Biology subjects

Gautam, C. K.

Publications and source records attributed to Gautam, C. K..

4 recordsLinked to original sources

bioRxiv2026

Systemic Iron Signaling via OPT3 Influences Reductive Uptake and Coumarin Secretion

Iron (Fe) availability is frequently restricted in soils, particularly under alkaline conditions, resulting in Fe-deficiency chlorosis and reduced plant growth. In Strategy I plants, Fe acquisition relies on ferric chelate reductase (FCR) activity and the secretion of Fe-mobilizing compounds like coumarins; however, how these pathways are integrated through systemic Fe signaling remains poorly understood. In this study, coordination between reductive Fe uptake, coumarin biosynthesis, external pH, and systemic signaling was investigated in Arabidopsis thaliana. Physiological readouts, including chlorophyll content, root FCR activity, and coumarin fluorescence, were compared among wild-type Col-0, the systemic signaling mutant opt3-2, and the coumarin-deficient mutant f6h1-1 under Fe-sufficient, alkaline, and Fe-free conditions. Under alkaline Fe limitation, opt3-2 sustained higher chlorophyll levels, persistent FCR activity, and strongly enhanced coumarin secretion, whereas f6h1-1 exhibited severe chlorosis accompanied by compensatory FCR induction. Time-resolved analyses showed that external pH restricts FCR responsiveness, while loss of OPT3-mediated systemic signaling profoundly alters the timing and amplitude of coumarin deployment. Co-cultivation assay further demonstrated that coumarins released by opt3-2 partially alleviate Fe-deficiency symptoms in f6h1-1. Together, these results identify systemic signaling as a key integrator of reductive Fe uptake and coumarin-mediated Fe mobilization, establishing a unified framework for Fe homeostasis.

plant biology↗

bioRxiv2025

Host-Specific Fluorescence Dynamics in Legume-Rhizobia Symbiosis During Nodulation

The legume-rhizobia symbiosis is a cornerstone of sustainable agriculture due to its ability to facilitate biological nitrogen fixation. Still, real-time visualization and quantification of this interaction remain technically challenging, especially across different host backgrounds. In this study, we systematically evaluate the efficacy of the nitrogenase system nifH promoter (PnifH) in driving expression of distinct fluorescent reporters; superfolder yellow fluorescent protein (sfYFP), superfolder cyan fluorescent protein (sfCFP), and various red fluorescent proteins (RFPs) within root nodules of determinate (Lotus japonicus-Mesorhizobium japonicum) and indeterminate (Pisum sativum-Rhizobium leguminosarum) systems. We show that PnifH-driven sfYFP and sfCFP yield strong, uniform, and reproducible fluorescence in nodules of both systems, facilitating reliable quantification of nodulation traits and strain occupancy. In contrast, RFPs including monomeric (mScarlet-I, mRFP1, mARs1) and multimeric (AzamiRed1.0) variants exhibited weak or inconsistent signals in pea. Notably, fluorescent labeling did not impair rhizobial competitiveness for root nodule occupancy, and PnifH-driven sfYFP and sfCFP reporters enabled robust multiplexed imaging in single-root and split-root assays. In the lotus, mScarlet-I worked robustly and facilitated a tripartite strain labeling system. Complementing our molecular toolkit, we established a deep learning-based analytical pipeline for high-throughput, automated quantification of nodulation traits, validated against standard ImageJ analysis. Altogether, our results identify PnifH-driven sfYFP and sfCFP as robust, broadly applicable reporters for legume-rhizobia symbiosis studies, while highlighting the need for optimized red fluorophores in some contexts. The integration of validated promoter-reporter constructs with state-of-the-art computational approaches provides a scalable framework for dissecting the spatial and competitive dynamics of plant-microbe mutualisms. IMPORTANCEThe legume-rhizobia symbiosis is central to sustainable agriculture through its capacity for biological nitrogen fixation, yet tools for real-time, quantitative visualization of this interaction remain limited. Here, we demonstrate that the nifH promoter (PnifH) effectively drives expression of superfolder yellow (sfYFP) and cyan (sfCFP) fluorescent proteins in both determinate (Lotus japonicus-Mesorhizobium japonicum) and indeterminate (Pisum sativum-Rhizobium leguminosarum) nodules. These reporters enable robust, reproducible fluorescence without impairing rhizobial competitiveness, supporting multiplexed imaging and quantitative nodulation analyses. By contrast, red fluorescent proteins exhibited host-dependent variability, underscoring the need for improved red fluorophores. Integration of validated promoter-reporter constructs with a deep learning-based image analysis pipeline establishes a scalable framework for high-throughput assessment of nodule occupancy and symbiotic dynamics. This work provides a practical molecular and computational toolkit for dissecting plant-microbe mutualisms across diverse host systems.

bioengineering↗

bioRxiv2024

Medicago truncatula CORYNE regulates inflorescence meristem branching, nutrient signaling, and arbuscular mycorrhizal symbiosis

The CLAVATA signaling pathway regulates plant development and plant-environment interactions. CLAVATA signaling consists of mobile, cell-type or environment-specific CLAVATA3/ESR-related (CLE) peptides, which are perceived by a receptor complex consisting of leucine-rich repeat receptor-like kinases such as CLAVATA1 and receptor-like proteins such as CLAVATA2, which often functions with the pseudokinase CORYNE (CRN). CLAVATA signaling has been extensively studied in various plant species for its role in meristem maintenance and in legumes for modulating root interactions with nitrogen-fixing rhizobia. Some signaling proteins involved in development and nodulation, including CLAVATA1, also regulate plant interactions with mutualistic arbuscular mycorrhizal (AM) fungi. However, our knowledge on AM symbiosis regulation by CLAVATA signaling remains limited and only a handful of genetic regulators have been identified. Here we report that Medicago truncatula CRN controls inflorescence meristem branching and negatively regulates root interactions with AM fungi. MtCRN functions partially independently of the AM autoregulation signal MtCLE53. Transcriptomic data revealed that crn roots display signs of perturbed nutrient, symbiosis, and stress signaling, suggesting that MtCRN plays various roles in plant development and interactions with the environment.

plant biology↗

bioRxiv2021

IRONMAN Tunes Responses to Iron Deficiency in Concert with Environmental pH

Iron (Fe) is an essential mineral element which governs the composition of natural plant communities and limits crop yield in agricultural ecosystems due to its extremely low availability in most soils, particularly at alkaline pH. To extract sufficient Fe from the soil under such conditions, some plants including Arabidopsis thaliana secrete Fe-mobilizing phenylpropanoids, which mobilize sparingly soluble Fe hydroxides by reduction and chelation. We show here that ectopic expression of the IRONMAN peptides IMA1 and IMA2 improves growth on calcareous soil by inducing the biosynthesis and secretion of the catecholic coumarin fraxetin (7,8-dihydroxy-6-methoxycoumarin) through increased expression of MYB72 and SCOPOLETIN 8-HYDROXYLASE (S8H), a response which is strictly dependent on elevated environmental pH (pHe). By contrast, transcription of the cytochrome P450 family protein CYP82C4, catalyzing the subsequent hydroxylation of fraxetin to sideretin, which forms less stable complexes with iron, was strongly repressed under such conditions. Luciferase reporter assays in transiently transformed protoplasts showed that IMA1/IMA2 peptides are translated and modulate the expression of CYP82C4 and MYB72 by acting as transcriptional coactivators. It is concluded that IMA peptides regulate processes supporting Fe uptake at both acidic and elevated pH by controlling gene expression upstream of or in concert with a putative pHe signal to adapt the plant to the prevailing edaphic conditions. This regulatory pattern confers tolerance to calcareous soils by extending the pH range in which Fe can be efficiently absorbed from the soil. Altering the expression of IMA peptides provides a novel route for generating plants adapted to calcareous soils. One sentence summaryEctopic expression of IRONMAN peptides improves growth under iron-limiting conditions by inducing responses to limited iron availability in accordance with the environmental pH. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Wolfgang Schmidt (wosh@gate.sinica.edu.tw).

plant biology↗