Browsing by Author "Pandey, Ashutosh"

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Attenuation of inorganic arsenic exposure-induced cognitive impairments by polyphenols-rich fraction of wild Rubus ellipticus berries via reshaping gut microbiota and reduction of oxidative stress-lead neuro-intestinal inflammation
(Elsevier B.V., 2026) Vandana; Gupta, Shweta; Sharma, Rajni; Pandey, Ashutosh; Bishnoi, Mahendra; Rawal, Rakesh; Singh, Dhirendra Pratap; Das, Santasabuj
The neurotoxic effects of inorganic arsenic exposure and consequential neurobehavioral outcomes involve activation of inflammatory cascades and reactive oxygen species (ROS)-mediated neuronal damage. Functional foods with characterized bioactive(s) are gaining attention in environmental contaminants-exposure induced pathologies. Here, we investigated the use of an ultrasonication-assisted extraction (UAE) and response surface methodology (RSM)-optimized process for polyphenols-rich extract from a Himalayan berry, Rubus ellipticus, against inorganic arsenic [iAs(III)]-induced cognitive impairments in mice. Total phenolic content (TPC), in-vitro antioxidant activity and cytotoxicities, along with UHPLC and LC-MS based polyphenolic profiles were determined. iAs(III)-exposure-induced spatial navigation tasks and passive avoidance-based learning performances were assessed. Neurochemical estimations, oxido-nitrosative stress markers, histological analysis and qRT-PCR-based gene expression in brain, ileum and, colon, pro-inflammatory cytokines and LPS levels, gut permeability, short chain fatty acids (SCFAs) levels, along with nanopore-based 16s rRNA metagenomics were performed. RSM-optimized UAE methods showed high TPC and antioxidant activities in polyphenol-rich (flavanols, phenolic acids and, proanthocyanidins) extract from R. ellipticus. The extract showed no potential cytotoxicity and significantly prevented iAs(III)-exposure-induced cognitive impairment, especially long-term spatial learning and memory. It also prevented altered neurotransmitter turnover, neuro-/ ileal/ colonic inflammation, and ROS-induced damages, increased ileum permeability, reduced SCFA level, and gut perturbations caused by iAs(III)-exposure. These findings suggest that the polyphenol-rich extract from Rubus ellipticus may offer protection against environmental toxicant [iAs(III)]-induced neurotoxicity and behavioral effects, potentially through combined modulation of oxidative stress, neuroinflammation, and gut-related pathways.
Biochemical analysis of anthocyanin and proanthocyanidin and their regulation in determining chickpea flower and seed coat colours
(Oxford University Press, 2023) Pal, Lalita; Dwivedi, Vikas; Gupta, Santosh Kumar; Saxena, Samiksha; Pandey, Ashutosh; Chattopadhyay, Debasis
Flower and seed coat colour are important agronomic traits in chickpea (Cicer arietinum L.). Cultivated chickpeas are of two types namely, desi (dark seeded, purple flower) and kabuli (light colour seeded, white flower). There has been limited information about the molecular mechanism underlying the colour variation of flower and seed coats in desi and kabuli chickpea. We profiled the anthocyanin and proanthocyanidin (PA) contents in chickpea flowers and seed coats. Tissue-specific silencing of two genes encoding a basic helix-loop-helix (CabHLH) protein and a tonoplast-localized multidrug and toxic compound extrusion (CaMATE1) transporter in a desi genotype resulted in the reduction in expressions of anthocyanin and PA biosynthetic genes and anthocyanin and PA contents in the flower and seed coat and produced flowers and seeds with kabuli characteristics. Transcriptional regulation of a subset of anthocyanin and PA biosynthetic genes by a natural CabHLH variant and transport assay of a natural CaMATE1 variant explained the association of these alleles with the kabuli phenotype. We carried out a detailed molecular characterization of these genes, and provided evidences that kabuli chickpea flower and seed colour phenotype can be derived by manipulation of single genes in a desi chickpea background.
Bioefficacy of Sida cordifolia L. phytoextract against foodborne bacteria: optimization and bioactive compound analysis
(Future Medicine Ltd, 2023) Kumar, Sachin; Kumar, Sandeep; Mir, M Amin; Vishnoi, Vineet Kumar; Pandey, Ashutosh; Pandey, Akanksha
Aim: To elucidate the antibacterial activity of Sida cordifolia L. phytoextract, evaluate its polyphenol profile and optimize conditions against certain common foodborne bacteria. Methods: After polarity-based sequential extraction, S. cordifolia phytoextracts were tested for antibacterial potential against antibiotic-resistant bacteria. Box-Behnken design was used to optimize several process parameters and ultra-performance liquid chromatography confirmed the phenolic composition of the best possible outcome. Results: Agar well diffusion and MIC/MBC assay confirmed a strong bactericidal effect of ethanolic (SC04-ET) extract against ampicillin and colistin-resistant Escherichia coli, Listeria monocytogenes and Staphylococcus aureus. The direct interactive effect of optimized conditions showed maximum antibacterial performance and ultra-performance liquid chromatography revealed a high amount of phenolic compounds. Conclusion: The results confirmed that ethanolic extract of S. cordifolia has potent bactericidal action against foodborne bacteria.
Bread wheat with enhanced grain carotenoid content: a novel option for wheat biofortification
(Springer Nature Publishing AG, 2022) Padhy, Asish Kumar; Sharma, Achla; Sharma, Himanshu; Rajput, Ruchika; Pandey, Ashutosh; Srivastava, Puja; Kaur, Satinder; Kaur, Harinderjit; Singh, Satinder; Kashyap, Lenika; Mavi, Gurvinder Singh; Kaur, Jaspal; Sohu, Virinder Singh; Chhuneja, Parveen; Bains, Navtej Singh
Colored wheat has piqued the interest of breeders and consumers alike. The chromosomal segment from 7E of Thinopyrum ponticum, which carries a leaf rust resistant gene, Lr19, has been rarely employed in wheat breeding operations due to its association with the Y gene, which gives a yellow tint to the flour. By prioritizing nutritional content over color preferences, consumer acceptance has undergone a paradigm change. Through marker-assisted backcross breeding, we introduced an alien segment harboring the Y (PsyE1) gene into a high yielding commercial bread wheat (HD 2967) background to generate rust resistant carotenoid biofortified bread wheat. Agro-morphological characterization was also performed on a subset of developed 70 lines having enhanced grain carotene content. In the introgression lines, carotenoid profiling using HPLC analysis demonstrated a considerable increase in β-carotene levels (up to 12 ppm). Thus, the developed germplasm caters the threat to nutritional security and can be utilized to produce carotenoid fortified wheat.
Broadening the epigenetic horizon of abiotic stress response in plants
(Springer Nature Publishing AG, 2024) Chhatwal, Himani; Naik, Jogindra; Pandey, Ashutosh; Trivedi, Prabodh Kumar
Plants, unlike animals, cannot move from one place to another and have to face different climatic disturbances wherever they are growing. So, they have innumerable built-in mechanisms to adapt to various abiotic stressful conditions like drought, heat, cold, and salinity. The changing environmental conditions influence the expression patterns of genes. Epigenetics involves heritable changes in DNA bases or histone proteins, which ultimately create different conformational states of chromatin. The regulatory enzymes of epigenetic modifications are grouped as writers, readers and erasers, which add, recognize and remove the epigenetic marks, respectively. Here, we provide a comprehensive overview of the mechanism of DNA methylation by the RdDM pathway, its maintenance and removal, and different histone modification categories like acetylation, methylation, phosphorylation and ubiquitination. This review further discusses in detail the crucial role these modifications play in adapting to major abiotic stresses and how plants preserve these experiences as stress memory to respond to recurring stresses. It emphasizes the role of epigenetic modifications as a crucial mechanism for building plant’s tolerance and how it can be an important research priority to improve plant growth and development under abiotic stress conditions.
CaLAP1 and CaLAP2 orchestrate anthocyanin biosynthesis in the seed coat of Cicer arietinum
(Springer Nature Publishing AG, 2024) Singh, Samar; Pal, Lalita; Rajput, Ruchika; Chhatwal, Himani; Singh, Nidhi; Chattopadhyay, Debasis; Pandey, Ashutosh
The seed coat color is a major economic trait in leguminous crop chickpea (Cicer arietinum). Anthocyanins and proanthocyanidins (PAs) are two classes of flavonoids that mainly contribute to the flower, seed coat and color of Desi chickpea cultivars. Throughout the land plant lineage, the accumulation of anthocyanins and PAs is regulated by MYB and bHLH transcription factors (TFs), which form an MBW (MYB, bHLH, and WD40) complex. Here, we report two R2R3-MYB TFs in chickpea belonging to the anthocyanin-specific subgroup-6, CaLAP1 (Legume Anthocyanin Production 1), and CaLAP2 (Legume Anthocyanin Production 2), which are mainly expressed in the flowers and developmental stages of the seeds. CaLAP1 and CaLAP2 interact with TT8-like CabHLH1 and WD40, forming the MBW complex, and bind to the promoter sequences of anthocyanin- and PA biosynthetic genes CaCHS6, CaDFR2, CaANS, and CaANR, leading to anthocyanins and PA accumulation in the seed coat of chickpea. Moreover, these CaLAPs partially complement the anthocyanin-deficient phenotype in the Arabidopsis thaliana sextuple mutant seedlings. Overexpression of CaLAPs in chickpea resulted in significantly higher expression of anthocyanin and PA biosynthetic genes leading to a darker seed coat color with higher accumulation of anthocyanin and PA. Our findings show that CaLAPs positively modulate anthocyanin and PA content in seed coats, which might influence plant development and resistance to various biotic and abiotic stresses.
Chlorpyrifos degradation by Zhihengliuella sp. ISTPL4: An esterase-driven actinobacterial platform for organophosphorus bioremediation
(Elsevier B.V., 2026) Aggarwal, Himanshi; Chaudhary, Divya; Kumari, Taruna; Pradhan, Nischal; Mishra, Vaibhav; Kumar, Antresh; Singh, Anamika; Pandey, Ashutosh; Chaturvedi, Navaneet; Dufossé, Laurent; Mishra, Arti; Joshi, Naveen Chandra
Organophosphorus pesticides (OPs) are widely used agrochemicals that pose serious risks to the environmental and human health due to their persistence and toxicity. This study reports, for the first time, chlorpyrifos (CPF) degradation by actinobacterium Zhihengliuella sp. ISTPL4. Strain ISTPL4 utilized various OPs, including dimethoate, monocrotophos, CPF, and malathion, with the highest growth observed in the presence of CPF as the sole carbon and energy source. Optimal growth and degradation occurred at 28 °C, pH 5, and 3% inoculum in minimal salt medium (MSM). Under optimized conditions, strain ISTPL4 degraded 76.95% of 600 mg L-1 CPF within 7 days. GC-MS analysis identified benzene, 1,3-bis(1,1-dimethylethyl) and phenol, 2,4-bis(1,1-dimethylethyl) as intermediates without the formation of toxic metabolite 3,5,6-trichloro-2-pyridinol (TCP). Whole genome analysis revealed five putative esterase genes potentially associated with CPF degradation. Molecular docking identified carboxylesterase B as the most favorable CPF-binding enzyme, while molecular dynamics simulations supported the stability of the enzyme-substrate complex. A putative metabolic pathway for CPF degradation by strain ISTPL4 was proposed. These findings highlight the potential of Zhihengliuella sp. ISTPL4 as a promising candidate for sustainable bioremediation of OP-contaminated environments.
Climate change impact on human health
(CABI, 2024) Singh, Samar; Chhatwal, Himani; Pandey, Ashutosh
Variations in environmental conditions caused by natural or anthropogenic activities have been exhibiting their impacts on climate change in the form of heat waves, drought, acid rain, floods, and storms throughout the decades. The resulting climate change has perturbated the interrelated threats to the ecosystem. Climate change affects human health, causing mental illness, undernutrition, and cardiovascular, respiratory, and infectious diseases. This outcome is observed in terms of worldwide disturbance in social dynamics such as health status, socioeconomic status, and public health infrastructure. This chapter explores the adverse climate conditions and highlights footprints on human health. Strategies to reduce the catastrophic impact of climate change on humans have been discussed in the latter sections.
Comparative assessment of flavonoid content in banana pulp and peel and their role in mitigating bone loss conditions and promoting osteoblast differentiation
(Royal Society of Chemistry, 2025) Sinha, Shradha; Sardar, Anirban; Rai, Divya; Tripathi, Ashish Kumar; Kothari, Priyanka; Rajput, Ruchika; Pandey, Ashutosh; Trivedi, Ritu
Banana fruit is widely grown and serves as a source of income across the tropics. It is known for its nutritional qualities and well-recognized medicinal applications. Given that banana pulp and peel are rich in flavonoids, such as naringenin, kaempferol, and quercetin, which are already known for their role in bone health, we hypothesize that banana pulp and peel can accelerate fracture healing, mitigate bone loss in post-menopausal conditions, and promote osteoblast differentiation. The current study was proposed to assess a comparative and parallel investigation of the differential flavonoid expression in banana pulp and peel and their concomitant bone anabolic effects. The pulp extract exhibited its osteogenic potential when administered orally for 2 weeks at doses of 250, 500 and 750 mg per kg per day in the osteotomy Balb/c mice model (n = 10), while the peel extract showed similar effects at comparatively much lower doses of 50, 100 and 250 mg per kg per day for the same duration. The effective lower doses in both cases, i.e., 250 mg per kg per day for the pulp and 50 mg per kg per day for the peel, were used to further investigate the anti-osteoporotic potential in vivo over a span of 8 weeks (n = 10). Banana pulp ameliorated the microarchitectural deterioration of the bones by increasing the rate of bone formation while simultaneously limiting exaggerated resorption, as assessed by micro-CT, calcein labelling, TRAP staining, bone strength parameters and measurement of bone formation and resorption markers in serum. Similar results were obtained with the banana peel extract at considerably lower doses. The osteogenic potential of the pulp and peel extracts was also tested in an in vitro setup. Osteoblast viability and differentiation, as assessed by MTT, ALP, mineralization and RT-PCR, demonstrated that bone formation potential was observed at 2.5 μg ml−1 and 5 μg ml−1 of the pulp extract, whereas in the case of the peel extract, it was observed at 0.625 μg ml−1 and 1.25 μg ml−1. These findings indicate that banana peel can exert similar osteogenic and osteoprotective effects as the pulp but at a much lower dose. This highlights banana peel as a prospective, sustainable feedstock for the healthcare sector, providing an alternative to its disposal.
Comparative genomic analysis of GARP transcription factor family in legumes and identification of stress-responsive candidate genes
(Springer Nature Publishing AG, 2023) Singh, Ritu; Pandey, Ashutosh; Verma, Praveen K.
The GARP transcription factors have been identified for multiple biological functions throughout the life cycle of a plant. Despite of its involvement in crucial functions, systematic study of GARPs remains obscure in plants. In this study, we explored the genomic, molecular, and evolutionary perspectives of the GARP gene family in the three major leguminous plants, namely chickpea (Cicer arietinum), soybean (Glycine max), and barrel clover (Medicago truncatula). Here, we identified 53, 56, and 107 GARP genes in Cicer, Medicago, and Glycine, respectively. They were classified into four clades and two sub-clades as per phylogenetic analysis, and the result was supported by consensus motifs, domain organization, and exon–intron structures. Detailed comparative analysis indicates conservation of the GARP gene family in plants. Identification of paralogous and orthologous gene pairs revealed that the expansion of this family occurs mainly through genome duplication in legumes. Additionally, the three-dimensional structure and functional enrichment analysis indicated their major role in signaling, growth, development, and stress processes. The chickpea GARP genes were also characterized for their transcript modulation in diverse plant organs and during pathogenic stress. Differential regulation of 24 CaGARP genes was observed during Ascochyta Blight (AB) stress. Characterization of AB-responsive genes reveals an over-representation of stress and hormone-binding elements on the promoter of CaGARPs. Additionally, interactome analysis also confirms the role of GARPs in plant stress and development. Our findings not only provide a handful of stress-responsive genes but also lay the foundation for prospective functional studies of GARPs in legumes.
Compendium of plant-specific CRISPR vectors and their technical advantages
(MDPI AG, 2021) Alok, Anshu; Chauhan, Hanny; Upadhyay, Santosh Kumar; Pandey, Ashutosh; Kumar, Jitendra; Singh, Kashmir
CRISPR/Cas mediated genome editing is a revolutionary approach for manipulating the plant genome. However, the success of this technology is highly dependent on selection of a specific vector and the other components. A plant-specific CRISPR/Cas vector usually consists of a Cas gene, target-specific gRNA, leader sequence, selectable marker gene, precise promoters, and other accessories. It has always been challenging to select the specific vector for each study due to a lack of comprehensive information on CRISPR vectors in one place. Herein, we have discussed every technical aspect of various important elements that will be highly useful in vector selection and efficient editing of the desired plant genome. Various factors such as the promoter regulating the expression of Cas and gRNA, gRNA size, Cas variants, multicistronic gRNA, and vector backbone, etc. influence transformation and editing frequency. For example, the use of polycistronic tRNA-gRNA, and Csy4-gRNA has been documented to enhance the editing efficiency. Similarly, the selection of an efficient selectable marker is also a very important factor. Information on the availability of numerous variants of Cas endonucleases, such as Cas9, Cas12a, Cas12b, Casɸ, and CasMINI, etc., with diverse recognition specificities further broadens the scope of editing. The development of chimeric proteins such as Cas fused to cytosine or adenosine deaminase domain and modified reverse transcriptase using protein engineering enabled base and prime editing, respectively. In addition, the newly discovered Casɸ and CasMINI would increase the scope of genetic engineering in plants by being smaller Cas variants. All advancements would contribute to the development of various tools required for gene editing, targeted gene insertion, transcriptional activation/suppression, multiplexing, prime editing, base editing, and gene tagging. This review will serve as an encyclopedia for plant-specific CRISPR vectors and will be useful for researchers.
COP1 mediates light-dependent regulation of flavonol biosynthesis through HY5 in Arabidopsis
(Elsevier B.V., 2021) Bhatia, Chitra; Gaddam, Subhash Reddy; Pandey, Ashutosh; Trivedi, Prabodh Kumar
Flavonols, a class of flavonoids, accumulate as protective agents in response to various stresses. Among various environmental stimuli, light is one of the factors regulating flavonol production. MYB12/11/111, members of the R2R3 MYBs family, regulates spatio-temporal flavonol accumulation in Arabidopsis. Although various studies indicate at the involvement of an E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and ELONGATED HYPOCOTYL 5 (HY5) in flavonoid biosynthesis in response to UV-B, the regulatory roles of these components under visible light are yet to be investigated. Here, we demonstrate that flavonol accumulation in Arabidopsis is light-regulated. Furthermore, our analysis suggests that MYB12 is a HY5-dependent light-inducible gene and plays a key role in the activation of the flavonol biosynthesis in response to light. Our results indicate the involvement of COP1 in the dark-dependent repression of MYB12 expression and flavonol accumulation. In addition, results also suggest that the effect of COP1 on MYB12 is indirect and is mediated through HY5, a direct transcriptional activator of the MYB12. Together these findings indicate that COP1 acts as a master negative regulator of flavonol biosynthesis in the dark.
CRISPR/Cas9 directed editing of lycopene epsilon-cyclase modulates metabolic flux for β-carotene biosynthesis in banana fruit
(Elsevier B.V., 2020) Kaur, Navneet; Alok, Anshu; Shivani; Kumar, Pankaj; Kaur, Navjot; Awasthi, Praveen; Chaturvedi, Siddhant; Pandey, Pankaj; Pandey, Ashutosh; Pandey, Ajay K.; Tiwari, Siddharth
Banana is one of the most economically important fruit crops worldwide. Genetic improvement in banana is a challenging task due to its parthenocarpic nature and triploid genome. Genetic modification of crops via the CRISPR/Cas9 module has emerged as a promising tool to develop important traits. In the present work, a CRISPR/Cas9-based approach was used to develop the β-carotene-enriched Cavendish banana cultivar (cv.) Grand Naine (AAA genome). The fifth exon of the lycopene epsilon-cyclase (LCYε) gene was targeted. The targeting specificity of the designed guide-RNA was also tested by its ability to create indels in the LCYε gene at the A genome of cv. Rasthali (AAB genome). Sequence analysis revealed multiple types of indels in the genomic region of Grand Naine LCYε (GN-LCYε). Metabolic profiling of the fruit pulp of selected edited lines showed enhanced accumulation of β-carotene content up to 6-fold (~24 μg/g) compared with the unedited plants. These lines also showed either an absence or a drastic reduction in the levels of lutein and α-carotene, suggesting metabolic reprogramming, without any significant effect on the agro-morphological parameters. In addition, differential expression of carotenoid pathway genes was observed in the edited lines in comparison to unedited plants. Overall, this is the first report in banana to improve nutritional trait by using a precise genome editing approach.
CRISPR/Cas9 edited StbHLH47 lines exhibit altered expression profiling of iron regulating genes and increased iron content in Solanum tuberosum
(Elsevier B.V., 2024) Chauhan, Hanny; Alok, Anshu; Aiana; Upadhyay, Santosh K.; Pandey, Ashutosh; Singh, Kashmir
Iron is an essential plant nutrient, and a continuous supply of it is required as it is a key factor in various metabolic processes, including photosynthesis, chlorophyll synthesis, and respiration. Various transcription factors are known to regulate iron homeostasis in plants, and the bHLH transcription factor family is one of them. The StbHLH47 is a homologue of the Arabidopsis POPEYE (PYE), which is known to repress iron homeostasis-related genes in Arabidopsis. Potato is the most consumed vegetable in the world and is low in iron content. We have generated CRISPR/Cas9-edited StbHLH47 lines and performed a detailed analysis of these lines. The analysis revealed that the roots of StbHLH47 edited lines have decreased ferric chelate reductase (FCR) activity compared to the roots of the wild-type (WT) plant. We also observed that CRISPR/Cas9 edited lines have fewer trichomes when compared to the WT plant. The expression of genes associated with iron homeostasis was also measured. Compared to the control, the expression of StbHLH47 was downregulated in the edited lines, while the expression of StNAS4, StOPT3, and StFRO3 was upregulated. This suggests the negative regulation of StbHLH47 in modulating iron. The iron content was also quantified using inductively coupled plasma mass spectrometry (ICP-MS) and found to be increased in the generated transgenic lines when compared to WT plants. Overall, this study reveals that StbHLH47 negatively regulates the expression of iron homeostasis-related genes. StbHLH47 edited lines exhibited decreased FCR activity, changes in phenotype, and increased iron content in the potato plants.
CRISPR/dCas9-KRAB mediated transcriptional suppression of NtbHLH47 enhances tolerance to iron stress and modulates iron content in tobacco
(Elsevier B.V., 2025) Alok, Anshu; Chauhan, Hanny; Rout, Biswaranjan; Pandey, Ashutosh; Singh, Kashmir
Iron homeostasis is a multifaceted regulatory process that needs to be studied to elucidate iron distribution, uptake, and storage in plants. NtbHLH47, a homologue to AtbHLH47, is a negative regulator of iron. The current study deploys CRISPR interference-dCas9-KRAB (Krüppel-associated box) in the transcriptional suppression of NtbHLH47 and its effect on iron uptake by plants. The pHSN6I01 harbouring dCas9-KRAB and gRNA targeting NtbHHLH47 was constructed. Four gRNAs were designed, G1, G2, G3, and G4, located at + 19, + 111, + 232, and + 335 bp upstream from the ATG start codon in the promoter region of NtbHLH47. The NtbHLH47 was repressed in the developed transgenic lines of tobacco and the qRT-PCR analysis showed that target sites G1 and G2 suppressed NtbHLH47 effectively. The transgenic pHSN6I01 +G1 plants were tolerant to the elevated levels of iron, copper, zinc, and magnesium. The root Ferric chelate reductase activity of pHSN6I01 +G1 lines was reduced against wild type. The Perl staining showed high iron content in the roots of the pHSN6I01 +G1 plants. ICP-MS analysis showed increased Fe content in the roots of pHSN6I01 +G1 line suggesting that NtbHLH47 modulates it. The expression of NtbHLH38, NtbHLH100, NtbHLH101, and NtFIT was found to be upregulated in the pHSN6I01 +G1 line. This is the first report of using CRISPRi based on dCas9-KRAB in tobacco and its application in the functional validation of a gene. Using this, NtbHLH47 was transcriptionally suppressed and the generated lines expressed increased levels of iron in the roots of N. tabacum and gave insight in the iron homeostasis.
Cytokinin-mediated repression of anthocyanin biosynthesis in banana fruits
(John Wiley & Sons, 2025) Rajput, Ruchika; Tyagi, Shivi; Anchal, Kumar; Singh, Samar; Laxmi, Ashverya; Misra, Prashant; Pandey, Ashutosh
Anthocyanins are pigments responsible for vibrant plant colors and play vital roles in plant physiology. This study compares two banana cultivars, Grand Naine (GN) and Red Banana (RB), which exhibit significant differences in anthocyanin pigmentation. Transcriptomic profiling of peel (PL) and pulp (PP) tissues revealed cytokinin-responsive type-B response regulators (RRs), MaRR_B9 and MaRR_B12, as key modulators of anthocyanin biosynthesis. Cytokinin treatment of PP tissues increased the expression of MaRR_B9 and MaRR_B12, while significantly reducing the expression of dihydroflavanol reductase (MaDFR1, MaDFR2) and anthocyanidin synthase (MaANS) genes along with anthocyanin content. Through a combination of physiological, molecular, and biochemical analyses, we demonstrate that MaRR_B9 and MaRR_B12 exert direct regulatory control over key structural genes of anthocyanin biosynthesis, MaDFRs and MaANS. Additionally, a type B-RRs motif (AGATT) was identified in the promoter regions of MaDFR2 and MaANS, suggesting that MaRRs might directly regulate the transcription of MaDFR2 and MaANS. MaRR_B9 and MaRR_B12 interact with the promoters of MaDFR2 and MaANS, repressing these genes in vivo. Overexpression of MaRR_B9 and MaRR_B12 in banana fruits leads to a reduction in anthocyanin content, notably the cyanidin derivative, accompanied by altered expression patterns of MaDFRs and MaANS. Thus, the present study identifies MaRR_B9 and MaRR_B12 as novel regulators of anthocyanin biosynthesis in banana and provides further evidence that the cytokinin regulatory network modifies anthocyanin accumulation in plants. In conclusion, our findings reveal new molecular targets, in the form of MaRRs, for the genetic optimization aimed at enhancing anthocyanin content, stress resilience, and nutritional value in crop plants.
Deciphering the complexity of terpenoid biosynthesis and its multi-level regulatory mechanism in plants
(Springer Nature Publishing AG, 2024) Singh, Samar; Chhatwal, Himani; Pandey, Ashutosh
Terpenoids are one of the essential plant metabolites which are known to play vital roles in plants' primary growth and development including protection from biotic and abiotic stresses. They have huge structural diversity and are known to provide various health benefits, flavors, fragrances, essential oils, cosmetics, pigments, insecticides, etc. The biosynthesis of terpenoids by mevalonic acid (MVA) and methylerythritol pathway (MEP) occurs inside the cytoplasm and the chloroplast, respectively. Here, we provide a comprehensive overview of synthesis, metabolic, and regulatory pathways of terpenoid, their different classes and ecological roles. We also discuss in detail the key transcription factors (TFs) like WRKY, AP2/ERF, bHLH, MYB, NAC, and bZIP which reprogram and modulate the terpenoid pathway in plants. It also includes the post-transcriptional and post-translational modifications of these pathways. The post-transcriptional regulation by microRNA plays a critical role in the synthesis and regulation of the terpenoid. MAP kinases also regulate the stability of biosynthetic enzymes and transcription factors to regulate terpenoid biosynthesis. High-throughput sequencing technology and functional genomics have further strengthened our understanding of this pathway and associated regulatory genes which control it. As a future perspective, modifying these transcription factors via various strategies holds promise for improvement of agricultural crop plants in terms of nutritional enrichment, stress responsiveness, and resistance.
Differential response of rice genotypes to nitrogen availability is associated with the altered nitrogen metabolism and ionomic balance
(Elsevier B.V., 2022) Kumari, Priyanka; Devi, Loitongbam Lorinda; Kumar, Amresh; Pandey, Ashutosh; Sinha, Subodh Kumar; Singh, Amar Pal
Nitrogen (N) uptake and its assimilation are crucial steps for plant growth and productivity. Plant's N balance largely depends on nitrate (NO3-) and ammonium (NH4+) forms present in the rhizosphere. Due to the fluctuating and heterogeneous availability of these N forms in the soils, plants encounter low to N deficiency. In contrast to low nitrogen, high N in the form of ammonium (NH4+) severely hampers plant development and causes NH4+ toxicity. In this study, we assessed eleven rice genotypes under sufficient (SN) and low N (LN) conditions. From the analysis, we identified a rice genotype, PB1, which is hypersensitive to SN and showed reduced root and shoot growth. In contrast to the SN condition, PB1 showed improved growth performance under the LN condition. Our data show that compromised growth of PB1 under SN condition is associated with increased activity of N responsive genes such as OsAMT1.1, OsAMT2.3, OsAMT3.1 and OsAMT3.2, OsNRT1.1A and OsNRT1.1B. Strikingly, LN treatment improved the root and shoot biomass with a concomitant increase in levels of NO3- and NH4+ transporter genes along with an increase in shoot: root NO3- ratio. Additionally, we show that increased levels of N in PB1 under SN condition are associated with the enhanced activity of the GS-GOGAT pathway. Further, our ionomic analysis highlighted the role of N-defined Fe accumulation which is partially associated with the N toxicity. Taken together, our study led to identifying a rice genotype (Oryza sativa L.) which is associated with enhanced N levels and assimilation and could be used for raising N use efficient rice varieties using breeding approaches.
Emerging tools and paradigm shift of gene editing in cereals, fruits, and horticultural crops for enhancing nutritional value and food security
(John Wiley & Sons, 2021) Tiwari, Manish; Trivedi, Prabodh Kumar; Pandey, Ashutosh
Gene editing using sequence‐specific nucleases, particularly CRISPR/Cas ribonucleoprotein, has drawn enormous attention in plant research in recent years. Nearly a decade ago, Cas9 protein was initially discovered for a role in adaptive immunity in bacteria. Owing to vast potential, a large number of reports came out in a short span of time, comprising the identification of Cas protein from different bacterial sources, new Cas9 variants with reduced off‐targets, multiplexing, base editing, prime editing, and RNA manipulation in plants. Studies revealed that CRISPR/Cas‐based gene editing can play a major role in ensuring food security via developing resilient commercial crops with improved yield and nutritional value. Use of the CRISPR/Cas9 system for creating mutation in genes and regulatory regions of promoter generated a number of alleles with variable phenotypes, which can serve as an excellent genetic resource in the breeding program. In this review, we provide a recent overview of state‐of‐art discoveries in the CRISPR/Cas system comprised of new Cas proteins, modifications of existing Cas9, refinements in CRISPR/Cas‐induced gene editing, applications, and outcome emphasizing on major cereals and horticultural crops. We also highlight the current global policy framework for the regulation of gene‐edited crops.
Endophytic Burkholderia: Multifunctional roles in plant growth promotion and stress tolerance
(Elsevier B.V., 2022) Pal, Gaurav; Saxena, Samiksha; Kumar, Kanchan; Verma, Anand; Sahu, Pramod K.; Pandey, Ashutosh; White, James F.; Verma, Satish K.
The genus Burkholderia has proven potential in improving plant performance. In recent decades, a huge diversity of Burkholderia spp. have been reported with diverse capabilities of plant symbiosis which could be harnessed to enhance plant growth and development. Colonization of endophytic Burkholderia spp. have been extensively studied through techniques like advanced microscopy, fluorescent labelling, PCR based assays, etc., and found to be systemically distributed in plants. Thus, use of these biostimulant microbes holds the promise of improving quality and quantity of crops. The endophytic Burkholderia spp. have been found to support plant functions along with boosting nutrient availability, especially under stress. Endophytic Burkholderia spp. improve plant survival against deadly pathogens via mechanisms like competition, induced systemic resistance, and antibiosis. At the same time, they are reported to extend plant tolerance towards multiple abiotic stresses especially drought, salinity, and cold. Several attempts have been made to decipher the potential of Burkholderia spp. by genome mining, and these bacteria have been found to harbour genes for plant symbiosis and for providing multiple benefits to host plants. Characteristics specific for host recognition and nutrient acquisition were confirmed in endophytic Burkholderia by genomics and proteomics-based studies. This could pave the way for harnessing Burkholderia spp. for biotechnological applications like biotransformation, phytoremediation, insecticidal activity, antimicrobials, etc. All these make Burkholderia spp. a promising microbial agent in improving plant performance under multiple adversities. Thus, the present review highlights critical roles of endophytic Burkholderia spp., their colonization, alleviation of biotic and abiotic stresses, biotechnological applications and genomic insights.