Biology subjects

Singh, V.

Publications and source records attributed to Singh, V..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Characterization of human lightness discrimination thresholds for independent spectral variations

The lightness of an object is an intrinsic property that depends on its surface reflectance spectrum. The visual system estimates an objects lightness from the light reflected off its surface. The light reflected also depends on object extrinsic properties of the scene. For stable perception, the visual system needs to discount variations due to extrinsic properties. We characterize this perceptual stability for variation in two spectral properties of the scene: the reflectance spectra of background objects and the intensity of light sources. We use a two-alternative forced-choice task to measure human observers thresholds of discriminating computer-generated images of 3D scenes based on the lightness of a spherical target object in the scene. We measured how the discrimination thresholds changed as we varied the reflectance spectra of the objects and the intensity of the light sources in the scene, both individually and simultaneously. For small amounts of extrinsic variations, the thresholds of discrimination remained constant indicating that the thresholds were dominated by observers intrinsic representation of lightness. As extrinsic variation increased, it started affecting observers lightness judgment and the thresholds increased. We estimated that the effects of extrinsic variations were comparable to observers intrinsic variation in the representation of object lightness. Moreover, for simultaneous variation of these spectral properties, the increase in threshold square compared to no variation condition was a linear sum of the corresponding increase in threshold squares for the individual properties, indicating that the variation from these independent sources combines linearly.

animal behavior and cognition↗

bioRxiv2023

The basis of antigenic operon fragmentation in Bacteroidota and commensalism

The causes for variability of pro-inflammatory surface antigens that affect gut commensal/opportunistic dualism within the phylum Bacteroidota remain unclear (1, 2). Using the classical lipopolysaccharide/O-antigen rfb operon in Enterobacteriaceae as a surface antigen model (5-gene-cluster rfbABCDX), and a recent rfbA-typing strategy for strain classification (3), we characterized the architecture/conservancy of the entire rfb operon in Bacteroidota. Analyzing complete genomes, we discovered that most Bacteroidota have the rfb operon fragmented into non-random gene-singlets and/or doublets/triplets, termed minioperons. To reflect global operon integrity, duplication, and fragmentation principles, we propose a five-category (infra/supernumerary) cataloguing system and a Global Operon Profiling System for bacteria. Mechanistically, genomic sequence analyses revealed that operon fragmentation is driven by intra-operon insertions of predominantly Bacteroides-DNA (thetaiotaomicron/fragilis) and likely natural selection in specific micro-niches. Bacteroides-insertions, also detected in other antigenic operons (fimbriae), but not in operons deemed essential (ribosomal), could explain why Bacteroidota have fewer KEGG-pathways despite large genomes (4). DNA insertions overrepresenting DNA-exchange-avid species, impact functional metagenomics by inflating gene-based pathway inference and overestimating extra-species abundance. Using bacteria from inflammatory gut-wall cavernous micro-tracts (CavFT) in Crohns Disease (5), we illustrate that bacteria with supernumerary-fragmented operons cannot produce O-antigen, and that commensal/CavFT Bacteroidota stimulate macrophages with lower potency than Enterobacteriaceae, and do not induce peritonitis in mice. The impact of foreign-DNA insertions on pro-inflammatory operons, metagenomics, and commensalism offers potential for novel diagnostics and therapeutics.

microbiology↗

bioRxiv2023

Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications

The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 [A] resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNAVal. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transition in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide the most complete description so far of the structure and function of the human mitoribosome.

biochemistry↗

bioRxiv2023

Computational workflow for predicting transcriptional modulation to achieve therapeutically desired cellular conversion for regenerative medicine

IntroductionRegenerative medicine promises a cure for currently incurable diseases and pathological conditions. Its central idea is to leverage healthy cells to regenerate diseased cells, tissues or organs through the process of cellular reprogramming. The most common method to achieve this is by modulating the activity of specific transcription factors. However, the large number of protein-coding genes and transcription factors in humans and their complex interactions poses a challenge in identifying the most suitable ones for modulation. Here, we propose a computational workflow that facilitates the prediction of such transcription factors for achieving desired cellular reprogramming, along with highlighting their mechanistic basis in terms of the gene regulatory network of the target cell type. MethodsIn this paper, we propose a synergistic workflow that leverages existing computational tools: TransSynW, PAGA and SIGNET, a software - Cytoscape and two databases - TRRUST and UniProt. It uses single-cell transcriptome data of the starting and target cell types as inputs. We demonstrate this workflow by predicting suitable transcriptional modulations for reprogramming of human foreskin fibroblasts to oculomotor neurons. ResultsUsing the workflow, we hypothesized the core drivers for specific cellular reprogramming along with their functional understanding for experimental applications. The workflow predicted the transcription factors for modulation and provided insight into their differential expression dynamics and influence on the predicted gene regulatory network of the target cells. ConclusionOur computational workflow helps extract meaningful predictive and mechanistic insights from high-dimensional biological data, which otherwise is difficult to accomplish from individual tools alone. We believe this workflow can help researchers generate mechanistically founded hypotheses for achieving desired cellular reprogramming as a step towards regenerative medicine. HighlightsO_LICombine computational tools as workflows to gain predictive and mechanistic insights C_LIO_LIThe workflow predicts suitable transcription factors for targeted cellular reprogramming C_LIO_LIGain insight into the influence of transcriptional modulation on gene regulatory network C_LIO_LIThe workflow generates mechanistically founded hypotheses for transcriptional modulation C_LIO_LIRationalized experimental design for targeted cellular reprogramming for regenerative therapies C_LI

bioinformatics↗

bioRxiv2023

An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis

As one of the top value-added chemicals, succinic acid has been the focus of numerous metabolic engineering campaigns since the 1990s. However, microbial production of succinic acid at an industrially relevant scale has been hindered by high downstream processing costs arising from neutral pH fermentation. Here we describe the metabolic engineering of Issatchenkia orientalis, a non-conventional yeast with superior tolerance to highly acidic conditions, for cost-effective succinic acid production. Through deletion of byproduct pathways, transport engineering, and expanding the substrate scope, the resulting strains could produce succinic acid at the highest titers in sugar-based media at low pH (pH 3) in fed-batch fermentations using bench-top reactors, i.e. 109.5 g/L in minimal medium and 104.6 g/L in sugarcane juice medium. We further performed batch fermentation in a pilot-scale fermenter with a scaling factor of 300x, achieving 63.1 g/L of succinic acid using sugarcane juice medium. A downstream processing comprising of two-stage vacuum distillation and crystallization enabled direct recovery of succinic acid, without further acidification of fermentation broth, with an overall yield of 64.0%. Finally, we simulated an end-to-end low-pH succinic acid production pipeline, and techno-economic analysis and life cycle assessment indicate our process is financially viable and can reduce life cycle greenhouse gas emissions by 34-90% relative to fossil-based production processes. We expect I. orientalis can serve as a general industrial platform for the production of a wide variety of organic acids.

synthetic biology↗

bioRxiv2023

O-GlcNAc modification forces the formation of an α-Synuclein amyloid-strain with notably diminished seeding activity and pathology

The process of amyloid fibril formation remains one of the primary targets for developing diagnostics and treatments for several neurodegenerative diseases (NDDs). Amyloid-forming proteins such -Synuclein and Tau, which are implicated in the pathogenesis of Alzheimers and Parkinsons disease, can form different types of fibril structure, or strains, that exhibit distinct structures, toxic properties, seeding activities, and pathology spreading patterns in the brain. Therefore, understanding the molecular and structural determinants contributing to the formation of different amyloid strains or their distinct features could open new avenues for developing disease-specific diagnostics and therapies. In this work, we report that O-GlcNAc modification of -Synuclein monomers results in the formation of amyloid fibril with distinct core structure, as revealed by Cryo-EM, and diminished seeding activity in seeding-based neuronal and rodent models of Parkinsons disease. Although the mechanisms underpinning the seeding neutralization activity of the O-GlcNAc modified fibrils remain unclear, our in vitro mechanistic studies indicate that heat shock proteins interactions with O-GlcNAc fibril inhibit their seeding activity, suggesting that the O-GlcNAc modification may alter the interactome of the -Synuclein fibrils in ways that lead to reduce seeding activity in vivo. Our results show that post-translational modifications, such as O-GlcNAc modification, of -Synuclein are key determinants of -Synuclein amyloid strains and pathogenicity. These findings have significant implications for how we investigate and target amyloids in the brain and could possibly explain the lack of correlation between amyloid burden and neurodegeneration or cognitive decline in some subtypes of NDDs.

biochemistry↗

bioRxiv2023

Structural insights into agonist-binding and activation of the human complement C3a receptor

The complement cascade is an integral part of innate immunity, and it plays a crucial role in our bodys innate immune response including combating microbial infections. Activation of the complement cascade results in the generation of multiple peptide fragments, of which complement C3a and C5a are potent anaphylatoxins. The complement C3a binds and activates a G protein-coupled receptor (GPCR) known as C3aR while C5a activates two distinct receptors namely C5aR1 and C5aR2. Our current understanding of complement peptide recognition by their corresponding receptors is limited primarily to biochemical studies, and direct structural visualization of ligand-receptor complexes is still elusive. Here, we present structural snapshots of C3aR in complex with heterotrimeric G-proteins, with the receptor in ligand-free state, activated by full-length complement C3a, and a peptide agonist EP54, derived based on the carboxyl-terminal sequence of C5a. A comprehensive analysis of these structures uncovers the critical residues involved in C3a-C3aR interaction, and also provides molecular insights to rationally design carboxyl-terminal fragments of C3a and C5a to act as potent agonists of the receptor. Surprisingly, a comparison of C3a-C3aR structure with C5a-C5aR1 structure reveals diagonally opposite placement of these two complement peptides on their respective receptors, which helps explain the subtype selectivity of these complement peptides. Finally, taking lead from the structural insights, we also identify EP141, a peptide derived from the carboxyl-terminus of C3a, as a G-protein-biased agonist at C3aR. Taken together, our study illuminates the structural mechanism of complement C3a recognition by C3aR, and it also offers the first structural template for designing novel C3aR ligands with therapeutic potential for inflammatory disorders.

biochemistry↗

bioRxiv2023

A very-low carbohydrate content in a high-fat diet modifies the plasma metabolome and alleviates experimental atherosclerosis

Ketogenic diets (KD) are very low-carbohydrate diets that promote nutritional ketosis and are widely used for weight loss, although concerns about potential adverse cardiovascular effects remain. In this study, we used apolipoprotein E deficient (ApoE -/-) mice to investigate the vascular impact and plasma metabolic signature of a very high-fat KD compared to a non-ketogenic high-fat diet (HFD). Plasma samples were collected after 4, 8, and 12 weeks on the experimental diets and used to quantify the major ketone body {beta}-hydroxybutyrate (BHB), inflammatory cytokines (interleukin 6, IL-6; monocyte chemoattractant protein 1, MCP-1; and tumor necrosis factor , TNF-), and targeted metabolomic profiling by mass spectrometry. Moreover, aortic atherosclerotic lesions were quantified ex vivo by magnetic resonance imaging (MRI) on a 14-tesla system. The results showed that, relative to HFD mice, the KD mice had markedly higher levels of BHB and lower levels of cytokines, confirming the presence of ketosis that alleviated the well-established fat-induced systemic inflammation. Moreover, mice under nutritional ketosis displayed a distinct plasma amino acid profile evidencing a KD-induced alteration in protein metabolism. Significant changes in the plasma metabolome in KD mice included a decrease in lipophilic and increase in hydrophilic metabolites. Despite the higher fat content of the KD versus the HFD, KD mice presented significantly lower levels of several lipid metabolites, including phosphatidylcholines, cholesterol esters, sphingomyelins, and ceramides. Consistent with the shift in energy metabolism toward fatty acid oxidation caused by the KD, the ratio of acylcarnitines to free carnitine was significantly higher in KD than in HFD mice., the aortic plaque burden was significantly lower in the KD versus the HFD group. In conclusion, nutritional ketosis induced by the KD was associated with specific metabolic changes and an atheroprotective phenotype versus the HFD.

biochemistry↗

bioRxiv2023

A large-scale Boolean model of the Rheumatoid Arthritis Fibroblast-Like Synoviocytes predicts drug synergies in the arthritic joint

Rheumatoid arthritis (RA) is a complex autoimmune disease with an unknown aetiology. However, rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS) play a significant role in initiating and perpetuating destructive joint inflammation by expressing immuno-modulating cytokines, adhesion molecules, and matrix remodelling enzymes. In addition, RA-FLS are primary drivers of inflammation, displaying high proliferative rates and an apoptosis-resistant phenotype. Thus, RA-FLS-directed therapies could become a complementary approach to immune-directed therapies by predicting the optimal conditions that would favour RA-FLS apoptosis, limit inflammation, slow the proliferation rate and minimise bone erosion and cartilage destruction. In this paper, we present a large-scale Boolean model for RA-FLS that consists of five submodels focusing on apoptosis, cell proliferation, matrix degradation, bone erosion and inflammation. The five phenotype-specific submodels can be simulated independently or as a global model. In-silico simulations and perturbations reproduced the expected biological behaviour of the system under defined initial conditions and input values. The model was then used to mimic the effect of mono or combined therapeutic treatments and predict novel targets and drug candidates through drug repurposing analysis.

systems biology↗

bioRxiv2023

Structural insights into ligand-recognition, activation, and signaling-bias at the complement C5a receptor, C5aR1

Activation of the complement cascade is a critical part of our innate immune response against invading pathogens, and it operates in a concerted fashion with the antibodies and phagocytic cells towards the clearance of pathogens. The complement peptide C5a, generated during the activation of complement cascade, is a potent inflammatory molecule, and increased levels of C5a are implicated in multiple inflammatory disorders including the advanced stages of COVID-19 pathophysiology. The proximal step in C5a-mediated cellular and physiological responses is its interaction with two different seven transmembrane receptors (7TMRs) known as C5aR1 and C5aR2. Despite a large body of functional data on C5a-C5aR1 interaction, direct visualization of their interaction at high-resolution is still lacking, and it represents a significant knowledge gap in our current understanding of complement receptor activation and signaling. Here, we present cryo-EM structures of C5aR1 activated by its natural agonist C5a, and a G-protein-biased synthetic peptide ligand C5apep, in complex with heterotrimeric G-proteins. The C5a-C5aR1 structure reveals the ligand binding interface involving the N-terminus and extracellular loops of the receptor, and we observe that C5a exhibits a significant conformational change upon its interaction with the receptor compared to the basal conformation. On the other hand, the structural details of C5apep-C5aR1 complex provide a molecular basis to rationalize the ability of peptides, designed based on the carboxyl-terminus sequence of C5a, to act as potent agonists of the receptor, and also the mechanism underlying their biased agonism. In addition, these structural snapshots also reveal activation-associated conformational changes in C5aR1 including outward movement of TM6 and a dramatic rotation of helix 8, and the interaction interface for G-protein-coupling. In summary, this study provides previously lacking molecular basis for the complement C5a recognition and activation of C5aR1, and it should facilitate structure-based discovery of novel lead molecules to target C5aR1 in inflammatory disorders.

biophysics↗

bioRxiv2022

Air-Liquid-Interface Reorganizes Membrane Lipid and Enhance Recruitment of Slc26a3 to Lipid-Rich Domains in Human Colon

Background and AimsCholesterol-rich membrane domains, also called lipid rafts (LR), are specialized membrane domains that provide a platform for intracellular signal transduction. Membrane proteins often cluster in LR that further aggregate into larger platform-like structures that are enriched in ceramide and are called ceramide-rich platforms (CRPs). The role of CRPs in the regulation of intestinal epithelial functions remains unknown. Down Regulated in Adenoma (DRA) is an intestinal Cl-/HCO3- antiporter which is enriched in LR. However, little is known regarding the mechanisms involved in the regulation of DRA activity. MethodsAir liquid interface (ALI) was created by removing apical media for a specified number of days from 12-14 days post confluency Caco-2/BBe cells or confluent colonoid monolayer grown as submerged cultures. Confocal imaging was used to examine the dimensions of membrane microdomains that contain DRA. ResultsDRA expression and activity were enhanced by culturing Caco-2/BBe cells and human colonoids using an ALI culture method. ALI causes an increase in acid sphingomyelinase (ASMase) activity, an enzyme responsible for enhancing ceramide content in the plasma membrane. ALI cultures expressed a larger number of DRA-containing platforms with dimensions >2 m compared to cells grown as submerged cultures. ASMase inhibitor, desipramine disrupted CRPs and reduced the ALI-induced increase in DRA expression in the apical membrane. Exposing normal human colonoid monolayers to ALI increased the ASMase activity and enhanced differentiation of colonoids along with enhancing basal and forskolin-stimulated DRA activity. ConclusionsALI increases DRA activity and expression by increasing ASMase activity and platform formation in Caco-2/BBe cells and by enhancing the differentiation of normal human colonoids. SynopsisAir-liquid interface (ALI) enhances total and brush border DRA expression and activity in Caco-2/BBe cells and human colonoids by causing differentiation of enterocytes and acid sphingomyelinase-dependent enhanced retention of DRA in ceramide-rich platform-like structures at the plasma membrane.

cell biology↗

bioRxiv2022

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Community-driven and highly interdisciplinary, the project is collaborative and supports community standards, open access, and the FAIR data principles. The coordination of community work allowed for an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework links key molecules highlighted from broad omics data analysis and computational modeling to dysregulated pathways in a cell-, tissue- or patient-specific manner. We also employ text mining and AI-assisted analysis to identify potential drugs and drug targets and use topological analysis to reveal interesting structural features of the map. The proposed framework is versatile and expandable, offering a significant upgrade in the arsenal used to understand virus-host interactions and other complex pathologies.

systems biology↗

bioRxiv2022

SLC26A3 (DRA) is stimulated in a synergistic, intracellular Ca2+ dependent manner by cAMP AND ATP in intestinal epithelial cells

In polarized intestinal epithelial cells, DRA is a brush border (BB) Cl-/HCO3- exchanger that is part of neutral NaCl absorption under baseline conditions but in cAMP driven diarrheas it is stimulated and contributes to increased anion secretion. To further understand regulation of DRA in conditions mimicking some diarrheal diseases, differentiated Caco-2/BBE cells were exposed to forskolin and ATP. Forskolin and ATP both acutely stimulated DRA in a concentration dependent manner. Forskolin at 1{micro}M and ATP at 0.25 {micro}M had minimal to no effect on DRA activity given individually; however, together, they stimulated DRA activity to levels seen with maximum concentrations of forskolin and ATP alone. In Caco-2/BBE cells expressing the Ca2+ indicator GCaMP6s, ATP alone increased Ca2+ in a concentration dependent manner, while forskolin (1 {micro}M), that by itself did not significantly alter Ca2+, followed by 0.25 {micro}M ATP produced a large increase in Ca2+ that was [~]equal to the elevation caused by 1 {micro}M ATP. BAPTA-AM pretreatment prevented the ATP and forskolin/ATP synergistic increased DRA activity and the increase in intracellular Ca2+ caused by ATP/forskolin. Conclusion: In Caco-2/BBE cells subthreshold concentrations of forskolin (cAMP) and ATP (Ca2+) synergistically increased intracellular Ca2+ and stimulated DRA activity with both being blocked by BAPTA-AM pretreatment. Diarrheal diseases such as bile acid diarrhea, in which both cAMP and Ca2+ are elevated, are likely to be associated with stimulated DRA activity contributing to increased anion secretion, while separation of DRA from NHE3 contributes to reduced NaCl absorption.

physiology↗

bioRxiv2022

Examining Anxiety and Risk-taking in Healthy Male and Female Wistar Rats using Spatial and Temporal Analysis of Elevated Plus Maze

The Elevated Plus Maze (EPM) offers a standard set up for understanding anxiety, unconditioned risk-avoidance in rodents. The animal shows a preference for enclosed safe arms and avoids risky, open arms that evoke anxiety due to elevated platform (unconditioned response to elevation). A few rodent studies aiming to understand sex-skewed representation in anxiety disorders use the maze and report that more females compared to males show high levels of anxiety and risk-avoidance on an elevated platform. Ethograms derived from examining animal behaviour in the EPM provide precise measures of behaviour of interest, enabling objective assessment of anxiety and risk behaviour. We report two new parameters that might be critical for quantitative analysis of EPM task as a measure of anxiety with reference to sex-differences in risk-taking: (a) spatial preference for arms (open & closed) (b) temporal shift in arm preference in task trials. We first report results from the conventionally derived measures confirming that males spent more time in the open arms indicating low anxiety and higher risk-taking. Preferences for the two open and two closed arms were non-uniform for males and females; male showed stronger preference for one of the two risky open arms, and females showed a stronger preference for one of the two safe closed arms. Temporal analyses indicated that males spent more time in open arms in 3 out of 6 time bins (time blocks), and females spent more time in the closed arms in 5 out of 6 time bins (time blocks), however, counter-intuitively, females showed larger increase in time spent in open arms in the last phase potentially indicating greater regulation of anxiety and increased risk-taking. Inclusion of spatial and temporal parameters in EPM studies might improve our understanding of cognitive and biological sex-differences pertaining to anxiety, and risky behaviour.

animal behavior and cognition↗

bioRxiv2022

Peyers Patch B cells undergo cell death via neutrophil-released toxic DNA following sterile tissue injury

Lymphocyte contraction (LC) in central immune organs is a concomitant of sterile tissue injury, for example after stroke. Intestinal Peyers patches (PP) harbor large numbers of B cells, but how sterile tissue injury leads to LC in PP has not been explored. We observed rapid and macroscopically evident shrinkage of PP after stroke and myocardial infarction. Light-sheet fluorescence microscopy and flow cytometry revealed a strong reduction in the number of PP-resident B cells. Mechanistically, tissue injury triggered the activation of neutrophils that released B cell-toxic neutrophil extracellular traps (NETs) decorated with citrullinated histone-H3. Antibody-mediated or genetically induced neutrophil-loss, NETs-degradation or blockade of their generation completely reversed B cell loss and preserved the tissue architecture of PP. We also found NET-like elements in human post-stroke plasma. Hence, we propose that targeting NET-generation or -function counteracts post-injury B cell contraction in PP and thereby maintains immune homeostasis at mucosal barriers. In briefHigh numbers of B cells reside in the intestinal Peyers patches. Tuz et al. revealed that in response to sterile tissue injury, activated neutrophils release histone-decorated DNA into the circulation which induces B cell death. The loss of B cells results in the shrinkage of Peyers patches and reduced amounts of secretory IgA. HighlightsO_LIStroke and myocardial infarction induce the melting of Peyers patch C_LIO_LILight-sheet microscopy and cytometry revealed B cell loss in Peyers patch C_LIO_LIPost-injury activated neutrophils release NETs and trigger B cell death C_LIO_LIInhibition of NETs rescues B cell loss and degeneration of Peyers patch C_LI

immunology↗

bioRxiv2022

Structural snapshots uncover a lock-and-key type conserved activation mechanism of β-arrestins by GPCRs

Agonist-induced phosphorylation of G protein-coupled receptors (GPCRs) is a key determinant for the binding and activation of multifunctional regulatory proteins known as {beta}-arrestins ({beta}arrs). Although the primary sequence and phosphorylation pattern of GPCRs are poorly conserved, the downstream functional responses mediated by {beta}arrs such as receptor desensitization, endocytosis and signaling are broadly applicable across GPCRs. A conserved principle of {beta}arr activation, if any, upon their interaction with different GPCRs harboring divergent phosphorylation patterns remains to be visualized, and it represents a major knowledge gap in our current understanding of GPCR signaling and regulatory paradigms. Here, we present four structural snapshots of activated {beta}arrs, in complex with distinct phosphorylation patterns derived from the carboxyl-terminus of three different GPCRs, determined using cryogenic-electron microscopy (cryo-EM). These structures of activated {beta}arrs elucidate a "lock-and-key" type conserved mechanism of {beta}arr activation wherein a P-X-P-P phosphorylation pattern in GPCRs interacts with a spatially organized K-K-R-R-K-K sequence in the N-domain of {beta}arrs. Interestingly, the P-X-P-P pattern simultaneously engages multiple structural elements in {beta}arrs responsible for maintaining the basal conformation, and thereby, leads to efficient {beta}arr activation. The conserved nature of this lock-and-key mechanism is further illustrated by a comprehensive sequence analysis of the human GPCRome, and demonstrated in cellular context with targeted mutagenesis including "loss-of-function" and "gain-of-function" experiments with respect to {beta}arr activation measured by an intrabody-based conformational sensor. Taken together, our findings uncover previously lacking structural insights, which explain the ability of distinct GPCRs to activate {beta}arrs through a common mechanism, and a key missing link in the conceptual framework of GPCR-{beta}arr interaction and resulting functional outcomes.

biochemistry↗

bioRxiv2022

Novel triplex nucleic acid lateral flow immuno-assay (NALFIA) for rapid detection of Nipah virus, Middle East respiratory syndrome coronavirus and Reston ebolavirus

We report the development of the first triplex Nucleic Acid Lateral Flow Assay (NALFIA) for detection of genomes of Nipah virus (NiV), Middle East respiratory syndrome coronavirus (MERS-CoV) and Reston ebolavirus (REBOV), intended for screening of bats as well as other hosts and reservoirs of these three viruses. Our triplex NALFIA is a two-step assay format wherein the target nucleic acid in sample is first amplified using tagged primers, and the tagged ds DNA amplicons are captured by immobilized antibodies on NALFIA device resulting to signal development from binding of streptavidin-colloidal gold conjugate to biotin tag on the captured amplicons. Triplex amplification of N gene of NiV, UpE gene of MERS-CoV, and Vp40 gene of REBOV was optimized using primers adapted from validated real-time RT-PCR assays of previous studies and the compatible combinations of hapten-labels and antibodies for triplex NALFIA device were identified. Digoxigenin, rhodamine red and alexa fluor 488 were identified as suitable 5 labels on forward primers. The lowest copy number detected by the triplex NALFIA with 2 l of triplex RT-PCR product were up to 8.21e4 for NiV N target, 7.09e1 for MERS-CoV UpE target, and 1.83e4 for REBOV Vp40 target. Using simulated samples and Taqman real-time RT-PCR as standard, the sensitivity and positive predictive values were found to be 100% for MERS-CoV UpE and REBOV Vp40 targets and 91% for NiV N target while the specificity and negative predictive values were 100% for MERS-CoV UpE targets and REBOV Vp40, and 93.3% for NiV N target.

molecular biology↗

bioRxiv2022

Toroidal displacement of Klebsiella pneumoniae by Pseudomonas aeruginosa is a unique mechanism to avoid competition for iron

Competition for resources is one of the major drivers for evolution and retention of new traits in microbial communities. Quorum-dependent traits of opportunistic human pathogen Pseudomonas aeruginosa allow it to survive and thrive in nature. Here, we report a unique surfactant-driven pushing mechanism that P. aeruginosa employs specifically against Klebsiella pneumoniae. The pushing is accomplished in a manner that is dependent on nutrient limitation and quorum sensing. We find that P. aeruginosa employs neither proteases nor toxic secondary metabolites against K. pneumoniae. Rhamnolipid biosurfactant appears to be the only factor required to displace Klebsiella effectively. Both rhamnolipid production and the pushing ability of P. aeruginosa are suppressed by iron supplementation. We show that both these bacteria produce several siderophores in minimal medium and rapidly deplete iron. Under these conditions, P. aeruginosa pushes Klebsiella away from the substratum using rhamnolipid, reducing the competition for iron. Our study describes a unique quorum and iron-responsive mechanism in P. aeruginosa to support its own growth during resource competition.

microbiology↗