Institutional Publications
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Item Evaluation of the parameters affecting agrobacterium-mediated transformation process to produce cold stress-tolerant tomato by targeting Solanum lycopersicumC-repeat binding factor 2 gene(Springer Nature Publishing AG, 2026) Halder, Koushik; Chaudhuri, Abira; Abdin, Malik Z.; Datta, AsisC-repeat binding factors (CBFs) are a part of the AP2/ERF superfamily of transcription factors, which are known to regulate gene expression under different abiotic stress conditions, especially cold. In this study, when tomato cultivar Pusa Ruby (PR) was subjected to cold stress at 4 °C for 24 h, SlCBF2, along with SlCBF1, was found to be simultaneously induced at the early hours (3rd to 24th) of cold exposure. Similar simultaneous induction observed in another tomato variety, Arka Rakshak (AR), at the 3rd hour post-cold exposure. This brief yet strong simultaneous induction of both SlCBF1 and SlCBF2 provides a new insight into the initial induction of CBFs in cold-stressed tomato, which was not previously reported in PR or AR. To elucidate the SlCBF2-mediated cold response in tomato, we have developed stable overexpression lines that showed better cold tolerance than the wild-type PR. We have also evaluated and optimized two important parameters in the Agrobacterium-mediated transformation process and reported an improved transformation efficiency of 28.33% using 1 mg/L zeatin alone and 25% using a combination of 2 mg/L BAP and 0.1 mg/L IAA. Considering the varying degree of transformation efficiency in PR, this optimization will surely be of interest to future researchers to generate stable tomato transgenic lines. However, further works such as generating stable mutant lines targeting SlCBF2 and studying how it reacts to cold-stress, whether SlCBF2 directly regulates SlCBF1 or other downstream cold-responsive genes would provide a more definitive framework for establishing SlCBF2 as an important cold-stress-related transcription factor in tomato.Item N-glycan remodeling by α-D-mannosidase and β-D-N-acetylhexosaminidase regulates fruit softening, redox balance, and post-harvest pathogen resistance(John Wiley & Sons, 2025) Irfan, Mohammad; Kumar, Pankaj; Kumar, Vinay; Ahmad, Irshad; Ansari, Sekhu; Ghosh, Sumit; Datta, AsisPost-harvest loss of fruits and vegetables poses significant challenges to food security and economic sustainability, primarily due to ripening-associated excessive softening that shortens shelf life and increases susceptibility to pathogens. N-glycans, N-glycoproteins, and their processing enzymes are integral to various plant processes, including fruit ripening. Among these, α-D-mannosidase (α-Man) and β-D-N-acetylhexosaminidase (β-Hex) are key ripening-specific enzymes that modulate fruit softening. Previously, we have shown that RNAi-mediated suppression of α-Man or β-Hex improves fruit shelf life and firmness in both climacteric and non-climacteric fruits. However, the underlying molecular and biochemical basis of fruit softening regulation by α-Man and β-Hex was not well understood. In this study, we developed transgenic tomato (Solanum lycopersicum) plants by silencing α-Man and β-Hex simultaneously using RNAi. Suppression of these enzymes reduces N-glycoprotein degradation, downregulates pectin dissolution, and inhibits ripening-related gene expression. RNAi fruits exhibited enhanced shelf life, greater firmness, reduced reactive oxygen species (ROS) accumulation and increased resistance against post-harvest pathogens without affecting plant growth, fruit development, yield, or nutritional quality. To further explore the molecular mechanism of α-Man and β-Hex function, we purified and quantified N-glycans in RNAi fruits and other ripening-impaired mutants, identifying key N-glycan species. We also carried out iTRAQ-based quantitative proteome profiling to investigate the abundance of proteins in ripened fruit affected by silencing of α-Man and β-Hex. Molecular insights revealed that N-glycan processing and degradation are key events during ripening, influencing cell wall softening, fruit redox state, and post-harvest quality attributes. This study highlights the potential of co-silencing α-Man and β-Hex as a novel approach to extending the shelf life of fruits, regardless of their climacteric behavior, without compromising quality or yield.Item Ethylene-mediated regulation of a ripening-specific N-glycan-processing enzyme β-D-N-Acetylhexosaminidase(Springer Nature Publishing AG, 2025) Irfan, Mohammad; Kumar, Pankaj; Datta, AsisN-glycoproteins in plants play a critical role in various biological processes such as plant stress response, seed development, and fruit ripening. Further, N-glycans and N-glycan-processing enzymes have been identified as critical regulators of fruit ripening in various fruit crop including tomato. Fruit ripening, a multifaceted process influenced by diverse factors is controlled by the upregulation of cell wall degradation enzymes. Among these, N-glycan-processing enzymes, specifically β-D-N-acetylhexosaminidase (β-Hex), are involved in ripening-associated fruit softening, and its suppression enhances fruit shelf life and firmness in both climacteric and non-climacteric fruits. Ethylene is among the various factors that regulates the ripening-specific expression of β-Hex. Notably, ethylene response factor 6 (SlERF6), also known as SlERF.E4, has been identified as a potential transcriptional regulator of β-Hex expression. However, in order to get deeper insights, a thorough understanding of the specific ethylene-mediated control of β-Hex during ripening is crucial. Thus, we present a protocol for investigating the ethylene-mediated regulation of this crucial ripening-related enzyme β-D-N-acetylhexosaminidase.Item Tweaking the small non-coding RNAs to improve desirable traits in plant(MDPI AG, 2023) Halder, Koushik; Chaudhuri, Abira; Abdin, Malik Z; Datta, AsisPlant transcriptome contains an enormous amount of non-coding RNAs (ncRNAs) that do not code for proteins but take part in regulating gene expression. Since their discovery in the early 1990s, much research has been conducted to elucidate their function in the gene regulatory network and their involvement in plants' response to biotic/abiotic stresses. Typically, 20-30 nucleotide-long small ncRNAs are a potential target for plant molecular breeders because of their agricultural importance. This review summarizes the current understanding of three major classes of small ncRNAs: short-interfering RNAs (siRNAs), microRNA (miRNA), and transacting siRNAs (tasiRNAs). Furthermore, their biogenesis, mode of action, and how they have been utilized to improve crop productivity and disease resistance are discussed here.Item Abiotic stress tolerance in plants: Brassinosteroids navigate competently(MDPI AG, 2022) Chaudhuri, Abira; Halder, Koushik; Abdin, Malik Z; Majee, Manoj; Datta, AsisBrassinosteroid hormones (BRs) multitask to smoothly regulate a broad spectrum of vital physiological processes in plants, such as cell division, cell expansion, differentiation, seed germination, xylem differentiation, reproductive development and light responses (photomorphogenesis and skotomorphogenesis). Their importance is inferred when visible abnormalities arise in plant phenotypes due to suboptimal or supraoptimal hormone levels. This group of steroidal hormones are major growth regulators, having pleiotropic effects and conferring abiotic stress resistance to plants. Numerous abiotic stresses are the cause of significant loss in agricultural yield globally. However, plants are well equipped with efficient stress combat machinery. Scavenging reactive oxygen species (ROS) is a unique mechanism to combat the deleterious effects of abiotic stresses. In light of numerous reports in the past two decades, the complex BR signaling under different stress conditions (drought, salinity, extreme temperatures and heavy metals/metalloids) that drastically hinders the normal metabolism of plants is gradually being untangled and revealed. Thus, crop improvement has substantial potential by tailoring either the brassinosteroid signaling, biosynthesis pathway or perception. This review aims to explore and dissect the actual mission of BRs in signaling cascades and summarize their positive role with respect to abiotic stress tolerance.Item Fruit ripening specific expression of β-D-N-acetylhexosaminidase (β-Hex) gene in tomato is transcriptionally regulated by Ethylene Response Factor SlERF.E4(Elsevier B.V., 2022) Irfan, Mohammad; Kumar, Pankaj; Kumar, Vinay; Datta, AsisN-glycans and N-glycan processing enzymes are key players in regulating the ripening of tomato (Solanum lycopersicum) fruits, a model for fleshy fruit ripening. β-D-N-acetylhexosaminidase (β-Hex) is a N-glycan processing enzyme involved in fruit ripening. The suppression of β-Hex results in enhanced fruit shelf life and firmness in both climacteric and non-climacteric fruits. Previously, we have shown that ripening specific expression of β-Hex is regulated by RIPENING INHIBITOR (RIN), ABSCISIC ACID STRESS RIPENING 1 (SlASR1) and ethylene. However, the precise mechanism of ethylene-mediated regulation of β-Hex remains elusive. To gain insights into this, we have performed 5’ deletion mapping of tomato β-Hex promoter and a shorter promoter fragment (pD-200, 200 bp upstream to translational start site) is identified, which was found critical for spatio-temporal transcriptional regulation of β-Hex. Further, site specific mutagenesis in RIN and ASR1 binding sites in pD-200 provides key insights into ripening specific promoter activity. Furthermore, induction of GUS activity by ethylene, yeast one hybrid assay and EMSA identify Ethylene Response Factor SlERF.E4 as a positive regulator of β-Hex. Taken together, our study suggest that SlERF.E4 together with RIN and SlASR1 transcriptionally regulates β-Hex and all these three proteins are essential for fruit ripening specific expression of β-Hex in tomato.Item Chromatin-based transcriptional reprogramming in plants under abiotic stresses(MDPI AG, 2022) Halder, Koushik; Chaudhuri, Abira; Abdin, Malik Z.; Majee, Manoj; Datta, AsisPlants’ stress response machinery is characterized by an intricate network of signaling cascades that receive and transmit environmental cues and ultimately trigger transcriptional reprogramming. The family of epigenetic regulators that are the key players in the stress-induced signaling cascade comprise of chromatin remodelers, histone modifiers, DNA modifiers and regulatory noncoding RNAs. Changes in the histone modification and DNA methylation lead to major alterations in the expression level and pattern of stress-responsive genes to adjust with abiotic stress conditions namely heat, cold, drought and salinity. The spotlight of this review falls primarily on the chromatin restructuring under severe abiotic stresses, crosstalk between epigenetic regulators along with a brief discussion on stress priming in plants.Item RNA interference for improving disease resistance in plants and its relevance in this clustered regularly interspaced short palindromic repeats-dominated era in terms of dsRNA-based biopesticides(Frontiers Media S.A., 2022) Halder, Koushik; Chaudhuri, Abira; Abdin, Malik Z.; Majee, Manoj; Datta, AsisRNA interference (RNAi) has been exploited by scientists worldwide to make a significant contribution in the arena of sustainable agriculture and integrated pest management. These strategies are of an imperative need to guarantee food security for the teeming millions globally. The already established deleterious effects of chemical pesticides on human and livestock health have led researchers to exploit RNAi as a potential agri-biotechnology tool to solve the burning issue of agricultural wastage caused by pests and pathogens. On the other hand, CRISPR/Cas9, the latest genome-editing tool, also has a notable potential in this domain of biotic stress resistance, and a constant endeavor by various laboratories is in progress for making pathogen-resistant plants using this technique. Considerable outcry regarding the ill effects of genetically modified (GM) crops on the environment paved the way for the research of RNAi-induced double-stranded RNAs (dsRNA) and their application to biotic stresses. Here, we mainly focus on the application of RNAi technology to improve disease resistance in plants and its relevance in today’s CRISPR-dominated world in terms of exogenous application of dsRNAs. We also focused on the ongoing research, public awareness, and subsequent commercialization of dsRNA-based biocontrol products.Item N-acetylglucosamine sensing and metabolic engineering for attenuating human and plant pathogens(MDPI AG, 2022) Ansari, Sekhu; Kumar, Vinay; Bhatt, Dharmendra Nath; Irfan, Mohammad; Datta, AsisDuring evolution, both human and plant pathogens have evolved to utilize a diverse range of carbon sources. N-acetylglucosamine (GlcNAc), an amino sugar, is one of the major carbon sources utilized by several human and phytopathogens. GlcNAc regulates the expression of many virulence genes of pathogens. In fact, GlcNAc catabolism is also involved in the regulation of virulence and pathogenesis of various human pathogens, including Candida albicans, Vibrio cholerae, Leishmania donovani, Mycobacterium, and phytopathogens such as Magnaporthe oryzae. Moreover, GlcNAc is also a well-known structural component of many bacterial and fungal pathogen cell walls, suggesting its possible role in cell signaling. Over the last few decades, many studies have been performed to study GlcNAc sensing, signaling, and metabolism to better understand the GlcNAc roles in pathogenesis in order to identify new drug targets. In this review, we provide recent insights into GlcNAc-mediated cell signaling and pathogenesis. Further, we describe how the GlcNAc metabolic pathway can be targeted to reduce the pathogens’ virulence in order to control the disease prevalence and crop productivity.Item Classification of CRISPR/Cas system and its application in tomato breeding(Springer Nature Publishing AG, 2022) Chaudhuri, Abira; Halder, Koushik; Datta, AsisRemarkable diversity in the domain of genome loci architecture, structure of effector complex, array of protein composition, mechanisms of adaptation along with difference in pre-crRNA processing and interference have led to a vast scope of detailed classification in bacterial and archaeal CRISPR/Cas systems, their intrinsic weapon of adaptive immunity. Two classes: Class 1 and Class 2, several types and subtypes have been identified so far. While the evolution of the effector complexes of Class 2 is assigned solely to mobile genetic elements, the origin of Class 1 effector molecules is still in a haze. Majority of the types target DNA except type VI, which have been found to target RNA exclusively. Cas9, the single effector protein, has been the primary focus of CRISPR-mediated genome editing revolution and is an integral part of Class 2 (type II) system. The present review focuses on the different CRISPR types in depth and the application of CRISPR/Cas9 for epigenome modification, targeted base editing and improving traits such as abiotic and biotic stress tolerance, yield and nutritional aspects of tomato breeding.