Institutional Publications

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Start date: 2020Subject: search.filters.subject.Arabidopsis thaliana

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    Temperature regulation of cell cycle and growth dynamics in Arabidopsis
    (Portland Press, 2026) Sundaravadivelu, Vasundara; Raipuria, Ritesh Kumar; Ranjan, Aashish
    The plant cell cycle is a highly coordinated and regulated process that integrates endogenous and environmental signals to control cell division, meristem maintenance, and cell fate specification for growth and development. Temperature is a critical environmental signal that regulates the cell cycle to manifest developmental plasticity in Arabidopsis roots and shoots. Arabidopsis plants exhibit either adaptive growth responses or arrested growth, depending on the temperature regime. The temperature-mediated growth dynamics in Arabidopsis involve altered cell-cycle regulation. While plant developmental and physiological responses to temperature have been extensively studied, the integration of temperature signalling cues with cell-cycle dynamics to regulate growth adaptation remains poorly understood. The present review not only compiles existing information on temperature-mediated regulation of cell-cycle dynamics but also provides a perspective on multidisciplinary approaches to investigate cell-cycle dynamics at spatiotemporal resolution in Arabidopsis adaptive growth responses.
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    AtFusionDB: A comprehensive database of fusion transcripts in model plant Arabidopsis thaliana
    (Springer Nature Publishing AG, 2026) Shree, Tanu; Kumar, Shailesh
    Fusion transcripts are chimeric RNAs, produced by the joining of two different RNAs at the RNA level or as a product of gene fusion at the DNA level. In this era of high-throughput sequencing technologies, it is easy to identify novel molecules like fusion transcripts in different systems. That's because, initially, supposed to be the well-known cancer biomarkers, fusion transcripts are also validated in normal human physiology. In Planta, discrete reports are available, indicating the presence of fusion transcripts but no dedicated web resource is available for the plant-specific fusion transcripts. This chapter describes the first plant-specific database of fusion transcripts, i.e., AtFusionDB ( http://www.nipgr.res.in/AtFusionDB ), which contains the information on fusion transcripts identified in the model plant Arabidopsis thaliana. This database can be exploited to get significant information about gene/transcript fusion in plants.
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    Validation of plant fusion peptides using proteomics data
    (Springer Nature Publishing AG, 2026) Hamid, Fiza; Aftab, Sahrish; Shree, Tanu; Kumar, Shailesh
    Fusion transcripts and their fused protein products are emerging as exciting entities in molecular biology, offering potential applications in diagnostics and therapeutics. These fusion proteins, derived from the translation of fusion transcripts, hold promise as unique biomarkers and targets for intervention. While numerous algorithms exist to identify fusion RNAs, the detection and validation of their protein counterparts through proteomics remains a growing area of research. This challenge is particularly intriguing in plant biology, where fusion events may affect stress responses, development, and adaptation. This chapter provides an accessible and practical workflow for validating plant fusion peptides using publicly available proteomics datasets.
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    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, Ashverya
    Root 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.
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    CBL1/9-CIPK6 complex negatively regulates respiratory burst oxidase homolog D in Arabidopsis thaliana
    (John Wiley & Sons, 2026) Vishwakarma, Niraj Kumar; Yadav, Shalini; Sardar, Atish; Choudhary, Megha; Chattopadhyay, Debasis
    Plant innate immune response is a well-balanced process with positive and negative regulations for the plants to survive. Calcium signaling is essential for pathogen-associated molecular pattern (PAMP)-driven respiratory burst oxidase homolog D (RBOHD)-mediated reactive oxygen species (ROS) burst. We show that calcium sensors calcineurin B like protein 1 (CBL1) and CBL9 and their interacting protein kinase CIPK6 negatively regulate RBOHD activity and immune response in Arabidopsis thaliana. Arabidopsis mutant cbl1cbl9, like cipk6, exhibited enhanced resistance and ROS production when infected with the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). CBL1 and CBL9 enhanced kinase activity of CIPK6. CBL1/9-CIPK6 module interacts with RBOHD at the plasma membrane. CIPK6 along with CBL1 reduces RBOHD activity in planta. CIPK6 phosphorylates the N-terminal cytoplasmic domain of RBOHD at a non-conserved (S33) and a conserved (S39) serine residue. While S39 phosphorylation increased RBOHD activity, S33 phosphorylation drastically reduced it and superseded the effect of S39 phosphorylation. We propose a model that CIPK6 phosphorylates RBOHD at S33 to suppress its activity to balance ROS generation in post-PTI situation in Arabidopsis. Our study reports a direct mechanism of negative regulation of ROS production and plant immune response by a calcium-signaling module in Arabidopsis thaliana.
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    Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana
    (Springer Nature Publishing AG, 2026) Vivek, AT; Kiran, Harikumar; Sahu, Namrata; Kalakoti, Garima; Kumar, Shailesh
    Background:- Long non-coding RNAs (lncRNAs) play key roles in regulating plant growth, development, and stress responses. Despite their increasing identification in plant transcriptomes, a systematic characterization of lncRNAs is still lacking, leaving a significant knowledge gap. To address this, we systematically identified and characterized Arabidopsis lncRNAs through integrative analysis of strand-specific RNA sequencing data and multi-omics datasets, revealing their genomic features, regulatory interactions, and evolutionary characteristics. Results:- Using a custom pipeline applied to hundreds of stranded RNA-seq datasets, we assembled a comprehensive catalog of 4,772 intergenic and antisense Arabidopsis lncRNAs. In comparing multiple key features of lncRNAs with those of protein-coding genes, we found that intergenic lncRNAs contain high transposable element-derived fragments and display broader TE diversity. Distinct DNA methylation and histone modification signatures further distinguished lncRNAs from protein-coding genes. We additionally uncovered R-loop connections and associations with sRNAs involved in post-transcriptional regulation and RNA-directed DNA methylation, with a minor subset classified as Pol V–transcribed. Of note, our results revealed lncRNAs mediating stress-responsive cis interactions and others linked to trait-associated loci. Probing further, an experimental evidence resource confirmed small peptide production from multiple lncRNA loci. Extending our investigation, comparative analyses across Brassicaceae species revealed syntenic lncRNAs enriched for shared sequence motifs despite substantial sequence divergence. Conclusions:- This study provides a valuable and extensively annotated catalog of Arabidopsis lncRNAs, revealing their diverse genomic features, regulatory interactions, and evolutionary characteristics. Altogether, our work advocates for multi-omics integrative analysis as a potent strategy to efficiently enhance lncRNA annotation, providing insights into functionality and addressing annotation limitations. Our comprehensive bioinformatic analyses of Arabidopsis lncRNAs pave the way for future functional characterization of these transcripts.
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    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 Krishna
    Auxin 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.
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    A method for isolation and transfection of arabidopsis protoplast for sucrose feeding assay
    (Springer Nature Publishing AG, 2026) Anjali, Anjali; Senthil-Kumar, Muthappa
    Protoplasts serve as a powerful system to study various plant physiological processes and to understand crucial signaling pathways within the plant system. The isolation of Arabidopsis protoplasts is a well-established technique and being utilized for wide range of assays. The method described herein includes the precise cutting of Arabidopsis leaves using extraction buffer containing cellulase and macerozyme. Further we present a polyethylene glycol [PEG]-mediated protoplast transformation method. Here, we have elucidated the methodology for isolation of protoplast for the AtSWEET-mediated sucrose uptake assay in control, and Pseudomonas syringe pv tomato DC3000 (Pst DC3000) treated leaves by utilizing GC/MS analysis. Our approach includes certain modifications to the previously published protoplast isolation technique, streamlining the process and providing a more accessible alternative to the highly specialized Xenopus oocyte uptake assay.
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    ANNInter: A platform to explore ncRNA-ncRNA interactome of Arabidopsis thaliana
    (Elsevier B.V., 2025) Vivek, AT; Sahu, Namrata; Kalakoti, Garima; Kumar, Shailesh
    Eukaryotic transcriptomes are remarkably complex, encompassing not only protein-coding RNAs but also an expanding repertoire of noncoding RNAs (ncRNAs). In plants, ncRNA-ncRNA interactions (NNIs) have emerged as pivotal regulators of gene expression, orchestrating development and adaptive responses to stress. Despite their critical roles, the functional significance of NNIs remains poorly understood, largely due to a lack of comprehensive resources. Here, we present ANNInter, a comprehensive platform that integrates computational predictions with experimental datasets to systematically identify and analyze NNIs. The current version catalogs over 90,000 interactions spanning eight categories of sRNA-to-longer ncRNAs, each extensively annotated with interaction types, identification methods, and functional descriptions. The integrated schema and advanced visualization framework in ANNInter enable users to explore intricate interaction networks, providing system-wide insights into ncRNA-mediated regulation. These interaction data provide unparalleled opportunities to uncover the regulatory roles of NNIs in key biological processes such as growth regulation, stress adaptation, and cellular signaling. By providing an extensive, curated repository of computational and degradome-based interaction data, ANNInter will provide a platform to the study of ncRNA biology, elucidating the complex mechanisms of NNIs and supporting the concept of competing endogenous RNAs (ceRNAs) in gene regulation. The platform is freely accessible at https://www.nipgr.ac.in/ANNInter/.
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    Yield loss and growth-defense trade-offs: impact of engineering amino acid transporters
    (Springer Nature Publishing AG, 2024) Dhatterwal, Pinky; Prasad, Manoj; Mehrotra, Sandhya; Mehrotra, Rajesh
    Recent studies recognize the importance of membrane transporters as vital targets for global food security, with amino acid transporters playing a key role in various plant processes afecting growth, productivity, and nutritional value. The manipulation of amino acid transporters in crop plants ofers a promising avenue for enhancing their nutritional profles, improving seed yield, and ensuring better survival under environmental stresses. However, such genetic modifcations often result in pleiotropic efects, including alterations in seed weight, starch, and sucrose levels, as well as compromised plant growth over improved stress tolerance and nutritional enhancement. These unintended phenotypic trade-ofs consequences underscore the importance of careful consideration in genetic engineering to achieve desired agricultural outcomes without compromising overall plant health and yield.