Biology subjects

Mukherjee, T.

Publications and source records attributed to Mukherjee, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Angiogenin activity regulates RNA remodeling during the maternal-to-zygotic transition in early mouse embryogenesis

Angiogenin (ANG), a member of the RNase A superfamily, regulates multiple aspects of RNA metabolism, including rRNA processing and the generation of tRNA-derived small RNAs. However, its function during early mammalian embryogenesis remains unknown. Here, we identify a previously unrecognized requirement for ANG activity during early mouse embryonic development. Pharmacological inhibition of ANG during the first embryonic cell cycle did not prevent progression to the 2-cell stage but markedly impaired subsequent development to the 4-cell stage, indicating a critical requirement for ANG activity during the maternal-to-zygotic transition. Transcriptome-wide analysis revealed that ANG inhibition disrupted the normal remodeling of the embryonic transcriptome, characterized by persistent accumulation of a subset of transcripts that are normally reduced during the 2-cell transition, including many maternally deposited RNAs, together with altered expression of transcripts associated with zygotic genome activation. Small-RNA profiling further revealed widespread alterations in miRNA and tRNA-derived small-RNA populations. Notably, a large proportion of transcripts retained following ANG inhibition contained predicted target sites for miRNAs that were concomitantly reduced, suggesting a potential link between ANG-dependent small-RNA regulation and maternal transcript clearance. ANG inhibition was also associated with altered abundance and organization of components of RNA regulatory granules, including Tudor, TIAR, Dcp1a and Ago2, and increased association of selected retained transcripts Reep4 and Esrrb with Tudor-positive structures. Together, these findings identify ANG activity as an important regulator of RNA remodeling during the maternal-to-zygotic transition and suggest that ANG coordinates maternal transcript clearance, small-RNA dynamics and mRNP organization to support early mouse embryonic development.

developmental biology↗

bioRxiv2026

An Eco-Evolutionary Modelling Framework for Mosquito Host Specialisation

Host preference varies widely across mosquitoes, with many species feeding opportunistically on diverse vertebrate hosts, while others show strong fidelity to specific hosts. Anthropophilia, the behavioural preference for feeding on humans, is a defining characteristic of some mosquito species responsible for the transmission of major human diseases, including malaria, dengue, and yellow fever. The evolution of anthropophilia therefore has profound epidemiological implications because increased human biting elevates vectorial capacity and disease transmission potential. However, the ecological and evolutionary mechanisms driving this extreme specialisation have not yet been fully elucidated and remain difficult to unify across laboratory and field studies. Here we present an eco-evolutionary modelling framework that links genetically determined mosquito traits with spatially structured host environments. Our framework integrates innate olfactory sensitivity, blood meal-derived fitness benefits, and spatio-temporal host accessibility. Two complementary indices are introduced: a local specialisation index, capturing short-term ecological feeding strategies, and a co-evolutionary index, capturing long-term genetic coupling between host detection and resource utilisation. Our results demonstrate that host specialisation is not a default evolutionary outcome but an environmentally gated process, which is favoured in resource-poor or temporally varying habitats and strongly filtered by seasonality. The framework yields testable predictions regarding when specialisation emerges, persists, or collapses, with direct implications for predicting vector-borne disease risk in changing environments

evolutionary biology↗

bioRxiv2026

Strategic Segmentation: A Nash Equilibrium based Approach for Weed Segmentation in Agricultural Fields

Weeds present a major challenge to agricultural productivity, competing with crops for critical resources like water, nutrients, and sunlight, resulting in significant yield reductions. Prompt weed identification is essential for enabling effective control strategies, such as the application of herbicides or mechanical removal, to minimize their impact on crop growth. This research focuses on developing a deep learning approach based on game theory for detecting weeds. Using CWFID dataset captured at various times and days, along with multispectral data in the visible and near-infrared spectrum, the study aims to improve early detection methods for more efficient weed management in agricultural settings. A novel segmentation technique for weed regions is introduced, employing a zero-sum game theory model to reconcile conflicting classifications from different weed detectors. These regions are treated as zones of conflict between weeds and crops, with each detector representing a different strategy. By defining an appropriate utility function, the method identifies the Nash equilibrium, effectively minimizing false positive detections of weeds.

plant biology↗

bioRxiv2025

Modular to cyclic TCA governs hematopoiesis in Drosophila

TCA cycle is well known for its role in bioenergetics and also a hub for metabolic exchange, here we identify a developmentally programmed, non-uniform TCA architecture that is required for hematopoietic state transitions in the Drosophila lymph gland. Early blood progenitors operate a modular TCA configuration, in which a CS/mAcon1-derived citrate node preserves progenitor identity, while a Gdh/Kdh mediated -ketoglutarate to succinyl-CoA branch, not succinate, supports proliferative potential. As cells exit the progenitor state and initiate lineage commitment, the cells undergo metabolic reorganization and engage a fully cyclic, Pdh- and Idh-dependent oxidative TCA cycle whose cataplerotic activity keeps the levels of TCA metabolites in check as their excess otherwise induces differentiation. Blocking these metabolic transitions disrupts progenitor homeostasis, compromises proliferative competency of transitional progenitors, and distorts balanced differentiation. These findings establish a developmentally regulated alternative to the traditional TCA cycle and reveals that appropriate engagement of modular versus cyclic TCA modes is required for orchestrating hematopoietic fate transitions. This work highlights TCA topology and not flux alone functions as a core determinant of stemness, proliferation, and lineage progression during hematopoiesis. Significance StatementHematopoietic development requires precise metabolic control to maintain progenitors while enabling their transition into differentiated lineages. We show that the Drosophila lymph gland achieves this through a developmentally programmed switch in TCA-cycle configuration where early progenitors rely on a modular TCA architecture that independently sustains identity and proliferation, whereas later stages require a fully cyclic, oxidative TCA mode to maintain homeostasis and balanced differentiation. Disrupting either phase perturbs hematopoietic organization, demonstrating that TCA topology itself regulates cell-state transitions. These findings reveal TCA architecture as the determinant of hematopoietic fate and provides a conceptual framework relevant to hematopoiesis and also stem cell biology.

developmental biology↗

bioRxiv2025

Calcium: Modulator of Post-transcriptional and post-translational process in mESCs

Calcium ion (Ca2+) is a ubiquitous intracellular and extracellular messenger that regulates several cellular activities. Previous findings have reported the presence of active Ca2+ receptors in mouse embryonic stem cells (mESCs) but the fundamental requirement of Ca2+ signalling remains unclear. We have noted the presence of high Ca2+ in undifferentiated mESCs and showed that its depletion exerts G2/M cell cycle arrest, spontaneous differentiation of mESCs towards mesoderm lineage and mitochondrial biogenesis. Further, our data demonstrates that Ca2+ regulates the homeostasis and stability of Oct4 and Nanog at the post-translational level through pCamkII dependent mechanism independent of polyubiquitin system, JAK-STAT3 pathway, transcriptional and translational control. Our data also signifies the role of Ca2+ at the post-transcriptional level in regulating p-bodies and stress granule markers (Dcp1a, XRN1, Tudor and EDC4), splicing-dependent and 3UTR-dependent NMD activity. Together, this study identifies the broad role of Ca2+ in modulating key processes in mESCs. HighlightsCa2+ is present at elevated levels in mESCs and is important for pluripotency Ca2+ depletion accelerates G2/M cell cycle arrest and mesoderm differentiation Ca2+ regulates pluripotency and p-bodies markers at the post-translational level Ca2+ regulates Oct4, Nanog, dcp1a through pCaMKII dependent mechanism

cell biology↗

bioRxiv2025

Tretinoin, a Vitamin A derivative, exerts antiviral effects against Chikungunya virus infection through the nuclear retinoid receptor signaling pathways

Chikungunya virus (CHIKV) has reemerged as a global pathogen causing serious public health threat and socio-economic damage, particularly due to the absence of specific antivirals. Retinoids have been reported to exhibit antiviral potentials against multiple viral infections. In the present study, Tretinoin (TR) or all-trans retinoic acid (ATRA) was evaluated for its anti-CHIKV activity using in vitro, in vivo, and ex vivo models. TR was able to impede CHIKV infection efficiently in Vero and physiologically relevant muscle cells, C2C12, with drastic reduction in the viral RNA, proteins and progeny formation. The IC50 of TR against CHIKV was estimated to be 20.05 {micro}M and 19.71 {micro}M in Vero and C2C12 cells, respectively. In addition, the inhibition was effective during entry as well as in the early stages of post CHIKV-infection. Notably, TR showed remarkable virucidal activity. Next, global transcriptome profile demonstrated that the signaling by Retinoic acid pathway was highly upregulated after CHIKV infection and Retinoic acid receptors (RAR), specifically RAR-{beta} are the key mediators for the anti-CHIKV effect of TR. Further, the drug was also capable to modulate CHIKV-induced inflammatory responses by reducing the phosphorylated MAPKs, NF-{kappa}B and proinflammatory cytokines. Interestingly, TR protected C57BL/6 mice from CHIKV challenge by diminishing viral burden leading to reduced clinical scores and better survival. Similar observation was also noticed in the ex vivo model of CHIKV-infected hPBMC-derived monocyte-macrophage populations. In conclusion, this work demonstrated the repurposing potential of TR against CHIKV infection for the first time, encouraging its clinical validation towards future therapeutics. IMPORTANCECHIKV is an arbovirus causing Chikungunya Fever (CHIKF) leading to debilitating arthralgia and myalgia. The unavailability of licensed antivirals or potent vaccines against CHIKV encourages extensive research to find a therapeutic cure. Retinoids, the derivatives of vitamin A, have been repurposed as antiviral agents against a broad range of viruses; however, their efficacy against alphaviruses remains unexplored. Accordingly, Tretinoin (TR), also known as all-trans retinoic acid (ATRA), was validated for anti-CHIKV efficacy in this investigation. Significant perturbation of CHIKV titer through the modulation of Retinoic acid receptors (RAR) was observed upon drug-treatment. Further, TR reduced major inflammatory markers (MAPKs and proinflammatory cytokines) supporting its anti-inflammatory effect. Further, its anti-CHIKV potential was validated in the mouse model and hPBMC-derived monocyte-macrophage cells, indicating the pre-clinical efficacy. Finally, this is the first study to report the anti-CHIKV property of Tretinoin using in vitro, in vivo, and ex vivo approaches suggesting its repurposing potential.

microbiology↗

bioRxiv2025

Exploring the Microbial Geobiological Pattern Across the Serpentinization Sites through Metagenomic and Elemental Composition Analyses

It is well-known that ultramafic rocks can continuously generate hydrogen through the serpentinization process associated with dynamic geochemical and geobiological interactions. This study aims to gain an improved understanding of these dynamic processes through the understanding of diverse microbial populations in order to maximize the geologic hydrogen production potential. The water samples were collected from a near surface serpentinite site in Northern California, USA. Elemental analyses of these water samples revealed the presence of essential dissolved minerals such as magnesium, calcium, and potassium, along with trace elements including iron, cobalt, and nickel. These elements act as cofactors for enzymes involved in microbial metabolic processes and Non-metric Multidimensional Scaling analysis supports this corelation. Furthermore, the analysis of total organic carbon (TOC) showed significant levels of organic carbon, suggesting a link with biological carbon cycling processes. Metagenomic analysis uncovered a diverse microbial community of hydrogen-fueled microbial consortia at the sampling sites, encompassing hydrogenogenic and hydrogenotrophic microorganisms. We examine hydrogen-metabolizing communities, including sulfate-reducing bacteria, acetogens, and methanogens, supported by diversity in hydrogenase enzymes across various sampling sites. These observations are corroborated by genomic accession data and abundance profiling of genes associated with acetogenesis, methanogenesis, and carbon monoxide metabolism. These investigations provide new insights into hydrogen-metabolizing microorganisms in northern California and propose frameworks for optimizing hydrogen production through the inhibition of hydrogen metabolism. O_FIG O_LINKSMALLFIG WIDTH=155 HEIGHT=200 SRC="FIGDIR/small/678891v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@11e5041org.highwire.dtl.DTLVardef@126ea56org.highwire.dtl.DTLVardef@1e2cd4forg.highwire.dtl.DTLVardef@11537f2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe association of the serpentinization process with dynamic geochemical and geobiological interactions. C_LIO_LIMetagenomic study found an assorted microbial community of hydrogen-fueled consortia at the different sampling sites in Northern California C_LIO_LIHydrogen-metabolizing communities counted, including sulfate-reducing bacteria, acetogens, and methanogens. C_LI

microbiology↗

bioRxiv2025

Endothelial cell-intrinsic NOD2 signaling regulates the intestinal immune response through the generation of effector and memory T cells.

Crohns disease (CD) is marked by vascular endothelial dysfunction and aberrant T cell immunity in the gastrointestinal tract. However, mechanistic understanding is lacking of how CD-associated gene variants, particularly those that compromise NOD2 function, impact the intestinal vascular endothelium and orchestration of T cell immunity. Here, we find that NOD2, when triggered by its ligand, muramyl dipeptide, is unique among pattern recognition receptors in its ability to induce endothelial cell expression of chemokines and immune adhesion molecules. Consequently, NOD2 signaling promoted T cell homing specifically to gut-associated lymphoid tissue during intestinal infection. Endothelial cell-specific deletion of Nod2 resulted in fewer effector and memory T cells in the small intestine, impacting the hosts ability to clear secondary infection. Together, our findings suggest that vascular endothelial cell expression of NOD2 coordinates intestinal immune responses, and that CD-associated loss of NOD2 function promotes aberrant inflammation due to alterations in the magnitude and specificity of host defense within the intestine.

immunology↗

bioRxiv2025

Comparative genome analysis of tea rhizosphere dwelling Paenarthrobacter nicotinovorans AB444: Uncovering Physiological Resilience and Ecological Adaptability

Plant growth-promoting rhizobacteria (PGPR) can be considered a promising tool for sustainable agriculture. The recent scenario of growing demand for higher crop yields, with declining soil fertility and impacts of climate change, promotes the global shift towards eco-friendly agricultural practices, emphasising the significance of PGPR as a sustainable solution. In this study, a PGPR Paenarthrobacter sp. AB444 was isolated from the rhizosphere of tea plants at the Longview and Makaibari tea estates in the Darjeeling District of West Bengal. Based on the draft genome sequence along with comprehensive chemotaxonomic analyses, strain AB444 was identified as Paenarthrobacter nicotinovorans. The pangenomic analysis with phylogenetically close strains revealed the gene clusters that are common and unique to the isolate. The plant growth-promoting attributes of AB444 were explored with different assays like phosphate solubilisation, IAA and siderophore production, ACC deaminase, nitrogen fixation, and protease activity. The colonization of the isolate to the plant root and in-planta growth were also assessed. The presence of biosynthetic gene clusters of AB444 related to plant growth was also extensively studied, highlighting the unmapped disposition of Paenarthrobacter nicotinovorans.

microbiology↗

bioRxiv2025

Antioxidant role of the GABA shunt in regulating redox balance in blood progenitors during Drosophila hematopoiesis

Redox balance is crucial for normal development of stem and progenitor cells that reside in oxidative environments. This study explores the mechanisms of redox homeostasis in such niches and investigates myeloid-like blood progenitor cells that generate reactive oxygen species (ROS) and moderate it developmentally. Our findings reveal that during lymph gland development, as the blood-progenitor cells oxidize pyruvate via the TCA cycle leading to the generation of ROS, these cell also de novo synthesize GSH to counter excessive ROS and ensure redox balance. GABA metabolism, through GABA-shunt, restricts pyruvate dehydrogenase (PDH) activity and consequently TCA rate. This allows a metabolic route to sustain serine levels in these cells which is the rate limiting precursor controlling de novo GSH production. Disruption of GABA metabolism leads to a metabolic imbalance, characterized by excessive PDH activity, heightened TCA rate leading to impaired serine/GSH production and overall ROS dysregulation. Overall, the study presents a unique metabolic state whereby, in the blood-progenitor cells, by keeping PDH and TCA activity in check and promoting serine/GSH generation, GABA metabolism establishes a metabolic framework that optimises the use of ROS in blood-progenitors, while ensuring redox homeostasis.

developmental biology↗

bioRxiv2024

Computational modeling of left ventricular flow using PC-CMR-derived four-dimensional wall motion

Intracardiac hemodynamics plays a crucial role in the onset and development of cardiac and valvular diseases. Simulations of blood flow in the left ventricle (LV) have provided valuable insight into assessing LV hemodynamics. While fully coupled fluid-solid modelings of the LV remain challenging due to the complex passive-active behavior of the LV wall myocardium, the integration of imaging-driven quantification of structural motion with computational fluid dynamics (CFD) modeling in the LV holds the promise of feasible and clinically translatable characterization of patient-specific LV hemodynamics. In this study, we propose to integrate two magnetic resonance imaging (MRI) modalities with the moving-boundary CFD method to characterize intracardiac LV hemodynamics. Our method uses the standard cine cardiac magnetic resonance (CMR) images to estimate four-dimensional myocardial motion, eliminating the need for involved myocardial material modeling to capture LV wall behavior. In conjunction with CMR, phase contrast-MRI (PC-MRI) was used to measure temporal blood inflow rates at the mitral orifice, serving as an additional boundary condition. Flow patterns, including velocity streamlines, vortex rings, and kinetic energy, were characterized and compared to the available data. Moreover, relationships between LV wall kinematic markers and flow characteristics were determined without myocardial material modeling and using a non-rigid image registration (NRIR) method. The fidelity of the simulation was quantitatively evaluated by validating the flow rate at the aortic outflow tract against respective PC-MRI measures. The proposed methodology offers a novel and feasible toolset that works with standard PC-CMR protocols to improve the clinical assessment of LV characteristics in prognostic studies and surgical planning.

bioengineering↗

bioRxiv2024

In-silico heart model phantom to validate cardiac strain imaging

The quantification of cardiac strains as structural indices of cardiac function has a growing prevalence in clinical diagnosis. However, the highly heterogeneous four-dimensional (4D) cardiac motion challenges accurate "regional" strain quantification and leads to sizable differences in the estimated strains depending on the imaging modality and post-processing algorithm, limiting the translational potential of strains as incremental biomarkers of cardiac dysfunction. There remains a crucial need for a feasible benchmark that successfully replicates complex 4D cardiac kinematics to determine the reliability of strain calculation algorithms. In this study, we propose an in-silico heart phantom derived from finite element (FE) simulations to validate the quantification of 4D regional strains. First, as a proof-of-concept exercise, we created synthetic magnetic resonance (MR) images for a hollow thick-walled cylinder under pure torsion with an exact solution and demonstrated that "ground-truth" values can be recovered for the twist angle, which is also a key kinematic index in the heart. Next, we used mouse-specific FE simulations of cardiac kinematics to synthesize dynamic MR images by sampling various sectional planes of the left ventricle (LV). Strains were calculated using our recently developed non-rigid image registration (NRIR) framework in both problems. Moreover, we studied the effects of image quality on distorting regional strain calculations by conducting in-silico experiments for various LV configurations. Our studies offer a rigorous and feasible tool to standardize regional strain calculations to improve their clinical impact as incremental biomarkers.

bioengineering↗

bioRxiv2024

Rosettes in a matrix: Predicting spatial variation in density of a large felid in a forest-production mosaic

Large carnivores are keystone for ecosystems and flagships for conservation efforts but face severe threats globally. Protected Areas are vital for the conservation of these charismatic species along with a host of ecological processes. However, the extent and scope of protected areas for conservation of all threatened species is limited, especially in the global south. Considering larger landscapes that can be compatible with large carnivore conservation goals is an alternative approach to ensure their persistence. This study explores the potential of multi-use landscapes for the persistence of a globally threatened large felid, the leopard. This study investigated the spatial variability of leopard densities across a land-use gradient using spatially explicit capture-recapture framework in a tea-plantation dominated forest-production landscape mosaic. While the density of leopards in this landscape was estimated to be 7.96 {+/-} 1.56 (SE) per 100 km2, significant (p=0.048, t=2.02, df=61) differences in estimates were observed between tea-plantations (11.53 {+/-} 2.72 (SE) leopards per 100 km2) and the forested habitats (4.67 {+/-} 2.07 (SE) per 100 km2). Densities between tea plantations and Protected Areas (a subset of the forested habitat) were found to be comparable (9.19 {+/-} 4.55 (SE) per 100 km2). The study posits that conservation-compatible land use in landscapes shared with people can host a higher density of large felids than forested areas and that conservation planning needs to move beyond the dominant PA-centric paradigm. The study also reinforces the importance of multi-use landscapes for wildlife conservation, especially for an adaptable large felid.

ecology↗

bioRxiv2024

Complete spatiotemporal quantification of cardiac motion in mice through enhanced acquisition and super-resolution reconstruction

The quantification of cardiac motion using cardiac magnetic resonance imaging (CMR) has shown promise as an early-stage marker for cardiovascular diseases. Despite the growing popularity of CMR-based myocardial strain calculations, measures of complete spatiotemporal strains (i.e., three-dimensional strains over the cardiac cycle) remain elusive. Complete spatiotemporal strain calculations are primarily hampered by poor spatial resolution, with the rapid motion of the cardiac wall also challenging the reproducibility of such strains. We hypothesize that a super-resolution reconstruction (SRR) framework that leverages combined image acquisitions at multiple orientations will enhance the reproducibility of complete spatiotemporal strain estimation. Two sets of CMR acquisitions were obtained for five wild-type mice, combining short-axis scans with radial and orthogonal long-axis scans. Super-resolution reconstruction, integrated with tissue classification, was performed to generate full four-dimensional (4D) images. The resulting enhanced and full 4D images enabled complete quantification of the motion in terms of 4D myocardial strains. Additionally, the effects of SRR in improving accurate strain measurements were evaluated using an in-silico heart phantom. The SRR framework revealed near isotropic spatial resolution, high structural similarity, and minimal loss of contrast, which led to overall improvements in strain accuracy. In essence, a comprehensive methodology was generated to quantify complete and reproducible myocardial deformation, aiding in the much-needed standardization of complete spatiotemporal strain calculations.

bioengineering↗

bioRxiv2024

Multi-Modality Deep Infarct: Non-invasive identification of infarcted myocardium using composite in-silico-human data learning

Myocardial infarction (MI) continues to be a leading cause of death worldwide. The precise quantification of infarcted tissue is crucial to diagnosis, therapeutic management, and post-MI care. Late gadolinium enhancement-cardiac magnetic resonance (LGE-CMR) is regarded as the gold standard for precise infarct tissue localization in MI patients. A fundamental limitation of LGE-CMR is the invasive intravenous introduction of gadolinium-based contrast agents that present potential high-risk toxicity, particularly for individuals with underlying chronic kidney diseases. Herein, we develop a completely non-invasive methodology that identifies the location and extent of an infarct region in the left ventricle via a machine learning (ML) model using only cardiac strains as inputs. In this transformative approach, we demonstrate the remarkable performance of a multi-fidelity ML model that combines rodent-based in-silico-generated training data (low-fidelity) with very limited patient-specific human data (high-fidelity) in predicting LGE ground truth. Our results offer a new paradigm for developing feasible prognostic tools by augmenting synthetic simulation-based data with very small amounts of in-vivo human data. More broadly, the proposed approach can significantly assist with addressing biomedical challenges in healthcare where human data are limited.

biophysics↗

bioRxiv2024

Dietary stress induced macrophage metabolic reprogramming, a determinant of animal growth

Nutrient sensing and signaling play pivotal roles in animal growth. However, under dietary stress, this system falters, leading to growth defects. While immune cells are increasingly recognized as key nutrient sensors, their impact on animal growth remains poorly understood. In this study, we investigate how Drosophila larval macrophages respond to excessive dietary sugar and identify a reconfiguration of their metabolic state. They undergo a glycolytic shift, intensify TCA activity, and elevate TAG synthesis. While typical of sugarinduced nutrient stress, these changes interestingly exert contrasting effects on animal growth: glycolysis and increased TCA activity inhibit growth, while the lipogenic shift promotes it. However, the lipogenic response is insufficient to counteract the metabolic events suppressing growth, resulting in an overall reduction in adult fly size under high sugar conditions. Stimulating a pro-lipogenic immune state facilitates growth recovery, suggesting a growth paradigm governed by immune-metabolic transitions. This study unveils the unexpected influence of macrophage metabolic reprogramming on organismal growth homeostasis during Drosophila development, highlighting immune cell states as central determinants of growth, particularly under dietary stress.

developmental biology↗

bioRxiv2023

Nuclear localization of HD-Zip IV transcription factor GLABRA2 is driven byImportin α

GLABRA2 (GL2), a class IV homeodomain leucine-zipper (HD-Zip IV) transcription factor (TF) from Arabidopsis, is a developmental regulator of specialized cell types in the epidermis. GL2 contains a putative monopartite nuclear localization sequence (NLS) partially overlapping with its homeodomain (HD). We demonstrate that NLS deletion or alanine substitution of its basic residues (KRKRKK) affects nuclear localization and results in a loss-of-function phenotype. Fusion of the predicted NLS (GTNKRKRKKYHRH) to the fluorescent protein EYFP is sufficient for its nuclear localization in roots and trichomes. The functional NLS is evolutionarily conserved in a distinct subset of HD-Zip IV members including PROTODERMAL FACTOR2 (PDF2). Despite partial overlap of the NLS with the HD, genetic dissection of the NLS from PDF2 indicates that nuclear localization and DNA binding are separable functions. Affinity purification of GL2 from plant tissues followed by mass spectrometry-based proteomics identified Importin (IMP) isoforms as potential GL2 interactors. NLS structural prediction and molecular docking studies with IMP-3 revealed major interacting residues. Split-ubiquitin cytosolic yeast two-hybrid assays suggest interaction between GL2 and four IMP isoforms from Arabidopsis. Direct interactions were verified in vitro by co-immunoprecipitation with recombinant proteins. IMP triple mutants (imp- 1,2,3) exhibit defects in EYFP:GL2 nuclear localization in trichomes but not in roots, consistent with tissue-specific and redundant functions of IMP isoforms in Arabidopsis. Taken together, our findings provide mechanistic evidence for IMP-dependent nuclear localization of GL2 and other HD-Zip IV TFs in plants. One sentence summaryGLABRA2, a representative HD-Zip IV transcription factor from Arabidopsis, contains an evolutionarily conserved monopartite nuclear localization sequence that is recognized by Importin for translocation to the nucleus, a process that is necessary for cell-type differentiation of the epidermis.

plant biology↗

bioRxiv2023

HIV-differentiated metabolite N-Acetyl-L-Alanine dysregulates human natural killer cell responses to Mycobacterium tuberculosis infection

BackgroundMycobacterium tuberculosis (Mtb) has latently infected over two billion people worldwide (LTBI) and causes 1.8 million deaths each year. Human immunodeficiency virus (HIV) co-infection with Mtb will affect the Mtb progression and increase the risk of developing active tuberculosis by 10-20 times compared to the HIV-LTBI+ patients. It is crucial to understand how HIV can dysregulate immune responses in LTBI+ individuals. MethodsPlasma samples collected from healthy and HIV-infected individuals were investigated by liquid chromatography-mass spectrometry (LC-MS), and the metabolic data were analyzed using an online platform Metabo-Analyst. ELISA, surface and intracellular staining, flow cytometry, quantitative reverse transcription PCR (qRT-PCR) were performed by standard procedure to determine the surface markers, cytokines and other signaling molecule expression. Seahorse extra cellular flux assays were used to measure the mitochondrial oxidative phosphorylation and glycolysis. ResultsSix metabolites were significantly less abundant, and two were significantly higher in abundance in HIV+ individuals compared to healthy donors. One of the HIV-upregulated metabolites, N-Acetyl-L-Alanine (ALA), inhibits pro-inflammatory cytokine IFN-{square} production by NK cells of LTBI+ individuals. ALA inhibits glycolysis of LTBI+ individuals NK cells in response to Mtb. ConclusionsOur findings demonstrate that HIV infection enhances plasma ALA levels to inhibit NK cell-mediated immune responses to Mtb infection, offering a new understanding of the HIV-Mtb interaction and providing the implication of nutrition intervention and therapy for HIV-Mtb co-infected patients.

immunology↗