Browsing by Author "Tiwari, Siddharth"

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Analysis of TCP Transcription Factors Revealed Potential Roles in Plant Growth and Fusarium oxysporum f.sp. cubense Resistance in Banana (cv. Rasthali)
(Springer, 2022-07-05T00:00:00) Chaturvedi, Siddhant; Khan, Shahirina; Usharani, T.R.; Tiwari, Siddharth
The TCP transcription factor gene family is highly conserved among the plant species. It plays a major role in the regulation of flower symmetry, cell division, and development of leaf, fibre, and nodule in the plants by controlling the synthesis of various plant hormones. Banana is a major staple crop in the world. However, Fusarium oxysporum f. sp. cubense (Foc) infection is a major threat to banana production. The role of TCP gene family during the Foc infection is not explored till now. Herein, a total of 27 non-redundant TCP (MaTCP) gene sequences were retrieved from the banana genome and analysed for structural characteristics, phylogenetic correlation, subcellular, and chromosomal localizations. Phylogenetic analysis showed that the MaTCP proteins were highly conserved among different species and found to be the closest relative of the Oryza sativa and Zea mays. Promoter analysis of the TCP sequences showed that the cis-acting regulatory elements are associated with various stresses and environmental and hormonal signals. The higher transcript accumulation in developing tissues (fruit finger, leaves, and stem) than of mature tissues (peel and pulp) showed a significant role of MaTCP in banana (cv. Rasthali) growth and development. Further, higher expression of the certain MaTCPs in Foc race 1-infected root (MaTCP2, MaTCP4, MaTCP6) and leaf (MaTCP9 and MaTCP11) tissues of Rasthali indicated their promising role during Fusarium infection. This study will underpin the facet of TCP transcription factors on the development of biotic (Foc) stress resistance in banana. � 2022, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Analysis of TCP Transcription Factors Revealed Potential Roles in Plant Growth and Fusarium oxysporum f.sp. cubense Resistance in Banana (cv. Rasthali)
(Springer, 2022-07-05T00:00:00) Chaturvedi, Siddhant; Khan, Shahirina; Usharani, T.R.; Tiwari, Siddharth
The TCP transcription factor gene family is highly conserved among the plant species. It plays a major role in the regulation of flower symmetry, cell division, and development of leaf, fibre, and nodule in the plants by controlling the synthesis of various plant hormones. Banana is a major staple crop in the world. However, Fusarium oxysporum f. sp. cubense (Foc) infection is a major threat to banana production. The role of TCP gene family during the Foc infection is not explored till now. Herein, a total of 27 non-redundant TCP (MaTCP) gene sequences were retrieved from the banana genome and analysed for structural characteristics, phylogenetic correlation, subcellular, and chromosomal localizations. Phylogenetic analysis showed that the MaTCP proteins were highly conserved among different species and found to be the closest relative of the Oryza sativa and Zea mays. Promoter analysis of the TCP sequences showed that the cis-acting regulatory elements are associated with various stresses and environmental and hormonal signals. The higher transcript accumulation in developing tissues (fruit finger, leaves, and stem) than of mature tissues (peel and pulp) showed a significant role of MaTCP in banana (cv. Rasthali) growth and development. Further, higher expression of the certain MaTCPs in Foc race 1-infected root (MaTCP2, MaTCP4, MaTCP6) and leaf (MaTCP9 and MaTCP11) tissues of Rasthali indicated their promising role during Fusarium infection. This study will underpin the facet of TCP transcription factors on the development of biotic (Foc) stress resistance in banana. � 2022, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Carotenoid cleavage dioxygenases (HD-CCD1A and B) contribute as strong negative regulators of ?-carotene in Indian bread wheat (cv. HD2967)
(Springer Science and Business Media Deutschland GmbH, 2021-04-16T00:00:00) Thakur, Nandita; Flowerika; Thakur, Neha; Khan, Shahirina; Pandey, Ajay K.; Tiwari, Siddharth
Wheat (Triticum aestivum L.) is the most common cereal crop that is considered to be deficient in provitamin A carotenoids. Carotenoids are prone to degrade into apocarotenoids by the activity of carotenoid cleavage dioxygenases (CCDs). Hence, in this study, multiple CCDs were cloned from commercial Indian wheat cultivar HD2967 to understand their role in provitamin A carotenoids degradation. The homoeolog specific expression of HD-CCD1 and HD-CCD4 at different grain filling stages revealed the higher expression of transcripts arising from the A and B subgenomes of HD-CCD1. Furthermore, the grain development stages showed a strong negative correlation of HD-CCD1A (r = ? 0.969) and B (r = ? 0.970) homoeologs expression to that of ?-carotene accumulation. It suggested that they could be potentially involved in deciding the turn-over of ?-carotene in wheat grain. Three-dimensional (3D) structures for all six homoeologs of HD-CCD1 and HD-CCD4 were predicted using maize VP14 template to gain better insight into their molecular mechanism. Ramachandran plot assessment revealed that ~ 90% of residues are in the most favoured region. Docking studies with various carotenoid substrates revealed the higher affinity of HD-CCD1A and B for ?-carotene and ?-cryptoxanthin. Bacterial complementation analysis validated the functional role of all six homoeologs with HD-CCD1B showing the highest activity followed by HD-CCD1A for ?-carotene degradation. Results of this study provide valuable insights into the characteristics of HD-CCDs in wheat and thereby justifying them (HD-CCD1A and B) as the candidate genes for employing genome editing tools for developing ?-carotene enriched wheat grains. � 2021, King Abdulaziz City for Science and Technology.
Carotenoid cleavage dioxygenases (HD-CCD1A and B) contribute as strong negative regulators of ?-carotene in Indian bread wheat (cv. HD2967)
(Springer Science and Business Media Deutschland GmbH, 2021-04-16T00:00:00) Thakur, Nandita; Flowerika; Thakur, Neha; Khan, Shahirina; Pandey, Ajay K.; Tiwari, Siddharth
Wheat (Triticum aestivum L.) is the most common cereal crop that is considered to be deficient in provitamin A carotenoids. Carotenoids are prone to degrade into apocarotenoids by the activity of carotenoid cleavage dioxygenases (CCDs). Hence, in this study, multiple CCDs were cloned from commercial Indian wheat cultivar HD2967 to understand their role in provitamin A carotenoids degradation. The homoeolog specific expression of HD-CCD1 and HD-CCD4 at different grain filling stages revealed the higher expression of transcripts arising from the A and B subgenomes of HD-CCD1. Furthermore, the grain development stages showed a strong negative correlation of HD-CCD1A (r = ? 0.969) and B (r = ? 0.970) homoeologs expression to that of ?-carotene accumulation. It suggested that they could be potentially involved in deciding the turn-over of ?-carotene in wheat grain. Three-dimensional (3D) structures for all six homoeologs of HD-CCD1 and HD-CCD4 were predicted using maize VP14 template to gain better insight into their molecular mechanism. Ramachandran plot assessment revealed that ~ 90% of residues are in the most favoured region. Docking studies with various carotenoid substrates revealed the higher affinity of HD-CCD1A and B for ?-carotene and ?-cryptoxanthin. Bacterial complementation analysis validated the functional role of all six homoeologs with HD-CCD1B showing the highest activity followed by HD-CCD1A for ?-carotene degradation. Results of this study provide valuable insights into the characteristics of HD-CCDs in wheat and thereby justifying them (HD-CCD1A and B) as the candidate genes for employing genome editing tools for developing ?-carotene enriched wheat grains. � 2021, King Abdulaziz City for Science and Technology.
Genome-wide identification and gene expression analysis of GHMP kinase gene family in banana cv. Rasthali
(Springer Science and Business Media B.V., 2023-09-20T00:00:00) Chaturvedi, Siddhant; Khan, Shahirina; Thakur, Neha; Jangra, Alka; Tiwari, Siddharth
Background: The GHMP kinase gene family encompasses ATP-dependent kinases, significantly involved in the biosynthesis of isoprenes, amino acids, and metabolism of carbohydrates. Banana is a staple tropical crop that is globally consumed but known for high sensitivity to salt, cold, and drought stresses. The GHMP kinases are known to play a significant role during abiotic stresses in plants. The present study emphasizes the role of GHMP kinases in various abiotic stress conditions in banana. Methods and results: We identified 12 GHMP kinase (MaGHMP kinase) genes in the banana genome database and witnessed the presence of the conserved Pro-X-X-X-Gly-Leu-X-Ser-Ser-Ala domain in their protein sequences. All genes were found to be involved in ATP-binding and carried kinase activity confronting their biological roles in the isoprene (27%) and amino acid (20%) biosyntheses. The expression analysis of genes during cold, drought, and salt stress conditions in tissue culture grown banana cultivar Rasthali plants showed a significant involvement of MaGHMP kinase genes in these stress conditions. The highest expression of MaGHMP kinase3 (8.5 fold) was noted during cold stress, while MaGHMP kinase1 (25 fold and 40.01 fold) showed maximum expression during drought and salt stress conditions in leaf tissue of Rasthali. Conclusion: Our findings suggested that MaGHMP kinase1 (MaHSK) and MaGHMP kinase3 (MaGlcAK) could be considered promising candidates for thwarting the abiotic stresses in banana. � 2023, The Author(s), under exclusive licence to Springer Nature B.V.
Genome-wide identification and gene expression analysis of GHMP kinase gene family in banana cv. Rasthali
(Springer Science and Business Media B.V., 2023-09-20T00:00:00) Chaturvedi, Siddhant; Khan, Shahirina; Thakur, Neha; Jangra, Alka; Tiwari, Siddharth
Background: The GHMP kinase gene family encompasses ATP-dependent kinases, significantly involved in the biosynthesis of isoprenes, amino acids, and metabolism of carbohydrates. Banana is a staple tropical crop that is globally consumed but known for high sensitivity to salt, cold, and drought stresses. The GHMP kinases are known to play a significant role during abiotic stresses in plants. The present study emphasizes the role of GHMP kinases in various abiotic stress conditions in banana. Methods and results: We identified 12 GHMP kinase (MaGHMP kinase) genes in the banana genome database and witnessed the presence of the conserved Pro-X-X-X-Gly-Leu-X-Ser-Ser-Ala domain in their protein sequences. All genes were found to be involved in ATP-binding and carried kinase activity confronting their biological roles in the isoprene (27%) and amino acid (20%) biosyntheses. The expression analysis of genes during cold, drought, and salt stress conditions in tissue culture grown banana cultivar Rasthali plants showed a significant involvement of MaGHMP kinase genes in these stress conditions. The highest expression of MaGHMP kinase3 (8.5 fold) was noted during cold stress, while MaGHMP kinase1 (25 fold and 40.01 fold) showed maximum expression during drought and salt stress conditions in leaf tissue of Rasthali. Conclusion: Our findings suggested that MaGHMP kinase1 (MaHSK) and MaGHMP kinase3 (MaGlcAK) could be considered promising candidates for thwarting the abiotic stresses in banana. � 2023, The Author(s), under exclusive licence to Springer Nature B.V.
Iron transport and homeostasis in plants: current updates and applications for improving human nutrition values and sustainable agriculture
(Springer Science and Business Media B.V., 2023-02-23T00:00:00) Khan, Shahirina; Kaur, Karambir; Kumar, Vinay; Tiwari, Siddharth
Agriculture and plant science face a formidable challenge in feeding the world�s expanding population in a sustainable, sufficient, and nutrient-rich manner. The mineral micronutrient composition of food crops merits special consideration. Globally, cultivated soil and plant micronutrient deficits have negative impacts on crop yield, plant nutritional value, human health and well-being. This article reviews the present knowledge on iron (Fe) uptake, transport, subcellular translocation, and its regulation at the molecular level mainly on Oryza sativa and Arabidopsis thaliana, which typically represent graminaceous and non-graminaceous plants, respectively. This study emphasizes the recent advancements in various approaches, including high-throughput technologies (NGS, proteomics, ionomics) and genetic engineering such as CRISPR/Cas for Fe biofortification in crop plants and their subsequent impact on human health. The aforementioned information can be applied to elevate the Fe content in model plants along with various fruit and vegetable crops. This might be helpful for nutritious food production for large human population in the world to achieve one of the most important Sustainable Development Goals (SDGs) for nutrition security. � 2023, The Author(s), under exclusive licence to Springer Nature B.V.
Iron transport and homeostasis in plants: current updates and applications for improving human nutrition values and sustainable agriculture
(Springer Science and Business Media B.V., 2023-02-23T00:00:00) Khan, Shahirina; Kaur, Karambir; Kumar, Vinay; Tiwari, Siddharth
Agriculture and plant science face a formidable challenge in feeding the world�s expanding population in a sustainable, sufficient, and nutrient-rich manner. The mineral micronutrient composition of food crops merits special consideration. Globally, cultivated soil and plant micronutrient deficits have negative impacts on crop yield, plant nutritional value, human health and well-being. This article reviews the present knowledge on iron (Fe) uptake, transport, subcellular translocation, and its regulation at the molecular level mainly on Oryza sativa and Arabidopsis thaliana, which typically represent graminaceous and non-graminaceous plants, respectively. This study emphasizes the recent advancements in various approaches, including high-throughput technologies (NGS, proteomics, ionomics) and genetic engineering such as CRISPR/Cas for Fe biofortification in crop plants and their subsequent impact on human health. The aforementioned information can be applied to elevate the Fe content in model plants along with various fruit and vegetable crops. This might be helpful for nutritious food production for large human population in the world to achieve one of the most important Sustainable Development Goals (SDGs) for nutrition security. � 2023, The Author(s), under exclusive licence to Springer Nature B.V.
Metabolic engineering in food crops to enhance ascorbic acid production: crop biofortification perspectives for human health
(Springer, 2022-04-19T00:00:00) Chaturvedi, Siddhant; Khan, Shahirina; Bhunia, Rupam Kumar; Kaur, Karambir; Tiwari, Siddharth
Ascorbic acid (AsA) also known as vitamin C is considered as an essential micronutrient in the diet of humans. The human body is unable to synthesize AsA, thus solely dependent on exogenous sources to accomplish the nutritional requirement. AsA plays a crucial role in different physiological aspects of human health like bone formation, iron absorption, maintenance and development of connective tissues, conversion of cholesterol to bile acid and production of serotonin. It carries antioxidant properties and is involved in curing various clinical disorders such as scurvy, viral infection, neurodegenerative diseases, cardiovascular diseases, anemia, and diabetes. It also plays a significant role in COVID-19 prevention and recovery by improving the oxygen index and enhancing the production of natural killer cells and T-lymphocytes. In plants, AsA plays important role in floral induction, seed germination, senescence, ROS regulation and photosynthesis. AsA is an essential counterpart of the antioxidant system and helps to defend the plants against abiotic and biotic stresses. Surprisingly, the deficiencies of AsA are spreading in both developed and developing countries. The amount of AsA in the major food crops such as wheat, rice, maize, and other raw natural plant foods is inadequate to fulfill its dietary requirements. Hence, the biofortification of AsA in staple crops would be feasible and cost-effective means of delivering AsA to populations that may have limited access to diverse diets and other interventions. In this review, we endeavor to provide information on the role of AsA in plants and human health, and also perused various biotechnological and agronomical approaches for elevating AsA content in food crops. � 2022, Prof. H.S. Srivastava Foundation for Science and Society.
Metabolic engineering in food crops to enhance ascorbic acid production: crop biofortification perspectives for human health
(Springer, 2022-04-19T00:00:00) Chaturvedi, Siddhant; Khan, Shahirina; Bhunia, Rupam Kumar; Kaur, Karambir; Tiwari, Siddharth
Ascorbic acid (AsA) also known as vitamin C is considered as an essential micronutrient in the diet of humans. The human body is unable to synthesize AsA, thus solely dependent on exogenous sources to accomplish the nutritional requirement. AsA plays a crucial role in different physiological aspects of human health like bone formation, iron absorption, maintenance and development of connective tissues, conversion of cholesterol to bile acid and production of serotonin. It carries antioxidant properties and is involved in curing various clinical disorders such as scurvy, viral infection, neurodegenerative diseases, cardiovascular diseases, anemia, and diabetes. It also plays a significant role in COVID-19 prevention and recovery by improving the oxygen index and enhancing the production of natural killer cells and T-lymphocytes. In plants, AsA plays important role in floral induction, seed germination, senescence, ROS regulation and photosynthesis. AsA is an essential counterpart of the antioxidant system and helps to defend the plants against abiotic and biotic stresses. Surprisingly, the deficiencies of AsA are spreading in both developed and developing countries. The amount of AsA in the major food crops such as wheat, rice, maize, and other raw natural plant foods is inadequate to fulfill its dietary requirements. Hence, the biofortification of AsA in staple crops would be feasible and cost-effective means of delivering AsA to populations that may have limited access to diverse diets and other interventions. In this review, we endeavor to provide information on the role of AsA in plants and human health, and also perused various biotechnological and agronomical approaches for elevating AsA content in food crops. � 2022, Prof. H.S. Srivastava Foundation for Science and Society.
Overexpression of banana GDP-L-galactose phosphorylase (GGP) modulates the biosynthesis of ascorbic acid in Arabidopsis thaliana
(Elsevier B.V., 2023-03-24T00:00:00) Chaturvedi, Siddhant; Thakur, Neha; Khan, Shahirina; Sardar, Mithilesh Kumar; Jangra, Alka; Tiwari, Siddharth
L-Ascorbic acid (AsA) is a potent antioxidant and essential micronutrient for the growth and development of plants and animals. AsA is predominantly synthesized by the Smirnoff-Wheeler (SW) pathway in plants where the GDP-L-galactose phosphorylase (GGP) gene encodes the rate-limiting step. In the present study, AsA was estimated in twelve banana cultivars, where Nendran carried the highest (17.2 mg/100 g) amount of AsA in ripe fruit pulp. Five GGP genes were identified from the banana genome database, and they were located at chromosome 6 (4 MaGGPs) and chromosome 10 (1 MaGGP). Based on in-silico analysis, three potential MaGGP genes were isolated from the cultivar Nendran and subsequently overexpressed in Arabidopsis thaliana. Significant enhancement in AsA (1.52 to 2.20 fold) level was noted in the leaves of all three MaGGPs overexpressing lines as compared to non-transformed control plants. Among all, MaGGP2 emerged as a potential candidate for AsA biofortification in plants. Further, the complementation assay of Arabidopsis thaliana vtc-5-1 and vtc-5-2 mutants with MaGGP genes overcome the AsA deficiency that showed improved plant growth as compared to non-transformed control plants. This study lends strong affirmation towards development of AsA biofortified plants, particularly the staples that sustain the personages in developing countries. � 2023 Elsevier B.V.
Overexpression of banana GDP-L-galactose phosphorylase (GGP) modulates the biosynthesis of ascorbic acid in Arabidopsis thaliana
(Elsevier B.V., 2023-03-24T00:00:00) Chaturvedi, Siddhant; Thakur, Neha; Khan, Shahirina; Sardar, Mithilesh Kumar; Jangra, Alka; Tiwari, Siddharth
L-Ascorbic acid (AsA) is a potent antioxidant and essential micronutrient for the growth and development of plants and animals. AsA is predominantly synthesized by the Smirnoff-Wheeler (SW) pathway in plants where the GDP-L-galactose phosphorylase (GGP) gene encodes the rate-limiting step. In the present study, AsA was estimated in twelve banana cultivars, where Nendran carried the highest (17.2 mg/100 g) amount of AsA in ripe fruit pulp. Five GGP genes were identified from the banana genome database, and they were located at chromosome 6 (4 MaGGPs) and chromosome 10 (1 MaGGP). Based on in-silico analysis, three potential MaGGP genes were isolated from the cultivar Nendran and subsequently overexpressed in Arabidopsis thaliana. Significant enhancement in AsA (1.52 to 2.20 fold) level was noted in the leaves of all three MaGGPs overexpressing lines as compared to non-transformed control plants. Among all, MaGGP2 emerged as a potential candidate for AsA biofortification in plants. Further, the complementation assay of Arabidopsis thaliana vtc-5-1 and vtc-5-2 mutants with MaGGP genes overcome the AsA deficiency that showed improved plant growth as compared to non-transformed control plants. This study lends strong affirmation towards development of AsA biofortified plants, particularly the staples that sustain the personages in developing countries. � 2023 Elsevier B.V.
Transgene-free genome editing supports the role of carotenoid cleavage dioxygenase 4 as a negative regulator of ?-carotene in banana
(Oxford University Press, 2022-02-01T00:00:00) Awasthi, Praveen; Khan, Shahirina; Lakhani, Hiralben; Chaturvedi, Siddhant; Shivani, S.; Kaur, Navneet; Singh, Jagdeep; Kesarwani, Atul Kumar; Tiwari, Siddharth
Carotenoid cleavage dioxygenases (CCDs) belong to a small gene family and have an important role in the intricate metabolism of carotenoids in plants. In this study we aimed to understand the regulatory mechanism of ?-carotene homeostasis by establishing transgene-free genome editing in banana. We found that the expression patterns of multiple CCDs were correlated with the concentrations of carotenoids in two cultivars with contrasting contents of ?-carotene, Nendran (high) and Rasthali (low). Higher expression of CCD4 in Rasthali (RAS-CCD4) was negatively correlated with ?-carotene accumulation in the fruit-pulp. Docking analysis and enzyme assays of purified RAS-CCD4 suggested that ?-carotene and 10-Apo-?-carotenal were the preferred substrates of RAS-CCD4. Bacterial complementation assays demonstrated the role of RAS-CCD4 in ?-carotene degradation, and this was further confirmed by in vivo overexpression of RAS-CCD4 in Arabidopsis, which resulted in significant reduction in ?-carotene concentration. CRISPR/Cas9-mediated editing of CCD4 was conducted in protoplasts and embryogenic cell lines of Rasthali, and carotenoid profiling in the resulting stable mutant lines showed greater increases in ?-carotene accumulation in the roots than in the leaves compared with unedited controls. The differences in expression of carotenoid pathway genes were correlated with differences in metabolites in the edited lines. Overall, our study suggests that carotenoid catabolism is regulated by CCD4 in ways that are tissue-and cultivar-specific, and it also demonstrates the successful use of the genome-editing tool in developing transgene-free biofortified lines of banana. � 2022 The Author(s) 2022.
Transgene-free genome editing supports the role of carotenoid cleavage dioxygenase 4 as a negative regulator of ?-carotene in banana
(Oxford University Press, 2022-02-01T00:00:00) Awasthi, Praveen; Khan, Shahirina; Lakhani, Hiralben; Chaturvedi, Siddhant; Shivani, S.; Kaur, Navneet; Singh, Jagdeep; Kesarwani, Atul Kumar; Tiwari, Siddharth
Carotenoid cleavage dioxygenases (CCDs) belong to a small gene family and have an important role in the intricate metabolism of carotenoids in plants. In this study we aimed to understand the regulatory mechanism of ?-carotene homeostasis by establishing transgene-free genome editing in banana. We found that the expression patterns of multiple CCDs were correlated with the concentrations of carotenoids in two cultivars with contrasting contents of ?-carotene, Nendran (high) and Rasthali (low). Higher expression of CCD4 in Rasthali (RAS-CCD4) was negatively correlated with ?-carotene accumulation in the fruit-pulp. Docking analysis and enzyme assays of purified RAS-CCD4 suggested that ?-carotene and 10-Apo-?-carotenal were the preferred substrates of RAS-CCD4. Bacterial complementation assays demonstrated the role of RAS-CCD4 in ?-carotene degradation, and this was further confirmed by in vivo overexpression of RAS-CCD4 in Arabidopsis, which resulted in significant reduction in ?-carotene concentration. CRISPR/Cas9-mediated editing of CCD4 was conducted in protoplasts and embryogenic cell lines of Rasthali, and carotenoid profiling in the resulting stable mutant lines showed greater increases in ?-carotene accumulation in the roots than in the leaves compared with unedited controls. The differences in expression of carotenoid pathway genes were correlated with differences in metabolites in the edited lines. Overall, our study suggests that carotenoid catabolism is regulated by CCD4 in ways that are tissue-and cultivar-specific, and it also demonstrates the successful use of the genome-editing tool in developing transgene-free biofortified lines of banana. � 2022 The Author(s) 2022.