Browsing by Author "Sharma, Namisha"

Now showing 1 - 20 of 28

Characterization of DEAD-box family of RNA helicases in tomato provides insights into their roles in biotic and abiotic stresses
(Elsevier B.V., 2019) Pandey, Saurabh; Muthamilarasan, Mehanathan; Sharma, Namisha; Chaudhry, Vaishali; Dulani, Priya; Shweta, Shweta; Jha, Sarita; Mathur, Saloni; Prasad, Manoj
In plants, RNA helicases play significant roles in growth, development and stress response. In a previous study, a three-fold upregulation of a DEAD-box RNA helicase in a tomato cultivar tolerant to Tomato leaf curl New Delhi virus (ToLCNDV) as compared to susceptible cultivar during virus infection was shown. Given this, a comprehensive study was performed to identify the members of RNA helicase family in tomato and analyze their functional properties in response to abiotic stresses, hormone treatments and ToLCNDV infection. A total of 131 genes were identified and classified into DEAD- (42), DEAH- (38), and DExD/H-box (51) RNA helicases. Expression profiling of candidate genes in response to abiotic stresses and ToLCNDV infection in contrasting tomato cultivars suggested the putative roles of SlDEAD23 and SlDEAD35 in biotic and abiotic stresses. Heterologous overexpression of these genes in yeast enhanced the tolerance of transgenic cells to salt and cold stresses. Further, virus-induced silencing of SlDEAD35 in ToLCNDV tolerant cultivar resulted in susceptibility to virus infection, thus suggesting its involvement in tolerance mechanism. Altogether, this study provides novel insights into the structure, organization and involvement of DEAD-box RNA helicase genes in biotic and abiotic stress responses in tomato.
Chromatin-based epigenetic regulation of plant abiotic stress response
(Bentham Science, 2016) Pandey, Garima; Sharma, Namisha; Sahu, Pranav Pankaj; Prasad, Manoj
Plants are continuously exposed to various abiotic and biotic factors limiting their growth and reproduction. In response, they need various sophisticated ways to adapt to adverse environmental conditions without compromising their proper development, reproductive success and eventually survival. This requires an intricate network to regulate gene expression at transcriptional and post-transcriptional levels, including epigenetic switches. Changes in chromatin modifications such as DNA and histone methylation have been observed in plants upon exposure to several abiotic stresses. In the present review, we highlight the changes of DNA methylation in diverse plants in response to several abiotic stresses such as salinity, drought, cold and heat. We also discuss the progresses made in understanding how these DNA methylation changes might contribute to the abiotic stress tolerance.
CRISPR/Cas9: A novel weapon in the arsenal to combat plant diseases
(Frontiers Media S.A., 2019) Das, Ayan; Sharma, Namisha; Prasad, Manoj
Plant pathogens like virus, bacteria, and fungi incur a huge loss of global productivity. Targeting the dominant R gene resulted in the evolution of resistance in pathogens, which shifted plant pathologists’ attention toward host susceptibility factors (or S genes). Herein, the application of sequence-specific nucleases (SSNs) for targeted genome editing are gaining more importance, which utilize the use of meganucleases (MN), zinc finger nucleases (ZFNs), transcription activator-like effector-based nucleases (TALEN) with the latest one namely clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). The first generation of genome editing technologies, due to their cumbersome nature, is becoming obsolete. Owing to its simple and inexpensive nature the use of CRISPR/Cas9 system has revolutionized targeted genome editing technology. CRISPR/Cas9 system has been exploited for developing resistance against virus, bacteria, and fungi. For resistance to DNA viruses (mainly single-stranded DNA viruses), different parts of the viral genome have been targeted transiently and by the development of transgenic plants. For RNA viruses, mainly the host susceptibility factors and very recently the viral RNA genome itself have been targeted. Fungal and bacterial resistance has been achieved mainly by targeting the host susceptibility genes through the development of transgenics. In spite of these successes CRISPR/Cas9 system suffers from off-targeting. This and other problems associated with this system are being tackled by the continuous discovery/evolution of new variants. Finally, the regulatory standpoint regarding CRISPR/Cas9 will determine the fate of using this versatile tool in developing pathogen resistance in crop plants.
Decoding the functionality of plant transcription factors
(Oxford University Press, 2024) Dhatterwal, Pinky; Sharma, Namisha; Prasad, Manoj
Transcription 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.
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.
Epigenetic mechanisms of plant stress responses and adaptation
(Springer, 2013) Sahu, Pranav Pankaj; Pandey, Garima; Sharma, Namisha; Puranik, Swati; Muthamilarasan, Mehanathan; Prasad, Manoj
Epigenetics has become one of the hottest topics of research in plant functional genomics since it appears promising in deciphering and imparting stress-adaptive potential in crops and other plant species. Recently, numerous studies have provided new insights into the epigenetic control of stress adaptation. Epigenetic control of stress-induced phenotypic response of plants involves gene regulation. Growing evidence suggest that methylation of DNA in response to stress leads to the variation in phenotype. Transposon mobility, siRNA-mediated methylation and host methyltransferase activation have been implicated in this process. This review presents the current status of epigenetics of plant stress responses with a view to use this knowledge towards engineering plants for stress tolerance.
Geminivirus-induced reprogramming of plant defense mechanisms: molecular insights and research frontiers
(Annual Reviews, 2026) Sharma, Namisha; Sett, Susmita; Prasad, Manoj
Geminiviruses employ multifunctional protein ammunition to evade robust plant defense pathways. Key viral proteins effectively manipulate host signaling mechanisms to create a permissive environment for viral replication. Rapid evolutionary adaptation of geminiviruses, synergized by the proliferation of insect vectors, creates a challenge for effective disease control. Current plant resistance against geminiviruses primarily relies on antiviral RNA silencing and the localized cell death mechanism as an outcome of the hypersensitive response. To win the escalating arms race between geminivirus manipulation and subsequent plant counteracting strategies and effectively restrict viral invasion, these defense strategies need to be updated or supplemented with novel engineering approaches. In this review, we provide a critical contemporary understanding of viral reprogramming pathways and host counter-defense responses that provide new avenues to improve plant immunity against geminiviruses.
Genomic dissection of ROS detoxifying enzyme encoding genes for their role in antioxidative defense mechanism against Tomato leaf curl New Delhi virus infection in tomato
(Elsevier B.V., 2021) Sharma, Namisha; Muthamilarasan, Mehanathan; Dulani, Priya; Prasad, Manoj
In the present study, genes encoding for six major classes of enzymatic antioxidants, namely superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), Peroxidase (Prx) and glutathione S-transferase (GST) are identified in tomato. Their expression was studied in tomato cultivars contrastingly tolerant to ToLCNDV during virus infection and different hormone treatments. Significant upregulation of SlGR3, SlPrx25, SlPrx75, SlPrx95, SlGST44, and SlGST96 was observed in the tolerant cultivar during disease infection. Virus-induced gene silencing of SlGR3 in the tolerant cultivar conferred disease susceptibility to the knock-out line, and higher accumulation (~80%) of viral DNA was observed in the tolerant cultivar. Further, subcellular localization of SlGR3 showed its presence in cytoplasm, and its enzymatic activity was found to be increased (~65%) during ToLCNDV infection in the tolerant cultivar. Knock-out lines showed ~3- and 3.5-fold reduction in GR activity, which altogether underlines that SlGR3 is vital component of the defense mechanism against ToLCNDV infection.
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.
Histone deacetylase 9 interacts with SiHAT3.1 and SiHDA19 to repress dehydration responses through H3K9 deacetylation in foxtail millet
(Oxford University Press, 2024) Kumar, Verandra; Singh, Babita; Singh, Roshan Kumar; Sharma, Namisha; Muthamilarasan, Mehanathan; Sawant, Samir V; Prasad, Manoj
Climate change inflicts several stresses on plants, of which dehydration stress severely affects growth and productivity. C4 plants possess better adaptability to dehydration stress; however, the role of epigenetic modifications underlying this trait is unclear. Particularly, the molecular links between histone modifiers and their regulation remain elusive. In this study, genome-wide H3K9 acetylation (H3K9ac) enrichment using ChIP-seq was performed in two foxtail millet cultivars contrastingly differing in dehydration tolerance (IC403579; cv. IC4 – tolerant, and IC480117; cv. IC41 – sensitive). It revealed that a histone deacetylase, SiHDA9, was significantly up-regulated in the sensitive cultivar. Further characterization indicated that SiHDA9 interacts with SiHAT3.1 and SiHDA19 to form a repressor complex. SiHDA9 might be recruited through the SiHAT3.1 recognition sequence onto the upstream of dehydration-responsive genes to decrease H3K9 acetylation levels. The silencing of SiHDA9 resulted in the up-regulation of crucial genes, namely, SiRAB18, SiRAP2.4, SiP5CS2, SiRD22, SiPIP1;4 and SiLHCB2.3, which imparted dehydration tolerance in the sensitive cultivar (IC41). Overall, the study provides mechanistic insights into SiHDA9-mediated regulation of dehydration stress response in foxtail millet.
An insight into plant–Tomato leaf curl New Delhi virus interaction
(Springer Nature, 2017) Sharma, Namisha; Prasad, Manoj
Plants being sessile are constantly exposed to several stresses, which involve different types of abiotic and biotic stress factors. Biotic stress in plants is caused by various living organisms called plant pathogens including bacteria, viruses, fungi and parasites. Among these pathogens, plant viruses cause severe damage to world agricultural productivity. The reason behind such widespread destruction caused by viruses is their ability to frequently evolve them through mutation and genetic recombination, to succeed over the unfavourable conditions. The virus infects both susceptible and tolerant/resistant plants by the similar and systematic manner but resistant/tolerant plants combat the virus spread and suppress the viral growth. When pathogen enters the plant system, diverse defense responses are initiated which are mediated by plant disease resistance genes (R genes) mediated resistance and hormone based signaling pathways which restrict the viral spread by initiating hypersensitive response. To further enhance our knowledge regarding resistance mechanisms, the virus infection pattern and interactions of virus within resistant and susceptible plants needs to be analysed. At present, most successful strategy involves deployment of crops possessing resistance/tolerance against viruses with the foremost interest of detecting genes associated with resistance or recovery. Among several plant viruses, ‘Geminiviruses’ are the most devastating. In this article we have provided a comprehensive overview of Tomato leaf curl New Delhi virus (ToLCNDV), a member of family Geminiviridae and the plant defense system initiated against this virus. The evaluation of ToLCNDV infection in a variety of hosts differing in their tolerance and identification of differentially expressed genes would be helpful in speculating the threats associated with similar begomoviral invasions.
Involvement of host regulatory pathways during geminivirus infection: a novel platform for generating durable resistance
(Springer, 2014) Sahu, Pranav Pankaj; Sharma, Namisha; Puranik, Swati; Muthamilarasan, Mehanathan; Prasad, Manoj
Geminiviruses are widely distributed throughout the world and cause devastating yield losses in almost all the economically important crops. In this review, the newly identified roles of various novel plant factors and pathways participating in plant–virus interaction are summarized with a particular focus on the exploitation of various pathways involving ubiquitin/26S proteasome pathway, small RNA pathways, cell division cycle components, and the epigenetic mechanism as defense responses during plant–pathogen interactions. Capturing the information on these pathways for the development of strategies against geminivirus infection is argued to provide the basis for new genetic approaches to resistance.
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.
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.
OsPSKR15, a phytosulfokine receptor from rice enhances abscisic acid response and drought stress tolerance
(John Wiley & Sons, 2022) Nagar, Preeti; Sharma, Namisha; Jain, Muskan; Sharma, Gauri; Prasad, Manoj; Mustafiz, Ananda
Abscisic acid (ABA) is a major phytohormone that acts as stimuli and plays an important role in plant growth, development, and environmental stress responses. Membrane-localized receptor-like kinases (RLKs) help to detect extracellular stimuli and activate downstream signaling responses to modulate a variety of biological processes. Phytosulfokine receptor (PSKR), a Leu-rich repeat (LRR)-RLK, has been characterized for its role in growth, development and biotic stress. Here, we observed that OsPSKR15, a rice PSKR, was upregulated by ABA in Oryza sativa. We demonstrated OsPSKR15 is a positive regulator in plant response to ABA. Ectopic expression of OsPSKR15 in Arabidopsis thaliana increased the sensitivity to ABA during germination, growth and stomatal closure. Consistently, the expression of ABA-inducible genes was significantly upregulated in these plants. OsPSKR15 also regulated reactive oxygen species (ROS)-mediated ABA signaling in guard cells, thereby governing stomatal closure. Furthermore, the constitutive expression of OsPSKR15 enhanced drought tolerance by reducing the transpirational water loss in Arabidopsis. We also reported that OsPSKR15 directly interacts with AtPYL9 and its orthologue OsPYL11 of rice through its kinase domain in the plasma membrane and nucleus. Altogether, these results reveal an important role of OsPSKR15 in plant response toward abiotic stress in an ABA-dependent manner.
Post-transcriptional and epigenetic arms of RNA silencing: a defense machinery of naturally tolerant tomato plant against Tomato leaf curl New Delhi virus
(Springer, 2014) Sahu, Pranav Pankaj; Sharma, Namisha; Puranik, Swati; Prasad, Manoj
Tomato leaf curl disease (ToLCD), caused by strains of Tomato leaf curl virus, is major constraint to tomato production globally. The present study was aimed to understand the mechanisms of ToLCD tolerance in a naturally tolerant tomato cultivar through post-transcriptional and DNA methylation-specific RNA silencing. We evaluated the distribution of virus-derived short-interfering RNAs (siRNAs) throughout the Tomato leaf curl New Delhi virus (ToLCNDV) genome along with DNA methylation patterns in intergenic (IR) and Rep (AC1) regions in two tomato cultivars differing in their ToLCNDV tolerance. The methylation pattern was correlated by expression analysis of key methyltransferases genes. In the tolerant cultivar, higher accumulation of viral IR-specific 24-nucleotides (nt) siRNA and AC1-specific 21-nt siRNA were found. Higher methylation levels were observed in various regions of IR. Additionally, AC1 region which facilitates binding of plant nuclear proteins was hypermethylated. DNA methylation in the key regulating region may control the expression of AC1, AC2, and AC3 genes. Components of RNA silencing and DNA methylation machinery were found to be differentially expressed in both the cultivar of tomato at 21 dpi. Thus, we infer that both viral DNA methylation and siRNA-mediated RNA degradation play an important role in conferring tolerance against Tomato leaf curl New Delhi virus. Due to the inability to achieve field resistance in transgenic tomato by deploying the viral genes, targeting the viral genomic regions through RNAi technology reported here could offer an alternate defense strategy for generating transgenics to prevent yield loss.
Recent advances in plant-virus interaction with emphasis on small interfering RNAs (siRNAs)
(Springer, 2013) Sharma, Namisha; Sahu, Pranav Pankaj; Puranik, Swati; Prasad, Manoj
Regulation of several biological functions in plants has now been known to involve diverse RNA silencing pathways. These vital pathways involve various components such as dsRNA, Dicer, RNA-dependent RNA polymerase and Argonaute proteins, which lead to the production of several small RNAs (sRNAs) varying in their sizes. These sRNAs have significant role in the regulation of gene expression at transcriptional and translational levels. Among them, small interfering RNAs (siRNAs; majorly 21, 22 and 24 nt) have been shown to play an important role in plants' resistance against many viruses by inhibiting the viral gene expression. Furthermore, it has also been highlighted that siRNA-mediated methylation of viral DNA confers resistance to various plant DNA viruses. In this review, we have outlined the recent advances made using the siRNA-mediated antiviral strategy, along with methylation-based epigenetic defensive mechanisms as a protective measure against diverse plant viruses.
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.
Role of RNA-interacting proteins in modulating plant-microbe interactions
(Elsevier B.V., 2020) Pandey, Saurabh; Sharma, Namisha; Prasad, Manoj
Successful infection of a pathogen in its host plant depends on the complex molecular interplay between host and the invading microbe. Plant-microbe interactions are primarily governed by signal interchange amid both the organisms. Effective passage of the pathogen into the plant system requires the circumvention of signal detection mechanisms and subsequent immune responses. As a mechanism to counteract defense response, pathogens deploy several RNA-interacting proteins (RIPs) or RNA molecules which interrupt the host transcriptional as well as signaling pathways, leading to successful infection and symptom development. The interference by pathogen-derived small RNAs (sRNA) in the gene silencing machinery of the host has been recently reported. In this context, the present review describes the pathogen- and host-specific RNA molecules and chaperones, their roles in modulating host immune response as well as pathogenesis, and the possible targets for manipulating the molecular mechanism to develop durable tolerance/resistance against diseases in crops.
Role of Sw5 gene cluster in the fight against plant viruses
(American Society for Microbiology, 2022) Sharma, Namisha; Prasad, Ashish; Prasad, Manoj
The Sw5 gene cluster furnishes robust resistance to Tomato spotted wilt virus in tomato, which has led to its widespread applicability in agriculture. Among the five orthologs, Sw5b functions as a resistance gene against a broad-spectrum Tospovirus and is linked with Tospovirus resistance. However, its paralog, Sw5a, has been recently implicated in providing resistance against Tomato leaf curl New Delhi virus, broadening the relevance of the Sw5 gene cluster in promoting defense against plant viruses. We propose that plants have established modifications within the homologs of R genes that permit identification of different effector proteins and provide broad and robust resistance against different pathogens through activation of hypersensitive response and cell death.