Publications of NIPGR Scientists

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Subject: search.filters.subject.Small RNA

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Now showing 1 - 9 of 9
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    Regulation of small RNA-mediated high temperature stress responses in crop plants
    (Springer Nature Publishing AG, 2022) Singh, Roshan Kumar; Prasad, Ashish; Maurya, Jyoti; Prasad, Manoj
    Throughout their life cycle, plants have to regulate their gene expression at various developmental phases, physiological changes, and in response to biotic or environmental stress. High temperature is one the most common abiotic stress for crop plants, that results in impaired morphology, physiology, and yield. However, plants have certain mechanisms that enable them to withstand such conditions by modulating the expression of stress-related genes. Small RNA (sRNA)-regulated gene expression is one such mechanism which is ubiquitous in all eukaryotes. The sRNAs mainly include micro RNAs (miRNAs) and small interfering RNAs (siRNAs). They are primarily associated with the gene silencing either through translation inhibition, mRNA degradation, or DNA methylation. During high temperature stress the increased or decreased level of miRNAs altered the protein accumulation of target transcripts and, therefore, regulate stress responses. Several reports are available in plants which are genetically engineered through expressing artificial miRNAs resulted in thermotolerance. sRNAs have also been reported to bring the epigenetic changes on chromatin region through RNA-dependent DNA methylation (RdDM). The present article draws a brief illustration of sRNA origin, their functional mechanisms, role in high temperature stress, and possible application for developing stress tolerant crop plants.
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    Sequestering miR165/166 enhances seed germination in Arabidopsis thaliana under normal condition and ABA treatment
    (Springer Nature Publishing AG, 2020) Sarkar Das, Shabari; Majee, Manoj; Nandi, Asis K.; Karmakar, Prakash
    Seed germination is a dynamic process involving imbibition, increased metabolic activity and protrusion of a tiny plantlet rupturing the seed coat. Many genes, phytohormones like ABA and GA have been implicated in germination of Arabidopsis thaliana seeds. Although many microRNAs (miRNAs) have been shown to be differentially expressed during seed germination process, their role remains mostly unaddressed. Here we address the role of developmentally important miR165/166 in the process of seed germination. We demonstrate that the seeds of transgenic A. thaliana having target mimic-miR165/166 (eTM-miR165/166), where miR165/166 is sponged, show better germination efficiency. The seeds of this line also maintain better germination even under ABA treatment, which is a negative regulator of seed germination. Thus, our results suggest that, sequestering miR165/166 activity enhances seed germination efficiency under normal and ABA-stress condition.
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    Role of RNA-interacting proteins in modulating plant-microbe interactions
    (Elsevier B.V., 2020) Pandey, Saurabh; Sharma, Namisha; Prasad, Manoj
    Successful infection of a pathogen in its host plant depends on the complex molecular interplay between host and the invading microbe. Plant-microbe interactions are primarily governed by signal interchange amid both the organisms. Effective passage of the pathogen into the plant system requires the circumvention of signal detection mechanisms and subsequent immune responses. As a mechanism to counteract defense response, pathogens deploy several RNA-interacting proteins (RIPs) or RNA molecules which interrupt the host transcriptional as well as signaling pathways, leading to successful infection and symptom development. The interference by pathogen-derived small RNAs (sRNA) in the gene silencing machinery of the host has been recently reported. In this context, the present review describes the pathogen- and host-specific RNA molecules and chaperones, their roles in modulating host immune response as well as pathogenesis, and the possible targets for manipulating the molecular mechanism to develop durable tolerance/resistance against diseases in crops.
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    Improved laser capture microdissection (LCM)‑based method for isolation of RNA, including miRNA and expression analysis in woody apple bud meristem
    (Springer Nature, 2019) Verma, Swati; Gautam, Vibhav; Sarkar, Ananda K.
    Isolation of high-quality RNA, including miRNA, from microscopic woody apple bud meristem using laser capture microdissection-based method. It is often challenging to study the expression of microRNAs (miRNAs) or genes in less accessible inner tissues of tree species rich in polyphenols or polysaccharides. Here, we report a laser capture microdissection (LCM)-based method for efficient and cost-effective isolation and expression analysis of miRNAs and genes in the meristem tissue of woody apple bud. The tissue fixation, processing, infiltration, and sectioning steps were optimized for LCM-based excision and subsequent RNA isolation. Further, we have confirmed that RNA isolated from LCM-derived apple bud meristem contained miRNAs and was of good quantity and quality, sufficient for downstream expression analysis.
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    Identification and co-evolution pattern of stem cell regulator miR394s and their targets among diverse plant species
    (BioMed Central Ltd, 2019) Kumar, Ashutosh; Gautam, Vibhav; Kumar, Pramod; Mukherjee, Shalini; Verma, Swati; Sarkar, Ananda K.
    Background Micro RNAs (miRNAs), a class of small non-coding RNAs, have been implicated in various aspects of plant development. miR394 is required for shoot apical meristem organization, stem cell maintenance and abiotic stress responses in Arabidopsis, where it functions by negatively regulating the transcript level of target LEAF CURLING RESPONSIVENESS (LCR), which is an F-box protein-coding gene. The evolutionary conservation of stem cell regulatory miR394-LCR module among plants remains elusive. Results Our study has identified 79 miR394 and 43 target sequences across 40 plant species using various homology based search tools and databases, and analysed their co-evolution pattern. We customised an annotation workflow which computationally validates 20 novel miR394s from 14 plant species. Independent phylogenetic trees were reconstructed with precursor MIR394s, mature miR394s, and their target sequences along with complementary miR394 binding sites. The phylogeny revealed that mature sequences of miR394s as well as their targets belonging to the F-box protein encoding gene families, were highly conserved. Though, miR394–3p were complementary to miR394s/miR394–5p, they clustered separately. Conclusion The existence and separate clustering of miR394–3p and miR394s/miR394–5p indicate their independent regulation. The phylogeny also suggests that miR394s had evolved at the beginning of gymnosperm-angiosperm divergence. Despite strong conservation, some level of sequence variation in miR394s and the complementary binding sites of their targets suggests possible functional diversification of miR394-LCR mediated stem cell regulation in plants.
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    Plant small RNAs: advancement in the understanding of biogenesis and role in plant development
    (Springer Nature, 2018) Singh, Archita; Gautam, Vibhav; Singh, Sharmila; Das, Shabari Sarkar; Verma, Swati; Mishra, Vishnu; Mukherjee, Shalini; Sarkar, Ananda K.
    Main conclusion: Present review addresses the advances made in the understanding of biogenesis of plant small RNAs and their role in plant development. We discuss the elaborate role of microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs) in various aspects of plant growth and development and highlight relevance of small RNA mobility. Small non-coding RNAs regulate various aspects of plant development. Small RNAs (sRNAs) of 21–24 nucleotide length are derived from double-stranded RNAs through the combined activity of several biogenesis and processing components. These sRNAs function by negatively regulating the expression of target genes. miRNAs and ta-siRNAs constitute two important classes of endogenous small RNAs in plants, which play important roles in plant growth and developmental processes like embryogenesis, organ formation and patterning, shoot and root growth, and reproductive development. Biogenesis of miRNAs is a multistep process which includes transcription, processing and modifcation, and their loading onto RNA-induced silencing complex (RISC). RISC-loaded miRNAs carry out post-transcriptional silencing of their target(s). Recent studies identifed orthologues of diferent biogenesis components of novel and conserved small RNAs from diferent model plants. Although many small RNAs have been identifed from diverse plant species, only a handful of them have been functionally characterized. In this review, we discuss the advances made in understanding the biogenesis, functional conservation/divergence in miRNA-mediated gene regulation, and the developmental role of small RNAs in diferent plant species.
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    Insights into the small RNA-mediated networks in response to abiotic stress in plants
    (Springer, 2015) Balyan, Sonia C.; Mutum, Roseeta D.; Kansal, Shivani; Kumar, Santosh; Mathur, Saloni; Raghuvanshi, Saurabh
    Under natural conditions, plants are constantly exposed to various environmental stresses such as drought, extreme temperature, salt, UV, mechanical, or nutrient starvation. To cope with these adverse conditions, plants have evolved cascade of molecular networks to perceive and transduce the stress signals, resulting into the reprogramming of gene expression. The stress-regulated reprogramming of gene expression at post-transcriptional regulation has been emphasized with the discovery of small regulatory RNAs. Plant small RNAs represent non-coding RNAs in the size range of 20–24 nucleotides and categorized into hairpin RNAs (hpRNAs) and siRNAs. The first category includes miRNAs, lmiRNAs, and nat-miRNAs while the siRNA group includes hc-siRNA, secondary siRNAs and nat-siRNAs. Studies have shown that small RNAs, especially miRNAs, are dynamically regulated by a variety of abiotic stress conditions. Such sRNAs target a variety of downstream targets including regulatory proteins as well as metabolic enzymes and thus play pivotal role in the regulation of plant abiotic stress response. Stress appears to regulate miRNA biogenesis as well as its activity. Several miRNA gene:target pairs respond to multiple stress conditions and are conserved in various plant species indicating that miRNAs may define pivotal regulatory nodes involved in the regulation of the plant stress response. On the other hand, miRNAs also show variety-/cultivar-specific stress response indicating that they themselves are under a very dynamic regulation. The world of small RNAs is gradually unfolding and much remains to be explored, nevertheless, it has been conclusively demonstrated that small RNAs define a new dimension in the molecular regulatory network regulating the plant stress response.
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    Balanced activity of microRNA166/165 and its target transcripts from the class III homeodomain leucine-zipper family regulates root growth in Arabidopsis thaliana
    (Springer, 2014) Singh, Archita; Singh, Sharmila; Panigrahi, Kishore C. S.; Reski, Ralf; Sarkar, Ananda K.
    Overexpression of miR166/165 down-regulates target HD - ZIP IIIs and promotes root growth by enhancing cell division and meristematic activity, whereas overexpression of HD - ZIP IIIs inhibits root growth in Arabidopsis thaliana. Post-embryonic growth of higher plants is maintained by active meristems harbouring undifferentiated cells. Shoot and root apical meristems (SAM and RAM) utilize both similar and distinct signalling mechanisms for their maintenance in Arabidopsis thaliana. An important regulatory role in this context has the interaction of microRNAs with their target mRNAs, mostly encoding transcription factors. One class of microRNA166/165 (miR166/165) has been implicated in the maintenance of SAM and vascular patterning. Here, we show that miR166/165 plays an important role in root growth also by negatively regulating its target transcripts, HD-ZIP IIIs, in the RAM. While overexpression of miR166 promotes RAM activity, overexpression of its targets reduces RAM activity. These results reveal a conserved role of miR166/165 in the maintenance of SAM and RAM activity in A. thaliana.
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    Recent advances in plant-virus interaction with emphasis on small interfering RNAs (siRNAs)
    (Springer, 2013) Sharma, Namisha; Sahu, Pranav Pankaj; Puranik, Swati; Prasad, Manoj
    Regulation of several biological functions in plants has now been known to involve diverse RNA silencing pathways. These vital pathways involve various components such as dsRNA, Dicer, RNA-dependent RNA polymerase and Argonaute proteins, which lead to the production of several small RNAs (sRNAs) varying in their sizes. These sRNAs have significant role in the regulation of gene expression at transcriptional and translational levels. Among them, small interfering RNAs (siRNAs; majorly 21, 22 and 24 nt) have been shown to play an important role in plants' resistance against many viruses by inhibiting the viral gene expression. Furthermore, it has also been highlighted that siRNA-mediated methylation of viral DNA confers resistance to various plant DNA viruses. In this review, we have outlined the recent advances made using the siRNA-mediated antiviral strategy, along with methylation-based epigenetic defensive mechanisms as a protective measure against diverse plant viruses.