Institutional Publications

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Subject: search.filters.subject.Biotic stress

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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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    Comprehensive study of tRNA-derived fragments in plants for biotic stress responses
    (Springer Nature Publishing AG, 2025) Swain, Supriya P. ; Bisht, Niyati ;  Kumar, Shailesh
    Plant growth and development are often disrupted by biological stressors as they interfere with the regulatory pathways. Among the key regulators, transfer-RNA-derived fragments (tRFs) have emerged as key players in plant defense mechanisms. While tRF-mediated responses to abiotic stress have been well studied, their role in biotic stress remains less understood, as various stressors may elicit different regulatory systems. In this study, tRF-mediated biotic responses in three species, viz. Arabidopsis thaliana, Oryza sativa, and Solanum lycopersicum are investigated using in-silico approaches. Analysis of predicted tRFs across various biotic stress conditions reveals specific interactions with mRNA targets, microRNAs (miRNAs), and transposable elements (TEs), highlighting their regulatory significance in plant adaptation mechanisms. These findings provide new insights into tRF-mediated stress responses and establish a computational framework for further functional studies. The study’s database is publicly available at http://www.nipgr.ac.in/PbtRFdb.
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    Lignin: the building block of defense responses to stress in plants
    (Springer Nature Publishing AG, 2023) Yadav, Shalini; Chattopadhyay, Debasis
    Lignin is a complex aromatic biopolymer important for providing mechanical strength to the cell wall and resistance against both biotic and abiotic stresses. It helps in plant growth by providing physical strength and helping in long distance transport of water and minerals. Lignin biosynthetic genes are known to be induced under both biotic and abiotic stresses, and perturbations in lignin biosynthesis has shown to result in changes in plants defense responses against these stresses. It’s important to understand how these sophisticated mechanisms are employed by the plants to adapt to the adverse climatic conditions and develop more resilient plant varieties. In this review, we try to deliver a thorough comprehension of how lignin biosynthesis is altered under various environmental conditions. We believe this information will be useful in understanding the role of diferent lignin biosynthetic genes in conferring resistance against diferent stresses.
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    Plant phosphate status influences root biotic interactions
    (Oxford University Press, 2023) Pazhamala, Lekha T; Giri, Jitender
    Phosphorus (P) deficiency stress in combination with biotic stress(s) severely impacts crop yield. Plant responses to P deficiency overlapping with that of other stresses exhibit a high degree of complexity involving different signaling pathways. On one hand, plants engage with rhizosphere microbiome/ arbuscular mycorrhizal fungi for improved phosphate (Pi) acquisition and plant stress response upon Pi deficiency, on the other, this association is inhibited under Pi sufficiency. This nutrient-dependent response is highly regulated by phosphate starvation response (PSR) mediated by the master regulator, PHR1 and its homolog, PHL. It is interesting to note that Pi status (deficiency/sufficiency) has a varying response (positive/negative) to different biotic encounters (beneficial microbes/opportunistic pathogens/insect herbivory), through a coupled PSR-PHR1-immune response. This also involves crosstalk among multiple players including transcription factors, defense hormones, microRNAs, and phosphate transporters, among others influencing the plant-biotic-phosphate interactions. We provide a comprehensive view of these key players involved in maintaining a delicate balance between Pi homeostasis and plant immunity. Finally, we propose strategies to utilize this information to improve crop resilience to P deficiency in combination with biotic stresses.
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    DNA methylation dynamics in response to abiotic and pathogen stress in plants
    (Springer Nature Publishing AG, 2022) Arora, Heena; Singh, Roshan Kumar; Sharma, Shambhavi; Sharma, Namisha; Panchal, Anurag; Das, Tuhin; Prasad, Ashish; Prasad, Manoj
    DNA methylation is a dynamic epigenetic mechanism that plays a significant role in gene expression and also maintains chromatin stability. The process is conserved in both plants and animals, and crucial for development and stress responses. Differential DNA methylation during adverse environmental conditions or pathogen attack facilitates the selective expression of defense-related genes. Both stress-induced DNA hypomethylation and hypermethylation play beneficial roles in activating the defense response. These DNA marks may be carried to the next generation making the progenies ‘primed’ for abiotic and biotic stress responses. Over the recent years, rapid advancements in the area of high throughput sequencing have enabled the detection of methylation status at genome levels in several plant species. Epigenotyping offers an alternative tool to plant breeders in addition to conventional markers for the selection of the desired offspring. In this review, we briefly discuss the mechanism of DNA methylation, recent understanding of DNA methylation-mediated gene regulation during abiotic and biotic stress responses, and stress memory in plants.
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    BURP domain-containing genes in legumes: genome-wide identification, structure, and expression analysis under stresses and development
    (Springer Nature Publishing AG, 2022) Chitkara, Pragya; Poddar, Nikita; Singh, Amarjeet; Kumar, Shailesh
    BURP domain-containing proteins are a plant-specific protein family which play an important role in plant metabolism and development. These proteins have also been involved in various abiotic and biotic stress responses. In this study, genome-wide identification and characterization of BURP domain protein encoding gene family is performed in four important legumes, Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Vigna radiata. BURP genes were distributed randomly across chromosomes in all four legume plants. The phylogenetic analysis classified all BURP proteins into five major subfamilies, namely, USP-like, RD22-like, BNM2-like, PG1β-like, and BURPV. Our findings revealed that BURP gene family descended from common ancestors with segmental gene duplication events playing a critical role in their evolution and expansion in legumes. The intron–exon and conserved protein motifs analysis revealed that BURP genes are structurally conserved in legumes. The promoter analysis revealed the presence of hormone, and stress-responsive cis-regulatory elements in BURP promoters, implying that BURP functions in both hormone and abiotic stress signaling. Global expression analysis revealed that several BURP genes in all four legumes express differentially during plant development, and under biotic and abiotic stresses. This indicates crucial role of BURP proteins in regulating the development of legumes and adaptation to different abiotic/biotic stresses. This study will provide the starter for cloning and detail functional investigation of BURP proteins in legume crops.
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    Complex molecular mechanisms determine fitness of plants to biotic and abiotic stresses
    (Springer Nature Publishing AG, 2021) Prasad, Ashish; Senthil-Kumar, Muthappa; Prasad, Manoj
    The mode of growth and development of plants does not allow them to change their habitat upon stress imposition. Through the course of evolution, plants have acquired complex molecular pathways to deal with abiotic and biotic factors to ensure their survival. The changing climatic conditions have led to unprecedented weather patterns resulting in increased crop losses. Similarly, the spread of pathogens in an era of increasing international trade has resulted in introduction and adaptation of these pathogens to new areas and cause frequent epidemics. There is an increasing need to understand the molecular mechanisms underlying stress responses in plants and envision ways to develop new crop varieties with improved features.
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    Linking the plant stress responses with RNA helicases
    (Elsevier B.V., 2020) Pandey, Saurabh; Prasad, Ashish; Sharma, Namisha; Prasad, Manoj
    RNA helicases are omnipresent plant proteins across all kingdoms and have been demonstrated to play an essential role in all cellular processes involving nucleic acids. Currently, these proteins emerged as a new tool for plant molecular biologists to modulate plant stress responses. Here, we review the crucial role of RNA helicases triggered by biotic, abiotic, and multiple stress conditions. In this review, the emphasis has been given on the role of these proteins upon viral stress. Further, we have explored RNA helicase mediated regulation of RNA metabolism, starting from ribosome biogenesis to its decay upon stress induction. We also highlighted the cross-talk between RNA helicase, phytohormones, and ROS. Different overexpression and transgenic studies have been provided in the text to indicate the stress tolerance abilities of these proteins.
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    Concurrent overexpression of rice G-protein β and γ subunits provide enhanced tolerance to sheath blight disease and abiotic stress in rice
    (Springer Nature Publishing AG, 2019) Swain, Durga Madhab; Sahoo, Ranjan Kumar; Chandan, Ravindra Kumar; Ghosh, Srayan; Kumar, Rahul; Jha, Gopaljee; Tuteja, Narendra
    The heterotrimeric G-proteins act as signalling molecules and modulate various cellular responses including stress tolerance in eukaryotes. The gamma (γ) subunit of rice G-protein (RGG1) was earlier reported to promote salinity stress tolerance in rice. In the present study, we report that a rice gene-encoding beta (β) subunit of G-protein (RGB1) gets upregulated during both biotic (upon a necrotrophic fungal pathogen, Rhizoctonia solani infection) and drought stresses. Markerfree transgenic IR64 rice lines that simultaneously overexpress both RGB1 and RGG1 genes under CaMV35S promoter were raised. The overexpressing (OE) lines showed enhanced tolerance to R. solani infection and salinity/drought stresses. Several defense marker genes including OsMPK3 were signifcantly upregulated in the R. solani-infected OE lines. We also found the antioxidant machineries to be upregulated during salinity as well as drought stress in the OE lines. Overall, the present study provides evidence that concurrent overexpression of G-protein subunits (RGG1 and RGB1) impart multiple (both biotic and abiotic) stress tolerance in rice which could be due to the enhanced expression of stress-marker genes and better management of reactive oxygen species (ROS)-scavenging/photosynthetic machinery. The current study suggests an improved approach for simultaneous improvement of biotic and abiotic stress tolerance in rice which remains a major challenge for its sustainable cultivation.
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    Ubiquitination: a tool for plant adaptation to changing environments
    (Springer Nature, 2018) Mandal, Arunava; Sharma, Namisha; Muthamilarasan, Mehanathan; Prasad, Manoj
    Post-translational modifcations namely ubiquitination, phosphorylation, methylation and acetylation play distinct roles in regulating the growth and development of plants. Among these, the ubiquitination regulates the abundance, activities, subcellular compartmentalization and trafcking of regulatory proteins involved in diverse developmental as well as stress-responsive processes. The ubiquitin–proteasome system (UPS) involves fve essential components namely ubiquitin, ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), ubiquitin ligase (E3) and the intact 26S proteasome. The E3 ubiquitin ligase is the major component of UPS that recognizes and tethers poly-ubiquitins on the target proteins. Owing to its specifcity of substrate recognition, the E3 ubiquitin ligase contributes not only to the proteome plasticity of the cell but also regulates the plant’s response to environmental cues. In this context, the review summarizes the components involved in UPS and elaborates the role of E3 ubiquitin ligase in biotic and abiotic stress responses.