Acidification of the cytoplasm as a poorly understood stimulus for the activation of acid stress adaptation in Escherichia coli

• Applicant: Professorin Dr. Kirsten Jung
• Subject Area: Metabolism, Biochemistry and Genetics of Microorganisms
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 471254198

On Earth, there are many habitats that have a low pH, such as the gastrointestinal tract of vertebrates or areas with acidic soils. Although most bacteria are neutralophiles, they are able to survive in acidic environments. Acid stress sensing and adaptation allow these bacteria to maintain a constant intracellular pH under moderate acid stress. However, under strong acid stress, the intracellular pH of neutralophilic bacteria decreases by approximately one pH unit, which has a considerable impact on the protonation states of all biological molecules, and can affect their charge, structure and function. In the preliminary work for this project, we have gained evidence that this acidification of the cytoplasm of Escherichia coli is used as stimulus to activate regulatory processes that contribute to acid stress resistance. The aim of the project is to identify and characterize regulators that become active in response to a fall in the pH of the cytoplasm.To achieve this goal, we have divided the project into two parts. In the first part, we will apply a systemic approach to quantify cellular changes in response to the strength of acid stress. Based on our preliminary work, we will perform ribosome profiling to measure the changes in the rates of synthesis of all proteins and thus determine their copy numbers per cell. We will then characterize all newly identified regulators and ascertain their cellular functions under acid stress. In the second part of the project, we plan an in-depth characterization of the transcription factor AdiY, the activator of the Adi system in E. coli, which is activated upon acidification of the cytoplasm. The investigations focus on pH-dependent structure-function studies and the identification of the ligand that binds to AdiY. Furthermore, we will test the exciting hypothesis that increased protonation enables AdiY to find its binding sites faster by promoting 1D sliding along the DNA. With the investigations on the molecular characterisation of the cellular processes as a result of an acidification of the cytoplasm, we focus on a poorly understood stimulus in the acid stress adaptation of E. coli, as a representative of the Gram-negative bacteria.

• DFG Programme: Research Grants