SYSTEMATIC INVESTIGATION OF QUORUM SENSING IN Escherichia coli

High throughput techniques and advanced mathematical tools have enabled systematic investigations of biological systems with unparalleled precision. Not only molecular interactions between components but mechanisms and the dynamic behaviors associated with these systems are revealed, suggesting that comprehensive systems biology can be realized in the near future. Quorum sensing, especially the auto-inducer2 (AI-2) system, has been extensively studied due to its commonality among bacteria and connections to pathogenic phenotypes. In this study, the E. coli quorum sensing AI-2 system was studied combing system-based mathematical modeling and high throughput genomic profiling. First, a Stochastic Petri Network (SPN) model was constructed based on available regulatory information. Simulations together with experimental data demonstrated that the apparent stimulation of AI-2 in the presence of glucose is not from the increased transcriptional or translational expression of AI-2 synthases luxS and pfs, nor from the increased metabolic flux associated with LuxS-related pathways but from an alternative AI-2 synthesis pathway. The conversion of adenosine with cellular extracts from both luxS and pfs mutants validated our prediction about the existence of an alternative non-LuxS related AI-2 synthesis pathway. Second, AI-2 uptake regulatory network was investigated in detail: lsrR-lacZ, lsrK-lacZ fusion reporters were constructed and the analysis found that lsrR is subject to its own repression and is induced by both lsrK and luxS. Further transcriptome analysis demonstrated that lsrR and lsrK, together with quorum signal AI-2, coregulate lsrRK regulon, which influences phenotypes (biofilm, small RNAs). Importantly, this regulation is in a distinctly different manner than that mediating the lsr operon. We hypothesize that lsrR acts together with AI-2 to mediate cellular processes and that the phosphorylation of AI-2 molecule through lsrK triggers different response pathways. These investigations demonstrated that lsrR, lsrK are indispensable for AI-2 uptake. These newly elucidated regulatory mechanisms and associations undoubtedly broaden the scope of the AI-2 quorum sensing system, and provide a solid foundation for further mathematical modeling of the dynamics and system behaviors in E. coli . Finally, a tight coupling of experimental manipulation with mathematical analysis, as demonstrated in this study, provides a good example for systematically investigating biological systems

Microbial stress. From sensing to intracellular and population responses

We initially devised this Research Topic (RT) as a valuable initiative to collect high-quality scientific articles from the participants of the 4th European Federation of Biotechnology (EFB) Microbial Stress meeting held in Kinsale, Ireland, April 2018. The scope of the RT is based on the scientific content of that “Microbial Stress: from Systems to Molecules and back” meeting. Indeed, over 40% of the articles eventually accepted for publication were contributed by meeting participants, but notably the remaining 60% was contributed by authors that work in this field. The collection of 22 original research and 2 review articles, contributed by 163 authors collectively, deal with the many different aspects of the microbial responses to biotic and abiotic stresses, relevant to many fields: from host-pathogen interactions to biotechnology, from bioremediation to food processing, from molecular and single-cell to population studies. The RT showcases the rapid developments of the microbial stress research on a range of microorganisms and stress conditions, and confirms that understanding microbial physiology under stress can be a trigger for the development of new methodologies as well as helping to integrate the knowledge from many different microbiological fields of research. The retrospective analysis of the articles contributed to this RT allowed them to be assigned to one of four main sub-topics: (i) impact of weak organic acids and low pH on micro-organisms, from clinical to biotechnological contexts; (ii) adaptive responses in microbial pathogens to abiotic/environmental stress; (iii) oxidative and metal stress, from clinical to bioremediation contexts, and (iv) regulation of transcription and translation under stress, from epigenetic aspects to the role of second messengers and sRNA

Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli

Bacteria have developed a repertoire of signalling mechanisms that enable adaptive responses to fluctuating environmental conditions. The formation of biofilm, for example, allows persisting in times of external stresses, e.g. induced by antibiotics or a lack of nutrients. Adhesive curli fibers, the major extracellular matrix components in Escherichia coli biofilms, exhibit heterogeneous expression in isogenic cells exposed to identical external conditions. The dynamical mechanisms underlying this heterogeneity remain poorly understood. In this work, we elucidate the potential role of post- translational bistability as a source for this heterogeneity. We introduce a structured modelling workflow combining logical network topology analysis with time-continuous deterministic and stochastic modelling. The aim is to evaluate the topological structure of the underlying signalling network and to identify and analyse model parameterisations that satisfy observations from a set of genetic knockout experiments. Our work supports the hypothesis that the phenotypic heterogeneity of curli expression in biofilm cells is induced by bistable regulation at the post-translational level. Stochastic modelling suggests diverse noise-induced switching behaviours between the stable states, depending on the expression levels of the c-di-GMP-producing (diguanylate cyclases, DGCs) and -degrading (phosphodiesterases, PDEs) enzymes and reveals the quantitative difference in stable c-di-GMP levels between distinct phenotypes. The most dominant type of behaviour is characterised by a fast switching from curli-off to curli-on with a slow switching in the reverse direction and the second most dominant type is a long-term differentiation into curli-on or curli-off cells. This behaviour may implicate an intrinsic feature of the system allowing for a fast adaptive response (curli-on) versus a slow transition to the curli-off state, in line with experimental observations. The combination of logical and continuous modelling enables a thorough analysis of different determinants of bistable regulation, i.e. network topology and biochemical kinetics, and allows for an incorporation of experimental data from heterogeneous sources. Our approach yields a mechanistic explanation for the phenotypic heterogeneity of curli fiber expression. Furthermore, the presented work provides a detailed insight into the interactions between the multiple DGC- and PDE-type enzymes and the role of c-di-GMP in dynamical regulation of cellular decisions

Contributions to the Mathematical Systems Medicine of Antimicrobial Therapy and Genotype-Phenotype Inference.

The following summary of my publications describes the main ideas in the corresponding research articles and clarfifies my contribution in multi-author publications. I decided to apply for habilitation according to x2.I.1.(c) of the Habilitationsordnung (this path is usually referred as Kumulative Habilitation"). I selected 13 first- or last author publications for this habilitation that concern contributions to the mathematical systems medicine of antiviral therapy [tMH10, tMS+11, FtK+11, tMMS12, DSt12, DWSt15, Dt16, DSt16, DDKt18, DSD+19, DDKt19], as well as inference of genotype-phenotype associations [SDH+15, SSJ+18]. The selected publications represent my major contributions in this research eld since submitting my doctoral thesis in September 2009