Browsing by Author "Singh, Amarjeet"

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Abscisic acid, a principal regulator of plant abiotic stress responses
(Elsevier B.V., 2019) Sagar, Sushma; Singh, Amarjeet
Plants are routinely troubled by various abiotic stresses such as high salinity, dehydration, and low temperature during their life span. These abiotic stresses have detrimental effect on plant development, longevity, and productivity. Plants have evolved with a sessile nature, and unlike animals, they cannot move away from adverse growth conditions. Rather, they are destined to combat these stress conditions in their stationary habitat. Therefore, plants have devised an adaptive mechanism that entails the activation of several signal transduction pathways, leading to diverse molecular, cellular, and physiological changes (Singh et al., 2016, 2018). Most signal transduction pathways triggered in response to biotic or abiotic stresses are mediated by one or more plant hormones. Therefore, plant hormones are a crucial player in regulating plants’ response to various environmental cues (Iqbal et al., 2017; Khan et al., 2015a,b; Khan and Khan, 2014; Kazan, 2015; Per et al., 2018). Generally, phytohormones like salicylic acid (SA), jasmonic acid (JAs), and ethylene (ET) are implicated in plant response to pathogens, wounding, and other biotic stresses, whereas gibberellins (GAs), auxins (IAAs), brassinosteroids (BRs), and cytokinins are known to regulate plant development. However, recent advancements in plant stress related research have shown that all plant hormones could control multiple plant processes and are involved in crosstalk of signaling pathways. For example, SA, JA, and ET, apart from biotic stresses, are also involved in plant development and responses to abiotic stresses. Similarly, auxins and GA are crucial in abiotic and biotic stress responses (Colebrook et al., 2014; Kazan, 2013; Khan and Khan, 2013; Santino et al., 2013). Abscisic acid (ABA) is the key hormone that primarily regulates plants’ responses to various abiotic stresses; however, like other phytohormones ABA is also known to regulate plants’ response to biotic stress and development (Singh et al., 2016). The discovery of the vital phytohormone ABA dates way back to the 1960s. Several independent and convergent experiments carried out by various research groups led to the discovery of ABA (Cracker and Abeles, 1969). However, the earliest and most convincing was the discovery of ABA in cotton, where it was involved in fruit abscission and dormancy (Li et al., 2017). As time and research progressed, newer functions of ABA were unveiled, including adaptation to various stresses, stomatal closure, sugar accumulation, seed development, etc. Due to its crucial role in abiotic and biotic stresses, ABA is known as a “stress hormone”. Plenty of research on ABA accumulated ample information on its biosynthesis, storage, catabolism, site of action, and its possible targets. During the last decade, the ABA receptors and their crystal structures have been elucidated (Ma et al., 2009; Park et al., 2009). This information has provided a clear cut paradigm of the ABA signal transduction pathway. Moreover, recruiting the combinations of different key players such as PP2C phosphatase and SnRK2 kinases has helped to understand the signal transduction pathway. Recent studies have provided newer insights into the functional roles of the ABA signaling cascade in various aspects of plant growth and development. In this chapter, we discuss different facets of ABA in plants, including its biosynthesis, catabolism, ABA signaling pathway and various signaling components, and the role of ABA in abiotic stresses and plant development.
BURP domain-containing genes in legumes: genome-wide identification, structure, and expression analysis under stresses and development
(Springer Nature Publishing AG, 2022) Chitkara, Pragya; Poddar, Nikita; Singh, Amarjeet; Kumar, Shailesh
BURP domain-containing proteins are a plant-specific protein family which play an important role in plant metabolism and development. These proteins have also been involved in various abiotic and biotic stress responses. In this study, genome-wide identification and characterization of BURP domain protein encoding gene family is performed in four important legumes, Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Vigna radiata. BURP genes were distributed randomly across chromosomes in all four legume plants. The phylogenetic analysis classified all BURP proteins into five major subfamilies, namely, USP-like, RD22-like, BNM2-like, PG1β-like, and BURPV. Our findings revealed that BURP gene family descended from common ancestors with segmental gene duplication events playing a critical role in their evolution and expansion in legumes. The intron–exon and conserved protein motifs analysis revealed that BURP genes are structurally conserved in legumes. The promoter analysis revealed the presence of hormone, and stress-responsive cis-regulatory elements in BURP promoters, implying that BURP functions in both hormone and abiotic stress signaling. Global expression analysis revealed that several BURP genes in all four legumes express differentially during plant development, and under biotic and abiotic stresses. This indicates crucial role of BURP proteins in regulating the development of legumes and adaptation to different abiotic/biotic stresses. This study will provide the starter for cloning and detail functional investigation of BURP proteins in legume crops.
Calcium dependent protein kinase, a versatile player in plant stress management and development
(Taylor & Francis Group, 2018) Singh, Amarjeet; Sagar, Sushma; Biswas, Dipul Kumar
Calcium-dependent protein kinases (CDPKs) form the major and unique group of calcium (Ca2+) sensors in plants. Attributed to their peculiar structural features, CDPKs play a dual role of “Ca2+ sensor and responder” and translate the message from specific Ca2+ signature to phosphorylation events. Most of the stress and developmental triggers instigate an increase in Ca2+ level and consequently Ca2+ signaling in plants. Expression and functional analyses across plant species have revealed differential regulation of CDPK transcripts, activity, protein interactions and substrate targeting under different cues, including biotic and abiotic stresses and plant development. Thus, vital roles of CDPKs are proposed in perpetuating stress and development triggered Ca2+ signaling to adaptive responses in plants. Genetic engineering using CDPK genes could be utilitarian in the agricultural biotechnology for imparting higher degree of biotic and abiotic stress tolerance and better productivity. Here, we discuss the recent advancements and update of CDPK gene family organization, domain structure and regulatory mechanism, the role of CDPKs in abiotic stress, biotic stress, development signaling and responses in the model and crop plants.
Cellular transport and multifaceted roles of jasmonates in nutrient deficiency response in plants
(Springer Nature Publishing AG, 2025) Kamali, Saravanappriyan; Sonkar, Kamankshi; Singh, Amarjeet
Jasmonates (JAs) are well documented for their role in plant defense and growth regulation. Cellular transport of JAs during their biosynthesis and signaling constitutes an important layer of their functional regulation. However, most of the information about JAs transport has been gathered in recent years. Therefore, understanding the mechanism of intracellular transport of JAs in plants is of great importance to comprehend their function. In addition, in recent years, JAs have emerged as key regulators of nutrient deficiency response in plants. Under nutrient deficiency, plants show unique adaptive responses, including altered root growth, remodeling of root system architecture (RSA), triggering nutrient uptake-related genes, and activation of nutrient transporters. JAs have been found to regulate these responses in relation to the variable availability of macro- and micronutrients. Evidence indicates that in response to deficiencies of macronutrients such as nitrogen (N), phosphorus (P), and potassium (K+), the JA biosynthesis pathway is modulated, leading to higher JA accumulation. Furthermore, the JA-signaling pathway has been shown to regulate nutrient deficiency-related transcription factors, transporters, and RSA for optimum plant development. In this review, recent developments and updates on molecular mechanisms of cellular transport of JAs during JA biosynthesis and signaling are presented. In addition, new insights on involvement of JAs in nutrient uptake, homeostasis, deficiency response, and plant development have been provided.
Comprehensive expression analysis of rice Armadillo gene family during abiotic stress and development
(Oxford University Press, 2014) Sharma, Manisha; Singh, Amarjeet; Shankar, Alka; Pandey, Amita; Baranwal, Vinay; Kapoor, Sanjay; Tyagi, Akhilesh K.; Pandey, Girdhar K.
Genes in the Armadillo (ARM)-repeat superfamily encode proteins with a range of developmental and physiological processes in unicellular and multicellular eukaryotes. These 42 amino acid, long tandem repeat-containing proteins have been abundantly recognized in many plant species. Previous studies have confirmed that Armadillo proteins constitute a multigene family in Arabidopsis. In this study, we performed a computational analysis in the rice genome (Oryza sativa L. subsp. japonica), and identified 158 genes of Armadillo superfamily. Phylogenetic study classified them into several arbitrary groups based on a varying number of non-conserved ARM repeats and accessory domain(s) associated with them. An in-depth analysis of gene expression through microarray and Q-PCR revealed a number of ARM proteins expressing differentially in abiotic stresses and developmental conditions, suggesting a potential roles of this superfamily in development and stress signalling. Comparative phylogenetic analysis between Arabidopsis and rice Armadillo genes revealed a high degree of evolutionary conservation between the orthologues in two plant species. The non-synonymous and synonymous substitutions per site ratios (Ka/Ks) of duplicated gene pairs indicate a purifying selection. This genome-wide identification and expression analysis provides a basis for further functional analysis of Armadillo genes under abiotic stress and reproductive developmental condition in the plant lineage.
Comprehensive genomic analysis and expression profiling of phospholipase C gene family during abiotic stresses and development in rice
(PLOS, 2013) Singh, Amarjeet; Kanwar, Poonam; Pandey, Amita; Tyagi, Akhilesh K.; Sopory, Sudhir K.; Kapoor, Sanjay; Pandey, Girdhar K.
BACKGROUND: Phospholipase C (PLC) is one of the major lipid hydrolysing enzymes, implicated in lipid mediated signaling. PLCs have been found to play a significant role in abiotic stress triggered signaling and developmental processes in various plant species. Genome wide identification and expression analysis have been carried out for this gene family in Arabidopsis, yet not much has been accomplished in crop plant rice. METHODOLOGY/PRINCIPAL FINDINGS: An exhaustive in-silico exploration of rice genome using various online databases and tools resulted in the identification of nine PLC encoding genes. Based on sequence, motif and phylogenetic analysis rice PLC gene family could be divided into phosphatidylinositol-specific PLCs (PI-PLCs) and phosphatidylcholine- PLCs (PC-PLC or NPC) classes with four and five members, respectively. A comparative analysis revealed that PLCs are conserved in Arabidopsis (dicots) and rice (monocot) at gene structure and protein level but they might have evolved through a separate evolutionary path. Transcript profiling using gene chip microarray and quantitative RT-PCR showed that most of the PLC members expressed significantly and differentially under abiotic stresses (salt, cold and drought) and during various developmental stages with condition/stage specific and overlapping expression. This finding suggested an important role of different rice PLC members in abiotic stress triggered signaling and plant development, which was also supported by the presence of relevant cis-regulatory elements in their promoters. Sub-cellular localization of few selected PLC members in Nicotiana benthamiana and onion epidermal cells has provided a clue about their site of action and functional behaviour. CONCLUSION/SIGNIFICANCE: The genome wide identification, structural and expression analysis and knowledge of sub-cellular localization of PLC gene family envisage the functional characterization of these genes in crop plants in near future.
Dark-induced hormonal regulation of plant growth and development
(Frontiers Media S.A., 2020) Deepika; Ankit; Sagar, Sushma; Singh, Amarjeet
The sessile nature of plants has made them extremely sensitive and flexible towards the constant flux of the surrounding environment, particularly light and dark. The light is perceived as a signal by specific receptors which further transduce the information through the signaling intermediates and effector proteins to modulate gene expression. Signal transduction induces changes in hormone levels that alters developmental, physiological and morphological processes. Importance of light for plants growth is well recognized, but a holistic understanding of key molecular and physiological changes governing plants development under dark is awaited. Here, we describe how darkness acts as a signal causing alteration in hormone levels and subsequent modulation of the gene regulatory network throughout plant life. The emphasis of this review is on dark mediated changes in plant hormones, regulation of signaling complex COP/DET/FUS and the transcription factors PIFs which affects developmental events such as apical hook development, elongated hypocotyls, photoperiodic flowering, shortened roots, and plastid development. Furthermore, the role of darkness in shade avoidance and senescence is discussed.
Emerging role of phospholipase C mediated lipid signaling in abiotic stress tolerance and development in plants
(Springer Nature Publishing AG, 2021) Sagar, Sushma; Singh, Amarjeet
Environmental stimuli are primarily perceived at the plasma membrane. Stimuli perception leads to membrane disintegration and generation of molecules which trigger lipid signaling. In plants, lipid signaling regulates important biological functions however, the molecular mechanism involved is unclear. Phospholipases C (PLCs) are important lipid-modifying enzymes in eukaryotes. In animals, PLCs by hydrolyzing phospholipids, such as phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] generate diacylglycerol (DAG) and inositol- 1,4,5-trisphosphate (IP3). However, in plants their phosphorylated variants i.e., phosphatidic acid (PA) and inositol hexakisphosphate (IP6) are proposed to mediate lipid signaling. Specifc substrate preferences divide PLCs into phosphatidylinositol–PLC (PI–PLC) and non-specifc PLCs (NPC). PLC activity is regulated by various cellular factors including, calcium (Ca2+) concentration, phospholipid substrate, and post-translational modifcations. Both PI–PLCs and NPCs are implicated in plants’ response to stresses and development. Emerging evidences show that PLCs regulate structural and developmental features, like stomata movement, microtubule organization, membrane remodelling and root development under abiotic stresses. Thus, crucial insights are provided into PLC mediated regulatory mechanism of abiotic stress responses in plants. In this review, we describe the structure and regulation of plant PLCs. In addition, cellular and physiological roles of PLCs in abiotic stresses, phosphorus defciency, aluminium toxicity, pollen tube growth, and root development are discussed.
Expression dynamics indicate the role of Jasmonic acid biosynthesis pathway in regulating macronutrient (N, P and K+) deficiency tolerance in rice (Oryza sativa L.)
(Springer Nature Publishing AG, 2021) Deepika; Singh, Amarjeet
Key message: Expression pattern indicates that JA biosynthesis pathway via regulating JA levels might control root system architecture to improve nutrient use efciency (NUE) and N, P, K+ defciency tolerance in rice. Abstract: Defciencies of macronutrients (N, P and K+) and consequent excessive use of fertilizers have dramatically reduced soil fertility. It calls for development of nutrient use efcient plants. Plants combat nutrient defciencies by altering their root system architecture (RSA) to enhance the acquisition of nutrients from the soil. Amongst various phytohormones, Jasmonic acid (JA) is known to regulate plant root growth and modulate RSA. Therefore, to understand the role of JA in macronutrient defciency in rice, expression pattern of JA biosynthesis genes was analyzed under N, P and K+ defciencies. Several members belonging to diferent families of JA biosynthesis genes (PLA1, LOX, AOS, AOC, OPR, ACX and JAR1) showed diferential expression exclusively in one nutrient defciency or in multiple nutrient defciencies. Expression analysis during developmental stages showed that several genes expressed signifcantly in vegetative tissues, particularly in root. In addition, JA biosynthesis genes were found to have signifcant expression under the treatment of diferent phytohormones, including Auxin, cytokinin, gibberellic acid (GA), abscisic acid (ABA), JA and abiotic stresses, such as drought, salinity and cold. Analysis of promoters of these genes revealed various cis-regulatory elements associated with hormone response, plant development and abiotic stresses. These fndings suggest that JA biosynthesis pathway by regulating the level of JA might control the RSA thus, it may help rice plant in combating macronutrient defciency.
Genome-wide characterization and comparative analysis of the OSCA gene family and identification of its potential stress-responsive members in legumes
(Nature Publishing Group, 2023) Chakraborty, Srija; Gangwar, Rashmi; Zahra, Shafaque; Poddar, Nikita; Singh, Amarjeet; Kumar, Shailesh
Cicer arietinum, Cajanus cajan, Vigna radiata, and Phaseolus vulgaris are economically important legume crops with high nutritional value. They are negatively impacted globally by different biotic and abiotic stresses. Hyperosmolality-gated calcium-permeable channels (OSCA) have been characterized as osmosensors in Arabidopsis thaliana but have not previously reported in legumes. This study provides a genome-wide identification, characterization, and comparative analysis of OSCA genes in legumes. Our study identified and characterized 13 OSCA genes in C. cajan, V. radiata, P. vulgaris, and 12 in C. arietinum, classified into four distinct clades. We found evidence to suggest that the OSCAs might be involved in the interaction between hormone signalling pathways and stress signalling pathways. Furthermore, they play a major role in plant growth and development. The expression levels of the OSCAs vary under different stress conditions in a tissue-specific manner. Our study can be used to develop a detailed understanding of stress regulatory mechanisms of the OSCA gene family in legumes.
Genome-wide expressional and functional analysis of calcium transport elements during abiotic stress and development in rice
(John Wiley & Sons, 2014) Singh, Amarjeet; Kanwar, Poonam; Yadav, Akhilesh K.; Mishra, Manali; Jha, Saroj K.; Baranwal, Vinay; Pandey, Amita; Kapoor, Sanjay; Tyagi, Akhilesh K.; Pandey, Girdhar K.
Ca²⁺ homeostasis is required to maintain a delicate balance of cytosolic Ca²⁺ during normal and adverse growth conditions. Various Ca²⁺ transporters actively participate to maintain this delicate balance especially during abiotic stresses and developmental events in plants. In this study, we present a genome-wide account, detailing expression profiles, subcellular localization and functional analysis of rice Ca²⁺ transport elements. Exhaustive in silico data mining and analysis resulted in the identification of 81 Ca²⁺ transport element genes, which belong to various groups such as Ca²⁺-ATPases (pumps), exchangers, channels, glutamate receptor homologs and annexins. Phylogenetic analysis revealed that different Ca²⁺ transporters are evolutionarily conserved across different plant species. Comprehensive expression analysis by gene chip microarray and quantitative RT-PCR revealed that a substantial proportion of Ca²⁺ transporter genes were expressed differentially under abiotic stresses (salt, cold and drought) and reproductive developmental stages (panicle and seed) in rice. These findings suggest a possible role of rice Ca²⁺ transporters in abiotic stress and development triggered signaling pathways. Subcellular localization of Ca²⁺ transporters from different groups in Nicotiana benthamiana revealed their variable localization to different compartments, which could be their possible sites of action. Complementation of Ca²⁺ transport activity of K616 yeast mutant by Ca²⁺-ATPase OsACA7 and involvement in salt tolerance verified its functional behavior. This study will encourage detailed characterization of potential candidate Ca²⁺ transporters for their functional role in planta.
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.
Genome-wide identification, structure analysis and expression profiling of phospholipases D under hormone and abiotic stress treatment in chickpea (Cicer arietinum)
(Elsevier B.V., 2021) Sagar, Sushma; Deepika; Biswas, Dipul Kumar; Chandrasekar, Ramsankar; Singh, Amarjeet
Phospholipases D (PLDs) are phospholipid hydrolyzing enzymes and crucial components of lipid signaling in plants. PLDs are implicated in stress responses in different plants however, characterization of PLDs in chickpea is missing. Here, we identify 13 PLD genes in the chickpea genome. PLD family could be divided into α, β, δ, ε and ζ isoforms based on sequence and structure. Protein remodeling described that chickpea PLDs are composed of defined arrangements of α-helix, β-sheets and short loops. Phylogenetic analysis suggested evolutionary conservation of chickpea PLD family with dicots. In-planta subcellular localization showed the plasma membrane localization of chickpea PLDs. All PLD promoters had hormone and stress related cis-regulatory elements, which suggested overlapping function of PLDs in hormone and abiotic stress signaling. The qRT-PCR expression analysis revealed that most PLD genes are differentially expressed in multiple abiotic stresses (drought, salt and cold stress). Moreover, several PLD genes had overlapping expression in abiotic stress and ABA and JA treatment. These observations indicate the involvement of PLD gene family in cross-talk of phytohormone and abiotic stress signaling in chickpea. Thus, present study opens new avenues of utilizing PLD related information for understanding hormone-regulated abiotic stress signaling in legume crops.
Genomic & structural diversity and functional role of potassium (K+) transport proteins in plants
(Elsevier B.V., 2022) Ankit, Ankit; Kamali, Saravanappriyan; Singh, Amarjeet
Potassium (K+) is an essential macronutrient for plant growth and productivity. It is the most abundant cation in plants and is involved in various cellular processes. Variable K+ availability is sensed by plant roots, consequently K+ transport proteins are activated to optimize K+ uptake. In addition to K+ uptake and translocation these proteins are involved in other important physiological processes like transmembrane voltage regulation, polar auxin transport, maintenance of Na+/K+ ratio and stomata movement during abiotic stress responses. K+ transport proteins display tremendous genomic and structural diversity in plants. Their key structural features, such as transmembrane domains, N-terminal domains, C-terminal domains and loops determine their ability of K+ uptake and transport and thus, provide functional diversity. Most K+ transporters are regulated at transcriptional and post-translational levels. Genetic manipulation of key K+ transporters/channels could be a prominent strategy for improving K+ utilization efficiency (KUE) in plants. This review discusses the genomic and structural diversity of various K+ transport proteins in plants. Also, an update on the function of K+ transport proteins and their regulatory mechanism in response to variable K+ availability, in improving KUE, biotic and abiotic stresses is provided.
Genomic and expression analysis indicate the involvement of phospholipase C family in abiotic stress signaling in chickpea (Cicer arietinum)
(Elsevier B.V., 2020) Sagar, Sushma; Biswas, Dipul Kumar; Singh, Amarjeet
Phospholipase C proteins are phospholipid hydrolysing enzymes and crucial components of abiotic stress triggered lipid signaling in plants. PLCs are implicated in plant reaction to drought, salinity, and cold stress responses, however, characterization of the PLC family in the legume crop chickpea is missing. Here, we identify and describe nine PLC encoding genes in the chickpea genome. Phylogenetic analysis showed that the chickpea PLC family has evolved through a common path in dicots. Subcellular localization of fluorescence tagged proteins confirmed cytoplasmic and plasma membrane bound forms of PLCs in chickpea. The promoters of all the PLC genes are comprised of several hormone response related, development and abiotic stress related cis-regulatory elements. Expression analysis in five developmental stages (germination, seedling, vegetative, reproductive and senescence) showed significant expression of multiple PLCs in germination, vegetative and reproductive stages, suggesting their diverse role in various developmental processes. qRT-PCR expression analysis of the entire PLC gene family under drought, salt and cold stresses revealed that most PLC genes are differentially expressed in multiple abiotic stresses. These observations indicate the involvement of PLC gene family in abiotic stress signaling and responses in important legume crop. The present study opens new avenues for utilizing PLC- related information in biotechnological programs for abiotic stress tolerance and legume crop improvement.
Genomic and transcriptomic approaches to developing abiotic stress-resilient crops
(MDPI AG, 2023) Kamali, Saravanappriyan; Singh, Amarjeet
In the realm of agriculture, a pressing concern remains the abiotic stresses, such as temperature fluctuation, drought, soil salinity, and heavy metal contamination. These adverse growth conditions hamper crop yields and global food security. In this review, we present a comprehensive examination of the recent advancements in utilizing genomics and transcriptomics, tools to enhance crop resilience against these stress factors. Genomics aids in the identification of genes responsive to stress, unravels regulatory networks, and pinpoints genetic variations linked to stress tolerance. Concurrently, transcriptomics sheds light on the intricate dynamics of gene expression during stress conditions, unearthing novel stress-responsive genes and signaling pathways. This wealth of knowledge shapes the development of stress-tolerant crop varieties, achieved through conventional breeding programs and state-of-the-art genetic engineering and gene editing techniques like CRISPR-Cas9. Moreover, the integration of diverse omics data and functional genomics tools empowers precise manipulation of crop genomes to fortify their stress resilience. In summary, the integration of genomics and transcriptomics holds substantial promise in elucidating the molecular mechanisms behind crop stress tolerance, offering a path towards sustainable agriculture and safeguarding food security amidst shifting environmental challenges.
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.
Jasmonates as emerging regulators of plants response to variable nutrient environment
(Taylor & Francis Group, 2022) Kamali, Saravanappriyan; Singh, Amarjeet
Jasmonates (JAs) are known for their roles in plant defense and growth regulation. In recent years their roles in nutrient uptake and homeostasis have been explored. Regulation of nutrients uptake is crucial to maintain their optimum level in normal and deficient conditions. Under the deficiency of different nutrients, plants show unique responses like altered root growth, remodeling of root system architecture (RSA), induction of nutrient uptake-related genes, activation of nutrient transporters, and nutrient reallocation. JAs have been shown to regulate these responses in the variable availability of macro-and micronutrients. Emerging evidences revealed that in response to deficiency of macronutrients, such as nitrogen (N), phosphorous (P), and potassium (K+), JA biosynthesis pathway is activated. JA signaling pathway has been implicated in regulating nutrient deficiency-related transcription factors, transporters, and various facets of RSA for optimum plant development. In addition, JA pathway cross-talks with other phytohormones like auxin and ethylene for improving plant growth and adaptive response under nutrient deficiencies. In this review, emerging evidences and the latest developments on involvements of JAs in macro- and micronutrient uptakes, homeostasis, deficiency response, and plant development are discussed.
Jasmonic acid biosynthesis pathway and its functional role in plants
(Elsevier B.V., 2023) Ankit, Ankit; Kamali, Saravanappriyan; Singh, Amarjeet
Plants encounter various abiotic and biotic stresses including drought, heat, cold, salinity, osmotic stress, fungal infection, herbivore attacks in their natural habitat. In these unavoidable circumstances various phytohormones play crucial roles in regulating plant growth and development (Khan et al., 2019, 2020a, 2020b; Nazir et al., 2019, 2021, 2022; Poo´r et al., 2021). Jasmonic acid (JA) is a lipid-derived phytohormone which acts as a signal as well as regulator in various physiological processes and stress conditions. Methyl ester of JA (MeJA) is the first active jasmonate which was detected and isolated as an odorant from Jasminium grandiflorum flowers (Demole et al., 1962). Among the conjugates of JA, JA-Ile is the most biologically active form (Fonseca et al., 2009). Recently, cis-(1)-12- oxophytodienoic acid (OPDA) an intermediate in the lipoxygenases (LOX) pathway for JA biosynthesis has been shown to be functional signaling molecule instead of JA in lower plants, such as Marchantia polymorpha (liverworts), Physcomitrella patens (moss) and Selaginella martensii (spikemoss) (Ogorodnikova et al., 2015; Stumpe et al., 2010; Yamamoto et al., 2015). Apart from bryophytes, fungus species such as Fusarium oxysporum have JA and/or JA-Ile conjugate (Miersch et al., 1999). Although, JA and its derivatives are distributed among bryophytes and fungi, most of the homologs of JA biosynthesis enzymes are present in major lineages of land plants (Han, 2017). In last decade, studies have been performed in both monocotyledons as well as dicotyledons plants to better understand the JA biosynthesis mechanism. In Arabidopsis, JA biosynthesis mainly occurs in chloroplast, peroxisome and cytoplasm (Ruan et al., 2019). In chloroplast, OPDA is synthesized from unsaturated fatty acid α-linolenic acid (α-LeA) derived from the chloroplast membrane, followed by its conversion into JA in peroxisome. The conversion of JA into different functional and structural metabolites takes place in the cytoplasm. JA and its other derivatives like MeJA and JA-Ile are collectively known as jasmonates.
Metabolic and physiological functions of patatin-like phospholipase-A in plants
(Elsevier B.V., 2025) Sonkar, Kamankshi; Singh, Amarjeet
Patatin-like phospholipase-A (pPLA) is a class of lipid acyl hydrolase enzymes found in both the animal and plant kingdoms. Plant pPLAs are related to the potato tuber storage protein patatin in solanaceous plants. Despite extensive investigation of pPLA functions in the animal system, the mechanistic functional details and regulatory roles of pPLA are poorly understood in plants. In recent years, research pertaining to pPLAs has gain some momentum as some of the key members of pPLA family have been characterized functionally. These findings have provided key insights into the structural features, biochemical activities, and functional roles of plant pPLAs. In this review, we are presenting a holistic overview of pPLAs in plants and providing the latest updates on pPLA research. We have highlighted the genomic diversity and structural features of pPLAs in plants. Importantly, we have discussed the role of pPLAs in lipid metabolism, including sphingolipid metabolism, lignin and cellulose accumulation, lipid breakdown and seed oil content enhancement. Moreover, regulatory roles of pPLAs in physiological processes, such as plant stress response, plant-pathogen interactions and plant development have been discussed. This information will be critical in the biotechnological programs for crop improvement.