Biology subjects

Chakraborty, A.

Publications and source records attributed to Chakraborty, A..

At least 91 records · Page 5Linked to original sources

bioRxiv2024

Diet breadth in two polyphagous Spodoptera moths in a wide range of host and non-host plants and the potential for range expansion

O_LISeveral polyphagous moths are severe crop pests. Diet breadth patterns and mechanisms among polyphagous insects provide an excellent system to study ecological and evolutionary processes in herbivores, driving dietary specialization. However, studies of diet breadth on more than a handful of crops are scarce. C_LIO_LIHere, we estimated the diet breadth in two species of lepidopteran herbivores from the genus Spodoptera: S. littoralis (SL), with host range including both mono- and dicotyledonous plants and S. frugiperda (SF) Corn strain, primarily adapted to different grass species. C_LIO_LILarval performance on 23 crop and wild plant species from 17 families from terrestrial and wetland habitats was compared to an artificial diet in no-choice feeding bioassays. SL survived and performed better on most tested plants, particularly on the family level, except on two monocot plants (maize and leek), where SF performed well. There were five wild non-host plants where both generalists failed to survive. Nutrition indices assay corroborates the findings on a subset of plants. C_LIO_LIIn a subset of plants, larval feeding preference correlated partly, and larval attraction correlated well with larval performance. Female oviposition choice showed a weak correlation with larval performance. This weak correlation implies that these traits are decoupled, and other factors are crucial for female host plant selection. C_LIO_LIDuring larval dispersal greenhouse experiments, SL and SF larvae strongly tended to migrate onto their suitable host plants, indicating that this is one factor that modulates female host plant selection. C_LIO_LIIn summary, SL has a broader diet breath compared to SF, surviving on wild plants with no previous exposure. The present study provides the first comprehensive data on the diet breadth of two range-expanding and highly invasive polyphagous herbivores. C_LI

ecology↗

bioRxiv2024

Early 2022 breakthrough infection sera from India target the conserved cryptic class 5 epitope to counteract immune escape by SARS-CoV-2 variants

During the COVID-19 pandemic, the vast majority of epitope mapping studies have focused on sera from mRNA-vaccinated populations from high-income countries. In contrast, here we report an analysis of 164 serum samples isolated from breakthrough infection patients in India during early 2022 who received two doses of the ChAdOx viral vector vaccine. Sera were screened for neutralization breadth against wildtype, Kappa, Delta, and Omicron BA.1 viruses. Three sera with the highest neutralization breadth and potency were selected for epitope mapping using charged scanning mutagenesis coupled to yeast surface display and Next Generation Sequencing. All of these sera primarily targeted the recently identified class 5 cryptic epitope along with the class 1 and class 4 epitopes, targeted to a lesser extent. The class 5 epitope is completely conserved across all SARS-CoV-2 variants and for the majority of the Sarbecoviruses. In line with these observations, a major fraction of the serum samples, including the selected three, show broad neutralizing activity against recent Omicron subvariants including XBB.1.5. This is in contrast with the results obtained with the sera from individuals receiving multiple doses of original and updated mRNA vaccines, where impaired neutralization of XBB and later variant of concerns was observed. Our study demonstrates that two doses of the ChAdOx vaccine in a highly exposed population was sufficient to drive substantial neutralization breadth against emerging and upcoming variants of concern, thus paves the path towards the development of future vaccine candidates. ImportanceWorldwide implementation of COVID19 vaccine and parallel emergence of newer SARS-CoV-2 variants has shaped the humoral immune response in a population specific manner. While characterization of this immune response is important for monitoring the disease progression at population level, it is also imperative for the development of effective countermeasures in the form of novel vaccines and therapeutics. India has implemented the worlds second largest COVID19 vaccination drive and also encountered large number of post vaccination "breakthrough" infections. From a cohort of breakthrough infection patients, we identified individuals whose sera showed broadly cross-reactive immunity against different SARS-CoV-2 variants. Interestingly, these sera primarily target a novel cryptic epitope which was not identified in previous population level studies conducted in western countries. This rare cryptic epitope remains conserved across all SARS-CoV-2 variants including the recently emerged ones and also for the SARS-like coronaviruses that may cause future outbreaks, thus representing a potential target for future vaccines.

molecular biology↗

bioRxiv2024

Identification of ABHD6 as a regulator of lysophosphatidylserines in the mammalian liver and kidneys

Lysophosphatidylserine (lyso-PS) is a potent hormone-like signaling lysophospholipid, which regulates many facets of mammalian biology and dysregulation in its metabolism is associated with several human neurological and autoimmune diseases. Despite the physiological importance and causal relation with human pathophysiology, little is known about the metabolism of lyso-PS in tissues other than the nervous and immune systems. To address this problem, here, we attempted to identify one (or more) lipase(s) capable of degrading lyso-PS in different mammalian tissues. We found that the membrane proteomic fraction of most mammalian tissues possess lyso-PS lipase activity, yet interestingly, the only bona fide lyso-PS lipase ABHD12 displays this enzymatic activity and has control over lyso-PS metabolism only in the mammalian brain. Using an in vitro inhibitor screen against membrane proteomic fractions of different tissues, we find that another lipase from the metabolic serine hydrolase family, ABHD6, is a putative lyso-PS lipase in the mouse liver and kidney. Finally, using pharmacological tools, we validate the lyso-PS lipase activity of ABHD6 in vivo, and functionally designate this enzyme as a major lyso-PS lipase in primary hepatocytes, and the mammalian liver and kidneys. HIGHLIGHTSO_LILyso-PS lipase enzymatic activity is present in the membrane proteomic fraction of most mammalian tissues C_LIO_LIAn in vitro inhibitor screen identifies ABHD6 as a putative lyso-PS lipase in the liver and kidney C_LIO_LIABHD6 functions as a lyso-PS lipase in primary hepatocytes C_LIO_LIABHD6 also performs lyso-PS lipase activity in vivo and regulates lyso-PS levels in the liver and kidney C_LI

biochemistry↗

bioRxiv2024

Skeletal Muscle Mitochondrial Dysfunction Mediated by Pseudomonas aeruginosa Quorum Sensing Transcription Factor MvfR: Reversing Effects with Anti-MvfR and Mitochondrial-Targeted Compounds

Sepsis and chronic infections with Pseudomonas aeruginosa, a leading "ESKAPE" bacterial pathogen, are associated with increased morbidity and mortality and skeletal muscle atrophy. The actions of this pathogen on skeletal muscle remain poorly understood. In skeletal muscle, mitochondria serve as a crucial energy source, which may be perturbed by infection. Here, using the well-established backburn and infection model of murine P. aeruginosa infection, we deciphered the systemic impact of the quorum sensing (QS) transcription factor MvfR by interrogating five days post-infection its effect on mitochondrial-related functions in the gastrocnemius skeletal muscle and the outcome of the pharmacological inhibition of MvfR function and that of the mitochondrial-targeted peptide, Szeto-Schiller 31 (SS-31). Our findings show that the MvfR perturbs ATP generation, oxidative phosphorylation (OXPHOS), and antioxidant response, elevates the production of reactive oxygen species, and promotes oxidative damage of mitochondrial DNA in the gastrocnemius muscle of infected mice. These impairments in mitochondrial-related functions were corroborated by the alteration of key mitochondrial proteins involved in electron transport, mitochondrial biogenesis, dynamics and quality control, and mitochondrial uncoupling. Pharmacological inhibition of MvfR using the potent anti-MvfR lead, D88, we developed, or the mitochondrial-targeted peptide SS-31 rescued the MvfR- mediated alterations observed in mice infected with the wild-type strain PA14. Our study provides insights into the actions of MvfR in orchestrating mitochondrial dysfunction in the skeletal murine muscle, and it presents novel therapeutic approaches for optimizing clinical outcomes in affected patients.

microbiology↗

bioRxiv2024

HOP/STIP1 is required for KSHV lytic replication.

Kaposi sarcoma associated herpesvirus (KSHV) is a DNA virus that causes Kaposi sarcoma, a cancer of endothelial origin. KSHV uses the activity of host molecular chaperones like Hsp70 and Hsp90 for the folding of host and viral proteins required for productive infection. Hsp70 and Hsp90 chaperones form proteostasis networks with several regulatory proteins known as co-chaperones. Of these, Hsp90-Hsp70 organising protein (HOP) is an early-stage co-chaperone that regulates transfer of folding substrate proteins between the Hsp70 and Hsp90 chaperone systems. While roles for Hsp90 and Hsp70 in KSHV biology have been described, HOP has not previously been studied in this context despite its prominent interaction with both chaperones. Here we demonstrate a novel function for HOP as a new host factor required for effective lytic replication of KSHV in primary effusion cell lines. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2024

The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection

Pseudomonas aeruginosa is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it is available to serve as a carbon source for P. aeruginosa in the diverse settings it inhabits. Here, we evaluate P. aeruginosas production and use of its redundant L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses lldD and identify a new transcription factor, called LldS, that activates lldA; these distinct regulators and the genomic contexts of lldD and lldA contribute to their differential expression. We demonstrate that the lldD and lldA genes are conditionally controlled in response to lactate isomers as well as to glycolate and {square}-hydroxybutyrate, which, like lactate, are {square}-hydroxycarboxylates. We also show that lldA is induced when iron availability is low. Our examination of lldD and lldA expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays revealed that both lldD and lldA contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during P. aeruginosa-eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote P. aeruginosas success as a resident of contaminated environments and animal hosts. ImportancePseudomonas aeruginosa is a major cause of lung infections in people with cystic fibrosis, hospital-acquired infections, and wound infections. It consumes L-lactate, which is found at substantial levels in human blood and tissues. In this study, we investigated the spatial regulation of two redundant enzymes, called LldD and LldA, which enable L-lactate metabolism in P. aeruginosa biofilms. We uncovered mechanisms and identified compounds that control P. aeruginosas LldD/LldA preference. We also showed that both enzymes contribute to its ability to survive within macrophages, a behavior that is thought to augment the chronicity and recalcitrance of infections. Our findings shed light on a key metabolic strategy used by P. aeruginosa and have the potential to inform the development of therapies targeting bacterial metabolism during infection.

microbiology↗

bioRxiv2024

Developing Bioactive Hydrogels Containing Cell-derived Extracellular Matrix: Implications in Drug and Cell-free Bone and Cartilage Repair

The prevalence of osteoarthritis has been increasing in aging populations, which has necessitated the use of advanced biomedical treatments. These involve grafts or delivering drug molecules entrapped in scaffolds. However, such treatments often show suboptimal therapeutic effects due to poor half-life and off-target effects of drug molecules. This study aims to overcome these limitations by 3D printing gelatin-based hydrogel scaffolds containing cell-derived extracellular matrix (ECM) as the bioactive therapeutic cargo. Here, pre-osteoblastic and pre-chondrogenic murine cells were differentiated in vitro, decellularized, and incorporated into methacrylated gelatin (GelMA) solutions to form osteogenic (GelO) and chondrogenic (GelC) hydrogels, respectively. The integration of the bioactive decellularized extracellular matrix (dECM) allows GelO and GelC to induce differentiation in human adipose-derived stem cells (hADSCs) toward osteogenic and chondrogenic lineages. GelO and GelC can be covalently adhered using carbodiimide coupling reaction, forming bioactive osteochondral plug. Moreover, this osteochondral plug can also induce differentiation of hADSCs. To conclude, this ECM-based bioactive hydrogel offers a promising new drug-free and cell-free treatment strategy for bone and cartilage repair, and future osteoarthritis management.

bioengineering↗

bioRxiv2024

The Bacterial Quorum-Sensing Signal 2-Aminoacetophenone Rewires Immune Cell Bioenergetics through the PGC-1α/ERRα Axis to Mediate Tolerance to Infection

How bacterial pathogens exploit host metabolism to promote immune tolerance and persist in infected hosts remains elusive. To achieve this, we show that Pseudomonas aeruginosa (PA), a recalcitrant pathogen, utilizes the quorum sensing (QS) signal 2-aminoacetophenone (2-AA). Here, we unveil how 2-AA-driven immune tolerization causes distinct metabolic perturbations in macrophages mitochondrial respiration and bioenergetics. We present evidence indicating that these effects stem from decreased pyruvate transport into mitochondria. This reduction is attributed to decreased expression of the mitochondrial pyruvate carrier (MPC1), which is mediated by diminished expression and nuclear presence of its transcriptional regulator, estrogen-related nuclear receptor alpha (ERR). Consequently, ERR exhibits weakened binding to the MPC1 promoter. This outcome arises from the impaired interaction between ERR and the peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1). Ultimately, this cascade results in diminished pyruvate influx into mitochondria and, consequently reduced ATP production in tolerized macrophages. Exogenously added ATP in infected macrophages restores the transcript levels of MPC1 and ERR- and enhances cytokine production and intracellular bacterial clearance. Consistent with the in vitro findings, murine infection studies corroborate the 2-AA-mediated long-lasting decrease in ATP and acetyl-CoA and its association with PA persistence, further supporting this QS signaling molecule as the culprit of the host bioenergetic alterations and PA persistence. These findings unveil 2-AA as a modulator of cellular immunometabolism and reveal an unprecedented mechanism of host tolerance to infection involving the PGC-1/ERR axis in its influence on MPC1/OXPHOS-dependent energy production and PA clearance. These paradigmatic findings pave the way for developing treatments to bolster host resilience to pathogen-induced damage. Given that QS is a common characteristic of prokaryotes, it is likely that 2-AA-like molecules with similar functions may be present in other pathogens.

immunology↗

bioRxiv2024

Comparative metagenomic study unveils bacterial communities and their putative involvement in ecological success of two pine-feeding Ips beetle holobionts

Climate change has recently boosted the severity and frequency of the pine bark beetle attacks. The bacterial community associated with these beetles acts as "hidden players", enhancing their ability to infest and thrive on defence-rich pine trees. There is limited understanding of the environmental acquisition of these hidden players and their life stage-specific association with different pine-feeding bark beetles. There is inadequate knowledge on novel bacterial introduction to pine trees after the beetle infestation. Hence, we conducted the first comparative bacterial metabarcoding study comprehensively revealing the bacterial communities in the pine trees before and after beetle feeding and in different life stages of two dominant pine-feeding bark beetles, namely Ips sexdentatus and Ips acuminatus. We also evaluated the bacterial association between wild and lab-bred beetles to measure the deviation due to inhabiting a controlled environment. Significant differences in bacterial amplicon sequence variance (ASVs) abundance existed among different life stages within and between the pine beetles. Such observations endorsed that the bark beetle life stage shaped bacterial assemblage. Furthermore, lab-bred and wild-collected adult beetles had distinct bacterial assemblages, implying that the breeding environment induced crucial changes. Alteration of pine wood bacteriome after beetle feeding is an intriguing observation in the present study, which demands further investigation. We validated the relative abundances of selected bacterial taxa estimated by metagenomic sequencing with quantitative PCR. Functional predictions revealed that these bacterial genera might execute conserved functions, aiding the ecological success of these beetles. Nevertheless, these findings shed new insights into bacterial associations and their putative metabolic roles in pine beetles under the influence of various drivers such as environment, host, and life stages and provide the foundation for future downstream functional investigations. ImportanceThe current understanding of bark beetle as holobiont is restricted. Most studies lack information on microbial community assembly in bark beetle microhabitats. No data comprehensively reveals the influence of lab breeding on pine beetle microbial associations. It is unknown if there is any adaptive convergence in beetle microbial assemblage due to feeding on the same host. Such information is essential to developing a bark beetle management strategy to restore forests from beetle-mediated damage. Our study shows that lab-breeding considerably influences beetle bacterial community assembly. We documented that beetle feeding alters bacteriome at the microhabitat level, and the beetle life stage shapes the bacterial associations. Nevertheless, our study revisited the bark beetle symbiosis under the influence of different drivers and revealed intriguing insight into bacterial community assembly, facilitating future functional studies.

microbiology↗

bioRxiv2024

Cellular heterogeneity in the developing forebrain masks transcriptional outcomes and principles of Evf2 enhancer lncRNA-Dlx5/6UCE-gene guidance

During mouse embryonic brain development, the Evf2 ultraconserved enhancer (UCE) lncRNA guides the Dlx5/6UCE to [~]129 sites across chr6. However, previous work identified only 4 transcriptionally regulated targets associated with Evf2-Dlx5/6UCE enhancer-gene guided sites (EGGs), raising questions about the significance of the majority of Evf2-EGGs. Here, single cell transcriptomics (scRNAseq) shows that Evf2-EGGs on chr6 coincide with subpopulation-specific Evf2 transcriptional targets, revealing far greater alignment between EGGs and transcriptional targets than previously reported. Surprisingly, subpopulation-specific Evf2 regulated gene networks in embryonic progenitors predict adult synaptic and seizure defects. Evf2 regulation of EGGs to gene bodies (GB, Dlx5/6UCE locations within {+/-}5kb of the target gene) divides chr6 into short-range (<10Mb distant), highly activated genes, and long/super-long-range (10-129Mb), moderately repressed genes. Clustering of Evf2 transcriptionally regulated chr6 targets in populations where Evf2 is first activated supports that Evf2-EGG transcriptional effects can occur from EGG shifts as far as 3Mb, uncoupling enhancer shift distance and transcriptional direction from transcriptional outcome. Evf2 RNA binding sites (RBSs) divide chr6 into 4 major regions, consistent with a role for RBS chromosomal spacing in long-and super-long-range EGG selectivity. Surprisingly, 95% of 147 RBSs genome-wide potentially form inter-chromosomal DNA loops. Evf2-regulated combinatorial recruitment of Evf2-ribonucleoproteins at EGGs and RBSs, together with effects on homeodomain transcription factor DNA motif recognition, support a novel model of lncRNA directed multi-modal EGG selectivity during intra- and inter-chromosomal gene regulation.

molecular biology↗

bioRxiv2024

Chromatin structure and var2csa - a tango in regulation of var gene expression in the human malaria parasite Plasmodium falciparum?

Over the last few decades, novel methods have been developed to study how chromosome positioning within the nucleus may play a role in gene regulation. Adaptation of these methods in the human malaria parasite, Plasmodium falciparum, has recently led to the discovery that the three-dimensional structure of chromatin within the nucleus may be critical in controlling expression of virulence genes (var genes). Recent work has implicated an unusual, highly conserved var gene called var2csa in contributing to coordinated transcriptional switching, however how this gene functions in this capacity is unknown. To further understand how var2csa influences var gene switching, targeted DNA double-strand breaks (DSBs) within the sub-telomeric region of chromosome 12 were used to delete the gene and the surrounding chromosomal region. To characterize the changes in chromatin architecture stemming from this deletion and how these changes could affect var gene expression, we used a combination of RNA-seq, Chip-seq and Hi-C to pinpoint epigenetic and chromatin structural modifications in regions of differential gene expression. We observed a net gain of interactions in sub-telomeric regions and internal var gene regions following var2csa knockout, indicating an increase of tightly controlled heterochromatin structures. Our results suggest that disruption of var2csa results not only in changes in var gene transcriptional regulation but also a significant tightening of heterochromatin clusters thereby disrupting coordinated activation of var genes throughout the genome. Altogether our result confirms a strong link between the var2csa locus, chromatin structure and var gene expression. AUTHOR SUMMARYMalaria remains one of the deadliest parasite-borne diseases, causing not only over a half million deaths annually, but also infecting hundreds of millions more. Plasmodium falciparum, the protozoan parasite that is responsible for the most virulent form of human malaria, is transmitted to humans by infected female mosquitoes during a blood meal. Due to a growing resistance to all existing antimalarials, there is a need to identify novel targets to design new antimalarial strategies. Our research builds on the growing body of evidence that supports the role of genome organization or chromatin structure within the nucleus in controlling the parasite development as well as virulence factors designed to circumvent the host immune response. This study identifies genes and structural elements within the Plasmodium falciparum genome that are controlled, at least partially, by the expression of a single unique and highly conserved virulence gene.

systems biology↗

bioRxiv2024

KR158 spheres harboring slow-cycling cells recapitulate GBM features in an immunocompetent system

Glioblastoma (GBM) poses a significant challenge in clinical oncology due to its aggressive nature, heterogeneity, and resistance to therapies. Cancer stem cells (CSCs) play a critical role in GBM, particularly in treatment-resistance and tumor relapse, emphasizing the need to comprehend the mechanisms regulating these cells. Also, their multifaceted contributions to the tumor-microenvironment (TME) underline their significance, driven by their unique properties. This study aimed to characterize glioblastoma stem cells (GSCs), specifically slow-cycling cells (SCCs), in an immunocompetent murine GBM model to explore their similarities with their human counterparts. Using the KR158 mouse model, we confirmed that SCCs isolated from this model exhibited key traits and functional properties akin to human SCCs. KR158 murine SCCs, expanded in the gliomasphere assay, demonstrated sphere forming ability, self-renewing capacity, positive tumorigenicity, enhanced stemness and resistance to chemotherapy. Together, our findings validate the KR158 murine model as a framework to investigate GSCs and SCCs in GBM-pathology, and explore specifically the SCC-immune system communications, understand their role in disease progression, and evaluate the effect of therapeutic strategies targeting these specific connections.

cancer biology↗

bioRxiv2023

Adaptation to ER Stress by Slt2, Counterpart of Human MAP Kinase ERK1/2, via Enhancing Splicing and Translation of HAC1 mRNA in Saccharomyces cerevisiae

Unfolded protein response (UPR) is a cellular strategy to increase the protein folding capacity of cells in response to stress within the endoplasmic reticulum (ER). In metazoan cells, three major UPR sensors Ire1, PERK and ATF6 work in concert by simultaneously activating intracellular signaling pathways and modulating a series of physiological processes such as attenuation of the general protein synthesis and expression of protein chaperones. In yeast Saccharomyces cerevisiae, Ire1 is known to be the only UPR sensor, which mediates splicing of HAC1 mRNA in the cytoplasm and derepresses its translation. Hac1 is a transcription factor that increases the expression of protein folding enzymes and chaperones, thus enhancing the protein folding capacity of cells. In this study, we provide compelling evidence that kinase Slt2 plays a significant role in facilitating both the splicing and translation of HAC1 mRNA, while also serving as a key mediator in the activation of UPR genes through an alternative route. We also provide evidence that human extracellular signal-regulated kinase 1 (ERK1) or ERK2 served as a functional substitute for yeast Slt2 in the context of UPR. Furthermore, ERK1 exhibits an enhanced activation in human primary cells when grown in the presence of ER stressor. These findings collectively suggest that Slt2 responds to ER stress by activating the Ire1 pathway as well as initiating a parallel signaling pathway.

molecular biology↗

bioRxiv2023

Master transcription factor binding sites are necessary for early replication control element activity

Eukaryotic genomes replicate in a defined temporal order called the replication timing (RT) program. RT is developmentally regulated with potential to drive cell fate transitions, but mechanisms controlling RT remain elusive. We previously identified "Early Replication Control Elements" (ERCEs) necessary for early RT, domain-wide transcription, 3D chromatin architecture and compartmentalization in mouse embryonic stem cells (mESCs) but, deletions identifying ERCEs were large and encompassed many putative regulatory elements. Here, we show that ERCEs are compound elements whose RT activity can largely be accounted for by multiple sites of diverse master transcription factor binding (subERCEs), distinguished from other such sites by their long-range interactions. While deletion of subERCEs had large effects on both transcription and RT, deleting transcription start sites eliminated nearly all transcription with moderate effects on RT. Our results suggest a model in which subERCEs respond to diverse master transcription factors by functioning both as transcription enhancers and as elements that organize chromatin domains structurally and support early RT, potentially providing a feed-forward loop to drive robust epigenomic change during cell fate transitions.

molecular biology↗

bioRxiv2023

Suppression of the Integrated Stress Response in Islet β Cells Decreases Risk of Autoimmune Diabetes

Preventing the onset of autoimmune type 1 diabetes (T1D) is feasible through pharmacological interventions that target molecular stress-responsive mechanisms. Cellular stresses, such as nutrient deficiency, viral infection, or unfolded proteins, trigger the integrated stress response (ISR), which curtails protein synthesis by phosphorylating eIF2. In T1D, maladaptive unfolded protein response (UPR) in insulin-producing {beta} cells renders these cells susceptible to autoimmunity. We show that inhibition of the eIF2 kinase PERK, a common component of the UPR and ISR, reverses the mRNA translation block in stressed human islets and delays the onset of diabetes, reduces islet inflammation, and preserves {beta} cell mass in T1D-susceptible mice. Single-cell RNA sequencing of islets from PERK-inhibited mice shows reductions in the UPR and PERK signaling pathways and alterations in antigen processing and presentation pathways in {beta} cells. Spatial proteomics of islets from these mice shows an increase in the immune checkpoint protein PD-L1 in {beta} cells. Golgi membrane protein 1, whose levels increase following PERK inhibition in human islets and EndoC-{beta}H1 human {beta} cells, interacts with and stabilizes PD-L1. Collectively, our studies show that PERK activity enhances {beta} cell immunogenicity, and inhibition of PERK may offer a strategy to prevent or delay the development of T1D.

cell biology↗

bioRxiv2023

Mitochondrial genes affect the immune response against bacterial infection (Duck Pasteurellosis) through a cascade of mechanisms mediated by nuclear immune genes- a cross talk with nuclear and mitochondrial gene

Mitochondria possess 37 genes of its own, helpful for carrying out various functions including oxidative phosphorylation. But the mitochondria is neither independent in terms of its structure, nor its function, it depend upon nuclear gene for its functionality and replication. Our lab has earlier reported the role of mitochondrial genome in controlling health and reproduction in animal model. Reports also indicate that mitochondria have role in immune response against bacterial infection. In our current study, we depict the role of two polypeptide coding mitochondrial gene as cytochrome B and cytochrome C in providing host immunity against bacterial disease (Duck Pasteurellosis). We further observe that the mechanism was governed by cascade of mechanisms mediated through nuclear genes NRLP3, IL18 and Sting. In the first phase of the study, we have characterized Cytochrome B and Cytochrome C genes from Bengal duck and quantified through the assesment of the expression profiling with respect to healthy and Pasteurella infected ducks following a natural challenge with Pasteurella multocida. In the next phase of our study, we have characterized the above nuclear genes in Bengal duck and attempted to correlate the expression with mitochondrial genes. We attempted to explore the mechanism of pathway how mitochondrial DNA triggers the nuclear immune response leading to destruction of bacterial pathogen. Molecular docking revealed how IL18 directly binds with the pathogen. This is the first report in animal model.

genomics↗

bioRxiv2023

Role of NUMTs (Nuclear mitochondrial DNA) genes in affecting disease resistance in duck against Pasteurellosis

Ducks are mostly resistant to common avian diseases, but frequent occurrence of duck pasteurellosis, commonly kown as Duck Cholera, caused by Pasteurella multocida may cause a loss. In our earlier studies, we have identified certain immune response genes of nuclear origin as well as mitochondrial genes in duck, conferring resistance against duck cholera. In our current study, we have detected certain NUMT (Nuclear mitochondrial) genes in duck with certain role in disease resistance in case of duck cholera. NUMT genes are basically nuclear genes, but they act through mitochondria. Identified NUMT genes (Thymidine phosphorylase/ endothelial cell growth factor1 gene, TFAM Transcription factor A, mitochondrial, TK2 Thymidine kinase 2) were characterized and certain important domains were identified. Differential mRNA expression profiling revealed upregulation of the genes in healthy ducks compared to that of infected ducks. Exploitation of the identified genes may lead to development of ducks resistant to duck Cholera.

genomics↗

bioRxiv2023

Genome sequencing of Syzygium cumini (Jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties

Syzygium cumini, also known as jambolan or jamun, is an evergreen tree widely known for its medicinal properties, fruits, and ornamental value. To understand the genomic and evolutionary basis of its medicinal properties, we sequenced S. cumini genome, which is the largest genome sequenced for the first time from the worlds largest tree genus Syzygium using Oxford Nanopore and 10x Genomics sequencing technologies. The tetraploid and highly heterozygous draft genome of S. cumini had a total size of 709.9 Mbp with 61,195 coding genes. The phylogenetic position of S. cumini was established using a comprehensive genome-wide analysis including species from 18 Eudicot plant orders. The existence of neopolyploidy in S. cumini was evident from the higher number of coding genes and expanded gene families compared to the other two sequenced species from this genus. Comparative evolutionary analyses showed the adaptive evolution of genes involved in the phenylpropanoid-flavonoid (PF) biosynthesis pathway and other secondary metabolites biosynthesis such as terpenoid and alkaloid in S. cumini, along with genes involved in stress tolerance mechanisms, which was also supported by leaf transcriptome data generated in this study. The adaptive evolution of secondary metabolism pathways is associated with the wide range of pharmacological properties, specifically the anti-diabetic property, of this species conferred by the bioactive compounds that act as nutraceutical agents in modern medicine.

genomics↗