Institutional Publications
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Item Decoding the functionality of plant transcription factors(Oxford University Press, 2024) Dhatterwal, Pinky; Sharma, Namisha; Prasad, ManojTranscription factors (TFs) intricately govern cellular processes and responses to external stimuli by modulating gene expressions. TFs help plants to balance the trade-off between stress tolerance and growth, thus ensuring their long-term survival in challenging environments. Understanding the factors and mechanisms that define the functionality of plant TFs is of paramount importance for unravelling the intricate regulatory networks governing development, growth, and responses to environmental stimuli in plants. The article provides a comprehensive understanding of these factors and mechanisms defining the activity of TFs. Understanding the dynamic nature of TFs has practical implications for modern molecular breeding programs, as it provides insights into how to manipulate gene expression to optimize desired traits in crops. Moreover, recent studies also report the functional duality of transcription factors, highlighting their ability to switch between activation and repression modes, this represents an important mechanism for attuning gene expression. Here we discuss what possible reasons for dual nature of TFs are and how this duality instructs the cell fate decision during development, and fine-tunes stress responses in plants, enabling them to adapt to various environmental challenges.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 Seedling-stage salinity tolerance in rice: decoding the role of transcription factors(John Wiley & Sons, 2022) Tiwari, Shalini; Nutan, Kamlesh Kant; Deshmukh, Rupesh; Sarsu, Fatma; Gupta, Kapuganti Jagadis; Singh, Anil K.; Singla-Pareek, Sneh L.; Pareek, AshwaniRice is an important staple food crop that feeds over half of the human population, particularly in developing countries. Increasing salinity is a major challenge for continuing rice production. Though rice is affected by salinity at all the developmental stages, it is most sensitive at the early seedling stage. The yield thus depends on how many seedlings can withstand saline water at the stage of transplantation, especially in coastal farms. The rapid development of ‘omics’ approaches has assisted researchers in identifying biological molecules that are responsive to salt stress. Several salinity-responsive quantitative trait loci (QTL) contributing to salinity tolerance have been identified and validated, making it essential to narrow down the search for the key genes within QTLs. Owing to the impressive progress of molecular tools, it is now clear that the response of plants towards salinity is highly complex, involving multiple genes, with a specific role assigned to the repertoire of transcription factors. Targeting the transcription factors for improving salinity tolerance can have an inbuilt advantage of influencing multiple downstream genes, which in turn can contribute towards tolerance to multiple stresses. This is the first comparative study for TF-driven salinity tolerance in contrasting rice cultivars at the seedling stage that shows how tolerant genotypes behave differently than sensitive ones in terms of stress tolerance. Understanding the complexity of salt-responsive transcription factor networks at the seedling stage will be helpful to alleviate crop resilience and prevent crop damage at an early growth stage in rice.Item Molecular components associated with the regulation of flavonoid biosynthesis(Elsevier B.V., 2022) Naik, Jogindra; Misra, Prashant; Trivedi, Prabodh Kumar; Pandey, AshutoshFlavonoids exhibit amazing structural diversity and play different roles in plants. Besides, these compounds have been associated with several health benefits in humans. Several exogenous and endogenous cues, for example, light, temperature, nutrient status, and phytohormones have been reported as modulators of biosynthesis and accumulation of flavonoids. Thus, multiple hormones and stress-related signaling pathways are involved in the regulation of gene expression associated with this pathway. The transcriptional regulators belonging to the MYB and bHLH family transcription factors are well documented as the direct regulators of the structural genes associated with flavonoid biosynthesis. Recent studies also suggest that some of these factors are regulated by molecular components involved in stress and hormone signaling pathways. Adapter proteins for transcriptional activation or repression via recruitment of co-activators and co-repressors, respectively, E2 ubiquitin ligases, miRNA processing complex, and DNA methylation/demethylation factors have been recently discovered in various plants to play key roles in fine-tuning flavonoids synthesis. In the present review, we aim to provide comprehensive information about the role of different factors in the regulation of flavonoid biosynthesis. Besides, we describe the potential upstream regulators involved in the regulation of flavonoid biosynthesis within the context of available information. To sum up, the present review furnishes an updated account of signal transduction pathways modulating the biosynthesis of flavonoids.Item Role of WRKY transcription factors in plant defense against lepidopteran insect herbivores: an overview(Springer Nature Publishing AG, 2021) Kundu, Pritha; Vadassery, JyothilakshmiPlants, in nature are challenged by various environmental stresses (both biotic and abiotic), which distort the plant growth, development and crop yield. A wide range of insect herbivores attack plants across the globe, throughout the year, causing huge loss to the productivity of crop species. Being sessile, the plants respond to the crisis using a wide range of defense responsive elements which at the transcriptional level, includes the transcription factors, like WRKY, NAC, AP2/ERF, MYB, MYC, bZIP, bHLH and others. Increasing evidences suggest a pivotal role of WRKY TFs in the regulation of plant defense response against herbivory in Arabidopsis and other important crop plants. Unlike pathogenic attack, very limited information is available on the role of different WRKYs in herbivore-plant interaction. In this review, we will thus majorly focus on the role of WRKY transcription factors and its regulation in response to herbivore attack while summarizing the recent developments from the field of transcriptional, post-transcriptional and epigenetic regulation of WRKYs in response to herbivory attack with the prospects for future implementation in research.Item Identification and downstream analyses of domains amplified in plant genomes: The case of StAR-related lipid transfer (START) domains in rice(Springer Nature Publishing AG, 2021) Mahtha, Sanjeet Kumar; Purama, Ravi Kiran; Kumari, Renu; Yadav, GitanjaliPlant genomes can withstand small- and large-scale duplications, at a far greater success than any other kingdom in the tree of life, resulting in the existence and evolution of gene families, often with over a hundred members! The gene families, in turn, go through subfunctionalization or neofunctionalization, to form protein domains performing unique or grouped functions in context of the original activity. Due to the large number of such cases in the plant kingdom, it has become a routine task for plant biologists to investigate their specific gene family of interest. In this chapter, we provide a simple and standard pipeline for this effort, taking the example of steroidogenic acute regulatory protein (StAR) related lipid transfer (START) domains in rice, as reference. We describe the extraction, processing, and downstream analysis of Oryza sativa var. japonica proteome towards identification and comparative exploration of START domains. This was done by training profile Hidden Markov Models (HMM) of 35 reported START domains in Arabidopsis, which were then used to search potential homologs in rice. Downstream investigations included domain structure analysis, visualization of exon–intron patterns, chromosomal localization of START genes, and phylogenetic studies, followed by identification of cis-regulatory elements and gene regulatory network construction. Additionally, we have also highlighted various alternative tools and techniques that can be used to perform similar analyses, along with salient features.Item The R2R3-MYB gene family in banana (Musa acuminata): Genome-wide identification, classification and expression patterns(PLOS, 2020) Pucker, Boas; Pandey, Ashutosh; Weisshaar, Bernd; Stracke, RalfThe R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, defense responses and metabolite accumulation. To date MYB family genes have not yet been comprehensively identified in the major staple fruit crop banana. In this study, we present a comprehensive, genome-wide analysis of the MYB genes from Musa acuminata DH-Pahang (A genome). A total of 285 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Organ- and development-specific expression patterns were determined from RNA-Seq data. For 280 M. acuminata MYB genes for which expression was found in at least one of the analysed samples, a variety of expression patterns were detected. The M. acuminata R2R3-MYB genes were functionally categorised, leading to the identification of seven clades containing only M. acuminata R2R3-MYBs. The encoded proteins may have specialised functions that were acquired or expanded in Musa during genome evolution. This functional classification and expression analysis of the MYB gene family in banana establishes a solid foundation for future comprehensive functional analysis of MaMYBs and can be utilized in banana improvement programmes.Item Genetic determinants of drought stress tolerance in Setaria(Springer, 2017) Muthamilarasan, Mehanathan; Prasad, ManojCultivated foxtail millet (Setaria italica) and its wild progenitor (S. viridis) have collectively been considered as tractable model species for studying C4 photosynthesis, stress biology, and biofuel traits. Being cultivated in arid and semiarid tropics of the world, these species are well adapted to harsh environments such as drought, heat, and salinity. This adaptation or acclimation potential of Setaria spp. has drawn research interest, and attempts have been made to dissect the molecular mechanisms of stress tolerance. Compared to other stresses, drought response has been studied extensively in S. italica and many drought-responsive genes encoding for transcription factors, signaling molecules, and enzymes have been identified and characterized. Several genome-wide studies have reported on identification of stress-responsive gene family members, and speculated on the potential for expansion and neofunctionalization of paralogs in these gene families. In this context, this chapter discusses the key genetic determinants identified for stress tolerance in S. italica and demonstrates their use in improving drought tolerance. In addition, strategies for identification of genes underlying stress tolerance are also described. Little effort has so far been made towards understanding the stress-tolerance characteristics of Setaria as compared to studies reported in other crops. Comprehensive functional studies along with the use of integrated -omics approaches are required to elucidate the genetics and genomics of stress tolerance in Setaria, as it is important to develop climate change resilient crops to meet the growing demand for food and feed.Item Drought stress responses and signal transduction in plants(Springer, 2015) Lata, Charu; Muthamilarasan, Mehanathan; Prasad, ManojNature provides all necessary components for healthy growth and development of plants in the form of air, water, light, nutrients, and soil. Any imbalance in the environmental harmony may cause stress to them. Stresses encountered by plants can broadly be categorized into biotic and abiotic stresses. Biotic stresses are mainly caused by pathogens and herbivory, whereas abiotic stresses include the threat imposed by drought, salinity, and extremes of temperature, heavy metals, and pollution. Drought stress is a major cause of yield instability in crops across diverse eco-geographic regions worldwide. A variety of biochemical, molecular, and physiological changes are manifested by plants in response to drought stress. The cellular abscisic acid (ABA) concentration increases on water deficit leading to the activation of a number of stress-responsive genes and the patterns of expression of these genes are very complex, with some genes being induced early while others respond slowly. In general, drought-responsive genes respond to salt and cold stresses as well as to exogenous ABA treatment. However, there are several genes, which express themselves in an ABA-independent manner suggesting that both ABA-dependent and -independent signal transduction cascades exist for drought stress perception, response, and adaptation. Drought stress response and adaptation in plants involves an array of pathways for signal perception, transduction, gene expression and synthesis of proteins, and other stress metabolites. Drought-responsive genes can mainly be classified into two groups. First group constitutes genes whose products provide osmotolerance and protection to plants thus directly functioning in tolerance to stress, while the second group includes genes playing a role in signal transduction as well as regulation of gene expression. This chapter summarizes the complex molecular mechanisms of drought stress response and adaptation in plants, highlighting the transcriptional regulation of stress-responsive gene expression. It also focuses on the recent advances in analyzing various stress-responsive pathways with prime emphasis on ABA-dependent and -independent pathways.Item Genome-scale transcriptomic insights into molecular aspects of abiotic stress responses in chickpea(Springer, 2015) Garg, Rohini; Bhattacharjee, Annapurna; Jain, MukeshChickpea is an important legume crop plant and various abiotic stresses are the major constraints affecting its overall productivity. For discovery of candidate genes involved in abiotic stress responses, we employed RNA sequencing for transcriptome profiling of roots and shoots of chickpea seedlings subjected to desiccation, salinity, and cold stresses. In total, we generated more than 250 million high-quality reads from non-stressed and stressed tissue samples. Data analyses provided a comprehensive view of the dynamic transcriptional response of chickpea tissues to different abiotic stresses. Differential expression analysis identified a total of 11,640 chickpea transcripts showing response to at least one of the stress conditions. The reference-based transcriptome assembly was generated and at least 3,536 previously unannotated gene loci differentially expressed under abiotic stress conditions were identified. We observed extensive transcriptional reprogramming of genes involved in transcription regulation, energy metabolism, photosynthesis, hormonal responses, secondary metabolite biosynthesis and osmoprotectant metabolism under stress conditions. In addition, genes involved in post-translational modifications, RNA metabolic processes, and epigenetic regulation were also significantly highlighted. The comprehensive transcriptome analyses presented in this study revealed several potential key regulators of plant response to abiotic stresses and open avenues to carry out functional and applied genomic studies for improving abiotic stress tolerance in chickpea.