Publications of NIPGR Scientists

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Subject: search.filters.subject.RNA silencing

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    In-silico prediction of coat protein structure of Indian citrus ringspot virus and their interactions with the Argonaut2/DCL4 proteins
    (Springer Nature Publishing AG, 2025) Angira, Aniket; Yadav, Siddharth; Mathur, Puniti; Baranwal, V. K.; Ranjan, Aashish; Choudhary, Nandlal
    The RNA silencing mechanism is a crucial regulatory system in plants, particularly in antiviral defense. However, most of the plant viruses encode a specifc protein called RNA silencing suppressor protein that suppress the RNA silencing mechanism of host. This study employs the bioinformatics tools, including SWISS homology model and I-TASSER, to predict the coat protein (CP) tertiary structure of Indian citrus ringspot virus (ICRSV). Then, fve protein–protein docking servers (GRAMM, pyDockWEB, HawkDock, ZDOCK and ClusPro) were utilized to investigate interactions of CP of ICRSV with Argonaut2/Dicer-Like (DCL4) protein 4 of RNA silencing pathway of host. In blind docking experiments, the CP consistently engaged in docking interactions with DCL4, while with AGO2, it interacted near the PIWI and MID domains. The AGO2-CP cluster demonstrated 4 salt bridges, 30 hydrogen bonds, and 328 non-bonded contacts, with interface areas spanning 2529 in AGO2 and 2424 in CP, involving 50 and 51 interface residues, respectively. Similarly, the DCL4-CP cluster showed 5 hydrogen bonds and 122 non-bonded contacts, with interface areas spanning 965 in DCL4 and 987 in CP, involving 16 and 19 interface residues, respectively. The established phenomenon of CP interaction with AGO2/DCL4, may resulting in the inhibition of the RNA silencing mechanism and shedding light on the suppression mechanisms of host defense responses.
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    Selective autophagy: the fulcrum of plant-virus interaction
    (Elsevier B.V., 2024) Sharma, Shambhavi; Prasad, Ashish; Prasad, Manoj
    Selective autophagy receptors play both proviral and antiviral roles during plant-virus interaction. However, little is known about the balance between such contradictory dual roles of these receptors. Tong et al. have deciphered the temporal regulation of antiviral and antiplant roles of a selective autophagy receptor, a virus-induced small peptide 1 (VISP1).
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    Plant-virus-abiotic stress interactions: A complex interplay
    (Elsevier B.V., 2022) Prasad, Ashish; Sett, Susmita; Prasad, Manoj
    Under field conditions, plants are subjected to a wide array of biotic and abiotic stresses. These are detrimental to the survival of plants and adversely affects global crop productivity. Changing climate has led to elevated temperatures and unpredicted whether patterns across the world leading to suboptimal crop performance. This is coupled by the emergence of novel pathogen strains which are resistant to anti-pathogenic agents. The situation is even worse in case of viruses where antiviral agents for controlling viral diseases in plants is lacking. The explosion of international trade has helped in the sharing of surplus resources from one location to the other and benefitted the economy of most countries however, this has also resulted in the spread of viruses and other pathogens. Recent years have seen a paradigm shift in the research methodology with combined stress gaining major attention instead of solitary stress. Viruses influence a plant’s response to various abiotic stresses, similarly, abiotic stress imposition has a great effect on viral disease progression. The recent developments associated with plant-virus-abiotic stress interactions along with the way forward to tackle such stresses has been discussed in the present review.
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    Non-host resistance to plant viruses: What do we know?
    (Elsevier B.V., 2020) Baruah, Aiswarya; Sivalingam, Palaiyur Nanjappan; Fatima, Urooj; Senthil-Kumar, Muthappa
    Non-host resistance (NHR) is a prevalent mode of plant defense against invading pathogens, including viruses. Being hard to circumvent, NHR has considerable potential to provide durable resistance against virus infection. This review systematically analyzes recent research findings demonstrating NHR mechanisms and chronologically enumerates the defense strategies contributing to NHR. Conventionally, the NHR mechanisms that operate by restricting viral entry and multiplication are termed “true NHR.” Here, we propose NHR mechanisms operating beyond viral multiplication in non-host plants as “apparent NHR.” This review elucidates both categories of NHR and provides insights into the mechanisms involved in NHR.
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    Application of RNA silencing in improving plant traits for industrial use
    (CABI, 2017) Ghosh, Sumit; Irfan, Mohammad; Datta, Asis
    The discovery of RNA silencing mechanisms has transformed research into gene function and has also allowed novel traits to be developed in plants, including some for industrial applications. To silence the expression of an undesirable gene, RNA silencing may be preferable over direct gene mutation as it leads to a dominant trait. This helps in straightforward screening of the desirable phenotypes. Moreover, RNA silencing is useful in tissue, organ and time-specific silencing of the genes that may play essential roles in plant life and, therefore, direct gene mutation may not be effective. This chapter summarizes the implication of RNA silencing in improving plant traits for industrial applications. Plants developed after RNA silencing of genes that act on cellular organization or metabolism are emerging as convenient and renewable raw materials for industries producing fuels, oils, pharmaceuticals, fibres, papers, seeds and processed foods. Several genetically modified plants, which may not have use in human consumption, have nevertheless been developed for specific industrial applications and await commercial-scale cultivation. Many more industrial crops are under different stages of development by industry and research organizations.