Browsing by Author "Sharma, Shambhavi"

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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).
Delineating microRNA169-Nuclear Factor Y-Subunit a module for its potential implications in crop improvement
(John Wiley & Sons, 2026) Chakraborty, Anirban; Sharma, Shambhavi; Pandey, Girdhar K.; Bhatia, Sabhyata; Prasad, Manoj
Climate change considerably impacts plant growth and productivity by inducing stress responses. This, along with the problems of feeding the ever-increasing global population, could be mitigated by generating climate-resilient crop varieties with enhanced productivity. However, an exhaustive account of the key regulatory processes that underlie developmental and stress-responsive pathways is a prerequisite for generating improved crop varieties. Towards this, our study, for the first time, provides an exhaustive compilation of the potential regulatory pathways impacted by the miR169-NFYA network in plants. The NFYA transcription factors belong to a class of nuclear factor-encoding genes directly influencing the transcription of many genes involved in developmental and stress responses. Meanwhile, miR169 provides a layer to NFYA-mediated gene regulation by post-transcriptionally suppressing the expression of these transcription factors. Evidence from several studies shed light on key molecular signatures related to hormone synthesis and signaling, calcium signaling, epigenetic regulation, nutrient starvation and miRNA biogenesis that could serve as downstream components of the miR169-NFYA cascade in plants. This ability of miR169-NFYA nexus to impact a wide range of biological processes makes it a suitable toolbox for developing tailor-made crop varieties through appropriate genetic manipulation strategies.
Diverse roles of phytohormonal signaling in modulating plant-virus interaction
(Oxford University Press, 2025) Sharma, Shambhavi; Prasad, Manoj
Virus infection brings about changes in the transcriptome, proteome and metabolome status of the infected plant wherein substantial alterations in the abundance of phytohormones and associated components involved in their signaling pathways have been observed. In the recent years, extensive research in the field of plant virology has showcased the undisputable significance of phytohormone signaling during plant-virus interactions. Apart from acting as growth regulators, phytohormones elicit robust immune response, which restricts the viral multiplication within the plant as well as its propagation by vector. Interestingly, these pathways have been shown to not only act as isolated mechanisms but as complex intertwined regulatory cascades where, the cross-talk among different phytohormones and with other antiviral pathways takes place during plant-virus interplay. Viruses cleverly disrupt phytohormone homeostasis via their multifunctional effectors that seems to be smart approach adopted by viruses to circumvent phytohormone-mediated plant immune responses. In this review, we summarize the current understanding of role of phytohormone signaling pathways during plant-virus interaction in activating antiviral immune responses of plant and also, how viruses exploit these signaling pathways favoring their pathogenesis.
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.
FERONIA, the kinase that phosphorylates PhyB
(Elsevier B.V., 2023) Sharma, Shambhavi; Prasad, Manoj
The phosphorylation status of phyB changes dynamically in response to environmental conditions and critically governs the corresponding plant’s responses. However, the kinase(s) that phosphorylates phyB is/are still unknown. Liu et al. have not only identified the kinase that phosphorylates phyB but also revealed its biological implications during salt stress.
Genomics resources for abiotic stress tolerance in solanaceae crops
(Springer, 2017) Sharma, Shambhavi; Pandey, Saurabh; Muthamilarasan, Mehanathan; Chaudhry, Vaishali; Dulani, Priya; Prasad, Manoj
The study of abiotic stresses in plants is crucial for an understanding of the mechanisms involved in responses to these stresses. The complex nature of abiotic stress-related traits and the occurrence of more than one stress simultaneously further complicate the study. The availability of genomic tools and resources allows a leap in plant breeding by facilitating the study of the genotype and its relationship with the phenotype. The development of techniques such as Next-Generation Sequencing (NGS) allowed the sequencing of genomes of cultivars and their wild relatives, enriching the available genetic as well as genomic resources. Genome-wide discovery of markers and quantitative trait loci are used for marker-assisted selection and breeding. The availability of the genome sequence information has expedited several downstream analyses, including genome-wide identification and expression profiling of the genes associated with stress response. This is coupled with the use of mutants and transgenics to elucidate and verify the function of genes in a high-throughput fashion. In this chapter, the progress made in the generation and enrichment of genomic resources of Solanum tuberosum and S. lycopersicum are discussed from the point of view of genetic improvement for abiotic stress tolerance.
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.
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.
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 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.
Role of ubiquitination enzymes in abiotic environmental interactions with plants
(Elsevier B.V., 2021) Sharma, Shambhavi; Prasad, Ashish; Sharma, Namisha; Prasad, Manoj
Ubiquitination, 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.
Selective autophagy: the fulcrum of plant-virus interaction
(Elsevier B.V., 2024) Sharma, Shambhavi; Prasad, Ashish; Prasad, Manoj
Selective autophagy receptors play both proviral and antiviral roles during plant-virus interaction. However, little is known about the balance between such contradictory dual roles of these receptors. Tong et al. have deciphered the temporal regulation of antiviral and antiplant roles of a selective autophagy receptor, a virus-induced small peptide 1 (VISP1).
Suppressing plant defence: Scavenge the ROS!
(John Wiley & Sons, 2023) Prasad, Ashish; Sharma, Shambhavi; Prasad, Manoj
ROS-mediated defence against fungal pathogens is an essential arm of plant immunity. As a counter defence, these pathogens synthesize antioxidant enzymes that scavenge the ROS produced by plants. The molecular mechanism behind the upregulation of these enzymes in fungal pathogens was unknown. A recent study by Zhang and colleagues has shed light on the mechanism, and it has been shown that deacetylation of FolSrpk1 protein on the K304 residue following oxidative stress is an important event in the signalling cascade leading to ROS detoxification in Fusarium oxysporum f. sp. lycopersici. Deacetylated FolSrpk1 moves to the nucleus where it hyperphosphorylates FolSr1, which further regulates the transcription of antioxidant enzymes (Zhang et al. 2023). This mechanism of ROS detoxification is conserved in Botrytis cinerea as well. Several other phytopathogenic fungi have a corresponding K304 site and NLS present in their Srpk1, suggesting a similar mechanism of ROS detoxification and suppression of plant defence. In this article, we have presented our views on how future studies can be synthesized based on the pathway deciphered by Zhang et al. 2023.
Ubiquitination from the perspective of plant pathogens
(Oxford University Press, 2023) Sharma, Shambhavi; Prasad, Ashish; Prasad, Manoj
The constant battle of survival between pathogens and host plants has played a crucial role in shaping the course of their co-evolution. However, the major determinants of the outcome of this ongoing arms race are the effectors secreted by pathogens into the host cells. These effectors perturb the defense responses of plants to promote their successful infection. In recent years, the extensive research in the area of effector biology has reported an increase in the repertoire of pathogenic effectors that mimics or targets the conserved ubiquitin proteasomal pathway. The role of ubiquitin mediated degradation pathway has been well known to be indispensable for various aspects of plant’s life, thus targeting or mimicking it seems to be a smart strategy adopted by pathogens in their favor. Therefore, this review summarizes the recent findings on how some pathogenic effectors mimics or act as one of the components of ubiquitin proteasomal machinery while others directly target the plant’s ubiquitin proteasomal system.