typhimurium hatte zum Ziel, Gene zu identifizieren, deren Produkte für das Überleben dieses Gram-negativen Keims in Vollmedium unter Laborbedingungen essentiell sind. Ausgehend von 14.000 S. typhimurium Fragmentbank-Klonen konnten durch Induktion der Integration des Vektors 262 Klone identifiziert werden, für welche die Mutation zu einem lethalen Phänotyp führte. 116 der 262 entsprechenden Proteine konnte durch IDM erstmalig eine essentielle Funktion für die Vitalität von S. typhimurium zugewiesen werden. Darunter befinden sich sowohl Proteine, die homolog sind zu Proteinen anderer klinisch-relevanter Keime, als auch Proteine, die Salmonella-spezifisch sind. Der größte Teil der identifizierten Proteine ist in die Speicherung und Weitergabe von Information (Transkription, Translation, DNA-Reparatur etc.) involviert, viele sind allerdings auch Proteine unbekannter Funktion. Die Essentialität der durch IDM identifizierten Gene konnte durch die Konstruktion von konditional lethalen Mutanten bestätigt werden. IDM ist demnach das erste Mutagenese-Verfahren, welches das essentielle Gen-Set von S. typhimurium für das Überleben in Vollmedium zu definieren vermochte. Basierend auf den IDM Daten konnte es auf 511 Gene, d.h. auf 11 % des Gesamt-Genoms beziffert werden. Bei der Applikation von IDM auf L. monocytogenes lag der Fokus auf der Identifizierung von Genen, die für das Überleben dieses Gram-positiven Bakteriums im Zytosol von eukaryontischen Zellen von Bedeutung sind. Im Screening von bis dato 720 der 1491 L. monocytogenes Insertionsmutanten auf ein attenuiertes Replikationsverhalten in Caco-2 Zellen konnten 69 Mutanten selektioniert werden. In diesen Mutanten sind Gene ausgeknockt, deren Produkte hauptsächlich wichtige Funktionen in der Nährstoffbereitstellung, in der Energiesynthese und im Metabolismus inne haben. Mit der Insertions-Duplikations-Mutagenese IDM steht ein molekulares Werkzeug zur Verfügung, welches für die Identifzierung neuer targets für sowohl Breitband- als auch Spezies-spezifische Antiinfektiva eingesetzt werden kann und welches unbekannten Proteinen eine biologische Funktionen zuweisen kann. / Using insertion-duplication-mutagenesis IDM, that has been established in this work, it is possible to mutate the genome of pathogenic bacteria and to generate a mutant bank. This bank can be screened in a high throughput format on genes that are relevant under certain conditions for the infectious potential and the survival of these germs. IDM is based on a conditionally replicating vector which integrates into the chromosome under non-permissive replication conditions via homologous recombination after having cloned a gene bank from the host organism into it. The vector integration causes a knockout of the respective gene. In contrast to transposon mutagenesis, the IDM approach has the advantage that the whole genome is mutated and that no mutation hot spots occur. Furthermore, after having screened the mutant bank, the mutated gene locus can be identified very quickly by applicating PCR: excision of the vector is induced and the cloned, homologous fragment is sequenced. Integration of the vector into the chromosome and therefore the gene knockout is very stable even without any selection so that the mutants can be examined in the cell culture and animal model. In this work IDM has been applicated successfully to Salmonella enterica Servovar typhimurium and Listeria monocytogenes. Application of IDM to S. typhimurium aimed to identify genes whose products are essential for the survival of that Gram negative germ in rich medium under laboratory conditions. Starting with 14.000 S. typhimurium fragment-bank clones, induction of integration of the vector led to the identification of 262 clones for which the mutation resulted in a lethal phenotype. For 116 of the 262 respective proteins, this is the first data that assigns to these proteins an essential function for viability of S. typhimurium. Amongst them are proteins that are homologue to proteins of other clinically relevant germs, as well as proteins that are Salmonella specific. Most of the identified proteins are involved in information storage and processing (transcription, translation, DNA repair etc.), but many are proteins of unknown function. The essentiality of the identified genes could be confirmed by construction of conditionally lethal mutants. Hence, IDM is the first mutagenesis approach that reached to define the essential gene-set of S. typhimurium for survival in rich medium. Based on the IDM data it could be estimated at 511 genes, that means at 11 % of the whole genome. The application of IDM to L. monocytogenes focussed on the identification of genes that play an important role for the survival of that Gram-positive bacterium in the cytosol of eucaryotic cells. Until now 720 of the 1491 L. monocytogenes mutants have been screened on a attenuated replication behaviour in Caco-2 cells and 69 mutants have been selected. These mutants harbour mutations in genes whose products mainly hold important functions in nutrient uptake, energy synthesis and metabolism. The insertion-duplication-mutagenesis IDM has proven to be a suitable molecular tool that can be used for the identification of novel targets for both broad spectrum and species-specific antibiotics and that can assign a biological function to unknown proteins.

by Tam Fung-ping. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1993. / Includes bibliographical references (leaves 254-264). / Chapter I. --- Title page --- p.I / Chapter II. --- Abstract --- p.II / Chapter III. --- Acknowlegements --- p.III / Chapter IV. --- Table of contents --- p.IV / Chapter V. --- List of tables --- p.V / Chapter VI. --- List of figures --- p.VI / Chapter VII. --- Abbreviations --- p.VII / Chapter Chapter 1. --- Literature Reviews / Chapter 1.1 --- Modes of energy generation in facultative bacteria --- p.1 / Chapter 1.1.1 --- Difference in energy generation mechanism between respiratory and fermentative pathways --- p.2 / Chapter 1.1.2 --- Difference in carbon metabolism during anaerobiosis --- p.6 / Chapter 1.2 --- Repression and derepression of genes during anaerobiosis --- p.8 / Chapter 1.3 --- Global regulatory network for respiratory control --- p.8 / Chapter 1.3.1 --- Fnr-regulated gene expression --- p.10 / Chapter 1.3.2 --- NarL-regulated gene expression --- p.11 / Chapter 1.3.3 --- Crp-regulated gene expression --- p.12 / Chapter 1.3.4 --- ArcA-regulated gene expression --- p.13 / Chapter 1.3.5 --- Overlapping control of gene expression --- p.14 / Chapter 1.3.6 --- Regulatory mechanism of respiratory control --- p.16 / Chapter 1.4 --- Other regulatory systems in respiratory control --- p.19 / Chapter 1.5 --- The puzzle of regulatory network in anaerobiosis --- p.22 / Chapter 1.6 --- ArcA-ArcB system in Escherichia coli --- p.24 / Chapter 1.6.1 --- Arc A and ArcB for aerobic respiratory control --- p.24 / Chapter 1.6.2 --- arcA/dye/msp/fex/sfrA/cpxC gene are on identical genetic locus --- p.26 / Chapter 1.6.3 --- Arc function and Sfr function of Arc A protein are separately regulated --- p.28 / Chapter 1.6.4 --- ArcB-ArcA as sensor regulator in two component system for respiratory control --- p.29 / Chapter 1.7 --- Objectives and strategies of present study --- p.37 / Chapter Chapter 2. --- Materials / Chapter 2.1 --- Bacterial strains --- p.41 / Chapter 2.2 --- Culture mediums --- p.44 / Chapter 2.3 --- "Buffers, chemicals and antibiotics" --- p.46 / Chapter 2.4 --- DNA primers --- p.53 / Chapter Chapter 3. --- Primer extension analysis for locating the transcriptional start point of anaerobic inducible arcA in pFS --- p.34 / Chapter 3.1 --- Introduction --- p.55 / Chapter 3.2 --- Methods --- p.57 / Chapter 3.2.1 --- Preparation of total RNA --- p.59 / Chapter 3.2.2 --- Formaldeyde agarose gel electrophoresis of RNA --- p.60 / Chapter 3.2.3 --- Spectrometric estimation of RNA --- p.61 / Chapter 3.2.4 --- End-labelling of arcAusp primer with 32P --- p.62 / Chapter 3.2.5 --- Precipitation of arcAusp primer with samples RNA --- p.63 / Chapter 3.2.6 --- Primer extension reaction --- p.63 / Chapter 3.3 --- Results / Chapter 3.3.1 --- Preparation of RNA --- p.67 / Chapter 3.3.2 --- Determination of transcription start site by primer extension --- p.67 / Chapter 3.4 --- Discussions --- p.76 / Chapter 3.4.1 --- Selective activations of aerobic and anaerobic transcripts in response to oxygen level --- p.76 / Chapter 3.4.2 --- The arcA promoter is a sigma-70 dependent promoter --- p.77 / Chapter 3.4.3 --- Experimental design --- p.77 / Chapter Chapter 4. --- In vitro chemical mutagensis for finding some important regulatory elements of arcA in pFS --- p.34 / Chapter 4.1 --- Introduction / Chapter 4.2 --- Methods --- p.84 / Chapter 4.2.1 --- Large scale preparation of pFS34 plasmid --- p.84 / Chapter 4.2.2 --- PCR-mediated chemical mutagenesis of pFS34 --- p.86 / Chapter 4.2.3 --- Restriction enzyme digestion of PCR-amplified arcA insert after phenol extraction --- p.90 / Chapter 4.2.4 --- Large scale preparation of vector pFZYl and restriction enzyme digestion --- p.91 / Chapter 4.2.5 --- Ligation of EcoRI-SalI digested pFS34 fragment and vector pFZYl --- p.91 / Chapter 4.2.6 --- Preparation of electrotcompetent cell Salmonella typhymurium JR502 and electro-transformation --- p.92 / Chapter 4.2.7 --- Screening of transformed clones by LB-amp50-xgal plates --- p.93 / Chapter 4.2.8 --- Screening of recombinants colonies by Polymerase chain reaction (PCR) --- p.94 / Chapter 4.2.9 --- Screening of single-point mutated clones by PCR-single stranded conformational polymorphism (PCR-SSCP) technique --- p.96 / Chapter 4.2.10 --- Screening of mutated pFS34 clones with altered promoter activities byβ-gal assay --- p.98 / Chapter 4.2.11 --- Sequencing of mutated clones --- p.101 / Chapter 4.2.11.1 --- Recombinant M13 single-stranded sequencing of the mutated clones --- p.101 / Chapter 4.2.11.2 --- pUC18 double-stranded DNA sequencing of mutated clones --- p.105 / Chapter 4.3 --- Results --- p.108 / Chapter 4.3. --- l PCR-mediated chemical mutagenesis of pFS34 --- p.108 / Chapter 4.3.2 --- Screening of transformed clones by LB-amp50-xgal plate --- p.112 / Chapter 4.3.3 --- Screening of recombinants colonies by polymerase chain reaction (PCR) --- p.112 / Chapter 4.3.4 --- Screening of single-point mutated clones by PCR-single stranded conformational polymorphism (PCR-SSCP) technique --- p.114 / Chapter 4.3.5 --- Screening of mutated pFS34 clones with altered promoter activities byβ-gal assay --- p.117 / Chapter 4.3.6 --- Sequencing of mutated clones --- p.123 / Chapter 4.4 --- Discussions --- p.135 / Chapter 4.4.1 --- The possible mechanisms in anaerobic transcription --- p.135 / Chapter 4.4.2 --- The possible mechanisms in aerobic transcription --- p.143 / Chapter 4.4.3 --- Experimental design --- p.146 / Chapter Chapter 5 --- Investigation of the effect of integration host factor (IHF) and autoregulation on the expression of pFS34 / Chapter 5.1 --- Introduction --- p.152 / Chapter 5.2 --- Methods --- p.154 / Chapter 5.2.1 --- Construction of Escherichia coli mutant --- p.155 / Chapter 5.2.2 --- PCR check of mutant for the presence of pFS34 and pFZYl plasmid --- p.157 / Chapter 5.2.3 --- β-galactosidase assay of aerobic and anaerobic activities change of pFS34 --- p.157 / Chapter 5.3 --- Results / Chapter 5.3.1 --- Effect of integration factor (IHF) on pFS34 --- p.158 / Chapter 5.3.1.1 --- PCR analysis of E. coli. himA and himD mutant for the presence of pFS34 and pFZYl plasmid --- p.158 / Chapter 5.3.1.2 --- β-galatosidase assay of aerobic and anaerobic activities of pFS34 in E. coli. himA and himD mutant --- p.158 / Chapter 5.3.2 --- Autoregultion on expression of pFS34 --- p.162 / Chapter 5.3.2.1 --- PCR analysis of E. coli. arcA mutant for the presence of pFS34 plasmid --- p.162 / Chapter 5.3.2.2 --- β-galctosidase assay of aerobic and anaerobic activities of pFS34 (arcA-lacZ) in E. coli. arcA mutant --- p.162 / Chapter 5.4 --- Discussions --- p.167 / Chapter 5.4.1 --- Effect of IHF on aerobic and anaerobic expression of arcA --- p.167 / Chapter 5.4.1.1 --- Possible regulatory mechanism of IHF on aerobic transcription --- p.167 / Chapter 5.4.1.2 --- Possible regulatory mechanism of IHF on anaerobic transcription --- p.170 / Chapter 5.4.1.3 --- Affinity binding of IHF depends on topological state of arcA --- p.172 / Chapter 5.4.1.4 --- Possible role of IHF in global regulation of anaerobiosis --- p.173 / Chapter 5.4.1.5 --- Experimental design --- p.174 / Chapter 5.4.2 --- Autoregulatory expression of arcA in pFS34 --- p.176 / Chapter Chapter 6. --- PCR walking of arcA from Salmonella typhimurium LT2 / Chapter 6.1 --- Introduction --- p.177 / Chapter 6.2 --- Methods --- p.186 / Chapter 6.2.1 --- Preparation of chromosomal DNA from Salmonella typhimurium LT2 --- p.186 / Chapter 6.2.2 --- Amplification of genomic arcA by linear PCR with arcAcds primer --- p.187 / Chapter 6.2.3 --- Low stringency PCR amplification of single-stranded arcA gene fragment and genomic DNA with anchor- random primer (delC-32R & delC-34R) --- p.188 / Chapter 6.2.4 --- High stringency PCR amplification with arcAcds primer and delC-23 primer --- p.189 / Chapter 6.2.5 --- High stringency PCR amplification with arcAusp2 and delC-23 primer --- p.190 / Chapter 6.2.6 --- "High stringency PCR amplification with delC-23 primer only, arcAusp2 primer only and mixture of delC-23 and arcAusp2 primer" --- p.191 / Chapter 6.2.7 --- High stringency PCR amplification with arcAusp2 only and Sau3A restriction enzyme digestion of PCR products --- p.192 / Chapter 6.2.8 --- Cloning of PCR walking products into pUC18 and heat shock transforming into E.coli. JM83 --- p.193 / Chapter 6.2.9 --- Confirmation of inserts in the clones and estimation of inserts size by PCR --- p.194 / Chapter 6.2.10 --- Dideoxy sequencing of PCR walking arcA fragments in pUC18 --- p.194 / Chapter 6.2.11 --- Subcloning of arcA fragment into pFZYl and PCR analysis for insertion of one insert with proper orientation --- p.195 / Chapter 6.2.12 --- arcA-galactosiadase assay of PCR walking arcA fragment-lacZ fusion --- p.196 / Chapter 6.3 --- Results --- p.198 / Chapter 6.3.1 --- Preparation of chromosomal DNA from Salmonella typhimurium LT2 --- p.198 / Chapter 6.3.2 --- Amplification of genomic arcA by linear PCR with arcAcds primer --- p.198 / Chapter 6.3.3 --- Low stringency PCR amplification of single-stranded arcA gene fragment and genomic DNA with anchor- random primer (delC-32R and delC-34R) --- p.200 / Chapter 6.3.4 --- High stringency PCR amplification with arcAcds primer and delC-23 primer --- p.200 / Chapter 6.3.5 --- High stringency PCR amplification with arcAusp2 、 primer and delC-23 prime --- p.203 / Chapter 6.3.6 --- "High stringency PCR amplification with delC-23 primer only, arcAusp2 primer only and mixture of delC-23 and arcAusp2 primer to check for flanking ends of bands" --- p.205 / Chapter 6.3.7 --- High stringency PCR amplification with arcAusp2 primer and Sau3A restriction enzyme digestion of PCR products --- p.207 / Chapter 6.3.8 --- Cloning of PCR walking products into pUC18 and heat-shock transforming into E. coli. JM83 --- p.210 / Chapter 6.3.9 --- Confirmation of inserts in the clones and estimation of inserts size by PCR --- p.210 / Chapter 6.3.10 --- Dideoxy sequencing of arc A PCR walking fragment: :pUC18 --- p.210 / Chapter 6.3.11 --- Subcloning of arcA fragment into pFZYl and PCR check for right insertion of single insert with proper orientation --- p.226 / Chapter 6.3.12 --- β-galactosidase assay --- p.232 / Chapter 6.4 --- Discussions --- p.227 / Chapter 6.4.1 --- PCR based gene walking strategy --- p.227 / Chapter 6.4.2 --- Confirmation of cloned arcA gene in pFS34 was a geniune arcA gene of S. typhimurium --- p.240 / Chapter 6.4.3 --- Promoter activity of further upstream arcA clones - AU87::pFZYl --- p.241 / Chapter Chapter 7. --- Overall Discussion --- p.244 / Chapter 7.1 --- Summary --- p.244 / Chapter 7.2 --- Proposed Model of regulation of arcA in Salmonella typhimurium --- p.249 / Chapter 7.3 --- Further Studies --- p.251 / References --- p.254

by Cheung, Man Wai William. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1992. / Includes bibliographical references (leaves 113-123). / ABSTRACT --- p.i / ACKNOWLEDGMENTS --- p.ii / DEDICATION --- p.iii / TABLE OF CONTENTS --- p.iv / LIST OF FIGURES --- p.viii / LIST OF TABLES --- p.x / Chapter 1. --- Introduction --- p.1 / Chapter 1.1. --- General Introduction --- p.1 / Chapter 1.2. --- Purpose of Study --- p.3 / Chapter 2. --- Literature Review --- p.7 / Chapter 2.1. --- Central Pathways of Aerobic and Anaerobic Carbon Catabolism --- p.7 / Chapter 2.2. --- Global Regulation of Gene Expression by Oxygen --- p.10 / Chapter 2.2.1. --- Two approaches for the studies --- p.10 / Chapter 2.2.2. --- FNR regulation --- p.12 / Chapter 2.2.3. --- ArcAB regulation --- p.19 / Chapter 2.2.3.1. --- arcA --- p.19 / Chapter 2.2.3.2. --- arcB --- p.20 / Chapter 2.2.3.3. --- A member of the Two- Components regulatory systems --- p.21 / Chapter 2.3. --- Molecular Analysis of Promoters --- p.26 / Chapter 2.3.1. --- S1 mapping --- p.29 / Chapter 2.3.2. --- Primer extension --- p.29 / Chapter 2.3.3. --- DNaseI footprinting --- p.30 / Chapter 2.3.4. --- Mutational analysis of promoters --- p.32 / Chapter 3. --- Materials and Methods --- p.35 / Chapter 3.1. --- Bacterial strains and Plasmids --- p.35 / Chapter 3.2. --- Media --- p.35 / Chapter 3.3. --- Solutions --- p.38 / Chapter 3.4. --- Small Scale Preparation of Plasmid DNA --- p.40 / Chapter 3.5. --- Large Scale Preparation of Plasmid DNA --- p.41 / Chapter 3.5.1. --- Growth of bacterial culture --- p.41 / Chapter 3.5.2. --- Lysis by alkali --- p.43 / Chapter 3.5.3. --- Purification of closed circular DNA by cesium chloride gradient equilibrium centrifugation --- p.44 / Chapter 3.5.4. --- Digestion of DNA with restriction endonucleases --- p.45 / Chapter 3.6. --- Analysis of DNA Samples with Agarose Gel Electrophoresis --- p.45 / Chapter 3.7. --- Cloning of DNA Fragments from Nest-deleted M13mpl8 Clones to pFZYl --- p.47 / Chapter 3.8. --- Introduction of Plasmids into Cells --- p.48 / Chapter 3.8.1. --- Heat shock transformation --- p.48 / Chapter 3.8.1.1. --- Preparation of competent cells (I) --- p.48 / Chapter 3.8.1.2. --- Preparation of competent cells (II) --- p.49 / Chapter 3.8.2. --- High efficiency transformation by electroporation --- p.50 / Chapter 3.8.2.1. --- Preparation of electro- competent cells --- p.50 / Chapter 3.8.2.2. --- Electro-transformation --- p.51 / Chapter 3.9. --- DNA Sequencing by Chain Termination Method --- p.51 / Chapter 3.9.1. --- Preparation of single-stranded M13 templates for sequencing reaction --- p.51 / Chapter 3.9.2. --- Sequencing reactions using single- stranded templates --- p.53 / Chapter 3.9.3. --- Preparation of polyacrylamide gel for sequencing --- p.54 / Chapter 3.9.4. --- Electrophoresis of the DNA samples --- p.55 / Chapter 3.10. --- Construction of Nested Clones by Exonuclease III Unidirectional Deletions --- p.55 / Chapter 3.10.1. --- Unidirectional nested deletion of M13mpl8 clones --- p.55 / Chapter 3.10.2. --- Screening of nested clones by Direct gel electrophoresis --- p.56 / Chapter 3.10.3. --- Screening of nested clones of M13mpl8 and pFZYl by Polymerase Chain Reaction --- p.57 / Chapter 3.11. --- β-galactosidase Assay --- p.59 / Chapter 3.12. --- Primer Extension --- p.60 / Chapter 3.12.1. --- Preparation of total RNA from Gram- negative bacteria --- p.60 / Chapter 3.12.2. --- Labelling the 5' end of the oligonucleotides --- p.61 / Chapter 3.12.3. --- Hybridization and primer extension --- p.62 / Chapter 4. --- Result --- p.63 / Chapter 4.1. --- Subcloning of arcA promoter into M13mpl8/19 --- p.63 / Chapter 4.2. --- Sequencing of p34一18i and p3419i using M13 Sequencing primers (-47) and ArcA-cds Primers --- p.63 / Chapter 4.3. --- Unidirectional Nested Deletion of p3418i using Exonuclease III --- p.65 / Chapter 4.3.1. --- Large scale preparation of p3A18i DNA for Exonuclease III unidirectional nested deletion --- p.65 / Chapter 4.3.2. --- Construction of 3' and 5' overhangs --- p.65 / Chapter 4.3.3. --- Exonuclease III digestion --- p.67 / Chapter 4.3.4. --- Repairing of the 3' and 5' overhangs to generate blunt ends --- p.67 / Chapter 4.3.5. --- Blunt-end ligation of the nested deletion M13mpl8 subclones p3418i --- p.67 / Chapter 4.3.6. --- Transformation --- p.69 / Chapter 4.3.7. --- Screening of nest-deleted p3418i clones by Direct Gel --- p.71 / Chapter 4.3.8. --- Screening of nested deletion p3418i clones by PCR Screening --- p.73 / Chapter 4.3.9. --- Sequencing of the nested deletion p3418i clones --- p.76 / Chapter 4.4. --- Cloning of Nested Deletion DNA Fragments from M13mpl8 into pFZYl --- p.80 / Chapter 4.4.1. --- Screening of pFZYl clones using PCR Screening --- p.80 / Chapter 4.5. --- Expression of Nest-Deleted arcA Promoter Clones in E. coli MC1061-5 --- p.87 / Chapter 4.6. --- Expression of Nest-Deleted arcA Promoter Clones in S. typhimurium JR501 --- p.89 / Chapter 4.7. --- Primer Extension --- p.89 / Chapter 5. --- Discussion --- p.93 / Chapter 5.1. --- Sequencing of arcA Promoter --- p.93 / Chapter 5.2. --- Unidirectional Nested Deletion of p3A18i using Exonuclease III --- p.94 / Chapter 5.3. --- Screening of Nest-deletion p3418i Subclones --- p.95 / Chapter 5.4 --- Cloning of Nest-deleted DNA Fragments from M13mpl8 Subclones into pFZYl --- p.99 / Chapter 5.5. --- Screening of Nest-deleted pFZYl Subclones of p3418i --- p.101 / Chapter 5.6. --- The Effect of 5' Unidirectional Nested Deletion on the Expression of the Cloned arcA promoter in E. coli M1061-5 and S typhimurium JR501 --- p.102 / Chapter 5.7. --- Primer Extension --- p.102 / Chapter 5.8. --- Sequence Analysis of the Cloned arcA Promoter --- p.104 / Chapter 6. --- Conclusion and Further Studies --- p.111 / Chapter 7. --- Reference Cited --- p.113

食物中毒感染是常見但非常重要的全球性公共健康問題。沙門氏鼠傷寒桿菌乃常被分離出來的細菌性病原體之一。隨著實驗室參考菌株LT2的基因組序列於2001年被發表之後，另外9個沙門氏鼠傷寒菌菌株的基因序列均已陸續進行測序。最近，本實驗室亦對十個本地沙門氏鼠傷寒菌臨床分離菌株的基因序列進行了測序。為了為這些基因組序列提供高品質的註釋，我們把預測的基因組提交到質量控制工具GenePRIMP以識別有潛在錯誤或異常的預測基因。本研究針對血液分離菌株78896和糞便分離菌株1047518的GenePRIMP報告進行人工檢查，並對每個菌株超過270個的基因進行了修訂。此外，本研究亦對上述的10個本地菌株進行了功能註釋。註釋項目包括沙門氏菌致病島（SPIs）、致病因子、tRNA和非編碼小分子RNA、噬菌體和CRISPRs結構等基因組及致病元素。 KEGG通路則提供了進一步的功能註釋。 / 本研究同時對本地的血液和糞便分離菌株，連同國外的臨床分離菌株，進行了廣泛的比對，用以識別全身性沙門氏菌感染的潛在遺傳因素。 本研究進行了以下基因分析：（1）多位點序列分型（MLST）；（2）在小鼠全身性感染中涉及的主調控因子和關鍵元素; 及（3）人類腸胃道感染中涉及的基因。然而，這些分析產生只能對全身性沙門氏菌感染提供有限的見解。然而，透過使用RAST註釋系統，我們於其中三個血液分離菌株中發現了一個的額外的螯鐵蛋白aerobactin鐵採集系統。儘管在體外實驗中，這些血液分離菌株並沒有明顯的生長優勢，但實驗結果表明，在缺乏鐵的培養液中，aerobactin基因的表達水平是比較高的。此外，我們亦於其中四個血液分離菌株中，發現負責細胞色素c熟成(ccm)的基因座均被中斷。這可能改變了這些血液分離菌株中細胞色素c的生物合成途徑。這些鐵採集和同化機制的觀察均為未來全身性沙門氏菌感染的研究提供了可能的發展方向。 / 本研究同時識別了用以分別本地及海外的沙門氏鼠傷寒菌菌株的分子標記，並在鮭魚和生菜的接種實驗中，展現了它們分辨本地及海外菌株的能力。然而，在投入實際應用之前，這些標記尚需要進一步的驗證和測試，以便確定快速檢測方法的有效性。 / Foodborne infection is a common but important public health issue worldwide. Salmonella enterica serovar Typhimurium is frequently isolated from outbreaks as one of the common bacterial causative agents. Following the availability of the genome sequence of the reference lab strain LT2 in 2001, nine genomes of S. Typhimurium had been sequenced since then. Recently, genomes of ten local S. Typhimurium clinical isolates have been assembled in our laboratory. In order to provide high quality annotation of these genome sequences, the predicted gene sets were submitted to the quality control tool GenePRIMP (Gene PRediction IMprovement Pipeline) to identify potentially erroneous and abnormal gene calls. The GenePRIMP reports for the local blood isolate 78896 and stool isolate 1047518 were manually inspected and more than 270 genes were amended individually for each isolate. Functional annotation had also been performed for the 10 local isolates. Genomic and virulent elements including Salmonella Pathogenicity Islands (SPIs), virulence factors, tRNAs and small non-coding RNAs, prophage elements and CRISPRs structures had been annotated. The KEGG pathways provided a further means of functional annotation. / The local blood and stool isolates, together with the sequenced foreign clinical isolates, had also been extensively compared to identify potential genetic determinants of Salmonella systemic infection. (1) Multilocus sequence typing (MLST); (2) Alignment of master regulators and key players of systemic infection in mice; and (3) Analyses of the genes responsible for human gastrointestinal tract infection had been performed. However, these analyses yielded limited insights on systemic infection. Alternatively, using subsystems annotation by RAST, an additional aerobactin siderophore iron acquisition system was shown to be prevalent among three of the blood isolates. Despite no obvious growth advantage was offered to the blood isolates in an in vitro experiment, it was demonstrated that expression of the aerobactin genes was higher in iron-depleted culturing medium. In addition, a disrupted cytochrome c maturation (ccm) locus that may alter the cytochrome c biogenesis pathway was also identified in four of the blood isolates. These observations in iron acquisition and assimilation mechanisms suggest their potential in future direction of Salmonella systemic infection studies. / Molecular markers specific to local and foreign S. Typhimurium isolates were also identified and their utility in differentiating local and foreign isolates was demonstrated in a pilot spiking experiment using raw salmon and lettuce. These markers will require further verification and testing prior to actual application in real-world settings in order to examine the validity of the rapid detection method. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Cheng, Chi Keung. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 124-146). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese. / Abstract of thesis entitled --- p.iii / 摘要 --- p.v / Acknowledgements --- p.vii / Table of Contents --- p.viii / List of Tables --- p.xi / List of Figures --- p.xiii / Abbreviations --- p.xiv / Chapter Chapter 1 --- Literature Review --- p.1 / Chapter 1.1 --- Introduction and Taxonomy --- p.1 / Chapter 1.2 --- Epidemiology of Salmonella Typhimurium infections --- p.2 / Chapter 1.3 --- Pathogenesis of Salmonella Typhimurium infection --- p.4 / Chapter 1.3.1 --- Infection mechanisms --- p.4 / Chapter 1.3.2 --- Salmonella Pathogenicity Islands --- p.6 / Chapter 1.3.3 --- Regulation of virulence --- p.9 / Chapter 1.4 --- Non-typhoid Salmonella (NTS) systemic infection --- p.11 / Chapter 1.4.1 --- Epidemiology of NTS systemic infection --- p.11 / Chapter 1.4.2 --- Salmonella Typhimurium multidrug resistance --- p.12 / Chapter 1.5 --- Salmonella Typhimurium genomics --- p.15 / Chapter 1.5.1 --- Salmonella Typhimurium genome sequencing --- p.15 / Chapter 1.5.2 --- Comparative studies on Salmonella genomes --- p.17 / Chapter 1.6 --- Aims of project --- p.19 / Chapter Chapter 2 --- Curation and detailed annotation of genomes of local Salmonella Typhimurium clinical isolates --- p.22 / Chapter 2.1 --- Introduction --- p.22 / Chapter 2.2 --- Materials and Methods --- p.27 / Chapter 2.2.1 --- Manual curation of GenePRIMP results --- p.27 / Chapter 2.2.2 --- Salmonella Pathogenicity Islands (SPIs) and virulence factors annotation --- p.29 / Chapter 2.2.3 --- Small RNA and t-RNA annotation --- p.29 / Chapter 2.2.4 --- Phage elements annotation --- p.30 / Chapter 2.2.5 --- CRISPRs annotation --- p.30 / Chapter 2.2.6 --- KEGG annotation --- p.30 / Chapter 2.3 --- Results --- p.32 / Chapter 2.3.1 --- Manual curation of GenePRIMP results --- p.32 / Chapter 2.3.1.1 --- Short genes --- p.35 / Chapter 2.3.1.2 --- Long genes --- p.35 / Chapter 2.3.1.3 --- Unique genes --- p.36 / Chapter 2.3.1.4 --- Overlapped genes --- p.36 / Chapter 2.3.1.5 --- Broken genes --- p.37 / Chapter 2.3.2 --- Salmonella Pathogenicity Islands (SPIs) and virulence factors annotation --- p.37 / Chapter 2.3.2.1 --- Salmonella Pathogenicity Islands (SPIs) annotation --- p.37 / Chapter 2.3.2.2 --- Virulence factors annotation --- p.44 / Chapter 2.3.3 --- Small RNA and t-RNA annotation --- p.44 / Chapter 2.3.4 --- Phage elements annotation --- p.44 / Chapter 2.3.5 --- CRISPRs annotation --- p.50 / Chapter 2.3.6 --- KEGG annotation --- p.51 / Chapter 2.4 --- Discussion --- p.53 / Chapter 2.4.1 --- Manual curation of GenePRIMP results --- p.53 / Chapter 2.4.1.1 --- Gene amendment not required --- p.54 / Chapter 2.4.1.2 --- Genes with boundaries relocated --- p.54 / Chapter 2.4.1.3 --- Genes to be discarded --- p.55 / Chapter 2.4.1.4 --- Gene pairs to be fused --- p.55 / Chapter 2.4.1.5 --- Potential pseudogenes formation --- p.56 / Chapter 2.4.2 --- Salmonella Pathogenicity Islands (SPIs) annotation --- p.57 / Chapter 2.4.3 --- Virulence factors annotation --- p.57 / Chapter 2.4.4 --- Small RNA and t-RNA annotation --- p.58 / Chapter 2.4.5 --- Phage elements annotation --- p.59 / Chapter Chapter 3 --- Identification of genetic determinants of blood invasiveness in local S. Typhimurium clinical isolates --- p.61 / Chapter 3.1 --- Introduction --- p.61 / Chapter 3.2 --- Materials and Methods --- p.66 / Chapter 3.2.1 --- Multilocus Sequence Typing (MLST) --- p.66 / Chapter 3.2.2 --- Phage elements annotation for foreign isolates --- p.67 / Chapter 3.2.3 --- Alignment of genes inferred to play important roles in NTS systemic --- p.infection67 / Chapter 3.2.4 --- Alignment of genes inferred to involved during infection in the gastrointestinal (GI) tract --- p.68 / Chapter 3.2.5 --- Subsystems assignment using Rapid Annotation using Subsystem Technology (RAST) server --- p.68 / Chapter 3.2.6 --- Growth analysis of local S. Typhimurium clinical isolates in iron-limiting environment --- p.69 / Chapter 3.2.7 --- Reverse transcription and real-time PCR --- p.70 / Chapter 3.2.7.1 --- Primer design and verification --- p.70 / Chapter 3.2.7.2 --- cDNA synthesis and real-time PCR --- p.70 / Chapter 3.3 --- Results --- p.73 / Chapter 3.3.1 --- Multilocus Sequence Typing (MLST) --- p.73 / Chapter 3.3.2 --- Phage elements annotation for foreign isolates --- p.73 / Chapter 3.3.3 --- Alignment of genes inferred to play important roles in NTS systemic infection --- p.74 / Chapter 3.3.4 --- Alignment of genes inferred to involved during infection in the gastrointestinal (GI) tract --- p.79 / Chapter 3.3.4.1 --- Acid tolerance response --- p.79 / Chapter 3.3.4.2 --- Epithelial cells attachment --- p.80 / Chapter 3.3.4.3 --- Epithelial cells invasion --- p.83 / Chapter 3.3.4.4 --- Survival within macrophages --- p.83 / Chapter 3.3.5 --- RAST subsystem analysis --- p.86 / Chapter 3.3.6 --- Growth analysis and aerobactin genes expression --- p.87 / Chapter 3.4 --- Discussion --- p.93 / Chapter Chapter 4 --- Molecular markers identification and testing on selected foodstuff for local S. Typhimurium isolates --- p.97 / Chapter 4.1 --- Introduction --- p.97 / Chapter 4.2 --- Materials and Methods --- p.101 / Chapter 4.2.1 --- Molecular markers identification --- p.101 / Chapter 4.2.2 --- Primer design and verification --- p.101 / Chapter 4.2.3 --- Spiking experiments on selected food samples --- p.103 / Chapter 4.2.4 --- Quantitative TaqMan real-time PCR --- p.103 / Chapter 4.3 --- Results --- p.105 / Chapter 4.3.1 --- Molecular markers identification --- p.105 / Chapter 4.3.2 --- Spiking experiments and TaqMan real-time PCR --- p.109 / Chapter 4.4 --- Discussion --- p.113 / Chapter 4.4.1 --- Molecular markers identification --- p.113 / Chapter 4.4.2 --- Spiking experiments and TaqMan real-time PCR --- p.114 / Chapter Chapter 5 --- General discussion --- p.116 / Chapter 5.1 --- Manual curation of GenePRIMP results --- p.116 / Chapter 5.2 --- Functional annotation of local S. Typhimurium genomes --- p.118 / Chapter 5.3 --- Systemic infection studies --- p.120 / Chapter 5.4 --- Molecular markers identification and spiking experiments --- p.121 / Chapter 5.5 --- Conclusion and future perspectives --- p.122 / References --- p.124

Metals are used as cofactors for enzymes, but are toxic in excess. In order to avoid the deleterious effects posed by metals, the cell must employ strict metal homeostasis systems. One such system is the Cue copper-resistance system in Salmonella enterica serovar Typhimurium (S. Typhimurium) which includes the periplasmic copper binding protein CueP. Previous studies have shown CueP to be a major periplasmic copper-sequestering protein that has a role in supplying copper to, and thus activating, the periplasmic Cu,Zn-superoxide dismutase enzyme SodCII (Osman et al., 2013). SodCII protects the cell from reactive oxygen species (ROS), due for example to the actions of the respiratory burst oxidase in host macrophages. However, despite its ability to sequester copper and activate SodCII, the precise physiological role of CueP in S. Typhimurium has remained unresolved since cueP mutants of S. Typhimurium strain SL1344 (the wild-type stain used in this study) do not exhibit a phenotype with respect to tolerance to copper or reactive oxygen species. In addition, the copper-binding mechanism of CueP and its interactions with other copper-binding proteins, including SodCII, have not been examined. An aim of this study was to establish a phenotype for a cueP mutant of S. Typhimurium with respect to copper and/or ROS tolerance. It was hypothesised that the possession of KatG (catalase) and multiple superoxide dismutases (SodCI, SodA and SodB), in addition to SodCII, by S. Typhimurium may confer functional redundancy with respect to copper and ROS tolerance. Hence mutants lacking katG (ΔkatG) or the various superoxide dismutase encoding genes (ΔsodA/ΔsodB/ΔsodCI/ΔsodCII) with and without functional cueP were generated. The ΔkatG mutants exhibited reduced catalase activity and reduced tolerance to hydrogen peroxide, consistent with the loss of KatG, however the additional loss of cueP did not reduce tolerance to hydrogen peroxide further. Similarly, tolerance to copper and extracellular superoxide was also unaltered in the ΔkatG/ΔcueP mutant. The tolerance of the various superoxide dismutase mutants to copper and various ROS was also unaffected by the presence or absence of CueP. To examine the role of CueP in SodCII activation in vivo, SodCII was over-expressed in S. Typhimurium (in a ΔsodA/ΔsodB/ΔsodCI/ΔsodCII background) with and without functional cueP and superoxide dismutase activity measured in both whole cells and periplasmic extracts. SodCII-dependent superoxide dismutase activity was successfully identified within the periplasmic extracts. However, surprisingly, the level of activity was unaffected by the presence 16 or absence of CueP and/or the addition of copper. It is possible that SodCII is thus able to scavenge sufficient copper for activity from the reagents used in these assays. Similarly, in an alternative approach to examine the role of CueP in vitro, both SodCII and CueP (WT and potential metal-binding residue mutant forms) were successfully over-expressed in E. coli and methods for their purification optimised (without the use of affinity tags). ICP-MS analysis indicated that a CuePC104S mutant contains > 18-fold less copper than the CueP WT protein. Furthermore, superoxide dismutase activity assays using purified proteins, indicated that the CuePC104S mutant was less able to activate SodCII than the WT CueP. Taken together, these results are consistent with a role for the Cys104 residue in copper-binding by CueP. Bioinformatics results suggest the presence of CueP or homologous genes in the presence of other bacteria, including pathogens such as Klebsiella, Yersinia and Shigella spp. Further understanding of the role of CueP and the systems used by S. Typhimurium to avoid both copper and ROS stress may inform the development of novel treatment strategies for bacterial diseases.

Non-coding RNAs constitute a major class of regulators involved in bacterial gene expression. A group of riboregulators of heterogeneous size and shape referred to as small regulatory RNAs (sRNAs) control trans- or cis-encoded genes through direct base-pairing with their mRNAs. Although mostly inhibiting their target mRNAs, several sRNAs also induce gene expression. An important co-factor for sRNA activity is the RNA chaperone, Hfq, which is able to rearrange intramolecular secondary structures and to promote annealing of complementary RNA sequences. In addition, Hfq protects unpaired RNA from degradation by ribonucleases and thus increases sRNA stability. Co-immunoprecipitation of RNA with the Hfq protein, and further experimental as well as bioinformatical studies performed over the last decade suggested the presence of more than 150 different sRNAs in various Enterobacteria including Escherichia coli and Salmonellae. So-called core sRNAs are considered to fulfill central cellular activities as deduced from their high degree of conservation among different species. Approximately 25 core sRNAs have been implicated in gene regulation under a variety of environmental responses. However, for the majority of sRNAs, both the riboregulators’ individual biological roles as well as modes of action remain to be elucidated. The current study aimed to define the cellular functions of the two highly conserved, Hfq-dependent sRNAs, SdsR and RydC, in the model pathogen Salmonella Typhimurium. SdsR had been known as one of the most abundant sRNAs during stationary growth phase in E. coli. Examination of the conservation patterns in the sdsR promoter region in combination with classic genetic analyses revealed SdsR as the first sRNA under direct transcriptional control of the alternative σ factor σS. In Salmonella, over-expression of SdsR down-regulates the synthesis of the major porin OmpD, and the interaction site in the ompD mRNA coding sequence was mapped by a 3'RACE-based approach. At the post-transcriptional level, expression of ompD is controlled by three additional sRNAs, but SdsR plays a specific role in porin regulation during the stringent response. Similarly, RydC, the second sRNA adressed in this study, was initially discovered in E. coli but appeared to be conserved in many related γ-proteobacteria. An interesting aspect of this Hfq-dependent sRNAs is its secondary structure involving a pseudo-knot configuration, while the 5’ end remains single stranded. A transcriptomic approach combining RydC pulse-expression and scoring of global mRNA changes on microarrays was employed to identify the targets of this sRNA. RydC specifically activated expression of the longer of two versions of the cfa mRNA encoding for the phospholipid-modifying enzyme cyclopropane fatty acid synthase. Employing its conserved single-stranded 5' end, RydC acts as a positive regulator and masks a recognition site of the endoribonuclease, RNase E, in the cfa leader. / Die bakterielle Genexpression wird unter anderem maßgeblich von nicht-kodierenden RNAs bestimmt. Kleine regulatorische RNAs (sRNAs) sind eine bezüglich Größe und Struktur heterogene Gruppe von Riboregulatoren, die ihre in cis oder in trans-kodierten Zielgene mittels direkter Basenpaarungen kontrollieren. Während der Großteil der sRNAs reprimierend wirkt, konnte für einige RNAs gezeigt werden, dass sie die Expression ihres Zieltranskripts verstärken. Ein wichtiger Kofaktor für die regulatorische Funktion der sRNAs ist das RNA-Chaperon Hfq, welches sowohl die Umfaltung intramolekularer Sekundärstrukturen ermöglicht, als auch die Ausbildung von Basenpaarungen zwischen komplementären RNA-Sequenzen steuert. Zusätzlich schützt Hfq nicht-gepaarte RNAs vor dem Abbau durch Ribonukleasen, und trägt damit zur Stabilität der Moleküle bei. Durch Ko-Immunopräzipitation mit Hfq sowie in weiteren experimentellen als auch bioinformatischen Studien konnten im letzten Jahrzehnt in diversen Enterobakterien, wie z.B. auch Escherichia coli und Salmonellae, mehr als 150 verschiedene sRNAs bestimmt werden. Von so genannten "core sRNAs" (Kern-sRNAs) wird aufgrund ihres hohen Grades an Konservierung in unterschiedlichen Spezies angenommen, dass sie zentrale Funktionen erfüllen. Etwa 25 core sRNAs agieren unter verschiedenen Umweltbedingungen als Regulatoren. Ihre exakte biologische Rolle, sowie ihre Funktionsweise sind jedoch größtenteils noch unbekannt. In der vorliegenden Arbeit wurden die beiden konservierten, Hfq-abhängigen sRNAs, SdsR und RydC, im Modellpathogen Salmonella Typhimurium charakterisiert. SdsR war als eine der abundantesten sRNAs der stationären Phase in E. coli beschrieben worden. Durch Auswertung der Konservierungsmuster der sdsR Promotorsequenz sowie klassische genetische Analyse konnte SdsR als erste sRNA unter direkter Kontrolle des alternativen σ Faktors σS bestimmt werden. In Salmonella führt die Überexpression von SdsR zur Reprimierung des Membranporins OmpD, und die Bindestelle von SdsR auf dem ompD Transkript wurde mittels einer auf 3'-RACE basierenden Methode ermittelt. Obwohl die Expression von ompD auf post-transkriptionaler Ebene von drei weiteren sRNAs kontrolliert wird, konnte eine spezische Regulation des Porins durch SdsR während Aminosäure-Hungerung gezeigt werden. Auch RydC, die zweite in dieser Studie analysierte sRNA, wurde zunächst in E. coli beschrieben und ist aber auch in weiteren γ-Proteobakterien konserviert. Interessanterweise enthält die Sekundärstruktur dieser Hfq-abhängigen sRNA einen Pseudoknoten, während das 5'-Ende ungepaart ist. Die Zielgene von RydC wurden mittels einer Transkriptomanalyse bestimmt, in der die Änderung der Häufigkeitsverteilung aller mRNAs nach kurzzeitiger Überexpression der sRNA auf Microarrays untersucht wurde. RydC bewirkte die spezifische Aktivierung des längeren von insgesamt zwei Versionen der cfa mRNA, die für eine Cyclopropan-fettsäuresynthase kodiert, ein Enzym das zur Modifikation von Phospholipiden dient. Eine Basenpaarung über das freie 5'-Ende der sRNA RydC führt zur Aktivierung der cfa-Expression, und maskiert eine Erkennungssequenz der Endoribonuklease, RNase E, innerhalb des Transkripts.

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