1. Research Background

How form cellular organelles? We investigate this question in the new “Interfacial Cell Biology” working group at the Institute of Biochemistry IV. Our current focus are capillary phenomena, i.e., processes mediated by wetting contacts between novel liquidous compartments (condensates) and, for example, conventional membrane-bound organelles. Our aim is to decipher underlying fundamental molecular-physical interactions and to translate them into medical applications.

Our recent works has identified that autophagosomes, key organelles of a complex cellular recycling process, form at condensates with liquid-like material properties (Nature 2020)¹. We investigated how these properties facilitate the expansion and bending of autophagosomal membranes via wetting interactions and discovered that the interplay between condensate and membrane properties plays a decisive role in determining which cellular parts are recycled (Nature 2021)². This study demonstrated for the first time that capillary forces are essential for cell physiological processes^3,4.

During plant embryogenesis, proteins accumulate in storage vacuoles. These storage vacuoles are one of the most important sources of protein in our diet. We recently deciphered their formation process: at certain stages of embryonic development, micrometer-sized liquid condensates form inside of vacuoles through phase separation (PNAS 2021)⁵. The condensates contain storage proteins, wet and deform the surrounding vacuole membrane through capillary forces, and ultimately mediate the formation of several storage vacuoles.

Physically similar, but molecular and physiologically distinct processes mediate the morphogenesis of intraluminal vesicles during multivesicular body biogenesis. Surprisingly, we identified in this geometry that condensates can fission resulting membrane necks through line tension force (Nature 2024)⁶ and thus, release vesicles from the enclosing membrane. Our work revealed a previously unknown mechanism of membrane fission and highlights the essential role of condensates in cellular organization⁷.

2. Research questions addressed by the group:

We address several key questions of how condensates and their surfaces facilitate diverse morphogenetic processes in cells and ageing, for example:

1. How does the interplay of condensates with cellular substrates contribute to healthy development, diseases and memory?
2. Condensates are well known to age, i.e., undergo time-depended changes of their physical properties. Do aging dynamics of individual condensates correlate with the age of organisms?
3. Which interventions (e.g., pharmacological, physical) can modulate ageing?

To address these questions, our group follows a highly collaborative, iterative approach and employs a broad spectrum of methods, ranging from state-of-the-art cell biology and biochemistry via mathematical modelling to biophysics, while including considerations originating in interfacial sciences and synthetic biology. Drawing on the physiological relevance of in vivo data, simplicity of physical models and reproducibility of test-tube experiments, our multi-faceted approach aims at revealing fundamental insights into the physico-molecular mechanisms in cells.

3. Possible project(s):

… are not limited to the following topics. We understand those as potential frameworks within which CGA doctoral candidates start in our lab. Details will be discussed together with the candidate and continuously developed during the PhD. We encourage everyone in the group to collaborate with colleagues of the CGA network and beyond.

• Investigating mechanisms of how cells control of phase separation in space and time; exploring the mechanisms that allow condensates to contribute to cellular memory.
• Deciphering the role of condensate ageing on capillarity and the efficiency of membrane fission; quantifying underlying forces in vivo and in vitro  
• Dissecting the molecular foundation of protein storage vacuole morphogenesis 

4. Applied Methods and model organisms:

All projects build on our established in vitro and in vivo models, state-of-the-art quantitative imaging (advanced confocal methods, electron microscopy), a cutting-edge optical tweezer (direct force spectroscopy, allowing pN accurate measurements in living cells) and access to CECAD omics platforms. PhD students will receive training in project-relevant methods and tools, in ageing, metabolism, and quantitative multi-omics, preparing them for competitive careers in academic, translational or industry research. PhD students are encouraged to present on conferences, to engage in transferring novel methods and tools from partner labs worldwide, as well as to pursue side own projects outside of the host lab.

5. Desirable skills and qualifications:

We welcome super-motivated, curious PhD candidates with a strong interest in research between established disciplines, e.g., combining experimental with theoretical approaches, and an eagerness to work self-determined in an inclusive environment. We strongly encourage applications from students with diverse backgrounds and who followed unconventional careers. Applicants should demonstrate excellent basic knowledge in some methods, prior experience in all techniques is not required as candidates will be trained adequately.

6. References and key publications:

1. Fujioka, Y.; Alam, J. M.; Noshiro, D.; Mouri, K.; Ando, T.; Okada, Y.; May, A. I.; Knorr, R. L.; Suzuki, K.; Ohsumi, Y.; Noda, N. N. Phase Separation Organizes the Site of Autophagosome Formation.Nature2020, 578 (7794), 301–305. doi.org/10.1038/s41586-020-1977-6.
2. Agudo-Canalejo, J.; Schultz, S. W.; Chino, H.; Migliano, S. M.; Saito, C.; Koyama-Honda, I.; Stenmark, H.; Brech, A.; May, A. I.; Mizushima, N.; Knorr, R. L. Wetting Regulates Autophagy of Phase-Separated Compartments and the Cytosol. Nature2021, 591 (7848), 142–146. doi.org/10.1038/s41586-020-2992-3.
3. Kusumaatmaja, H.; May, A. I.; Knorr, R. L. Intracellular Wetting Mediates Contacts between Liquid Compartments and Membrane-Bound Organelles. J. Cell Biol.2021, 220 (10), e202103175. doi.org/10.1083/jcb.202103175.
4. Gouveia, B.; Kim, Y.; Shaevitz, J. W.; Petry, S.; Stone, H. A.; Brangwynne, C. P. Capillary Forces Generated by Biomolecular Condensates. Nature2022, 609 (7926), 255–264. doi.org/10.1038/s41586-022-05138-6.
5. Kusumaatmaja, H.; May, A. I.; Feeney, M.; McKenna, J. F.; Mizushima, N.; Frigerio, L.; Knorr, R. L. Wetting of Phase-Separated Droplets on Plant Vacuole Membranes Leads to a Competition between Tonoplast Budding and Nanotube Formation. Proc. Natl. Acad. Sci.2021, 118 (36), e2024109118. doi.org/10.1073/pnas.2024109118.
6. Wang, Y.; Li, S.; Mokbel, M.; May, A. I.; Liang, Z.; Zeng, Y.; Wang, W.; Zhang, H.; Yu, F.; Sporbeck, K.; Jiang, L.; Aland, S.; Agudo-Canalejo, J.; Knorr, R. L.; Fang, X. Biomolecular Condensates Mediate Bending and Scission of Endosome Membranes. Nature2024, 634 (8036), 1204–1210. doi.org/10.1038/s41586-024-07990-0.
7. Cell Membranes Shaped and Cut by Phase-Separated Liquid Protein Condensates. Nature2024. doi.org/10.1038/d41586-024-03495-y.