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Start date: 2025Subject: search.filters.subject.Abiotic stress

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    Genome-wide identification and expression analysis of chickpea U-box E3 ligases identifies CaPUB4 and CaPUB16 as candidate responsive genes for abiotic stress tolerance
    (Springer Nature Publishing AG, 2026) Fernandes, Nithya; Unnati, G. Meher; Bhattacharjee, Surjit; Pandey, Ashutosh; Mishra, Neelam
    U-box E3 ubiquitin ligases play a crucial role in post-translational protein modification, stress signaling, and cellular adaptation in plants. In this study, 38 non-redundant CaPUB genes were identified from the chickpea (Cicer arietinum) genome and characterized for their phylogenetic relationships, domain architecture, gene structures, and expression profiles. Synteny and gene ontology analyses revealed evolutionary conservation with Lotus japonicus and Arabidopsis thaliana, and functional involvement in processes such as ubiquitination, signaling, and stress responses. RNA sequencing and qPCR analyses demonstrated distinct tissue-specific expression patterns. Specifically, CaPUB14 and CaPUB2 were predominantly expressed in particular organs, whereas CaPUB4 and CaPUB16 were upregulated under drought and salt stress in the stress-tolerant ICC4958 cultivar. Functional interaction network analysis revealed that CaPUB4 and CaPUB16 proteins interact with an identical set of partner proteins, supporting the hypothesis that these ligases may function collaboratively in stress adaptation. Collectively, these findings provide insights into the diversity, expression patterns, and potential regulatory roles of the CaPUB gene family, highlighting promising candidate genes for future functional characterization and their possible utility in improving crop stress resilience.
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    AraNSdb: a dedicated database of stress-responsive non-coding RNAs in Arabidopsis thaliana
    (Springer Nature Publishing AG, 2026) Vivek, A.T.; Bhatia, Manika; Sahu, Namrata; Kalakoti, Garima; Kaushik, Love; Mukherjee, Kanka; Kumar, Shailesh
    Plants, as sessile organisms, are constantly exposed to biotic and abiotic stresses, making their ability to respond crucial for survival. Non-coding RNAs (ncRNAs) have emerged as key regulators in these stress responses, with several studies identifying numerous stress-responsive ncRNAs (SRNs). However, a comprehensive collection of SRNs derived from sequencing data in Arabidopsis thaliana has been lacking. To address this, we utilized high-throughput experimental data and mined published studies to construct AraNSdb (Arabidopsis ncRNA Stress Database), a systematic resource for storing and querying SRNs. AraNSdb documents over 1,000 expression profiles from diverse stress datasets, encompassing 6,616 SRNs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). The database features an intuitive web interface for exploring SRNs associated with specific stress types and provides detailed ncRNA annotations to support functional and regulatory studies. AraNSdb offers a valuable platform for advancing our understanding of ncRNA-mediated stress responses and is freely accessible at http://www.nipgr.ac.in/AraNSdb.
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    OsLdh3 interacts with OsGAPC3 and OsLos2 to maintain the glycolytic continuum for tolerance to multiple abiotic stresses in rice
    (Oxford University Press, 2026) Chatterjee, Yajnaseni; Babuta, Priyanka; Gupta, Kapuganti Jagadis; Pareek, Ashwani; Singla-Pareek, Sneh Lata
    Lactate dehydrogenases are oxidoreductases present in almost all living organisms. They catalyze the interconversion of pyruvate and L-lactate with simultaneous oxidation of NADH and reduction of NAD+. Since their function remains largely unexplored in rice, in this study we deciphered the role of the rice lactate dehydrogenase, OsLdh3. OsLdh3 showed optimum enzyme activity at pH 6.6 for the forward reaction (pyruvate to L-lactate) and pH 9 for the reverse reaction (L-lactate to pyruvate). Protein-protein interaction studies revealed that OsLdh3 interacts with the glycolytic enzymes glyceraldehyde 3-phosphate dehydrogenaseC3 (OsGAPC3) and Enolase2 (OsLos2), suggesting its role in regulating glycolytic flux. Further, overexpression of OsLdh3 in rice showed enhanced abiotic stress tolerance by exhibiting elevated NAD+ levels and OsGAPC3 activity, thereby facilitating an improved glycolytic continuum and higher pyruvate accumulation. Consequently, these lines also showed increased mitochondrial respiration and ATP synthesis, and reduced reactive oxygen species (ROS) accumulation. Further, enhanced photosynthetic efficiency and reduced yield penalty of the stress-imposed OsLdh3 overexpression lines underscore its importance in crop productivity under adverse climatic conditions. Thus, our findings show that OsLdh3 enhances stress tolerance in rice by regulating redox homeostasis and respiration, reducing ROS levels, and maintaining energy balance. This makes OsLdh3 a promising candidate gene for developing climate-resilient rice cultivars with reduced yield gap.
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    Genome-wide identification, functional characterization of protein phosphatase 2A (PP2A) gene family in Cicer arietinum reveals the potential role of CaPP2A-A1 under abiotic stress
    (Springer Nature Publishing AG, 2025) Fernandes, Nithya; Bhattacharjee, Surjit; Anusha, D. M.; Pandey, Ashutosh; Mishra, Neelam
    Drought and salt stress are among the primary abiotic factors that negatively impact crop productivity. To cope with these adverse conditions, plants have evolved various adaptive mechanisms, often mediated by specific genes that confer tolerance to different stresses. In this study, we performed a genome-wide identification of PP2A genes in Cicer arietinum using Arabidopsis thaliana genome as a reference. This study identified 21 CaPP2A members distributed across seven chromosomes. Phylogenetic analysis grouped these genes into six distinct subfamilies, each characterized by unique intron-exon structures and conserved motifs. Promoter analysis revealed the presence of cis-acting elements associated with hormone regulation and abiotic stress responsiveness. RNA sequencing analysis demonstrated that nine PP2A genes were significantly responsive to drought and salt stress which was corroborated by quantitative PCR. Notably, the CaPP2A-A1 gene was identified as a key stress responsive since it exhibited significant upregulation in a stress tolerant cultivar, whereas it was downregulated in a susceptible cultivar under both drought and salt stress conditions, suggesting its pivotal role in stress adaptation. Overall, these findings enhance our understanding of the PP2A gene family in chickpea providing a foundation for future functional studies to unravel the PP2A-mediated regulatory networks governing stress tolerance in C. arietinum and facilitate the development of improved breeding strategies for stress-resilient cultivars.
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    Genomic, structural, and molecular analysis of calmodulin-binding transcriptional activators (CAMTAs) suggests their role in plant development and abiotic stress tolerance in chickpea
    (Elsevier B.V., 2025) Sonkar, Kamankshi; Kamali, Saravanappriyan; Kumar, Atul; Deepika, Deepika; Ankit, Ankit; Singh, Amarjeet
    The calmodulin-binding transcriptional activator (CAMTA) transcription factors regulate the expression of target genes in Ca2 + dependent cellular functions. CAMTAs are known to regulate biotic and abiotic stress tolerance, and development in plants. CAMTA family has been characterized in Arabidopsis, it is yet to be explored in the legume plant chickpea. Here, we have identified and characterized the chickpea CAMTA family. Total seven CAMTA genes (CaCAMTA1–7) were identified in chickpea. Gene and domain structure analyses suggested that CAMTAs are structurally conserved. The phylogenetic analysis demarcated CaCAMTAs into three groups namely; group I, II and III, and indicated that CaCAMTAs have co-evolved in dicot leguminous plants whereas, they have divergent evolution in monocots. Protein homology modeling revealed their three-dimensional structure, and composition & conformations of α-helix, β-sheets and p-loops. Subcellular localization showed that CaCAMTA4 was localized both, in the nucleus and the cytosol whereas, CaCAMTA5 was localized in the nucleus. CaCAMTA promoters contain various cis-regulatory elements related to abiotic stresses and plant development. Expression profiling using RNA-seq data revealed differential expression of CaCAMTAs during various stages of plant development. RT-qPCR expression analysis showed that most CaCAMTA genes are drought, salt, and ABA responsive, suggesting their role in abiotic stress tolerance in chickpea. Moreover, CaCAMTA regulon was identified based on the presence of CAMTA binding motif (CGCG box) in the promoters of target genes, and in-silico interaction analysis of TF and putative targets. Overall, CaCAMTAs are crucial for abiotic stress tolerance and plant development in chickpea. Key CaCAMTA genes will be functionally characterized, and will be exploited for developing stress tolerant chickpea varieties.
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    Genome-wide identification and molecular characterization of core ABA signaling components under abiotic stresses and during development in chickpea
    (Springer Nature Publishing AG, 2025) Kamali, Saravanappriyan; Sonkar, Kamankshi; Ankit, Ankit; Deepika, Deepika; Sharma, Ankita; Singh, Amarjeet
    Abscisic acid (ABA) signaling is vital for plant's response to abiotic stresses and development. Core components of ABA signaling include ABA receptors PYR/PYL/RCAR, group-A PP2Cs (PP2C-As) and SnRK2 serine/threonine kinases. These have been well studied in Arabidopsis, but their knowledge in the legume crop chickpea is missing. Here, we identified 8 PYLs, 11 PP2C-As and 13 SnRK2s genes in the chickpea genome. Gene duplication events have been found to drive their evolution and expansion in chickpea. Protein homology modeling revealed three-dimensional structure, and arrangements of α-helix, β-sheets and p-loops in respective families. In-planta subcellular localization analysis revealed that CaPYL3 and CaPYL5 proteins were localized at the plasma membrane, and CaPP2CA-1 and CaSnRK2.7 were localized in the cytoplasm and the nucleus. RNA sequencing data analysis indicated the regulatory role of CaPYLs, CaPP2C-As and CaSnRK2s in developmental stages particularly, stages of early embryogenesis to seed maturity. Through RT-qPCR analysis drought, salt and ABA responsive CaPYL, CaPP2C-A and CaSnRK2 genes, which might regulate abiotic stress response in chickpea were identified. Importantly, key genes like CaPYL4, CaPP2C-A4, CaPP2C-A11 and CaSnRK2.9 with overlapping expression in drought, ABA and seed development were identified, which might determine chickpea crop yield. In-silico interaction analysis revealed specific and overlapping interaction among ABA signaling proteins indicating their functional relevance. Overall, core ABA signaling components are crucial for abiotic stress tolerance and development in chickpea. These genes will be functionally validated in the future and will be utilized to generate abiotic stress resilience and high-yielding chickpea varieties.