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Saini, D. K.

Publications and source records attributed to Saini, D. K..

15 recordsLinked to original sources

Mycobacterial MutT1 mediated dephosphorylation of the sensor kinases reveals a new link in the regulation of the two-component signaling in bacteria

Bacterial pathogens such as Mycobacterium tuberculosis majorly rely on two-component signaling (TCS) systems to sense and generate adaptive responses to the dynamic and stressful host environment. TCS comprises a sensor histidine kinase (SK) that perceives the environmental signal, and a response regulator (RR) that modulates the target gene expression. TCS occurs via a phosphotransfer event from SK to RR. However, the mechanisms that regulate phosphotransfer events are not well understood. We explored the role of MutT1, originally characterized to hydrolyze oxidized GTP (8-oxo-GTP) and dGTP (8-oxo-dGTP), in TCS regulation. Unlike other MutT proteins, mycobacterial MutT1 comprises two domains (N-terminal domain, NTD; and C-terminal domain, CTD). Structurally, MutT1 NTD is like MutT proteins in other organisms. However, the MutT1 CTD is similar to E. coli SixA, a histidine phosphatase with an RHG motif. We show that MutT1 CTD dephosphorylates many SKs and impacts expression of their target genes, highlighting the role of MutT1 in regulating TCS. These novel findings are of special significance because they provide us with an extrinsic phosphatase mechanism to reset TCS signaling. The study reveals an intricate interplay between an enzyme that sanitizes the cellular nucleotide pool, and bacterial signaling pathways, offering insights into the adaptation mechanisms.

cell biology↗

An unusual activity of mycobacterial MutT1 Nudix hydrolase domain as a protein phosphatase regulates nucleoside diphosphate kinase (NDK) function

MutT proteins are Nudix hydrolases characterized by the presence of a Nudix box, GX5EX7REUXEEXGU, where U is a bulky hydrophobic residue and X is any residue. Major MutT proteins hydrolyse 8-oxo-(d)GTP (8-oxo-GTP or 8-oxo-dGTP) to the corresponding 8-oxo-(d)GMP, preventing their incorporation into nucleic acids. Mycobacterial MutT1 comprises an N-terminal domain (NTD) harbouring the Nudix box motif, and a C-terminal domain (CTD) harbouring the RHG histidine phosphatase motif. Interestingly, unlike other MutTs, the MutT1 hydrolyses the mutagenic 8-oxo-(d)GTP to corresponding 8-oxo-(d)GDP. Nucleoside diphosphate kinase (NDK), a conserved protein, carries out reversible conversion of (d)NDPs to (d)NTPs through phospho-NDK (NDK-Pi) intermediate. Recently, we showed that NDK-Pi converts 8-oxo-dGDP to 8-oxo-dGTP and escalates A to C mutations in a MutT deficient Escherichia coli. We now show that both Mycobacterium tuberculosis MutT1, and M. smegmatis MutT1, through their NTD (Nudix hydrolase motifs) function as protein phosphatase to regulate the levels of NDK-Pi to NDK and prevent it from catalysing conversion of (d)NDPs to (d)NTPs (including conversion of 8-oxo-dGDP to 8-oxo-dGTP). To corroborate this function, we show that MsmMutT1 decreases A to C mutations in E. coli under the conditions of EcoNDK overexpression. ImportanceMutT proteins, having a Nudix box domain, hydrolyse the mutagenic 8-oxo-dGTP to 8-oxo-dGMP. However, mycobacterial MutT (MutT1) comprises an N-terminal domain (NTD) harboring a Nudix box, and a C-terminal domain (CTD) harboring an RHG histidine phosphatase. Unlike other MutTs, mycobaterial MutT1 hydrolyses 8-oxo-dGTP to 8-oxo-dGDP. Nucleoside diphosphate kinase (NDK), a conserved protein, converts 8-oxo-dGDP to 8-oxo-dGTP through phospho-NDK (NDK-Pi) intermediate, and escalates A to C mutations. Here, we show that the mycobacterial MutT1 is unprecedented in that its NTD (Nudix box), functions as protein phosphatase to regulate NDK-Pi levels and prevents it from converting dNDPs to dNTPs (including 8-oxo-dGDP to 8-oxo-dGTP conversion). In addition, mycobacterial MutT1 decreases A to C mutations in Escherichia coli under the conditions of NDK overexpression.

molecular biology↗

Oxysterol accumulation in aging cells alters GPCR signalling

Organismal aging is accompanied by the accumulation of senescent cells in the body, which drives tissue dysfunction. Senescent cells have a distinctive profile, including proliferation arrest, resistance to apoptosis, altered gene expression, and high inflammation. Despite global signalling and metabolic dysregulation during senescence, the underlying reasons for changes in signalling remain unclear. GPCRs are pivotal in cellular signalling, dynamically mediating the complex interplay between cells and their surrounding environment to maintain cellular homeostasis. The chemokine receptor CXCR4 plays a crucial role in modulating immune responses and inflammation. It has been shown that expression of CXCR4 increases in cells undergoing senescence, which enhances inflammation post-activation. Here we examine CXCR4 signalling in deeply senescent cells, where cholesterol and its oxidized derivatives, oxysterols, affect receptor function. We report elevated oxysterol levels in senescent cells, which altered classical CXCL12-mediated CXCR4 signalling. Tail-oxidized sterols disrupted signalling more than ring-oxidized counterparts. Molecular dynamics simulations revealed that 27-hydroxycholesterol displaces cholesterol and binds strongly to alter the conformation of critical signalling residues to modify the sterol-CXCR4 interaction landscape. Our study provides a molecular view of the observed mitigated GPCR signalling in the presence of oxysterols, which switched G-protein signalling from Gi/o to Gs class. Overall, we present an altered paradigm of GPCR signalling where cholesterol oxidation alters the signalling outcome in aged cells. Significance StatementOur study brings to light a novel and significant discovery in aged cells: the accumulation of oxysterols, oxidized forms of cholesterol, critically impairs CXCR4-dependent signalling and alters G-protein coupling specificity. This effect of oxysterols is demonstrated for the first time in aged cellular models, providing a molecular basis for a multitude of observed alterations in senescence, such as compromised immune functions and a decline in cellular responsiveness with age. Our research not only fills a crucial gap in understanding the aging process at the molecular level but also identifies potential targets for therapeutic interventions aimed at mitigating age-related cellular dysfunctions and diseases.

cell 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↗

The senescent mesothelial matrix accentuates colonization by ovarian cancer cells

Ovarian cancer is amongst the most morbid of gynecological malignancies due to its diagnosis at an advanced stage, a transcoelomic mode of metastasis, and rapid transition to chemotherapeutic resistance. Like all other malignancies, the progression of ovarian cancer may be interpreted as an emergent outcome of the conflict between metastasizing cancer cells and the natural defense mounted by microenvironmental barriers to such migration. Here, we asked whether senescence in coelom-lining mesothelia, brought about by drug exposure, affects their interaction with disseminated ovarian cancer cells. We observed that cancer cells adhered faster on, senescent human and murine mesothelial monolayers than non-senescent controls. Time-lapse epifluorescent microscopy showed that mesothelial cells were cleared by a host of cancer cells that surrounded the former, even under sub-confluent conditions. A multiscale computational model predicted that such colocalized mesothelial clearance under sub-confluence requires greater adhesion between cancer cells and senescent mesothelia. Consistent with the prediction, we observed that senescent mesothelia expressed extracellular matrix with higher levels of fibronectin, laminins and hyaluronan than non-senescent controls. On senescent matrix, cancer cells adhered more efficiently, spread better, and moved faster and persistently, aiding the spread of cancer. Inhibition assays using RGD cyclopeptides suggested the adhesion was predominantly contributed by fibronectin and laminin. These findings led us to propose that the senescence-associated matrisomal phenotype of peritoneal barriers enhances the colonization of invading ovarian cancer cells and their clearance contributing to the metastatic burden associated with the disease.

cancer biology↗

Modulated protein-sterol interactions drive oxysterol-induced impaired CXCR4 signalling

CXCR4 is a G-protein coupled receptor which mediates signalling for diverse functions such as cell proliferation and migration, hematopoiesis and plays a role in embryogenesis and development. Signal transduction occurs primarily through transmembrane helices that function in the multicomponent lipid environment of the plasma membrane. Elevated levels of plasma membrane oxysterols occur in cardiovascular and metabolic disorders, physiological stress and inflammatory conditions. We use experimental and simulation approaches to study the impact of oxysterol chemistry and composition on CXCL12-mediated CXCR4 signalling. Experiments on HeLa cells show a pronounced decrease in calcium oscillation response for the tail oxidized sterols in comparison with the ring oxidized sterols with 22(R) hydroxycholesterol showing a near complete loss of signalling followed by 27-hydroxycholesterol and 25-hydroxycholesterol. All-atom molecular dynamics simulations reveal that tail oxidized, 27-hydroxycholesterol, displaces cholesterol and ubiquitously binds to several critical signalling residues, as well as the dimer interface. Enhanced 27-hydroxycholesterol binding alters CXCR4 residue conformations, disrupts the toggle switch and induces secondary structure changes at both N and C termini. Our study provides a molecular view of the observed mitigated CXCR4 signalling in the presence of oxysterols revealing that disruption of cholesterol-protein interactions, important for regulating the active state, is a key factor in the loss of CXCR4 signalling. Additionally, a signalling class switching from Gi to Gs as revealed by increased CREB and ERK phosphorylation is observed in the experiments.

cell biology↗

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

In wheat, a meta-analysis was performed using previously identified QTLs associated with drought stress, heat stress, salinity stress, water-logging stress, pre-harvest sprouting, and aluminium stress which predicted a total of 134 meta-QTLs (MQTLs) that involved at least 28 consistent and stable MQTLs conferring tolerance to five or all six abiotic stresses under study. Seventy-six MQTLs out of the 132 physically anchored MQTLs were also verified with genome-wide association studies. Around 43% of MQTLs had genetic and physical confidence intervals of less than 1 cM and 5 Mb, respectively. Consequently, 539 genes were identified in some selected MQTLs providing tolerance to 5 or all 6 abiotic stresses. Comparative analysis of genes underlying MQTLs with four RNA-seq based transcriptomic datasets unravelled a total of 191 differentially expressed genes which also included at least 11 most promising candidate genes common among different datasets. The promoter analysis showed that the promoters of these genes include many stress responsiveness cis-regulatory elements, such as ARE, MBS, TC-rich repeats, As-1 element, STRE, LTR, WRE3, and WUN-motif among others. Further, some MQTLs also overlapped with as many as 34 known abiotic stress tolerance genes. In addition, numerous ortho-MQTLs among the wheat, maize, and rice genomes were discovered. These findings could help with fine mapping and gene cloning, as well as marker-assisted breeding for multiple abiotic stress tolerances in wheat.

bioinformatics↗

An evolutionary paradigm favoring crosstalk between bacterial two-component signaling systems

The prevalent paradigm governing bacterial two-component signaling systems (TCSs) is specificity, wherein the histidine kinase (HK) of a TCS exclusively activates its cognate response regulator (RR). Crosstalk, where HKs activate noncognate RRs, is considered evolutionarily disadvantageous because it can compromise adaptive responses by leaking signals. Yet, crosstalk is observed in several bacteria. Here, to resolve this paradox, we propose an alternative paradigm where crosstalk can be advantageous. We envisioned programmed environments, wherein signals appear in predefined sequences. In such environments, crosstalk that primes bacteria to upcoming signals may improve adaptive responses and confer evolutionary benefits. To test this hypothesis, we employed mathematical modeling of TCS signaling networks and stochastic evolutionary dynamics simulations. We considered the comprehensive set of bacterial phenotypes, comprising thousands of distinct crosstalk patterns, competing in varied signaling environments. Our simulations predicted that in programmed environments phenotypes with crosstalk facilitating priming would outcompete phenotypes without crosstalk. In environments where signals appear randomly, bacteria without crosstalk would dominate, explaining the specificity widely seen. Additionally, a testable prediction was that the phenotypes selected in programmed environments would display one-way crosstalk, ensuring priming to future signals. Interestingly, the crosstalk networks we deduced from available data on TCSs of Mycobacterium tuberculosis all displayed one-way crosstalk, offering strong support to our predictions. Our study thus identifies potential evolutionary underpinnings of crosstalk in bacterial TCSs, suggests a reconciliation of specificity and crosstalk, makes testable predictions of the nature of crosstalk patterns selected, and has implications for understanding bacterial adaptation and the response to interventions. IMPORTANCEBacteria use two-component signaling systems (TCSs) to sense and respond to environmental changes. The prevalent paradigm governing TCSs is specificity, where signal flow through TCSs is insulated; leakage to other TCSs is considered evolutionarily disadvantageous. Yet, crosstalk between TCSs is observed in many bacteria. Here, we present a potential resolution of this paradox. We envision programmed environments, wherein stimuli appear in predefined sequences. Crosstalk that primes bacteria to upcoming stimuli could then confer evolutionary benefits. We demonstrate this benefit using mathematical modeling and evolutionary simulations. Interestingly, we found signatures of predicted crosstalk patterns in Mycobacterium tuberculosis. Furthermore, specificity was selected in environments where stimuli occurred randomly, thus reconciling specificity and crosstalk. Implications follow for understanding bacterial evolution and for interventions.

microbiology↗

Cell adhesion strength and tractions are mechano-diagnostic features of cellular invasiveness

The adhesion of cells to substrates occurs via integrin clustering and binding to the actin cytoskeleton. Oncogenes modify anchorage-dependent mechanisms in cells during cancer progression. Fluid shear devices provide a label-free, non-invasive way to characterize cell-substrate interactions and heterogeneities in the cell populations. We quantified the critical adhesion strengths of MCF7, MDAMB-231, A549, HPL1D, HeLa, and NIH3T3 cells using a custom fluid shear device. The detachment response was sigmoidal for each cell type. A549 and MDAMB-231 cells had significantly lower adhesion strengths at {tau}50 than their non-invasive counterparts, HPL1D and MCF7. Detachment dynamics was inversely correlated with cell invasion potentials. A theoretical model, based on {tau}50 values and the distribution of cell areas on substrates, provided good fits to data from de-adhesion experiments. Quantification of cell tractions, using the Reg-FTTC method on 10 kPa polyacrylamide gels, showed highest values for invasive, MDAMB-231 and A549, cells compared to non-invasive cells. Immunofluorescence studies show differences in vinculin distributions: non-invasive cells have distinct vinculin puncta, whereas invasive cells have more dispersed distributions. The cytoskeleton in non-invasive cells was devoid of well-developed stress fibers, and had thicker cortical actin bundles in the boundary. These correlations in adhesion strengths with cell invasiveness, demonstrated here, may be useful in cancer diagnostics and other pathologies featuring misregulation in adhesion.

bioengineering↗

Sequestration of histidine kinases by non-cognate response regulators establishes a threshold level of stimulation for bacterial two-component signaling

Two-component signaling systems (TCSs) in bacteria are often positively auto-regulated, where the histidine kinase (HK) and response regulator (RR) proteins comprising a TCS are expressed downstream of the signal they transduce. This auto-regulation improves the sensitivity of the TCS to stimuli and amplifies adaptive responses. The downside, however, is that the TCS may mount disproportionately large responses to weak or fleeting signals. How bacteria prevent such disproportionate responses is not known. Here, we show that sequestration of phosphorylated HKs by non-cognate RRs serves as a design to prevent such disproportionate responses. Using TCSs of M. tuberculosis as model systems, we found that with every one of the five HKs we studied, there was at least one non-cognate RR with higher affinity than that of the cognate RR for the HK. Phosphorylated HKs would thus preferentially bind the non-cognate RRs, suppressing signal transduction through the cognate pathways, which we demonstrated in vitro. Using mathematical modeling of TCS signaling in vivo, we predicted that this sequestration would introduce a threshold level of stimulation for a significant response, preventing responses to signals below this threshold. Finally, we showed in vivo using tunable expression systems in M. bovis that upregulation of a higher affinity non-cognate RR substantially suppressed the output from the cognate TCS pathway, presenting strong evidence of sequestration by non-cognate RRs as a design to regulate TCS signaling. Blocking this sequestration may be a novel intervention strategy, as it would compromise bacterial fitness by letting it respond unnecessarily to signals.

systems biology↗

Unravelling consensus genomic regions associated with quality traits in wheat (Triticum aestivum L.) using meta-analysis of quantitative trait loci

A meta-analysis of quantitative trait loci (QTLs) associated with following six major quality traits (i) arabinoxylan, (ii) dough rheology properties, (iii) nutritional traits, (iv) polyphenol content, (v) processing quality traits, and (vi) sedimentation volume was conducted in wheat. For this purpose, as many as 2458 QTLs were collected from the 50 mapping studies published during 2013-20. Of the total QTLs, 1126 QTLs were projected on to the consensus map saturated with 2,50,077 markers resulting into the identification of 110 meta-QTLs (MQTLs) with average confidence interval (CI) of 5.6 cM. These MQTLs had 18.84 times reduced CI compared to CI of initial QTLs. Fifty-one (51) MQTLs were also verified with the marker-trait associations (MTAs) detected in earlier genome-wide association studies (GWAS). Physical region occupied by a single MQTL ranged from 0.12 to 749.71 Mb with an average of 130.25 Mb. Candidate gene mining allowed the identification of 2533 unique gene models from the MQTL regions. In-silico expression analysis discovered 439 differentially expressed gene models with >2 transcripts per million (TPM) expression in grains and related tissues which also included 44 high-confidence candidate genes known to be involved in the various cellular and biochemical processes related to quality traits. Further, nine functionally characterized wheat genes associated with grain protein content, high molecular weight glutenin and starch synthase enzymes were also found to be co-localized with some of the MQTLs. In addition, synteny analysis between wheat and rice MQTL regions identified 23 wheat MQTLs syntenic to 16 rice MQTLs. Furthermore, 64 wheat orthologues of 30 known rice genes were detected in 44 MQTL regions. These genes encoded proteins mainly belonging to the following families: starch synthase, glycosyl transferase, aldehyde dehydrogenase, SWEET sugar transporter, alpha amylase, glycoside hydrolase, glycogen debranching enzyme, protein kinase, peptidase, legumain and seed storage protein enzyme. Main ConclusionMeta-QTL analysis in wheat for major quality traits identified 110 MQTLs with reduced confidence interval. Candidate gene mining and expression analysis discovered differentially expressed genes involve in quality traits.

genetics↗

Meta-analysis of orthogonal OMICs data from COVID-19 patients unveils prognostic markers and antiviral factors.

While our battle with the COVID-19 pandemic continues, a multitude of Omics data has been generated from patient samples in various studies, which remains to be translated. We conducted a meta-analysis of published transcriptome and proteome profiles of nasal swab and bronchioalveolar lavage fluid (BALF) samples of COVID-19 patients, to shortlist high confidence upregulated host factors. Subsequently, mRNA overexpression of selected genes was validated in nasal swab/BALF samples from a cohort of COVID-19 positive/negative, symptomatic/asymptomatic individuals. Analysis of these data revealed S100 family genes (S100A6, S100A8, S100A9, and S100P) as prognostic markers of COVID-19 disease. Furthermore, Thioredoxin gene (TXN) was identified as a significant upregulated host factor in our overlap analysis. An FDA-approved drug Auranofin, which inhibits Thioredoxin reduction, was found to mitigate SARS-CoV-2 replication in vitro and in vivo in the hamster challenge model. Overall, this study translates COVID-19 host response Big Data into potential clinical interventions.

microbiology↗

Aging associated altered response to intracellular bacterial infections and its implication on the host

The effects of senescence and aging on geriatric diseases has been well explored but how these influence infections in the elderly have been scarcely addressed. Here, we show that several innate immune responses are elevated in senescent cells and old mice, allowing them to promptly respond to bacterial infections. We have identified higher levels of iNOS as a crucial host response and show that p38 MAPK in senescent cells acts as a negative regulator of iNOS transcription. In old mice, however the ability to impede bacterial proliferation does not correlate with increased survival as elevated immune responses persist unabated eventually affecting the host. The use of anti-inflammatory drugs that could consequently be recommended also decreases iNOS disarming the host of a critical innate immune response. Overall, our study highlights that infection associated mortality in the elderly is not merely an outcome of pathogen load but is also influenced by the hosts ability to resolve inflammation induced damage. Summary statementUsing cellular models and old mice we demonstrate the effect of aging on host response to bacterial infections. Aged systems mount a more effective anti-bacterial innate immune response but its persistence results in mortality of the host.

microbiology↗

The histidine kinase PdtaS is a cyclic di-GMP binding metabolic sensor that controls mycobacterial adaptation to nutrient deprivation

Cell signalling relies on second messengers to transduce signals from the sensory apparatus to downstream components of the signalling pathway. In bacteria, one of the most important and ubiquitous second messengers is the small molecule cyclic diguanosine monophosphate (c-di-GMP). While the biosynthesis, degradation and regulatory pathways controlled by c-di-GMP are well characterized, the mechanisms through which c-di-GMP controls these processes is not completely understood. Here we present the first report of a c-di-GMP regulated sensor histidine kinase previously named PdtaS (Rv3220c), which binds to c-di-GMP at sub-micromolar concentrations, subsequently perturbing signalling of the PdtaS-PdtaR (Rv1626) two component system. Aided by biochemical analysis, molecular docking and structural modelling, we have characterized the binding site of c-di-GMP in the GAF domain of PdtaS. We show that a pdtaS knockout in M. smegmatis is severely compromised in growth on amino acid deficient media and exhibits global transcriptional dysregulation. Perturbation of the c-di-GMP-PdtaS-PdtaR axis results in a cascade of cellular changes recorded by a multi-parametric systems approach of transcriptomics, unbiased metabolomics and lipid analyses.\n\nOne-sentence summaryThe universal bacterial second messenger cyclic di-GMP controls the mycobacterial nutrient stress response

microbiology↗

Sequence Analysis and Homology Modelling of SmHQT Protein, a Key Player in Chlorogenic Acid Pathway of Eggplant

Eggplant is an important vegetable that belongs to family Solanaceae. Fruits of eggplant are rich in phenolic acids. Chlorogenic acid makes up to 90 per cent of total phenolic acids present in the eggplants fruit flesh. Eggplant hydroxycinnamoyl CoA-quinate (SmHQT) is the central enzyme that modulates the last step of the chlorogenic acid pathway of eggplant. Here, we have analysed the sequence of eggplant SmHQT protein in eggplant. The sequence obtained from the NCBI was aligned using MUSCLE. After that, homology modelling was performed using MODELLER 9v15. Model with Dope Z-Score of -1.596 was selected and verified for viability under real conditions using several online tools. Also, the docking was performed with this model. Overall, this could be useful in developing eggplant varieties rich in phenolic acids especially chlorogenic acid.

bioinformatics↗