TY - JOUR A1 - Karl, Stefan A1 - Dandekar, Thomas T1 - Convergence behaviour and control in non-linear biological networks JF - Scientific Reports N2 - Control of genetic regulatory networks is challenging to define and quantify. Previous control centrality metrics, which aim to capture the ability of individual nodes to control the system, have been found to suffer from plausibility and applicability problems. Here we present a new approach to control centrality based on network convergence behaviour, implemented as an extension of our genetic regulatory network simulation framework Jimena (http://stefan-karl.de/jimena). We distinguish three types of network control, and show how these mathematical concepts correspond to experimentally verified node functions and signalling pathways in immunity and cell differentiation: Total control centrality quantifies the impact of node mutations and identifies potential pharmacological targets such as genes involved in oncogenesis (e.g. zinc finger protein GLI2 or bone morphogenetic proteins in chondrocytes). Dynamic control centrality describes relaying functions as observed in signalling cascades (e.g. src kinase or Jak/Stat pathways). Value control centrality measures the direct influence of the value of the node on the network (e.g. Indian hedgehog as an essential regulator of proliferation in chondrocytes). Surveying random scale-free networks and biological networks, we find that control of the network resides in few high degree driver nodes and networks can be controlled best if they are sparsely connected. KW - complex networks KW - control profiles KW - differentiation KW - pathways KW - tumors KW - models KW - centrality KW - chondrosarcoma KW - transcriptional regulation KW - regulatory networks Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148510 VL - 5 IS - 09746 ER - TY - JOUR A1 - Groma, Michaela A1 - Horst, Sarah A. A1 - Das, Sudip A1 - Huettel, Bruno A1 - Klepsch, Maximilian A1 - Rudel, Thomas A1 - Medina, Eva A1 - Fraunholz, Martin T1 - Identification of a Novel LysR-Type Transcriptional Regulator in Staphylococcus aureus That Is Crucial for Secondary Tissue Colonization during Metastatic Bloodstream Infection JF - mbio N2 - Staphylococcus aureus is a common cause of bacteremia that can lead to severe complications once the bacteria exit the bloodstream and establish infection in secondary organs. Despite its clinical relevance, little is known about the bacterial factors facilitating the development of these metastatic infections. Here, we used an S. aureus transposon mutant library coupled to transposon insertion sequencing (Tn-Seq) to identify genes that are critical for efficient bacterial colonization of secondary organs in a murine model of metastatic bloodstream infection. Our transposon screen identified a LysR-type transcriptional regulator (LTTR), which was required for efficient colonization of secondary organs such as the kidneys in infected mice. The critical role of LTTR in secondary organ colonization was confirmed using an isogenic mutant deficient in the expression of LTTR. To identify the set of genes controlled by LTTR, we used an S. aureus strain carrying the LTTR gene in an inducible expression plasmid. Gene expression analysis upon induction of LTTR showed increased transcription of genes involved in branched-chain amino acid biosynthesis, a methionine sulfoxide reductase, and a copper transporter as well as decreased transcription of genes coding for urease and components of pyrimidine nucleotides. Furthermore, we show that transcription of LTTR is repressed by glucose, is induced under microaerobic conditions, and required trace amounts of copper ions. Our data thus pinpoints LTTR as an important element that enables a rapid adaptation of S. aureus to the changing host microenvironment. IMPORTANCE Staphylococcus aureus is an important pathogen that can disseminate via the bloodstream and establish metastatic infections in distant organs. To achieve a better understanding of the bacterial factors facilitating the development of these metastatic infections, we used in this study a Staphylococcus aureus transposon mutant library in a murine model of intravenous infection, where bacteria first colonize the liver as the primary infection site and subsequently progress to secondary sites such as the kidney and bones. We identified a novel LysR-type transcriptional regulator (LTTR), which was specifically required by S. aureus for efficient colonization of secondary organs. We also determined the transcriptional activation as well as the regulon of LTTR, which suggests that this regulator is involved in the metabolic adaptation of S. aureus to the host microenvironment found in secondary infection sites. KW - Staphylococcus aureus KW - metabolic adaptation KW - secondary site infection KW - transcriptional regulation Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230473 VL - 11 IS - 4 ER - TY - THES A1 - Groma, Michaela T1 - Identification of a novel LysR-type transcriptional regulator in \(Staphylococcus\) \(aureus\) T1 - Identifizierung eines neuen Transkriptionsregulators vom LysR-Typ in \(Staphylococcus\) \(aureus\) N2 - Staphylococcus aureus is a facultative pathogen which causes a variety of infections. The treatment of staphylococcal infections is complicated because the bacteria is resistant to multiple common antibiotics. S. aureus is also known to express a variety of virulence factors which modulate the host’s immune response in order to colonize and invade certain host cells, leading to the host cell’s death. Among the virulence factors is a LysR-type transcriptional regulator (lttr) which is required for efficient colonization of secondary organs. In a recent report, which used transposon screening on S. aureus-infected mice, it was found that the amount of a novel lttr852 mutant bacteria recovered from the kidneys was significantly lower compared to the wildtype strains. This doctoral thesis therefore focused on phenotypical and molecular characterization of lttr852. An assessment of the S. aureus biofilm formation and the hemolysis revealed that lttr852 was not involved in the regulation of these virulence processes. RNA-sequencing for potential target genes of lttr852 identified differentially expressed genes that are involved in branched chain amino-acid biosynthesis, methionine sulfoxide reductase and copper transport, as well as a reduced transcription of genes encoding urease and of components of pyrimidine nucleotides. Promoter fusion with GFP reporters as as well as OmniLog were used to identify conditions under which the lttr852 was active. The promoter studies showed that glucose and high temperatures diminish the lttr852 promoter activity in a time-dependent manner, while micro-aerobic conditions enhanced the promoter activity. Copper was found to be a limiting factor. In addition, the impact on promoter activity of the lttr852 was tested in the presence of various regulators, but no central link to the genes involved in virulence was identified. The present work, thus, showed that lttr852, a new member of the class of LysR-type transcriptional regulators in S. aureus, has an important role in the rapid adaptation of S. aureus to the changing microenvironment of the host. N2 - Staphylococcus aureus ist ein fakultativer Erreger, der eine Vielzahl von Infektionen verursacht. Die Behandlung von Staphylokokken-Infektionen ist aufgrund des Auftretens einer Resistenz gegen mehrere gängige Antibiotika kompliziert. Es ist bekannt, dass S. aureus eine Vielzahl von Virulenzfaktoren exprimiert, um die Immunantwort des Wirts zu umgehen, und so in bestimmte Wirtszellen einzudringen und diese zu kolonisieren, was zum Tod von Wirtszellen führen kann. Unter den Virulenzfaktoren befindet sich ein Transkriptions-regulator vom LysR-Typ (lttr), der für eine effiziente Besiedlung von Sekundärorganen erforderlich ist. In einem kürzlich durchgeführten Transposon-Screen, bei dem Mäuse mit S. aureus infiziert wurden, wurde ein neuartiger lttr, der lttr852 identifiziert, bei dem aus den Nieren gewonnenen Bakterien signifikant dezimiert waren. Diese Doktorarbeit befasste sich mit der phänotypischen und molekularen Charakterisierung von lttr852. Die Auswertung der Biofilmbildung und der Hämolyse von S. aureus ergab, dass lttr852 nicht an der Regulation dieser Virulenzprozesse beteiligt war. Die RNA-Sequenzierung für potenzielle Zielgene von lttr852 identifizierte sowohl eine erhöhte Expression von Genen, die in der Aminosäuren-Biosynthese, Methionin-Sulfoxid-Reduktase und dem Kupfertransport involviert sind, als auch eine verringerte Transkription von codierenden Genen der Urease und Komponenten der Pyrimidin Nukleotide. Die Promotorfusion mit dem GFP-Reporter sowie das OmniLog System wurden verwendet, um Bedingungen zu identifizieren unter denen das lttr852 aktiv ist. Die Promotorstudien ergaben, dass die Anwesenheit von Glucose und eine erhöhte Temperatur die Promotoraktivität von lttr852 zeitabhängig herabsetzt, wobei die Aktivität durch mikroaerobe Bedingungen begünstigt wird. Kupfer wurde als limitierender Faktor identifiziert. Außerdem wurde der Einfluss diverser Regulatoren auf die transkriptionelle Regulation von lttr852 kontrolliert, jedoch keine zentrale Rolle in der Regulation von Virulenzgenen zugewiesen. Damit konnte innerhalb der vorliegenden Arbeit gezeigt werden, dass lttr852, ein neues Mitglied der Klasse der LysR-Typ Transkriptionsregulatoren in S. aureus, eine wichtige Rolle in der schnellen Adaption von S. aureus an die wechselnde Mikroumgebungen des Wirts hat. KW - Staphylococcus aureus KW - transcriptional regulation KW - metabolic adaptation KW - secondary site infection KW - LysR-type Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-246757 ER -