Institutional Publications
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Item Major transcription factor families at the nexus of regulating abiotic stress response in millets: a comprehensive review(Springer Nature Publishing AG, 2024) Prusty, Ankita; Panchal, Anurag; Singh, Roshan Kumar; Prasad, ManojMillets stand out as a sustainable crop with the potential to address the issues of food insecurity and malnutrition. These small-seeded, drought-resistant cereals have adapted to survive a broad spectrum of abiotic stresses. Researchers are keen on unravelling the regulatory mechanisms that empower millets to withstand environmental adversities. The aim is to leverage these identified genetic determinants from millets for enhancing the stress tolerance of major cereal crops through genetic engineering or breeding. This review sheds light on transcription factors (TFs) that govern diverse abiotic stress responses and play role in conferring tolerance to various abiotic stresses in millets. Specifically, the molecular functions and expression patterns of investigated TFs from various families, including bHLH, bZIP, DREB, HSF, MYB, NAC, NF-Y and WRKY, are comprehensively discussed. It also explores the potential of TFs in developing stress-tolerant crops, presenting a comprehensive discussion on diverse strategies for their integration.Item Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights(Elsevier B.V., 2023) Seni, Sushmita; Singh, Roshan Kumar; Prasad, ManojPlants control expression of their genes in a way that involves manipulating the chromatin structural dynamics in order to adapt to environmental changes and carry out developmental processes. Histone modifications like histone methylation are significant epigenetic marks which profoundly and globally modify chromatin, potentially affecting the expression of several genes. Methylation of histones is catalyzed by histone lysine methyltransferases (HKMTs), that features an evolutionary conserved domain known as SET [Su(var)3-9, E(Z), Trithorax]. This methylation is directed at particular lysine (K) residues on H3 or H4 histone. Plant SET domain group (SDG) proteins are categorized into different classes that have been conserved through evolution, and each class have specificity that influences how the chromatin structure operates. The domains discovered in plant SET domain proteins have typically been linked to protein-protein interactions, suggesting that majority of the SDGs function in complexes. Additionally, SDG-mediated histone mark deposition also affects alternative splicing events. In present review, we discussed the diversity of SDGs in plants including their structural properties. Additionally, we have provided comprehensive summary of the functions of the SDG-domain containing proteins in plant developmental processes and response to environmental stimuli have also been highlighted.Item An insight into the roles of regulatory ncRNAs in plants: An abiotic stress and developmental perspective(Elsevier B.V., 2023) Panchal, Anurag; Maurya, Jyoti; Seni, Sushmita; Singh, Roshan Kumar; Prasad, ManojDifferent environmental cues lead to changes in physiology, biochemistry and molecular status of plant's growth. Till date, various genes have been accounted for their role in regulating plant development and response to abiotic stress. Excluding genes that code for a functional protein in a cell, a large chunk of the eukaryotic transcriptome consists of non-coding RNAs (ncRNAs) which lack protein coding capacity but are still functional. Recent advancements in Next Generation Sequencing (NGS) technology have led to the unearthing of different types of small and large non-coding RNAs in plants. Non-coding RNAs are broadly categorised into housekeeping ncRNAs and regulatory ncRNAs which work at transcriptional, post-transcriptional and epigenetic levels. Diverse ncRNAs play different regulatory roles in nearly all biological processes including growth, development and response to changing environments. This response can be perceived and counteracted by plants using diverse evolutionarily conserved ncRNAs like miRNAs, siRNAs and lncRNAs to participate in complex molecular regimes by activating gene-ncRNA-mRNA regulatory modules to perform the downstream function. Here, we review the current understanding with a focus on recent advancements in the functional studies of the regulatory ncRNAs at the nexus of abiotic stresses and development. Also, the potential roles of ncRNAs in imparting abiotic stress tolerance and yield improvement in crop plants are also discussed with their future prospects.Item Recent advancements and future perspectives of foxtail millet genomics(Springer Nature Publishing AG, 2023) Panchal, Anurag; Singh, Roshan Kumar; Prasad, ManojOne of the oldest domesticated crops, foxtail millet (Setaria italica (L.) P. Beauv.) is known for its enormous seed production and ability to grow in unfavourable agro-economic conditions. This understudied diploid panicoid crop plant which performs C4 type of photosynthesis, contains approximately seven folds higher proteins with macro and micro-nutrients as compared to major cereals including rice and wheat. Encompassing a small genome size of ~ 515 Mb, short life cycle, and inbred properties make this orphan crop a potential model system to study abiotic stress tolerance mechanisms adopted by plants. Rich phenotypic variation and the largest available germplasm collection of cultivated and wild species exists for foxtail millet. Release of whole genome sequence in 2012, led to acceleration of functional genomic studies and molecular characterization of Setaria genes conferring stress tolerance. Recent advancements in integrative OMICS and NGS approaches are contributing in functional analysis, understanding complex gene regulatory networks and molecular mechanisms behind its growth and development. Abiotic stress tolerance traits of foxtail millet including drought, salinity, and its survival in nutrient-poor soil can be introduced in popular crop plants by genetic engineering techniques. Stable plant transformation system and precise gene editing in foxtail millet are under optimization which can revolutionize the theme of climate resilient future crops. Overall, foxtail millet has characteristics to serve as an excellent C4 model plant to study evolution, stress physiology and biomass production for bioenergy crops to serve sustainable global food security in near future.Item 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, ManojDNA 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.Item Plant-virus-abiotic stress interactions: A complex interplay(Elsevier B.V., 2022) Prasad, Ashish; Sett, Susmita; Prasad, ManojUnder 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.Item Complex molecular mechanisms determine fitness of plants to biotic and abiotic stresses(Springer Nature Publishing AG, 2021) Prasad, Ashish; Senthil-Kumar, Muthappa; Prasad, ManojThe 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.Item Role of ubiquitination enzymes in abiotic environmental interactions with plants(Elsevier B.V., 2021) Sharma, Shambhavi; Prasad, Ashish; Sharma, Namisha; Prasad, ManojUbiquitination, a post-translational modification, plays a crucial role in various aspects of plant development and stress responses. Protein degradation by ubiquitination is well established and ubiquitin is the main underlying component directing the turnover of proteins. Recent reports have also revealed the non-proteolytic roles of ubiquitination in plants. In the past decade, ubiquitination has emerged to be one of the most important players in modulating plant's responses to abiotic stresses, which led to identification of specific E3 ligases and their targets involved in the process. Most of the E3 ligases play regulatory roles by modifying the stability and accumulation of stress responsive regulatory proteins, such as transcription factors, thus, modifying the downstream responses, or by degrading the proteins involved in the downstream cascade itself. In this review, we summarize and highlight the recent advances in the field of ubiquitination-mediated regulation of plant's responses to various abiotic stresses including limited nutrient availability and metal toxicity. The non-proteolytic role of ubiquitination in epigenetic regulation of abiotic stress induced response has also been discussed.Item Linking the plant stress responses with RNA helicases(Elsevier B.V., 2020) Pandey, Saurabh; Prasad, Ashish; Sharma, Namisha; Prasad, ManojRNA 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.Item Ubiquitination: a tool for plant adaptation to changing environments(Springer Nature, 2018) Mandal, Arunava; Sharma, Namisha; Muthamilarasan, Mehanathan; Prasad, ManojPost-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.