Browsing by Author "Deepika, Deepika"

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Genome-wide identification and molecular characterization of core ABA signaling components under abiotic stresses and during development in chickpea
(Springer Nature Publishing AG, 2025) Kamali, Saravanappriyan; Sonkar, Kamankshi; Ankit, Ankit; Deepika, Deepika; Sharma, Ankita; Singh, Amarjeet
Abscisic acid (ABA) signaling is vital for plant's response to abiotic stresses and development. Core components of ABA signaling include ABA receptors PYR/PYL/RCAR, group-A PP2Cs (PP2C-As) and SnRK2 serine/threonine kinases. These have been well studied in Arabidopsis, but their knowledge in the legume crop chickpea is missing. Here, we identified 8 PYLs, 11 PP2C-As and 13 SnRK2s genes in the chickpea genome. Gene duplication events have been found to drive their evolution and expansion in chickpea. Protein homology modeling revealed three-dimensional structure, and arrangements of α-helix, β-sheets and p-loops in respective families. In-planta subcellular localization analysis revealed that CaPYL3 and CaPYL5 proteins were localized at the plasma membrane, and CaPP2CA-1 and CaSnRK2.7 were localized in the cytoplasm and the nucleus. RNA sequencing data analysis indicated the regulatory role of CaPYLs, CaPP2C-As and CaSnRK2s in developmental stages particularly, stages of early embryogenesis to seed maturity. Through RT-qPCR analysis drought, salt and ABA responsive CaPYL, CaPP2C-A and CaSnRK2 genes, which might regulate abiotic stress response in chickpea were identified. Importantly, key genes like CaPYL4, CaPP2C-A4, CaPP2C-A11 and CaSnRK2.9 with overlapping expression in drought, ABA and seed development were identified, which might determine chickpea crop yield. In-silico interaction analysis revealed specific and overlapping interaction among ABA signaling proteins indicating their functional relevance. Overall, core ABA signaling components are crucial for abiotic stress tolerance and development in chickpea. These genes will be functionally validated in the future and will be utilized to generate abiotic stress resilience and high-yielding chickpea varieties.
Genomic, structural, and molecular analysis of calmodulin-binding transcriptional activators (CAMTAs) suggests their role in plant development and abiotic stress tolerance in chickpea
(Elsevier B.V., 2025) Sonkar, Kamankshi; Kamali, Saravanappriyan; Kumar, Atul; Deepika, Deepika; Ankit, Ankit; Singh, Amarjeet
The calmodulin-binding transcriptional activator (CAMTA) transcription factors regulate the expression of target genes in Ca2 + dependent cellular functions. CAMTAs are known to regulate biotic and abiotic stress tolerance, and development in plants. CAMTA family has been characterized in Arabidopsis, it is yet to be explored in the legume plant chickpea. Here, we have identified and characterized the chickpea CAMTA family. Total seven CAMTA genes (CaCAMTA1–7) were identified in chickpea. Gene and domain structure analyses suggested that CAMTAs are structurally conserved. The phylogenetic analysis demarcated CaCAMTAs into three groups namely; group I, II and III, and indicated that CaCAMTAs have co-evolved in dicot leguminous plants whereas, they have divergent evolution in monocots. Protein homology modeling revealed their three-dimensional structure, and composition & conformations of α-helix, β-sheets and p-loops. Subcellular localization showed that CaCAMTA4 was localized both, in the nucleus and the cytosol whereas, CaCAMTA5 was localized in the nucleus. CaCAMTA promoters contain various cis-regulatory elements related to abiotic stresses and plant development. Expression profiling using RNA-seq data revealed differential expression of CaCAMTAs during various stages of plant development. RT-qPCR expression analysis showed that most CaCAMTA genes are drought, salt, and ABA responsive, suggesting their role in abiotic stress tolerance in chickpea. Moreover, CaCAMTA regulon was identified based on the presence of CAMTA binding motif (CGCG box) in the promoters of target genes, and in-silico interaction analysis of TF and putative targets. Overall, CaCAMTAs are crucial for abiotic stress tolerance and plant development in chickpea. Key CaCAMTA genes will be functionally characterized, and will be exploited for developing stress tolerant chickpea varieties.
Molecular analysis indicates the involvement of Jasmonic acid biosynthesis pathway in low-potassium (K+) stress response and development in chickpea (Cicer arietinum)
(Elsevier B.V., 2022) Deepika, Deepika; Ankit; Jonwal, Sarvesh; Mali, Komal Vitthalrao; Sinha, Alok Krishna; Singh, Amarjeet
K+ is a major macronutrient and its deficiency hampers plant growth and yield. Plants combat low-K+ stress by modifying their root system architecture (RSA). Here, morphophysiological analysis revealed that chickpea plants exhibit sensitivity to low-K+ stress as shown by impaired primary root growth. Phytohormone JA regulates various facets of plant root growth, however, information of JA biosynthesis genes in chickpea is missing. We performed genome-wide identification and molecular characterization of JA biosynthesis pathway genes in chickpea. Total 33 genes belonging to different families i.e., LOXs-18, AOSs-3, AOCs-2, OPRs-6 and JARs-4 were identified in the chickpea genome. In-planta analysis revealed the localization of CaLOX7, − 10, CaAOS1, − 2 and CaAOC1 at subcellular compartments, such as membrane, chloroplast and cytoplasm. Protein expression and in-vitro enzymatic activity analysis showed that CaAOS1 an CaOPR2 are the functional enzymes in chickpea. Promoters of most genes harboured abiotic stress, hormone and development related cis-regulatory elements, suggesting their role in nutrient deficiency, abiotic stress and plant development. qRT-PCR expression profiling showed that about 15 JA biosynthesis genes from different families express differentially whereas, JA catabolism genes were repressed in chickpea root and shoot under low-K+ stress. In addition, JA biosynthesis genes showed differential expression in vegetative and reproductive development, senescence stages, desiccation, salinity and cold stress. These findings indicate the involvement of JA biosynthesis pathway in low-K+ stress response and development in chickpea. Low-K+ stress and development related genes identified in this study could be utilized in genetic engineering of chickpea plants for improved traits.
Molecular and expression analysis indicate the role of CBL interacting protein kinases (CIPKs) in abiotic stress signaling and development in chickpea
(Springer Nature Publishing AG, 2022) Poddar, Nikita; Deepika, Deepika; Chitkara, Pragya; Singh, Amarjeet; Kumar, Shailesh
Calcineurin B-like proteins (CBL)-interacting protein kinases (CIPKs) regulate the developmental processes, hormone signal transduction and stress responses in plants. Although the genome sequence of chickpea is available, information related to the CIPK gene family is missing in this important crop plant. Here, a total of 22 CIPK genes were identified and characterized in chickpea. We found a high degree of structural and evolutionary conservation in the chickpea CIPK family. Our analysis showed that chickpea CIPKs have evolved with dicots such as Arabidopsis and soybean, and extensive gene duplication events have played an important role in the evolution and expansion of the CIPK gene family in chickpea. The three-dimensional structure of chickpea CIPKs was described by protein homology modelling. Most CIPK proteins are localized in the cytoplasm and nucleus, as predicted by subcellular localization analysis. Promoter analysis revealed various cis-regulatory elements related to plant development, hormone signaling, and abiotic stresses. RNA-seq expression analysis indicated that CIPKs are significantly expressed through a spectrum of developmental stages, tissue/organs that hinted at their important role in plant development. The qRT-PCR analysis revealed that several CaCIPK genes had specific and overlapping expressions in different abiotic stresses like drought, salt, and ABA, suggesting the important role of this gene family in abiotic stress signaling in chickpea. Thus, this study provides an avenue for detailed functional characterization of the CIPK gene family in chickpea and other legume crops.
Molecular characterization reveals the involvement of calcium dependent protein kinases in abiotic stress signaling and development in chickpea (Cicer arietinum)
(Frontiers Media S.A., 2022) Deepika, Deepika; Poddar, Nikita; Kumar, Shailesh; Singh, Amarjeet
Calcium-dependent protein kinases (CDPKs) are a major group of calcium (Ca2+) sensors in plants. CDPKs play a dual function of "Ca2+ sensor and responder." These sensors decode the "Ca2+ signatures" generated in response to adverse growth conditions such as drought, salinity, and cold and developmental processes. However, knowledge of the CDPK family in the legume crop chickpea is missing. Here, we have identified a total of 22 CDPK genes in the chickpea genome. The phylogenetic analysis of the chickpea CDPK family with other plants revealed their evolutionary conservation. Protein homology modeling described the three-dimensional structure of chickpea CDPKs. Defined arrangements of α-helix, β-strands, and transmembrane-helix represent important structures like kinase domain, inhibitory junction domain, N and C-lobes of EF-hand motifs. Subcellular localization analysis revealed that CaCDPK proteins are localized mainly at the cytoplasm and in the nucleus. Most of the CaCDPK promoters had abiotic stress and development-related cis-regulatory elements, suggesting the functional role of CaCDPKs in abiotic stress and development-related signaling. RNA sequencing (RNA-seq) expression analysis indicated the role of the CaCDPK family in various developmental stages, including vegetative, reproductive development, senescence stages, and during seed stages of early embryogenesis, late embryogenesis, mid and late seed maturity. The real-time quantitative PCR (qRT-PCR) analysis revealed that several CaCDPK genes are specifically as well as commonly induced by drought, salt, and Abscisic acid (ABA). Overall, these findings indicate that the CDPK family is probably involved in abiotic stress responses and development in chickpeas. This study provides crucial information on the CDPK family that will be utilized in generating abiotic stress-tolerant and high-yielding chickpea varieties.
Plant phospholipase D: novel structure, regulatory mechanism, and multifaceted functions with biotechnological application
(Taylor & Francis Group, 2022) Deepika, Deepika; Singh, Amarjeet
Phospholipases D (PLDs) are important membrane lipid-modifying enzymes in eukaryotes. Phosphatidic acid, the product of PLD activity, is a vital signaling molecule. PLD-mediated lipid signaling has been the subject of extensive research leading to discovery of its crystal structure. PLDs are involved in the pathophysiology of several human diseases, therefore, viewed as promising targets for drug design. The availability of a eukaryotic PLD crystal structure will encourage PLD targeted drug designing. PLDs have been implicated in plants response to biotic and abiotic stresses. However, the molecular mechanism of response is not clear. Recently, several novel findings have shown that PLD mediated modulation of structural and developmental processes, such as: stomata movement, root growth and microtubule organization are crucial for plants adaptation to environmental stresses. Involvement of PLDs in regulating membrane remodeling, auxin mediated alteration of root system architecture and nutrient uptake to combat nitrogen and phosphorus deficiencies and magnesium toxicity is established. PLDs via vesicle trafficking modulate cytoskeleton and exocytosis to regulate self-incompatibility (SI) signaling in flowering plants, thereby contributes to plants hybrid vigor and diversity. In addition, the important role of PLDs has been recognized in biotechnologically important functions, including oil/TAG synthesis and maintenance of seed quality. In this review, we describe the crystal structure of a plant PLD and discuss the molecular mechanism of catalysis and activity regulation. Further, the role of PLDs in regulating plant development under biotic and abiotic stresses, nitrogen and phosphorus deficiency, magnesium ion toxicity, SI signaling and pollen tube growth and in important biotechnological applications has been discussed.
Regulation of plants nutrient deficiency responses by phytohormones
(Elsevier B.V., 2023) Deepika, Deepika; Sonkar, Kamankshi; Singh, Amarjeet
Living organisms have the ability to acquire nutrients from their physical environment and subsequently convert them into an energy source for survival and growth. In plants, nutrients are involved in metabolism and physiology either as constituents of metabolites or enzymes for macromolecule biosynthesis. Based on their concentration in plant dry matter, the 14 essential inorganic elements are categorized into macronutrients and micronutrients. Macronutrients include six elements, nitrogen (N), phosphorus (P), potassium (K), sulfur (S), calcium (Ca), and magnesium (Mg), whereas the micronutrients comprised eight elements, chlorine (Cl), iron (Fe), boron (B), manganese (Mn), zinc (Zn), copper (Cu), molybdenum (Mo), and nickel (Ni) (de Bang et al., 2020; Sustr et al., 2019). Nutrients are distributed in a patchy manner in soil due to their variable interactions with spatially and temporally dispersed charged soil particles (Hodge, 2006). This, along with many other factors, leads to either low nutrient concentration in soil or low accessibility for plants. Low availability of a nutrient causes specific deficiency symptoms. But plants usually face multiple nutrient deficiencies simultaneously leading to a complex response and symptoms. Moreover, various biotic and abiotic stress factors, such as pests, pathogens, water deficit, salinity, and light, also interact to cause atypical nutrient deficiency symptoms (Amtmann et al., 2008; Troufflard et al., 2010; Atkinsonand Urwin., 2012). Globally, nutrient deficiencies are major threats to crop production, causing reduced yields and poor food and feed quality. The world food security challenge is being met by the use of chemical fertilizers (natural and anthropogenic).