Browsing by Author "Mehra, Poonam"

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Comparative morphophysiological analyses and molecular profiling reveal Pi-efficient strategies of a traditional rice genotype
(Frontiers Media S.A., 2016) Mehra, Poonam; Pandey, Bipin K.; Giri, Jitender
Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice genotypes are naturally compatible with low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes, Dular (low Pi tolerant), and PB1 (low Pi sensitive), have been selected. Comparative morphophysiological, global transcriptome and lipidome analyses of root and shoot tissues of both genotypes grown under Pi deficient and sufficient conditions revealed potential low Pi tolerance mechanisms of the traditional genotype. Most of the genes associated with enhanced internal Pi utilization (phospholipid remobilization) and modulation of root system architecture (RSA) were highly induced in the traditional rice genotype, Dular. Higher reserves of phospholipids and greater accumulation of galactolipids under low Pi in Dular indicated it has more efficient Pi utilization. Furthermore, Dular also maintained greater root growth than PB1 under low Pi, resulting in larger root surface area due to increased lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of the traditional genotype can be exploited to improve the low Pi tolerance of modern high yielding rice cultivars.
Genome-wide DNA polymorphisms in low phosphate tolerant and sensitive rice genotypes
(Nature Publishing Group, 2015) Mehra, Poonam; Pandey, Bipin K.; Giri, Jitender
Soil Phosphorus (P) deficiency is one of the major challenges to rice crop world-wide. Modern rice genotypes are highly P-responsive and rely on high input of P fertilizers. However, low P tolerant traditional cultivars and landraces have genetic potential to sustain well under low P. Identification of high resolution DNA polymorphisms (SNPs and InDels) in such contrasting genotypes is largely missing for low P response at gene levels. Here, we report high quality DNA polymorphisms in low P sensitive genotype, PB1 and tolerant traditional genotype, Dular. We performed whole genome resequencing using Illumina NGS platform and identified a total of 5,157,939 sequence variants in PB1 and Dular with reference to Nipponbare genome. We have identified approximately 2.3 million and 2.9 million high quality polymorphisms in PB1 and Dular, respectively, with an average read depth of ≥24X. We further mapped several DNA polymorphisms (non-synonymous and regulatory variants) having potential functional significance to key Phosphate Starvation Responsive (PSR) and root architecture genes in Dular and Kasalath using a compiled list of low P responsive genes. These identified variants can serve as a useful source of genetic variability for improving low P tolerance and root architecture of high yielding modern genotypes.
Identification of purple acid phosphatases in chickpea and potential roles of CaPAP7 in seed phytate accumulation
(Nature Publishing Group, 2017) Bhadouria, Jyoti; Singh, Ajit Pal; Mehra, Poonam; Verma, Lokesh; Srivastawa, Rishi; Parida, Swarup K.; Giri, Jitender
Purple acid phosphatases (PAPs) play important roles in phosphate (Pi) acquisition and utilization. These PAPs hydrolyze organic Phosphorus (P) containing compounds in rhizosphere as well as inside the plant cell. However, roles of PAPs in one of the most widely cultivated legumes, chickpea (Cicer arietnum L.), have not been unraveled so far. In the present study, we identified 25 putative PAPs in chickpea (CaPAPs) which possess functional PAP motifs and domains. Differential regulation of CaPAPs under different nutrient deficiencies revealed their roles under multiple nutrient stresses including Pi deficiency. Interestingly, most of the CaPAPs were prominently expressed in flowers and young pods indicating their roles in flower and seed development. Association mapping of SNPs underlying CaPAPs with seed traits revealed significant association of low Pi inducible CaPAP7 with seed weight and phytate content. Biochemical characterization of recombinant CaPAP7 established it to be a functional acid phosphatase with highest activity on most abundant organic-P substrate, phytate. Exogenous application of recombinant CaPAP7 enhanced biomass and Pi content of Arabidopsis seedlings supplemented with phytate as sole P source. Taken together, our results uncover the PAPs in chickpea and potential roles of CaPAP7 in seed phytate accumulation.
Improvement of phosphate acquisition and utilization by a secretory purple acid phosphatase (OsPAP21b) in rice
(John Wiley & Sons, 2017) Mehra, Poonam; Pandey, Bipin Kumar; Giri, Jitender
Phosphate (Pi) deficiency in soil system is a limiting factor for rice growth and yield. Majority of the soil Phosphorus (P) is organic in nature; not readily available for root uptake. Low Pi inducible purple acid phosphatases (PAPs) are hypothesized to enhance the availability of Pi in soil and cellular system. However, information on molecular and physiological roles of rice PAPs is very limited. Here, we demonstrate the role of a novel rice PAP, OsPAP21b in improving plant utilization of organic-P. OsPAP21b was found to be under the transcriptional control of OsPHR2 and strictly regulated by plant Pi-status at both transcript and protein levels. Biochemically, OsPAP21b showed hydrolysis of several organophosphates at acidic pH and possessed sufficient thermostability befitting for high temperature rice ecosystems with acidic soils. Interestingly, OsPAP21b was revealed to be a secretory PAP and encodes a distinguishable major APase (acid phosphatase) isoform under low Pi in roots. Further, OsPAP21b overexpressing transgenics showed increased biomass, APase activity and P content both in hydroponics supplemented with organic-P sources and soil containing organic manure as sole P source. Additionally, overexpression lines depicted increased root length, biomass and lateral roots under low Pi while RNAi lines showed reduced root length and biomass as compared to WT. In light of these evidences, present study strongly proposes OsPAP21b as a useful candidate for improving Pi acquisition and utilization in rice.
Morpho-physiological and transcriptome profiling reveal novel zinc deficiency-responsive genes in rice
(Springer, 2017) Bandyopadhyay, Tirthankar; Mehra, Poonam; Hairat, Suboot; Giri, Jitender
Intensive farming has depleted the soil zinc (Zn) availability resulting in decreased crop productivity. Here, we attempt to understand the Zn deficiency response in rice through temporal transcriptome analysis. For this, rice seedlings were raised under Zn-deficient conditions up to 4 weeks followed by Zn re-supply for 3 days. Zn-deficient plants developed characteristic deficiency symptoms such as leaf bronzing, decrease in biomass, total chlorophyll, PSII efficiency, decreased carbonic anhydrase activity and increased ROS production. Interestingly, severe alterations in root system architecture were also observed. Comprehensive transcriptome analyses of rice seedlings were carried out after 2 (DEF2W) and 4 weeks (DEF4W) of Zn deficiency with respect to transcriptome profiles of corresponding Zn sufficient conditions (SUF2W, SUF4W). Additionally, to detect the potential Zn-responsive genes, transcriptome profile of Zn-recovered seedlings was compared with DEF4W. All differentially expressed Zn-responsive genes were categorized into early and late Zn deficiency response, and a set of 77 genes, induced and repressed on Zn deficiency and re-supply, respectively, was identified. These genes could be used as low Zn-responsive marker genes. Further, genes involved in membrane transport, phytosiderophore activity and organic acid biosynthesis showed high differential expression. Additionally, the present study unravelled several genes putatively associated with alterations in root system architecture under Zn deficiency and provides novel insights into the interpretation of morpho-physiological, biochemical and molecular regulation of zinc deficiency responses in rice.
A novel glycerophosphodiester phosphodiesterase improves phosphate deficiency tolerance in rice
(John Wiley & Sons, 2019) Mehra, Poonam; Pandey, Bipin K.; Verma, Lokesh; Giri, Jitender
Soil phosphate (Pi) deficiency is major constraint for rice cultivation world‐wide. Cellular membranes account for one‐third of cellular P (Phosphorus) in the form of phospholipids. Therefore, remobilization of Pi from membrane phospholipids under Pi deficiency can be an important strategy to improve PUE (Phosphorus Use Efficiency). GDPDs (Glycerophosphodiester phosphodiesterases) hydrolyse intermediate product of phospholipid catabolism, glycerophosphodiesters to glycerol‐3‐phosphate (G3P); a precursor for P and non P‐lipid biosynthesis. Here, we show that OsGDPD2 is a Pi deficiency responsive gene which is transcriptionally regulated by OsPHR2. In silico analysis of active site residues and enzymatic assays confirmed phosphodiesterase activity of OsGDPD2. All overexpression lines showed higher GDPD activity, Pi content, root growth and biomass accumulation as compared to wild‐type. Conversely, silencing of OsGDPD2 led to decreased GDPD activity and Pi content. Notably, most of the P‐containing metabolites and fatty acids were elevated in transgenic lines. Further, quantitative analysis of polar lipids revealed higher accumulation of several classes of phospholipids and galactolipids in overexpression lines indicating a potential role of OsGDPD2 in de novo glycerolipid biosynthesis. Thus, present study provides insights into novel physiological roles of OsGDPD2 in low Pi acclimation in rice.
OsHAD1, a haloacid dehalogenase-like APase enhances phosphate accumulation
(American Society of Plant Biologists, 2017) Pandey, Bipin Kumar; Mehra, Poonam; Verma, Lokesh; Bhadouria, Jyoti; Giri, Jitender
Phosphorus (P) deficiency limits plant growth and crop yield. Since, plants can absorb only inorganic form of P (Pi), a large portion of soil P (organic and inorganic P complexes) remains largely unused. Here, we identified and characterized a PHR2 regulated; novel low Pi responsive haloacid dehalogenase (HAD)-like hydrolase, OsHAD1. While, OsHAD1 is a functional HAD protein having both acid phosphatase and phytase activity; it showed little homology with other known low Pi responsive HAD superfamily members. Recombinant OsHAD1 is highly active at acidic pH and dephosphorylates broad range of organic and inorganic P containing substrates including protein phosphates and Na-phytate. Exogenous application of recombinant OsHAD1 protein in growth media supplemented with phytate, led to marked increase in growth and total P content of Pi deficient WT rice seedlings. Further, overexpression of OsHAD1 in rice resulted in enhanced phosphatase activity, biomass, total and soluble P content in Pi deficient transgenic seedlings treated with phytate as restricted Pi source. Gene expression and metabolite profiling revealed enhanced Pi starvation responses such as upregulation of multiple genes involved in Pi uptake and solubilization, accumulation of organic acids, enhanced secretory phosphatase activity and depletion of ATP in overexpression lines as compared to WT. To elucidate the underlying regulatory mechanisms of OsHAD1, we performed in-vitro pull down assays which revealed association of OsHAD1 with protein kinases. We conclude that besides dephosphorylation of cellular organic-P, OsHAD1 in coordination with kinases may regulate phosphorylation status of downstream targets to accomplish Pi homeostasis under limited Pi supply.
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, Poonam
Jasmonic 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.
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.
OsJAZ9 overexpression modulates jasmonic acid biosynthesis and potassium deficiency responses in rice
(Springer Nature Publishing AG, 2020) Singh, Ajit Pal; Pandey, Bipin K.; Mehra, Poonam; Heitz, Thierry; Giri, Jitender
Potassium (K) represents up to 10% of the plant’s total dry biomass, and its deficiency makes plants highly susceptible to both abiotic and biotic stresses. K shortage results in the inhibition of root and shoots growth, but the underlying mechanism of this response is unclear. Our RNA-Seq and qPCR analysis suggested leading roles for JA pathway genes under K deficiency in rice. Notably, K deficiency and JA application produced similar phenotypic and transcriptional responses. Here, we integrated molecular, physiological and morphological studies to analyze the role of OsJAZ9 in JA homeostasis and K deficiency responses. We raised OsJAZ9 over-expression, knockdown, transcriptional reporter, translational reporter and C-terminal deleted translational reporter lines in rice to establish the role of JA signaling in K ion homeostasis. JA profiling revealed significantly increased JA-Ile levels in OsJAZ9 OE lines under K deficiency. Furthermore, we established that OsJAZ9 overexpression and knockdown result in K deficiency tolerance and sensitivity, respectively, by modulating various K transporters and root system architecture. Our data provide evidence on the crucial roles of OsJAZ9 for improving K deficiency tolerance in rice by altering JA levels and JA responses.
OsMED14_2, a tail module subunit of mediator complex, controls rice development and involves jasmonic acid
(Elsevier B.V., 2024) Prusty, Ankita; Mehra, Poonam; Sharma, Shivam; Malik, Naveen; Agarwal, Pinky; Parida, Swarup K.; Kapoor, Sanjay; Tyagi, Akhilesh K.
The Mediator complex is essential for eukaryotic transcription, yet its role and the function of its individual subunits in plants, especially in rice, remain poorly understood. Here, we investigate the function of OsMED14_2, a subunit of the Mediator tail module, in rice development. Overexpression and knockout of OsMED14_2 resulted in notable changes in panicle morphology and grain size. Microscopic analysis revealed impact of overexpression on pollen maturation, reflected by reduced viability, irregular shapes, and aberrant intine development. OsMED14_2 was found to interact with proteins involved in pollen development, namely, OsMADS62, OsMADS63 and OsMADS68, and its overexpression negatively affected the expression of OsMADS68 and the expression of other genes involved in intine development, including OsCAP1, OsGCD1, OsRIP1, and OsCPK29. Additionally, we found that OsMED14_2 overexpression influences jasmonic acid (JA) homeostasis, affecting bioactive JA levels, and expression of OsJAZ genes. Our data suggest OsMED14_2 may act as a regulator of JA-responsive genes through its interactions with OsHDAC6 and OsJAZ repressors. These findings contribute to better understanding of the Mediator complex's role in plant traits regulation.
Phosphate deficiency inducible OsGDPD5 affects root growth by regulating sugar-auxin crosstalk
(John Wiley & Sons, 2025) Verma, Lokesh; Pandey, Mandavi; Bhatia, Chitra; Mehra, Poonam; Singh, Bhagat; Giri, Jitender
Glycerophosphodiester phosphodiesterases (GDPDs) enzymes are known to be involved in phospholipids degradation pathways, where glycerophosphodiesters are hydrolyzed to glycerol-3-phosphate (G3P) and corresponding alcohol. In plants, GDPDs are involved in phosphate deficiency adaptive responses and have been shown to impact root length, but the precise mechanism remains unclear. This study focuses on the rice GDPD5 gene and its role in regulating primary root growth. Our research demonstrates that OsGDPD5 encodes a functional GDPD enzyme and could hydrolyze glycerophosphocholine and glycerophosphorylethanolamine. At transcriptional levels, OsGDPD5 is preferentially expressed in the root tip and regulated by transcription factor OsPHR2. We have used CRISPR/Cas9 to generate OsGDPD5 knock-out lines, allowing us to explore its role in root growth. Our findings show that osgdpd5 mutants had a shorter primary root, which could be restored to a normal level by the exogenous application of sugar or G3P. Further, knocking out OsGDPD5 alters endogenous levels of G3P and sugars, affecting auxin biosynthesis in the root and, ultimately, primary root growth. In this manner, OsGDPD5 has a crucial role in regulating physiological processes, specifically sugar and auxin signaling, which are known to be involved in root growth regulation in rice. Our research thus unraveled a link between rice phosphate deficiency-responsive lipid remodeling and root growth via sugar-hormone signaling.
Phosphorus starvation response in plants and opportunities for crop improvement
(Wiley, 2013) Pandey, Bipin K.; Mehra, Poonam; Giri, Jitender
Phosphorus (P) is one of the most essential nutrients for the adequate growth and development of plants as well as a crucial component of all life forms. Plants absorb P only in the inorganic form of orthophosphate (Pi). The availability of soluble Pi in most of the world's soil is poor as compared to its requirement for optimum growth and crop yield. Application of P fertilizers is a common practice to grow crop plants in P-poor soils. However, highly reactive Pi easily forms insoluble complexes in soil and a large fraction of applied Pi fertilizer becomes unavailable to plants. This problem is further compounded as the source of P fertilizers (i.e., P rocks) may be exhausted in the near future. Plants have evolved physiologically, biochemically, and morphologically to cope with Pi starvation through modification of the root system architecture for better Pi uptake and remobilize the internal Pi content. Genetic regulation of these adaptations has been explored to some extent and thus provides the resource for crop improvement using transgenics or plant breeding approaches. This complex network is regulated by transcription factors, microRNAs, membrane transporters, kinases/phosphatases, ubiquitin conjugase, and various hormones. Sugars have also been shown to play important roles in Pi starvation-mediated gene expression. Here, we review the recent progress made in delineating the functions of genetic elements in terms of modulating the Pi starvation response in plants. We further explore the possible strategies for crop improvement using available resources.
Root-expressed rice PAP3b enhances secreted APase activity and helps utilize organic phosphate
(Oxford University Press, 2023) Bhadouria, Jyoti; Mehra, Poonam; Verma, Lokesh; Pazhamala, Lekha T; Rumi, Rumi; Panchal, Poonam; Sinha, Alok Krishna; Giri, Jitender
Phosphate (Pi) deficiency leads to the induction of purple acid phosphatases (PAPs) in plants, which dephosphorylates organic phosphorus complexes in the rhizosphere and intracellular compartments to release Pi. In this study, we demonstrate that OsPAP3b belongs to group III low molecular weight PAP, and is low Pi responsive, preferentially in roots. The expression of OsPAP3b is negatively regulated with Pi re-supply. Interestingly, OsPAP3b was found to be dual localized to the nucleus and secretome. Furthermore, OsPAP3b is transcriptionally regulated by OsPHR2 as substantiated by DNA-protein binding assay. Through in-vitro biochemical assays, we further demonstrate that OsPAP3b is a functional acid phosphatase with broad substrate specificity. Overexpression of OsPAP3b in rice led to increased secreted APase activity and improved mineralization of organic P sources, reflected in better growth of transgenics compared to wild type when grown on organic P as exogenous P substrate. Under Pi deprivation, OsPAP3b knockdown and knockout lines showed no significant changes in total P content and dry biomass. However, the expression of other phosphate starvation-induced (PSI) genes and the levels of metabolites were found to be altered in the overexpression and knockdown lines. In addition, in-vitro pull-down assay revealed multiple putative interacting proteins of OsPAP3b. Our data collectively suggest that OsPAP3b can aid in organic P utilization in rice. The APase isoforms behavior and nuclear localization indicate its additional role, possibly in stress signaling. Considering its important roles, OsPAP3b could be a potential target for improving low Pi adaptation in rice.