Publications of NIPGR Scientists
Permanent URI for this communityhttps://ndkr-library.nipgr.ac.in/handle/123456789/1
Browse
44 results
Search Results
Item Genome wide investigation and transcriptional profiling of SWEET genes in two contrasting cultivars of foxtail millet under abiotic stresses(Elsevier B.V., 2025) Singh, Jitender; Singh, Kajol BM.; Sutar, Rashmi Ranjan; Kumar, Angad; Prasad, Manoj; Thakur, Jitendra K.The SWEET (Sugars will eventually be exported transporter) gene family is an important class of sugar transporters that regulates diverse aspects of plant physiology such as apoplastic phloem loading, plant-pathogen interactions and plant responses to abiotic stresses. While majority of the studies on SWEET family in plants have been performed in C3 species, there are limited reports on C4 plants. In this study we conducted genome wide investigation of the SWEET gene family in foxtail millet, a naturally stress tolerant C4 crop. In-silico analysis identified 24 SWEET genes in foxtail millet genome that were classified into 4 distinct clades. Domain analysis revealed the presence of conserved MtN3_slv/PQ-loop domains in all identified SWEET proteins. Interestingly, many SWEET proteins also harboured the prokaryotic SemiSWEET/PQ-loop domain suggesting an evolutionary link to their prokaryotic Semi-SWEET ancestors. In-silico analysis predicted the presence of abscisic acid and drought responsive cis-elements in the promoter region of SWEET genes. Transcriptional analysis under control, drought, and salinity stress revealed differential expression patterns of SWEET genes in stress resistant and stress susceptible foxtail millet cultivars. Moreover, the differential expression of SWEET genes altered the soluble sugar content in leaves and roots under stress conditions suggesting altered carbon re-allocation between source and sink tissues. This study significantly advances our understanding of the SWEET gene family in C4 plants, particularly in foxtail millet, and provides insights into its role in stress tolerance mechanisms and carbohydrate re-allocation under stress conditions.Item MediatorWeb: a protein-protein interaction network database for the RNA polymerase II Mediator complex(John Wiley & Sons, 2024) Maji, Sourobh; Waseem, Mohd; Sharma, Manish Kumar; Singh, Maninder; Singh, Anamika; Dwivedi, Nidhi; Thakur, Pallabi; Cooper, David G.; Bisht, Naveen C.; Fassler, Jan S.; Subbarao, Naidu; Khurana, Jitendra P.; Bhavesh, Neel Sarovar; Thakur, Jitendra K.The protein-protein interaction (PPI) network of the Mediator complex is very tightly regulated and depends on different developmental and environmental cues. Here, we present an interactive platform for comparative analysis of the Mediator subunits from humans, baker's yeast Saccharomyces cerevisiae, and model plant Arabidopsis thaliana in a user-friendly web-interface database called MediatorWeb. MediatorWeb provides an interface to visualize and analyze the PPI network of Mediator subunits. The database facilitates downloading the untargeted and unweighted network of Mediator complex, its submodules, and individual Mediator subunits to better visualize the importance of individual Mediator subunits or their submodules. Further, MediatorWeb offers network visualization of the Mediator complex and interacting proteins that are functionally annotated. This feature provides clues to understand functions of Mediator subunits in different processes. In an additional tab, MediatorWeb provides quick access to secondary and tertiary structures, as well as residue-level contact information for Mediator subunits in each of the three model organisms. Another useful feature of MediatorWeb is detection of interologs based on orthologous analyses, which can provide clues to understand the functions of Mediator complex in less explored kingdoms. Thus, MediatorWeb and its features can help the user to understand the role of Mediator complex and its subunits in the transcription regulation of gene expression.Item Serine hydroxymethyltransferase6 is involved in growth and resistance against pathogens via ethylene and lignin production in Arabidopsis(John Wiley & Sons, 2024) Singh, Pooja; Kumari, Aprajita; Khaladhar, Vemula Chandra; Singh, Namrata; Pathak, Pradeep Kumar; Kumar, Vinod; Kumar, Ritika Jantu; Jain, Priyanka; Thakur, Jitendra K.; Fernie, Alisdair R.; Bauwe, Hermann; Raghavendra, A.S.; Gupta, Kapuganti JagadisPhotorespiratory serine hydroxymethyltransferases (SHMTs) are important enzymes of cellular one-carbon metabolism. In this study, we investigated the potential role of SHMT6 in Arabidopsis thaliana. We found that SHMT6 is localized in the nucleus and expressed in different tissues during development. Interestingly SHMT6 is inducible in response to avirulent, virulent Pseudomonas syringae and to Fusarium oxysporum infection. Overexpression of SHMT6 leads to larger flowers, siliques, seeds, roots, and consequently an enhanced overall biomass. This enhanced growth was accompanied by increased stomatal conductance and photosynthetic capacity as well as ATP, protein, and chlorophyll levels. By contrast, a shmt6 knockout mutant displayed reduced growth. When challenged with Pseudomonas syringae pv tomato (Pst) DC3000 expressing AvrRpm1, SHMT6 overexpression lines displayed a clear hypersensitive response which was characterized by enhanced electrolyte leakage and reduced bacterial growth. In response to virulent Pst DC3000, the shmt6 mutant developed severe disease symptoms and becomes very susceptible, whereas SHMT6 overexpression lines showed enhanced resistance with increased expression of defense pathway associated genes. In response to Fusarium oxysporum, overexpression lines showed a reduction in symptoms. Moreover, SHMT6 overexpression lead to enhanced production of ethylene and lignin, which are important components of the defense response. Collectively, our data revealed that SHMT6 plays an important role in development and defense against pathogens.Item Co-overexpression of SWEET sucrose transporters modulates sucrose synthesis and defence responses to enhance immunity against bacterial blight in rice(John Wiley & Sons, 2024) Singh, Jitender; James, Donald; Das, Shubhashis; Patel, Manish Kumar; Sutar, Rashmi Ranjan; Achary, V. Mohan Murali; Goel, Naveen; Gupta, Kapuganti Jagadis; Reddy, Malireddy K.; Jha, Gopaljee; Sonti, Ramesh V.; Foyer, Christine H.; Thakur, Jitendra K.; Tripathy, Baishnab C.Enhancing carbohydrate export from source to sink tissues is considered to be a realistic approach for improving photosynthetic efficiency and crop yield. The rice sucrose transporters OsSUT1, OsSWEET11a and OsSWEET14 contribute to sucrose phloem loading and seed filling. Crucially, Xanthomonas oryzae pv. oryzae (Xoo) infection in rice enhances the expression of OsSWEET11a and OsSWEET14 genes, and causes leaf blight. Here we show that co‐overexpression of OsSUT1, OsSWEET11a and OsSWEET14 in rice reduced sucrose synthesis and transport leading to lower growth and yield but reduced susceptibility to Xoo relative to controls. The immunity‐related hypersensitive response (HR) was enhanced in the transformed lines as indicated by the increased expression of defence genes, higher salicylic acid content and presence of HR lesions on the leaves. The results suggest that the increased expression of OsSWEET11a and OsSWEET14 in rice is perceived as a pathogen (Xoo) attack that triggers HR and results in constitutive activation of plant defences that are related to the signalling pathways of pathogen starvation. These findings provide a mechanistic basis for the trade‐off between plant growth and immunity because decreased susceptibility against Xoo compromised plant growth and yield.Item Identification of novel inhibitors against Med15a KIX domain of Candida glabrata(Elsevier B.V., 2023) Waseem, Mohd; Das, Shubhashis; Mondal, Debarati; Jain, Monika; Thakur, Jitendra K.; Subbarao, NaiduCandida glabrata, the second most common cause of invasive fungal infections, exhibits multi-drug resistance to commonly used antifungal drugs. To counter this resistance, there is a critical need for novel antifungals. This study identifies small molecule inhibitors that target a three-helix bundle KIX domain in the Med15a Mediator subunit of Candida glabrata (CgMed15a KIX). This domain plays a crucial role by interacting with the Pleiotropic Drug Resistance transcription factor Pdr1, a key regulator of the multidrug resistance pathway in Candida glabrata. We performed high throughput computational screening of large chemical datasets against the binding sites of the CgMed15a KIX domain to identify novel inhibitors. We selected six potential candidates with high affinity and confirmed their binding with the CgMed15a KIX domain. A phytochemical compound, Chebulinic acid binds to the CgMed15a KIX domain with a KD value of 0.339 μM and shows significant inhibitory effects on the growth of Candida glabrata. Molecular dynamics simulation studies further revealed the structural stability of the CgMed15a KIX-Chebulinic acid complex. Thus, in conclusion, this study highlights Chebulinic acid as a novel potential antifungal compound against Candida glabrata.Item MEDIATOR SUBUNIT17 is required for transcriptional optimization of root system architecture in Arabidopsis(Oxford University Press, 2023) Agrawal, Rekha; Singh, Amrita; Giri, Jitender; Magyar, Zoltan; Thakur, Jitendra K.Sucrose and auxin are well-known determinants of root system architecture (RSA). However, the factors that connect the signaling pathways evoked by these two critical factors during root development are poorly understood. In this study, we report the role of MEDIATOR SUBUNIT17 (MED17) in RSA and its involvement in the transcriptional integration of sugar and auxin signaling pathways in Arabidopsis (Arabidopsis thaliana). Sucrose regulates root meristem activation through the TARGET OF RAPAMYCIN-E2 PROMOTER BINDING FACTOR A TOR-E2FA pathway, and auxin regulates lateral root (LR) development through AUXIN RESPONSE FACTOR-LATERAL ORGAN BOUNDARIES DOMAIN ARF-LBDs. Both sucrose and auxin play a vital role during primary and LR development. However, there is no clarity on how sucrose is involved in the ARF-dependent regulation of auxin-responsive genes. This study establishes MED17 as a nodal point to connect sucrose and auxin signaling. Transcription of MED17 was induced by sucrose in an E2FA/B-dependent manner. Moreover, E2FA/B interacted with MED17, which can aid in the recruitment of the Mediator complex on the target promoters. Interestingly, E2FA/B and MED17 also occupied the promoter of ARF7, but not ARF19, leading to ARF7 expression, which then activates auxin signaling and thus initiates LR development. MED17 also activated cell division in the root meristem by occupying the promoters of cell-cycle genes, thus regulating their transcription. Thus, MED17 plays an important role in relaying the transcriptional signal from sucrose to auxin-responsive and cell-cycle genes to regulate primary and lateral root development, highlighting the role of the Mediator as the transcriptional processor for optimal root system architecture in Arabidopsis.Item Physiological implications of SWEETs in plants and their potential applications in improving source-sink relationships for enhanced yield(John Wiley & Sons, 2023) Singh, Jitender; Das, Shubhashis; Gupta, Kapuganti Jagadis; Ranjan, Aashish; Foyer, Christine H; Thakur, Jitendra K.The SWEET (SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTERS) family of transporters in plants is identified as a novel class of sugar carriers capable of transporting sugars, sugar alcohols, and hormones. Functioning in intercellular sugar transport, SWEETs influence a wide range of physiologically important processes. SWEETs regulate the development of sink organs by providing nutritional support from source leaves, responses to abiotic stresses by maintaining intracellular sugar concentrations, and host-pathogen interactions through the modulation of apoplastic sugar levels. Many bacterial and fungal pathogens activate the expression of SWEET genes in species such as rice and Arabidopsis to gain access to the nutrients that support virulence. The genetic manipulation of SWEETs has led to the generation of Bacterial Blight (BB) resistant rice varieties. Similarly, while the overexpression of the SWEETs involved in sucrose export from leaves and pathogenesis led to growth retardation and yield penalties, plants overexpressing SWEETs show improved disease resistance. Such findings demonstrate the complex functions of SWEETs in growth and stress tolerance. Here, we review the importance of SWEETs in plant-pathogen and source-sink interactions and abiotic stress resistance. We highlight the possible applications of SWEETs in crop improvement programs aimed at improving sink and source strengths important for enhancing the sustainability of yield. We discuss how the adverse effects of the overexpression of SWEETs on plant growth may be overcome.Item Role of C4 photosynthetic enzyme isoforms in C3 plants and their potential applications in improving agronomic traits in crops(Springer Nature Publishing AG, 2022) Singh, Jitender; Garai, Sampurna; Das, Shubhashis; Thakur, Jitendra K.; Tripathy, Baishnab CharanAs compared to C3, C4 plants have higher photosynthetic rates and better tolerance to high temperature and drought. These traits are highly beneficial in the current scenario of global warming. Interestingly, all the genes of the C4 photosynthetic pathway are present in C3 plants, although they are involved in diverse non-photosynthetic functions. Non-photosynthetic isoforms of carbonic anhydrase (CA), phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), the decarboxylating enzymes NAD/NADP-malic enzyme (NAD/NADP-ME), and phosphoenolpyruvate carboxykinase (PEPCK), and finally pyruvate orthophosphate dikinase (PPDK) catalyze reactions that are essential for major plant metabolism pathways, such as the tricarboxylic acid (TCA) cycle, maintenance of cellular pH, uptake of nutrients and their assimilation. Consistent with this view differential expression pattern of these non-photosynthetic C3 isoforms has been observed in different tissues across the plant developmental stages, such as germination, grain filling, and leaf senescence. Also abundance of these C3 isoforms is increased considerably in response to environmental fluctuations particularly during abiotic stress. Here we review the vital roles played by C3 isoforms of C4 enzymes and the probable mechanisms by which they help plants in acclimation to adverse growth conditions. Further, their potential applications to increase the agronomic trait value of C3 crops is discussed.Item Root hair-specific transcriptome reveals response to low phosphorus in Cicer arietinum(Frontiers Media S.A., 2022) Kohli, Pawandeep Singh; Pazhamala, Lekha T; Mani, Balaji; Thakur, Jitendra K.; Giri, JitenderRoot hairs (RH) are a single-cell extension of root epidermal cells. In low phosphorus (LP) availability, RH length and density increase thus expanding the total root surface area for phosphate (Pi) acquisition. However, details on genes involved in RH development and response to LP are missing in an agronomically important leguminous crop, chickpea. To elucidate this response in chickpea, we performed tissue-specific RNA-sequencing and analyzed the transcriptome modulation for RH and root without RH (Root-RH) under LP. Root hair initiation and cellular differentiation genes like RSL TFs and ROPGEFs are upregulated in Root-RH, explaining denser, and ectopic RH in LP. In RH, genes involved in tip growth processes and phytohormonal biosynthesis like cell wall synthesis and loosening (cellulose synthase A catalytic subunit, CaEXPA2, CaGRP2, and CaXTH2), cytoskeleton/vesicle transport, and ethylene biosynthesis are upregulated. Besides RH development, genes involved in LP responses like lipid and/or pectin P remobilization and acid phosphatases are induced in these tissues summarizing a complete molecular response to LP. Further, RH displayed preferential enrichment of processes involved in symbiotic interactions, which provide an additional benefit during LP. In conclusion, RH shows a multi-faceted response that starts with molecular changes for epidermal cell differentiation and RH initiation in Root-RH and later induction of tip growth and various LP responses in elongated RH.Item Endosperm ontogeny through the lens of epigenetics(Elsevier B.V., 2023) Singh, Kajol B.M.; Thakur, Jitendra K.Endosperm tissue is crucial to seed development. Monocots and dicots have evolved different fates for their endosperm: it is usually consumed in dicots during seed development, while monocots seeds retain the endosperm till maturity. Recently, Wu et al. addressed the role of divergent epigenetic regulation over functionally conserved IKU2 gene contributing to silenced or persistent endosperm proliferation and has provided insights into diverged seed ontogeny pattern in plants. Here, we highlight the novel findings of this study and their potential significance. Seed production represents a remarkable life-history adaptation that has been established during plant evolution. In flowering plants, a double fertilization event initiates seed development, producing embryo and the endosperm. Endosperm (3n) is a triploid outcome of second fertilization, which occurs when a female central cell (2n) fuses with one of the two male gametes (n) carried by the pollen tube (Ingram, 2020). It develops precociously and is primed to perform nutritional and developmental functions for embryo growth (Povilus & Gehring, 2022). Different taxa have evolved specific seed formation patterns that elicit different levels of endosperm perseverance during development (Baroux et al., 2002). As a result of this, the endosperm-to-embryo ratio in mature seeds has varied gradually among different plants. As an example, endosperm in cereals is formed and retained as a nutritive reserve till seed maturity. In several eudicots such as Arabidopsis, early formed endosperm is substantially devoured to serve during embryo maturation. In peas with non-persistent endosperm, the tissue appears to be absorbed in the early free nuclear division phase before cell wall formation. The Podostomenaceae and Orchidaceae are the two endosperm-free lineages because their seeds lack or terminate endosperm nuclear divisions during early stages. Endosperm develops through two major phases: first syncytial involving continuous nuclear divisions, and the subsequent cellularization in which the free nuclear state develops cell wall (Baroux et al., 2002). Despite that the embryo produces the next generation progeny, endosperm proliferation and cellularization timing is crucial to embryo viability.