Institutional Publications
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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 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 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 Recent insights into plant circadian clock response against abiotic stress(Springer Nature Publishing AG, 2022) Sharma, Megha; Irfan, Mohammad; Kumar, Arun; Kumar, Pankaj; Datta, AsisThe circadian clock is a cell autonomously and endogenously regulated biological timekeeper that detects changes in environmental stimuli and generates 24-h rhythms that are synched with day to day and periodic oscillations to govern many biological functions. Plant's circadian clocks enable them to anticipate environmental changes by modifying their physiological and biological traits to improve plant fitness. The internal circadian clock not only aids fitness but also allows the plant to time-gate the response to environmental stimuli. The latest evidence on the circadian clock suggests that the clock regulates/modulates the expression of abiotic stress-responsive pathways to improve tolerance to stresses without hampering plant growth. In turn, stress signaling also influences the activity of several clock components. This review emphasizes the interplay of the biological circadian clock with abiotic stress-responsive pathways (drought, heat, cold, and salt) for plant growth and survival as well as for stress resilience. A better comprehension of these mechanisms could aid in the development of genetic tools to improve breeding procedures and plant stress tolerance, thereby increasing crop yield and quality under changing ecological conditions.Item Unraveling the role of tomato Bcl-2-associated athanogene (BAG) proteins during abiotic stress response and fruit ripening(Springer Nature Publishing AG, 2021) Irfan, Mohammad; Kumar, Pankaj; Ahmad, Irshad; Datta, AsisB-cell lymphoma2 (Bcl-2)-associated athanogene (BAG) family proteins are evolutionary conserved across all eukaryotes. These proteins interact with HSP70/HSC70 and function as co-chaperones during stress response and developmental pathways. Compared to the animal counterpart, the BAG proteins in plants are much less studied and primarily Arabidopsis BAG proteins have been identified and characterized for their role in programmed cell death, homeostasis, growth and development, abiotic and biotic stress response. Here, we have identified BAG protein family (SlBAGs) in tomato, an economically important and a model fruit crop using genome-wide scanning. We have performed phylogenetic analysis, genes architecture assessment, chromosomal location and in silico promoter analysis. Our data suggest that SlBAGs show differential tissue specific expression pattern during plant development particularly fruit development and ripening. Furthermore, we reported that expression of SlBAGs is modulated during abiotic stresses and is regulated by stress hormones ABA and ethylene. In planta subcellular localization reveals their diverse subcellular localization, and many members are localized in nucleus and cytoplasm. Like previous reports, our protein–protein interaction network and yeast two-hybrid analysis uncover that SlBAGs interact with HSP70. The current study provides insights into role of SlBAGs in plant development particualry fruit ripening and abiotic stress response.Item Manipulation of oxalate metabolism in plants for improving food quality and productivity(Elsevier B.V., 2019) Kumar, Vinay; Irfan, Mohammad; Datta, AsisOxalic acid is a naturally occurring metabolite in plants and a common constituent of all plant-derived human diets. Oxalic acid has diverse unrelated roles in plant metabolism, including pH regulation in association with nitrogen metabolism, metal ion homeostasis and calcium storage. In plants, oxalic acid is also a pathogenesis factor and is secreted by various fungi during host infection. Unlike those of plants, fungi and bacteria, the human genome does not contain any oxalate-degrading genes, and therefore, the consumption of large amounts of plant-derived oxalate is considered detrimental to human health. In this review, we discuss recent biotechnological approaches that have been used to reduce the oxalate content of plant tissues.Item A comprehensive analysis of Candida albicans phosphoproteome reveals dynamic changes in phosphoprotein abundance during hyphal morphogenesis(Springer Nature, 2018) Ghorai, Priyanka; Irfan, Mohammad; Narula, Alka; Datta, AsisThe morphological plasticity of Candida albicans is a virulence determinant as the hyphal form has significant roles in the infection process. Recently, phosphoregulation of proteins through phosphorylation and dephosphorylation events has gained importance in studying the regulation of pathogenicity at the molecular level. To understand the importance of phosphorylation in hyphal morphogenesis, global analysis of the phosphoproteome was performed after hyphal induction with elevated temperature, serum, and N-acetyl-glucosamine (GlcNAc) treatments. The study identified 60, 20, and 53 phosphoproteins unique to elevated temperature-, serum-, and GlcNAc-treated conditions, respectively. Distribution of unique phosphorylation sites sorted by the modified amino acids revealed that predominant phosphorylation occurs in serine, followed by threonine and tyrosine residues in all the datasets. However, the frequency distribution of phosphorylation sites in the proteins varied with treatment conditions. Further, interaction network-based functional annotation of protein kinases of C. albicans as well as identified phosphoproteins was performed, which demonstrated the interaction of kinases with phosphoproteins during filamentous growth. Altogether, the present findings will serve as a base for further functional studies in the aspects of protein kinase-target protein interaction in effectuating phosphorylation of target proteins, and delineating the downstream signaling networks linked to virulence characteristics of C. albicans.Item Application of RNA silencing in improving plant traits for industrial use(CABI, 2017) Ghosh, Sumit; Irfan, Mohammad; Datta, AsisThe discovery of RNA silencing mechanisms has transformed research into gene function and has also allowed novel traits to be developed in plants, including some for industrial applications. To silence the expression of an undesirable gene, RNA silencing may be preferable over direct gene mutation as it leads to a dominant trait. This helps in straightforward screening of the desirable phenotypes. Moreover, RNA silencing is useful in tissue, organ and time-specific silencing of the genes that may play essential roles in plant life and, therefore, direct gene mutation may not be effective. This chapter summarizes the implication of RNA silencing in improving plant traits for industrial applications. Plants developed after RNA silencing of genes that act on cellular organization or metabolism are emerging as convenient and renewable raw materials for industries producing fuels, oils, pharmaceuticals, fibres, papers, seeds and processed foods. Several genetically modified plants, which may not have use in human consumption, have nevertheless been developed for specific industrial applications and await commercial-scale cultivation. Many more industrial crops are under different stages of development by industry and research organizations.Item Improving food nutritional quality and productivity through genetic engineering(Juniper Publishers, 2017) Irfan, Mohammad; Datta, AsisGenetic engineering has provided new tools for effectively ensuring food and nutritional security to improve agriculture across the world. Conventional agricultural practices can be assisted by molecular biology and biotechnology tools to develop crops with superior traits in a relatively fast way. Genetic engineering allowed solving important problems in many crops such as susceptibility to pests, diseases, environmental stress and development of crops with higher productivity and enhanced nutritional quality. Genetically-modified (GM) crops can prove to be powerful complements to those produced by conventional methods for meeting the worldwide demand for quality foods.