Pathogen-host interaction - from bacterial secretome analysis to host metabolomics

Chlamydiae are intracellular bacteria that live inside eukaryotic host cells and comprise pathogens of humans and animals as well as symbionts of protists. This lifestyle requires intimate and orchestrated interactions with the respective hosts. Within the scope of this project, these bacteria and their host interplay were analyzed using a variety of state-of-the-art methods, ranging from genome and transcriptome analyses to metabolomics and the targeted analysis of protein-protein interactions. As part of the ERA-NET consortium Pathomics, we mainly focused our work on environmental chlamydiae such as the amoeba symbiont Protochlamydia amoebophila. Thus, our data complemented the analysis of other network partners who worked on chlamydial species infecting humans. This collaborative effort provided novel insights into the genetic basis and the molecular biology of different chlamydial species and the interaction with their respective host cells, and it illustrated not only commonalities but also differences between the diverse chlamydial organisms. For instance, we could show that Clavichlamydia salmonicola, a chlamydial species detected in the gills of salmonid fish is, like all known chlamydiae, an energy parasite highly dependent on their host. However, these bacteria are special as their metabolic capabilities are significantly more truncated than those of their relatives. Clavichlamydia salmonicola represents a unique case of host dependency among intracellular bacteria. The extracellular, infectious form of chlamydiae has been described as representing a metabolically inert, spore-like life stage. We demonstrated that this form of Protochlamydia amoebophila is in fact metabolically active. Challenging long-standing textbook knowledge, we could show that this activity is absolutely essential for a successful infection of new host cells, not only in Protochlamydia amoebophila but also in the human pathogen Chlamydia trachomatis. The life cycle of Protochlamydia amoebophila and the alternation between the extracellular infections form and the intracellular replicating form was further analysed by sequencing of RNA transcripts during infection. This transcriptome sequencing approach provided a first global view on differential gene expression during the Protochlamydia amoebophila infection cycle, as well as on the response of the amoebal host cell. This approach was complemented by the analysis of regulatory RNAs among different chlamydial species, representing the first targeted survey for small RNAs among chlamydial species. Taken together, our data contribute to a better understanding of chlamydiae, their lifestyle, and their interplay with their eukaryotic hosts.