Browsing by Author "Mishra, Vishnu"

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Identification and analysis of miRNAs-lncRNAs-mRNAs modules involved in stem-elongation of deepwater rice (Oryza sativa L.)
(John Wiley & Sons, 2022) Panda, Alok Kumar; Rawal, Hukam C.; Jain, Priyanka; Mishra, Vishnu; Nishad, Jyoti; Chowrasia, Soni; Sarkar, Ananda K.; Sen, Priyabrata; Naik, Soumendra Kumar; Mondal, Tapan Kumar
Deepwater is an abiotic stress that limits rice cultivation worldwide due to recurrent floods. The miRNAs and lncRNAs are two non-coding RNAs emerging as major regulators of gene expressions under different abiotic stresses. However, the regulation of these two non-coding RNAs under deepwater stress in rice is still unexplored. In this study, small RNA-seq and RNA-seq from internode and node tissues were analyzed to predict deepwater stress responsive miRNAs and lncRNAs, respectively. Additionally, a competitive endogenous RNA (ceRNA) study revealed about 69 and 25 lncRNAs acting as endogenous target mimics (eTM) with the internode and node miRNAs, respectively. In ceRNA analyses, some of the key miRNAs such as miR1850.1, miR1848 and IN-nov-miR145 were up-regulated while miR159e was down-regulated, and their respective eTM lncRNAs and targets were found to have opposite expressions. Moreover, we have transiently expressed one module (IN-nov-miR145–Cc-TCONS_00011544-Os11g36430.3) in tobacco leaves. The integrated analysis has identified differentially expressed miRNAs, lncRNAs and their target genes, and the complex regulatory network, which might lead to stem elongation under deepwater stress. In this novel attempt to identify and characterize miRNAs and lncRNAs under deepwater stress in rice, we have provided, probably for the first time, a reference platform to study the interactions of these two non-coding RNAs with respective target genes through transient expression analyses.
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.
Role of abiotic stress responsive miRNAs in Arabidopsis root development
(Springer Nature Publishing AG, 2020) Singh, Archita; Gandhi, Nidhi; Mishra, Vishnu; Yadav, Sandeep; Rai, Vandna; Sarkar, Ananda K.
Abiotic stresses like drought, extreme temperature, and lack of sufficient water or nutrients adversely affect plant growth and productivity. The physiological responses of higher plants to the environmental stresses are largely influenced by the root system, which can quickly modulate its developmental pattern under changing water, nutrient, and temperature, as an adaptive response. Protein coding genes, phytohormones and microRNAs (miRNAs) are among the key players which imparts crucial intrinsic role in shaping the root development and its environment adaptive growth pattern. Among these factors, miRNAs belong to a class of small non-coding RNAs of 21–24 nucleotides in length, which regulates various aspects of plant growth and development by negatively regulating their target genes through either transcriptional cleavage or translational inhibition. Although many miRNAs have been identified to be differentially regulated under various abiotic stress conditions, only a limited number of them have been characterized, due to the complex nature of its regulation. However, some of the miRNAs, such as miR156, miR165/166, miR169 etc., have recently been shown to be involved in both abiotic stress response and root development, indicating the diverse role of miRNA mediated gene regulation. The field of miRNA mediated gene regulation is dynamically expanding and more miRNAs are being characterized for their function. Current review focuses on miRNAs that are differentially regulated by major abiotic stresses as well as are involved in root development in Arabidopsis thaliana. We highlight their role in regulation of multiple and diverse aspects of developmental and physiological processes in Arabidopsis.
Role of miRNAs in root development of model plant Arabidopsis thaliana
(Springer, 2017) Gautam, Vibhav; Singh, Archita; Verma, Swati; Kumar, Ashutosh; Kumar, Pramod; Mahima; Singh, Sharmila; Mishra, Vishnu; Sarkar, Ananda K.
The molecular regulation of root development is relatively well studied in model plant Arabidopsis as compared to other plants. Besides phytohormones, transcription factors and environmental factors, other important regulators which have recently been shown to play crucial roles in controlling root development are the non-coding RNAs. Small non-coding RNAs of 21–24 nt length (miRNAs and ta-siRNAs) regulate various aspects of plant development by negatively regulating their target genes through transcript cleavage or translational inhibition. In recent past the microRNA-mediated regulation of root development has drawn significant interest in the area of plant research. Several reports have highlighted the role of many miRNAs and ta-siRNAs in root growth, vascular patterning, lateral root (LR) formation and elongation, and adventitious root development, Phytohormones like auxin, cytokinin and environmental factors like light, abiotic and biotic stresses, and nutrient availability influence many miRNA-mediated regulation of root growth and branching. In current review, we summarize the recent advances made in understanding the miRNA-mediated regulation of root development in the model plant Arabidopsis thaliana. The molecular crosstalk between different miRNAs, ta-siRNAs, and concerned target genes that regulate root growth and branching have been addressed.
Tweaking microRNA-mediated gene regulation for crop improvement
(Elsevier B.V., 2020) Yadav, Sandeep; Das, Shabari Sarkar; Kumar, Pramod; Mishra, Vishnu; Sarkar, Ananda K.
Many beneficial agronomic traits of crops have been lost in the course of domestication and selective introgression processes. One of the best strategies to prevent the exclusion of beneficial traits during the introgression of novel traits is to selectively fine-tune the expression of some candidate genes or microRNAs (miRNAs). Noncoding regulatory miRNAs of 20–24 nucleotide (nt) length have evolved as specific posttranscriptional regulators that negatively regulate the transcript abundance of their target genes via either cleavage of mRNAs or translational inhibition. In this chapter, we summarize the current knowledge on the role of miRNAs and elaborate their use in miRNA-mediated gene regulation for the improvement of agronomic traits in crop plants. Recent CRISPR-Cas9-based genome engineering technology can be applied to selectively tweak the specific miRNA-target regulation, and thus, the function of the candidate genes to improve crop plants by conferring better productivity or resistance to abiotic or biotic stresses.
A unique miR775-GALT9 module regulates leaf senescence in Arabidopsis during post-submergence recovery by modulating ethylene and the abscisic acid pathway
(The Company of Biologists, 2022) Mishra, Vishnu; Singh, Archita; Gandhi, Nidhi; Das, Shabari Sarkar; Yadav, Sandeep; Kumar, Ashutosh; Sarkar, Ananda K.
Submergence-induced hypoxic condition negatively affects the plant growth and development, and causes early onset of senescence. Hypoxia alters the expression of a number of microRNAs (miRNAs). However, the molecular function of submergence stress-induced miRNAs in physiological or developmental changes and recovery remains poorly understood. Here we show that miR775 is an Arabidopsis thaliana-specific young and unique miRNA that possibly evolved non-canonically. miR775 post-transcriptionally regulates Galactosyltransferase (GALT9) and their expression is inversely affected at 24 hours of complete submergence stress. The overexpression of miR775 (miR775-Oe) confers enhanced recovery from submergence stress and reduced accumulation of RBOHD and ROS, in contrast to wild type and MIM775 Arabidopsis shoot. A similar recovery phenotype of galt9 mutant indicates the role of miR775-GALT9 module in post-submergence recovery. We predicted Golgi-localized GALT9 to be potentially involved in protein glycosylation. The altered expression of senescence-associated genes (SAG12, SAG29, and ORE1), ethylene signalling (EIN2 and EIN3) and ABA biosynthesis (NCED3) pathway genes in miR775-Oe, galt9 and MIM775 plants. Thus, our results indicate the role of miR775-GALT9 module in post-submergence recovery through a crosstalk with ethylene and ABA pathway.