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Item Sweet shaping of root system architecture under water deficit(Oxford University Press, 2026) Singh, Dhriti; Awasthi, Prakhar; Sharma, Aishwarye; Samtani, Harsha; Shukla, Brihaspati Narayana; Laxmi, AshveryaRoot growth direction under water-deficit conditions is critical for plant survival. Increasing agar concentration in the growth medium simulates stress conditions, limiting water availability. Our study highlights the role of glucose (Glc) in orchestrating the root growth deviation in Arabidopsis under stress conditions. We demonstrate that Glc-TOR signaling plays a central role in modulating root growth direction under stress conditions. Conversely, cytokinin (CK) signaling reduces root deviation during water deficit. We further show that Glc downregulates CK signaling under water-deficit conditions, while CK negatively influences Glc–TOR activity. The interplay between Glc-TOR and CK signaling pathways fine-tunes root orientation by modulating auxin transport and signaling. Collectively, our findings show that in Arabidopsis, Glc-induced changes in root architecture are mediated through its antagonistic interaction with CK signaling, contributing to enhanced root plasticity and improved adaptation to water-limited conditions.Item Mitogen-activated protein kinase 3/6 regulates the stability of AtIAA3 and AtIAA7 during auxin signaling in Arabidopsis(Elsevier B.V., 2026) Noryang, Stanzin; Manna, Mrinalini; Verma, Neetu; Singh, Kirti; Tayyeba, Sumaira; Sinha, Alok KrishnaAuxin mediated Aux/IAA degradation is required to release the ARFs from the control of IAAs, and ARFs in the free forms perform their role of transcription activation or suppression in response to developmental ques. Auxin is known to tag IAAs for proteasomal degradation, but how this tagging is regulated has not been widely explored. Here we report that, in Arabidopsis, exogenous application of auxin activates MPK3/6 which in turn phosphorylate IAA3 and IAA7 at Ser-58 and Ser-26, respectively. Further, incubation of IAA3 and IAA7 with the protein extracts from auxin treated mpk3 or mpk6 single mutants increase the rate of degradation of IAAs. Consequently, the phospho-null mutants, IAA3S58A and IAA7S26A were observed to be comparatively more stable. Thus, MAP kinase-mediated phosphorylation destabilised IAA3 and IAA7 leading to their degradation. Additionally, over-expression of the phospho-dead mutant of IAA3 (35S:IAA3S58A) and complementation of iaa3 mutant with this phospho-dead mutant resulted in reduced primary root length because of increased stability and accumulation of IAA3. Interestingly, we found that a member of ARF, ARF7 regulated the expression of MPKs by binding to their respective promoters.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 Host manipulations within mutualisms: Role of plant hormones in selective resource allocation(Springer Nature Publishing AG, 2025) Kulkarni, Manasa; Vadassery, Jyothilakshmi; Borges, Renee M.In some mutualisms involving host plants, photoassimilates are provided as rewards to symbionts. Endophagous organisms often manipulate host plants to increase access to photoassimilates. Host manipulations by endophagous organisms that are also mutualists are poorly understood. We show host plant manipulations by symbionts and the role of phytohormones, i.e. the auxin indole-3-acetic acid (IAA), and the cytokinin trans-zeatin (tZ), in the brood-site pollination mutualism between fig trees and pollinator fig wasps. In this interaction, pollinator wasps pollinate Ficus flowers within an enclosed inflorescence called a syconium, in exchange for flowers that develop into galls nourishing pollinator offspring. To examine host manipulation by pollinator galls by affecting host fitness through seed reduction, we compared growth hormones released by syconial occupants within three experimentally produced treatment groups of syconia: S (containing only seeds), G (containing only pollinator galls) and SG (containing seeds and pollinator galls). We harvested syconia from each treatment in early and mid-phases of syconial maturation when maximal growth occurs and measured hormone levels. Hormones were reduced by mid-phase in general; however, their levels were mostly sustained in G syconia in the mid-phase, suggesting that galls manipulate the host to continuously access resources. We found no difference in IAA and tZ levels of S and G syconia. IAA concentrations were higher in SG syconia. From the perspective of the maintenance of mutualism, syconium volume and hormone concentrations were highest when both seeds and galls were present (SG treatment), indicating that both partners control allocation of resources to syconia.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 Genome-wide identification of auxin response factors (ARFs) in three different species of Arachis(Springer Nature Publishing AG, 2021) Raul, Bikash; Bhattacharjee, Oindrila; Tembhare, Kunal; Khanna, Tanyya; Shaheen, Tarannum; Sinharoy, Senjuti; Bandyopadhyay, KaustavThe phytohormone auxin is involved in the regulation of plant growth, nutrient acquisition, and response to environmental stimuli. Auxin response factors (ARFs) are transcription factors containing B3 DNA binding domain. ARFs play central role in auxin response, using Aux/IAA proteins as partners. Arachis is a genus within the Dalbergioid clade of papilionoid legumes, which out-branched from other members of papilionoids. Cultivated peanut (Arachis hypogaea L.) is an allotetraploid formed by hybridization of two parental genotypes Arachis duranensis, and Arachis ipaensis merely 10,000 years ago. We have made a genome-wide inventory of all the ARFs present in tetraploid A. hypogaea, as well as in two diploid parental genotypes. Our data show that Arachis contains more ARFs per diploid genome (around 31), compared to other legumes (around 25). We further observed few ARF-like genes which are defective in important domains. Most of the ARFs in tetraploid Arachis are redundant, representing the A and B sub-genomes. Some of the ARFs show expression bias from either A or B sub-genome, while some of the pairs are expressed from both sub-genomes. Many ARFs do not express in any of the conditions for which we have expression data. Finally, few pairs show diferential spatio-temporal expression pattern from A and B sub-genomes, indicative of diversifcation of function. This is the frst efort to list all the ARFs from an allotetraploid legume. The list of ARFs in all three species of Arachis will help the scientifc community working to understand auxin regulation in crop legumes.Item Expression profiling of miRNAs indicates crosstalk between phytohormonal response and rhizobial infection in chickpea(Springer Nature Publishing AG, 2020) Tiwari, Manish; Bhatia, SabhyataLegumes develop root nodules in which bacteria fix nitrogen for plants. The phytohormones auxin and cytokinin regulate nodule organogenesis by recruiting various genes to effect symbiosis. Moreover, these genes are regulated by the action of microRNAs also. To understand the complex regulatory network involving miRNAs in response to phytohormones and rhizobial interactions in chickpea roots, a miRNA expression profiling was performed. Indole acetic acid and 6-benzylaminopurine at concentrations of 0.1, 1 and 10 lM were used for auxin and cytokinin exogenous treatment and Mesorhizobium ciceri to study rhizobial interaction with chickpea root. Expression profiling of a set of 11 miRNAs was performed. Further, the targets of the candidate miRNAs were identified, followed by functional annotation. This analysis revealed that cat-miR160, cat-miR164, cat-miR396 and cat-miR398 were responsive to auxin and cytokinin. cat-miR319 was found to be only auxin responsive and is known to regulate auxin signalling by targeting TEOSINTE BRANCHED/ CYCLOIDEA/PCF (TCP) which interacts with auxin inducible genes. Further, cytokinin elicited a response at very low concentration of 0.1 lM, and most of the miRNAs investigated were responsive to cytokinin. Interactome analysis revealed that cat-miR164 and cat-miR168 work in conjunction to regulate auxin signalling. Interestingly, cat-miR169 and cat-miR482 were low expressing during auxin treatment and M. ciceri infection but their expression spiked during cytokinin treatment, indicating a cytokinin mediated mode of action. The miRNA expression profiling in response to phytohormones and rhizobia and the reported function of their target genes suggested a crosstalk among the phytohormonal responses during chickpea nodulation.Item Mediator subunit OsMED14_1 plays an important role in rice development(John Wiley & Sons, 2020) Malik, Naveen; Ranjan, Rajeev; Parida, Swarup K.; Agarwal, Pinky; Tyagi, Akhilesh K.Mediator, a multi‐subunit coactivator complex, regulates transcription in eukaryotes and is involved in diverse processes in Arabidopsis through its different subunits. Here, we have explored developmental aspects of one of the rice Mediator subunit gene OsMED14_1. We analyzed its expression pattern through RNA in‐situ hybridization and pOsMED14_1:GUS transgenics which showed its expression in roots, leaves, anthers and seeds prominently at younger stages, indicating possible involvement of this subunit in multiple aspects of rice development. To understand developmental roles of OsMED14_1 in rice, we generated and studied RNAi based knockdown rice plants which showed multiple effects including less height, narrower leaves and culms with reduced vasculature, lesser lateral root branching, defective microspore development, reduced panicle branching and seed set, and smaller seeds. Histological analyses showed that slender organs were caused by reduction in both cell number and cell size in OsMED14_1 knockdown plants. Flow cytometric analyses and expression analyses of cell‐cycle related genes revealed that defective cell‐cycle progression led to these defects. Expression analyses of auxin related genes and IAA immuno‐localization study indicated altered auxin level in these knockdown plants. Reduction of lateral root branching in knockdown plants was corrected by exogenous IAA supplement. OsMED14_1 physically interacts with transcription factors YABBY5, TDR and MADS29, possibly regulating auxin homeostasis and ultimately leading to lateral organ/leaf, microspore and seed development.Item Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thaliana(BioMed Central Ltd, 2019) Kumari, Sony; Yadav, Sandeep; Patra, Debadutta; Singh, Sharmila; Sarkar, Ananda K.; Panigrahi, Kishore C. S.Background Root morphology is known to be affected by light quality, quantity and direction. Light signal is perceived at the shoot, translocated to roots through vasculature and further modulates the root development. Photoreceptors are differentially expressed in both shoot and root cells. The light irradiation to the root affects shoot morphology as well as whole plant development. The current work aims to understand the white light intensity dependent changes in root patterning and correlate that with the global gene expression profile. Results Different fluence of white light (WL) regulate overall root development via modulating the expression of a specific set of genes. Phytochrome A deficient Arabidopsis thaliana (phyA-211) showed shorter primary root compared to phytochrome B deficient (phyB-9) and wild type (WT) seedlings at a lower light intensity. However, at higher intensity, both mutants showed shorter primary root in comparison to WT. The lateral root number was observed to be lowest in phyA-211 at intensities of 38 and 75 μmol m − 2 s − 1. The number of adventitious roots was significantly lower in phyA-211 as compared to WT and phyB-9 under all light intensities tested. With the root phenotypic data, microarray was performed for four different intensities of WL light in WT. Here, we identified ~ 5243 differentially expressed genes (DEGs) under all light intensities. Gene ontology-based analysis indicated that different intensities of WL predominantly affect a subset of genes having catalytic activity and localized to the cytoplasm and membrane. Furthermore, when root is irradiated with different intensities of WL, several key genes involved in hormone, light signaling and clock-regulated pathways are differentially expressed. Conclusion Using genome wide microarray-based approach, we have identified candidate genes in Arabidopsis root that responded to the changes in light intensities. Alteration in expression of genes such as PIF4, COL9, EPR1, CIP1, ARF18, ARR6, SAUR9, TOC1 etc. which are involved in light, hormone and clock pathway was validated by qRT-PCR. This indicates their potential role in light intensity mediated root development.Item Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate(Nature Publishing Group, 2018) Giri, Jitender; Bhosale, Rahul; Huang, Guoqiang; Pandey, Bipin K.; Parker, Helen; Zappala, Susan; Yang, Jing; Dievart, Anne; Bureau, Charlotte; Ljung, Karin; Price, Adam; Rose, Terry; Larrieu, Antoine; Mairhofer, Stefan; Sturrock, Craig J.; White, Philip; Dupuy, Lionel; Hawkesford, Malcolm; Perin, Christophe; Liang, Wanqi; Peret, Benjamin; Hodgman, Charlie T.; Lynch, Jonathan; Wissuwa, Matthias; Zhang, Dabing; Pridmore, Tony; Mooney, Sacha J.; Guiderdoni, Emmanuel; Swarup, Ranjan; Bennett, Malcolm J.Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice.