Refine
Has Fulltext
- yes (14)
Is part of the Bibliography
- yes (14)
Document Type
- Doctoral Thesis (14)
Keywords
- Fusobacterium nucleatum (2)
- Neisseria meningitidis (2)
- RNS (2)
- small RNA (2)
- Adhesion and Invasion (1)
- Angeborene Immunität (1)
- Annotation (1)
- Bacteria (1)
- Bacteria-Host Cell Interaction (1)
- Bacterial infection (1)
Institute
Sonstige beteiligte Institutionen
Neisseria meningitidis, a commensal β-proteobacterium residing exclusively in the human nasopharynx, is a leading cause of sepsis and epidemic meningitis worldwide. While comparative genome analysis was able to define hyperinvasive lineages that are responsible for most of the cases of invasive meningococcal disease (IMD), the genetic basis of their virulence remains unclear. Recent studies demonstrate that the type II C CRISPR/Cas system of meningococci is associated with carriage and less invasive lineages. CRISPR/Cas, an adaptive defence system against foreign DNA, was shown to be involved in gene regulation in Francisella novicida. This study shows that knockout strains of N. meningitidis lacking the Cas9 protein are impaired in the adhesion to human nasopharyngeal cells in a strain-dependant manner, which constitutes a central step in the pathogenesis of IMD. Consequently, this study indicates that the meningococcal CRISPR/Cas system fulfils functions beyond the defence of foreign DNA and is involved in the regulation of meningococcal virulence.
Flatworm parasites (platyhelminths) cause serious infection diseases in humans, such as schistosomiasis and hydatid disease, mainly prevalent in developing countries. However, the current repertoire of drug armamentarium used to combat flatworm infections is limited. For instance, praziquantel is the only drug available for mass treatment of Schistosoma infections. In contrast to their hosts, flatworm parasites possess a distinct redox arrangement of redox pathways in which the selenoenzyme thioredoxin glutathione reductase (TGR) controls the overall redox homeostasis. Interference with this enzyme leads to parasite death. Hence, this key redox enzyme seems to be a new promising drug target against flatworm infections.
Because most flatworms are difficult to cultivate in the laboratory (e.g. Echinococcus granulosus experimental infection in mice takes about 10 month to develop into cysts), this work was focused on Mesocestoides vogae (syn. corti), a non-human flatworm parasite which is an interesting laboratory model to study other flatworm infections: it is very rare in humans, can be easily manipulated both in vivo and in vitro and grows extremely fast in mice. With the aim to assess TGR inhibitors as possible drugs to treat flatworm infections, the thioredoxin and glutathione pathways of M.vogae were studied. Here, the objectives were to study whether the biochemical pathways that maintain the redox homeostasis in M. vogae conform to the general biochemical scenario proposed for other platyhelminth parasites.
Here, it was proven that M. vogae extracts possess both thioredoxin and glutathione reductase activities. The thioredoxin and glutathione reductase activities were partially purified from total extracts by a combination of ammonium sulfate precipitation, anion exchange and hydroxyapatite chromatography. Both activities co-purified in all steps which strongly indicates the existence of TGR rather than a single TR and GR. Furthermore partially purified activities could be inhibited by the organogold compound auranofin, a known TGR inhibitor. Moreover, the glutathione reductase activity displays hysteresis (a peculiar kinetic behavior) at high concentrations of oxidised glutathione, a feature typical of flatworm TGRs, but not of conventional GR. Although M. vogae activities could not be purified to homogeneity, the overall results strongly indicate that this flatworm possesses TGR and lacks conventional GR and TR.
Furthermore the thiadiazole WPQ75 and the N-oxide VL16E (a furoxan derivate) were identified as inhibitors of TGR activity of M.vogae at a 10 µM concentration. These inhibitors were able to kill M.vogae larval worms in vitro as well as in experimental infection in mice.
Due to the existence of TGR activity in M.vogae, the possibility to inhibit this activity with recently discovered inhibitors of flatworm TGR and the successes achieved by testing these inhibitors both in vitro and in vivo, it is strongly evident that M. vogae would be an excellent model to assess TGR inhibitors in flatworm infections.
Weltweit leben ca. 2,5 Mrd. Menschen im Dengue Virus Verbreitungsgebiet. Dengue Virus Infektionen führen zum Dengue Fieber und können bei Re-Infektionen
mit anderen Serotypen das sog. Dengue Schocksyndrom mit einer Letalität von 10% verursachen. Momentan stehen jedoch weder Impfstoffe noch antivirale Substanzen zur Verfügung.
In der vorliegenden Arbeit sollten DENV2-Proteaseinhibitoren entwickelt werden.
Dazu wurde ein in vitro DENV Proteasetest etabliert, für den die DENV Protease in Bakterien exprimiert und anschließend gereinigt wurde. Mit diesem System wurden 144 Verbindungen getestet und Diaryl-Thioether, Thiazole und Zimtsäurederivate als Dengue PIs charakterisiert. Ein Diarythioether (FM 47) wurde an die Proteasestruktur modelliert und nach den Strukturdaten zielgerichtet
derivatisiert. Diese Derivate ihibierten die Protease im mikromolaren Bereich und wurden anschließend in einer Zellkultur getestet. Drei Substanzen -
HWu 11, HWu 51, HWu 62 - zeigten gute bis sehr gute Hemmung in vivo bei 2,5 μM. Die Charakterisierung der Inhibitoren zeigte eine nicht-kompetitive Hemmung.
Die gefundenen Substanzen bilden eine gute Grundlage für die weitere Inhibitorforschung.
The infection of a eukaryotic host cell by a bacterial pathogen is one of the most intimate examples of cross-kingdom interactions in biology. Infection processes are highly relevant from both a basic research as well as a clinical point of view. Sophisticated mechanisms have evolved in the pathogen to manipulate the host response and vice versa host cells have developed a wide range of anti-microbial defense strategies to combat bacterial invasion and clear infections. However, it is this diversity and complexity that makes infection research so challenging to technically address as common approaches have either been optimized for bacterial or eukaryotic organisms. Instead, methods are required that are able to deal with the often dramatic discrepancy between host and pathogen with respect to various cellular properties and processes. One class of cellular macromolecules that exemplify this host-pathogen heterogeneity is given by their transcriptomes: Bacterial transcripts differ from their eukaryotic counterparts in many aspects that involve both quantitative and qualitative traits. The entity of RNA transcripts present in a cell is of paramount interest as it reflects the cell’s physiological state under the given condition. Genome-wide transcriptomic techniques such as RNA-seq have therefore been used for single-organism analyses for several years, but their applicability has been limited for infection studies.
The present work describes the establishment of a novel transcriptomic approach for infection biology which we have termed “Dual RNA-seq”. Using this technology, it was intended to shed light particularly on the contribution of non-protein-encoding transcripts to virulence, as these classes have mostly evaded previous infection studies due to the lack of suitable methods. The performance of Dual RNA-seq was evaluated in an in vitro infection model based on the important facultative intracellular pathogen Salmonella enterica serovar Typhimurium and different human cell lines. Dual RNA-seq was found to be capable of capturing all major bacterial and human transcript classes and proved reproducible. During the course of these experiments, a previously largely uncharacterized bacterial small non-coding RNA (sRNA), referred to as STnc440, was identified as one of the most strongly induced genes in intracellular Salmonella. Interestingly, while inhibition of STnc440 expression has been previously shown to cause a virulence defect in different animal models of Salmonellosis, the underlying molecular mechanisms have remained obscure. Here, classical genetics, transcriptomics and biochemical assays proposed a complex model of Salmonella gene expression control that is orchestrated by this sRNA. In particular, STnc440 was found to be involved in the regulation of multiple bacterial target mRNAs by direct base pair interaction with consequences for Salmonella virulence and implications for the host’s immune response. These findings exemplify the scope of Dual RNA-seq for the identification and characterization of novel bacterial virulence factors during host infection.
RNA-binding proteins (RBPs) have been extensively studied in eukaryotes, where they post-transcriptionally regulate many cellular events including RNA transport, translation, and stability. Experimental techniques, such as cross-linking and co-purification followed by either mass spectrometry or RNA sequencing has enabled the identification and characterization of RBPs, their conserved RNA-binding domains (RBDs), and the regulatory roles of these proteins on a genome-wide scale. These developments in quantitative, high-resolution, and high-throughput screening techniques have greatly expanded our understanding of RBPs in human and yeast cells. In contrast, our knowledge of number and potential diversity of RBPs in bacteria is comparatively poor, in part due to the technical challenges associated with existing global screening approaches developed in eukaryotes.
Genome- and proteome-wide screening approaches performed in silico may circumvent these technical issues to obtain a broad picture of the RNA interactome of bacteria and identify strong RBP candidates for more detailed experimental study. Here, I report APRICOT (“Analyzing Protein RNA Interaction by Combined Output Technique”), a computational pipeline for the sequence-based identification and characterization of candidate RNA-binding proteins encoded in the genomes of all domains of life using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences of an input proteome using position-specific scoring matrices and hidden Markov models of all conserved domains available in the databases and then statistically score them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them according to functionally relevant structural properties. APRICOT performed better than other existing tools for the sequence-based prediction on the known RBP data sets. The applications and adaptability of the software was demonstrated on several large bacterial RBP data sets including the complete proteome of Salmonella Typhimurium strain SL1344. APRICOT reported 1068 Salmonella proteins as RBP candidates, which were subsequently categorized using the RBDs that have been reported in both eukaryotic and bacterial proteins. A set of 131 strong RBP candidates was selected for experimental confirmation and characterization of RNA-binding activity using RNA co-immunoprecipitation followed by high-throughput sequencing (RIP-Seq) experiments. Based on the relative abundance of transcripts across the RIP-Seq libraries, a catalogue of enriched genes was established for each candidate, which shows the RNA-binding potential of 90% of these proteins. Furthermore, the direct targets of few of these putative RBPs were validated by means of cross-linking and co-immunoprecipitation (CLIP) experiments.
This thesis presents the computational pipeline APRICOT for the global screening of protein primary sequences for potential RBPs in bacteria using RBD information from all kingdoms of life. Furthermore, it provides the first bio-computational resource of putative RBPs in Salmonella, which could now be further studied for their biological and regulatory roles. The command line tool and its documentation are available at https://malvikasharan.github.io/APRICOT/.
The human-bacterial pathogen interaction is a complex process that results from
a prolonged evolutionary arms race in the struggle for survival. The pathogen employs
virulence strategies to achieve host colonization, and the latter counteracts using defense
programs. The encounter of both organisms results in drastic physiological changes
leading to stress, which is an ancient response accompanying infection. Recent evidence
suggests that the stress response in the host converges with the innate immune pathways
and influences the outcome of infection. However, the contribution of stress and the exact
mechanism(s) of its involvement in host defense remain to be elucidated. Using the model
bacterial pathogen Shigella flexneri, and comparing it with the closely related pathogen
Salmonella Typhimurium, this study investigated the role of host stress in the outcome of
infection.
Shigella infection is characterized by a pronounced pro-inflammatory response
that causes intense stress in host tissues, particularly the intestinal epithelium, which
constitutes the first barrier against Shigella colonization. In this study, inflammatory
stress was simulated in epithelial cells by inducing oxidative stress, hypoxia, and cytokine
stimulation. Shigella infection of epithelial cells exposed to such stresses was strongly
inhibited at the adhesion/binding stage. This resulted from the depletion of sphingolipidrafts
in the plasma membrane by the stress-activated sphingomyelinases. Interestingly,
Salmonella adhesion was not affected, by virtue of its flagellar motility, which allowed the
gathering of bacteria at remaining membrane rafts. Moreover, the intracellular replication
of Shigella lead to a similar sphingolipid-raft depletion in the membrane across adjacent
cells inhibiting extracellular bacterial invasion.
Additionally, this study shows that Shigella infection interferes with the host stress
granule-formation in response to stress. Interestingly, infected cells exhibited a nuclear
depletion of the global RNA-binding stress-granule associated proteins TIAR and TIA-1
and their accumulation in the cytoplasm.
Overall, this work investigated different aspects of the host stress-response in the
defense against bacterial infection. The findings shed light on the importance of the host
stress-pathways during infection, and improve the understanding of different strategies
in host-pathogen interaction.
Development and application of computational tools for RNA-Seq based transcriptome annotations
(2019)
In order to understand the regulation of gene expression in organisms, precise genome annotation is essential. In recent years, RNA-Seq has become a potent method for generating and improving genome annotations. However, this Approach is time consuming and often inconsistently performed when done manually. In particular, the discovery of non-coding RNAs benefits strongly from the application of RNA-Seq data but requires significant amounts of expert knowledge and is labor-intensive. As a part of my doctoral study, I developed a modular tool called ANNOgesic that can detect numerous transcribed genomic features, including non-coding RNAs, based on RNA-Seq data in a precise and automatic fashion with a focus on bacterial and achaeal species. The software performs numerous analyses and generates several visualizations. It can generate annotations of high-Resolution that are hard to produce using traditional annotation tools that are based only on genome sequences. ANNOgesic can detect numerous novel genomic Features like UTR-derived small non-coding RNAs for which no other tool has been developed before. ANNOgesic is available under an open source license (ISCL) at https://github.com/Sung-Huan/ANNOgesic.
My doctoral work not only includes the development of ANNOgesic but also its application to annotate the transcriptome of Staphylococcus aureus HG003 - a strain which has been a insightful model in infection biology. Despite its potential as a model, a complete genome sequence and annotations have been lacking for HG003. In order to fill this gap, the annotations of this strain, including sRNAs and their functions, were generated using ANNOgesic by analyzing differential RNA-Seq data from 14 different samples (two media conditions with seven time points), as well as RNA-Seq data generated after transcript fragmentation. ANNOgesic was
also applied to annotate several bacterial and archaeal genomes, and as part of this its high performance was demonstrated. In summary, ANNOgesic is a powerful computational tool for RNA-Seq based annotations and has been successfully applied to several species.
The expression of genetic information into proteins is a key aspect of life. The efficient and exact regulation of this process is essential for the cell to produce the correct amounts of these effector molecules to a given situation. For this purpose, eukaryotic cells have developed many different levels of transcriptional and posttranscriptional gene regulation. These mechanisms themselves heavily rely on interactions of proteins with associated nucleic acids. In the case of posttranscriptional gene regulation an orchestrated interplay between RNA-binding proteins, messenger RNAs (mRNA), and non-coding RNAs is compulsory to achieve this important function.
A pivotal factor hereby are RNA secondary structures. One of the most stable and diverse representatives is the G-quadruplex structure (G4) implicated in many cellular mechanisms, such as mRNA processing and translation. In protein biosynthesis, G4s often act as obstacles but can also assist in this process. However, their presence has to be tightly regulated, a task which is often fulfilled by helicases.
One of the best characterized G4-resolving factors is the DEAH-box protein DHX36. The in vitro function of this helicase is extensively described and individual reports aimed to address diverse cellular functions as well. Nevertheless, a comprehensive and systems-wide study on the function of this specific helicase was missing, so far.
The here-presented doctoral thesis provides a detailed view on the global cellular function of DHX36. The binding sites of this helicase were defined in a transcriptome-wide manner, a consensus binding motif was deviated, and RNA targets as well as the effect this helicase exerts on them were examined. In human embryonic kidney cells, DHX36 is a mainly cytoplasmic protein preferentially binding to G-rich and G4-forming sequence motifs on more than 4,500 mRNAs. Loss of DHX36 leads to increased target mRNA levels whereas ribosome occupancy on and protein output of these transcripts are reduced. Furthermore, DHX36 knockout leads to higher RNA G4 levels and concomitant stress reactions in the cell. I hypothesize that, upon loss of this helicase, translationally-incompetent structured DHX36 target mRNAs, prone to localize in stress granules, accumulate in the cell. The cell reacts with basal stress to avoid cytotoxic effects produced by these mis-regulated and structured transcripts.
Complex formation between macromolecules constitutes the foundation of most cellular processes. Most known complexes are made up of two or more proteins interacting in order to build a functional entity and therefore enabling activities which
the single proteins could otherwise not fulfill. With the increasing knowledge about
noncoding RNAs (ncRNAs) it has become evident that, similar to proteins, many of
them also need to form a complex to be functional. This functionalization is usually executed by specific or global RNA-binding proteins (RBPs) that are specialized
binders of a certain class of ncRNAs. For instance, the enterobacterial global RBPs
Hfq and ProQ together bind >80 % of the known small regulatory RNAs (sRNAs),
a class of ncRNAs involved in post-transcriptional regulation of gene expression.
However, identification of RNA-protein interactions so far was performed individually by employing low-throughput biochemical methods and thereby hindered the discovery of such interactions, especially in less studied organisms such
as Gram-positive bacteria. Using gradient profiling by sequencing (Grad-seq), the
present thesis aimed to establish high-throughput, global RNA/protein complexome resources for Escherichia coli and Streptococcus pneumoniae in order to provide a
new way to investigate RNA-protein as well as protein-protein interactions in these
two important model organisms.
In E. coli, Grad-seq revealed the sedimentation profiles of 4,095 (∼85 % of
total) transcripts and 2,145 (∼49 % of total) proteins and with that reproduced
its major ribonucleoprotein particles. Detailed analysis of the in-gradient distribution of the RNA and protein content uncovered two functionally unknown
molecules—the ncRNA RyeG and the small protein YggL—to be ribosomeassociated. Characterization of RyeG revealed it to encode for a 48 aa long, toxic protein that drastically increases lag times when overexpressed. YggL was shown to
be bound by the 50S subunit of the 70S ribosome, possibly indicating involvement
of YggL in ribosome biogenesis or translation of specific mRNAs.
S. pneumoniae Grad-seq detected 2,240 (∼88 % of total) transcripts and 1,301
(∼62 % of total) proteins, whose gradient migration patterns were successfully reconstructed, and thereby represents the first RNA/protein complexome resource
of a Gram-positive organism. The dataset readily verified many conserved major
complexes for the first time in S. pneumoniae and led to the discovery of a specific
interaction between the 3’!5’ exonuclease Cbf1 and the competence-regulating ciadependent sRNAs (csRNAs). Unexpectedly, trimming of the csRNAs by Cbf1 stabilized the former, thereby promoting their inhibitory function. cbf1 was further shown
to be part of the late competence genes and as such to act as a negative regulator of
competence.
Neisseria meningitidis (N. meningitidis) is a human commensal that occasionally causes life-threatening infections such as bacterial meningitis and septicemia. Despite experi-mental evidence that the expression of small non-coding RNAs (sRNAs) as well as the RNA chaperone Hfq affect meningococcal physiology, the impact of RNA-based regula-tion (riboregulation) on fitness and virulence in N. meningitidis is only poorly understood. Therefore, this study addressed these issues using a combination of high-throughput tech-nologies.
A differential RNA-sequencing (dRNA-seq) approach was applied to produce a single-nucleotide resolution map of the primary transcriptome of N. meningitidis strain 8013. The dRNA-seq analysis predicted 1,625 transcriptional start sites including 65 putative sRNAs, of which 20 were further validated by northern blot analysis. By Hfq RNA im-munopreci-pitation sequencing a large Hfq-centered post-transcriptional regulatory net-work comprising 23 sRNAs and 401 potential mRNA targets was identified. Rifampicin stability assays demonstrated that Hfq binding confers enhanced stability on its associat-ed sRNAs. Based on these data, the interactions of two paralogous sRNAs and their cog-nate target mRNA prpB were validated in vivo as well as in vitro. Both sRNAs directly repress prpB encoding a methylisocitrate lyse which was previously shown to be involved in meningococcal colonization of the human nasopharynx.
Besides the well-described RNA chaperone Hfq, FinO-domain proteins have recently been recognized as a widespread family of RNA-binding proteins (RBPs) with regulatory roles in diverse bacteria. They display an intriguing bandwidth of target sites, ranging from a single RNA pair as recognized by plasmid-encoded FinO to the global RNA regu-lons of enterobacterial ProQ proteins. To better understand the intrinsic targeting mode of this RBP family, in vivo targets of the minimal ProQ protein of N. meningitidis were de-termined. In vivo UV crosslinking with RNA deep sequencing (UV-CLIP) identified as-sociations of ProQ with 16 sRNAs and 166 mRNAs encoding a variety of biological functions and thus revealed ProQ as another global RBP in meningococci. It could be shown that meningococcal ProQ predominantly binds to highly structured RNA regions including DNA uptake sequences (DUS) and rho-independent transcription terminators and stabilizes many of its RNA targets as proved by rifampicin stability experiments. As expected from the large suite of ProQ-bound RNAs, proQ deletion globally affects both gene and protein expression in N. meningitidis, changing the expression levels of at least 244 mRNAs and 80 proteins. Phenotypic analyses suggested that ProQ promotes oxida-tive stress tolerance and UV damage repair capacity, both of which are required for full virulence of N. meningitidis.
Together, this work uncovers the co-existence of two major post-transcriptional regulons, one governed by ProQ, the other by Hfq, in N. meningitidis. It further highlights the role of these distinct RBPs and its associated sRNAs to bacterial virulence and indicates that riboregulation is likely to contribute to the way how meningococci adapt to different host niches.