Sadhukhan, Ayan

In the current study, gene network analysis revealed five novel disease-resistance proteins against bacterial leaf blight (BB) and rice blast (RB) diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (M. oryzae), respectively. In silico modeling, refinement, and model quality assessment were performed to predict the best structures of these five proteins and submitted to ModelArchive for future use. An in-silico annotation indicated that the five proteins functioned in signal transduction pathways as kinases, phospholipases, transcription factors, and DNA-modifying enzymes. The proteins were localized in the nucleus and plasma membrane. Phylogenetic analysis showed the evolutionary relation of the five proteins with disease-resistance proteins (XA21, OsTRX1, PLD, and HKD-motif-containing proteins). This indicates similar disease-resistant properties between five unknown proteins and their evolutionary-related proteins. Furthermore, gene expression profiling of these proteins using public microarray data showed their differential expression under Xoo and M. oryzae infection. This study provides an insight into developing disease-resistant rice varieties by predicting novel candidate resistance proteins, which will assist rice breeders in improving crop yield to address future food security through molecular breeding and biotechnology.

Aims: This study aimed to isolate plant growth and drought tolerance-promoting bacteria from the nutrient-poor rhizosphere soil of Thar desert plants and unravel their molecular mechanisms of plant growth promotion. Methods and results: Among our rhizobacterial isolates, Enterobacter cloacae C1P-IITJ, Kalamiella piersonii J4-IITJ, and Peribacillus frigoritolerans T7-IITJ, significantly enhanced root and shoot growth (4 - 5-fold) in Arabidopsis thaliana under PEG-induced drought stress. Whole genome sequencing and biochemical analyses of the non-pathogenic bacterium T7-IITJ revealed its plant growth-promoting traits, viz., solubilization of phosphate (40-73 μg/ml), iron (24 ± 0.58 mm halo on chrome azurol S media), and nitrate (1.58 ± 0.01 μg/ml nitrite), along with production of exopolysaccharides (125 ± 20 μg/ml) and auxin-like compounds (42.6 ± 0.05 μg/ml). Transcriptome analysis of A. thaliana inoculated with T7-IITJ and exposure to drought revealed the induction of 445 plant genes (log2fold-change > 1, FDR < 0.05) for photosynthesis, auxin and jasmonate signalling, nutrient uptake, redox homeostasis, and secondary metabolite biosynthesis pathways related to beneficial bacteria-plant interaction, but repression of 503 genes (log2fold-change < -1) including many stress-responsive genes. T7-IITJ enhanced proline 2.5-fold, chlorophyll 2.5 - 2.8-fold, iron 2-fold, phosphate 1.6-fold, and nitrogen 4-fold, and reduced reactive oxygen species 2 - 4.7-fold in plant tissues under drought. T7-IITJ also improved the germination and seedling growth of Tephrosia purpurea, Triticum aestivum, and Setaria italica under drought and inhibited the growth of two plant pathogenic fungi, Fusarium oxysporum, and Rhizoctonia solani. Conclusions: P. frigoritolerans T7-IITJ is a potent biofertilizer that regulates plant genes to promote growth and drought tolerance.

We sequenced the drought-response transcriptome of the keystone tree species Prosopis cineraria from the Indian Thar desert to understand the key factors in its drought tolerance mechanism. We identified a network of genes activated in P. cineraria involved in the biosynthesis of osmolytes, antioxidants, phytohormones, and signal transduction. Of these, up-regulation of 54 APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factor genes, validated by real-time PCR, suggests their key role in the drought tolerance of P. cineraria. We conducted a genome-wide study of the AP2/ERF superfamily in P. cineraria, classifying its 232 proteins into 15 clades and analyzing their protein structures, gene structure, and promoter organization. The P. cineraria genome contains more copies of AP2/ERF genes than drought-sensitive plants. Further, we identified sequence polymorphisms in AP2/ERF genes between Arabian and Indian cultivars of P. cineraria. We modeled the DNA–protein complex structures of AP2/ERFs from drought-tolerant and sensitive species using AlphaFold to compare their DNA-binding ability. Though the DNA-binding domain (DBD) is relatively conserved across species, the unstructured region of these proteins possesses different charge distributions, which might contribute differently to their DNA search and binding. Using all-atom molecular dynamics simulations, we teased out a higher number of specific DBD-DNA hydrogen bonds in P. cineraria, leading to a stronger DNA-binding affinity than drought-sensitive Arabidopsis thaliana. These results directly support copy number expansion of AP2/ERF transcription factors and the evolution of their structures for more efficient DNA search and binding as drought adaptation mechanisms in P. cineraria.

The combination of nanotechnology and hydroponics paves the way toward sustainable agriculture with less environmental footprints. We investigated the effects of a liquid nano urea formulation (NUF) marketed by Indian Farmers Fertilizer Cooperative (IFFCO) on the model plant Arabidopsis thaliana in hydroponics, comparing it to an equimolar bulk urea. Dynamic light scattering and transmission electron microscopy confirmed NUF’s negative surface charge and sub-100-nm size, suitable for its uptake and distribution in the plant. A two-week growth in a nitrogen-free hydroponic medium with 70 μM NUF led to a 20% higher biomass and 16% higher chlorophyll content than a medium with 70 μM urea. Higher doses of NUF inhibited growth, whereas higher equivalent urea doses did not. Transcriptome analysis revealed that NUF led to the differential expression of more genes than urea at 12 h to seven days of treatment. Nitrogen assimilation, growth, photosynthesis, and stress tolerance genes showed higher transcript levels in NUF than in urea. On the other hand, NUF led to greater suppression of many negative growth-regulating genes. After seven days of treatment, chlorophyll biosynthesis genes were up-regulated, while chlorophyll catabolism genes down-regulated at higher levels by NUF than by urea, correlating with the higher chlorophyll content of NUF-treated seedlings. In conclusion, NUF outperformed equimolar urea for the growth promotion of A. thaliana at a low concentration in hydroponics, leading to a greater regulation of genes for nitrogen metabolism and chlorophyll biosynthesis. Our results suggest a potential use of NUF as a nitrogen fertilizer for hydroponic agriculture. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2024.

We compared the efficacy of the Indian Farmers Fertilizer Cooperative (IFFCO) liquid nano urea formulation (NUF) and conventional urea on the model plant Arabidopsis thaliana. NUF and equimolar bulk urea were applied to vermiculite-grown one-month-old plants as 0.4% foliar sprays. NUF resulted in a 0.4 g increase in biomass, 0.5 mg g− 1 in chlorophyll, 0.17 mmol g− 1 in nitrogen, and 28.8 mg g− 1 in amino acid content of the leaves, compared to bulk urea. NUF’s zeta potential of -54.7 mV and particle size of ≃27.7 nm, measured by dynamic light scattering and transmission electron microscopy, is suitable for stomatal uptake. A differential gene expression analysis of NUF versus urea-treated plants showed significantly higher expression levels of 211 genes (log2fold-change > 0.5, FDR < 0.05) involved in the biosynthesis of carbohydrates, amino acids, nucleotides, lipids, phytohormones, and secondary metabolites, cell wall biosynthesis and modification, growth and developmental processes, cell cycle, and stress response than bulk urea. On the other hand, 1,286 genes (log2fold-change < -0.5) involved in cell death, abscission, senescence, nitrogen transport and metabolism, and biotic stress response showed lower expression levels upon NUF application than bulk urea. These suggest that although NUF suppresses nitrogen uptake genes, it enhances growth by higher induction of essential biomolecule synthesis and growth-promoting genes, than bulk urea. This research advances current knowledge in sustainable agriculture by elucidating the molecular mechanisms through which nano urea enhances plant productivity compared to bulk urea, potentially reducing fertilizer use. © The Author(s) 2025.

We sequenced the drought-response transcriptome of the keystone tree species Prosopis cineraria from the Indian Thar desert to understand the key factors in its drought tolerance mechanism. We identified a network of genes activated in P. cineraria involved in the biosynthesis of osmolytes, antioxidants, phytohormones, and signal transduction. Of these, up-regulation of 54 APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factor genes, validated by real-time PCR, suggests their key role in the drought tolerance of P. cineraria. We conducted a genome-wide study of the AP2/ERF superfamily in P. cineraria, classifying its 232 proteins into 15 clades and analyzing their protein structures, gene structure, and promoter organization. The P. cineraria genome contains more copies of AP2/ERF genes than drought-sensitive plants. Further, we identified sequence polymorphisms in AP2/ERF genes between Arabian and Indian cultivars of P. cineraria. We modeled the DNA–protein complex structures of AP2/ERFs from drought-tolerant and sensitive species using AlphaFold to compare their DNA-binding ability. Though the DNA-binding domain (DBD) is relatively conserved across species, the unstructured region of these proteins possesses different charge distributions, which might contribute differently to their DNA search and binding. Using all-atom molecular dynamics simulations, we teased out a higher number of specific DBD-DNA hydrogen bonds in P. cineraria, leading to a stronger DNA-binding affinity than drought-sensitive Arabidopsis thaliana. These results directly support copy number expansion of AP2/ERF transcription factors and the evolution of their structures for more efficient DNA search and binding as drought adaptation mechanisms in P. cineraria.

We sequenced the drought-response transcriptome of the keystone tree species Prosopis cineraria from the Indian Thar desert to understand the key factors in its drought tolerance mechanism. We identified a network of genes activated in P. cineraria involved in the biosynthesis of osmolytes, antioxidants, phytohormones, and signal transduction. Of these, up-regulation of 54 APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factor genes, validated by real-time PCR, suggests their key role in the drought tolerance of P. cineraria. We conducted a genome-wide study of the AP2/ERF superfamily in P. cineraria, classifying its 232 proteins into 15 clades and analyzing their protein structures, gene structure, and promoter organization. The P. cineraria genome contains more copies of AP2/ERF genes than drought-sensitive plants. Further, we identified sequence polymorphisms in AP2/ERF genes between Arabian and Indian cultivars of P. cineraria. We modeled the DNA–protein complex structures of AP2/ERFs from drought-tolerant and sensitive species using AlphaFold to compare their DNA-binding ability. Though the DNA-binding domain (DBD) is relatively conserved across species, the unstructured region of these proteins possesses different charge distributions, which might contribute differently to their DNA search and binding. Using all-atom molecular dynamics simulations, we teased out a higher number of specific DBD-DNA hydrogen bonds in P. cineraria, leading to a stronger DNA-binding affinity than drought-sensitive Arabidopsis thaliana. These results directly support copy number expansion of AP2/ERF transcription factors and the evolution of their structures for more efficient DNA search and binding as drought adaptation mechanisms in P. cineraria.

Essential plant nutrients encapsulated or combined with nano-dimensional adsorbents define nano fertilizers (NFs). Nanoformulation of non-essential elements enhancing plant growth and stress tolerance also comes under the umbrella of NFs. NFs have an edge over conventional chemical fertilizers, viz., higher plant biomass and yield using much lesser fertilization, thereby reducing environmental pollution. Foliar and root applications of NFs lead to their successful uptake by the plant, depending on the size, surface charge, and other physicochemical properties of NFs. Smaller NFs can pass through channels on the waxy cuticle depending on the hydrophobicity, while larger NFs pass through the stomatal conduits of leaves. Charge-based adsorption, followed by apoplastic movement and endocytosis, translocates NFs through the root, while the size of NFs influences passage into vascular tissues. Recent transcriptomic, proteomic, and metabolomic studies throw light on the molecular mechanisms of growth promotion by NFs. The expression levels of nutrient transporter genes are regulated by NFs, controlling uptake and minimizing excess nutrient toxicity. Accelerated growth by NFs is brought about by their extensive regulation of cell division, photosynthesis, carbohydrate, and nitrogen metabolism, as well as the phytohormone-dependent signaling pathways related to development, stress response, and plant defense. NFs mimic Ca,2+ eliciting second messengers and associated proteins in signaling cascades, reaching transcription factors and finally orchestrating gene expression to enhance growth and stress tolerance. Developing advanced nano fertilizers of the future must involve exploring molecular interactions with plants to reduce toxicity and improve effectiveness.

The combination of nanotechnology and hydroponics paves the way toward sustainable agriculture with less environmental footprints. We investigated the effects of a liquid nano urea formulation (NUF) marketed by Indian Farmers Fertilizer Cooperative (IFFCO) on the model plant Arabidopsis thaliana in hydroponics, comparing it to an equimolar bulk urea. Dynamic light scattering and transmission electron microscopy confirmed NUF’s negative surface charge and sub-100-nm size, suitable for its uptake and distribution in the plant. A two-week growth in a nitrogen-free hydroponic medium with 70 μM NUF led to a 20% higher biomass and 16% higher chlorophyll content than a medium with 70 μM urea. Higher doses of NUF inhibited growth, whereas higher equivalent urea doses did not. Transcriptome analysis revealed that NUF led to the differential expression of more genes than urea at 12 h to seven days of treatment. Nitrogen assimilation, growth, photosynthesis, and stress tolerance genes showed higher transcript levels in NUF than in urea. On the other hand, NUF led to greater suppression of many negative growth-regulating genes. After seven days of treatment, chlorophyll biosynthesis genes were up-regulated, while chlorophyll catabolism genes down-regulated at higher levels by NUF than by urea, correlating with the higher chlorophyll content of NUF-treated seedlings. In conclusion, NUF outperformed equimolar urea for the growth promotion of A. thaliana at a low concentration in hydroponics, leading to a greater regulation of genes for nitrogen metabolism and chlorophyll biosynthesis. Our results suggest a potential use of NUF as a nitrogen fertilizer for hydroponic agriculture.