Publications of NIPGR Scientists
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Item Chickpea chitinases responsive to Helicoverpa herbivory and phytohormone signaling: genome-wide identification, field expression profiling, and structure-guided prioritization(BioMed Central Ltd, 2026) Konda, Aravind Kumar; Annapragada, Harika; G K, Sujayanand; Singh, Pooja; Bhuvanachandra, Bhoopal; Chinnasamy, Hariharan V; Dixit, Girish Prasad; Gupta, Kapuganti Jagadis; Matheshwaran, SaravananBackground: Chitinases can contribute to plant defence against fungal pathogens and insect herbivores, but their family organization, inducible deployment, and putative ligand-recognition behaviour remain poorly resolved in chickpea. We combined genome-wide identification, field expression profiling under controlled Helicoverpa armigera infestation, hormone treatments, and structure-guided comparison of representative proteins to prioritize defence-associated chickpea chitinases. Results: We identified 28 chickpea chitinase loci (Car_Chits), comprising 22 glycosyl hydrolase family 18 (GH18) genes and 6 GH19 genes. Local duplication, especially tandem duplication within GH18, was the main contributor to family expansion, and interpretable duplicate pairs were retained mainly under purifying selection. Promoter scans indicated broad enrichment of defence- and hormone-associated cis-elements. Field quantitative real-time PCR (qRT-PCR) profiling of 11 candidate genes in field-grown plants subjected to controlled H. armigera infestation and hormone treatments showed treatment-specific temporal regulation. Car_Chit-4 (GH19) was strongly induced by salicylic acid (7.81-fold at 0.5 h; q < 0.05) but transiently repressed shortly after H. armigera feeding (0.15-fold at 0.5 h; q = 0.030). Car_Chit-19 (GH18) was the clearest herbivory-responsive gene, with late induction at 8 h (1.62-fold; q = 0.050) and 48 h (1.85-fold; q = 0.050). Jasmonic acid caused broad early repression across several genes, followed by delayed induction of Car_Chit-4 at 24 h. Seven Car_Chit-(GlcNAc)₄ complexes were modelled, docked, and simulated for 100 ns. GH18 proteins generally showed more favourable predicted MM-PBSA binding energies than GH19 proteins, but the structural metrics were interpreted as relative ligand-recognition indicators rather than direct evidence of anti-herbivore function. Car_Chit-17 had the most favourable predicted binding energy (ΔG_bind = - 18.51 ± 6.75 kcal/mol), whereas Car_Chit-14 and Car_Chit-27 retained the most stable ligand poses and Car_Chit-19 displayed the most stable protein scaffold. Conclusions: Chickpea chitinases show differentiated temporal responses to herbivory and hormone signalling. The study supports a working model in which GH19 Car_Chit-4 marks a rapid salicylic-acid-responsive arm, whereas GH18 Car_Chit-19 marks a delayed herbivory-responsive arm. A tiered prioritization framework separates expression-deployed candidates from structure-guided biochemical candidates, explaining why different genes emerge from qRT-PCR and molecular modelling analyses. The structural analyses provide complementary prioritization of Car_Chit-17, Car_Chit-14, and Car_Chit-27 for biochemical characterization. Together, these results provide a resource for dissecting chitinase-mediated defence in chickpea and for selecting candidates for functional validation.Item The confluence of TOR signaling and plant growth regulators in development and stress responses(Oxford University Press, 2026) Saksena, Harshita B; Kumar, Mukesh; Samtani, Harsha; Sharma, Aishwarye; Rawat, Sanjay Singh; Awasthi, Prakhar; Botta, Halidev Krishna; Sandhya, Shital; Pande, Anjali; Naaz, Sheeba; Kushwah, Sunita; Shukla, Brihaspati N; Laxmi, AshveryaThe Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that serves as a crucial signaling hub, seamlessly integrating a wide range of internal and external signals to meticulously regulate cellular and organismal physiology. TOR is crucial in regulating the different phases of lifecycle in plants including embryogenesis, seed germination, meristem activation, root and leaf development, flowering and senescence. Beyond its central role in growth and development, emerging research has revealed its significant involvement in the response to environmental stresses. Even though plant growth regulators such as auxin, cytokinin (CK), brassinosteroid (BR), gibberellin (GA), abscisic acid (ABA), ethylene (ET), salicylic acid (SA), jasmonic acid (JA) and nitric oxide (NO) function as pivotal signaling molecules in modulating plant development and stress responses, how they coordinate with the energy status still remains obscure. Here we summarize the current findings on the dynamic interconnection between TOR and these discrete phytoregulators and their potential role in executing diverse biological processes in plants.Item Jasmonic acid biosynthesis pathway and its functional role in plants(Elsevier B.V., 2023) Ankit, Ankit; Kamali, Saravanappriyan; Singh, AmarjeetPlants 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.Item OsJAZ11 regulates spikelet and seed development in rice(John Wiley & Sons, 2022) Mehra, Poonam; Pandey, Bipin K.; Verma, Lokesh; Prusty, Ankita; Singh, Ajit Pal; Sharma, Shivam; Malik, Naveen; Bennett, Malcolm J.; Parida, Swarup K.; Giri, Jitender; Tyagi, Akhilesh K.Seed size is one of the major determinants of seed weight and eventually, crop yield. As the global population is increasing beyond the capacity of current food production, enhancing seed size is a key target for crop breeders. Despite the identification of several genes and QTLs, current understanding about the molecular regulation of seed size/weight remains fragmentary. In the present study, we report novel role of a jasmonic acid (JA) signaling repressor, OsJAZ11 controlling rice seed width and weight. Transgenic rice lines overexpressing OsJAZ11 exhibited up to a 14% increase in seed width and ~30% increase in seed weight compared to wild type (WT). Constitutive expression of OsJAZ11 dramatically influenced spikelet morphogenesis leading to extra glume-like structures, open hull, and abnormal numbers of floral organs. Furthermore, overexpression lines accumulated higher JA levels in spikelets and developing seeds. Expression studies uncovered altered expression of JA biosynthesis/signaling and MADS box genes in overexpression lines compared to WT. Yeast two-hybrid and pull-down assays revealed that OsJAZ11 interacts with OsMADS29 and OsMADS68. Remarkably, expression of OsGW7, a key negative regulator of grain size, was significantly reduced in overexpression lines. We propose that OsJAZ11 participates in the regulation of seed size and spikelet development by coordinating the expression of JA-related, OsGW7 and MADS genes.Item OsJAZ11 regulates phosphate starvation responses in rice(Springer Nature Publishing AG, 2021) Pandey, Bipin K.; Verma, Lokesh; Prusty, Ankita; Singh, Ajit Pal; Bennett, Malcolm J.; Tyagi, Akhilesh K.; Giri, Jitender; Mehra, PoonamJasmonic Acid (JA) is a key plant signaling molecule which negatively regulates growth processes including root elongation. JAZ (JASMONATE ZIM-DOMAIN) proteins function as transcriptional repressors of JA signaling. Therefore, targeting JA signaling by deploying JAZ repressors may enhance root length in crops. In this study, we overexpressed JAZ repressor OsJAZ11 in rice to alleviate the root growth inhibitory action of JA. OsJAZ11 is a low phosphate (Pi) responsive gene which is transcriptionally regulated by OsPHR2. We report that OsJAZ11 overexpression promoted primary and seminal root elongation which enhanced Pi foraging. Expression studies revealed that overexpression of OsJAZ11 also reduced Pi starvation response (PSR) under Pi limiting conditions. Moreover, OsJAZ11 overexpression also suppressed JA signaling and biosynthesis as compared to wild type (WT). We further demonstrated that the C-terminal region of OsJAZ11 was crucial for stimulating root elongation in overexpression lines. Rice transgenics overexpressing truncated OsJAZ11ΔC transgene (i.e., missing C-terminal region) exhibited reduced root length and Pi uptake. Interestingly, OsJAZ11 also regulates Pi homeostasis via physical interaction with a key Pi sensing protein, OsSPX1. Our study highlights the functional connections between JA and Pi signaling and reveals JAZ repressors as a promising candidate for improving low Pi tolerance of elite rice genotypes.Item A novel role of salt and drought induced RING 1 protein in modulating plant defense against hemibiotrophic and necrotrophic pathogens(American Phytopathological Society, 2021) Ramu, Vemanna S.; Oh, Sunhee; Lee, Hee-Kyung; Nandety, Raja Sekhar; Oh, Youngjae; Lee, Seonghee; Nakashima, Jin; Tang, Yuhong; Senthil-Kumar, Muthappa; Mysore, Kirankumar S.Many plant encoded E3 ligases are known to be involved in plant defense. Here we report a novel role of E3 ligase SALT- AND DROUGHT-INDUCED RING FINGER1 (SDIR1) in plant immunity. Even though SDIR1 is reasonably well-characterized, its role in biotic stress response is not known. The silencing of SDIR1 in Nicotiana benthamiana reduced the multiplication of the virulent bacterial pathogen Pseudomonas syringae pv. tabaci. The Arabidopsis sdir1 mutant is resistant to virulent pathogens, whereas SDIR1 overexpression lines are susceptible to both host and nonhost hemibiotrophic bacterial pathogens. However, sdir1 mutant and SDIR1 overexpression lines showed hypersusceptibility and resistance, respectively, against the necrotrophic pathogen, Erwinia carotovora. The mutant of SDIR1 target protein, SDIR-interacting protein 1 (SDIR1P1), also showed resistance to host and nonhost pathogens. In SDIR1 overexpression plants, transcripts of NAC transcription factors were less accumulated and the levels of JA and abscisic acid (ABA) were increased. In sdir1 mutants, JA signaling genes JAZ7 and JAZ8 were downregulated. These data suggest that SDIR1 is a susceptibility factor, and its activation/overexpression enhances disease caused by P. syringae pv. tomato DC3000 in Arabidopsis. Our results show a novel role of SDIR1 in modulating plant defense gene expression and plant immunity.Item Jasmonic acid (JA) induced-calcium elevation in Arabidopsis is highly variable due to time of day and conversion to JA-Ile(Springer Nature Publishing AG, 2020) Prajapati, Ramgopal; Mittal, Deepika; Meena, Mukesh Kumar; Vadassery, JyothilakshmiPlants have evolved mechanisms to effectively anticipate environmental changes via diurnal rhythmicity (day/night) maintained by the circadian clock. Jasmonic acid biosynthesis and signalling are known to be under the control of the circadian clock. Both JA and its bioactive form jasmonoyl-L-isoleucine (JA-Ile) when externally added can induce a cytosolic Ca2? influx in Arabidopsis thaliana. JA and JA-Ile induced Ca2? is poorly understood and often used interchangeably to study Ca2? regulation of jasmonates. We attempted to understand if they are similar and if diurnal rhythms or time of day regulate them. JA induced Cacyt 2? signature is variable according to time-of-day in Arabidopsis. JA is sensed in two ways according to the time-of-day (a) directly sensed as JA and induces Cacyt 2? elevation (b) JA gets converted into the JA-Ile by JAR1 and is sensed as JA-Ile, which we proved using jar1-1*aequorin. This twin sensing mode is responsible for variability in JA induced Cacyt 2? signature. We further suggest caution when using JA as a stimulant for Cacyt 2? elevation measurements to compare wild-type (Col-0 transformed with pMAQ2; transgenic aequorin) and effect of different mutations. On the other hand bioactive JA-Ile induced Cacyt 2? signature is constant diurnally with maximum amplitude at dawn which coincides with maximum sensitivity of JA-Ile receptor, COI1 and increased VSP2 expression. From the above study we conclude that JA-Ile induced Cacyt 2? elevation is a better read-out than the highly variable JA-induced Cacyt 2? elevations to study the output pathways.