Browsing by Author "Prasad, Ashish"

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Advances in omics technology for improving crop yield and stress resilience
(John Wiley & Sons, 2021) Singh, Roshan Kumar; Sood, Priyanka; Prasad, Ashish; Prasad, Manoj
Global climate change has emerged as the utmost environmental threat for agriculture. To maintain a sustainable food supply, climate-resilient high-yielding crop plants need to be developed. Over the last decade, understanding the complexity of genotype underlying agronomic traits has prompted the integrated application of various omics tools to address specific biological questions. A multi-parallel qualitative and quantitative differential analysis of gene transcripts, proteins and metabolites provides a comprehensive picture of the interconnected gene networks and cellular signalling cascade of regulatory and effector proteins. Genetic determinants of adaptation to environmental stress and yield enhancement traits are being determined and introgressed into elite accessions through either molecular breeding or genetic engineering approaches to obtain future crops with improved traits.
Breeding and biotechnological interventions for trait improvement: status and prospects
(Springer Nature Publishing AG, 2020) Singh, Roshan Kumar; Prasad, Ashish; Muthamilarasan, Mehanathan; Parida, Swarup K.; Prasad, Manoj
Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the diferent genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.
Catalase regulation during plant-virus-vector interaction
(John Wiley & Sons, 2024) Sharma, Rohit; Pandey, Saurabh; Prasad, Manoj; Prasad, Ashish
Plant-virus-host interaction is a complex process involving several players. A constant arms race between the hosts and viruses has led to their co-evolution. Reactive oxygen species (ROS) are important signaling molecules that regulate plant growth, development, and stress responses. Barley yellow dwarf virus (BYDV) has a wide host range and infects several plant species such as barley, rice, oats, wheat, etc. A recent study by Tian et al. (2024) has highlighted that the movement protein (MP) of BYDV is involved in manipulation of the host ROS pathway to promote viral multiplication as well as transmission. The findings display the multifaceted role of a viral protein that is otherwise involved in movement. The limited coding ability of viruses is compensated by their proteins having multiple roles in the modulation of several different host molecular pathways. This is one of the key reasons for viruses being successful pathogens despite their limited coding ability.
Complex molecular mechanisms determine fitness of plants to biotic and abiotic stresses
(Springer Nature Publishing AG, 2021) Prasad, Ashish; Senthil-Kumar, Muthappa; Prasad, Manoj
The 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.
Deeper look into viruses: replication intermediates do code!
(Springer Nature Publishing AG, 2024) Prasad, Ashish; Sharma, Shambhavi; Prasad, Manoj
It is quite intriguing how viruses with their limited coding ability are able to infect their hosts. Processes like RNA editing, transcriptional slippage, RNA splicing, programmed ribosome frameshifting, ribosomal leaky scanning, translational initiation from non-AUG codons, alternative splicing and several other mechanisms greatly expand the coding capacity of viruses, resulting in a more diverse transcriptome and proteome which is conventionally predicted from the ORFs (Ho et al. 2021). Several studies have highlighted that viruses encode various small ORFs that play important roles in viral lifecycle and infection (Gong et al. 2021; Shi et al. 2023). Positive-sense single-stranded RNA (+ ssRNA) viruses have a RNA genome that can act as mRNA and can be translated directly (Louten 2016). These viruses synthesize an −RNA strand which has been long believed to be a replication intermediate without coding ability that serves as a template for synthesizing more + ssRNA strands. However, some studies have highlighted that −RNA replication intermediates do have coding ability expanding the transcriptome of such viruses (Dinan et al. 2020; Retallack et al. 2021; Zhang et al. 2023; Gong et al. 2023).
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, Manoj
DNA 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.
Genomics approaches to synthesis plant-based biomolecules for therapeutic applications to combat SARS-CoV-2
(Elsevier B.V., 2020) Sharma, Namisha; Muthamilarasan, Mehanathan; Prasad, Ashish; Prasad, Manoj
COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is devastative to the humankind for which neither vaccines nor precise therapeutic molecules for treatment are identified. The search for new drugs and repurposing of existing drugs are being performed; however, at the same time, research on plants to identify novel therapeutic compounds or testing the existing ones is progressing at a slower phase. In this context, genomics and biotechnology offer various tools and strategies to manipulate plants for producing those complex biopharmaceutical products. This review enumerates the scope for research on plant-based molecules for their potential application in treating SARS-CoV-2 infection. Strategies to edit gene and genome, overexpression and silencing approaches, and molecular breeding for producing target biomolecules in the plant system are discussed in detail. Altogether, the present review provides a roadmap for expediting research on using plants as a novel source of active biomolecules having therapeutic applications.
Horizontal gene transfer and the evolution of land plants
(Cell Press, 2022) Prasad, Ashish; Chirom, Oceania; Prasad, Manoj
Horizontal gene transfer (HGT) can be defined as the acquisition of genetic material from another organism without being its offspring. HGT is common in the microbial world including archaea and bacteria, where HGT mechanisms are widely understood and recognized as an important force in evolution. In eukaryotes, HGT now appears to occur more frequently than originally thought. Many studies are currently detecting novel HGT events among distinct lineages using next-generation sequencing. Most examples to date include gene transfers from bacterial donors to recipient organisms including fungi, plants, and animals. In plants, one well-studied example of HGT is the transfer of the tumor-inducing genes (T-DNAs) from some Agrobacterium species into their host plant genomes. Evidence of T-DNAs from Agrobacterium spp. into plant genomes, and their subsequent maintenance in the germline, has been reported in Nicotiana, Linaria and, more recently, in Ipomoea species. The transferred genes do not produce the usual disease phenotype, and appear to have a role in evolution of these plants. In this paper, we review previous reported cases of HGT from Agrobacterium, including the transfer of T-DNA regions from Agrobacterium spp. to the sweetpotato [Ipomoea batatas (L.) Lam.] genome which is, to date, the sole documented example of a naturally-occurring incidence of HGT from Agrobacterium to a domesticated crop plant. We also discuss the possible evolutionary impact of T-DNA acquisition on plants.
Host-virus interactions mediated by long non-coding RNAs
(Elsevier B.V., 2021) Prasad, Ashish; Prasad, Manoj
Viruses are obligate pathogens that cause a wide range of diseases across all kingdoms of life. They have a colossal impact on the economy and healthcare infrastructure world-wide. Plants and animals have developed sophisticated molecular mechanisms to defend themselves against viruses and viruses in turn hijack host mechanisms to ensure their survival inside their hosts. Long non-coding (lnc) RNAs have emerged as important macromolecules that regulate plant-virus and animal-virus interactions. Both pro-viral and anti-viral lncRNAs have been reported and they show immense potential to be used as markers and in therapeutics. The current review is focussed on the recent developments that have been made in viral interactions of animals and plants.
Insect herbivores benefit from horizontal gene transfer
(Elsevier B.V., 2021) Prasad, Ashish; Chirom, Oceania; Prasad, Manoj
Evidence suggests that horizontal gene transfer (HGT) is relatively common in eukaryotes, contrary to what was previously believed. For example, insects that feed on complex sugars and neutralize, degrade, and sequester toxic secondary metabolites have recently been shown to benefit by acquiring genes through HGT.
Interaction of ToLCNDV TrAP with SlATG8f marks it susceptible to degradation by autophagy
(Springer Nature Publishing AG, 2022) Prasad, Ashish; Prasad, Manoj
Tomato leaf curl New Delhi virus (ToLCNDV) is a devastating plant pathogen which causes significant losses in tomato yield. According to previous reports, proteins of geminiviruses like βC1 of Cotton leaf curl Multan virus and C1 of Tomato leaf curl Yunnan virus are degraded by the autophagy pathway. There are no reports on the role of autophagy in ToLCNDV pathogenesis. In this study, we have shown that SlATG8f interacts with the ToLCNDV Transcription activator protein (TrAP; AC2) to mediate its degradation by the autophagy pathway. Silencing of SlATG8f in a ToLCNDV tolerant tomato cultivar; H-88-78-1 resulted in enhanced viral symptoms and ToLCNDV accumulation suggesting an anti-viral role for SlATG8f against ToLCNDV. TrAP is a nucleus localized protein, but it interacts with SlATG8f in and outside the nucleus indicating its nuclear export. This export might be mediated by Exportin1 as treatment with Exportin1 inhibitor inhibits TrAP export outside the nucleus. ToLCNDV TrAP is known to possess host RNA silencing suppression (RSS) activity. Degradation of TrAP results in the attenuation of its RSS activity. To the best of our knowledge, we have shown for the first time that SlATG8f-TrAP interaction leads to TrAP degradation providing defence against ToLCNDV.
Linking the plant stress responses with RNA helicases
(Elsevier B.V., 2020) Pandey, Saurabh; Prasad, Ashish; Sharma, Namisha; Prasad, Manoj
RNA 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.
Molecular characterization of SlATG18f in response to Tomato leaf curl New Delhi virus infection in tomato and development of a CAPS marker for leaf curl disease tolerance
(Springer Nature Publishing AG, 2021) Prasad, Ashish; Hari‑Gowthem, Gunaseelen; Muthamilarasan, Mehanathan; Hussain, Zakir; Yadav, Pawan Kumar; Tripathi, Sandhya; Prasad, Manoj
Autophagy is a highly conserved catabolic process regulating cellular homeostasis and adaptation to different biotic and abiotic stress. Several autophagy-related proteins (ATGs) are reported to be involved in autophagic processes, and considering their importance in regulating growth and stress adaptation, these proteins have been identified and characterized in several plant species. However, there is no information available on the role of autophagy-related proteins regulating the tolerance of tomato to tomato leaf curl disease (ToLCD). Given this, the present genome-wide study identified thirty ATG-encoding genes (SlATG) in tomato, followed by their functional characterization. Expression profiling of the SlATG genes in contrasting tomato cultivars subjected to virus infection showed a 4.5-fold upregulation of SlATG18f in the tolerant cultivar. Further, virus-induced gene silencing of SlATG18f in the tolerant cultivar conferred disease susceptibility, which suggested the role of this gene in Tomato leaf curl New Delhi virus tolerance. Comparison of the gene sequence of both tolerant and susceptible cultivars along with the 5′ upstream regions identified an SNP (A/T) at -2916 upstream of the start codon. A cleaved amplified polymorphic sequence (CAPS) marker was developed targeting this region, which showed a significant association with the tolerance characteristics in the tomato germplasm (R2 = 0.1787). Altogether, the study identified a potential gene that could be used to develop ToLCNDV tolerant tomato cultivars using transgene-based or marker-assisted breeding-based approaches.
Multihost compatibility of Fusarium oxysporum: early root colonization effectors into the action!
(Springer Nature Publishing AG, 2023) Prasad, Ashish; Sharma, Shambhavi; Prasad, Manoj
Agricultural productivity is greatly afected by several biotic factors which include insects, nematodes, bacteria, fungi, and viruses. Fungal pathogens in particular are a major setback to optimum crop production. A fungal species causing huge agro-economic losses world-wide is the Fusarium oxysporum (Fo) species complex. Fo is known to cause cross-kingdom infections in plants and humans (Zhang et al. 2020). In plants, it causes vascular wilt in several species; however, any particular Fo formae speciales (Fo f. sp.) can cause symptomatic infection on one or a few related species by invading their vasculature. Some important Fo f. sp. include apii, conglutinans, cubense, lycopersici, and melongena (Arie 2019). These strains can also survive in the root cortex of other hosts without invading the vasculature resulting in asymptomatic root colonization. A study by Redkar et al. has revealed that such an endophytic growth in multiple hosts is regulated by a group of conserved fungal efectors known as early root colonization (ERC) efectors.
Noncoding but coding: pri-miRNA into the action
(Elsevier B.V., 2021) Prasad, Ashish; Sharma, Namisha; Prasad, Manoj
Some pri-miRNAs can code for short peptides called micropeptides (miPEPs) and it has been suggested that these peptides positively regulate the accumulation of their associated miRNAs. Recent data further support this model and point towards the potential for miPEPs to be used in the agricultural sector to improve crop agronomic traits.
Osmosensing in plants: mystery unveiled
(Elsevier B.V., 2023) Sharma, Shambhavi; Prasad, Ashish; Prasad, Manoj
Osmotic stress limits plant growth and productivity. The downstream signaling components involved in osmotic adjustments are well known, but our knowledge of the perception of osmotic stress is far too limited. Wang et al. have recently identified a lesser-known mechanism of bimolecular condensation that underlies osmotic stress perception in plants.
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.
Post translational modifications at the verge of plant-geminivirus interaction
(Elsevier B.V., 2023) Prasad, Ashish; Sharma, Shambhavi; Prasad, Manoj
Plant-virus interaction is a complex phenomenon and involves the communication between plant and viral factors. Viruses have very limited coding ability yet, they are able to cause infection which results in huge agro-economic losses throughout the globe each year. Post-translational modifications (PTMs) are covalent modifications of proteins that have a drastic effect on their conformation, stability and function. Like the host proteins, geminiviral proteins are also subject to PTMs and these modifications greatly expand the diversity of their functions. Additionally, these viral proteins can also interact with the components of PTM pathways and modulate them. Several studies have highlighted the importance of PTMs such as phosphorylation, ubiquitination, SUMOylation, myristoylation, S-acylation, acetylation and methylation in plant-geminivirus interaction. PTMs also regulate epigenetic modifications during geminivirus infection which determines viral gene expression. In this review, we have summarized the role of PTMs in regulating geminiviral protein function, influence of PTMs on viral gene expression and how geminiviral proteins interact with the components of PTM pathways to modulate their function.
Recent advances in small RNA mediated plant-virus interactions
(Taylor & Francis Group, 2019) Prasad, Ashish; Sharma, Namisha; Muthamilarasan, Mehanathan; Rana, Sumi; Prasad, Manoj
Small RNAs (sRNA) are reported to play pivotal roles in the epigenetic and post-transcriptional regulation of gene expression during growth, development, and stress response in plants. Recently, the involvement of two different classes of sRNAs namely, miRNAs (microRNAs), and siRNAs (small interfering RNAs) in biotic stress response has been underlined. Notably, during virus infection, these sRNAs deploy antiviral defense by regulating the gene expression of the modulators of host defense pathways. As a counter defense, viruses have evolved strategic pathways involving the production of suppressors that interfere with the host silencing machinery. This molecular arms race between the sophisticated gene regulatory mechanism of host plants fine-tuned by sRNAs and the defense response exhibited by the virus has gained much attention among the researchers. So far, several reports have been published showing the mechanistic insights on sRNA-regulated defense mechanism in response to virus infection in several crop plants. In this context, our review enumerates the molecular mechanisms underlying host immunity against viruses mediated by sRNAs, the counter defense strategies employed by viruses to surpass this immunogenic response and the advances made in our understanding of plant-virus interactions. Altogether, the report would be insightful for the researchers working to decode the sRNA-mediated defense response in crop plants challenged with virus infection.
Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction
(Elsevier B.V., 2023) Sharma, Shambhavi; Sett, Susmita; Das, Tuhin; Prasad, Ashish; Prasad, Manoj
In natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.