Biology subjects

Patil, G.

Publications and source records attributed to Patil, G..

4 recordsLinked to original sources

bioRxiv2026

A spatiotemporal single-cell atlas reveals coordinated immune, metabolic, and nutrient exchange programs and a coumarin-centered metabolic switch during soybean arbusular mycorrhizal symbiosis

Arbuscular mycorrhizal fungi (AMF) establish intimate symbiosis with plant roots, yet the cell-type-specific regulatory and metabolic programs governing this interaction remain poorly resolved. Here, we integrate single-nucleus RNA sequencing (snRNA-seq) with spatial metabolomics across a temporal gradient of soybean root colonization (2-8 weeks post inoculation) to construct a high-resolution, multi-omic atlas of AMF symbiosis. Profiling 33,410 nuclei spanning all major root cell types, we uncover dynamic, cell-type-resolved transcriptional reprogramming coupled to spatially localized metabolite accumulation. Early colonization triggers a robust, epidermis-localized immune response alongside cortex-specific epigenetic reprogramming, mediated by RNA-directed DNA methylation machinery, suggesting active suppression of defense in fungal accommodation zones. Spatial metabolomics reveals a biphasic metabolic transition from flavonoid- and terpenoid-rich signaling states to lipid-dominated nutrient exchange, aligned with colonization progression. In parallel, coordinated carbon allocation and lipid biosynthesis pathways were activated in cortex and vascular tissues, supporting fungal dependence on host-derived fatty acids and sugars. Nutrient exchange programs, particularly nitrogen and phosphorus transport, exhibit strong pericycle and phloem specificity, highlighting systemic integration of symbiotic benefits. Through co-expression network analysis, we identify a previously uncharacterized coumarin-centered metabolic switch, governed by GmF6H1-2, that is essential for efficient colonization, as validated by natural loss-of-function variants. Collectively, this study provides a comprehensive, spatially resolved framework linking gene regulation, metabolism, and cell identity, revealing that AMF symbiosis is orchestrated through coordinated immune modulation, metabolic rewiring, and nutrient flux partitioning at single-cell resolution. Key pointsO_LIMulti-omic integration reveals cell-type-resolved symbiotic programs C_LIO_LISymbiosis requires spatially coordinated immune reprogramming C_LIO_LIA biphasic metabolic shift underpins colonization dynamics C_LIO_LICarbon and nutrient flux are partitioned across specialized cell types C_LIO_LIDiscovery of a coumarin-driven "metabolic GO-switch" controlling symbiosis C_LI

plant biology↗

bioRxiv2026

Nuclear mTOR-Polycomb synergism at developmental gene promoters prone to activation

Pluripotent cells hold the capacity to differentiate into cells with diverse functions, enabling development and regeneration. The balance between local epigenetic repression and maintaining the potential for prompt transcriptional activation supports pluripotency while allowing imminent differentiation. How the activation of developmental pathways is correctly timed in sync with the environment remains poorly understood. Here we find that the cellular growth regulator mTOR selectively binds developmental gene promoters in pluripotent mouse embryonic stem cells. mTOR binding at target genes correlates with and depends on histone H2AK119 monoubiquitination (H2AK119ub1) deposited by the Polycomb Repressor Complex 1 (PRC1). Acute depletion of the whole PRC1 complex or its catalytic activity leads to depletion of mTOR at target gene promoters, whereas forced PRC1 recruitment to an artificial site brings along mTOR. At target genes, mTOR colocalizes with components of the transcription machinery and we find that mTOR-bound genes are distinctly characterized by high levels of RNA Polymerase II pausing. Our findings reveal a role of mTOR in pluripotency regulation and highlight the tight crosstalk between gene regulatory and cell growth machineries in stem cells.

molecular biology↗

bioRxiv2023

Klebsiella pneumoniae Co-infection Leads to Fatal Pneumonia in SARS-CoV-2-infected Mice

SARS-CoV-2 patients have been reported to have high rates of secondary Klebsiella pneumoniae infections. Klebsiella pneumoniae is a commensal that is typically found in the respiratory and gastrointestinal tracts. However, it can cause severe disease when a persons immune system is compromised. Despite a high number of K. pneumoniae cases reported in SARS-CoV-2 patients, a co-infection animal model evaluating the pathogenesis is not available. We describe a mouse model to study disease pathogenesis of SARS-CoV-2 and K. pneumoniae co-infection. BALB/cJ mice were inoculated with mouse-adapted SARS-CoV-2 followed by a challenge with K. pneumoniae. Mice were monitored for body weight change, clinical signs, and survival during infection. The bacterial load, viral titers, immune cell accumulation and phenotype, and histopathology were evaluated in the lungs. The co-infected mice showed severe clinical disease and a higher mortality rate within 48 h of K. pneumoniae infection. The co-infected mice had significantly elevated bacterial load in the lungs, however, viral loads were similar between co-infected and single-infected mice. Histopathology of co-infected mice showed severe bronchointerstitial pneumonia with copious intralesional bacteria. Flow cytometry analysis showed significantly higher numbers of neutrophils and macrophages in the lungs. Collectively, our results demonstrated that co-infection of SARS-CoV-2 with K. pneumoniae causes severe disease with increased mortality in mice.

immunology↗

bioRxiv2020

Traceback of Core Transcription Factors for Soybean Root Growth Maintenance under Water Deficit

Some crops inhibit shoot growth but maintain root growth under water-deficit conditions. Unraveling the molecular mechanisms of root plasticity under water deficit conditions in plants remains a major challenge. We developed an efficient platform for identifying core transcription factors (TFs) that collectively regulate each other and/or themselves in response to water stress, and exploring their interconnected regulatory circuitry involved in root growth maintenance under water deficit in soybean. We performed multi-species phylogenetic footprinting combined with spatial-temporal transcriptome analysis of soybean (Glycine max) roots under water deficit to identify conserved motifs that function in the water-stress response. Using these functional conserved cis-motifs, we applied a new approach to trace back motifs-associated core TFs ingroup as signal mediators, which mediate signaling between abiotic and endogenous stimuli. We integrated a co-functional TF-TF network and conserved motif-centered TF-DNA networks to construct a core TF network defined by mutual cross-regulation among core TFs. We found that core TF ARG (Abscisic acid response element binding factor-like Root Growth regulator) represses BRG (Brassinosteroid enhanced expression-like Root Growth regulator) expression through binding to its promoter at a conserved binding site. ARG and BRG antagonistically regulate Phytochrome-interacting factor-like Root Growth regulator (PRG) and combinatorially regulate some other core TFs. These core TFs form complex regulatory circuits to integrate light and multiple hormone signaling pathways and maintain root growth in response to varying degrees of water stress. Our study provides valuable information to unravel the complicated mechanisms of molecular networks involved in the regulation of root growth under water deficit.

plant biology↗