Understanding the self-organization of prokaryotic protein systems

Advisor: Beatrice Ramm

Location: Friedrich Miescher Laboratory of the Max Planck Society

Our interdisciplinary group sits at the interface of biochemistry, biophysics, and synthetic biology and works towards a deeper understanding of spatiotemporal organization in biology across different scales. In this project we are interested in investigating how relatively simple prokaryotic protein systems can organize cellular content in space and time.

Prokaryotes, bacteria and archaea, long thought to be just simple "bags of molecules", actually have a rather sophisticated intracellular organization. Moreover, their species diversity is reflected in the variety of distinct protein systems that organize their cellular content and determine their shape. These prokaryotic protein systems are usually rather simple, i.e., consist of just a few proteins. Their activity is fueled by ATP or GTP, which often induces binding to a reaction matrix, for example the membrane or the nucleoid DNA. Despite their simplicity when compared to the complex eukaryotic cytoskeleton and motor proteins, they nevertheless exhibit rich dynamics and perform sophisticated functions, such as determining the cell division site and positioning plasmids, chromosomes, and motility structures within the cell. Examples of interesting prokaryotic protein systems include the E. coli MinDE system and the PomXYZ system from M. xanthus.

In this project you will recreate such cellular processes in the test tube to study them in detail. You will reconstitute the self-organization and self-assembly of these protein systems in vitro and quantitatively analyze their behavior using quantitative microscopy and biochemical assays. What is the minimal set of proteins to generate dynamics? How are these proteins influenced by properties of their reaction matrix (membrane or nucleoid) and how do they in turn affect the reaction matrix? What role does liquid-liquid phase separation play in these systems? Does the system’s self-organization generate diffusive fluxes that lead to diffusiophoretic transport of other molecules?

We are looking for an enthusiastic PhD student to carry out this project in our group. You should have a basic background in molecular biology and biochemistry techniques, be curious and motivated, and enjoy working in a collaborative and interdisciplinary team. Experience with protein expression and purification, model membranes, biochemical assays, fluorescence microscopy, quantitative image analysis and computer programming (python, MATLAB) would be advantageous, but can be compensated for with a strong motivation to acquire these skills.

More information about the research of Beatrice Ramm and a selection of recent publications can be found on her faculty page.

To apply

• Check that you meet our requirements
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Application deadline: 27 January 2025