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Sengupta, S.

Publications and source records attributed to Sengupta, S..

At least 55 records · Page 3Linked to original sources

Dishevelled localization and function are differentially regulated by structurally distinct sterols

The Dishevelled (DVL) family of proteins form supramolecular protein and lipid complexes at the cytoplasmic interface of the plasma membrane to regulate tissue patterning, proliferation, cell polarity, and oncogenic processes through DVL-dependent signaling, such as Wnt/{beta}-catenin. While DVL binding to cholesterol is required for its membrane association, the specific structural requirements and cellular impacts of DVL-sterol association are unclear. We report that intracellular sterols which accumulate within normal and pathological conditions cause aberrant DVL activity. In silico and molecular analyses suggested orientation of the {beta}- and -sterol face within the DVL-PDZ domain regulates DVL-sterol binding. Intracellular accumulation of naturally occurring sterols impaired DVL2 plasma membrane association, inducing DVL2 nuclear localization via Foxk2. Changes to intracellular sterols also selectively impaired DVL2 protein-protein interactions This work identifies sterol specificity as a regulator of DVL signaling, suggests intracellular sterols cause distinct impacts on DVL activity, and supports a role for intracellular sterol homeostasis in cell signaling.

cell biology↗

Identification of distinct genotypes in circulating RSV A strains based on variants on the virus replication-associated genes

Respiratory syncytial virus is a common cause of respiratory infection that often leads to hospitalization of infected younger children and older adults. RSV is classified into two strains, A and B, each with several subgroups or genotypes. One issue with the definition of these subgroups is the lack of a unified method of identification or genotyping. We propose that genotyping strategies based on the genes coding for replication-associated proteins could provide critical information on the replication capacity of the distinct subgroup, while clearly distinguishing genotypes. Here, we analyzed the virus replication-associated genes N, P, M2, and L from de novo assembled RSV A sequences obtained from 31 newly sequenced samples from hospitalized patients in Philadelphia and 78 additional publicly available sequences from different geographic locations within the US. In-depth analysis and annotation of the protein variants in L and the other replication-associated proteins N, P, M2-1, and M2-2 identified the polymerase protein L as a robust target for genotyping RSV subgroups. Importantly, our analysis revealed non-synonymous variations in L that were consistently accompanied by conserved changes in its co-factor P or the M2-2 protein, suggesting associations and interactions between specific domains of these proteins. These results highlight L as an alternative to other RSV genotyping targets and demonstrate the value of in-depth analyses and annotations of RSV sequences as it can serve as a foundation for subsequent in vitro and clinical studies on the efficiency of the polymerase and fitness of different virus isolates. IMPORTANCEGiven the historical heterogeneity of Respiratory Syncytial Virus (RSV) and the disease it causes, there is a need to understand the circulating RSV strains each season. This requires an informative and consensus method of genotype definition. Here, we carried out a variant analysis that shows a pattern of specific variations among the replication-associated genes of RSV A across different seasons. Interestingly, these variation patterns point to previously defined interactions of domains within these genes, suggesting co-variation in the replication-associated genes. Our results also suggest a genotyping strategy that can prove to be particularly important in understanding the genotype-phenotype correlation in the era of RSV vaccination, where selective pressure on the virus to evolve is anticipated. More importantly, the categorization of RSV strains based on these patterns may prove to be of prognostic value.

microbiology↗

Microbiota-derived inosine programs protective CD8+ T cell responses against influenza in newborns

The immunological defects causing susceptibility to severe viral respiratory infections due to early-life dysbiosis remain ill-defined. Here, we show that influenza virus susceptibility in dysbiotic infant mice is caused by CD8+ T cell hyporesponsiveness and diminished persistence as tissue-resident memory cells. We describe a previously unknown role for nuclear factor interleukin 3 (NFIL3) in repression of memory differentiation of CD8+ T cells in dysbiotic mice involving epigenetic regulation of T cell factor 1 (TCF 1) expression. Pulmonary CD8+ T cells from dysbiotic human infants share these transcriptional signatures and functional phenotypes. Mechanistically, intestinal inosine was reduced in dysbiotic human infants and newborn mice, and inosine replacement reversed epigenetic dysregulation of Tcf7 and increased memory differentiation and responsiveness of pulmonary CD8+ T cells. Our data unveils new developmental layers controlling immune cell activation and identifies microbial metabolites that may be used therapeutically in the future to protect at-risk newborns.

immunology↗

Requirement of a Wnt5A-Microbiota Axis in the Maintenance of Gut B Cell Repertoire and Protection from Infection

We investigated the influence of a Wnt5A-gut microbiota axis on gut B cell repertoire and protection from infection, having previously demonstrated that Wnt5A in association with gut commensals help shape gut T cell repertoire. Accordingly, Wnt5A heterozygous mice, which express less than wild type level of Wnt5A, and their isolated Peyers patches (PP), were studied in comparison with the wild type counterparts. The percentages of IgM and IgA expressing B cells were quite similar in the PP of both sets of mice. However, the PP of the Wnt5A heterozygous mice harbored significantly higher than wild type levels of microbiota bound B cell secreted IgA (sIgA), indicating the prevalence of a microbial population therein, that is significantly altered from that of wild type. Additionally, the percentage of PP IgG1 expressing B cells was appreciably depressed in the Wnt5A heterozygous mice in comparison to wild type. Wnt5A heterozygous mice, furthermore, exhibited notably higher than the wild type levels of morbidity and mortality following infection with Salmonella enterica, a common gut pathogen. Difference in morbidity/mortality correlated with considerable disparity between the PP-B cell repertoires of the Salmonella infected Wnt5A heterozygous and wild type mice, the percentage of IgG1 expressing B1b cells in the PP of heterozygous mice remaining significantly low as compared to wild type. Overall, these results suggest that a gut Wnt5A-microbiota axis is intrinsically associated with the maintenance of gut B cell repertoire and protection from infection. ImportanceAlthough it is well accepted that B cells and microbiota are required for protection from infection and preservation of gut health, a lot remains unknown about how the optimum B cell repertoire and microbiota are maintained in the gut. The importance of this study lies in the fact that it unveils a potential role of a growth factor termed Wnt5A in the safeguarding of the gut B cell population and microbiota, thereby protecting the gut from the deleterious effect of infections by common pathogens. Documentation of the involvement of a Wnt5A-microbiota axis in the shaping of a protective gut B cell repertoire, furthermore, opens up new avenues of investigations for understanding gut disorders related to microbial dysbiosis and B cell homeostasis that till date, are considered incurable.

immunology↗

Cell-type specific contributions to theta-gamma coupled rhythms in the hippocampus

Distinct inhibitory cell types participate in cognitively relevant nested brain rhythms, and particular changes in such rhythms are known to occur in disease states. Specifically, the co-expression of theta and gamma rhythms in the hippocampus is believed to represent a general coding scheme, but cellular-based generation mechanisms for these coupled rhythms are currently unclear. We develop a population rate model of the CA1 hippocampus that encompasses circuits of three inhibitory cell types (bistratified cells, parvalbumin (PV)-expressing and cholecystokinin (CCK)-expressing basket cells) and pyramidal cells to examine this. We constrain parameters and perform numerical and theoretical analyses. The theory, in combination with the numerical explorations, predicts circuit motifs and specific cell-type mechanisms that are essential for the co-existence of theta and gamma oscillations. We find that CCK-expressing basket cells initiate the coupled rhythms and regularize theta, and PV-expressing basket cells enhance both theta and gamma rhythms. Pyramidal and bistratified cells govern the generation of theta rhythms, and PV-expressing basket and pyramidal cells play dominant roles in controlling theta frequencies. Our circuit motifs for theta-gamma coupled rhythm generation could be applicable to other brain regions. AUTHOR SUMMARYThere are many different types of inhibitory cells in our brains that are differentially affected in disease. Concomitantly, coupled rhythms change in particular ways with disease. To help understand cell-type specific changes in coupled rhythms, we develop a mathematical network model that is both respective of the cell type and also amenable to analyses. We focus on theta-gamma coupled rhythms in the hippocampus and include three different inhibitory cell types in our model circuits. By combining theoretical analysis and numerical explorations, we find distinct contributions of these inhibitory cell types to coupled rhythms, and predict motifs that are essential for the expression of theta-gamma coupled rhythms. Moving forward, we can leverage our model insights to help unravel cell-type contributions in disease states.

neuroscience↗

Early-stage lung adenocarcinoma is driven by an injury-associated, plastic cell state dependent on a KRAS-ITGA3-SRC axis

Glycine 12 mutations in the GTPase KRAS (KRASG12) are a known initiating event for lung adenocarcinoma (LUAD) with broad clinical relevance. KRASG12 mutations promote cell-intrinsic rewiring of the lung alveolar type II progenitor (AT2) cells, but to what extent such changes interplay with pathways essential for lung homeostasis and cell fate is unclear. We used single-cell RNA-seq (scRNA-seq) from AT2-mesenchyme organoid co-cultures, mouse models, and stage IA LUAD patient samples to identify conserved regulators of AT2 cell transcriptional dynamics and the impact of KRASG12D with temporal resolution. In AT2WT organoids, a transient injury/plasticity state preceded AT2 self-renewal and AT1 differentiation. Early-stage AT2KRAS cells exhibited perturbed gene expression dynamics most noted by retention of the injury/plasticity state. At later time points in tumorigenesis, AT2KRAS cells consisted of heterogeneous populations that could be defined by either the injury state or high expression of an AT2 cell signature. The injury state in AT2KRAS cells of LUAD in patients, mice, and organoids was distinguishable from AT2WT states by altered receptor expression, including co-expression of ITGA3 and SRC. The combination of clinically relevant KRASG12D and SRC inhibitors to target the oncogenic injury cell state impaired AT2KRAS organoid growth. Thus, an injury/plasticity signature characterized as an essential step in lung repair is used during alveolar cell self-renewal and during initiation and progression of LUAD. Early-stage lung cancer may be susceptible to intervention by targeting the oncogenic-specific nature of this cell state.

cancer biology↗

Prognostic relevance of correlated co-expression of coding and noncoding RNAs in cervical cancers

Human papillomavirus (HPV) drives cervical cancer (CaCx) pathogenesis and viral oncoproteins jeopardize global gene expression in such cancers. We aimed to identify differentially expressed coding (DEcGs) and long noncoding (sense intronic and Natural Antisense Transcripts) RNA genes (DElncGs) in HPV16-positive CaCx patients (N=44) compared to HPV-negative normal individuals (N=34). Thereby, employing strand-specific RNA-seq, we determined the relationships between DEcGs and DElncGs and their clinical implications. Gene set enrichment and protein-protein interaction analyses of DEcGs revealed enrichment of processes crucial for abortive virus life cycle and cancer progression. The DEcGs formed 16 gene clusters, portraying cancer-related functions. We recorded significantly correlated co-expression of 79 DElncGs with DEcGs at proximal genomic loci, and 24 such pairs portrayed significantly altered correlation coefficients among patients, compared to normal individuals. Of these, 6 DEcGs belonged to 5 gene clusters, one of which was survival-associated. Out of the 24 correlated DEcG: DElncG pairs, 3 pairs were identified, where expression of both members was significantly associated with patient overall survival. Besides being prognostically relevant, disruption of the significant correlative relationships of such gene pairs in CaCx bears immense potential for patient-targeted therapy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/573593v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@19091c8org.highwire.dtl.DTLVardef@52fbeaorg.highwire.dtl.DTLVardef@18ecf3org.highwire.dtl.DTLVardef@6c5e30_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO A schematic representation of the analyses undertaken to draw insights on the biological relevance of joint analysis of co-expressed and significantly correlated DElncGs and DEcGs considering the ncNATs and sense intronic DElncGs, in HPV16-positive CaCx patients compared with HPV-negative normal individuals. C_FIG

cancer biology↗

GABA(A) receptor activation drives GABARAP-Nix mediated autophagy to radiation-sensitize primary and brain-metastatic lung adenocarcinoma tumors

In non-small cell lung cancer (NSCLC) treatment, targeted therapies benefit only a subset of NSCLC, while radiotherapy responses are not durable and toxicity limits therapy. We find that a GABA(A) receptor activator, AM-101, impairs viability and clonogenicity of NSCLC primary and brain metastatic cells. Employing an ex vivo chip, AM-101 is as efficacious as the chemotherapeutic docetaxel, which is used with radiotherapy for advanced-stage NSCLC. In vivo, AM-101 potentiates radiation, including conferring a survival benefit to mice bearing NSCLC intracranial tumors. GABA(A) receptor activation stimulates a selective-autophagic response via multimerization of GABA(A) Receptor-Associated Protein (GABARAP), stabilization of mitochondrial receptor Nix, and utilization of ubiquitin-binding protein p62. A targeted-peptide disrupting Nix binding to GABARAP inhibits AM-101 cytotoxicity. This supports a model of GABA(A) receptor activation driving a GABARAP-Nix multimerization axis triggering autophagy. In patients receiving radiotherapy, GABA(A) receptor activation may improve tumor control while allowing radiation dose de-intensification to reduce toxicity. HighlightsO_LIActivating GABA(A) receptors intrinsic to lung primary and metastatic brain cancer cells triggers a cytotoxic response. C_LIO_LIGABA(A) receptor activation works as well as chemotherapeutic docetaxel in impairing lung cancer viability ex vivo. C_LIO_LIGABA(A) receptor activation increases survival of mice bearing lung metastatic brain tumors. C_LIO_LIA selective-autophagic response is stimulated by GABA(A) receptor activation that includes multimerization of GABARAP and Nix. C_LIO_LIEmploying a new nanomolar affinity peptide that abrogates autophagosome formation inhibits cytotoxicity elicited by GABA(A) receptor activation. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/569295v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1df2f4eorg.highwire.dtl.DTLVardef@19ac26forg.highwire.dtl.DTLVardef@1533986org.highwire.dtl.DTLVardef@e59653_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

DIGEST: An online tool for designing of multiple reaction monitoring assays

Targeted proteomics using multiple reaction monitoring (MRM) assays enables fast and sensitive detection of a preselected set of target peptides. This technique utilizes the specificity of precursors to product transitions for quantitative analysis of multiple proteins in a single sample. The success of an MRM experiment depends on the selection of transitions however, given the existing resources, accurately predicting signal intensity of peptides and their fragmentation patterns ab initio is challenging task. We present an alternative for rapid design of MRM transitions for proteomics research: DIGEST. Our method predicts the b and y ions with +1 and +2 charge produced in a collision cell of a mass spectrometer from peptides of multiple proteotypically digested proteins. Additionally, by using the existing knowledge of the fundamental rules for designing transitions, the tool provides optimal MRM transitions, negating the need to undertake prior "discovery" MS studies. We demonstrate that our algorithm is directed toward the selection of MRM precursor and product-ions pairs, and can avoid the pitfalls of interference due to cross-contamination of samples by selecting ion combinations that uniquely map to target peptides. Comparison with SRMAtlas showed that DIGEST successfully predicted the peptide and production pairs in the majority of cases. We believe that DIGEST will facilitate rapid design of MRM assays with increased specificity, reducing the overall time required to design an MRM assay for routine mass-spectrometry. DIGEST is available as a web-based tool at https://digest.raylab.iiitd.edu.in/

bioinformatics↗

Fibrinogen and complement factor H: The two crucial markers of Parkinson's disease with cognitive impairment

Animal model-assisted validation is vital for biomarker studies. It provides better means for understanding disease pathogenesis and opens avenues for addressing therapeutics. Our earlier non-targeted label free proteomics-based biomarker study on CSF of Parkinsons disease (PD) patients with cognitive impairment (PDCI), revealed the presence of elevated levels of fibrinogen and complement factor H (CFAH) in PDCI-CSF. In the present study, we aimed to determine if these proteins harbor a pathogenic potential, when present above physiological levels. Native fibrinogen and recombinant CFAH were intraperitoneally injected in adult C57BL/6J mice and 48h later, motor and cognitive behavioral deficits as well as their neuroanatomical correlates were noted. The reduction in stride length in fibrinogen and CFAH injected mice indicate shuffling gait, often seen in PD patients. Motor deficit was complemented by the loss of dopaminergic (DA) neurons in SNpc, compensatory hypertrophy of the surviving neurons, and reduction in TH expression in striatum, thus reminiscing PD pathology. The low discrimination index in (novel object recognition) NOR test complemented by morphological alterations in Nissl-stained CA-1 and subiculum neurons in the fibrinogen-injected mice imply recognition memory deficits. Thus, our study provides objective evidence that fibrinogen and CFAH harbor the potential to induce motor deficits and cognitive impairments in mice, akin to the PDCI-associated neuro-pathological deficits, and thus are potential biomarkers.

neuroscience↗

Nucleo-cytoplasmic environment modulates spatio-temporal p53 phase separation

Phase separation of various transcription factors and nucleic acids into biomolecular condensates is known to play an essential role in the regulation of gene expression. Here, we show that p53, a tumor suppressor and transcription factor, phase separates and forms biomolecular condensates in the nucleus of cancer cells as well as when overexpressed in the various cell lines. Although the nuclear condensates of wild-type (WT) p53 maintain their liquid state and are able to bind DNA, cancer-associated mutations not only promote misfolding but also partially rigidify the p53 condensates, which are unable to bind the DNA. Irrespective of WT or mutant form, the cytoplasmic partitioning of p53 with time also results in biomolecular condensate formation, which eventually undergoes rigidification. In vitro, WT p53 core domain (p53C) forms biomolecular condensates, which rigidify with time and the process is further promoted by cancer-associated mutations. Both RNA and non-specific DNA promote LLPS of p53C, but specific DNA promotes the dissolution of p53C condensates. The result suggests that the cellular microenvironment regulates p53 LLPS, material property and its functions.

biophysics↗

Reproductive biology of the mudskippers Boleophthalmus boddarti and Periophthalmus novemradiatus in the Indian Sundarbans

Reproductive biology of mudskippers Boleophthalmus boddarti and Periophthalmus novemradiatus are investigated along the mudflats of the Indian Sundarbans. We investigated a total of 794 sampes for both male and female Boleophthalmus boddarti and Periophthalmus novemradiatus fish species to explore properties such as the size-at-50% maturity, fecundity, spawning, gona-dosomatic and hepatosomatic indices along with the characterization of the macroscopic and histological attributes of the female gonads. Our work reports for the first time the weight-length relationships for these fish species in the Sundarbans region depicting a negative allometric growth pattern. The size-at-50% maturity which is often a crucial parameter for stock and reserve management is found for the female and male Boleophthalmus boddarti as 10.2 cm and 9.9 cm respectively, whereas, for the Periophthalmus novemradiatus, the same were 4.0 cm and 4.4 cm, respectively. Fully matured female Boleophthalmus boddarti were found to be multiple spawners in comparison to Periophthalmus novemradiatus with monthly variation of Le Crens relative condition [≤]1, indicating good physiological conditions of the fish. The relationships between batch fecundity (F), body weight (i.e., BW, gm) and total length (i.e., TL, cm) were Log10F = 1.12 Log10BW + 2.41 and Log10F = 1.93 Log10TL + 1.82, respectively for Boleoph-thalmus boddarti and for the Periophthalmus novemradiatus, it was Log10F = 2.15 Log10BW + 2.57 and Log10F = 5.43 Log10TL - 0.81. The reproductive parameters estimated in this study are important information for studying population dynamics and stock assessments of these mudskippers in the Indian Sundarbans and will contribute to the management, conservation and prediction of environmental changes as these mudskippers are often studied as bio-indicators for climate-change effects.

zoology↗

p53 amyloid pathology with cancer grades and p53 mutations

p53 mutation and amyloid formation are implicated with cancer pathogenesis, but the direct demonstration of the link between p53 amyloid load and cancer progression is lacking. Using multi-disciplinary techniques and a cohort of 59 tumor tissues (53 from Indian cancer patients and six normal tissues) of oral and stomach cancer types, we showed that p53 amyloid load and cancer grades are highly correlated. Further, next-generation sequencing (NGS) data suggest that not only mutant p53 (e.g., SNVs, deletions, and insertions) but wild-type p53 also formed amyloids either in the nucleus (50%) and/or in the cytoplasm in most cancer tissues. Interestingly, in all these cancer tissues, p53 displays a loss of DNA binding and transcriptional activities, which is highly aggravated with the amyloid load and cancer grades. The p53 amyloids also sequester higher amounts of p63/p73 isoforms in higher-grade of tumor tissues. The data suggest p53 misfolding/aggregation and subsequent amyloid formation lead to loss and gain of p53 tumorigenic function, aggravation of which might determine the cancers grades.

cancer biology↗

BEERS2: RNA-Seq simulation through high fidelity in silico modeling

Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking, and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully-length mRNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM, or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in PCR amplification, barcode read errors, and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.

bioinformatics↗

The RNA-DNA world and the emergence of DNA-encoded heritable traits

The RNA world hypothesis confers a central role to RNA molecules in information encoding and catalysis. Even though evidence in support of this hypothesis has accumulated from both experiments and computational modelling, the transition from an RNA world to a world where heritable genetic information is encoded in DNA remains an open question. Recent experiments show that both RNA and DNA templates can extend complementary primers using free RNA/DNA nucleotides, either non-enzymatically or in the presence of a replicase ribozyme. Guided by these experiments, we analyse protocellular evolution with an expanded set of reaction pathways made possible through the presence of DNA nucleotides. By en-capsulating these reactions inside three different types of protocellular compartments, each subject to distinct modes of selection, we show how protocells containing DNA-encoded replicases in low copy numbers and replicases in high copy numbers can dominate the population. This is facilitated by a reaction that leads to auto-catalytic synthesis of replicase ribozymes from DNA templates encoding the replicase, after the chance emergence of a replicase through non-enzymatic reactions. Our work unveils a pathway for the transition from an RNA world to a mixed RNA-DNA world characterized by Darwinian evolution, where DNA sequences encode heritable phenotypes.

evolutionary biology↗

Treg cells drive MYCN-mediated immunosuppression and tumor aggressiveness in high-risk neuroblastoma

Solid tumors, especially those with aberrant MYCN activation, harbor an immunosuppressive microenvironment to fuel malignant growth and trigger treatment resistance1,2, yet the underlying mechanisms are elusive and effective strategies to tackle this challenge are lacking. Here we demonstrated the crucial role of T regulatory (Treg) cells in MYCN-mediated immune repression and tumor aggression using high-risk neuroblastoma (NB) as a model system. Human MYCN-activated NB attracts CD4+ Treg cells, which are also found enriched in MYCN-high primary patient samples. Zebrafish MYCN-overexpressing neural crests recruit Cd4+ cells before tumor formation and induce an immunosuppressive microenvironment, thereby promoting tumor onset and progression. Strikingly, disruption of Treg cells through depletion of forkhead box protein 3a restores anti-tumor immunity and impairs NB development. Together, our studies establish Treg cells as the key driver of MYCN-mediated immunosuppression and tumor aggressiveness, providing mechanistic insights and therapeutic implications.

cancer biology↗

Rational engineering of a β-glucosidase (H0HC94) from glycosyl family I (GH1) to improve catalytic performance on cellobiose

The conversion of lignocellulosic feedstocks by cellulases to glucose is a critical step in biofuel production. {beta}-glucosidases catalyze the final step in cellulose breakdown, producing glucose, and is often the rate-limiting step in biomass hydrolysis. Rationally engineering previously characterized enzymes may be one strategy to increase catalytic activity and the efficiency of cellulose hydrolysis. The specific activity of most natural and engineered {beta}-glucosidase is higher on the artificial substrate p-Nitrophenyl {beta}-D-glucopyranoside (pNPGlc) than on the natural substrate, cellobiose. Based on our hypothesis of increasing catalytic activity by reducing the interaction of residues present near the active site tunnel entrance with glucose without disturbing any existing interactions with cellobiose, we report an engineered {beta}-glucosidase (Q319A H0HC94) with a 1.8-fold specific activity increase (366.3 {+/-} 36 {micro}mol/min/mg), an almost 1.5-fold increase in kcat (340.8 {+/-} 27 s-1), and a 3-fold increase in Q319A H0HC94 cellobiose specificity (236.65 mM-1 s-1) over HOHC94. Molecular dynamic simulations and protein structure network analysis indicate that Q319A significantly increased the dynamically stable communities and hub residues, leading to a change in enzyme conformation and higher enzymatic activity. This study shows the impact of rational engineering of non-conserved residue to increase {beta}-glucosidase substrate accessibility and enzyme specificity. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/505235v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@392a36org.highwire.dtl.DTLVardef@10252d4org.highwire.dtl.DTLVardef@18c1749org.highwire.dtl.DTLVardef@4cc8c6_HPS_FORMAT_FIGEXP M_FIG A rationally engineered -glucosidase with a 1.5-fold increase in kcat, and a 3-fold increase in cellobiose specificity over the wild-type C_FIG

bioengineering↗

Wnt5A Signaling Regulates Gut Bacterial Survival and T cell Homeostasis

In light of the demonstrated antagonism of Wnt5A signaling toward the growth of several bacterial pathogens, it was important to study the influence of Wnt5A on gut resident bacteria, and its outcome. Here we demonstrate that in contrast to inhibiting the survival of the established gut pathogen Salmonella enterica, Wnt5A clearly promotes the survival of the common gut commensals Enterococcus faecalis and Lactobacillus rhamnosus within macrophages through a self-perpetuating Wnt5A-Actin axis. A Wnt5A - Actin axis furthermore regulates the subsistence of the natural bacterial population of the Peyers patches, as is evident from the diminution in the countable bacterial colony forming units therein through the application of Wnt5A signaling and actin assembly inhibitors. Wnt5A dependency of the gut resident bacterial population is also manifested in the notable difference between the bacterial diversities associated with the feces and Peyers patches of Wnt5A heterozygous mice, which lack a functional copy of the Wnt5A gene, and the wild type counterparts. Alterations in gut commensal bacterial population resulting from either the lack of a copy of the Wnt5A gene or inhibitor mediated attenuation of Wnt5A signaling correlate with significantly different ratios of regulatory vs. activated CD4 T cells associated with the Peyers patches. Taken together, our study reveals the importance of Wnt5A signaling in shaping the gut commensal bacterial population and the T cell repertoire linked to it, thus unveiling a crucial control device for the maintenance of gut bacterial diversity and T cell homeostasis. Significance StatementGut commensal bacterial diversity and T cell homeostasis are crucial entities of the host innate immune network. Yet molecular details of host directed signaling pathways that sustain the steady state of gut bacterial colonization and T cell activation remain unclear. Here we describe the protective role of a Wnt5A-Actin axis in the survival of several gut bacterial commensals, and its importance in shaping gut bacterial colonization and the associated T cell repertoire. This study opens up new avenues of investigation into the role of the Wnt5A-Actin axis in protection of the gut from dysbiosis related inflammatory disorders.

immunology↗