Biology subjects

Biswas, A.

Publications and source records attributed to Biswas, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Inhomogeneous Tau polymerization, core-shell organization, and seed formation during Tau condensate aging

Several proteins aggregating in neurodegenerative diseases spontaneously segregate into liquid condensates, which can catalyze protein aggregation. How liquid-solid transitions are catalyzed in the confined condensate volume is not clear. For the microtubule associated protein Tau, aggregating intra-neuronally in Alzheimer's disease, we show that, during maturation, Tau condensates convert into elastic protein networks, accompanied by inhomogeneous polymerization of the condensate interior and the formation of high-density nodes and a 'shell'. During condensation, Tau molecules extend, favoring intermolecular interactions and priming for progressive parallel Tau arrangement that can enable amyloid-like Tau oligomerization. In cells, aged condensates seed small Tau clusters in cytosol and at the nuclear envelope, precursors of larger aggregates. By bridging molecular to condensate level, we present mechanistic insight into how Tau condensates evolve into pathological, beta-structure containing seeds. The interior of aged Tau condensates remains accessible for smaller molecules, providing the opportunity to molecularly target Tau seed formation inside condensates.

biochemistry↗

bioRxiv2026

Theca cell mechanosensing and regulation of follicular extracellular matrix during ovarian follicle development

Mammalian folliculogenesis is essential for female hormonal regulation and successful reproduction. While the steroidogenic functions of theca cells (TCs) have been implicated in ovarian diseases and infertility, the physico-structural properties of TCs and their associated extracellular matrix (ECM), or theca matrix, remain poorly understood. Using murine ovaries, we show that a stiff basement membrane (BM) and theca matrix constitute a mechanically instructive niche that modulates TC proliferation and Yes-associated protein (YAP) signalling in secondary follicles. We identify hyaluronic acid (HA) as a key matrix component that is actively secreted by contractile TCs. The HA scaffold, in turn, regulates TC proliferation, YAP signalling and motility, and is required for overall follicle growth. We showed that stiffer substrates enhance YAP nuclear transport in TCs, while mechanical stretch, cell packing, and curvature affect TC proliferation. In addition, TCs exhibit directed migration towards regions of positive curvature. Together, this study reveals a mechanochemical feedback mechanism that establishes TC mechanics and HA as key regulators of theca matrix formation that is essential for mammalian folliculogenesis. SIGNIFICANCEThe structural properties and mechanical functions of the basement membrane and theca cell-matrix encapsulating mammalian ovarian follicles are poorly understood. Our findings reveal that during early stage of follicle development, the basement membrane remains thin and stiff, while the theca cells actively secrete hyaluronic acid in a contractility-dependent manner. The hyaluronic acid scaffold, in turn, regulates theca cell YAP signalling, proliferation and motility that are required for functional growth of follicles. We further showed that the theca cells are mechanosensitive and fine-tune their proliferative capacity and Hippo pathways in response to substrate stiffness, stretch and curvature. Together, our study uncovers mechanoregulatory feedback between theca cells and associated extracellular matrix, offering new insights into environmental control of folliculogenesis in female reproduction.

developmental biology↗

bioRxiv2026

Ribosome Processing Factor-2 Interacts with RPL10A to Regulate Selective Translation during Plant Immunity and Drought Stress

Processing of ribosomal RNA (rRNA) is essential for ribosome biogenesis, translation, plant development, and stress adaptation. Ribosome processing factor-2 (RPF2), which plays a role in the later stages of rRNA maturation, interacts with ribosomal protein L10A (RPL10A). RPF2 overexpression in Arabidopsis and Nicotiana benthamiana showed enhanced plant growth and trichome development due to increased gibberellic acid (GA) levels. Conversely, RPF2-silenced and mutant plants had a dwarf phenotype, reduced stomatal apertures, and decreased glucosinolate accumulation. RPF2 silenced and mutant plants also showed compromised nonhost disease resistance, whereas RPF2 overexpression lines exhibited enhanced disease resistance to both host and nonhost pathogens. RPL10A and RPF2 overexpression lines were sensitive to abscisic acid (ABA) and tolerant to drought, which is attributed to their unique roles in translation regulation. Despite having larger stomatal apertures, RPF2 overexpression plants displayed low pathogen multiplication rates and reduced water loss, indicating independent resistance mechanisms associated with ribosomal functions in translation regulation. Although both RPL10A and RPF2 proteins interact with each other and are involved in translation regulation, proteomic analysis suggests that they regulate the translation of distinct sets of genes during pathogen or drought stress. These findings indicate that RPF2 and RPL10A play independent roles in the regulation of unique protein translation.

plant biology↗

bioRxiv2026

Integrated proteomic and phosphoproteomic profiling reveals mechanisms of Bisphenol-A induced placental toxicity

The global industrialization and rapid urbanization elevated the risk of toxic pollutant exposure, which affects human health specially during pregnancy. Pregnant mothers are daily exposed to bisphenol-A (BPA), which is a common plastic leachate and a prominent toxic pollutant present in our environment. BPA act as an endocrine disrupting chemical (EDCs) by altering feto-placental homeostasis. This persistent and potent exposure of BPA during gestation can trigger placental damage affecting trophoblast cell function and survival. BPA even disrupts specific signalling cascades by altering post translational protein phosphorylation. However, this BPA mediated dysregulation of signalling nodes in early trimester placenta is still unexplored. Therefore, this study investigates the global proteome changes in post-BPA exposed extravillous trophoblast (EVTs) cells, which revealed a BPA mediated dynamic regulation of phosphoproteome-signatures and their associated kinases. Further inspection showed that the altered phosphorylation of c-JUN (S63) and GSK3 (Y279) is associated with BPA toxicity in EVTs and placenta. This altered phosphorylation affects the cellular signalling downstream, imparting damage upon the growing feto-placental unit. This highlights an altered phosphorylation mediated mechanism of BPA toxicity in placenta which can cause an onset of adverse pregnancy outcome. Data are available via ProteomeXchange with the identifiers PXD074780.

biochemistry↗

bioRxiv2026

Cytosolic interaction with RNA-helicase DDX39A titrates viral RNA G-quadruplex mediated α-Synuclein amyloidogenesis

Amyloid aggregates of -Synuclein are hallmark of Parkinsons Disease (PD) and related neurodegenerative diseases. -Synuclein, being an non-canonical RNA-binding protein (RBP), associates with other RBPs within cytosolic RNA-protein granules to modulate mRNA-stability. Conversely, mRNA G-quadruplexes (rG4s) expedite -Synuclein amyloidogenesis. However, spatiotemporal control on -Synuclein amyloidogenesis by other RBPs remains unexplored. Here, we report that RNA-dependent cytosolic interaction with DEAD-box RNA-helicase DDX39A decelerates -Synuclein amyloidogenesis. Viral infections transiently elevate rG4s in cytoplasm. Perturbing interactions between Synuclein and DDX39A using viral rG4s from H1N1-influenza and SARS-CoV-2 genomes expedites intracellular amyloidogenesis. Conversely, DDX39A overexpression alleviates -Synuclein amyloidogenesis in mouse primary neurons triggered by SARS-CoV-2 infection. We demonstrate that while DDX39A unwinds viral rG4s to mitigate -Synuclein sol-gel transition, its reciprocal cooperative phase separation with -Synuclein enhances the helicases rG4-unwinding activity. We propose that accelerated -Synuclein amyloidogenesis represents a trade-off within this RNA-protein interaction equilibrium, contributing to the viral etiology of PD.

biochemistry↗

bioRxiv2026

Spatiotemporal variation in habitat suitability predicts genomic diversity and structure in a Western Ghats endemic Tarantula (Thrigmopoeus truculentus)

Physical barriers are well known to restrict gene flow and generate population structure, yet what drives genetic differentiation in the absence of such barriers remains less understood. In these cases, long-term climatic fluctuations may shape genomic variation by altering habitat connectivity through time. The Western Ghats mountains in Peninsular India, marked by high endemism and in-situ radiations, provide a compelling natural laboratory to understand how historical climate change can shape genetic diversity. While the role of topographic barriers in generating diversity in this landscape is well documented, the influence of paleoclimatic processes has rarely been examined, especially from a genomic perspective. Here, we combine genome-wide SNPs and ecological niche modelling with present and past climatic data to test the role of elevation, geographic distance, environment and paleohabitat dynamics in shaping the genetic diversity and structure in a wet-adapted tarantula species endemic mostly to the central Western Ghats. Despite overall genomic admixture and continuity, populations show little north-south structuring, and genetically distinct central populations. Paleoclimate projections from the present to the Last Glacial Maximum reveal that northern and southern regions maintained stable habitat suitability for Thrigmopoeus, whereas central regions experienced high temporal variability. Linear mixed models identify historical stability of suitable habitats as the strongest predictor of genetic structure. Central populations occupying historically unstable habitats also show reduced heterozygosity, elevated inbreeding, and smaller historical effective population sizes. These results demonstrate that, even in the absence of physical barriers, long-term climate dynamics can generate and maintain fine-scale, within-species genetic diversity.

zoology↗

bioRxiv2026

Gamma oscillations across recording scales show a preference for saturated long-wavelength (reddish) hues in the primate visual cortex

Stimulus-induced narrowband gamma oscillations (30-70 Hz) arise due to excitatory-inhibitory interactions and have been proposed to carry feedforward prediction errors during visual processing. However, the dependence of gamma on stimulus color is not well characterized, with some studies showing a preference for saturated long-wavelength (reddish) hues in invasive recordings from the primary visual cortex (V1), while others showing no preference for red in luminance and cone-contrast balanced colors spanning the Derrington-Krauskopf-Lennie (DKL) isoluminant plane in non-invasive magnetoencephalography (MEG) recordings. To address these discrepancies, we simultaneously recorded local field potentials (LFPs) from V1 (n=2 monkeys) along with scalp electroencephalography (EEG), while presenting luminance-matched hues spanning the entire permissible range of colors. We found that saturated reddish hues produced the strongest gamma in both LFP and EEG in both monkeys. However, gamma was reduced when the colors were desaturated, so that selectivity for reddish hues was diminished or absent on the DKL space, as shown previously. Interestingly, selectivity was further reduced in EEG compared to LFP. Simultaneous recordings from an intermediate visual area (V4, n=1) revealed weak color-induced gamma, partially explaining the weakening of hue selectivity in macro-signals. Gamma power increased with increasing activation along the red-green (L-M) cardinal axis but was virtually absent along the blue-yellow (S-(L+M)) axis, suggesting that gamma could be a reflection of the L-M cone-contrast mechanism. These results comprehensively resolve the earlier discrepancy and shed light about the neural mechanisms underlying gamma generation in primate V1. Significance StatementGamma-band brain rhythms are markers of cortical computation and disease, yet their dependence on color has remained controversial because studies using different recording methods and stimulus color spaces yielded conflicting results. By densely sampling colors across the entire monitor gamut in an isoluminant space and mapping brain rhythms across multiple neural scales in primates, we show that primary visual cortex generates exceptionally strong gamma for saturated reddish hues. Crucially, this effect is driven by contrast in specific cone pathways (specifically, L-M cone contrast), and the selectivity diminishes in desaturated color spaces, downstream visual areas and scalp recordings. This explains why the "red bias" observed invasively often vanishes in non-invasive recordings and demonstrates that color-induced gamma reflects pathway-specific circuit engagement.

neuroscience↗

bioRxiv2026

Emergence of diverse ligase reactivities from a single RNA evolution experiment

RNA enzymes that assemble RNA from shorter pieces would have been important for primordial RNA-based biology. To explore the scope of RNA-catalyzed RNA assembly, we used directed evolution to re-engineer a ligase ribozyme that uses 5'-phosphorimidazolide RNA substrates into a ribozyme that ligates RNA substrates carrying the biologically relevant 5'-triphosphate group. Unexpectedly, this single RNA evolution experiment generated, in addition to the desired triphosphate ligase, four other distinct classes of ligase ribozymes. Three of these four ligase classes were isolated at extremely low abundances, collectively covering <0.1% of the selected RNA population. One class exhibits strict specificity for 5'-phosphorimidazolide substrates, even though these substrates were never presented during evolution. Another ligase class mediates a reaction between its 5'-triphosphate and the substrate's terminal 2'-OH, but only when the substrate carries a 3'-phosphate. This reaction resembles those catalyzed by protein enzymes such as RtcB ligase and plant RNA splicing ligases in RNA repair pathways. The remaining classes catalyze two different but related reactions, each involving the 5'-triphosphate groups on the ribozyme and a distinct internal hydroxyl group on the substrate. These reactions resemble branching reactions catalyzed by naturally occurring ribozymes such as the group II intron and the spliceosome, even though these ribozymes emerged from a synthetic RNA library with no relation to biological catalysts. The emergence of such catalytic diversity from a single RNA evolution experiment under highly constrained selection pressures and the discovery of new enzyme reactivities in rare RNA sequences highlight the catalytic flexibility and evolutionary potential of RNA. These findings strengthen the plausibility that an RNA World could have supported a wide range of chemistries essential for the emergence of life.

biochemistry↗

bioRxiv2025

Planar cell polarity-directed cell crawling drives polarized hair follicle morphogenesis

During epithelial morphogenesis, cell polarity aligns individual cell behaviors into collective motions that shape developing tissues. Here, we combine experiments with computational modeling to investigate how cell-scale forces oriented by Planar Cell Polarity (PCP) direct the collective, counter-rotational cell flows that occur during hair placode morphogenesis. We rule out that PCP directs apical neighbor exchanges, as junctional myosin and PCP protein localization are not co-correlated with junction shrinkage. Instead, we find that PCP directs anterior-directed crawling of placode cells along the basal surface of the tissue through a mechanism that requires cell crawling regulator Rac1. Modeling the placode as a continuum viscoelastic fluid, we find that active forces from cell crawling at the basal surface is sufficient to generate the experimentally observed counter-rotational cell motion at the apical surface. Our results show an unexpected role for PCP in epithelial morphogenesis, centering the basal surface as the site of force generation.

developmental biology↗

bioRxiv2025

Inhibitory Motifs Quench Synchrony Induced by Excitatory Motifs in Biological Neuronal Networks

AO_SCPLOWBSTRACTC_SCPLOWThe connectivity in biological neuronal networks is known to deviate significantly from the random network (Erd[o]s-Renyi) model. Specifically, di-synaptic motifs like reciprocal, convergent, divergent, and chain are found to be either over-represented or under-represented in certain brain regions. Over-representation of such motifs among excitatory neurons is known to induce synchrony. However, cortical activity is typically asynchronous. Thus, it remains unclear how synchrony induced by excitatory motifs may be reduced to physiological levels. To address this question, we systematically vary the prevalence of these four motifs in an Excitatory-Inhibitory (EI) network. We found that over-representation of chain and convergent motifs in the excitatory population led to increased firing rates and greater synchrony. However, this excess synchrony was quenched when we introduced the same type of motifs among inhibitory neurons. Because of the overabundance of motifs, some inhibitory neurons received fewer recurrent inhibitory inputs. Such weakly coupled neurons were primarily driven by uncorrelated external inputs, and therefore, these neurons exerted stronger inhibition on excitatory neurons and reduced both synchrony and firing rates. Thus, we also provide a new mechanism by which synchrony can be controlled in excitatory-inhibitory networks. We predict that the same kind of di-synaptic motifs should be present in both excitatory and inhibitory neurons. Significance StatementComputational models predict that over-representation of di-synaptic motifs among excitatory neurons (as is experimentally observed) should lead to highly synchronous network activity. However, cortical activity is largely asynchronous. To reconcile this mismatch between structural connectivity and network activity we propose a novel mechanism to quench the synchrony. We show that motifs in the inhibitory population can quench the synchrony produced by excitatory motifs. We found that inhibitory neurons that received fewer inhibitory inputs are crucial for quenching the synchrony. Thus, we predict the existence of di-synaptic motifs among inhibitory neurons and argue that modulation of inhibitory neurons with less recurrent connectivity (e.g. SST+ neurons) have a more prominent role in controlling network activity state.

neuroscience↗

bioRxiv2025

Nested Effects of Climate and Substrate in Functional Trait Investment: Insights from Chemical Communication in Geckos

Chemical communication is a crucial signalling mode in lizards, yet its ecological and evolutionary drivers remain poorly understood. In geckos, chemical cues are secreted by follicular glands, whose numbers vary widely across species. To test whether this variation reflects phylogenetic conservatism or ecological adaptation, we assembled trait and ecological data for 659 species (Infraorder: Gekkota) and analysed three predictors--substrate use, diel activity, and climatic regime--using phylogenetic comparative models and path analysis. We detected partial phylogenetic conservatism, but ecological factors explained substantial additional variation within the trait. Substrate exerted the strongest direct effect: terrestrial species consistently had fewer glands than arboreal or rupicolus species, likely reflecting differences in signal persistence across habitats. Climatic factors predominantly exerted an indirect effect, by influencing substrate availability and modulating its influence. Arid conditions selected for reduced chemical investment, whereas mesic, structurally complex forests favoured elevated gland numbers, likely to compensate for faster chemical degradation. These results demonstrate that chemical signalling in geckos evolves under a nested hierarchy of constraints, with climate setting broad ecological limits and substrate imposing the strongest immediate selection. This multiscale framework refines sensory evolution theory and clarifies how communication traits respond to ecological and climatic contexts.

ecology↗

bioRxiv2025

Synapse-related protein alterations and estradiol deficiency associate with early Parkinsonism in female A53T-α-synuclein transgenic mice fed on a high-fat diet

Substantial evidence highlights the detrimental impact of a fat-rich diet on cognitive and emotional behaviour. Epidemiological studies have linked the consumption of saturated fat with an increased risk of Parkinsons disease (PD), whereas a low-fat or ketogenic diet is reported to improve both motor and non-motor symptoms. Several animal model studies further support these associations. However, the impact of a high-fat diet (HFD) on sex-specific behavioural alterations and the underlying molecular mechanism in PD remains poorly studied. In the present study, we investigated the impact of HFD on PD progression in a sex-specific manner using the A53T transgenic mouse model of PD. Behavioural and pathophysiological analyses revealed a faster onset and progression of PD-like phenotype in female mice exposed to HFD compared with the male mice. Proteomics profiling of brain tissues demonstrated positive enrichment of immune system-related pathways in males, while females exhibited considerable downregulation of synapse-associated pathways under HFD conditions. The reduced estradiol level was identified as a potential factor contributing to synaptic dysfunction and the subsequent early onset of PD in female mice. These findings provide novel insights into the sex-specific consequences of HFD on PD pathogenesis and highlight the role of estrogen-linked synaptic vulnerability in mediating diet-induced PD onset.

neuroscience↗

bioRxiv2025

The mechanical code of DNA impacts its interaction with DNA gyrase

DNA:protein interactions involving large structural deformations of DNA underpin essential biological processes. Although correlative evidence suggests that local, sequence-encoded, mechanical properties of DNA can modulate its interactions with large bent-DNA complexes like nucleosomes, direct high-throughput measurements of programmable mechanical modulation of DNA:protein interactions remain lacking. DNA gyrase is a type II topoisomerase that introduces negative supercoils in bacterial chromosomes via a process that involves extensive, nucleosome-scale, DNA wrapping around its two C-terminal domains (CTDs). Here we combine Systematic Evolution of Ligands by EXponential enrichment (SELEX), neural network predictions of DNA intrinsic cyclizability, and high-throughput DNA-compete binding assays to broadly reveal that sequence-encoded DNA mechanics tunes gyrase:DNA interactions by modulating wrapping of DNA around the CTDs. Further, we find that both genomic gyrase cleavage sites, and SELEX-enriched strong gyrase-binding sequences, display marked mechanical asymmetry: an extended region of flexible DNA facilitating wrapping around only one CTD exists on one half of the enzyme footprint. High throughput binding assays further reveal that strong binding to one CTD alone can compensate for weaker dual binding, suggesting that asymmetric attachment may have evolved to balance the need for stable anchoring with conformational flexibility required for catalytic remodelling. Additionally, we identify key GC-rich motifs that independently enhance gyrase:DNA interactions, also in an asymmetric fashion. Our findings establish sequence-encoded DNA mechanics as a tunable determinant of protein:DNA interactions and illustrate how functional asymmetry within a symmetric enzyme can couple stable substrate association with structural plasticity.

biophysics↗

bioRxiv2025

SEASONAL PM2.5 DIFFERENTIALLY REGULATES JAK2/STAT3 SIGNALING IN RURAL AND URBAN COHORTS

Ambient particulate matter (PM2.5) is a major environmental carcinogen linked to lung cancer, yet its molecular insights on asymptomatic non-smokers remains unclear. This study examined the effect of seasonal fluctuations of PM2.5 on oxidative stress and pro-oncogenic signaling in rural (RU) and urban (UR) cohorts from West Bengal, India. Environmental monitoring revealed higher PM2.5 and associated benzo[]pyrene in UR, during winter, induced oxidative stress (elevated ROS, 8-OHdG), reduced antioxidants (SOD, catalase, GPx), and promoted airway inflammation. Transcriptomic and bioinformatic analyses identified activation of IL-6/EGFR-driven JAK2/STAT3 signaling and its crosstalk with Ras/Raf/MAPK, leading to increased expression of downstream effectors (BCL-2, MCL-1, c-MYC, cyclin D1) and repression of tumor suppressors (BAX, p21). Notably, downregulation of JAK/STAT inhibitors PIAS2 and SOCS2 suggested persistent activation of oncogenic signaling. Linear mixed-effects models linked winter PM2.5 surges to oxidative stress, inflammation, and altered JAK2/STAT3 signaling, while regression models showed stronger responses in UR. Risk modeling predicted significantly higher lung cancer mortality in UR, underscoring the role of seasonal PM2.5 surges in JAK2/STAT3-driven carcinogenic susceptibility and the urgent need for targeted interventions.

cancer biology↗

bioRxiv2025

The mechanical code of DNA links DNA bending nucleosome organization and codon choice

Nucleosomes are the fundamental units of chromatin, yet how DNA sequence encodes the mechanics required for their formation remains incompletely understood. Using high-throughput measurements and predictive modeling, we show that nucleosomal DNA is distinguished not only by enhanced isotropic bendability but by coherent anisotropic bending aligned with the DNA helical repeat. Within nucleosome footprints, anisotropy vectors are phase-aligned across thousands of sequences, yielding ensemble-level signatures--such as [~]15 full rotations of bending direction--that directly mirror histone-DNA wrapping. We show that within nucleosomes, reinforcement of bending direction every helical repeat pre-disposes DNA to wrap smoothly around histones, lowering the energetic cost of nucleosome formation. Extending these principles to coding regions, we demonstrate that synonymous codon usage bias varies systematically around nucleosomes in a manner that optimizes DNA mechanical and structural features around nucleosomes and suggest that degeneracy of the genetic code has been exploited to encode both proteins and chromatin architecture. Together, our findings establish DNA anisotropy as a pervasive, sequence-encoded feature of nucleosomal DNA and identify codon usage as a key contributor to this hidden mechanical code.

biophysics↗

bioRxiv2025

Critical phenomenon underlies de novo luminogenesis during mammalian follicle development

A key process during mammalian folliculogenesis is the formation of a fluid-filled antrum around the oocyte. While it is known that the antrum is critical for oocyte maturation and the eventual ovulation, the detailed process underlying de novo luminogenesis remains poorly understood. In this study, we investigated the spatiotemporal dynamics of lumen growth and the cellular mechanism driving this process, using advanced microscopy, molecular perturbations and computational modelling. We found that in secondary follicles, the interstitial gaps exist in a near-critical regime, characterised by a highly dynamic and interconnected fluid network with gap size obeying a power-law distribution. Above a critical size of 180 m, we observed an onset of cell death and the emergence of a stably growing dominant fluid cavity resembling phase separation. By modelling the granulosa cells and the interstitial fluid as a binary fluid, we reproduced the near-critical and phase-separated regimes and found that a spatial gradient of cell-fluid interfacial tension, as observed experimentally, is sufficient to robustly maintain the secondary follicles in a near-critical state. Reducing cell-fluid interfacial tension globally by weakening the cell-cell adhesion between granulosa cells leads to fragmentation of fluid and growth arrest of the dominant cavity, as predicted by the model. Importantly, perturbing the critical state in secondary follicles leads to impaired follicle growth. Altogether, our study reveals how collective spatiotemporal regulation of cell junction mechanics and cell death can contribute to the effective transition between distinct regimes of fluids, which are indispensable for functional maturation of follicles.

developmental biology↗

bioRxiv2025

Dynamic and atypical E-cadherin-based attachments mediate melanoblast migration through confined epithelial spaces

Epithelial tissues are populated with accessory cells such as immune cells, sensory cells, and pigment-producing melanocytes, which must migrate through and intercalate between tightly adherent epithelial cells. Although much is known about how cells migrate through interstitial spaces consisting of predominantly of collagen-rich ECM and mesenchyme, how cells migrate through confined epithelial spaces without impairing barrier function is far less understood. Here, using live imaging of the mouse epidermis, we captured the migration of embryonic melanocytes (melanoblasts) while simultaneously visualizing the basement membrane or epithelial surfaces. We show that melanoblasts migrate through both basal and suprabasal layers of the epidermis and hair follicles where they use keratinocyte surfaces, as well as the basement membrane, as substrates for migration. We show that melanoblasts form atypical and dynamic E-cadherin based attachments to surrounding keratinocytes that largely lack the cytoplasmic catenins known to anchor E-cadherin to the actin cytoskeleton. We show E-cadherin is needed in both melanoblasts and keratinocytes to stabilize migratory protrusions, and that depleting E-cadherin in melanoblasts results in reduced motility and ventral depigmentation in adult mice. These findings illustrate how migratory cells co-opt the cell-cell adhesion machinery connecting adjacent epithelial cells to invade between and migrate through them without interrupting the skin barrier.

cell biology↗

bioRxiv2025

Predicting compatibility between ferredoxins and the Fe protein of nitrogenase using in silico protein modeling

Biological nitrogen fixation is the process by which certain bacteria and archaea use the enzyme nitrogenase to reduce atmospheric nitrogen into bioavailable ammonium. Engineering non-nitrogen-fixing organisms, like plants, to use nitrogenase could reduce dependency on synthetic fertilizer and mitigate the environmental impacts of industrial fertilizer production. However, nitrogenase activity requires delivery of reducing power by small electron carrying proteins known as ferredoxins and flavodoxins, and successfully engineering nitrogenase into new systems will require a mechanistic understanding of electron delivery by these proteins. Most organisms often have multiple ferredoxins, raising the question of which ferredoxin can support nitrogenase activity. The purpose of this study is to gain insight into how we can predict which ferredoxin is compatible with the Fe protein, the component of nitrogenase that interacts with ferredoxin or flavodoxin. Our in silico protein-protein docking simulations reveal that ferredoxins and flavodoxins involved in nitrogen fixation have a distance [≤] 10 [A] between their redox cofactor and the [4Fe-4S] cluster of the Fe protein. We found shorter cofactor distance contributes to faster intermolecular electron tunneling rates (> 106 sec-1). These nitrogen-fixing bacterial ferredoxins also form more complementary interactions with the Fe protein compared to non-nitrogen-fixing bacterial and plant ferredoxins. Heterologous expression of a set of ferredoxins from both nitrogen-fixing and non-nitrogen-fixing bacteria in the diazotroph Rhodopseudomonas palustris support our model-derived prediction that cofactor distances of [≤] 10 [A] favor nitrogenase compatibility. These findings offer a framework to predict and potentially enhance ferredoxin-nitrogenase compatibility, which will help to improve our ability to engineer nitrogen fixation into non-nitrogen-fixing organisms like plants.

microbiology↗