Biology subjects

Rawal, S.

Publications and source records attributed to Rawal, S..

10 recordsLinked to original sources

bioRxiv2026

A histidine switch controls the pH-responsive self-assembly of a helical protein filament

Self-assembling helical protein filaments underlie diverse biological processes, from signaling pathways to cell motility. Encoding tunable self-assembly into the sequences of filamentous proteins remains a major challenge. Here, we discovered that the caspase-9 CARD can natively self-assemble into helical filaments in a pH-regulated manner. We defined the determinants of filament assembly using an integrative structural, biophysical, and computational approach. Using NMR spectroscopy, we found that the protonation of a single histidine residue near an N-terminal helix dipole, H38, regulates the pH-dependent self-assembly process. Charge-altering mutations at this site tune thermodynamic stability and filament self-assembly across solution and pH conditions. We solved 3.3- and 3.5-[A] cryo-EM structures of the wild-type and H38R filaments, respectively, which show H38 positioned directly at a filament interface. Molecular dynamics simulations show that H38 functions as a molecular switch, whereby protonation rotates its positively charged side-chain toward solvent and away from the partial-positive charge at the N-terminal helix dipole. This reflects a fine balance between stabilizing intermolecular association and a destabilizing intramolecular electrostatic clash at the helix dipole. More broadly, across 350 helix-containing protein domains we identified electrostatic contributions to protein stability near helix dipoles by integrating AlphaFold2 predictions with deep mutational scanning data. Together, our results identify a native, pH-sensitive histidine switch that regulates a self-assembling helical protein filament. Our results establish a mechanism by which charge-altering mutations near helical N-termini can be engineered to control side-chain rotamers, protein stability, and self-assembly.

biophysics↗

bioRxiv2025

A histidine switch regulates pH-dependent filament formation by the caspase-9 CARD

The caspase activation and recruitment domain (CARD) mediates protein-protein interactions in apoptotic and inflammatory signaling pathways. In humans, more than 30 proteins contain a CARD, several of which have been reported to polymerize into helical filaments. Here we found that the CARD from the apoptotic protease caspase-9 (C9CARD) self assembles into filaments in vitro at physiological pH and salt concentrations. The C9CARD more readily polymerizes under low-salt or mildly acidic conditions, suggesting a significant role for electrostatic interactions in mediating filament formation. Using NMR spectroscopy, we determined the pKa of the lone histidine residue, H38, which supports a role for histidine protonation in enhancing filament formation. Indeed, mutation of H38 to introduce a positive (H38R) or negative (H38D) charge, or to remove the pH-dependence of the side chain at this site altogether (H38N), dramatically alters the filament propensity of the domain. Using cryo-election microscopy, we determined 3.4- and 3.2-[A] structures of the wild-type and H38R C9CARD filaments, respectively, which provide new insights into the molecular basis of C9CARD polymerization and its pH dependence via H38.

biophysics↗

bioRxiv2025

Curvature-dependent morphological reorganization of the endoplasmic reticulum determines the mode of epithelial migration

From single-cell extrusion to centimeter-sized wounds, epithelial gaps of various sizes and geometries appear in all organisms. For gap closure, epithelial cells invoke two orthogonal modes: lamellipodial crawling at the convex edge and purse-string-like movements at the concave edge. The mechanisms underlying these differential responses to geometric cues remain elusive. Here we perform an intracellular cartography to reveal that in both micropatterned and naturally arising gaps, the endoplasmic reticulum (ER) undergoes edge curvature-dependent morphological reorganizations with convex and concave edges promoting ER tubules and sheets, respectively. This reorganization depends on cytoskeleton-generated protrusive and contractile forces. Additionally, theoretical modeling predicts that the curvature-specific ER morphology leads to a lower strain energy state. ER tubules at the convex edge favor perpendicularly oriented focal adhesions, supporting lamellipodial crawling while ER sheets at the concave edge favor parallelly oriented focal adhesions, supporting purse-string-like movements. Altogether, ER emerges as a central player in cellular mechanotransduction, which orchestrates two orthogonal modes of cell migration by integrating signals from cytoskeletal networks.

cell biology↗

bioRxiv2023

HDL regulates TGFβ-receptor lipid raft partitioning, restoring contractile features of cholesterol-loaded vascular smooth muscle cells

BackgroundCholesterol-loading of mouse aortic vascular smooth muscle cells (mVSMCs) downregulates miR-143/145, a master regulator of the contractile state downstream of TGF{beta} signaling. In vitro, this results in transitioning from a contractile mVSMC to a macrophage-like state. This process likely occurs in vivo based on studies in mouse and human atherosclerotic plaques. ObjectivesTo test whether cholesterol-loading reduces VSMC TGF{beta} signaling and if cholesterol efflux will restore signaling and the contractile state in vitro and in vivo. MethodsHuman coronary artery (h)VSMCs were cholesterol-loaded, then treated with HDL (to promote cholesterol efflux). For in vivo studies, partial conditional deletion of Tgf{beta}r2 in lineage-traced VSMC mice was induced. Mice wild-type for VSMC Tgf{beta}r2 or partially deficient (Tgf{beta}r2+/-) were made hypercholesterolemic to establish atherosclerosis. Mice were then treated with apoA1 (which forms HDL). ResultsCholesterol-loading of hVSMCs downregulated TGF{beta} signaling and contractile gene expression; macrophage markers were induced. TGF{beta} signaling positively regulated miR-143/145 expression, increasing Acta2 expression and suppressing KLF4. Cholesterol-loading localized TGF{beta} receptors into lipid rafts, with consequent TGF{beta} signaling downregulation. Notably, in cholesterol-loaded hVSMCs HDL particles displaced receptors from lipid rafts and increased TGF{beta} signaling, resulting in enhanced miR-145 expression and decreased KLF4-dependent macrophage features. ApoA1 infusion into Tgf{beta}r2+/- mice restored Acta2 expression and decreased macrophage-marker expression in plaque VSMCs, with evidence of increased TGF{beta} signaling. ConclusionsCholesterol suppresses TGF{beta} signaling and the contractile state in hVSMC through partitioning of TGF{beta} receptors into lipid rafts. These changes can be reversed by promotion of cholesterol efflux, consistent with evidence in vivo. Condensed abstractMany cells identified as macrophage-like in human and mouse atherosclerotic plaques are thought to be of VSMC origin. We identified cholesterol-mediated downregulation of TGF{beta} signaling in vitro in human (h)VSMCs by localization of TGF{beta} receptors in membrane lipid rafts, which was reversed by HDL-mediated cholesterol efflux. This restored VSMC contractile marker (Acta2) and suppressed macrophage marker (CD68) expression by promoting TGF{beta} enhancement of miR-145 expression. In vivo, administration of apoA1 (which forms HDL) to atherosclerotic mice also promoted VSMC Acta2 expression and reduced CD68 expression. Because macrophage-like VSMC are thought to have adverse properties, our studies not only show mechanistically how cholesterol causes their transition, but also suggest that efflux-competent HDL particles may have a therapeutic role by restoring a more favorable phenotypic state of VSMC in atherosclerotic plaques.

molecular biology↗

bioRxiv2023

Matrix stiffening promotes perinuclear clustering of mitochondria

Mechanical cues from the tissue microenvironment, such as the stiffness of the extracellular matrix, modulate cellular forms and functions. As numerous studies have shown, this modulation depends on the stiffness-dependent remodeling of cytoskeletal elements. In contrast, very little is known about how the intracellular organelles such as mitochondria respond to matrix stiffness and whether their form, function, and localization change accordingly. Here, we performed an extensive quantitative characterization of mitochondrial morphology, subcellular localization, dynamics and membrane tension on soft and stiff matrices. This characterization revealed that while matrix stiffness affected all these aspects, matrix stiffening most distinctively led to an increased perinuclear clustering of mitochondria. Subsequently, we could identify the matrix stiffness-sensitive perinuclear localization of filamin as the key factor dictating this perinuclear clustering. Photo-conversion labeling and fluorescent recovery after photobleaching experiments revealed that perinuclear and peripheral mitochondrial populations differed in their motility on the soft matrix but surprisingly they did not show any difference on the stiff matrix. Finally, perinuclear mitochondrial clustering appeared to be crucial for priming human mesenchymal stem cells towards osteogenesis on the stiff matrix. Taken together, we elucidate a dependence of mitochondrial localization on matrix stiffness, which possibly enables a cell to adapt to its microenvironment.

cell biology↗

bioRxiv2022

Mechanosensitive dynamics of lysosomes regulates the emergence of leader cells during collective cell migration

Collective cell migration during embryonic development, wound healing, and cancer metastasis entails the emergence of leader cells at the migration front. These cells with conspicuous lamellipodial structures provide directional guidance to the collective. Despite their physiological relevance, the mechanisms underlying the emergence of leader cells remain elusive. Here we report that in diverse model systems for wound healing, including cultured epithelial monolayer, Drosophila embryo, and mouse embryonic skin, leader cells display a peripheral accumulation of lysosomes. This accumulation appears essential for leader cell emergence, involves lysosomal movement along microtubules, and depends on the actomyosin contractility-generated cellular forces. Peripheral lysosomes associate with inactive Rac1 molecules to remove them from the leading periphery, which increases local Rac1-activity, triggering actin polymerization and promoting lamellipodium formation. Taken together, we demonstrate that beyond their catabolic role, lysosomes act as the intracellular platform that links mechanical and biochemical signals to control the emergence of leader cells.

cell biology↗

bioRxiv2022

Cas9+ conditionally immortalized neutrophil progenitors as a tool for genome wide CRISPR screening for neutrophil differentiation and function

Neutrophils are short-lived cells of the innate immune system that play numerous roles in defense against infection, regulation of immune responses, tissue damage and repair, autoimmunity, and other non-communicable diseases. Understanding neutrophil function at a mechanistic level has been hampered by the difficulty of working with primary neutrophils, which die rapidly upon isolation, and the relative paucity of neutrophil cell lines. Murine neutrophil progenitors that are immortalized with estrogen-regulated expression of Hoxb8 differentiate into neutrophils upon withdrawal of estrogen and facilitate the quantitative production of neutrophils in vitro. Here we report the creation of a Cas9+ER-Hoxb8 neutrophil progenitor cell line that enables both forward and reverse genetic analysis of neutrophils for the first time. By editing progenitors via transduction with sgRNAs, and then withdrawing estrogen, Cas9 edited neutrophils are produced with high efficiency. Importantly, neutrophil differentiation of edited progenitors occurs both in vitro in cell culture and when transferred into murine recipients. To demonstrate the utility of Cas9+ER-Hoxb8 progenitors for forward genetics, we performed a pooled CRISPR screen to identify factors required for survival during neutrophil differentiation. This screen identified hundreds of genes both negatively and positively selected under differentiation conditions. One of the top hits from this screen was Cebpe, a transcription factor known to be required for neutrophil differentiation from pre-neutrophils to immature neutrophils. Using the progenitor cell line, we also confirmed that Cepbe is required for neutrophil differentiation in vivo, validating the utility of this cell line both for screening and for studying in vivo phenotypes. The genome-wide screen also identified all components of the WASH complex as being required for neutrophil differentiation, a finding that extends the known role of WASH in hematopoietic stem cell differentiation to later stages of neutrophil development. Taken together, we demonstrate that Cas9+ER-Hoxb8 immortalized neutrophils can be used to study neutrophil function both in vitro and in vivo. This new resource will enable the analysis of the role of neutrophils in numerous disease states using genetics for the first time.

immunology↗

bioRxiv2021

IFN-γ-independent control of M. tuberculosis requires CD4 T cell-derived GM-CSF and activation of HIF-1α

The prevailing model of protective immunity to tuberculosis is that CD4 T cells produce the cytokine IFN-{gamma} to activate bactericidal mechanisms in infected macrophages. Recent evidence has expanded this model, and it is now clear that CD4 T cells can control M. tuberculosis infection in the absence of IFN-{gamma} production. To identify factors and pathways involved in IFN-{gamma}-independent control, we developed a co-culture model using CD4 T cells isolated from the lungs of infected mice and M. tuberculosis-infected murine bone marrow-derived macrophages (BMDMs). We show that IFN-{gamma}-independent control is primarily mediated by CD4 T cell production of the cytokine GM-CSF and requires activation of the macrophage transcription factor HIF-1. HIF-1 activation drives a metabolic shift toward aerobic glycolysis and leads to the production of lipid droplets, both of which support host defense against infection. Surprisingly, recombinant GM-CSF is insufficient to rescue the absence of control by GM-CSF-deficient CD4 T cells during co-culture with BMDMs. In peritoneal macrophages, GM-CSF is sufficient to control growth, induces lipid droplet biogenesis, and requires HIF-1 expression for control. While HIF-1-mediated control following IFN-{gamma} stimulation requires nitric oxide, we find that HIF-1 activation by CD4 T cells and recombinant GM-CSF is nitric oxide-independent, implying a distinct pathway of activation. In addition to GM-CSF, CD4 T cells produce a factor that helps maintain phagosome membrane integrity during infection and blocks bacterial access to host lipids, a primary nutrient source. These results advance our understanding of CD4 T cell-mediated immunity to M. tuberculosis, clarify the role of nitric oxide as primarily immunomodulatory during M. tuberculosis infection, and reveal a novel mechanism for the activation of HIF-1. Furthermore, we establish a previously unknown functional link between GM-CSF and HIF-1 and provide evidence that CD4 T cell-derived GM-CSF is a potent bactericidal effector.

immunology↗

bioRxiv2020

Transcriptional regulation of ACSL1 by CHREBP and NF-kappa B in macrophages during hyperglycemia and inflammation

Acyl-CoA synthetase 1 (ACSL1) is an enzyme that converts fatty acids to acyl-CoA-derivatives for use in both lipid catabolism and lipid synthesis, including of arachidonic acid mediators that promote inflammation. ACSL1 has also been linked to the pro-atherosclerotic effects of diabetes in mice. ACSL1 expression has been reported to be upregulated in monocytes and macrophages by hyperglycemia, as well as enhanced by inflammatory stimuli, yet surprisingly little is known about the mechanisms underlying its transcriptional regulation. Here we show that increased Acsl1 mRNA expression in mouse macrophages by hyperglycemia is via transcription initiation such that nascent ACSL1 RNA and Acsl1 promoter activity are increased. We further demonstrate that the hyperglycemic-dependent induction of Acsl1 mRNA is governed by the glucose-sensing transcription factor, Carbohydrate Response Element Binding Protein (CHREBP), since the hyperglycemic upregulation of Acsl1 mRNA is lost in mouse bone marrow derived macrophages (BMDMs) from Chrebp knock out mice. In addition, we show that LPS treatment of mouse BMDMs increased Acsl1 mRNA, and this is attenuated by an NF-kappa B inhibitor that blocks p65 subunit binding to DNA. We further show that LPS treatment increased ACSL1 protein abundance and stimulated ACSL1 protein localization to membranes where it likely exerts its activity. Using an ACSL1 reporter gene containing the promoter and 1.6 Kb of upstream regulatory region, which contain multiple predicted CHREBP and NF-kappa B (RELA) binding sites conserved between the human and mouse ACSL1 gene, we found a synergistic increase of ACSL1 promoter activity when CHREBP and RELA were co-expressed. Thus, we have identified pathways controlling the expression of ACSL1 by hyperglycemia and inflammation through CHREBP and NF-kappa B.

molecular biology↗

bioRxiv2019

Activation of GPR56, a novel adhesion GPCR, is necessary for nuclear androgen receptor signaling in prostate cells

The androgen receptor (AR) is activated in patients with castration resistant prostate cancer (CRPC) despite low circulating levels of androgen, suggesting that intracellular signaling pathways and non-androgenic factors may contribute to AR activation. Many G-protein coupled receptors (GPCR) and their ligands are also activated in these cells indicating a role for these in CRPC. Although a cross talk has been suggested between the two pathways, yet, the identity of GPCRs which may play a role in androgen signaling, is not established yet. We demonstrate that adhesion GPCR 205, also known as GPR56, can be activated by androgens to stimulate the Rho signaling pathway, a pathway that plays an important role in prostate tumor cell metastasis. Testosterone stimulation of GPR56 also activates the cAMP/ Protein kinase A (PKA) pathway, that is necessary for AR signaling. Knocking down the expression of GPR56 using siRNA, disrupts nuclear translocation of AR and transcription of prototypic AR target genes such as PSA. GPR56 expression is higher in all prostate tumor samples tested and cells expressing GPR56 exhibit increased proliferation. These findings provide new insights about androgen signaling and identify GPR56 as a possible therapeutic target in advanced prostate cancer patients.

cancer biology↗