Biology subjects

Weber, S. C.

Publications and source records attributed to Weber, S. C..

9 recordsLinked to original sources

bioRxiv2026

3D Electron Microscopy Reveals Diverse Chromosome Morphologies Across Dinoflagellate Species

Dinoflagellate chromosomes adopt a highly condensed and organized morphology, with periodic bands and arches observed by traditional Transmission Electron Microscopy (TEM). However, the limited two-dimensional field of view of TEM has prevented a precise characterization of the inherently three-dimensional organization of dinoflagellate chromosomes. Moreover, given the vast diversity among dinoflagellate species and the lack of a systematic comparison of their chromosomes, it remains unclear whether dinoflagellate chromosomes share common organizational features or instead exhibit significant cell- or species-specific differences. Here, we acquire three whole-nucleus 3D Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) datasets at 4 nm voxel size for each of four dinoflagellate species: Symbiodinium microadriaticum, Breviolum minutum, Fugacium kawagutii, and Crypthecodinium cohnii. We compile these data with previously published image volumes from four additional species and present an analysis of the largest collection of dinoflagellate FIB-SEM images to date. Common features observed across all eight species include the absence of physical confinement or spatial clustering of chromosomes in the nucleus. In addition, by decomposing each chromosome into a weighted sum of orthogonal shapes using Spherical Harmonics Expansion, we find a principal component encapsulating 88% of the total shape variance that is common to all species. However, our analysis also reveals differences in chromosome morphology across species. First, while many chromosomes exhibit surface ridges with left-handed helical twist, the proportion of chromosomes with such ridges varies extensively across species. Second, while chromosomes in most species are discrete and well-separated, chromosomes in F. kawagutii are interconnected in a single contiguous network. Lastly, to our knowledge, we report the first observation in eukaryotic cells of toroid-shaped DNA objects, whose numbers vary dramatically across cells and species. Overall, our results show that dinoflagellate chromosomes exhibit both shared organizational features and pronounced species-specific deviations.

cell biology↗

bioRxiv2026

Nuclear envelope-dependent heterochromatin positioning gates the timing of nucleolar assembly in the early embryo

The nucleolus is the largest nuclear condensate, yet how its assembly is developmentally timed remains poorly understood. In the Caenorhabditis elegans embryo, nucleoli normally appear at the 6- to 8-cell stage. Here we show that the LINC complex and nuclear lamina restrain premature nucleolar assembly through heterochromatin organization. Depletion of the embryonic LINC complex proteins SUN-1 or ZYG-12 induces precocious FIB-1-positive nucleoli at the 4-cell stage, particularly in the EMS and P2 blastomeres. LMN-1 depletion produces a more severe phenotype combining premature assembly with impaired disassembly. Loss of the heterochromatin anchor CEC-4 alone has modest effects but strongly suppresses precocious nucleolar assembly caused by LINC complex depletion. LINC complex and lamin perturbations alter the heterogeneity of HPL-2-marked chromatin, and FIB-1 condensates occupy locally HPL-2-depleted regions. These findings identify nuclear envelope-dependent heterochromatin organization as a developmental gate for nucleolar condensate assembly.

cell biology↗

bioRxiv2026

A winding road to coexistence: Interdependence of niche and fitness differences in E. coli with targeted resource uptake gene deletions

Resource competition theory typically assumes static traits and continuous supply of resources. Yet microbial communities often experience feast-famine cycles and rapid trait change. To investigate coexistence under these nonequilibrium conditions, we integrate modern coexistence theory (MCT) with a genome-scale metabolic model that explicitly links resource use (traits) to metabolic fluxes and growth. MCT partitions competitive interactions into niche and fitness differences, to predict when trait-driven departures from neutrality result in coexistence or exclusion. Using dynamic flux balance analysis, we define a function that maps trait-resource matching to niche and fitness differences between species in a two-species two-resource system. This mapping shows that niche and fitness differences are not independently tunable under resource competition: changes in transporter-mediated resource uptake and changes in resource concentration ratios generate constrained trajectories through coexistence space. Specifically, we show that the minimum niche difference required for coexistence increases linearly with the absolute difference in maximal growth rates on limiting resources, showing how limiting similarity between species can emerge from intracellular metabolic constraints. Furthermore, we find that in batch culture simulations, initial conditions (inoculum size, total resource concentration) determine the timescale of the transient growth phase, with niche differences saturating and fitness differences increasing as the timescale grows, thereby governing competition outcomes. Finally, we test these predictions experimentally using E. coli strains with targeted resource transporter knockouts under both equal and skewed resource concentrations. Our results confirm that transporter-mediated trait changes and resource concentration ratio modulation can be harnessed to engineer coexistence. Together, our work demonstrates that trait-resource matching imposes structured constraints on the joint evolution of niche and fitness differences, thereby shaping biodiversity maintenance in microbial communities under nonequilibrium conditions.

ecology↗

bioRxiv2026

Omega stabilizes RNA polymerase condensates andcontributes to cellular fitness during acid stress

In eukaryotes, organization of the nucleolus is tightly linked to ribosomal RNA (rRNA) synthesis. External stresses, such as heat shock and acidosis, induce a transition of the nucleolus from a liquid- to solid-like state. Bacterial RNA polymerase (RNAP) condensates share similarities with the nucleolus as they colocalize with pre-rRNA synthesis and their assembly correlates with high rRNA synthesis. In addition, their organization is growth dependent, highlighted by dissolution upon nutritional stress. However, their behavior and biophysical properties during other stresses remain unknown. Here, we find that RNAP condensates persist during acid stress despite an arrest in cell growth. In contrast to fast-growth RNAP condensates, acid-stabilized RNAP condensates become insensitive to drug treatments, suggesting a change in their dynamics. We identify both passive and active mechanisms that contribute to the maintenance of RNAP condensates during acid stress: a drop in intracellular pH and the stringent response. Specifically, the omega subunit of RNAP, which contributes to (p)ppGpp binding site 1, is critical for condensate maintenance during acid stress. In contrast, we show that DksA, a major stress regulator that binds to RNAP, does not contribute to RNAP condensate stabilization. Interestingly, we find that maintenance of RNAP condensates correlates with survival during recovery from acid stress. Our work sheds light on a new aspect of bacterial stress tolerance through regulation of RNAP codensates and a new role for the omega subunit. Our data bring RNAP condensates conceptually one step closer to nucleoli.

microbiology↗

bioRxiv2025

Labeling of Nascent RNA in C. elegans Intestine

Transcriptional regulation in C. elegans has been difficult to study at the level of nascent RNA because nucleotide analogs do not readily penetrate the cuticle. Here, we establish an ex vivo EU-click labeling protocol that enables sensitive microscopy detection of newly transcribed RNA in dissected intestines. Using worms expressing fluorescent nucleolar markers, we show that EU incorporation faithfully reports on rRNA nascent transcription and is abolished by RNA polymerase I inhibition. Spatial analysis further reveals that the majority of nascent rRNA transcripts localize to the fibrillar zone (FZ) of intestinal nucleoli, consistent with the conserved role of this compartment in rRNA synthesis. In addition to imaging applications, this workflow can be adapted for gene expression assays, providing a versatile approach for quantitative analysis of nascent transcription in C. elegans. By enabling direct visualization of nucleolar transcription in intact intestine tissue, this method opens new opportunities to investigate how nucleolar activity is regulated across development, aging, and disease contexts.

cell biology↗

bioRxiv2025

3D Reconstruction of Dinoflagellate Chromosomes from Hi-C Data Refutes the Cholesteric Liquid Crystal Hypothesis

Dinoflagellates have permanently condensed chromosomes that are often described as liquid crystalline. Specifically, a Cholesteric Liquid Crystal (CLC) model was proposed in which DNA is organized into parallel fibers within stacked discs, such that the fiber orientation rotates by a constant angle between adjacent discs. Extrachromosomal loops extending from the discs were hypothesized to be more accessible and thus to contain transcriptionally active genes. Although the CLC model captures some features of dinoflagellate chromosome structure, its validity has not been rigorously tested against modern genomic data. Here, we use chromatin conformation capture (Hi-C) data to simulate 3D conformations of chromosome scaffolds for three dinoflagellate species: Fugacium kawagutii, Symbiodinium microadriaticum, and Breviolum minutum. Consensus and population-based modeling generate diverse polymer conformations with moderate orientational and nematic order. However, we find no evidence of cholesteric discs. Moreover, contact probability curves from empirical Hi-C data are inconsistent with the CLC model. Nevertheless, we show that introducing locus-specific boundaries into the CLC model can produce simulated Hi-C contact maps with topologically associating domains (TADs), which are observed in experimental Hi-C contact maps for these species. Finally, by mapping RNA-seq data onto our simulated conformations, we show that actively transcribed genes are present throughout entire chromosomes, and not exclusively on extrachromosomal loops or at the surface. Our results challenge the long-standing CLC model and suggest that dinoflagellate chromosomes are organized into condensed but non-crystalline structures that do not impede transcription.

biophysics↗

bioRxiv2024

Resource-use plasticity governs the causal relationship between traits and community structure in model microbial communities

Resolving the relationship between species traits and their relative abundance is a central challenge in ecology. Current hypotheses assume relative abundances either result from or are independent of traits. However, despite some success, these hypotheses do not integrate the reciprocal and feedback interactions between traits and abundances to predictions of community structure such as relative abundance distributions. Here we study how plasticity in resource-use traits govern the causal relationship between traits and relative abundances. We adopt a consumer-resource model that incorporates resource-use plasticity that operates to optimize organism growth, underpinned by investment constraints in physiological machinery for acquisition of resources. We demonstrate that the rate of plasticity controls the coupling strength between trait and abundance dynamics, predicting species relative abundance variation. We first show how plasticity in a single species in a community allows all other non-plastic species to coexist, a case of facilitation emerging from competitive interactions where a plastic species minimizes its similarity with competitors and maximizes resource-use efficiency in its environment. We apply this environment-competition trade-off to predict trait-abundance relationships and reveal that initial traits are better predictors of equilibrium abundances than final trait values. This result highlights the importance of transient dynamics that drive species sorting. The temporal scale of transients determines the strength of species sorting due to the emergence of ecological equivalence at equilibrium. We propose trait-abundance feedback as an eco-evolutionary mechanism linking community structure and assembly, highlighting trait plasticitys role in community dynamics.

ecology↗

bioRxiv2024

Transcription templated assembly of the nucleolus in the C. elegans embryo

The nucleolus is a multicomponent structure made of RNA and proteins that serves as the site of ribosome biogenesis within the nucleus. It has been extensively studied as a prototype of a biomolecular condensate whose assembly is driven by phase separation. While the steady-state size of the nucleolus is quantitatively accounted for by the thermodynamics of phase separation, we show that experimental measurements of the assembly dynamics are inconsistent with a simple model of a phase-separating system relaxing to its equilibrium state. Instead, we show that the dynamics are well described by a model in which the transcription of ribosomal RNA actively drives nucleolar assembly. We find that our model of active transcription-templated assembly quantitatively accounts for the rapid kinetics observed in early embryos at different developmental stages, and for different RNAi perturbations of embryo size. Our model predicts a scaling of the time to assembly with the volume of the nucleus to the one-third power, which is confirmed by experimental data. Our study highlights the role of active processes such as transcription in controlling the placement and timing of assembly of membraneless organelles. Significance statementHow membraneless organelles like nucleolus assemble within cells is not well understood. Recent experiments suggest that transcription of ribosomal RNA actively drives nucleolar assembly. Our proposed model of active transcription-templated assembly quantitatively accounts for the rapid kinetics observed in early worm embryos at different developmental stages. Further, it predicts a scaling of the time to assembly with the volume of the nucleus that is confirmed by experimental data. This work describes how active processes such as transcription can control the placement and timing of assembly of membraneless organelles.

cell biology↗

bioRxiv2020

Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation

Once described as mere "bags of enzymes", bacterial cells are in fact highly organized, with many macromolecules exhibiting non-uniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid-liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) in E. coli. Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and suggests that this process serves as a universal mechanism for intracellular organization across the tree of life. SignificanceBacterial cells are small and were long thought to have little to no internal structure. However, advances in microscopy have revealed that bacteria do indeed contain subcellular compartments. But how these compartments form has remained a mystery. Recent progress in larger, more complex eukaryotic cells has identified a novel mechanism for intracellular organization known as liquid-liquid phase separation. This process causes certain types of molecules to concentrate within distinct compartments inside the cell. Here, we demonstrate that the same process also occurs in bacteria. This work, together with a growing body of literature, suggests that liquid-liquid phase separation is a universal mechanism for intracellular organization that extends across the tree of life.

cell biology↗