Global mapping of second messenger c-di-GMP signaling networks in bacteria using proteomics

Project Information

SNiB-cdG-P

Grant agreement ID: 101024238

DOI

10.3030/101024238

Project closed

EC signature date 22 February 2021

Start date 1 March 2021

End date 28 February 2023

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 191 149,44

EU contribution

€ 191 149,44

Coordinated by

UNIVERSITAT BASEL
Switzerland

Periodic Reporting for period 1 - SNiB-cdG-P (Global mapping of second messenger c-di-GMP signaling networks in bacteria using proteomics)

Reporting period: 2021-03-01 to 2023-02-28

Summary of the context and overall objectives of the project

Bacteria are masters in sensing environmental cues and in processing this information to adequately adjust their behavior. A key element of bacterial signal transduction is the nucleotide second messenger cyclic di-guanosine-monophosphate (c-di-GMP). This powerful signalling molecule acts in minute amounts to control important cellular functions, such as motility, biofilm formation, or bacterial virulence and persistence. Despite of its global importance in regulating bacterial growth and behavior, studies systematically investigating the c-di-GMP network in bacteria are missing. To address this, the project aimed to employ recently developed quantitative proteomics techniques to identify and characterize proteins involved in c-di-GMP signaling pathways in bacterial model organisms.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

For this project, we adapted and optimised a quantitative proteomics method called thermal proteome profiling (TPP) to study c-di-GMP signalling in two bacterial model organisms, Escherichia coli and Caulobacter crescentus. Recording differential thermal stability of proteins at different intracellular concentrations of c-di-GMP levels not only uncovered known c-di-GMP pathway proteins but also generated datasets with novel candidate proteins and pathways regulated by c-di-GMP. The generated new hypothesis include the involvement of c-di-GMP in biological processes important for bacterial survival, such as bacterial surface attachment and stress response.

We are currently in the process of publishing these findings and depositing the data in an open access format.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

In this project we have successfully adapted TTP technology to the investigation of a small molecule-based signaling network in different bacteria in vivo. By establishing a robust technology to globally investigate the interaction of proteins with their small-molecule ligands, we have provided a highly useful experimental tool for researchers in similar fields. We are confident that this technique will have an impact and will be used by other scientists in the field of microbiology and beyond. At the same time, we have generated high-quality datasets of proteins directly or indirectly interacting with c-di-GMP. This is a highly valuable resource for the field and provides a direct entry point into mechanistic follow-up studies that will help uncover this prototypical bacterial signaling systems and by that contribute to a better understanding of bacterial growth and growth control.

Thermal Proteome Profiling for bacterial second messenger c-di-GMP