Biology subjects

Mayor, S.

Publications and source records attributed to Mayor, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Tropomyosin and Vinculin antagonistically mediate GPI-anchored protein nanoclustering

The plasma membrane is laterally organised into dynamic nanoscale and mesoscale domains. Glycosylphosphatidylinositol-anchored proteins (GPI-APs) form actomyosin dependent nanoclusters at the outer leaflet of the plasma membrane via transbilayer coupling to inner leaflet lipids. These nanoclusters are nucleated downstream of integrin activation in a mechanochemical fashion and require vinculin and myosin 1 activity. Here, we identify an antagonistic relationship between vinculin and a negative regulator of myosin 1, tropomyosin, in regulating GPI-AP nanoclustering. We show vinculin mediated restoration of clustering is myosin-1 sensitive. The actin and lipid-binding vinculin tail is sufficient to restore clustering, indicating that vinculin, in particular its actin and lipid-proximal tail promote nanoclustering. Furthermore, re-expression of the non-muscle tropomyosin isoform Tpm2.1 in Tpm2-deficient MDA-MB-231 cells suppress GPI-AP nanoclustering while Tpm2.1 mutants defective in stable actin-filament association do not. Structural superposition of actin-bound vinculin tail and tropomyosin assemblies suggests that vinculin and tropomyosin engage overlapping or closely adjacent surfaces on actin filaments. Consistent with this, depletion of tropomyosin in vinculin-null cells restores GPI-AP nanoclustering. Together these results suggest that competitive interactions between tropomyosin and vinculin regulate actin availability for myosin 1 and hence contribute to the regulation of GPI-AP nanoclusters.

cell biology↗

bioRxiv2025

Two-colour Imaging Fluorescence Correlation Spectroscopy (ImFCS) probes the influence of the juxta-membrane actin-cortex

Here we extend Imaging Fluorescence Correlation Spectroscopy (ImFCS), together with bright, photostable fluorophores, to quantify how the juxta-membranous actin cortex influences plasma membrane dynamics. This problem is technically challenging because the membrane is only a few nanometres thick, whereas the axial resolution of live-cell fluorescence imaging is on the order of 100 nm. We address this by engineering a membrane-anchored actin reporter that combines a weakly interacting actin-binding domain with bright, photostable fluorophores optimized for two-colour ImFCS. This design enables the generation of simultaneous, co-registered diffusion maps where the mobility of the reporter serves as a dynamic sensor for the local density of the cortical actin network. The actin-binding reporter displays diffusion coefficients spanning more than two orders of magnitude, in stark contrast to an otherwise similar reporter that cannot bind actin, which diffuses much faster and within a much narrower range. Thus, the mobility of the reporter becomes a sensitive spatial readout of actin-mediated constraints. By comparing, on a pixel-by-pixel basis, the diffusion of the actin-binding reporter with that of the non-binding mutant, we construct an actin-occupancy map that quantifies the fraction of the membrane functionally influenced by cortical actin. Using this approach, we find that the juxta-membrane actin cortex modulates transport over more than 80% of the cell surface. Our two-channel ImFCS strategy establishes diffusion-based comparison as a general methodology to map the functional footprint of the cortical cytoskeleton on live cell membranes.

biophysics↗

bioRxiv2025

Diverse ancestral myosin motors generate and segregate distinct types of nanocluster-rich domains at the plasma membrane

Molecular organization of the plasma membrane (PM) at nano and micron scales is critical for its function in all living cells. This emerges not only from the self-assembly of lipids and proteins but also from active forces originating in the underlying cytoskeletal cortex. These forces drive membrane molecules into non-equilibrium steady state patterns such as nanoclusters. However, the molecular agents connecting membrane organization with cytoskeletal dynamics and stresses have remained unknown. Here we show that two classes of ubiquitous ancestral non-muscle myosins are deployed for the organization of different types of membrane components. Inner-leaflet localized Class I myosins link outer-leaflet GPI-anchored molecules to juxta-membrane actin-filaments, whereas the more cortically-localized Class II myosins operate on transmembrane proteins endowed with actin-binding capacity. Consistent with an active Flory Huggins theory for phase separation, these observations show that the distinct motor-driven membrane molecules generate spatially segregated mesoscale domains, enriched in nanoclusters derived from different myosin classes. Moreover, chemically reversible post-translational modifications such as palmitoylation enable concatenation of these domains by enhancing affinity of the membrane domain constituents for each other. We anticipate that the segregation potential of the ATP-fueled cell membrane is made available for the crucial purpose of modulating information transduction because it can be regulated in space and time during the construction of signaling cascades, underpinning functional plasma membrane organization.

cell biology↗

bioRxiv2025

Active flows drive clustering and sorting of membrane components with differential affinity to dynamic actin cytoskeleton

Several cell membrane proteins, including signalling receptors and cell adhesion receptors, bind to contractile cortical F-actin at the cytoplasmic leaflet. Interaction with contractile actomyosin and associated actin flows drives these proteins into nanoscale clusters and mesoscopic assemblies of physiological relevance. In the context of diverse actin-binding membrane proteins, we ask how a specific composition of the local cluster/assembly may be achieved. Using in vitro reconstitution together with kinetic Monte Carlo simulations our studies reveal that an interplay between differential actin-binding affinity, protein-protein interactions and actomyosin remodelling leads to specific molecular patterning within a cluster and sorting between clusters. We show that in the lamellipodia of spreading cells in vivo, actin flows also result in the sorting of high and low-affinity actin-binders. This affinity-based sorting mechanism provides an attractive means for locally controlling cell membrane composition via engagement with the active cortical meshwork beneath.

cell biology↗

bioRxiv2025

Assessing plant phenological changes based on drivers of spring phenology

Understanding plant phenological responses to climate warming is crucial for predicting changes in plant communities and ecosystems but challenging when relying on sensitivity analysis that is not based on drivers of spring phenology. In this article, we present a new measure phenological lag to quantify the overall effect of phenological constraints including insufficient winter chilling, photoperiod, and environmental stresses, based on observed response and that expected from species-specific changes in spring temperatures, i.e., changes in spring forcing (degree days) from warming and average temperature at budburst with the warmer climate. We applied this new analytical framework to a global dataset with 980 species and 1527 responses to synthesize observed changes in spring budburst (leafing or flowering) and investigate the mechanisms of differential phenological responses reported previously. We found longer phenological lags with experimental studies and native plants in flowering, likely due to more stressful environments associated with warmer and drier climate. Less forcing changes were mainly responsible for the smaller responses in leafing and flowering in boreal region (compared to temperate region) and in grass leafing (compared to trees and shrubs). Higher budburst temperatures also contributed to the smaller responses in flowering for experimental studies and with herbs and grasses. The effects of altitude, latitude, MAT, and average spring temperature change were minor (all combined <2.5% variations), while those of photoperiod and long-term precipitation were not significant in influencing spring phenology. Our method helps to determine mechanisms responsible for changes in spring phenology and differences in plant phenological responses.

ecology↗

bioRxiv2024

Solvatochromic reporter to image plasma membrane order leaflet by leaflet reveals ahighly asymmetric bilayer locally modulated by transbilayer interactions

The plasma membrane (PM) of cells is an asymmetric bilayer composed of a complex mixture of lipids and proteins. The emergent biophysical properties of its leaflets and their consequence on cellular function remain unexplored owing to the limitation in available probes. In this manuscript, we report on the design and characterisation of a PM-localised solvatochromic probe, C3L, based on the established reporter Laurdan. C3L is retained at the inner-leaflet due to flippase and scramblase activity, as determined by Bovine Serum Albumin-based back exchange experiments. By measuring the Generalized Polarization of C3L we are able to determine membrane order, leaflet-by-leaflet at the PM. Our results reveal that the PM is made of a tightly-packed outer/exofacial-leaflet in contrast to a disordered inner/cytoplasmic-leaflet. This differential packing is established by the maintenance of lipid asymmetry, the presence of specific lipids, Sphingomyelin in the outer-leaflet and Phosphatidylserine at the inner-leaflet, and exaggerated during mesenchymal to epithelial transition. We find spatial signatures of local modulation of the inner leaflet by protein scaffolds which promote trans-bilayer coupling of lipids. C3L thus informs on steady state lipid organisation at the asymmetric membrane while allowing further exploration of spatial regulation of lateral heterogeneity at each leaflet.

cell biology↗

bioRxiv2024

Causal discovery in biodiversity-mediated social-ecological systems

Global biodiversity loss and climate change exacerbate feedbacks within social-ecological systems, i.e., between ecosystems, their services and well-being of human societies. Our ability to mediate these feedbacks is hampered by incomplete understanding of the underlying causal links, which could benefit from interdisciplinary approaches to discover theoretical or empirical links from heterogeneous data characteristic of social-ecological studies. We propose a novel framework connecting literature-based causal knowledge with data-driven inference of causality. We test this framework for the highly biodiverse island of Borneo by conducting a systematic literature review of 7473 studies over 170 years, and a causal inference analysis for three conceptual causal diagrams connecting global change, socio-economics, ecosystem services, and biodiversity-ecosystem function using a set of 227 spatially explicit variables. We find that, while natural or social processes have been mostly studied independently, a set of studies already documents causal links across social-ecological domains for processes related to deforestation, food or energy. Causal discovery unveiled consistent negative causal links between global change, social-economic landscape, and biodiversity-ecosystem function, and positive causal links between global change and socio-economics, and these links were robust to indicator selection and addition. We detected few and weak links between social-economic landscape, global change, and ecosystem services. When comparing the data-driven inferred causal links to those documented by the literature, we find that links between biodiversity and ecosystem function with global change, and links between social-economic landscape and ecosystem services were also consistent, and causal analysis uncovered new (potential) causal links not yet described in the literature. Significance StatementAddressing climate change and biodiversity loss in the Anthropocene requires us to recognize that human societies and ecological systems are inherently interconnected in complex adaptive systems. Causal understanding in social-ecological systems enables understanding system dynamics and response to pressures and shocks. While promising, few studies have studied these systems using a combination of big literature which provides the state-of-the-knowledge and big data that provides the underlying information for causal discovery. With this framework, we can specify and rigorously test, causal links in biodiversity-mediated social-ecological processes under global change and examine potential interventions that lead to much needed sustainable outcomes.

ecology↗

bioRxiv2023

Growth factor-induced desialylation for the fast control of endocytosis

It is commonly assumed that the glycan makeup of glycoproteins that reach the cell surface is final and static. Here, we challenge this notion by the discovery of a molecular switch that induces acute and reversible changes of glycans on the plasma membrane. We demonstrate that within minutes, the epidermal growth factor triggers the galectin-driven endocytosis of cell surface glycoproteins, such as integrins, that are key regulators of cell adhesion and migration. The onset of this process, mediated by the Na+/H+ antiporter NHE-1 and the neuraminidases Neu1/3, requires the pH-triggered enzymatic removal of sialic acids whose presence otherwise prevents galectin binding. Desialylated glycoproteins are then retrogradely transported to the Golgi apparatus where their glycan makeup is reset, and their function is repurposed to regulate EGF-dependent invasive cell migration. Glycosylation at the cell surface thereby emerges as a dynamic and reversible regulatory post-translational modification that controls a highly adaptable trafficking pathway.

cell biology↗

bioRxiv2023

Genomic surveillance reveals circulation of multiple variants and lineages of SARS-CoV-2 during COVID-19 pandemic in Indian city of Bengaluru

Genomic surveillance in response to coronavirus disease (COVID-19) pandemic is crucial for tracking spread, identify variants of concern (VoCs) and understand the evolution of its etiological agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). India has experienced three waves of COVID-19 cases, which includes a deadly wave of COVID-19 that was driven by the Delta lineages (second/Delta wave) followed by another wave driven by the Omicron lineages (third/Omicron wave). These waves were particularly dramatic in the metropolitan cities due to high population density. We evaluated the prevalence, and mutational spectrum of SARS-CoV-2 variants/lineages in one such megapolis, Bengaluru city, across these three waves between October 2020 and June 2022. 15,134 SARS-CoV-2 samples were subjected to whole genome sequencing (WGS). Phylogenetic analysis revealed, SARS-CoV-2 variants in Bengaluru city belonged to 18 clades and 196 distinct lineages. As expected, the Delta lineages were the most dominant lineages during the second wave of COVID-19. The Omicron lineage BA.2 and its sublineages accounted for most of the COVID-19 cases in the third wave. Most number of amino acid changes were observed in spike protein. Among the 18 clades, majority of the mutations and least similarity at nucleotide sequence level with the reference genome were observed in Omicron clades.

genomics↗

bioRxiv2022

Quantitative fluorescence emission anisotropy microscopy for implementing homo-FRET measurements in living cells.

Quantitative fluorescence emission anisotropy microscopy reveals the organization of fluorescently labelled cellular components and allows for their characterization in terms of changes in either rotational diffusion or homo-Forsters energy transfer characteristics in living cells. These properties provide insights into molecular organization, such as orientation, confinement and oligomerization in situ. Here we elucidate how quantitative measurements of anisotropy using multiple microscope systems may be made, by bringing out the main parameters that influence the quantification of fluorescence emission anisotropy. We focus on a variety of parameters that contribute to errors associated with the measurement of emission anisotropy in a microscope. These include the requirement for adequate photon counts for the necessary discrimination of anisotropy values, the influence of extinction coefficients of the illumination source, the detector system, the role of numerical aperture and excitation wavelength. All these parameters also affect the ability to capture the dynamic range of emission anisotropy necessary for quantifying its reduction due to homo-FRET and other processes. Finally, we provide easily implementable tests to assess whether homo-FRET is a cause for the observed emission depolarization.

biophysics↗

bioRxiv2022

Quantitative analysis of three-dimensional cell organisation and concentration profiles within curved epithelial tissues

Organogenesis involves folding of flat epithelial tissues into three-dimensional (3D) shapes. Quantitative analysis in 3D of the concentration gradients of biochemical and mechano-chemical cues that shape the tissue has remained a challenge, due to the complex tissue geometries. Towards addressing this, we present a methodology that transforms the cartesian images acquired by high-resolution confocal microscopy of curved tissues into a laminar organisation from the outer-most tissue surface. We further detail a data-based intensity correction method to account for the intensity variations that arise as a consequence of the global geometry. Applying our approach to the dome-shaped Drosophila wing disc, we quantitatively estimate the concentration profiles of different biochemical signals, including the Wingless morphogen gradient. The laminar data-organisation method also enabled visualisation of apical and basal layers facilitating an accurate 3D reconstruction of cell shapes within the pseudostratified epithelium. We find that the columnar disc proper cells have irregular 3D shapes and undergo frequent apico-basal cell intercalations, concomitantly leading to cell neighbour exchanges along the apico-basal axis. The workflow of image processing described here may be employed to quantify 3D concentration gradients and 3D cellular organisation in any layered curved tissue, provided a marker describing the reference surface manifold is available.

developmental biology↗

bioRxiv2022

Active emulsions in living cell membranes driven by contractile stresses and transbilayer coupling

The spatiotemporal organisation of proteins and lipids on the cell surface has direct functional consequences for signaling, sorting and endocytosis. Earlier studies have shown that multiple types of membrane proteins including transmembrane proteins that have cytoplasmic actin binding capacity and lipid-tethered GPI-anchored proteins (GPI-APs) form nanoscale clusters driven by active contractile flows generated by the actin cortex. To gain insight into the role of lipids in organizing membrane domains in living cells, we study the molecular interactions that promote the actively generated nanoclusters of GPI-APs and transmembrane proteins. This motivates a theoretical description, wherein a combination of active contractile stresses and transbilayer coupling drive the creation of active emulsions, mesoscale liquid ordered (lo) domains of the GPI-APs and lipids, at temperatures greater than equilibrium lipid-phase segregation. To test these ideas we use spatial imaging of homo-FRET combined with local membrane order and demonstrate that mesoscopic domains enriched in nanoclusters of GPI-APs are maintained by cortical actin activity and transbilayer interactions, and exhibit significant lipid order, consistent with predictions of the active composite model.

cell biology↗

bioRxiv2022

Cellular compartmentalisation and receptor promiscuity as a strategy for accurate and robust inference of position during morphogenesis

Precise spatial patterning of cell fate during morphogenesis requires accurate inference of cellular position. In making such inferences from morphogen profiles, cells must contend with inherent stochasticity in morphogen production, transport, sensing and signalling. Motivated by the multitude of signalling mechanisms in various developmental contexts, we show how cells may utilise multiple tiers of processing (compartmentalisation) and parallel branches (multiple receptor types), together with feedback control, to bring about fidelity in morphogenetic decoding of their positions within a developing tissue. By simultaneously deploying specific and nonspecific receptors, cells achieve a more accurate and robust inference. We explore these ideas in the patterning of Drosophila melanogaster wing imaginal disc by Wingless morphogen signalling, where multiple endocytic pathways participate in decoding the morphogen gradient. The geometry of the inference landscape in the high dimensional space of parameters provides a measure for robustness and delineates stiff and sloppy directions. This distributed information processing at the scale of the cell highlights how local cell autonomous control facilitates global tissue scale design.

biophysics↗

bioRxiv2021

Inhibition of HIV-1 immune modulation by small molecules targeting viral Nef-host CD80 interface

HIV-1 causes diverse immunomodulatory responses in the host, including the down-regulation of co-stimulatory proteins CD80/86, mediated by HIV-1 protein Nef, blunting T-cell activation. Using a screening cascade of biochemical and cell-based assays, we identified potent small molecules representing three chemical scaffolds namely amino pyrimidine, phenoxy acetamide and bi-aryl heteroaryl carbamate which target the protein-protein interaction interface of CD80/86 and Nef with sub-micromolar potency. These molecules restore CD80/86 surface levels in HIV-1-Nef infected antigen presenting cells and T-cell activation. Nef-CD80 interface and small molecule binding sites were mapped by using computational docking and structural studies, followed by validation by mutational analysis. This analysis resulted in the identification of two key residues, K99 and R111, which were associated with down-modulation of CD80 surface levels by Nef and important for small molecule binding. Targeting these interacting residues disabled Nef-mediated down-modulation of CD80 surface levels, consequently restoring T-cell activation. Thus, we validate a new target, the Nef-CD80/86 protein-protein interaction interface, with a potential to develop new inhibitors to counteract the immunomodulatory consequences of HIV-1.

microbiology↗

bioRxiv2021

Cortical actin flow activates an alpha-catenin clutch to assemble adherens junctions

Adherens junctions allow cell contact to inhibit epithelial migration. But a long-standing puzzle is how locomotion is downregulated when E-cadherin adhesions form at surfaces perpendicular, but not those parallel, to the direction of migration. We now show that this arises from coupling between E-cadherin adhesions and the retrograde cortical flows of leader cells in migrating epithelia. At interfaces perpendicular to the direction of motion, such flows are antiparallel, which generates a tensile signal that induces the actin-binding domain of -catenin to promote lateral growth of nascent adhesions and inhibit the lamellipodial activity necessary for migration. At interfaces parallel to the direction of motion, by contrast, cortical flows are aligned and no such mechanical inhibition takes place. Therefore, -catenin mechanosensitivity in the clutch between E-cadherin and cortical F-actin allows cells to interpret the direction of motion via cortical flows and trigger the first signal for contact to inhibit locomotion.

cell biology↗

bioRxiv2020

Niclosamide inhibits SARS-CoV2 entry by blocking internalization through pH-dependent CLIC/GEEC endocytic pathway

Many viruses utilize the host endo-lysosomal network to infect cells. Tracing the endocytic itinerary of SARS-CoV2 can provide insights into viral trafficking and aid in designing new therapeutic targets. Here, we demonstrate that the receptor binding domain (RBD) of SARS-CoV2 is internalized via the clathrin and dynamin-independent, pH-dependent CLIC/GEEC (CG) endocytic pathway. Endosomal acidification inhibitors like BafilomycinA1 and NH4Cl, which inhibit the CG pathway, strongly block the uptake of RBD. Using transduction assays with SARS-CoV2 Spike-pseudovirus, we confirmed that these acidification inhibitors also impede viral infection. By contrast, Chloroquine neither affects RBD uptake nor extensively alters the endosomal pH, yet attenuates Spike-pseudovirus entry, indicating a pH-independent mechanism of intervention. We screened a subset of FDA-approved acidification inhibitors and found Niclosamide to be a potential SARS-CoV2 entry inhibitor. Niclosamide, thus, could provide broader applicability in subverting infection of similar category viruses entering host cells via this pH-dependent endocytic pathway.

cell biology↗

bioRxiv2020

Cargo-specific recruitment in clathrin and dynamin-independent endocytosis

Spatially controlled, cargo-specific endocytosis is essential for development, tissue homeostasis, and cancer invasion and is often hijacked by viral infections 1. Unlike clathrin-mediated endocytosis, which exploits cargo-specific adaptors for selective protein internalization, the clathrin and dynamin-independent endocytic pathway (CLIC-GEEC, CG-pathway) has until now been considered a bulk internalization route for the fluid phase, glycosylated membrane proteins and lipids 2,3. Although the core molecular players of CG endocytosis have been recently defined, no cargo-specific adaptors are known and evidence of selective protein uptake into the pathway is lacking 3. Here, we identify the first cargo-specific adaptor for CG-endocytosis and demonstrate its clinical relevance in breast cancer progression. By combining unbiased molecular characterization and super-resolution imaging, we identified the actin-binding protein swiprosin-1 (EFHD2) as a cargo-specific adaptor regulating integrin internalization via the CG-pathway. Swiprosin-1 couples active Rab21-associated integrins with key components of the CG-endocytic machinery, IRSp53 and actin. Swiprosin-1 is critical for integrin endocytosis, but not for other CG-cargo and supports integrin-dependent cancer cell migration and invasion, with clinically relevant implications for breast cancer. Our results demonstrate a previously unknown cargo selectivity for the CG-pathway and opens the possibility to discover more adaptors regulating it.

cell biology↗

bioRxiv2020

PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak

The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium has achieved its initial goal of completing the sequencing of 1000 SARS-CoV-2 genomes from nasopharyngeal and oropharyngeal swabs collected from individuals testing positive for COVID-19 by Real Time PCR. The samples were collected across 10 states covering different zones within India. Given the importance of this information for public health response initiatives investigating transmission of COVID-19, the sequence data is being released in GISAID database. This information will improve our understanding on how the virus is spreading, ultimately helping to interrupt the transmission chains, prevent new cases of infection, and provide impetus to research on intervention measures. This will also provide us with information on evolution of the virus, genetic predisposition (if any) and adaptation to human hosts. One thousand and fifty two sequences were used for phylodynamic, temporal and geographic mutation patterns and haplotype network analyses. Initial results indicate that multiple lineages of SARS-CoV-2 are circulating in India, probably introduced by travel from Europe, USA and East Asia. A2a (20A/B/C) was found to be predominant, along with few parental haplotypes 19A/B. In particular, there is a predominance of the D614G mutation, which is found to be emerging in almost all regions of the country. Additionally, mutations in important regions of the viral genome with significant geographical clustering have also been observed. The temporal haplotype diversities landscape in each region appears to be similar pan India, with haplotype diversities peaking between March-May, while by June A2a (20A/B/C) emerged as the predominant one. Within haplotypes, different states appear to have different proportions. Temporal and geographic patterns in the sequences obtained reveal interesting clustering of mutations. Some mutations are present at particularly high frequencies in one state as compared to others. The negative estimate Tajimas D (D = -2.26817) is consistent with the rapid expansion of SARS-CoV-2 population in India. Detailed mutational analysis across India to understand the gradual emergence of mutants at different regions of the country and its possible implication will help in better disease management.

genomics↗