Biology subjects

Basak, S.

Publications and source records attributed to Basak, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Non-canonical NF-κB signaling in dendritic cells promotes intestinal inflammation by restraining the tolerogenic β-catenin-Raldh2 axis

Dendritic cell (DC) dysfunctions exacerbate intestinal pathologies. However, the mechanisms compromising DC-mediated immune controls remain unclear. We found that intestinal DCs from mice subjected to experimental colitis possessed heightened non-canonical NF-{kappa}B signaling, which activates the RelB:p52 heterodimer. Genetic inactivation of this pathway in DCs alleviated inflammation in colitogenic mice. Unexpectedly, RelB:p52 deficiency diminished the transcription of Axin1, a critical component of the {beta}-catenin destruction complex. This reinforced {beta}-catenin-driven expression of Raldh2, which imparts tolerogenic DC attributes by promoting retinoic acid (RA) synthesis. Indeed, DC-specific non-canonical NF-{kappa}B impairment improved the colonic frequency of Tregs and IgA+ B cells, which fostered luminal IgA and eubiosis. Introducing {beta}-catenin haploinsufficiency in non-canonical NF-{kappa}B-deficient DCs moderated Raldh2 activity, reinstating colitogenic sensitivity in mice. Finally, IBD patients displayed a deleterious non-canonical NF-{kappa}B signature in intestinal DCs. In sum, we establish a DC network that integrates non-canonical NF-{kappa}B signaling to subvert RA metabolic pathway in fueling intestinal inflammation. Significance (100)Distorted dendritic cell (DC) functions have been implicated in aberrant intestinal inflammation; however, the underlying mechanism remains obscure. We discovered that the non-canonical NF-{kappa}B pathway exacerbates inflammation in the colitogenic gut by downmodulating {beta}-catenin-driven synthesis of Raldh2 in DCs. Raldh2 represents a key enzyme involved in the production of tolerogenic retinoic acid in intestinal DCs. Beyond regulating immune genes, therefore, non-canonical NF-{kappa}B signaling appears to instruct retinoic acid-mediated control of gut health. While we illustrate a DC network integrating immune signaling and micronutrient metabolic pathways in the intestine, our finding may have broad relevance for nutritional interventions in inflammatory ailments. eToCDeka and Kumar et al. illustrate a DC-circuitry that exacerbates intestinal inflammation in IBD patients and colitogenic mice. Non-canonical NF-{kappa}B signaling restrains {beta}-catenin in DCs to downmodulate Raldh2, which promotes tolerogenic RA synthesis, leading to diminished Treg and IgA+ cell frequencies in the gut. HighlightsO_LIAberrant intestinal inflammation is associated with and exacerbated by non-canonical NF-{kappa}B signaling in DCs. C_LIO_LINon-canonical signaling restrains the tolerogenic {beta}-catenin-Raldh2 axis in DCs by upregulating Axin1. C_LIO_LIDC-specific RelB:p52 impairment promotes {beta}-catenin-dependent Treg accumulation in the gut. C_LIO_LIA DC defect of non-canonical signaling causes {beta}-catenin-dependent increase in luminal sIgA, fostering the gut microbiome. C_LI One sentenceThe non-canonical NF-{kappa}B pathway fuels intestinal inflammation by waning the tolerogenic {beta}-catenin-Raldh2-retinoic acid axis in DCs.

immunology↗

bioRxiv2023

A hepatocyte-specific transcriptional program driven by Rela and Stat3 exacerbates experimental colitis in mice by modulating bile synthesis

Hepatic factors secreted by the liver promote homeostasis and are pivotal for maintaining the liver-gut axis. Bile acid metabolism is one such example wherein, bile acid synthesis occurs in the liver and its biotransformation happens in the intestine. Dysfunctional interactions between the liver and the intestine stimulate varied pathological outcomes through its bidirectional portal communication. Indeed, aberrant bile acid metabolism has been reported in inflammatory bowel disease (IBD). However, the molecular mechanisms underlying these crosstalks that perpetuate intestinal permeability and inflammation remain obscure. Here, we identify a novel hepatic gene program regulated by Rela and Stat3 that accentuates the inflammation in an acute experimental colitis model. Hepatocyte-specific ablation of Rela and Stat3 reduces the levels of primary bile acids in both the liver and the gut and shows a restricted colitogenic phenotype. On supplementation of chenodeoxycholic acid (CDCA), knock-out mice exhibit enhanced colitis-induced alterations. This study provides persuasive evidence for the development of multi-organ strategies for treating IBD and identifies a hepatocyte-specific rela-stat3 network as a promising therapeutic target.

immunology↗

bioRxiv2023

Downregulation of a cell polarity protein potentiates Chikungunya Virus infection in host cells

During cellular infections, alphaviruses produce a 6 kDa membrane protein (6K) and a transframe variant (TF) of 6K through ribosomal frameshifting. The role of these proteins in alphavirus biology is largely unknown. Here, we show that TF of Chikungunya virus plays a unique and critical role in promoting virus propagation by manipulating host cell boundaries. TF achieves this by targeting and downregulating human Scribble, a component of the polarity complex that controls cellular morphology and apoptosis, leading to its punctate localization, ubiquitination, and subsequent degradation via the proteasomal pathway. The TF-Scribble interaction is mediated by a newly discovered PDZ-domain binding motif (PBM) in TF, with the PDZ domains of Scribble, as demonstrated by co-localization during viral infection and further by co-immunoprecipitation and proteomics analysis. This PBM is unique to TF and is absent in 6K; thus, 6K cannot modulate Scribble localization in infected cells. shRNA-mediated knockdown of Scribble potentiates CHIKV propagation highlighting the requirement of TF for the downregulation of Scribble. While wildtype CHIKV drastically alters cell-cell boundaries, a mutated version of CHIKV generated through reverse genetics ({Delta}TF CHIKV), which produces 6K but not TF, is unable to trigger similar morphological alterations due to its inability to engage Scribble, ultimately resulting in suboptimal virus propagation. A cryoEM reconstruction of {Delta}TF CHIKV at a global resolution of 3.6 [A], one of the highest reported among all alphavirus structures, indicates that the assembly of glycoprotein spikes and nucleocapsid is unaffected. Thus, the loss of TF affects the ultimate stage of cellular egress in the virus life cycle, and not earlier stages such as entry, replication or assembly. Our work thus establishes a novel function for the TF component of alphaviruses in modulating host morphology, potentiating virus transmission, and also distinguishes the functionality of TF from that of 6K in alphavirus biology. TeaserA novel functionality of Chikungunya Virus in modulating cell boundaries to allow efficient virus propagation

cell biology↗

bioRxiv2023

Gestational exposure to bisphenol S induces microvesicular steatosis by promoting lipogenesis and inflammation in male rat offspring

Fetal exposure to endocrine-disrupting bisphenol A (BPA) showed a long-lasting programming effect on organ development and predisposed to the metabolic risk of adult diseases. However, limited data on developmental exposure to BPA-substitute bisphenol S (BPS) in predisposing liver metabolic disease is available. Here, the effects of BPS exposure were assessed on hepatic metabolism by examining adiposity and inflammation in the adipose and liver of the 90-day male offspring. Pregnant Wistar rats were exposed to BPA and BPS (0.0, 0.4, 4.0 {micro}g/kg bw) via gavage from gestational day 4 to 21. Prenatal BPS-exposed offspring exhibited a higher obesogenic effect than BPA, including changes in body weight, body fat, feed efficiency, and leptin signalling. The fasting blood glucose did not change, but BPS exposure elevated plasma corticosterone levels and adipocyte hypertrophy of the visceral adipose tissue (VAT) to a greater extent than BPA. Adipocyte hypertrophy was augmented by modulated expression of lipid uptake (PPAR{gamma}, FABP4), glucocorticoid (HSD11{beta}1), inflammation (IL6, IL1{beta}, CRP, COX2), oxidative stress (CHOP) and apoptotic (Caspase 3) mediators. Liver histology showed numerous lipid droplets, and hepatocyte ballooning, associated with upregulated expression of cholesterol, lipid biogenesis and glucocorticoid activators, indicating microvesicular steatosis in the prenatally BPS-exposed adult offspring. The upregulated PPAR, ADRP, and FGF21 expression and increased lipid peroxidation in the offsprings liver suggest metaflammation due to fetal exposure to BPS. Fetal BPS exposure demonstrated a more significant disruption in metabolism involving adiposity, liver fat, inflammation in excess, and predisposition to hepatic steatosis in the male offspring. HighlightsO_LIFetal BPS exposure exhibited enlarged and inflamed adipocytes more than BPA C_LIO_LIPrenatal BPS exposure induced excess lipid droplets & hepatocyte ballooning in liver C_LIO_LIIn utero exposure to BPS induces microvesicular steatosis in adult rats C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/543354v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@89c53org.highwire.dtl.DTLVardef@14f176borg.highwire.dtl.DTLVardef@18a934corg.highwire.dtl.DTLVardef@cc7af6_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

Fetal exposure to endocrine disrupting-bisphenol A (BPA) alters testicular fatty acid metabolism in the adult offspring: relevance to sperm maturation and quality

Daily exposure to bisphenols can affect reproductive functions due to their pseudo-estrogenic and/or anti-androgenic effects. Testicular lipids contain high levels of polyunsaturated fatty acids necessary for sperm maturity, motility, and spermatogenesis. Whether prenatal exposure to bisphenols alters testicular fatty acid metabolism in adult offspring is unknown. Pregnant Wistar rats were gavaged from gestational day 4 to 21 with BPA and BPS (0.0, 0.4, 4.0, 40.0 g/kg bw/d). Despite increased body and testis weight, the total testicular cholesterol, triglyceride, and plasma fatty acids were unaffected in offspring. Lipogenesis was upregulated by increased SCD-1, SCD-2, and expression of lipid storage (ADRP) and trafficking protein (FABP4). The arachidonic acid, 20:4 n-6 (ARA) and docosapentaenoic acid, 22:5 n-6 (DPA) levels were decreased in the BPA-exposed testis, while BPS exposure had no effects. The expression of PPAR, PPAR{gamma} proteins and CATSPER2 mRNA were decreased, which are important for energy dissipation and motility of the sperm in the testis. The endogenous conversion of linoleic acid,18:2n-6 (LA), to ARA was impaired by a reduced ARA/LA ratio and decreased FADS1 expression in BPA-exposed testis. Collectively, fetal BPA exposure affected endogenous long-chain fatty acid metabolism and steroidogenesis in the adult testis, which might dysregulate sperm maturation and quality. HighlightsO_LIIn utero BPA exposure not BPS affected testicular long-chain n-6 PUFA metabolism in offspring C_LIO_LIFetal exposure to BPA alters delta-9-desaturase indices in the adult testis C_LIO_LIBPA exposure reduced fatty acid desaturase1 expression in offspring testis C_LIO_LIFetal BPA exposure dysregulated lipogenesis in offspring testis C_LI

developmental biology↗

bioRxiv2022

Maternal omega-3 fatty acid deficiency affects fetal thermogenic development and postnatal musculoskeletal growth in mice

Maternal omega-3 (n-3) polyunsaturated fatty acids (PUFAs) deficiency can affect offsprings adiposity and metabolism by modulating lipid and glucose metabolism. However, the impact of n-3 PUFA deficiency on the development of fetal thermogenesis and its consequences is not reported. Using an n-3 PUFA deficient mice, we assessed fetal interscapular brown adipose tissue (iBAT), body fat composition, insulin growth factor-1 (IGF-1), glucose transporters (GLUTs), and expression of lipid storage & metabolic proteins in the offspring. The n-3 PUFA deficiency did not change the pups calorie intake, organ weight, and body weight. However, the offsprings skeletal growth was altered due to excess fat to lean mass, reduced tibia & femur elongation, dysregulated IGF-1 in the mother and pups (p<0.05). Localization of uncoupling protein 1 (UCP1) in iBAT exhibited a reduced expression in the deficient fetus. Further, UCP1, GLUT1, GPR120 were downregulated while FABP3, ADRP, GLUT4 expressions were upregulated in the BAT of the deficient offspring (p<0.05). The deficiency decreased endogenous conversion of the n-3 LCPUFAs from their precursors and upregulated SCD1, FASN, and MFSD2A mRNAs in the liver (p<0.05). An altered musculoskeletal growth in the offspring is associated with impaired browning of the fetal adipose, dysregulated thermogenesis, growth hormone, and expression of glucose and fatty acid metabolic mediators due to maternal n-3 PUFA deficiency. BAT had higher metabolic sensitivity compared to WAT in n-3 PUFA deficiency. Maternal n-3 PUFA intake may prevent excess adiposity by modulating fetal development of thermogenesis and skeletal growth dynamics in the mice offspring. HighlightO_LIMaternal n-3 PUFA deficiency dysregulated the development of fetal adipose browning C_LIO_LIN-3 PUFA regulates fetal thermogenic development by altering UCP1 expression C_LIO_LIBAT had higher metabolic sensitivity compared to WAT in n-3 PUFA deficiency C_LIO_LIIncreased fat mass and IGF-1 played a role in promoting adiposity in n-3 PUFA deficiency C_LI

developmental biology↗

bioRxiv2022

Dietary omega-3 fatty acid deficiency from pre-pregnancy to lactation affects expression of genes involved in neurogenesis of the offspring

Maternal n-3 PUFA (omega-3) deficiency can affect brain development in utero and postnatally. Despite the evidence, the impacts of n-3 PUFA deficiency on the expression of neurogenesis genes in the postnatal brain remained elusive. Since postnatal brain development requires PUFAs via breast milk, we examined the fatty acid composition of breast milk and hippocampal expression of neurogenesis genes in n-3 PUFA deficient 21d mice. In addition, expression of fatty acid desaturases, elongases, signalling receptors of free fatty acids, insulin and leptin, and glucose transporters were measured. Among the genes involved in neurogenesis, the expression of brain-specific tenascin-R (TNR) was downregulated to a greater extent ([~]31 folds), followed by adenosine A2A receptor (A2AAR), dopamine receptor D2 (DRD2), glial cell line-derived neurotrophic factor (GDNF) expression in the n-3 PUFA deficient hippocampus (p<0.05). Increasing dietary LA to ALA (50:1) elevated ARA to DHA ratio by [~]8 folds in the n-3 PUFA deficient breast milk, with an overall increase of total n-6/n-3 PUFAs by [~]15:1 (p<0.05) compared to n-3 PUFA sufficient (LA to ALA: 2:1) diet. The n-3 PUFA deficient brain exhibited upregulation of FADS1, FADS2, ELOVL2, ELOVL5, ELOVL6, GPR40, GPR120, LEPR, IGF1 and downregulation of GLUT1, GLUT3, and GLUT4 mRNA expression (p<0.05). Maternal n-3 PUFA deficiency affects the expression of key neurogenesis genes in the offspring with concomitant expression of desaturases and elongases genes suggesting the importance of dietary n-3 PUFA for neurodevelopment.

developmental biology↗

bioRxiv2022

Fuzzy Supertertiary Interactions within PSD-95 Enable Ligand Binding

The scaffold protein PSD-95 links postsynaptic receptors to sites of presynaptic neurotransmitter release. Flexible linkers between folded domains in PSD-95 enable a dynamic supertertiary structure. Interdomain interactions within the PSG supramodule, formed by PDZ3, SH3 and GuK domains, regulate PSD-95 activity. Here we combined Discrete Molecular Dynamics and single molecule FRET to characterize the PSG supramodule, with time resolution spanning picoseconds to seconds. We used a FRET network to measure distances in full-length PSD-95 and model the conformational ensemble. We found that PDZ3 samples two conformational basins, which we confirmed with disulfide mapping. To understand effects on activity, we measured binding of the synaptic adhesion protein neuroligin. We found that PSD-95 bound neuroligin well at physiological pH while truncated PDZ3 bound poorly. Our hybrid structural models reveal how the supertertiary context of PDZ3 enables recognition of this critical synaptic ligand.

biophysics↗

bioRxiv2021

A vitamin D-RelB/NF-κB pathway limits Chandipura virus multiplication by rewiring the homeostatic state of autoregulatory type 1 interferon-IRF7 signaling

Besides its functions in the skeletomuscular system, vitamin D also promotes protective immunity against viral pathogens. Viral sensing by mammalian cells triggers nuclear activation of RelA/NF-{kappa}B and IRF3 factors, which collaborate in mediating the early induction of antiviral type 1 interferons (T1-IFNs). Autocrine T1-IFN signaling further accumulates otherwise negligibly expressed IRF7 in virus-infected cells that then sustains T1-IFN production in a positive feedback. Surprisingly, prior cell-culture studies revealed that vitamin D actually suppresses signal-induced RelA activation. Indeed, it remains unclear how vitamin D limits viral multiplication in a cell-autonomous manner. Here, we examined the role of vitamin D in controlling cellular infections by the Chandipura virus (CHPV), a cytoplasmic RNA virus implicated in human epidemics. We found that vitamin D conditioning produced an altered cell state less permissive for CHPV multiplication because of the heightened expression of T1-IFNs. It is thought that viruses also induce a distinct RelB/NF-{kappa}B activity, which counteracts RelA-driven T1-IFN expressions in infected cells. Our analyses instead characterized a basal nuclear RelB activity, which was downregulated upon vitamin D-mediated suppression of RelB synthesis. Interestingly, this vitamin D-RelB pathway provoked IRF7-mediated positive autoregulation augmenting constitutive T1-IFN expressions even in the absence of viral infections. Accordingly, RelB deficiency rendered redundant, while IRF7 depletion abrogated antiviral vitamin D actions. In sum, our study suggests that the homeostatic state of the signaling circuitry comprising of the NF-{kappa}B and T1-IFN pathways connects micronutrients to antiviral immunity at the cellular level. Significance statementVitamin D limits viral infections, but the underlying mechanism remains unclear. Linking micronutrients to antiviral immunity, Ratra et al. characterize an immune signaling circuitry engaged by vitamin D that generates a cellular state less permissive to infections by Chandipura virus, a pathogen of public health importance.

immunology↗

bioRxiv2021

Underlying selection for the diversity of Spike protein sequences of SARS-CoV-2

The global spread of SARS-CoV-2 is fast moving and has caused a worldwide public health crisis. In the present manuscript we analyzed spike protein sequences of SARS-CoV-2 genomes to assess the impact of mutational diversity. We observed from amino acid usage patterns that spike proteins are associated with a diversity of mutational changes and most important underlying cause of variation of amino acid usage is the changes in hydrophobicity of spike proteins. The changing patterns of hydrophobicity of spike proteins over time and its influence on the receptor binding affinity provides crucial information on the SARS-CoV-2 interaction with human receptor. Our results also show that spike proteins have evolved to prefer more hydrophobic residues over time. The present study provides a comprehensive analysis of molecular sequence data to consider that mutational variants might play a crucial role in modulating the virulence and spread of the virus and has immediate implications for therapeutic strategies.

bioinformatics↗

bioRxiv2021

Selective estrogen receptor modulators limit alphavirus infection by targeting the viral capping enzyme nsP1

Alphaviruses cause animal or human diseases that are characterized by febrile illness, debilitating arthralgia, or encephalitis. Selective estrogen receptor modulators (SERMs), a class of FDA-approved drugs, have been shown to possess antiviral activities against multiple viruses, including Hepatitis C virus, Ebola virus, dengue virus, and vesicular stomatitis virus. Here, we evaluated three SERM compounds, namely 4-hydroxytamoxifen, tamoxifen, and clomifene, for plausible antiviral properties against two medically important alphaviruses, chikungunya virus (CHIKV) and Sindbis virus (SINV). In cell culture settings, these SERMs displayed potent activity against CHIKV and SINV at non-toxic concentrations with EC50 values ranging between 400 nM and 3.9 M. Further studies indicated that these compounds inhibit a post-entry step of the alphavirus life cycle, while enzymatic assays involving purified recombinant proteins confirmed that these SERMs target the enzymatic activity of non-structural protein 1 (nsP1), the capping enzyme of alphaviruses. Finally, tamoxifen treatment restrained CHIKV growth in the infected mice and diminished musculoskeletal pathologies. Combining biochemical, cell culture-based studies, and in vivo analyses, we strongly argue that SERM compounds, or their derivatives, may provide for attractive therapeutic options against alphaviruses.

immunology↗

bioRxiv2021

Cryo-EM Structure of Bacterioferritin Nanocages Provides Insight into the Bio-mineralization of Ferritins

Iron is an essential element involved in various metabolic processes. The ferritin family of proteins forms nanocage assembly and are involved in iron oxidation, storage and mineralization. Although several structures of human ferritin and bacterioferritin subunits have been resolved, there is still no complete structure that shows both the trapped Fe-biomineral cluster along with the nanocage. Furthermore, whereas the mechanism of iron trafficking has been explained using various approaches, an atomic-level description of the pathway and the biomineralization that occurs inside the cavity are lacking. Here, we report three cryo-EM structures of different states of the Streptomyces coelicolor bacterioferritin nanocage (i.e., apo, holo) at 3.4 [A] to 4.6 [A] resolution and the subunit crystal structure at 2.6 [A] resolution. The holo forms show different stages of Fe-biomineral accumulation inside the nanocage and suggest the possibility of a different Fe biomineral accumulation process. The cryo-EM map shows connections between the Fe-biomineral cluster and residues such as Thr157 and Lys42 from the protein shell, which are involved in iron transport. Mutation and truncation of the bacterioferritin residues involved in these connections can significantly reduce iron binding as compared with wild type bacterioferritin. Moreover, S. coelicolor bacterioferritin binds to various DNA fragments, similar to Dps (DNA-binding protein from starved cells) proteins. Collectively, our results represent a prototype for the ferritin nanocage, revealing insight into its biomineralization and the potential channel for ferritin-associated iron trafficking.

biophysics↗

bioRxiv2020

Overexpression of EiKCS confers paraquat-tolerance in rice (Oryza sativa L.) by promoting polyamine pathway

Paraquat is an important bipyridine herbicide by acting on the photosynthetic system of the plants and generating reactive oxygen species leading to cell death, whereas the mechanism of the paraquat resistance remains to be explored. In this study, a putative paraquat-resistant gene EiKCS from goosegrass (Eleusine indica L.) was isolated and overexpressed in a transgenic rice (Oryza sativa L.). This transgenic rice (KCSox) was treated by exogenous spermidine and paraquat and then was analyzed by qualitative and quantitative proteomics. Overexpressing of EiKCS enhanced paraquat tolerance in KCSox by the accumulation of endogenous polyamines whose dominant presences of polyamines benzoylation derivatizations in rice were C18H20N2O2, C28H31N3O3, and C38H42N4O4. The mechanism underlying the improving tolerance enhanced antioxidant capacity of ROS systems and light-harvesting in photosynthesis in KCSox rice leaves to reducing paraquat toxicity. The protein {beta}-Ketoacyl-CoA Synthase (EiKCS) encoded by the EiKCS gene promoted the synthesis and metabolism of proteins of the polyamine pathway. Three cofactors CERs were identified and positively correlated with the function of EiKCS on very-long-chain fatty acids (VLCFAs) biosynthesis via promoting the polyamine pathway and inhibiting the links with the TCA pathway and fatty acid pathway to responding to the paraquat tolerance in the KCSox rice, which also caused the prolongation of the overproduction of spermine and a transient increase of intracellular malondialdehyde (MDA). These results expanded the polyamines pathway manipulated in cereals using genetic engineering to clarify the mechanism of paraquat-tolerance. One Sentence SummaryA putative paraquat-resistant EiKCS gene from the goosegrass overexpressing in the rice resulted in the accumulation of polyamines, especially the spermine, and promoted the proteins in polyamine pathways by its EiKCS protein under paraquat stress.

physiology↗

bioRxiv2020

An epithelial Nfkb2 pathway exacerbates intestinal inflammation by supplementing latent RelA dimers to the canonical NF-κB module

Aberrant inflammation associated with human ailments, including inflammatory bowel disease (IBD), is typically fuelled by the inordinate activity of RelA/NF-{kappa}B transcription factors. As such, the canonical NF-{kappa}B module mediates controlled nuclear activation of RelA dimers from the latent cytoplasmic complexes. What provokes pathological RelA activity in the colitogenic gut remains unclear. The noncanonical NF-{kappa}B pathway promotes immune organogenesis involving Nfkb2 gene products. Because NF-{kappa}B pathways are intertwined, we asked if noncanonical signaling aggravated inflammatory RelA activity. Our investigation revealed frequent engagement of the noncanonical pathway in human IBD. In a mouse model, an Nfkb2 function exacerbated gut inflammation by amplifying the epithelial RelA activity induced upon intestinal injury. Our mechanistic studies clarified that cell-autonomous Nfkb2 signaling supplemented latent NF-{kappa}B dimers leading to hyperactive canonical RelA response in the inflamed colon. In sum, regulation of latent NF-{kappa}B dimers links noncanonical signaling to RelA-driven inflammatory pathologies and may provide for therapeutic targets. In briefNoncanonical NF-{kappa}B signals in intestinal epithelial cells supplement latent RelA dimers that, in turn, aggravated canonical NF-{kappa}B response in the colitogenic gut exacerbating intestinal inflammation. HighlightsO_LIHuman IBD involves the frequent engagement of the noncanonical NF-{kappa}B pathway. C_LIO_LIMice deficient in the noncanonical signal transducer Nfkb2 are resistant to experimental colitis. C_LIO_LINoncanonical NF-{kappa}B signaling supplements latent RelA NF-{kappa}B dimers. C_LIO_LINoncanonical NF-{kappa}B signaling amplifies canonical NF-{kappa}B response to TLR ligands. C_LI

immunology↗

bioRxiv2020

High-resolution Structures of multiple 5-HT3AR-setron complexes reveal a novel mechanism of competitive inhibition

Serotonin receptors (5-HT3AR) play a crucial role in regulating gut movement, and are the principal target of setrons, a class of high-affinity competitive antagonists, used in the management of nausea and vomiting associated with radiation and chemotherapies. Structural insights into setron-binding poses and their inhibitory mechanisms are just beginning to emerge. Here, we present high-resolution cryo-EM structures of full-length 5-HT3AR in complex with palonosetron, ondansetron, and alosetron. Each structure reveals a distinct interaction fingerprint between the setron and binding-pocket residues that may underlie their diverse affinities. In addition, setrons elicit varying degrees of conformational change throughout the channel that, quite surprisingly, lie along the channel activation pathway, suggesting a novel mechanism of competitive inhibition. Molecular dynamic simulations were used to assess binding-poses and the drug-target interaction dynamics. Together, this study provides a molecular basis for setron binding affinities and their inhibitory effects.

biophysics↗

bioRxiv2019

Mechanisms of activation and desensitization of full-length glycine receptor in membranes

Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyR) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structural studies have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unknown. Here, we present Cryo-EM structures of the full-length GlyR protein reconstituted into lipid nanodiscs that are captured in the unliganded (closed) and glycine-bound (open and desensitized) conformations. A comparison of the three states reveals global conformational changes underlying GlyR channel gating. The functional state assignments were validated by molecular dynamics simulations of the structures incorporated in a lipid bilayer. Observed permeation events are in agreement with the anion selectivity of the channel and the reported single-channel conductance of GlyR. These studies establish the structural basis for gating, selectivity, and single-channel conductance of GlyR in a physiological environment.

biophysics↗

bioRxiv2019

Chandipura virus requires pro-survival RelA NF-κB function for its propagation

In response to infection by RNA viruses, mammalian cells typically activate RelA-containing NF-{kappa}B heterodimers, which induce genes encoding interferon-{beta} and other antiviral mediators. Therefore, RelA is commonly thought to function as an anti-viral transcription factor. Notably, virus-specific mechanisms often modify mainstay immune pathways. Despite its human health relevance, how Chandipura virus (CHPV) per se interacts with the cellular signaling machinery has not been investigated. Here, we report that RelA deficiency abrogated antiviral gene expressions and yet surprisingly caused diminished growth of CHPV in mouse embryonic fibroblasts. Our experimental studies clarified that RelA-dependent synthesis of pro-survival factors restrained infection-inflicted cell death, and that exacerbated cell death processes prevented multiplication of CHPV in RelA-deficient cells. In sum, we identify a pro-viral function of the immune-activating transcription factor RelA NF-{kappa}B linked to its pro-survival properties.\n\nHighlightsO_LILack of RelA NF-{kappa}B leads to reduced growth of CHPV ex vivo\nC_LIO_LIRelA deficiency exacerbates cell-death processes upon CHPV infection\nC_LIO_LIInhibition of cell-death processes restores CHPV multiplication in RelA-deficient MEFs\nC_LI

immunology↗

bioRxiv2018

Rational Design of Peptide Vaccines for the Highly Lethal Nipah and Hendra Viruses

The Nipah virus disease is a lethal infection that has led to 40% to 75% fatalities in Malaysia, Bangladesh and India. The reports of human-to-human transmission documented in Bangladesh has raised the specter of pandemic potential and has caused the World Health Organization to list the Nipah virus as one of the pathogens to be considered for development of drugs and vaccines on urgent basis, neither of which exist against the Nipah virus as of now, although many proposals have been made and trials initiated. Given that there are established country-specific differences in the virus effects and fatalities, meeting the sudden need for a vaccine in case of an epidemic will require design, development and preparation for a peptide vaccine. Thus, we propose a protocol for creating peptide vaccines that can be tailor-made for these specific countries, an approach which is being advocated for the first time. Here, we analyze the surface proteins, Fusion protein and Glycoprotein, of the strains currently affecting the three countries on a large scale and determine the specific country-based epitope differences.

bioinformatics↗