Biology subjects

Nandi, M.

Publications and source records attributed to Nandi, M..

6 recordsLinked to original sources

bioRxiv2025

Phase separation as a tunable regulator of canonical gene regulatory motifs

Gene regulatory networks govern essential cellular processes such as signal transduction, metabolism, and cell fate control. Within these networks, canonical motifs such as genetic toggle switches and repressilators serve as building blocks that generate bistable and oscillatory behaviors. An open question is how cells regulate the dynamical behavior of such motifs, both in natural contexts and in synthetic systems. Recent studies highlight phase separation of transcription factors (TFs) and nucleic acids as a key organizing principle of intracellular biochemistry. In this work, we explore how phase separation of TFs influences the dynamics of toggle switch and repressilator using mean-field theory and stochastic simulations. Our mean-field analysis reveals that phase separation reshapes motif dynamics by altering fixed-point stability and basin geometry in toggle switch, and by altering oscillatory cycles in repressilator. A key finding for both motifs is that when multiple TFs undergo phase separation, the one with the lowest saturation concentration for phase separation dominates system dynamics. Interestingly, stochastic simulations show that the impact of phase separation on fluctuations (or noise) in the abundance of transcription factors within network motifs is architecture-dependent and sharply contrasts with its buffering effect on noise in the expression of isolated genes. Overall, our results show that biomolecular phase separation acts as a physical principle for tuning stability and noise in gene regulatory networks, providing new insights into cellular decision-making.

biophysics↗

bioRxiv2024

A generalized theoretical framework to investigate multicomponent actin dynamics

The length of actin filaments is regulated by the combined action of hundreds of actin-binding proteins. While the roles of individual proteins are well understood, how they combine to regulate actin dynamics in vivo remains unclear. Recent advances in microscopy have enabled precise, high-throughput measurements of filament lengths over time. However, the absence of a unified theoretical framework has hindered a mechanistic understanding of the multicomponent regulation of actin dynamics. To address this, we propose a general kinetic model that captures the combined effects of multiple regulatory proteins on actin dynamics. We provide closed-form expressions for both time-dependent and steady-state moments of the filament length distribution. Our framework not only differentiates between various regulatory mechanisms but also serves as a powerful tool for interpreting current data and driving future experiments.

biophysics↗

bioRxiv2024

Emergence of temporal noise hierarchy in co-regulated genes of multi-output feed-forward loop

Natural variations in gene expression, called noise, are fundamental to biological systems. The expression noise can be beneficial or detrimental to cellular functions. While the impact of noise on individual genes is well-established, our understanding of how noise behaves when multiple genes are co-expressed by shared regulatory elements within transcription networks remains elusive. This lack of understanding extends to how the architecture and regulatory features of these networks influence noise. To address this gap, we study the multi-output feed-forward loop motif. The motif is prevalent in bacteria and yeast and influences co-expression of multiple genes by shared transcription factors. Focusing on a two-output variant of the motif, the present study explores the interplay between its architecture, co-expression patterns of the two genes (including symmetric and asymmetric expressions), and the associated noise dynamics. We employ a stochastic modeling approach to investigate how the binding affinities of the transcription factors influence symmetric and asymmetric expression patterns and the resulting noise dynamics in the co-expressed genes. This knowledge could guide the development of strategies for manipulating gene expression patterns through targeted modulation of transcription factor binding affinities.

systems biology↗

bioRxiv2024

Activation and regulation of a p38α MAPK by its downstream MAPKAP kinase through feedback phosphorylation and LLPS-driven condensate formation.

MAP kinases (MAPKs) represent a class of evolutionarily conserved stress and extracellular stimuli responsive signaling molecules. p38 group of MAPKs known to be activated by dual-specific upstream MAPK kinases and also by autophosphorylation. They activate MAPK activated protein kinases (MAPKAPKs) in a context dependent manner by specific phosphorylation, and together, they play crucial biological roles. One such pair is PMK3, p38-MAPK and its cognate MAPKAPK, MAK2, downstream of DLK1 (MAPK kinase kinase) and MKK4 (MAPK kinase) in C. elegans. They are implicated in axonal regeneration, degeneration and synaptic pruning in response to neuronal injury. Here, we report that PMK3 and MAK2 engage in a feedback relationship, leading to phosphorylation-mediated activation of both kinases. Interaction of PMK3 with MAK2 through the canonical docking site leads to negligible de novo autophosphorylation of PMK3. Phosphorylation of both Thr and Tyr residues on the TxY-motif necessary for the full activation of PMK3 requires catalytic activity of MAK2 as confirmed by mass spectrometry. Distribution of phosphorylation sites on either kinase when incubated together, and presence of long intrinsically disordered regions in each kinase indicate that PMK3:MAK2 complex is conformationally plastic in nature. MAK2 increases bioavailability of aggregation-prone PMK3 by virtue of its ability to form LLPS-driven condensates in vitro, wherein they retain enzymatic activities and phosphorylate each other. Furthermore, experiments with transgenic C. elegans reveal that MAK2 controls stability of PMK3 and localization of PMK3 puncta in touch neuron. Our observations offer an unreported activation mechanism of a p38-MAPK by its downstream MAPKAPK. Significance StatementMAPK kinases are evolutionarily conserved, and are key players in stress response, cell survival, differentiation, metabolic processes and neuronal response to injury. MAPK pathways are primarily activated through unidirectional flow of phosphorylation-signal MAP3K to MAP2K to MAPK, and in some cases to a downstream MAPKAPK. We found that a C. elegans MAPK (PMK3) can also be activated by its downstream MAPKAPK (MAK2) through feedback phosphorylation that ensures robust activation of PMK3 by MAK2 without requiring the MAP2K. Furthermore, MAK2 increases bioavailability of activation-competent and active PMK3 by preventing its aggregation through LLPS-driven condensate formation in vitro and in the worm neuron. This feedback relationship might ensure rapid activation of such MAPK pathways in response to nervous system injury or stress.

biochemistry↗

bioRxiv2024

Real-time visualization reveals Mycobacterium tuberculosis ESAT-6 disrupts phagosome via fibril-mediated vesiculation

Mycobacterium tuberculosis (Mtb) evades host defense by hijacking and rupturing the phagosome, enabling it to escape to the host cytosol for its survival. ESAT-6, a secreted virulence protein of Mtb, is known to be critical for phagosome rupture. However, the mechanism of ESAT-6-mediated disruption of the phagosomal membrane remains unknown. Using in vitro reconstitution and numerical simulations, we discover that ESAT-6 polymerization remodels and vesiculates phagosomal membrane. In contrast to the pore formation triggered by a bilayer-spanning conformation, we find that the binding of ESAT-6 to the phagosomal membrane is shallow. Such shallow insertion leads to membrane shape transition leading to tubular and bud-like deformations on the membrane in a concentration-dependent manner, facilitated by the reduction in membrane tension and compressibility modulus. Strikingly, our observations suggest that ESAT-6 polymerizes in bulk and on the membrane, both in vitro and in macrophage. Numerical simulations demonstrate that growing fibrils generate both radial and tangential forces causing local remodeling and shape transition of the membrane. Using micropipette aspiration, we quantitatively show that ESAT-6 bound tensed membrane undergoes local changes in membrane curvature and lipid phase separation, also facilitated by the direct contact of the bacteria inside the phagosome. Nonetheless, the vesiculation of the buds is primarily driven by the forces exerted by the polymerization of ESAT-6. Such ESAT-6 mediated vesiculation induces apoptosis and host cell death in a concentration and time-dependent manner that promotes infection. Overall, the findings provide mechanistic insights into the long-standing question of phagosome disruption by Mtb for its escape.

biophysics↗

bioRxiv2023

SARS-CoV-2 spike antigen-specific B cell and antibody responses in pre-vaccination period COVID-19 convalescent males and females with or without post-covid condition

BackgroundFollowing SARS-CoV-2 infection a significant proportion of convalescent individuals develop the post-COVID condition (PCC) that is characterized by wide spectrum of symptoms encompassing various organs. Even though the underlying pathophysiology of PCC is not known, detection of viral transcripts and antigens in tissues other than lungs raise the possibility that PCC may be a consequence of aberrant immune response to the viral antigens. To test this hypothesis, we evaluated B cell and antibody responses to the SARS-CoV-2 antigens in PCC patients who experienced mild COVID-19 disease during the pre-vaccination period of COVID-19 pandemic. MethodsThe study subjects included unvaccinated male and female subjects who developed PCC or not (No-PCC) after clearing RT-PCR confirmed mild COVID-19 infection. SARS-CoV-2 D614G and omicron RBD specific B cell subsets in peripheral circulation were assessed by flow cytometry. IgG, IgG3 and IgA antibody titers toward RBD, spike and nucleocapsid antigens in the plasma were evaluated by ELISA. ResultsThe frequency of the B cells specific to D614G-RBD were comparable in convalescent groups with and without PCC in both males and females. Notably, in females with PCC, the anti-D614G RBD specific double negative (IgD-CD27-) B cells showed significant correlation with the number of symptoms at acute of infection. Anti-spike antibody responses were also higher at 3 months post-infection in females who developed PCC, but not in the male PCC group. On the other hand, the male PCC group also showed consistently high anti-RBD IgG responses compared to all other groups. ConclusionsThe antibody responses to the spike protein, but not the RBD-specific B cell responses diverge between convalescent males and females, and those who develop PCC or not. Our findings suggest that sex-related factors may also be involved in the development of PCC via modulating antibody responses to the SARS-CoV-2 antigens. Short SummaryPost-COVID Condition (PCC) is lingering illness that afflicts a significant proportion of COVID-19 patients from three months after clearing SARS-CoV-2 infection. Therapy for PCC is only palliative and the underlying disease mechanisms are unclear. The wide spectrum of PCC symptoms that can affect different organs and the detection of viral components in tissues distant from lungs raise the possibility that PCC may be associated with aberrant immune response due to presence of viral antigens. Therefore, we studied B cell and antibody responses to the spike and nucleoprotein antigens in PCC patients who cleared mild SARS-CoV-2 infection during the pre-vaccination COVID-19 pandemic period. We observed divergent patterns of immune reactivity to the spike protein in PCC males and females at different times post-infection, suggesting that the immune responses in PCC may also be influenced by sex-related factors.

immunology↗