PHD2020-03
Distribution and dynamics of energy-conserving processes in bacteria
Host laboratory and collaborators
Didier Marguet / CIML / marguet@ciml.univ-mrs.fr
Axel Magalon / LCB / magalon@imm.cnrs.fr
Abstract
Compartmentalization and the emergence of physical barriers are fundamental parts of life and have been crucial steps in the evolution process. Despite decades of studies, how oxidative phosphorylation (OXPHOS) is spatially and temporally organized in the membrane to account for efficient energy conservation is largely unknown. We have recently evidenced that several membrane-associated OXPHOS complexes are unevenly distributed in the bacterial cell. The overarching goal of this project is to deepen our knowledge about OXPHOS organization in bacterial cells and gain molecular-level understanding of the biological importance of spatiotemporal organization on OXPHOS. To this end, the candidate will develop and use spatially and temporally resolutive high end fluorescence microscopy approaches at the single cell level. These measurements will be combined with computational tools and feed theoretical models to delineate how dynamic spatial organization impacts OXPHOS outcome.
Keywords
Bioenergetics; Biophysics; Fluorescence; Image data processing; computational analysis; Molecular interactions
Objectives
The objectives of this project aiming at investigating the mechanisms behind OXPHOS are (i) to provide a comprehensive picture of the distribution and dynamics of OXPHOS complexes in bacterial cells, (ii) to develop computational modeling of the recorded signals at the single molecule and cell levels and (iii) to employ mathematical models to predict the impact of spatial organization and dynamics on the OXPHOS outcome.
Proposed approach (experimental / theoretical / computational)
SMLM will be conducted on an existing versatile setup built by Marguet’s group which, in conjunction with specific algorithms, will provide detailed information about the distribution of OXPHOS complexes with spatial resolution scales up to 20 nm. Such experiments will also benefit from the recent acquisition of a 3D-SIM at the IMM. In-depth dynamic view of their distribution will be provided with diffusion measurements by fluorescence correlation spectroscopy (FCS)-related methods with the requested sensitivity and robustness. Computational modeling of the recorded signals will be developed by N. Bertaux currently hosted at CIML. Overall, these approaches will allow us to record biologically relevant parameters over multiple decades in time and to resolve dynamic biomolecular heterogeneity on different spatial scales of observations. Mathematical modeling fueled by those parameters will be conducted in collaboration with A. Parmeggiani (L2C, Montpellier). Microbial genetic will be conducted in Magalon’s group.
Interdisciplinarity
This project will be conducted in a cross-disciplinary environment combining physics, mathematics and biology. The two supervisors have highly complementary expertise on bacterial genetics, biochemistry, microbial physiology, cutting-edge microscopy and signal processing providing a stimulating environment for the candidate. Signal processing and modeling will be supervised by N. Bertaux (MdC) currently hosted at CIML. This project will further involve mathematical modeling taking advantage on existing collaborations. Importantly, development and implementation of novel cutting-edge nanoscopy approaches combining super-resolution with FCS measurements in bacterial cells will provide the scientific community with new tools. In this context, the successful candidate will thus take part of an innovative and interdisciplinary project which will act as an exemplar of what can be achieved using membrane complexes.