Development of synthetic, methylation based, epigenetic gene circuits

• Applicants: Professor Dr. Albert Jeltsch; Professorin Dr. Nicole Radde
• Subject Area: Bioinformatics and Theoretical Biology ; Biochemistry
• Term: since 2018
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 401437149

In the previous grant period, we have developed and characterized artificial bacterial memory circuits, which behave as bistable switches with positive feedback and use DNA methylation to store biological input information. Potential applications of such synthetic epigenetic memory systems are manifold and include the development of bacteria that could be used as live sensors to monitor environmental pollution next to production sites or atomic power plants, or passage through the human body and collect input about disease markers and metabolic states. We aim here to further develop fundamental properties of these epigenetic memory systems to improve their potential applicability. For this, we will implement novel input systems able to detect radioactivity, fluoride and theophylline, and integrate riboswitches as new input components. To collect many different input signals and carry out basic input processing, additional DNA methyltransferases shall be integrated. This will allow us to store information of different input signals in different DNA methylation codes in one bacterial cell. The different input channels will be combined to generate logic gates exhibiting AND or OR behavior. We aim to use quantitative dynamic modelling both at the bulk level and at the level of single cells as a powerful tool to facilitate the mechanistic understanding of regulation principles, information processing and storage by epigenetic circuits thereby supporting the entire design and implementation cycle. Our work will further pave the way towards the application of designer bacteria containing synthetic, epigenetic circuits in the detection of biological signals as live biosensors, storing the information in DNA methylation patterns as bacterial storage devices, and performing initial data processing as bacterial microprocessors. Our project is based on a close collaboration between the Jeltsch and Radde groups for advanced biochemical studies combined with expert modelling that was established in the last grant period. As in the previous application, the Jeltsch group will be mainly responsible for the experimental parts of this application. They will closely interact with the Radde group by basing experimental studies on predictions from modelling and providing experimental data, like FACS data and absolute cellular concentrations of relevant molecules and plasmids, which are needed to develop and improve modelling. The Radde group is responsible for the modelling part of the project, aiming to support the detailed understanding of the underlying mechanisms of the epigenetic memory systems at molecular level. Modelling results will provide valuable insights for the design and improvement of these systems, in particular, for the case of combining modules towards processing and storing multi-input information as logical gates.

• DFG Programme: Research Grants