EtransColi: A multidisciplinary study of Escherichia coli's trans-translation regulation under stress conditions

• Applicant: Dr. Adelaide Raguin
• Subject Area: Bioinformatics and Theoretical Biology
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 470067901

EtransColi is a multidisciplinary project that integrates experiments and computational modelling in a Systems Biology approach. Our aim is to understand how trans-translation regulates protein production by degrading mRNAs where stalled ribosomes are detected. We will establish new fundamental knowledge on the mechanistics and kinetics of this regulatory process, and we will demonstrate the ability of our computational model to predict recombinant protein expression, in order to design genes of improved expression. The project is organised in three phases to progressively elaborate the predictive strength of the model. We will first calibrate the model to E. Coli grown under normal conditions, then we will mimic a sudden acute starvation stress by chemically depleting charged tRNAs, and finally we will predict recombinant protein expression, which is also a milder amino acid stress. In this last step, the recombinant expression of high value human antibodies will be tested. The project will deliver pioneering knowledge and a powerful theoretical tool based on stochastic simulations, which will be fully calibrated with experimental data. We will implement most advanced programming methods to develop a model with unprecedented simulation efficiency and accuracy. In the model, detailed translation processes will be described for the complete set of E. coli mRNAs, and resolved at the codon scale. Trans-translation is ubiquitous in bacteria, analogous to ribosome rescue processes in yeast and mammals, and it has recently emerged as an antibiotic target. As the model will be freely and openly shared, we thus expect great reuse and interest. An important part of the project will be the training of a PhD student, so we have designed the EtransColi project such that they will benefit from close collaboration with theory, while being trained on cutting-edge experimental techniques. The various specific methods of the project will be supported by a broad team of committed and enthusiastic partners.

• DFG Programme: Research Grants
• Co-Investigator: Professorin Dr. Zoya Ignatova