bioRxiv ScienceSearch

Biology subjects

Humbel, B. M.

Publications and source records attributed to Humbel, B. M..

4 recordsLinked to original sources

Progenitor cell integration into a barrier epithelium during adult organ turnover

Barrier epithelial organs face the constant challenge of sealing the interior body from the external environment while simultaneously replacing the cells that contact this environment. These replacement cells--the progeny of basal stem cells--are born without apical, barrier-forming structures such as a protective, lumen-facing membrane and occluding junctions. How stem cell progeny acquire these structures to become part of the barrier is unknown. Here we use Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM), Correlative Light-Electron Microscopy (CLEM), and volumetric imaging of live and fixed organs to investigate progenitor integration in the intestinal epithelium of adult Drosophila. We find that stem cell daughters gestate their future lumenal-apical membrane beneath a transient, basal niche formed by an umbrella-shaped occluding junction that shelters the growing cell and adheres it to mature neighbor cells. The umbrella junction both targets formation of a deep, microvilli-lined, apical invagination and closes it off from the contents of the gut lumen. When the growing cell is sufficiently mature, the umbrella junction retracts to expose this Pre-Assembled Apical Compartment (PAAC) to the gut lumen, thus incorporating the new cell into the intestinal barrier. When we block umbrella junctions, stem cell daughters grow and attempt to differentiate but fail to integrate; when we block cell growth, no umbrella junctions form and daughters arrest in early differentiation. Thus, stem cell progeny build new barrier structures in the shelter of a transient niche, where they are protected from lumenal insults until they are prepared to withstand them. By coordinating this dynamic junctional niche with progenitor cell differentiation, a physiologically active epithelial organ incorporates new cells while upholding integrity of its barrier.

developmental biology

A Novel Membrane Protein in the Rhodobacter sphaeroides LH1-RC Photocomplex

We present a cryo-EM structure of the monomeric light-harvesting-reaction center (LH1-RC) core complex from photosynthetic purple bacterium Rhodobacter (Rba.) sphaeroides at 2.9 [A] resolution. The LH1 complex forms a C-shaped structure composed of 14 {beta}-polypeptides around the RC with a large ring opening. From the cryo-EM density map, a previously unrecognized integral membrane protein, referred to as protein-U, was identified. Protein-U has a U-shaped conformation near the LH1-ring opening and was annotated as a hypothetical protein in the Rba. sphaeroides genome. Deletion of protein-U resulted in a mutant strain that expressed a much-reduced amount of the dimeric LH1-RC, indicating an important role for protein-U in dimerization of the LH1-RC complex. PufX was located opposite protein-U on the LH1-ring opening, and both its position and conformation differed from that of previous reports of dimeric LH1-RC structures obtained at low-resolution. Twenty-six molecules of the carotenoid spheroidene arranged in two distinct configurations were resolved in the Rba. sphaeroides LH1 and were positioned within the complex to block its pores. Our findings offer a new view of the core photocomplex of Rba. sphaeroides and the connections between structure and function in bacterial photocomplexes in general.

biochemistry

An interactive deep learning-based approach reveals mitochondrial cristae topologies

Outer and inner mitochondrial membranes are highly specialized structures with distinct functional properties. Reconstructing complex 3D ultrastructural features of mitochondrial membranes at the nanoscale requires analysis of large volumes of serial scanning electron tomography data. While deep-learning-based methods improved in sophistication recently, time-consuming human intervention processes remain major roadblocks for efficient and accurate analysis of organelle ultrastructure. In order to overcome this limitation, we developed a deep-learning image analysis platform called Python-based Human-In-the-LOop Workflows (PHILOW). Our implementation of an iterative segmentation algorithm and Three-Axis-Prediction method not only improved segmentation speed, but also provided unprecedented ultrastructural detail of whole mitochondria and cristae. Using PHILOW, we found that 42% of cristae surface exhibits tubular structures that are not recognizable in light microscopy and 2D electron microscopy. Furthermore, we unraveled a fundamental new regulatory function for the dynamin-related GTPase Optic Atrophy 1 (OPA1) in controlling the balance between lamellar versus tubular cristae subdomains.

cell biology

Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum

We present a cryo-EM structure of the light-harvesting-reaction center (LH1-RC) core complex from purple phototrophic bacterium Rhodospirillum (Rsp.) rubrum at 2.76 [A] resolution. The LH1 complex forms a closed, slightly elliptical ring structure with 16 {beta}-polypeptides surrounding the RC. Our biochemical analysis detected rhodoquinone (RQ) molecules in the purified LH1-RC, and the cryo-EM density map specifically positions RQ at the QA site in the RC. The geranylgeraniol sidechains of bacteriochlorophyll (BChl) aG coordinated by LH1 {beta}-polypeptides exhibit a highly homologous tail-up conformation that allows for interactions with the bacteriochlorin rings of nearby LH1 -associated BChls aG. The structure also revealed key protein-protein interactions in both N- and C-terminal regions of the LH1 {beta}-polypeptides, mainly within a face-to-face structural subunit. Our findings enable to evaluate past experimental and computational results obtained with this widely used organism and provide crucial information for more detailed exploration of light-energy conversion, quinone transport, and structure-function relationships in pigment-protein complexes.

biochemistry