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Biology subjects

Malhotra, V.

Publications and source records attributed to Malhotra, V..

At least 19 recordsLinked to original sources

p125A (Sec23ip) couples COPII coat assembly with donor-acceptor membrane organization to facilitate tunnel-based traffic.

COPII-coat proteins play a crucial role in generating small vesicles at endoplasmic reticulum (ER) exit sites (ERES). However, they also assemble at the necks of tunnels and tubules connecting the ER exit site (donor) to the ERGIC/cis-Golgi cisterna (acceptor). How can COPII support these two traffic mechanisms? Through cell-free reconstitutions, we have found that the apposition of donor and acceptor membranes is important for the assembly of the outer layer of the COPII coat (Sec13/31) but had minimal impact on Sar1-induced COPII inner layer (Sec23/24) recruitment. The expression of the adaptor protein p125A, which binds to phosphatidylinositol 4-phosphate (PI4P), Sec31 and Sec23, stabilized the contact between the donor and acceptor membranes and promoted COPII outer layer assembly. A p125A-chimera expressing a Golgi-targeted PI4P-binding domain could also support outer layer assembly. Notably, the C-terminal helical domain of Sec31A, which interacts with p125A, was essential for its assembly at ERES. In cells lacking p125A, the assembly of the COPII outer layer was selectively destabilized. Transcriptome and secretome analyses reveal selective adjustments to extracellular matrix remodeling and collagen secretion, which corresponded with selective inhibition of fibrillar collagen traffic from the ER. Thus, p125A connects the outer COPII layer at ERES with PI4P-rich ERGIC/cis-Golgi membranes, coordinating COPII assembly with tunnel-driven collagen traffic.

cell biology↗

Imaging-based screen identifies novel natural compounds that perturb cell and chloroplast division in Chlamydomonas reinhardtii

Successful cell division requires faithful division and segregation of organelles into daughter cells. The unicellular alga Chlamydomonas reinhardtii has a single, large chloroplast whose division is spatiotemporally coordinated with furrowing. Cytoskeletal structures form in the same plane at the midzone of the dividing chloroplast (FtsZ) and the cell (microtubules), but how these structures are coordinated is not understood. Previous work showed that loss of F-actin blocks chloroplast division but not furrow ingression, suggesting that pharmacological perturbations can disorganize these events. In this study, we developed an imaging platform to screen natural compounds that perturb cell division while monitoring FtsZ and microtubules and identified 70 unique compounds. One compound, curcumin, has been proposed to bind to both FtsZ and tubulin proteins in bacteria and eukaryotes, respectively. In C. reinhardtii, where both targets coexist and are involved in cell division, curcumin at a specific dose range caused a severe disruption of the FtsZ ring in chloroplast while leaving the furrow-associated microtubule structures largely intact. Time-lapse imaging showed that loss of FtsZ and chloroplast division failure delayed the completion of furrowing but not the initiation, suggesting that the chloroplast-division checkpoint proposed in other algae requires FtsZ or is absent altogether in C. reinhardtii. SIGNIFICANCE STATEMENTO_LISuccessful cell division requires the coordination of both organelle inheritance and cytokinesis. The unicellular alga Chlamydomonas reinhardtii, which spatiotemporally coordinates the division of its chloroplast with cytokinesis, is an excellent model to study the regulation. C_LIO_LIWe screened libraries of natural compounds for perturbations of cell and/or chloroplast division, identifying 70 unique chemicals. By time-lapse microscopy using one of the hits, curcumin, we demonstrate that although chloroplast division failures delay the completion of cytokinesis, it does not impair initiation. C_LIO_LIThese findings suggest that the chloroplast-division checkpoint proposed in other algae requires FtsZ or is absent altogether in C. reinhardtii. C_LI

cell biology↗

Selective promotion of oligonucleotides in the course of evolution

Evolution shapes the structure and content of genomes, yet the contribution of local sequence composition to variant selection remains poorly understood. While traditional models emphasize protein function or cross-species conservation, we propose that intra-genomic patterns of oligonucleotide (k-mer) frequencies also reflect selective forces. To explore this, we developed kGain score, a metric that quantifies the frequency shift of a k-mer upon single-nucleotide substitution, using the surrounding genomic context as a baseline. We hypothesize that variants arising in high-kGain contexts are more likely to persist due to evolutionary favorability. We validated this hypothesis across multiple systems. In E. coli and S. cerevisiae long-term evolution experiments, we found that fixed, essential, and parallel mutations consistently show elevated kGain scores. This trend held in SARS-CoV-2 variants of concern and in an in-house antibiotic adaptation experiment, where a high-kGain fusA Y515N mutation conferred resistance and maintained fitness when overexpressed, demonstrating a causal link between kGain and adaptive potential. To enable cross-species generalization, we trained a transformer-based neural network regressor on LTEE-derived mutations to predict kGain from sequence alone. The model achieved high correlation in held-out in-domain data (Pearson r = 0.81) and accurately predicted kGain trends in out-of-domain data (Pearson r = 0.82), demonstrating that k-mer-based sequence constraints learned from one genome can be effectively transferred to others. Together, our results establish kGain as a biologically meaningful, scalable metric for probing within-genome sequence selection, offering a complementary lens to existing conservation-based frameworks for understanding evolutionary fitness and variant persistence.

evolutionary biology↗

Anti-cancer drug Tamoxifen interferes with Mycobacterium tuberculosis PhoPR mediated signaling and inhibits mycobacterial growth

Two-component signaling (TCS) systems empower all bacteria, including intracellular pathogens like Mycobacterium tuberculosis (M. tb) to regulate key pathways governing growth, physiology and virulence. Amongst all M. tb TCS systems, PhoPR and DevRS have been studied extensively for their roles in regulating persistence and virulence. Here, we report that besides its cognate response regulator PhoP, the PhoR sensor kinase displays several non-cognate interactions that augment its role in pathogenesis. We demonstrate that PhoR phosphorylates the DevR response regulator and furthermore, is itself subjected to O-phosphorylation by PknK, a Ser/Thr protein kinase (STPK), connecting TCS pathways with "eukaryotic-like" STPK driven phosphosignaling. This intersection of non-canonical regulatory pathways and the coregulation of PhoP and DevR regulons make M. tb PhoR a potentially attractive drug target. We rationalized that disruption of PhoPR signaling cascade and the resulting dysregulation may result in decreased virulence of M. tb. We tested this hypothesis by performing a high-throughput screen for compounds that inhibit autophosphorylation of PhoR sensor kinase. Screening of pharmacologically active, small molecule libraries yielded 11 potential inhibitors, of which one compound, Tamoxifen was able to attenuate PhoR autophosphorylation at micromolar concentrations in vitro and in vivo. Tamoxifen not only inhibited growth of Mycobacterium bovis BCG in culture but also interrupted PhoPR-mediated downstream signaling. Quantitative expression analysis revealed suppression of target gene, aprA under acidic conditions. Our findings highlight TCS sensor kinases as promising drug targets and underscore the applicability of clinically relevant anti-cancer drug tamoxifen as a repurposed anti-TB drug.

biochemistry↗

Ser/Thr Phosphorylation of Mycobacterium tuberculosis Type II Rel TA module by Protein Kinase K interferes with toxin neutralization: A novel mode of TA regulation.

Toxin-Antitoxin (TA) modules represent genetic elements implicated in bacterial persistence and antibiotic tolerance. Remarkably, Mycobacterium tuberculosis encodes 90+ TA modules, the majority of which are Type II TA comprising of a toxin component and an antitoxin counterpart that neutralizes the toxin. Upon exposure to stress, the antitoxin is degraded, releasing the toxin which then acts to halt cellular growth. Given that TA modules dictate social behavior of a population, we hypothesize that their regulation must be exquisitely controlled to avoid superfluous growth inhibition and initiation of persistence. However, the regulation and coordination of TA modules is poorly understood. Herein, we describe for the first time, a novel regulatory mechanism for Type II TA modules involving post-translational modification (PTM). Using computational tools, we observed that over 85 % of the M. tuberculosis TA proteins possess potential Ser/Thr phosphosites highlighting them as putative substrates for M. tuberculosis Ser/Thr protein kinases (STPK). We demonstrate that members of the RelBE family are subjected to O-phosphorylation by PknK, a stress-responsive growth regulatory STPK. Mass spectrometry confirmed multiple sites of PknK-mediated phosphorylation in the RelJK TA module. To gain insights into the functional impact of this PTM, we conducted in vitro binding and phenotypic growth studies with the wild type and mutant RelJK proteins. Our findings indicate that phosphorylation of Thr77 residue in RelK toxin compromises its binding to the RelJ antitoxin. These results suggest a potential role for O-phosphorylation in influencing the interaction dynamics of the TA module components. ImportanceBacterial pathogens rely on the phenomenon of persistence as a survival strategy to combat the adverse environmental conditions encountered during infection. As a stochastic process, the driving force(s) that potentiate the formation of persisters in a bacterial population are largely unclear. This study is a step towards the discovery of intricate regulatory mechanisms that coordinate a synchronized TA cellular program. We propose a model wherein the TA module is regulated post translationally, specifically via Ser/Thr phosphorylation disrupting the interaction between the toxin and antitoxin proteins as a mechanism to regulate TA function.

biochemistry↗

Endoplasmic reticulum exit sites are segregated for secretion based on cargo size

TANGO1-family proteins (TANGO1, TANGO1S and cTAGE5) form stable complexes at the Endoplasmic Reticulum Exit Sites (ERES) and mediate export of bulky cargoes. The C-terminal proline rich domain (PRD) of these proteins binds Sec23A and affects COPII assembly at ERES. These PRD interactions were replaced with light-responsive domains to control the binding between TANGO1S-DPRD and Sec23A. TANGO1S{Delta}PRD was dispersed in the ER membrane but relocated rapidly, yet reversibly, to pre-exiting ERES by binding to Sec23A upon light-activation. Prolonged binding of these two proteins concentrated ERES in the juxtanuclear region by a microtubule dependent process, blocked secretory cargo export and relocated ERGIC53 into the ER, but had limited impact on Golgi complex organization. Under these conditions, bulky collagen VII, and endogenous collagen I were collected at less than 47% of the stalled ERES, whereas small cargo molecules were halted uniformly across the ER, indicating that ERES differentially adapt to cargo size. We suggest these differences in cargo-accumulation at ERES permit cells to balance trafficking of cargoes of different sizes and optimize secretion.

cell biology↗

A model for collagen secretion by intercompartmental continuities

Newly synthesized secretory proteins are exported from endoplasmic reticulum (ER) at specialized subcompartments called exit sites (ERES). Cargoes like procollagen are too large for export by the standard COPII-coated vesicle of 60 nm average diameter. We have previously suggested that procollagen is transported from the ER to the next secretory organelle, the ERGIC, in TANGO1-dependent inter-organelle tunnels. Here, we show that intrinsically disordered domains of TANGO1 in the ER lumen generate an entropic contraction that pulls procollagen towards the ERES. Molecular gradients of pH and HSP47 between the ER and ERGIC generate a force in the range of tens of femtoNewtons (fN), which is sufficient to propel procollagen from the ER at a speed of [~]1 nm.s-1. This calculated speed and the quantities of collagen secreted are similar to its observed physiological secretion rate in fibroblasts, consistent with the proposal that ER export is the rate limiting step for procollagen secretion. Our theoretical model explains how cells can utilize molecular gradients to export procollagens at a rate commensurate with physiological needs. Significance StatementProcollagen cannot be exported from the endoplasmic reticulum (ER) by standard COPII-coated vesicle of 60 nm average diameter. We have previously suggested that collagen is transported from the ER to the next secretory organelle, the ERGIC, in TANGO1-dependent inter-organelle tunnels. ER and ERGIC differ in molecular composition including their pH and protein composition. We propose a mechanical/entropic ratchet model whereby molecular gradients of pH and the collagen chaperone HSP47, provide the energy to propel procollagen from the ER at a speed that matches the physiological rate of collagen secretion.

biophysics↗

Defects in lipid homeostasis reflect the function of TANGO2 in Acyl-CoA metabolism

We show that TANGO2, which lacks a transmembrane domain localizes predominantly to mitochondria and transiently to endoplasmic reticulum (ER) and lipid droplets (LDs). Evaluation of lipids in HepG2 cells lacking TANGO2 revealed an increase in the size of lipid droplets and reactive oxygen species production. There is also a marked increase lysophosphatidic acid (LPA) and a concomitant decrease in its biosynthetic precursor phosphatidic acid (PA). These changes are exacerbated in nutrient starved cells. Based on our data, we suggest that the principle function of TANGO2 is in acyl-CoA metabolism, which is necessary for the acylation of LPA to generate PA. This defect subsequently affects metabolism of many other fatty acids. These data help explain the physiological consequence of TANGO2 that induce acute metabolic crisis including rhabdomyolysis, cardiomyopathy and cardiac arrhythmias often leading to fatality upon starvation and stress.

cell biology↗

Biphasic release propensity of mucin granules is supervised by TSPAN8

Agonist-mediated stimulated pathway of mucin and insulin release is biphasic in which a rapid fusion of pre-docked granules is followed by slow docking and fusion of granules from the reserve pool. The sustained neurotransmitter release also necessitates docking of vesicles from a reserve pool. We present here a surprising finding that plasma membrane-located tetraspanin-8 (Tspan-8) sequesters syntaxin-2 (Stx2) to control external agonist-dependent mucin release. Tspan-8 specifically affects fusion of granules in reserve during the second phase of stimulated mucin release. The Tspan-8 and Stx2 complex does not contain VAMP-8 and Munc18, which are required for fusion of mucin granules. We suggest that by sequestering Stx2, Tspan-8 prevents docking granules in the reserve pool. In the absence of Tspan-8, granules in reserve pool are free to dock to Stx2 and their fusion doubles the quantities of mucins secreted. Tspan-8 thus emerges as the long-sought component that controls biphasic mucin release. We suggest a similar mechanism likely controls biphasic insulin and sustained neurotransmitter release.

cell biology↗

Pla2g12b is Essential for Expansion of Nascent Lipoprotein Particles

SUMMARYTriglyceride-rich lipoproteins (TRLs) are micelle-like particles that enable efficient transport of lipids throughout the bloodstream, but also promote atherosclerotic cardiovascular disease. Despite this central relevance to cardiovascular disease, very little is known about how lipids are loaded onto nascent TRLs prior to secretion. Here we show that Pla2g12b, a gene with no previously described function, concentrates components of the TRL biogenesis machinery along the ER membrane to ensure efficient delivery of lipids to nascent TRLs. We find that the lipid-poor TRLs secreted in PLA2G12B-/- mice and zebrafish support surprisingly normal growth and physiology while conferring profound resistance to atherosclerosis, and demonstrate that these same processes are conserved in human cells. Together these findings shed new light on the poorly understood process of TRL expansion, ascribe function to the previously uncharacterized gene Pla2g12b, and reveal a promising new strategy to remodel serum lipoproteins to prevent cardiovascular disease.

cell biology↗

Sorting of secretory proteins at the trans-Golgi network by TGN46

Secretory proteins are sorted at the trans-Golgi network (TGN) for export into specific transport carriers. However, the molecular players involved in this fundamental process remain largely elusive. Here, we identified the human transmembrane protein TGN46 as a receptor for the export of secretory cargo protein PAUF in CARTS - a class of protein kinase D-dependent TGN-to-plasma membrane carriers. We show that TGN46 is necessary for cargo sorting and loading into nascent carriers at the TGN. By combining quantitative fluorescence microscopy and mutagenesis approaches, we further discovered that the lumenal domain of TGN46 encodes for its cargo sorting function. In summary, our results define a cellular function of TGN46 in sorting secretory proteins for export from the TGN.

cell biology↗

The ulcerative colitis associated gene FUT8 regulates the quantity and quality of secreted mucins

Fucosylation of mucins, the main macrocomponents of the mucus layer that protects the digestive tract from pathogens, increases their viscoelasticity and shear stress resistance. These properties are altered in patients with ulcerative colitis (UC), which is marked by a chronic inflammation of the distal part of the colon. Here we show that the levels of Fucosyltransferase 8 (FUT8) and specific mucins are increased in the distal inflamed colon of UC patients compared to normal individuals. Overexpressing FUT8, as observed in UC, in mucin-producing HT29-18N2 colonic cell line increases trafficking of MUC1 to plasma membrane and secretion of MUC2/MUC5AC. FUT8 depletion (FUT8 KD), instead, causes intracellular accumulation of MUC1 and alters the ratio of secreted MUC2 to MUC5AC. Mucins secreted by FUT8 overexpressing cells are more resistant to shear stress compared to mucins secreted by FUT8 KD cells. These data fit well with the Fut8-/- mice phenotype, which are protected against UC. Fut8-/- mice exhibit a thinner proximal colon mucus layer with an altered ratio of neutral to acidic mucins compared to Fut8+/+ mice. Together, these data reveal that FUT8 optimizes the viscoelastic properties of the extracellular mucous by controlling the quantities of mucins secreted. SIGNIFICANCE STATEMENTMucins, the major components of the mucous barrier that protects our body from pathogens, are heavily glycosylated proteins. Changes their amounts and properties will alter the viscosity of mucous. Here we show that FUT8, a glycosylation enzyme of the Golgi apparatus, can control the viscosity of secreted mucins. Mucin secreting cells of the distal colon express FUT8, but their levels are altered in Ulcerative colitis patients. As a result, mucous produced by these cells is easily washed away, which exposes them to pathogens. We suggest that a defective mucous production is the main cause of initial inflammation observed in disease. Our findings help in understanding how cells control the quality of mucins and provide a means to prevent Ulcerative colitis.

cell biology↗

Building new compartments for unconventional protein secretion from the early and late Golgi membranes

CUPS, a compartment for unconventional secretion of signal sequence lacking proteins, is built during starvation. CUPS, lacking the Golgi specific glycosyltransferases, form by COPI independent extraction of membranes from the early Golgi cisterna, require PI4P for their biogenesis and PI3P for stability. We now show that a PI4P effector Drs2 of the trans-Golgi network, relocates to a new compartment monikered TCUPS because it touches CUPS. Although localized to TCUPS, Drs2 is required for CUPS formation specifically by interacting with Rcy1, and this process is essential for unconventional secretion. Visualizing cells by 4D SCLIM technology revealed that tubules emanating from TCUPS are often collared by CUPS and severed. Incidentally, while CUPS are stable, TCUPS are vesiculated at late stages of starvation. This mirrors the dynamics of the early and late Golgi during conventional protein secretion. TCUPS and CUPS thus emerge as the functional equivalent of early and late Golgi of the conventional secretory pathway, thus representing key compartments in unconventional secretion.

cell biology↗

Reversing chemorefraction in colorectal cancer cells by controlling mucin secretion

15% of colorectal cancers (CRC) cells exhibit a mucin hypersecretory phenotype, which is suggested to provide resistance to immune surveillance and chemotherapy. We now formally show that colorectal cancer cells build a barrier to chemotherapeutics by increasing mucins secretion. We show that low levels of KChIP3, a negative regulator of mucin secretion (Cantero-Recasens et al., 2018), is a risk factor for CRC patients relapse in subset of untreated tumours. Our results also reveal that cells depleted of KChIP3 are four times more resistant (measured as cell viability and DNA damage) to chemotherapeutics 5-Fluorouracil plus Irinotecan (5-FU+iri.) compared to control cells, whereas KChIP3 overexpressing cells are 10 times more sensitive to killing by chemotherapeutics. Similar increase in tumour cell death is observed upon chemical inhibition of mucin secretion by the sodium/calcium exchanger (NCX) blockers (Mitrovic et al., 2013). Finally, sensitivity of CRC patient-derived organoids to 5-FU+iri increases 40-fold upon mucin secretion inhibition. Reducing mucin secretion thus provides a means to control chemoresistance of mucinous colorectal cancer cells and other mucinous tumours.

cell biology↗

Global gene-expression analysis reveals the molecular processes underlying ClC-5 loss-of-function in novel Dent Disease 1 cellular models

Dent disease 1 (DD1) is a rare X-linked renal proximal tubulopathy characterized by low molecular weight proteinuria (LMWP) and variable degree of hypercalciuria, nephrocalcinosis and/or nephrolithiasis with progression to chronic kidney disease (CKD). Although loss-of-function mutations in the gene CLCN5 encoding the electrogenic Cl-/H+ antiporter ClC-5, which impair endocytic uptake in proximal tubule cells, cause the disease, there is poor genotype-phenotype correlation and their contribution to proximal tubule dysfunction remains unclear. Here, in order to discover the mechanisms leading to proximal tubule dysfunction due to ClC-5 loss-of-function, we have generated and characterized new human cellular models of DD1 by silencing CLCN5 and introducing the ClC-5 pathogenic mutants V523del, E527D and I524K into the human proximal tubule-derived cell line RPTEC/TERT1. Depletion of CLCN5 or expression of mutant ClC-5 impairs albumin endocytosis, increases substrate adhesion and decreases collective migration, which correlates with a less differentiated epithelial phenotype. Interestingly, although all conditions compromised the endocytic capacity in a similar way, their impact on gene expression profiles was different. Our DNA microarray studies show that ClC-5 silencing or mutant re-introduction alter pathways related to nephron development, anion homeostasis, organic acid transport, extracellular matrix organization and cell migration, compared to control cells. Cells carrying the V523del ClC-5 mutation show the largest differences in gene expression vs WT cells, which is in agreement with the more aggressive clinical phenotype observed in some DD1 patients. Overall, this work emphasizes the use of human proximal tubule derived cell models to identify the molecular processes underlying ClC-5 deficiency.

pathology↗

Palmitoylation of KChIP3 controls baseline mucin secretion

Baseline mucin secretion (BMS) is independent of external agonists and controlled by a small calcium binding protein named KChIP3. KChIP3-hosting mucin granules are not released until intracellular cytosolic calcium oscillations reach a threshold, KChIP3 binds calcium and detaches from granules, allowing their fusion to plasma membrane. Loss of KChIP3 or blocking its membrane attachment causes mucin hypersecretion. How is KChIP3 recruited to mucin granules? We show here that zDHHC (aspartate-histidine-histidine-cysteine motif in a cysteine-rich, zinc finger-like domain) S-acyl-transferase dependent palmitoylation modulates binding of KChIP3 to mucin granules thereby affecting mucin secretion. We have found that inhibiting zDHHC-mediated palmitoylation in differentiated HT29-18N2, which express the Golgi-localized zDHHC3 and zDHHC4, releases KChIP3 from mucin granules and increases baseline mucin secretion. Mutation of the palmitoylation sites in KChIP3 (Cysteines 122 and 123 to Alanine) quantitatively reduces its attachment to mucin granules. Expression of KChIP3-WT in HT29-18N2 cell lines stably depleted of KChIP3 inhibits mucin secretion, whereas expression of non-palmitoylated KChIP3 (KChIP3-AA) only partially rescues the effect of KChIP3 depletion and the cells maintain higher levels of baseline secretion compared to KChIP3-WT cells. Altogether, our data suggest that zDHHC3 or zDHHC4-dependent palmitoylation is involved in KChIP3 recruitment to mucin granules to control the baseline mucin secretion.

cell biology↗

GORASPs link Golgi cisternae laterally to stabilize the rims and prevent vesiculation

In vitro experiments have shown GRASP65 (GORASP1) and GRASP55 (GORASP2) proteins function in stacking Golgi cisternae. However, in vivo depletion of GORASPs in metazoans have given equivocal results. We have generated a mouse lacking both GORASPs and find that Golgi cisternae remained stacked. However, the stacks are disconnected laterally from each other and the cisternal cross-sectional diameters are significantly reduced compared to their normal counterparts. These data support earlier findings on the role of GORASPs in linking stacks and we suggest that unlinking of stacks affects dynamic control of COPI budding and vesicle fusion at the rims. The net result is that cisternal cores remain stacked, but cisternal diameter is reduced by rim consumption.

cell biology↗

TANGO1 membrane helices create a lipid diffusion barrier at curved membranes

We have previously shown TANGO1 organises membranes at the interface of the endoplasmic reticulum (ER) and ERGIC/Golgi (Raote et al., 2018). TANGO1 corrals retrograde membranes at ER exit sites to create an export conduit. Here the retrograde membrane is, in itself, an anterograde carrier. This mode of forward transport necessitates a mechanism to prevent membrane mixing between ER and the retrograde membrane. TANGO1 has an unusual membrane helix organisation, composed of one membrane-spanning helix (TM) and another that penetrates the inner leaflet (IM). We have reconstituted these membrane helices in model membranes and shown that TM and IM together reduce the flow of lipids at a region of defined shape. We have also shown that the helices align TANGO1 around an ER exit site. We suggest this is a mechanism to prevent membrane mixing during TANGO1-mediated transfer of bulky secretory cargos from the ER to the ERGIC/Golgi via a tunnel.

cell biology↗