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Results for “Cell Biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2019

Evidence for a role for BK channels in the regulation of ADAM17 activity.

Large-conductance voltage and calcium activated channels, KCa1.1, have a large single conductance (~p250) and are highly selective for potassium ions. As a result they have been termed big potassium channels (BK channels). Because of the channels ability to integrate multiple physical and chemical signals they have received much attention in excitable cells. In comparison they have received relatively little attention in non-excitable cells in those of the immune system. Here we report evidence that the BK channel regulates ADAM17 activity. Upon macrophage activation, BK channels translocate to the cell membrane. Genetic or pharmacological inhibition of the cell membrane BK channels resulted in elevated TNF- release and increased metalloproteinase a disintegrin and metalloproteinase domain 17 (ADAM17) activity. Inhibitors of BK channels also increased IL-6R release, a second ADAM17 substrate. In comparison, a BK channel opener decreases TNF- release. Taken together, our results demonstrate a novel mechanism by which ion channel regulates ADAM17 activity. Given the broad range of ADAM17 substrates, this finding has implications in many fields of cell biology including immunology, neurology and cancer biology.

pharmacology and toxicology↗

bioRxiv2019

Neto-α controls synapse organization and homeostasis at the Drosophila neuromuscular junction

Glutamate receptor auxiliary proteins control receptor distribution and function, ultimately controlling synapse assembly, maturation and plasticity. At the Drosophila neuromuscular junction (NMJ), a synapse with both pre- and post-synaptic kainate-type glutamate receptors (KARs), we show that the auxiliary protein Neto evolved functionally distinct isoforms to modulate synapse development and homeostasis. Using genetics, cell biology and electrophysiology we demonstrate that Neto- functions on both sides of the NMJ. In muscle, Neto- limits the size of the postsynaptic receptors field. In motor neurons, Neto- controls neurotransmitter release in a KAR-dependent manner. Furthermore, Neto- is both required and sufficient for the presynaptic increase in neurotransmitter release in response to reduced postsynaptic sensitivity. This KAR-independent function of Neto- is involved in activity-induced cytomatrix remodeling. We propose that Drosophila ensured NMJ functionality by acquiring two Neto isoforms with differential expression patterns and activities.

neuroscience↗

bioRxiv2019

Polarly localized EccE1is required for ESX-1 function and stabilization of ESX-1 membrane proteins in Mycobacterium tuberculosis

Mycobacterium tuberculosis is a slow-growing intracellular bacterium with the ability to induce host cell death and persist indefinitely in the human body. This pathogen uses the specialized ESX-1 secretion system to secrete virulence factors and potent immunogenic effectors required for disease progression. ESX-1 is a multi-subunit apparatus with a membrane complex that is predicted to form a pore in the cytoplasmic membrane. In M. tuberculosis this complex is composed of five membrane proteins: EccB1, EccCa1, EccCb1, EccD1, EccE1. In this study, we have characterized the membrane component EccE1 and found that deletion of eccE1 lowers the levels of EccB1, EccCa1 and EccD1 thereby abolishing ESX-1 secretion and attenuating M. tuberculosis ex vivo. Surprisingly, secretion of EspB was not affected by loss of EccE1. Furthermore, EccE1 was found to be a membrane- and cell-wall associated protein that needs the presence of other ESX-1 components to assemble into a stable complex at the poles of M. tuberculosis. Overall, this investigation provides new insights into the role of EccE1 and its localization in M. tuberculosis.\n\nIMPORTANCETuberculosis (TB), the worlds leading cause of death of humans from an infectious disease, is caused by the intracellular bacterium Mycobacterium tuberculosis. The development of successful strategies to control TB requires better understanding of the complex interactions between the pathogen and human host. We investigated the contribution of EccE1, a membrane protein, to the function of the ESX-1 secretion system, the major virulence determinant of M. tuberculosis. By combining genetic analysis of selected mutants with eukaryotic cell biology and proteomics, we demonstrate that EccE1 is critical for ESX-1 function, secretion of effector proteins and pathogenesis. Our research improves knowledge of the molecular basis of M. tuberculosis virulence and enhances our understanding of pathogenesis.

microbiology↗

bioRxiv2019

ATP Binding Cassette Proteins ABCG37 and ABCG33 are required for potassium-independent cesium uptake in Arabidopsis roots

Radiocesium, accumulated in the soil by nuclear accidents is a major environmental concern. The transport process of cesium (Cs+) is tightly linked to the indispensable plant nutrient potassium (K+) as they both belong to the group I alkali metal with similar chemical properties. Most of the transporters that had been characterized to date as Cs+ transporters are directly or indirectly linked to K+. Using a combinatorial approach of physiology, genetics, cell biology and root uptake assay, here we identified two ATP-Binding Cassette (ABC) proteins, ABCG37 and ABCG33 as facilitators of Cs+ influx. The gain-of-function mutant of ABCG37 (abcg37-1) showed hypersensitive response to Cs+-induced root growth inhibition, while the double knock out mutant of ABCG33 and ABCG37 (abcg33-1abcg37-2) showed resistance. Single loss-of-function mutant of ABCG33 and ABCG37 did not show any alteration in Cs+ response. Short term uptake experiment with radioactive Cs+ revealed reduced Cs+ uptake in abcg33-1abgc37-2 compared with wild type in presence or absence of K+. Potassium response and content were unaffected in the double mutant background confirming that Cs+ uptake by ABCG33 and ABCG37 is independent of K+. Collectively, this work identified two ABC proteins as new Cs+ influx carriers, which act redundantly and independent of K+ uptake pathway.

plant biology↗

bioRxiv2019

Bayesian Modeling Reveals Ultrasensitivity Underlying Metabolic Compensation in the Cyanobacterial Circadian Clock

Mathematical models can enable a predictive understanding of mechanism in cell biology by quantitatively describing complex networks of interactions, but such models are often poorly constrained by available data. Owing to its relative biochemical simplicity, the core circadian oscillator in Synechococcus elongatus has become a prototypical system for studying how collective dynamics emerge from molecular interactions. The oscillator consists of only three proteins, KaiA, KaiB, and KaiC, and near-24-h cycles of KaiC phosphorylation can be reconstituted in vitro. Here, we formulate a molecularly-detailed but mechanistically agnostic model of the KaiA-KaiC subsystem and fit it directly to experimental data within a Bayesian parameter estimation framework. Analysis of the fits consistently reveals an ultrasensitive response for KaiC phosphorylation as a function of KaiA concentration, which we confirm experimentally. This ultrasensitivity primarily results from the differential affinity of KaiA for competing nucleotide-bound states of KaiC. We argue that the ultrasensitive stimulus-response relation is critical to metabolic compensation by suppressing premature phosphorylation at nighttime. SynopsisThis study takes a data-driven kinetic modeling approach to characterizing the interaction between KaiA and KaiC in the cyanobacterial circadian oscillator and understanding how the oscillator responds to changes in cellular metabolic conditions. O_LIAn extensive dataset of KaiC autophosphorylation measurements was gathered and fit to a detailed yet mechanistically agnostic kinetic model within a Bayesian parameter estimation framework. C_LIO_LIKaiA concentration tunes the sensitivity of KaiC autophosphorylation and the period of the full oscillator to %ATP. C_LIO_LIThe model reveals an ultrasensitive dependence of KaiC phosphorylation on KaiA concentration as a result of differential KaiA binding affinity to ADP- vs. ATP-bound KaiC. C_LIO_LIUltrasensitivity in KaiC phosphorylation contributes to metabolic compensation by suppressing premature phosphorylation at nighttime. C_LI

systems biology↗

bioRxiv2019

Effects of surfaces and macromolecular crowding on bimolecular reaction rates

Biological cells are complex environments that are densely packed with macromolecules and subdivided by membranes, both of which affect the rates of chemical reactions. It is well known that crowding reduces the volume available to reactants, which increases reaction rates, and also inhibits reactant diffusion, which decreases reaction rates. This work investigates these effects quantitatively using analytical theory and particle-based simulations. A reaction rate equation based on only these two processes turned out to be inconsistent with simulation results. However, accounting for diffusion inhibition by the surfaces of nearby obstacles, which affects access to reactants, led to perfect agreement for reactions near impermeable planar membranes and improved agreement for reactions in crowded spaces. A separate model that quantified reactant occlusion by crowders, and extensions to a thermodynamic "cavity" model proposed by Berezhkovskii and Szabo (J. Phys. Chem. B 120:5998, 2016), were comparably successful. These results help elucidate reaction dynamics in confined spaces and improve prediction of in vivo reaction rates from in vitro ones.

biophysics↗

bioRxiv2025

DUCs are C2 domain containing plant-specific deubiquitinases stabilizing endocytic cargo at the plasma membrane

Deubiquitinases (DUBs) remove ubiquitin modifications from proteins in a substrate- or linkage-selective manner and regulate numerous cell-biological processes, including endocytosis. By performing homology-agnostic bioinformatical screens for undescribed deubiquitinase classes, we identified the plant-specific DUC (deubiquitinase with C2) family, whose members are highly selective for cleaving K63-linked ubiquitin chains. The crystal structure of the Arabidopsis member AtDUC1 reveals that DUC enzymes display a papain-like fold with a characteristic DUB-like active site, despite the apparent absence of sequence similarity to other deubiquitinase families. The K63 linkage specificity is attributed to the recognition of both distal and proximal ubiquitin units via highly conserved contact residues. Arabidopsis DUC members localize to the plasma membrane by virtue of their lipid-binding C2-like domains. In protoplast experiments, all three Arabidopsis DUC enzymes demonstrate the capacity to stabilize an endocytotic model cargo at the plasma membrane, a process that requires both the C2-mediated membrane association and catalytic DUB activity.

biochemistry↗

bioRxiv2025

Modular to cyclic TCA governs hematopoiesis in Drosophila

TCA cycle is well known for its role in bioenergetics and also a hub for metabolic exchange, here we identify a developmentally programmed, non-uniform TCA architecture that is required for hematopoietic state transitions in the Drosophila lymph gland. Early blood progenitors operate a modular TCA configuration, in which a CS/mAcon1-derived citrate node preserves progenitor identity, while a Gdh/Kdh mediated -ketoglutarate to succinyl-CoA branch, not succinate, supports proliferative potential. As cells exit the progenitor state and initiate lineage commitment, the cells undergo metabolic reorganization and engage a fully cyclic, Pdh- and Idh-dependent oxidative TCA cycle whose cataplerotic activity keeps the levels of TCA metabolites in check as their excess otherwise induces differentiation. Blocking these metabolic transitions disrupts progenitor homeostasis, compromises proliferative competency of transitional progenitors, and distorts balanced differentiation. These findings establish a developmentally regulated alternative to the traditional TCA cycle and reveals that appropriate engagement of modular versus cyclic TCA modes is required for orchestrating hematopoietic fate transitions. This work highlights TCA topology and not flux alone functions as a core determinant of stemness, proliferation, and lineage progression during hematopoiesis. Significance StatementHematopoietic development requires precise metabolic control to maintain progenitors while enabling their transition into differentiated lineages. We show that the Drosophila lymph gland achieves this through a developmentally programmed switch in TCA-cycle configuration where early progenitors rely on a modular TCA architecture that independently sustains identity and proliferation, whereas later stages require a fully cyclic, oxidative TCA mode to maintain homeostasis and balanced differentiation. Disrupting either phase perturbs hematopoietic organization, demonstrating that TCA topology itself regulates cell-state transitions. These findings reveal TCA architecture as the determinant of hematopoietic fate and provides a conceptual framework relevant to hematopoiesis and also stem cell biology.

developmental biology↗

bioRxiv2025

Isolation of Crenothrix bacteria reveals the distinct ecophysiologies of filamentous methanotrophs and adaptations to redox stress

At the dawn of modern microbiology, Cohn observed abundant filamentous bacteria in drinking water wells that he named Crenothrix polyspora. Subsequent research has revealed the methanotrophic metabolism of Crenothrix bacteria and their disproportionately high activity in stratified lakes compared to unicellular strains, yet laboratory cultivation has proven elusive, leaving the ecophysiology of Crenothrix bacteria largely unknown. Here we report the isolation of two methanotroph strains of the "lacustrine Crenothrix" clade from an iron-rich wetland and reveal their highly unique cell biologies and potential ecological roles. Using physiological approaches, we demonstrate that the strains perform a microaerobic methane metabolism while growing distinct filaments having wide and directionally oriented connective structures. The strains further have broad genomic repertoires for addressing redox stress that we show are uniquely associated with lacustrine Crenothrix compared to related methanotrophs based on genome data. Aligning with laboratory observations, we identify lacustrine Crenothrix bacteria along potential redox gradients in the wetland at iron-rich snow sites, and we further detect such bacteria in diverse global ecosystems based on public metagenome searches. Together, our data strongly point to an ecophysiology of lacustrine Crenothrix bacteria that is tightly linked to redox stress, and we propose these bacteria may uniquely store or share metabolic intermediates via their filamentous lifestyle to thrive under such conditions. Our results provide a fresh view of the diversity, evolution, and ecology of aerobic methanotrophs, connecting over 150 years of microbiology research opening vast new opportunities to probe bacterial adaptations that drive global methane cycling under redox stress.

microbiology↗

bioRxiv2025

MONDE·T: A Database and Interactive Webserver for Non-Canonical Amino Acids (ncAAs) in the PDB

SummaryNon-canonical amino acids (ncAAs) are understood as amino acids that are not genetically encoded. They are of wide interest for protein design and applications in pharmaceutical and cell biological research, but their impact on protein structure has not been explored systematically. We therefore collected all ncAAs in the Protein Data Bank (PDB) into the MONDE{middle dot}T database, amounting to 1,875 different chemical types in >10,000 entries. They are made accessible through a webserver that allows for data download, visualization of the structures in which they occur, plots of their backbone torsion angles compared to canonical residues, and exploration of their similarity to these. Analyses can focus on a single ncAA or a specific protein structure, illustrated here by example applications. Availability and implementationMONDE{middle dot}T is hosted at the Max Planck Institute for Biology Tu bingen, accessible online at https://mondet.tuebingen.mpg.de. The database is available for download under the Creative Commons 4.0 License.

bioinformatics↗

bioRxiv2025

Coronavirus membrane protein with a fluorescent protein tag enables tracking of virus particles in live cells

Coronavirus particles assemble at endoplasmic reticulum Golgi intermediate compartment (ERGIC) membranes and exit from host cells via secretory organelles that are not well defined. The interplay between viral components and intracellular transport pathways that facilitate assembly and egress are not fully understood and recent studies suggest that multiple pathways maybe involved. Reverse genetics was used to develop a model system to further understand the assembly and egress processes. Mouse hepatitis coronavirus (MHV-A59) was genetically engineered to express the membrane (M) protein fused to green fluorescent protein (M-GFP), with the chimeric gene cloned in place of the open reading frame (ORF) 4 coding region in the RNA genome. The recovered M-GFP virus also expresses wild-type (WT) M protein (M WT) from its native ORF. The M-GFP virus exhibited morphology and growth properties like WT virus. M-GFP and WT M proteins colocalized early in infection, but less M-GFP trafficked toward the cell surface at later times, suggesting that the fusion protein is incorporated less efficiently into virus particles. M-GFP was stably expressed through at least four virus passages. Early passage virus M-GFP virus particles were visualized by confocal and Total Internal Reflection Fluorescence (TIRF) microscopy in live cells. The fluorescently labeled virus particles represent a new tool for coronavirus intracellular trafficking and egress studies. Such studies can also help provide a more detailed understanding of infection and disease processes to provide new insight for development of new therapeutic strategies. IMPORTANCECoronavirus assembly, intracellular transport, egress, and the virus-host interactions involved in these processes are not fully understood. The M protein is the most abundant virion structural component, which forms the scaffold for assembly of the viral envelope. It facilitates incorporation of the viral nucleocapsid and the other viral membrane proteins, spike (S) and envelope (E). In this study we engineered M protein tagged with GFP, which is expressed along with wild-type (WT) M from the viral genome. M-GFP interacted with WT M protein and co-assembled into virus particles. The resulting fluorescently labeled coronavirus particles open opportunities to use state of the art microscopy to monitor virus assembly, trafficking, and egress in live cells to facilitate deeper understanding of the molecular and cell biology of these processes. The ability to visualize particles also opens opportunities to help further understanding of steps in viral replication and pathogenesis for potential therapeutic targets.

microbiology↗

bioRxiv2026

The STA1-DOT2 interaction promotes nuclear speckle formation and splicing robustness in growth and heat stress responses

Pre-mRNA splicing is carried out by the spliceosome, a large and dynamic ribonucleoprotein complex. The spliceosome is known to be stored in nuclear speckles (NS), which are now recognized as active subnuclear organelles for splicing. However, it remains poorly understood how spliceosomal protein-protein interactions are functionally coupled to NS organization to maintain splicing robustness in plants. Here, we report the functional significance of a specific interaction between two U4/U6{middle dot}U5 tri-snRNP components of the spliceosome, STA1 and DOT2, in regulating NS organization, pre-mRNA splicing, and heat stress responses in Arabidopsis. We identified a missense mutation in DOT2 (a Snu66/SART1 homolog) from a genetic suppressor of the PRP6 homolog mutant sta1-1 (named S307). This mutation restored the weakened interaction between STA1 and DOT2 in the sta1-1 mutant background. Genetic, biochemical, and cell biological analyses showed that variation in the strength of the STA1-DOT2 interaction was closely associated with changes in NS formation, splicing efficiency, as well as growth and heat tolerance. Pharmacological inhibition of STA1-associated NS formation by tubercidin recapitulated sta1-1-like phenotypes and splicing defects, supporting a functional link between NS organization and splicing outcomes. In addition, heat-induced weakening of the STA1-DOT2 interaction was accompanied by reduced NS formation and increased intron retention at the transcriptome-wide level including key heat-responsive transcripts. Based on these observations, we propose that the STA1-DOT2 interaction, likely reflecting the assembly state of the U4/U6{middle dot}U5 tri-snRNP, functions as a heat-sensitive interaction node that couples spliceosome assembly to NS organization and splicing robustness under stress conditions.

plant biology↗

bioRxiv2026

Wash-Free Multi-Target Super-Resolution Microscopy with Photocaged DNA Labels

Super-resolution microscopy with DNA-fluorophore labels is primed for multi-target imaging of cell biological samples. However, direct interaction with the sample is required to exchange or add DNA-fluorophore labels in each imaging round, which can impair the accuracy of the imaging data at the nanometer scale. To bypass this requirement, we introduce a wash-free method that employs DNA oligonucleotides equipped with photocaging groups. Irradiation with light removes these photo-modulatable groups and changes the hybridization properties of DNA labels, enabling light-modulated targeting. We demonstrate this concept by imaging various cellular targets with confocal microscopy, single-molecule localization microscopy, and stimulated emission depletion (STED) microscopy.

biophysics↗

bioRxiv2026

Transcriptomic profiling of human γδ T cells reveals non-linear immune aging characterized by childhood transitions and relative stability in adulthood

{gamma}{delta} T cells are one of the first T cell subsets developing in early ontogeny and show various effector functions in immune homeostasis and response in the young and the old. However, their maturation trajectories from infancy to children, adults and elderly have not been systematically defined. Here, we generated a single-cell transcriptome atlas of 106,711 {gamma}{delta} T cells from 223 individuals spanning infancy to old age. Our analysis reveals that {gamma}{delta} T cell aging is non-linear, characterized by pronounced childhood transitions followed by relative stability throughout adulthood despite marked inter-individual variability. In childhood, changes from developmental and mitochondrial programs toward cytotoxicity and inflammaging were evident. This includes maturation trajectories from GZMK intermediates to GZMB+Perforin+ effectors at both RNA and protein levels. Taken together, our study delineates the aging trajectories of human {gamma}{delta} T cells, establishes {gamma}{delta} T cells as a cellular paradigm of non-linear immune aging, and provides a comprehensive resource for investigating {gamma}{delta} T cell biology across the human lifespan.

immunology↗

bioRxiv2026

Cysteine Glutathionylation as a Global Dynamic Regulator of Protein Active Site Accessibility and Protein Complex Formation

Protein-glutathionylation is traditionally viewed as a protective mechanism that shields cysteine-residues from irreversible oxidative damage. Its broader functional roles remain poorly understood, in part due to technical limitations in detecting this modification at scale. Here, we develop and leverage a new mass-spectrometry approach that preserves protein-glutathionylation, thereby revealing its widespread distribution across the proteome in cell models, worms, mice and human cardiac tissues. In all cases, we find that glutathionylation sites are enriched at both protein-protein interfaces and protein-active sites, and are highly conserved across species. We find that glutathionylation is dynamically redistributed in response to environmental challenges, thereby driving remodelling of cellular protein-protein interaction (PPI) networks, and access to protein active sites, with functional and phenotypic consequences. Finally, we show that glutathionylation accumulates on key cardiac-sarcomeric proteins in aged-mice and human cardiomyopathy biopsies, revealing its role in cardiovascular dysfunction. These findings reposition glutathionylation as a crucial regulatory PTM, akin to phosphorylation, that orchestrates adaptive cellular responses. This work redefines the role of glutathionylation, with broad implications for cell biology and disease.

molecular biology↗

bioRxiv2026

Bifunctional Lipid-Protein Crosslinking Efficiency and Reaction Products

Bifunctional diazirine lipids are valuable tools for mapping protein-lipid interactions and cellular localization by photocrosslinking. Yet, the crosslinking efficiency of these probes has not been systematically evaluated. Here, we use the lipid transfer protein STARD10, which binds phospholipids in a 1:1 stoichiometry within a hydrophobic pocket, to measure the upper limit of the photo-crosslinking efficiency of bifunctional lipid probes. We characterize reaction products using native and denaturing mass spectrometry. Our results show that approximately 5% of photoactivated lipids form covalent protein-lipid crosslinks, while the majority follow intramolecular reaction trajectories, resulting in the formation of products featuring alkene, ketone and hydroxyl moieties. These findings provide essential context for the use of bifunctional probes to uncover the cell biology of lipids and highlight the need for continuous improvement to experimental workflows. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/700185v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@15d1641org.highwire.dtl.DTLVardef@6024e0org.highwire.dtl.DTLVardef@1503dcorg.highwire.dtl.DTLVardef@1b067bd_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

SARS-CoV-2 membrane protein biogenesis

Viral protein biogenesis underpins every viral life cycle stage, and elucidating these processes could reveal fundamental principles of virus-host interaction, and vulnerabilities amenable to therapeutic targeting. Here we apply biophysical, molecular, and cell biology techniques to investigate the insertion, folding, and oligomerization of the SARS-CoV-2 M protein. We describe the sequential co-translational insertion of the hydrophobic core, and demonstrate that the cytosolic C-terminal domain undergoes slower adoption of its tertiary structure. Additionally, we characterize how the transmembrane domain bundle facilitates M-protein oligomerization. Our results reveal a hydrophobic residue cluster that is essential for protein folding and co-translational dimerization. Additionally, we identify the cellular machinery responsible for targeting and inserting the M protein into the ER membrane, and chaperones and cofactors that may contribute to proper folding.

molecular biology↗

bioRxiv2026

Generative modeling reveals the connection between cellular morphology and gene expression

The understanding of how transcriptional programs give rise to cellular morphology, and how morphological features reflect and influence cell identity and function remains limited. This is due in part to the lack of large-scale datasets pairing the two modalities as well as the absence of computational frameworks capable of modeling their cross-modal structure. Here, we introduce COSMIC, a bidirectional generative framework that enables quantitative decomposition of transcriptional variance reflected in morphology and morphological variance explained by gene expression. COSMIC builds on a foundation model trained on over 21 million segmented nuclei and couples it with existing transcriptomic embeddings. To enable cross-modal learning, we leveraged a newly generated multimodal dataset acquired using IRIS, a technology that captures high-resolution images and transcriptomes from the same single cells at scale. COSMIC accurately modeled cell type identity, as well as continuous dynamics such as cell-cycle progression, establishing a quantitative link between morphological phenotypes and underlying gene expression. In prostate cancer cells, COSMIC identified morphological and transcriptomic differences between chemotherapy drug treatment-responsive and -resistant cells, and revealed morphology-associated genes linked to tumor state. Together, these results demonstrate that generative modeling powered by paired single-cell measurements can capture the bidirectional flow of information between cellular form and gene expression, opening new avenues for mechanistic discovery and predictive modeling in both basic and translational cell biology.

bioinformatics↗