Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host–pathogen transcriptomes

Abstract

Pathogenic bacteria need to rapidly adjust their virulence and fitness program to prevent eradication by the host. So far, underlying adaptation processes that drive pathogenesis have mostly been studied in vitro, neglecting the true complexity of host-induced stimuli acting on the invading pathogen. In this study, we developed an unbiased experimental approach that allows simultaneous monitoring of genome-wide infection-linked transcriptional alterations of the host and colonizing extracellular pathogens. Using this tool for Yersinia pseudotuberculosis-infected lymphatic tissues, we revealed numerous alterations of host transcripts associated with inflammatory and acute-phase responses, coagulative activities, and transition metal ion sequestration, highlighting that the immune response is dominated by infiltrating neutrophils and elicits a mixed T H 17/T H 1 response. In consequence, the pathogen's response is mainly directed to prevent phagocytic attacks. Yersinia up-regulates the gene and expression dose of the antiphagocytic type III secretion system (T3SS) and induces functions counteracting neutrophil-induced ion deprivation, radical stress, and nutritional restraints. Several conserved bacterial riboregulators were identified that impacted this response. The strongest influence on virulence was found for the loss of the carbon storage regulator (Csr) system, which is shown to be essential for the up-regulation of the T3SS on host cell contact. In summary, our established approach provides a powerful tool for the discovery of infection-specific stimuli, induced host and pathogen responses, and underlying regulatory processes.tissue dual RNA-seq | host-pathogen interaction | host-adapted metabolism | noncoding RNAs | Yersinia

Chemical and Biological Aspects of Nutritional Immunity—Perspectives for New Anti‐Infectives that Target Iron Uptake Systems

“…Whereas pathogens can adapt central metabolic pathways to the respective available carbon and nitrogen sources,h osts have developed efficient means to limit the availability of essential metal ions.This is reflected in in vivo transcriptomic studies of bacteria from infection sites of animal models.T he bacteria in these studies showed astress response to metal-ion limitation. [5][6][7] Thebest studied example is the dependence of pathogens on iron, [8] and so most research approaches aiming at exploiting nutritional immunity as atherapeutic target address the iron acquisition systems.T his is the reason why iron acquisition systems and their respective chemical inhibitors are described predominantly in this Review,b ut where possible we also include chemical approaches to influence the uptake of other metal ions.F or various other aspects related to nutritional immunity,t he recent reviews on microbiological aspects, [9,10] the coordination chemistry of siderophores, [11] environmental applications of siderophores, [12] zinc homeostasis, [9,13] and the chemical synthesis of antibacterials [14] are highly recommended. More specific reviews can be found in the following chapters.…”

Chemische und biologische Aspekte von “Nutritional Immunity” – Perspektiven für neue Antiinfektiva mit Fokus auf bakterielle Eisenaufnahmesysteme

“…Baulamycin A( 5a)i st die aktivere der beiden Substanzen und inhibiert die Enzyme AsbA und SbnE mit IC 50 -Werten von 180 mm und 4.8 mm (Abbildung 4). Diese Enzyme katalysieren die Konjugation von Spermidin (9)oder l-2,3-Diaminopropionsäure (10)m it Citrat (8)w ährend der Biosynthese der Siderophore Staphyloferrin (6)u nd Petrobactin (7).…”

“…[5][6][7] Das am besten studierte Beispiel ist die Abhängigkeit von Pathogenen von Eisen, [8] sodass die meisten Forschungsansätze,d ie die Ausnutzung der Nährstoffimmunitätf ürt herapeutische Ansätze zum Ziel haben, sich mit Eisenaufnahmesystemen beschäftigen. Daher gehçrt es zur ersten Verteidigungsstrategie des Wirtes gegen Infektionen, dem Pathogen Nährstoffe zu entziehen, ein Phänomen, das als Nährstoffimmunitäto der "nutritional immunity" bezeichnet wird.…”

“…In ihnen wird häufig die Stressantwort der Bakterien auf eine begrenzte Metallionenverfügbarkeit sichtbar. [5][6][7] Das am besten studierte Beispiel ist die Abhängigkeit von Pathogenen von Eisen, [8] sodass die meisten Forschungsansätze,d ie die Ausnutzung der Nährstoffimmunitätf ürt herapeutische Ansätze zum Ziel haben, sich mit Eisenaufnahmesystemen beschäftigen. Diese und die entsprechenden chemischen Inhibitoren bilden daher den Schwerpunkt in diesem Aufsatz.…”

Omics in Aid of Host-pathogen Interaction Studies: A Bacterial Perspective

“…In another study, Peyer's patches from mice infected with Yersinia pseudotuberculosis were analyzed [52]. In both examples, infected tissues were isolated and homogenized prior to total RNA extraction for sequencing.…”