An important morphogenetic event of mammalian embryogenesis is the formation of a blastocyst with a fluid-filled cavity, blastocoel, and the establishment of three cell types essential for implantation. Morphogenesis of the blastocyst begins with the emergence of multiple nascent cavities, which progressively coalesce to form one cavity segregating the cavity-facing primitive endoderm from the epiblast within the inner cell mass. While cell-to-cell gene expression heterogeneity is well characterised during this lineage specification, little is known about the physical principles governing self-organized blastocyst morphogenesis and patterning. In particular, changes in fluid pressure, cell shape and polarity during blastocyst formation remain uncharacterized. In this project, I will study the roles of fluid cavities in coordinating tissue mechanics, polarity and lineage specification. I will establish a novel micropressure technique to quantify the growth of luminal pressure during blastocyst development. Combining micropipette aspiration with high-resolution live-embryo imaging, I will characterize the impact of fluid pressure on trophectoderm fate specification through dynamic changes in cell shape and adhesion, and cytoskeletal remodeling. To assess the impact of fluid pressure on inner cell mass, I will study if cavity expansion induces apical polarisation and enhances primitive endoderm differentiation in cavity-facing cells. Combining laser ablation with light-sheet microscopy, we will build a spatio-temporal map of intercellular forces in vivo during blastocyst development. We will further manipulate the cavity size to study if fluid pressure is functionally required and sufficient for driving lineage segregation. This interdisciplinary and quantitative study will establish the novel role of fluid cavities and elucidate their interplay with biochemical signaling within the multi-cellular self-organization process.

Mycobacterium abscessus (Mab) is an opportunistic-multidrug-resistant non-tuberculous mycobacteria responsible for multiple clinically-acquired infections both pulmonary and extrapulmonary. Unlike many rapidly growing mycobacteria (RGM), Mab is able to survive and multiply within macrophages, similar to slow growing mycobacteria (SGM) such as M. tuberculosis (Mtb). In Mtb, five T7SS (ESX-1-5) have been identified and shown to be essential for intracellular survival (ESX-1), virulence (ESX-1 and ESX-5) or growth (ESX-3). T7SS are composed of five protein components essential for function: EccB, EccC, EccD, EccE and MycP. Except for a low-resolution structure of the holo ESX-5 complex from the host lab at 13 Å resolution, no structural data on any T7SS have been published to date, rendering structural work timely and eagerly awaited by relevant communities. Deemed inactive due to its lack of one of the established T7SS components EccE4, ESX-4 has been considered an ancestral T7SS form. However, Mab possess a fully intact and functional ESX-4, essential for its intracellular survival, rendering it a highly attractive target for an in-depth characterization. Here, I propose an interdisciplinary project that includes both functional and structural investigation. As the 2 M Dalton-holo-complex crosses the Mab inner membrane, experimental structural work will be challenging and require an integrative modeling approach to combine diverse experimental data sets. Complementary infection biology experiments including microbiology, genetics and cell biology will be carried out by collaborators. With this work, I aim to respond to central questions related to T7SS in general and Mab ESX-4 specifically, such as: what is the mechanism of T7SS-mediated secretion? What makes ESX-4 specific and different from other T7SS? What is the specific role of EccE4 to establish a functionally active ESX4? and What are the substrates and specific mechanism of ESX-4 substrate recognition?

This proposal brings together two fields in biology, namely the emerging field of phase-separated assemblies in cell biology and state-of-the-art cellular cryo-electron tomography, to advance our understanding on a fundamental, yet illusive, question: the molecular organization of the cytoplasm. Eukaryotes organize their biochemical reactions into functionally distinct compartments. Intriguingly, many, if not most, cellular compartments are not membrane enclosed. Rather, they assemble dynamically by phase separation, typically triggered upon a specific event. Despite significant progress on reconstituting such liquid-like assemblies in vitro, we lack information as to whether these compartments in vivo are indeed amorphous liquids, or whether they exhibit structural features such as gels or fibers. My recent work on sample preparation of cells for cryo-electron tomography, including cryo-focused ion beam thinning, guided by 3D correlative fluorescence microscopy, shows that we can now prepare site-specific ‘electron-transparent windows’ in suitable eukaryotic systems, which allow direct examination of structural features of cellular compartments in their cellular context. Here, we will use these techniques to elucidate the structural principles and cytoplasmic environment driving the dynamic assembly of two phase-separated compartments: Stress granules, which are RNA bodies that form rapidly in the cytoplasm upon cellular stress, and centrosomes, which are sites of microtubule nucleation. We will combine these studies with a quantitative description of the crowded nature of cytoplasm and of its local variations, to provide a direct readout of the impact of excluded volume on molecular assembly in living cells. Taken together, these studies will provide fundamental insights into the structural basis by which cells form biochemical compartments.