Biology subjects

Biswas, A.

Publications and source records attributed to Biswas, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Distinct Proline residues in hinge-regions of SYMRK generates a phosphocode for releasing Malectin-like-Domain to allow progress of rhizobia-legume symbiosis at epidermal-cortical barrier.

Symbiosis Receptor Kinase (SYMRK), a malectin-like-domain/leucine-rich-repeat receptor-like-kinase (MLD-LRR-RLK), is the upstream most component in Common-Symbiosis-Signalling-Pathway. We highlight two Proline residues that were distinctly acquired by SYMRK orthologues in its hinge-regions to evolve a signalling module for allowing progress of symbionts across transcellular barriers during rhizobia-legume symbiosis. Within the Ectodomain hinge (EctoD-hinge) all MLD-LRR-RLKs have a conserved W1xnGDPCxnW2x4C motif, where SYMRK orthologues within legumes have a distinct signature with a Proline preceding W2 enabling cleavage of SYMRK-EctoD for releasing MLD. Within the kinase hinge (KD-hinge) at gatekeeper+1 position, a conserved Glutamate in MLD-LRR-RLKs is replaced by Proline in all SYMRK orthologues that enabled its dual-specific kinase activity for ensuring EctoD-cleavage. Substitution of either Proline restricted symbionts at the transcellular epidermal-cortical barrier forming infection patches in the nodule apex without affecting epidermal invasion and nodule organogenesis. This halt was entirely overcome by ectopic expression of free MLD demonstrating the released MLD to have an active role in progress of symbionts. Overall, we show that adaptations of distinct Prolines in hinge-regions of SYMRK orthologues in legumes have evolved a signalling module involving dimerization and optimal phosphorylation of SYMRK for releasing MLD as an active transducer of symbiosis signalling.

plant biology↗

bioRxiv2024

Mechanistic basis of temperature-adaptation in microtubule dynamics across frog species

Cellular processes are remarkably effective across diverse temperature ranges, even with highly conserved proteins. In the context of the microtubule cytoskeleton, which is critically involved in a wide range of cellular activities, this is particularly striking as tubulin is one of the most conserved proteins while microtubule dynamic instability is highly temperature sensitive. We thus lack a mechanistic framework that links functional adaptability with environmental pressures. Here, we leverage the diversity of natural tubulin variants from three closely related frog species that live at different temperatures: we combine in vitro reconstitution assays, quantitative biochemistry, and cryogenic electron microscopy to show how a small number of primary sequence changes influences the energy landscape of tubulin interactions and thereby mediates cold-adaptation and microtubule stability. This study thus broadens our conceptual framework for understanding microtubule dynamics and provides insights into how conserved cellular processes are tailored to different ecological niches.

biochemistry↗

bioRxiv2024

Cell State-Specific Cytoplasmic Material Properties Control Spindle Architecture and Scaling

Mitotic spindles are dynamically intertwined with the cytoplasm they assemble in. How the physicochemical properties of the cytoplasm affect spindle architecture and size remains largely unknown. Using quantitative biochemistry in combination with adaptive feedback microscopy, we investigated mitotic cell and spindle morphology during neural differentiation of embryonic stem cells. While tubulin biochemistry and microtubule dynamics remained unchanged, spindles changed their scaling behaviour: in differentiating cells, spindles were significantly smaller than those in equally-sized undifferentiated stem cells. Integrating quantitative phase imaging, biophysical perturbations and theory, we found that as cells differentiated, their cytoplasm became more dilute. The concomitant decrease in free tubulin activated CPAP (centrosomal P4.1-associated protein) to enhance the centrosomal nucleation capacity. As a consequence, in differentiating cells, microtubule mass shifted towards spindle poles at the expense of the spindle bulk, explaining the differentiation-associated switch in spindle architecture. This study shows that cell state-specific cytoplasmic density tunes mitotic spindle architecture. Thus, we reveal physical properties of the cytoplasm as a major determinant in organelle size control.

cell biology↗

bioRxiv2024

Modulation of ribosomal subunit associations by eIF6 is critical for mitotic exit and cancer progression.

Moderating the pool of active ribosomal subunits is critical for maintaining global translation rates. A factor crucial for modulating the 60S ribosomal subunits is eukaryotic translation initiation factor 6. Release of eIF6 from 60S is essential to permit 60S interactions with 40S. Here, using the N106S mutant of eIF6, we show that disrupting eIF6 interaction with 60S leads to an increase in vacant 80S. It further highlights a dichotomy in the anti-association activity of eIF6 that is distinct from its role in 60S biogenesis and shows that the nucleolar localization of eIF6 is not dependent on uL14-BCCIP interactions. Limiting active ribosomal pools markedly deregulates translation especially in mitosis and leads to chromosome segregation defects, mitotic exit delays and mitotic catastrophe. Ribo-Seq analysis of the eIF6-N106S mutant shows a significant downregulation in the translation efficiencies of mitotic factors and specifically transcripts with long 3'UTRs. eIF6-N106S mutation also limits cancer invasion, and this role is correlated with the overexpression of eIF6 only in high-grade invasive cancers suggesting that deregulation of eIF6 is probably not an early event in cancers. Thus, this study highlights the segregation of eIF6 functions and its role in moderating 80S availability for mitotic translation and cancer progression.

molecular biology↗

bioRxiv2024

Liver-specific Mettl14 deletion induces nuclear heterotypia and dysregulates RNA export machinery

Modification of RNA with N6-methyladenosine (m6A) has gained attention in recent years as a general mechanism of gene regulation. In the liver, m6A, along with its associated machinery, has been studied as a potential biomarker of disease and cancer, with impacts on metabolism, cell cycle regulation, and pro-cancer state signaling. However these observational data have yet to be causally examined in vivo. For example, neither perturbation of the key m6A writers Mettl3 and Mettl14, nor the m6A readers Ythdf1 and Ythdf2 have been thoroughly mechanistically characterized in vivo as they have been in vitro. To understand the functions of these machineries, we developed mouse models and found that deleting Mettl14 led to progressive liver injury characterized by nuclear heterotypia, with changes in mRNA splicing, processing and export leading to increases in mRNA surveillance and recycling.

molecular biology↗

bioRxiv2024

Multi-parametric thrombus profiling microfluidics detects intensified biomechanical thrombogenesis associated with hypertension and aging

Arterial thrombosis, which represents a critical complication of cardiovascular diseases, is a leading cause of death and disability worldwide with no effective bioassay for clinical prediction. As a symbolic feature of arterial thrombosis, severe stenosis in the blood vessel creates a high-shear, high-gradient flow environment that effectively facilitates platelet aggregation towards vessel occlusion even with platelet amplification loops inhibited. However, no approach is currently available to comprehensively characterize the size, composition and platelet activation status of thrombi forming under this biorheological condition. Here, we present a thrombus profiling assay that monitors the multi-dimensional attributes of thrombi forming in conditions mimicking the physiological scenario of arterial thrombosis. Using this platform, we demonstrate that different receptor-ligand interactions contribute distinctively to the composition and activation status of the thrombus. Our investigation into hypertensive and older individuals reveals intensified biomechanical thrombogenesis and multi-dimensional thrombus profile abnormalities, demonstrating a direct contribution of mechanobiology to arterial thrombosis and endorsing the diagnostic potential of the assay. Furthermore, we identify the hyperactivity of GPIb-integrin IIb{beta}3 mechanosensing axis as a molecular mechanism that contributes to hypertension-associated arterial thrombosis. By studying the interactions between anti-thrombotic inhibitors and hypertension, and the inter-individual variability in personal thrombus profiles, our work reveals a critical need for personalized anti-thrombotic drug selection that accommodates each patients pathological profile.

bioengineering↗

bioRxiv2024

The Hidden Potential of PDE4 Inhibitor Rolipram: A Multifaceted Examination of its Inhibition of MMP2/9 Reveals Theraputic Implications

A PDE4 inhibitor, Rolipram, was previously found to down-regulate (in a manner dependent on cAMP-PKA) MMP2 and MMP9 levels, important markers of epithelial-to-mesenchymal transition in human breast cancer cell lines. However, zymographic studies revealed that rolipram could also alter the enzymatic activities of these MMPs, even in the presence of the PKA inhibitor H89. This calls for more detailed investigations of the inhibitory mechanism of rolipram on MMP2 and MMP9. The prediction of ligand-based targets through online reverse screening indicated that proteases are likely targets of rolipram. Computational molecular docking also demonstrated significant binding affinities of rolipram for both MMP2 and MMP9 proteins. Concurrently, a well-known inhibitor of MMPs, SB3CT, was utilized as a positive control for this study. The best models of the docked complexes were used as initial conditions for molecular dynamics (MD) simulations to explore their dynamic behavior and stability. In particular, both the MMP2-rolipram and MMP9-rolipram complexes were found to be stable and compact for the duration of the simulation (300 ns). Several stable hydrogen bonds were also detected between the proteins and rolipram. In vitro experiments using primary cells from patients with breast cancer also showed that rolipram could alter the enzymatic activities of MMP2 and MMP9, independent of the cAMP-PKA signaling pathway. These observations indicate the ability of rolipram to control breast cancer by regressing the functions of MMP2 and MMP9, thus having off-targets other than PDE4 to have direct control over proteins that are involved in the advancement of metastasis.

cancer biology↗

bioRxiv2024

Theca cell mechanics and tissue pressure regulate mammalian ovarian folliculogenesis

The maturation of functional eggs within the ovaries is essential for successful reproduction and organismal functions in mammals. Yet, despite its biological and clinical importance, the underlying mechanisms regulating folliculogenesis remain enigmatic. Here, we report a novel role of the surface-anchoring theca cells (TCs) in regulating follicle growth through mechanical signalling. Direct mechanical measurements reveal that these TCs are highly contractile and exert compressive stress to the follicular interior, potentially through active assembly of fibronectin scaffold around the follicles. Abolishing TC contractility disrupts fibronectin assembly, increases follicle size, and decreases intrafollicular pressure and viscosity. We further reveal that the granulosa cells (GCs) within the follicles exhibit spatial patterns of YAP signalling and proliferation, which appear to be decoupled. Transient manipulation of tissue pressure through bulk follicle compression, laser ablation or pharmacological perturbation of TC contractility leads to changes in GC YAP signalling, proliferation, and oocyte-GC communications, while long term abrogation of TC contractility leads to impaired follicle growth. Altogether, our study unveils the unique role of TC-mediated tissue pressure in ensuring robust mammalian ovarian folliculogenesis.

developmental biology↗

bioRxiv2024

Globetrotting geckos: Historical biogeography suggests an Indian origin and an ''Out-Of-India'' dispersal for the cosmopolitan Hemidactylus geckos

AimFollowing the breakup of Gondwana, dispersal events both into and out of India have influenced the biotic assembly of the surrounding landmasses. The cosmopolitan Hemidactylus presents an intriguing group to examine these instances, particularly given its sister relationship with the endemic Dravidogecko found in Indias Western Ghats. Despite earlier theories of Afro-Arabian or Southeast Asian origins for Hemidactylus, its deep divergence from Dravidogecko ([~]57 million years ago) suggests a potential Indian origin, thus contradicting an "Into-India" scenario proposed for the current Indian tetrapod groups. We thus aim to resolve the origins and shed light on the inter-continental dispersals in Hemidactylus by reconstructing its biogeographic history. LocationWorldwide TaxonHemidactylus Geckos MethodsWe use six nuclear genes to reconstruct a reduced representation backbone phylogeny of Hemidactylus using likelihood, Bayesian, and coalescent based methods. We further assemble a timetree using a concatenated dataset of nuclear and mitochondrial markers from 132 of the 192 Hemidactylus species by constraining the topology with the backbone phylogeny and secondary calibrations. We use this chronogram to reconstruct ancestral geographic ranges using BioGeoBEARS, employing a time-stratified approach in conjunction with plate tectonics information to explicitly test four hypotheses regarding the origin of the genus -- An Indian origin, a Southeast Asian origin, a Saharo-Arabian origin, or an Afrotropical origin. ResultsOur findings suggest that the ancestral lineage of Hemidactylus and Dravidogecko colonized the drifting Indian plate from Southeast Asia approximately 57 million years ago, eventually evolving into the two genera in the Indian subcontinent. Following this, Hemidactylus dispersed multiple times from India to Africa and Asia. Main ConclusionThis study proposes an Indian origin for these widely distributed geckos, representing a rare instance of an "Out-of-India" dispersal scenario observed in a non-Gondwanan squamate group. Additionally, our research underscores the significance of incorporating sister taxa in biogeographic analyses to avoid misinterpretations of ancestral ranges.

evolutionary biology↗

bioRxiv2024

Designing Combinatorial Multiepitope Vaccine Candidates against Scrub Typus by a Proteome-wide Immunoinfomatics Approach.

Scrub typhus (ST) is a mite-borne infection caused by the bacteria Orientia tsutsugamushi and a major public health concern in eastern and south eastern Asia. Early diagnosis and immediate intervention with antibiotics are required to limit the severity of the infection. Prophylaxis is compromised by the absence of an effective vaccine against O. tsutsugamushi. Development an effective vaccine is impeded due to extreme divergence of major surface antigens limiting cross-protectivity. Adopting a proteome-wide immunoinformatic approach, here, immunodominant outer membrane proteins are identified and conserved regions enriched in B-cell, Tc-cell, and Th-cell epitopes were mapped. Similarly, immunodominant stretches from salivary proteins of the vector were identified. Fifteen independent MEVs were designed by combining such segments and were analysed for physicochemical and immunological properties. Tertiary structure of the prioritized MEV was modelled, and interaction with TLR2, 4, and 5 was profiled through molecular docking and MD simulation. A glycosylation-deficient version of the MEV was also designed and analysed similarly. Both the MEVs were immune-simulated, which indicated elicitation of effective immune response. In silico cloning and expression were performed for bacterial and mammalian expression systems. Though the proteome-wide combinatorial approach with immunodominant segments demonstrated prospect, experimental validation for its efficacy against ST is warranted.

bioinformatics↗

bioRxiv2024

Enhanced stimulus-induced and stimulus-free gamma in open-eye meditators

Visual stimuli induce "narrowband" gamma oscillations (30-70 Hz) that are linked to attention/binding and attenuate with aging and neurodegeneration. In contrast, meditation increases power in a broad frequency range (>25 Hz). However, the effect of meditation on stimulus-induced gamma is unknown. We recorded EEG from meditators and controls performing open-eye meditation while gamma-inducing stimuli were presented before, during and after meditation. We found that stimulus-induced gamma, like stimulus-free gamma, was stronger in meditators. Interestingly, both gamma signatures co-existed during meditation but were unrelated and prominent in occipital and fronto-temporal regions, respectively. Further, power spectral density (PSD) slope, which becomes shallower with aging, was steeper for meditators. Meditation could boost inhibitory mechanisms leading to stronger gamma and steeper PSDs, potentially providing protection against aging and neurodegeneration. One line summaryStimulus-induced and stimulus-free gamma are stronger in open-eye meditators.

neuroscience↗

bioRxiv2024

Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas syringae and Pseudomonas savastanoi

Microbial experimental evolution is commonly highly repeatable under identical conditions, indicating a potential for short-term evolutionary forecasting. However, it is unclear to what extent evolutionary predictions can be extrapolated to related species adapting in similar environments, which would enable direct testing of general forecasting models and biological assumptions. To further develop a model system for evolutionary forecasting based on adaptation to static culture conditions, we experimentally tested previous predictions for Pseudomonas syringae and Pseudomonas savastanoi. In addition to sequence divergence, these species also differ in their repertoire of diguanylate cyclases that can be mutationally activated to produce the adaptive wrinkly spreader (WS) phenotype and genes for biosynthesis of exopolysaccharides. After experimental evolution, we isolated 32 independent WS mutants for P. syringae and 37 WS mutants for P. savastanoi that had increased ability to colonize the air-liquid interface and reduced motility. As predicted, most mutants had mutations in the wsp operon followed by rarer promoter mutations upstream of uncharacterized diguanylate cyclases. Surprisingly, no mutations were found in wspF, the most commonly mutated gene in the previously characterized species, which was explained by differences in relative fitness. While prediction of mutated regions was largely successful for WspA, mutations in WspE had a divergent pattern for both species. Surprisingly, deletion of known exopolysaccharide loci previously shown to contribute to the adaptive WS phenotype in other species did not reduce fitness, suggesting the presence of additional adhesive components under c-di-GMP control. This study shows that evolutionary forecasts can be extended to related species, but that differences in the genotype-phenotype-fitness map and mutational biases limit predictability on a detailed molecular level. Author summaryBiological evolution is often observed to be repeatable in the short-term, which suggests that it might be possible to forecast and ultimately steer evolution. Evolutionary processes are fundamental to biology but are also central to major societal problems, including antibiotic resistance, cancer, and adaptation to climate change. Experimental evolution with microbes makes it possible to study evolutionary processes in real-time over many generations to allow direct tests of evolutionary forecasts. However, a fundamental problem is that predictive models are usually based on previous experimental data which limits the novelty of the prediction beyond simple repeatability. A more challenging issue is to predict to what degree similar species evolve in similar ways in similar environments. Here we show that one of the best characterized bacterial experimental evolution model systems, biofilm formation at the surface of static tubes in Pseudomonas, can be extended to related species evolving in similar environments. This allowed us to directly test previous evolutionary forecasts to show that similar phenotypes evolved in similar environments, but that predictions of molecular details often fail. This study also elucidates the causes for failed forecasts to allow continuous improvements in predictive models and to delineate the limits of evolutionary forecasting.

evolutionary biology↗

bioRxiv2024

Host response during unresolved urinary tract infection alters mammary tissue homeostasis through collagen deposition and TIMP1

Exposure to pathogens throughout a lifetime influences immunity and organ function. Here, we explored how the systemic host-response to bacterial urinary tract infection (UTI) induces tissue-specific alterations to the mammary gland. Utilizing a combination of histological tissue analysis, single cell RNA sequencing and flow cytometry, we identified that mammary tissue from UTI-bearing mice display collagen deposition, enlarged ductal structures, ductal hyperplasia with atypical epithelial transcriptomes and altered immune composition. Bacterial cells were absent in the mammary tissue and blood of UTI-bearing mice, therefore, alterations to the distal mammary tissue were mediated by the systemic host response to local infection. Furthermore, broad spectrum antibiotic treatment resolved the infection and restored mammary cellular and tissue homeostasis. Systemically, unresolved UTI correlated with increased plasma levels of the metalloproteinase inhibitor, TIMP1, which controls extracellular matrix (ECM) remodeling and neutrophil function. Treatment of nulliparous and post-lactation UTI-bearing female mice with a TIMP1 neutralizing antibody, or broad-spectrum antibiotic, prevented mammary collagen deposition, thus providing evidence for an unexpected link between the systemic host response during UTI and mammary alterations. SummaryThe systemic response during urinary tract infection induces TIMP1-driven collagen deposition specifically into the mammary gland.

developmental biology↗

bioRxiv2024

Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding

Integrase (IN) performs dual essential roles during HIV-1 replication. During ingress, IN functions within an oligomeric "intasome" assembly to catalyze viral DNA integration into host chromatin. During late stages of infection, tetrameric IN binds viral RNA and orchestrates the condensation of ribonucleoprotein complexes into the capsid core. The molecular architectures of HIV-1 IN assemblies that mediate these distinct events remain unknown. Furthermore, the tetramer is an important antiviral target for allosteric IN inhibitors. Here, we determined cryo-EM structures of wildtype HIV-1 IN tetramers and intasome hexadecamers. Our structures unveil a remarkable plasticity that leverages IN C-terminal domains and abutting linkers to assemble functionally distinct oligomeric forms. Alteration of a newly recognized conserved interface revealed that both IN functions track with tetramerization in vitro and during HIV-1 infection. Collectively, our findings reveal how IN plasticity orchestrates its diverse molecular functions, suggest a working model for IN-viral RNA binding, and provide atomic blueprints for allosteric IN inhibitor development.

biochemistry↗

bioRxiv2023

Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization

The first and second-generation clinically used HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the integration step in the HIV-1 replication cycle that is catalyzed by a nucleoprotein assembly called an intasome. However, resistance to even the latest clinically used INSTIs is beginning to emerge. Developmental third-generation INSTIs, based on naphthyridine scaffold, are promising candidates to combat drug-resistant viral variants. Among these novel INSTIs, compound 4f exhibits two distinct conformations when binding to intasomes from HIV-1 and the closely related prototype foamy virus (PFV), despite the high structural similarity of their INSTI binding pockets. The molecular mechanism and the key active site residues responsible for these differing binding modes in closely related intasomes remain elusive. To unravel the molecular determinants governing the two distinct binding modes, we employ a novel molecular dynamics-based free energy approach that utilizes alchemical pathways to overcome the sampling challenges associated with transitioning between two ligand conformations within crowded environments along physical pathways. The calculated conformational free energies successfully recapitulate the experimentally observed binding mode preferences in the two viral intasomes. Analysis of the simulated structures suggests that the observed binding mode preferences are caused by amino acid residue differences in both the front and the central catalytic sub-pocket of the INSTI binding site in HIV-1 and PFV. Additional free energy calculations on mutants of HIV-1 and PFV revealed that while both sub-pockets contribute to the binding mode selection, the central sub-pocket plays a more important role. These results highlight the importance of both side chain and solvent reorganization, as well as the conformational entropy in determining the ligand binding mode and will help inform the development of more effective INSTIs for combatting drug-resistant viral variants.

biophysics↗

bioRxiv2023

Myeloperoxidase-dependent tyrosine halogenation potentiates alpha-defensins functions

Neutrophils are immune cells that eliminate microbes using a powerful arsenal of reactive oxygen species, hypohalous acids, proteases, and antimicrobial peptides -- yet how these cytotoxic effectors act in concert remains poorly understood. Here, we identify an unrecognized synergy between oxidative and non-oxidative neutrophil defenses. We show that myeloperoxidase-derived hypohalous acids selectively halogenate -defensins (HNP1-3) at conserved tyrosine residues. This post-translational modification occurs in both human and rat neutrophils and is prominent in diseases marked by neutrophil-rich inflammation, including cystic fibrosis, bacterial pneumonia, and Staphylococcus aureus abscesses. Halogenation increases HNP1 hydrophobicity without altering its structure, reprogramming these peptides into potent immunomodulatory mediators. Using single-cell transcriptomics and a in vivo peritonitis model, we demonstrate that halogenated HNP1s amplify immune signaling. Our analysis of the human haloproteome reveals a novel oxidative mechanism by which hypohalous acids rewire immune protein functions, uncovering an unexpected layer of cooperation between neutrophil effector systems. The discovery of halogenated HNP1s represents, to our knowledge, the first characterization of a protein halogenation that has biologically significance in human immunity.

biochemistry↗

bioRxiv2023

A genome-wide CRISPR screen supported by human genetics identifies the TNRC18 gene locus as a novel regulator of inflammatory signaling

Interleukin-1{beta} (IL-1{beta}) is dysregulated in many chronic inflammatory diseases, yet the genetic factors influencing IL-1{beta} production and signaling remain largely unknown. Myeloid-derived cells are the primary producers of IL-1{beta}, prompting a genome-wide CRISPR knockout screen in the human myeloid-derived U937 cell model, treated with lipopolysaccharide (LPS) to mimic inflammatory conditions, and sorted for high and low intracellular IL-1{beta} levels. A total of 295 genes were identified as regulators of IL-1{beta} production, including known mediators, such as TLR4, JAK-STAT, IL-10 receptor, and the Cullin ring finger ligase complex. Notably, 57 out of the 295 genes overlapped with loci associated with human inflammatory diseases, including the TNRC18 gene on chromosome 7p22.1 associated with multiple diseases in the Finnish population. U937 cells engineered with the homozygous rs748670681 risk allele associated with inflammatory bowel disease, demonstrated decreased levels of mRNA for TNRC18 and an adjacent gene WIPI2, reduction in LPS-dependent gene activation and cytokine production, but elevation of interferon-responsive gene programs. Transcriptomic profiles for individual knockouts of TNRC18 and WIPI2 attributed the loss of LPS-dependent signaling primarily to TNRC18 while the exacerbation of interferon signaling is a hallmark of loss of WIPI2. Collectively, these findings delineate the global regulatory mechanisms of IL-1{beta} production and provide molecular insights to the role of the rs748670681 variant as a pleiotropic risk factor for inflammatory diseases.

genomics↗

bioRxiv2023

Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes

The packing and confinement of macromolecules in the cytoplasm and nucleoplasm has profound implications for cellular biochemistry. How intracellular density distributions vary and affect cellular physiology remains largely unknown. Here, we show that the nucleus is less dense than the cytoplasm and that living systems establish and maintain a constant density ratio between these compartments. Using label-free biophotonics and theory, we show that nuclear density is set by a pressure balance across the nuclear envelope in vitro, in vivo and during early development. Nuclear transport establishes a specific nuclear proteome that exerts a colloid osmotic pressure, which, assisted by entropic chromatin pressure, draws water into the nucleus. Using C. elegans, we show that while nuclear-to-cytoplasmic (N/C) volume ratios change during early development, the N/C density ratio is robustly maintained. We propose that the maintenance of a constant N/C density ratio is the biophysical driver of one of the oldest tenets of cell biology: the N/C volume ratio. In summary, this study reveals a previously unidentified homeostatic coupling of macromolecular densities that drives cellular organization with implications for pathophysiologies such as senescence and cancer.

biophysics↗