Biology subjects

Davies, K. M.

Publications and source records attributed to Davies, K. M..

6 recordsLinked to original sources

bioRxiv2022

A centimeter-long bacterium with DNA compartmentalized in membrane-bound organelles

Cells of most bacterial species are around 2 {micro}m in length, with some of the largest specimens reaching 750 {micro}m. Using fluorescence, x-ray, and electron microscopy in conjunction with genome sequencing, we characterized Ca. Thiomargarita magnifica, a bacterium with an average cell length greater than 9,000 {micro}m that is visible to the naked eye. We found that these cells grow orders of magnitude over theoretical limits for bacterial cell size through unique biology, display unprecedented polyploidy of more than half a million copies of a very large genome, and undergo a dimorphic life cycle with asymmetric segregation of chromosomes in daughter cells. These features, along with compartmentalization of genomic material and protein synthesis in membrane-bound organelles, indicate gain of complexity in the Thiomargarita lineage, and challenge traditional concepts of bacterial cells. One Sentence SummaryCa. T. magnifica are compartmentalized centimeter-long bacteria

cell biology↗

bioRxiv2022

Caulobacter requires anionic sphingolipids and deactivation of fur to lose lipid A

Lipid A, the membrane-anchored portion of lipopolysaccharide, is an essential component of the outer membrane (OM) of nearly all Gram-negative bacteria. Here, we identify regulatory and structural factors that together permit Caulobacter crescentus to eliminate lipid A from its OM. Mutations in the ferric uptake regulator fur allow Caulobacter to survive in the absence of either LpxC, which catalyzes an early step of lipid A synthesis, or CtpA, a tyrosine phosphatase homolog which we find is needed for wild-type lipid A structure and abundance. Alterations in Fur-regulated processes, rather than iron status per se, underlie the ability to eliminate lipid A. Fitness of lipid A-deficient Caulobacter requires a previously uncharacterized anionic sphingolipid, ceramide phosphoglycerate (CPG), which also mediates sensitivity to the antibiotic colistin. Our results demonstrate that, in an altered regulatory landscape, anionic sphingolipids can support the integrity of a lipid A-deficient OM.

microbiology↗

bioRxiv2021

Actin force generation in vesicle formation: mechanistic insights from cryo-electron tomography

Actin assembly provides force for a multitude of cellular processes. Compared to actin assembly- based force production during cell migration, relatively little is understood about how actin assembly generates pulling forces for vesicle formation. Here, cryo-electron tomography revealed actin filament number, organization, and orientation during clathrin-mediated endocytosis in human cells, showing that force generation is robust despite variance in network organization. Actin dynamics simulations incorporating a measured branch angle indicate that sufficient force to drive membrane internalization is generated through polymerization, and that assembly is triggered from [~]4 founding "mother" filaments, consistent with tomography data. Hip1R actin filament anchoring points are present along the entire endocytic invagination, where simulations show that it is key to pulling force generation, and along the neck, where it targets filament growth and makes internalization more robust. Actin cytoskeleton organization described here allowed direct translation of structure to mechanism with broad implications for other actin-driven processes. Highlights- Filament anchorage points are key to pulling force generation and efficiency. - Native state description of CME-associated actin force-producing networks. - Branched actin filament assembly is triggered from multiple mother filaments. - Actin force production is robust despite considerable network variability.

cell biology↗

bioRxiv2021

3D structure and in situ arrangements of CatSper channel in the sperm flagellum

The sperm calcium channel CatSper plays a central role in successful fertilization as a primary Ca2+ gateway into the sperm flagellum. However, CatSpers complex subunit composition has impeded its reconstitution in vitro and structural elucidation. Here, we applied cryo-electron tomography to visualize the macromolecular organization of the native CatSper channel complex in intact mammalian sperm, as well as identified three additional CatSper-associated proteins. The repeating CatSper units form long zigzag-rows in four nanodomains along the flagella. In both mouse and human sperm, each CatSper repeat consists of a tetrameric pore complex. Murine CatSper contains an additional outwardly directed wing-structure connected to the tetrameric channel. The majority of the extracellular domains form a canopy above each pore-forming channel that interconnects to a zigzag-shaped roof. The intracellular domains link two neighboring channel complexes to a diagonal array. The loss of this intracellular link in Efcab9-/- sperm distorts the longitudinally aligned zigzag pattern and compromises flagellar movement. This work offers unique insights into the mechanisms underlying the assembly and transport of the CatSper complex to generate the nanodomains and provides a long-sought structural basis for understanding CatSper function in the regulation of sperm motility.

biophysics↗

bioRxiv2020

Subcellular structure segmentation from cryo-electron tomograms via machine learning

We describe how to use several machine learning techniques organized in a learning pipeline to segment and identify subcellular structures from cryo electron tomograms. These tomograms are difficult to analyze with traditional segmentation tools. The learning pipeline in our approach starts from supervised learning via a special convolutional neural network trained with simulated data. It continues with semi-supervised reinforcement learning and/or a region merging techniques that try to piece together disconnected components that should belong to the same subcellular structure. A parametric or non-parametric fitting procedure is then used to enhance the segmentation results and quantify uncertainties in the fitting. Domain knowledge is used in generating the training data for the neural network and in guiding the fitting procedure through the use of appropriately chosen priors and constraints. We demonstrate that the approach proposed here work well for extracting membrane surfaces of protein reconstituted liposomes in a cellular environment that contains other artifacts.

cell biology↗

bioRxiv2018

Mitochondrial ATP synthase dimers spontaneously self-associate driven by a long-ranged membrane-induced force

ATP synthases populate the inner membranes of mitochondria, where they produce the majority of the ATP required by the cell. Cryo-electron tomograms of these membranes from yeast to vertebrates have consistently revealed a very precise organization of these enzymes. Rather than being scattered throughout the membrane, the ATP synthases form dimers, and these dimers are organized into rows that extend for hundreds of nanometers. These rows are only observed in the membrane invaginations known as cristae, specifically along their sharply curved edges. Although the presence of these macromolecular structures has been irrefutably linked to the proper development of cristae morphology, it has been unclear what drives the formation of the rows and why they are specifically localized in the cristae. We present the result of a quantitative molecular-simulation analysis that strongly suggests that the ATP synthase dimers organize into rows spontaneously, driven by a long-ranged attractive force that results from relief in the overall elastic strain of the membrane. This strain is caused by the V-like shape of the dimers, unique among membrane-protein complexes, which induces a strong deformation in the surrounding membrane. The process of row formation is therefore not a result of protein-protein interactions, or of a specific lipid composition of the membrane. We further hypothesize that once assembled, the ATP synthase dimer rows prime the inner mitochondrial membrane to develop folds and invaginations, by causing macroscopic membrane ridges that ultimately become the cristae edges. In this view, mitochondrial ATP synthases would contribute to the generation of a morphology that maximizes the surface area of the inner membrane, and thus ATP production. Finally, we outline the key experiments that would be required to verify or refute this hypothesis.

biophysics↗