Browsing by Author "Mishra, Divya"

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Carboxylate clamp tetratricopeptide repeat (TPR) domain containing Hsp90 cochaperones in Triticeace: an insight into structural and functional diversification
(Elsevier B.V., 2018) Mishra, Divya; Shekhar, Shubhendu; Chakraborty, Subhra; Chakraborty, Niranjan
The molecular chaperones serve as surveillance molecules that mediates regulatory crosstalk between protein folding and degradation pathways under natural and stress conditions. In present study, we focused on the diversification and role of tetratricopeptide repeat (TPR) domain containing Hsp90 cochaperones. These cochaperone were recognized by the presence of three motifs of TPR with the basic conserved residues often referred to as carboxylate clamp (CC). A total of 213 putative CC-TPRs were found in Triticeace, clustered into 16 groups, amongst which few CC-TPR families such as TPR-RPAP3 and TPR-SMYD were documented. Domain architecture and genomic organization revealed that CC-TPRs are very diverse in nature. Evolutionary analyses showed that CC-TPRs are conserved, stable and ubiquitous in nature. Analysis of available RNA-seq data revealed a high degree of tissue-specific expression of 1-TPR and TaTPR-FKBP family members at various developmental stages. The transcripts of TaCC-TPRs displayed differential expression in two contrasting wheat cultivars under abiotic stress conditions. Complementation and heterologous expression of TaTPR-FKBP5 in yeast conferred abiotic stress tolerance. Together, these results provide a glimpse into the genetic diversity and evolution of CC-TPRs in Triticeace, which would help to better understand of how TPR-domain cochaperones function in plants.
Comparative analysis of phytochemicals and nutrient availability in two contrasting cultivars of sweet potato (Ipomoea batatas L.)
(Elsevier B.V., 2014) Shekhar, Shubhendu; Mishra, Divya; Buragohain, Alak Kumar; Chakraborty, Subhra; Chakraborty, Niranjan
Sweet potato ranks as the world's seventh most important food crop, and has major contribution to energy and phytochemical source of nutrition. To unravel the molecular basis for differential nutrient availability, and to exploit the natural genetic variation(s) of sweet potato, a series of physiochemical and proteomics experiment was conducted using two contrasting cultivars, an orange-fleshed sweet potato (OFSP) and a white-fleshed sweet potato (WFSP). Phytochemical screening revealed high percentage of carbohydrate, reducing sugar and phenolics in WFSP, whereas OFSP showed increased levels of total protein, flavonoids, anthocyanins, and carotenoids. The rate of starch and cellulose degradation was found to be less in OFSP during storage, indicating tight regulation of gene(s) responsible for starch-degradation. Comparative proteomics displayed a cultivar-dependent expression of proteins along with evolutionarily conserved proteins. These results suggest that cultivar-specific expression of proteins and/or their interacting partners might play a crucial role for nutrient acquisition in sweet potato.
Comparison of proteomic and metabolomic profiles of two contrasting ecotypes of sweetpotato (Ipomoea batata L)
(Elsevier B.V., 2016) Shekhar, Shubhendu; Mishra, Divya; Gayali, Saurabh; Buragohain, Alak Kumar; Chakraborty, Subhra; Chakraborty, Niranjan
Sweetpotato has long been acknowledged as a significant contributor of global caloric needs, which continues to be of remarkable economic value. It is an important staple and emergency food in many countries and its annual world production hovers to about 130 million tons. The tubers act as sink and compete for the available photoassimilates eventually leading to the acquisition of nutrients and phytochemicals. Differential display of genes or gene-products, and metabolites causes differences in nutritive value of closely related ecotypes. To better understand the molecular basis for differential nutrient availability and phytochemicals, and exploit the natural genetic variation(s), we aimed at developing proteometabolic profiles of two contrasting ecotypes of sweetpotato. Proteomic analyses led to the identification of 1541 and 1201 proteins in orange fleshed and white fleshed sweetpotato ecotypes, respectively, presumably associated with binding, followed by catalytic, transferase, hydrolase, kinase and transporter activities. Furthermore, metabolome profiling revealed 148 and 126 metabolites in cv. OFSP and WFSP, respectively. This study would provide a basis for future comparative proteometabolomic efforts for sweetpotato, in particular and tuber crops in general. The results would expand our understanding of the proteome as well as metabolome and give new insights into how ecotype-specific traits are developed.
Critical compromise: Trade-off between symbiosis and water uptake
(Oxford University Press, 2024) Mishra, Divya
What is the difference between legume crops and other crop species? Legume roots possess specialized organs, nodules where symbiotic rhizobia fix atmospheric nitrogen into ammonia for plants, and, in turn, rhizobia receives the carbon, photosynthetic product from plants (Tiwari et al., 2021). How do the legumes control nodule numbers? Conserved autoregulation of nodulation (AON) signaling is found in legumes, which maintains the optimal nodule number by following root-to-shoot and back-to-root circuit (Roy and Müller, 2022). Disruption of the AON pathway leads to the aberrant formation of nodules, disturbing the metabolic exchange between legumes and rhizobia (Gautrat et al., 2019).
Cultivar-specific high temperature stress responses in bread wheat (Triticum aestivum L.) associated with physicochemical traits and defense pathways
(Elsevier B.V., 2017) Mishra, Divya; Shekhar, Shubhendu; Agrawal, Lalit; Chakraborty, Subhra; Chakraborty, Niranjan
The increasing global temperature by 1°C is estimated to reduce the harvest index in a crop by 6%, and this would certainly have negative impact on overall plant metabolism. Wheat is one of the most important crops with global annual production of over 600million tonnes. We investigated an array of physicochemical and molecular indexes to unravel differential response of nine commercial wheat cultivars to high temperature stress (HTS). The reduced rate in relative water content, higher membrane stability, slow chlorophyll degradation and increased accumulation of proline and secondary metabolites ingrained higher thermotolerance in cv. Unnat Halna, among others. The altered expression of several stress-responsive genes, particularly the genes associated with photosynthesis, heat shock proteins and antioxidants impinge on the complexity of HTS-induced responses over different genetic backgrounds and connectivity of adaptive mechanisms. This may facilitate the targeted manipulation of metabolic routes in crops for agricultural and industrial exploitation.
Ectopic expression of amaranth seed storage albumin modulates photoassimilate transport and nutrient acquisition in sweetpotato
(Nature Publishing Group, 2016) Shekhar, Shubhendu; Agrawal, Lalit; Mishra, Divya; Buragohain, Alak Kumar; Unnikrishnan, Mullath; Mohan, Chokkappan; Chakraborty, Subhra; Chakraborty, Niranjan
Storage proteins in plants, because of high nutrient value, have been a subject of intensive investigation. These proteins are synthesized de novo in the cytoplasm and transported to the storage organelles where they serve as reservoir of energy and supplement of nitrogen during rapid growth and development. Sweetpotato is the seventh most important food crop worldwide, and has a significant contribution to the source of nutrition, albeit with low protein content. To determine the behaviour of seed storage proteins in non-native system, a seed albumin, AmA1, was overexpressed in sweetpotato with an additional aim of improving nutritional quality of tuber proteins. Introduction of AmA1 imparted an increase in protein and amino acid contents as well as the phytophenols. The proteometabolomics analysis revealed a rebalancing of the proteome, with no significant effects on the global metabolome profile of the transgenic tubers. Additionally, the slower degradation of starch and cellulose in transgenic tubers, led to increased post-harvest durability. Present study provides a new insight into the role of a seed storage protein in the modulation of photoassimilate movement and nutrient acquisition.
Frost-fighter, SVALKA-PRC2: Winter, bring it on!
(Oxford University Press, 2024) Mishra, Divya
How does the plant survive in nature’s extremes? Plants possess different adaptive mechanisms, such as developing tolerance to low temperatures to thrive in harsh freezing conditions, a process known as cold acclimation. One of the major players in cold acclimation is C-REPEAT BINDING FACTORS (CBFs), a family of three tandemly duplicated CBF paralogs that activate cold-inducible genes (Novillo et al., 2007). The CBF family is induced during low temperatures, and its expression reaches the maximum in the initial phase of low temperatures, further decreasing in the later stages of low temperatures (Medina et al., 1999). While the role of CBF in cold induction has been extensively investigated, the underlying mechanisms of decline in CBF expression in later stages of low-temperature conditions remain elusive.
Heat shock proteins and abiotic stress tolerance in plants
(Springer Nature, 2018) Mishra, Divya; Shekhar, Shubhendu; Singh, Deepika; Chakraborty, Subhra; Chakraborty, Niranjan
Abiotic stresses restrict plant growth and development, and reduce harvest index of many crop species worldwide. Maintenance of native conformation of proteins and reducing the accumulation of non-native proteins are imperative for survival under stress conditions as such stresses frequently lead to protein aggregation causing metabolic dysfunction. Heat shock proteins (HSP) play a key role in conferring abiotic stress tolerance. Plants protect themselves from numerous stresses by inducing HSP, besides some stress-responsive proteins, suggesting analogous response mechanisms. A close association between the HSP and ROS also co-exists, indicating that plants have evolved to gain a higher degree of regulation over ROS toxicity and can use ROS as elicitor to induce HSP for better adaptations through activating an array of molecules. Therefore, unraveling the mechanisms of plant response against various stress and the role of HSP in acquired stress tolerance is utmost important to delineate their specific function as a part of stress-responsive module. The HSP have been well characterized in different crop species, albeit the knowledge about their correlation with genome sequence information as well as their functional plasticity is limited.
High temperature stress responses and wheat: Impacts and alleviation strategies
(Elsevier B.V., 2021) Mishra, Divya; Shekhar, Shubhendu; Chakraborty, Subhra; Chakraborty, Niranjan
Over the past century, the average surface temperature and recurrent heatwaves have been steadily rising, affecting the yield potential of most food crops including bread wheat, the second most important caloric source, but is particularly vulnerable to the impacts of elevated temperatures. Significantly, the past decade has witnessed tremendous advancements in multiomics approaches to extract the key regulators that influence the adaptive responses to high temperature stress (HTS). With the help of genetic engineering technologies, transgenic wheat plants have been developed showing resistance to HTS without hampering productivity. In this review, we described the effect of rising temperature at a global scale and the drastic impacts on crops, particularly on wheat production. Also, this review is focused on accomplishing a deeper understanding of the genetic and molecular basis of HTS responses of crop plants, wheat in particular along with current strategies and technologies to generate thermotolerant varieties. Collective strategy and identified thresholds of HTS tolerance and susceptibility will contribute to the value-added modelling of wheat growth and yield under predictable future climate conditions.
Nuclear proteome reprogramming and acquired thermotolerance in chickpea exposed to escalating high-temperature stress
(Elsevier B.V., 2026) Pareek, Akanksha; Wardhan, Vijay; Mishra, Divya; Rathi, Divya; Khan, Iqra Nafees; Subba, Pratigya; Saxena, Harshita; Jeevaraj, Theboral; Chakraborty, Subhra; Chakraborty, Niranjan
Global chickpea (Cicer arietinum L.) production amounted to ∼17.55 MMT during 2024-2025, whose market size is valued at ∼$16.83 billion. Chickpea is highly susceptible to high-temperature stress (HTS), and its yield declines 10-15% with the rise in each degree of temperature. In this study, the HTS-responsive nuclear proteome of a thermotolerant chickpea cultivar ICC 1205 was investigated, leading to the identification of 2705 proteins, including 424 differentially regulated proteins designated as HTS-responsive (HRPs). Of these, 212 were shared between immediate (day-1) and later (day-4) stages of HTS, with 117 proteins specific to day-1 and 95 to day-4. Functional network analysis revealed a complex network of nuclear proteins involved in regulatory and stress-related functions. Detailed analysis of the proteome revealed several non-canonical proteins, suggesting HTS-responsive reprograming of the nuclear proteome landscape. The cross-species multiple abiotic stress responses recognized unique HRPs, reflecting genetic foundation that leads to crop adaptation. Comparison of protein and mRNA expression shed light on the intricate regulatory mechanisms of thermotolerance response in chickpea. The characterization of root-phototropism 2 protein (CaRPT2), a member of the NPH3 gene-family, showed significant regulations, particularly under dehydration stress and ABA treatments. Subcellular localization of CaRPT2 demonstrated its dual localization in both plasma membrane and nucleus. Analysis of physiological indices in atrpt2 loss-of function mutants in Arabidopsis demonstrated better germination rate, resilience and growth under progressive HTS, suggesting the putative role of RPT2 in regulating multiple stress-responsive genes.
Performance of novel antimicrobial protein Bg_9562 and in silico predictions on its properties with reference to its antimicrobial efficiency against Rhizoctonia solani
(MDPI AG, 2022) Karnati, Pranathi; Gonuguntala, Rekha; Barbadikar, Kalyani M.; Mishra, Divya; Jha, Gopaljee; Prakasham, Vellaisamy; Chilumula, Priyanka; Shaik, Hajira; Pesari, Maruthi; Sundaram, Raman Meenakshi; Chinnaswami, Kannan
Bg_9562 is a potential broad-spectrum antifungal effector protein derived from the bacteria Burkholderia gladioli strain NGJ1 and is effective against Rhizoctonia solani, the causal agent of sheath blight in rice. In the present study, in vitro antifungal assays showed that Bg_9562 was efficient at 35 °C and 45 °C and ineffective either at high acidic pH (3.0) or alkaline pH (9.5) conditions. Compatibility studies between the native bioagents Trichoderma asperellum TAIK1 and Bacillus subtilis BIK3 indicated that Bg_9562 was compatible with the bioagents. A field study using foliar spray of the Bg_9562 protein indicated the need of formulating the protein before its application. In silico analysis predicted that Bg_9562 possess 111 amino acid residues (46 hydrophobic residues, 12 positive and 8 negative residues) with the high aliphatic index of 89.92, attributing to its thermostability with a half-life of 30 h. Bg_9562 (C491H813N137O166S5) possessed a protein binding potential of 1.27 kcal/mol with a better possibility of interacting and perturbing the membrane, the main target for antimicrobial proteins. The secondary structure revealed the predominance of random coils in its structure, and the best 3D model of Bg_9562 was predicted using an ab initio method with Robetta and AlphaFold 2. The predicted binding ligands were nucleic acids and zinc with confidence scores of 0.07 and 0.05, respectively. The N-terminal region (1–14 residues) and C-terminal region (101 to 111) of Bg_9562 residues were predicted to be disordered regions. Stability and binding properties of the protein from the above studies would help to encapsulate Bg_9562 using a suitable carrier to maintain efficiency and improve delivery against Rhizoctonia solani in the most challenging rice ecosphere.
Physiological plasticity to high temperature stress in chickpea: Adaptive responses and variable tolerance
(Elsevier B.V., 2019) Pareek, Akanksha; Rathi, Divya; Mishra, Divya; Chakraborty, Subhra; Chakraborty, Niranjan
High temperature stress (HTS) is one of the most crucial factors that limits plant growth and development, and reduces crop yields worldwide. Cool-season crops, particularly the legumes, are severely affected by increasing ambient temperature associated with global climate change. We characterized the HTS-induced modulations of morpho-physicochemical traits and gene expression of several chickpea genotypes and the metabolic profile of the tolerant cultivar. Higher water use efficiency and photosynthetic capacity, minimal membrane lipid peroxidation in conjunction with increased abundance of osmolytes and secondary metabolites depicted thermotolerance of ICC 1205. The adaptive responses were accompanied by high transcript abundance of heat shock proteins and antioxidant enzymes. To integrate stress-responsive signalling and metabolic networks, the HTS-induced physicochemical analysis was further extended to metabolite profiling of the thermotolerant cultivar. The screening of the metabolome landscape led to the identification of 49 HTS-responsive metabolites that include polycarboxylic acid, sugar acids, sugar alcohols and amino acids which might confer thermotolerance in chickpea. The present study, to our knowledge, is the most comprehensive of its kind in dissecting cultivar-specific differential adaptive responses to HTS in chickpea, which might potentiate the identification of genetic traits extendible to improvement of thermotolerance of crops.
ReDtool: a Python-based command line tool for restriction digestion analysis of large DNA sequences
(Springer Nature Publishing AG, 2024) Brahmam, Guntha Shiva; Mishra, Divya; Yadav, Vikash Kumar
Developing an in-silico restriction digestion tool is vital in modern molecular biology and genomics. We develop ReDtool, a Python 3-based command-line toolkit to simulate restriction digestion processes. ReDtool offers a virtual digestion function, simulating restriction digestion on a provided sequence by specifying any desired restriction site. We validated the output of ReDtool experimentally using restriction analysis and Sanger sequencing. ReDtool processes large genomic sequences efficiently, accepting FASTA or text format as input. The output file includes detailed information such as restriction site position, fragment length, and fragment sequence. With its high throughput and precision, ReDtool enables comprehensive restriction digestion analysis of chromosomes or genomes, addressing a critical need in genomic research with its straightforward approach (https://github.com/CBL205NIPGR/ReDtool).
The small heat shock proteins, chaperonin 10, in plants: An evolutionary view and emerging functional diversity
(Elsevier B.V., 2021) Pareek, Akanksha; Mishra, Divya; Rathi, Divya; Verma, Jitendra Kumar; Chakraborty, Subhra; Chakraborty, Niranjan
Small heat shock proteins (sHSPs) constitute a class of molecular chaperones, which are evolutionarily conserved yet diverse group of molecules, rapidly produced in response to stress. In this study, we sought to identify plant sHSPs, especially chaperonin 10 (Cpn10) family members in major evolutionary lineages, and determine their biological significance. Multiple sequence alignment of Cpn10 domains revealed divergent amino acids as well as conserved sites. Phylogenetic tree depicted the diversification and expansion of Cpn10 gene family. During the process of evolution, the Ka/Ks ratio of orthologous and paralogous pairs was <1, suggesting their evolutionary convergence and biological relevance. Functional annotations demonstrated that Cpn10 are involved in protein folding, regulation of metabolic processes and abiotic stress responses. Furthermore, subcellular localization prediction revealed that Cpn10 proteins are localized in multiple compartments, indicating a critical cell-coordinated defense. In-silico gene expression analysis exhibited their expression in most tissues examined, implying functional redundancy. Interactome analysis illustrated their interaction with chloroplast and mitochondrial genes, which are majorly involved in protein folding and assembly. The transcriptional regulation revealed their stress-responsive and distinct physiological roles. Our findings would contribute to new insights on the evolutionary history of Cpn10 gene family and the distinct biological roles.
Wheat 2-Cys peroxiredoxin plays a dual role in chlorophyll biosynthesis and adaptation to high temperature
(John Wiley & Sons, 2021) Mishra, Divya; Shekhar, Shubhendu; Chakraborty, Subhra; Chakraborty, Niranjan
The molecular mechanism of high temperature stress (HTS) response, in plants, has so far been investigated using transcriptomics, while the dynamics of HTS‐responsive proteome remain unexplored. We examined the adaptive responses of the resilient wheat cultivar ‘Unnat Halna’ and dissected the HTS‐responsive proteome landscape. This led to the identification of 55 HTS‐responsive proteins (HRPs), which are predominantly involved in metabolism and defense pathways. Interestingly, HRPs included a 2‐cysteine peroxiredoxin (2CP), designated Ta2CP, presumably involved in stress perception and adaptation. Complementation of Ta2CP in yeast and heterologous expression in Arabidopsis demonstrated its role in thermotolerance. Both Ta2CP silencing and overexpression inferred the involvement of Ta2CP in plant growth and chlorophyll biosynthesis. We demonstrated that Ta2CP interacts with protochlorophyllide reductase b, TaPORB. Reduced TaPORB expression was found in Ta2cp‐silenced plants, while upregulation was observed in Ta2CP‐overexpressed plants. Furthermore, the downregulation of Ta2CP in Taporb‐silenced plants and reduction of protochlorophyllide in Ta2cp‐silenced plants suggested the key role of Ta2CP in chlorophyll metabolism. Additionally, the transcript levels of AGPase1 and starch were increased in Ta2cp‐silenced plants. More significantly, HTS‐treated Ta2cp‐silenced plants showed adaptive responses despite increased reactive oxygen species and peroxide concentrations, which might help in rapid induction of high‐temperature acclimation.
Wheat TaNACα18 functions as a positive regulator of high-temperature adaptive responses and improves cell defense machinery
(John Wiley & Sons, 2024) Mishra, Divya; Shekhar, Shubhendu; Subba, Pratigya; Prasad, T S Keshava; Chakraborty, Subhra; Chakraborty, Niranjan
Global wheat production amounted to >780 MMT during 2022-2023 whose market size are valued at >$128 billion. Wheat is highly susceptible to high-temperature stress (HTS) throughout the life cycle and its yield declines 5-7% with the rise in each degree of temperature. Previously, we reported an array of HTS-response markers from a resilient wheat cv. Unnat Halna and described their putative role in heat acclimation. To complement our previous results and identify the key determinants of thermotolerance, here we examined the cytoplasmic proteome of a sensitive cv. PBW343. The HTS-triggered metabolite reprograming highlighted how proteostasis defects influence the formation of an integrated stress-adaptive response. The proteomic analysis identified several promising HTS-responsive proteins, including a NACα18 protein, designated TaNACα18, whose role in thermotolerance remains unknown. Dual localization of TaNACα18 suggests its crucial functions in the cytoplasm and nucleus. The homodimerization of TaNACα18 anticipated its function as a transcriptional coactivator. The complementation of TaNACα18 in yeast and overexpression in wheat demonstrated its role in thermotolerance across the kingdom. Altogether, our results suggest that TaNACα18 imparts tolerance through tight regulation of gene expression, cell wall remodeling and activation of cell defense responses.