Department Of Biochemistry And Microbial Sciences
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Item SUMO and SUMOylation in Plants: Ignored Arsenal to Combat Abiotic Stress(Springer, 2023-10-11T00:00:00) Yadav, Radheshyam; Chaudhary, Shivam; Ramakrishna, WusirikaPlants being fixed in one place are exposed to various episodes of different abiotic stresses such as drought, salinity, cold, and heat. SUMOylation is one of the ignored arsenals that help plants to develop tolerance to these external abiotic stresses. SUMOylation of target protein generally leads to changes in its transportation, transcriptional regulation, apoptosis, stability, and response to different stresses. de-SUMOylation of substrate proteins by SUMO proteases also play a crucial role in maintaining the cellular pool of SUMO. This review highlights different components of SUMOylation and their role in different abiotic stresses and their ability to contribute to plant abiotic stress tolerance. Furthermore, the current perspective of SUMOylation in phytochrome signaling, nutrient and ROS homeostasis is discussed. The full potential of SUMOylation in combination with other molecular approaches to combat abiotic stresses in plants is not yet realized. As research in this area continues to advance, it is crucial to explore the interplay between SUMOylation and other signaling networks, as well as the crosstalk with different stress-responsive pathways. Additionally, understanding the specificity and dynamics of SUMOylation in response to specific stressors can provide valuable insights for designing targeted interventions to enhance plant stress tolerance. In conclusion, the review highlights the emerging significance of SUMOylation in plant stress responses and its potential in contributing to plant resilience against abiotic stresses. � 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.Item Biochar as an Environment-Friendly Alternative for Multiple Applications(Multidisciplinary Digital Publishing Institute (MDPI), 2023-09-07T00:00:00) Yadav, Radheshyam; Ramakrishna, WusirikaThe climate crisis and years of unsustainable agricultural practices have reduced soil fertility and crop yield. In addition, agricultural lands contribute more than 10% of greenhouse gases (GHGs). These concerns can be addressed by using biochar for carbon neutralization, environmental restoration, and agricultural management. Biochar has a role in nitrous oxide and methane gas emission mitigation from agricultural soil. New methods are needed to link belowground processes to functioning in multi-species and multi-cultivar agroecosystems. The intricate relationship between biochar and the composition of soil microbial communities, along with its impacts on functions within the rhizosphere, constitutes a highly perplexing and elusive subject within microbial genomics. The present review discusses how biochar can mitigate climate change, enhance carbon sequestration, and support crop productivity. Biochar could be a potential solution to mitigate soil microplastics and heavy metal contamination. Applying a biochar-based microbiome reduces polycyclic aromatic hydrocarbons (PAHs) in soil. The current knowledge and perspectives on biochar�plant�microbial interactions for sustainable agriculture and ameliorating the adverse effects of climate change are highlighted. In this review, a holistic approach was used to emphasize the utility of biochar for multiple applications with positive and negative effects and its role in promoting a functional circular economy. � 2023 by the authors.Item Analysis of the Inhibitory Effect of hsa-miR-145-5p and hsa-miR-203a-5p on Imatinib-Resistant K562 Cells by GC/MS Metabolomics Method(American Chemical Society, 2023-09-14T00:00:00) Singh, Priyanka; Yadav, Radheshyam; Verma, Malkhey; Chhabra, RavindreshImatinib (IM) resistance is considered to be a significant challenge in the management of chronic myeloid leukemia (CML). Previous studies have reported that hsa-miR-145-5p and hsa-miR-203a-5p can overcome IM resistance and hsa-miR-203a-5p can alter glutathione metabolism in IM-resistant cells. The purpose of this study was to examine whether hsa-miR-145-5p or hsa-miR-203a-5p counters IM resistance by targeting the overall metabolic profile of IM-resistant K562 cells. The metablic profiling of cell lysates obtained from IM-sensitive, IM-resistant, and miR-transfected IM-resistant K562 cells was carried out using the GC-MS technique. Overall, 75 major metabolites were detected, of which 32 were present in all samples. The pathway analysis of MetaboAnalyst 5.0 revealed that the majorly enriched pathways included glucose metabolism, fatty acid biosynthesis, lipogenesis, and nucleotide metabolism. Eleven of identified metabolites, l-glutamine, l-glutamic acid, l-lactic acid, phosphoric acid, 9,12-octadecadienoic acid, 9-octadecenoic acid, myristic acid, palmitic acid, cholesterol, and ?-alanine, appeared in enriched pathways. IM-resistant cells had comparatively higher concentrations of all of these metabolites. Notably, the introduction of hsa-miR-145-5p or hsa-miR-203a-5p into resistant cells resulted in a decrease in levels of these metabolites. The efficacy of miR-203a-5p was particularly remarkable in comparison with miR-145-5p, as evidenced by partial least-squares-discriminant analysis (PLS-DA), which showed a high level of similarity in metabolic profile between IM-sensitive K562 cells and IM-resistant cells transfected with hsa-miR-203a-5p. The results indicate that GC-MS-based metabolic profiling has the potential to distinguish between drug-resistant and -sensitive cells. This approach can also be used to routinely monitor therapeutic response in drug-resistant patients, thus, enabling personalized therapy. � 2023 American Society for Mass Spectrometry. Published by American Chemical Society. All rights reserved.Item MicroRNAs Involved in Nutritional Regulation During Plant�Microbe Symbiotic and Pathogenic Interactions with Rice as a Model(Springer, 2023-07-19T00:00:00) Yadav, Radheshyam; Ramakrishna, WusirikaPlants are constantly challenged with numerous adverse environmental conditions, including biotic and abiotic stresses. Coordinated regulation of plant responses requires crosstalk between regulatory pathways initiated by different external cues. Stress induced by excessiveness or deficiency of nutrients has been shown to positively or negatively interact with pathogen-induced immune responses. Also, colonization by arbuscular mycorrhizal (AM) fungi can improve plant nutrition, mainly phosphorus and resistance to pathogen infection. The proposed review addresses these issues about a new question that integrates adaptation to nutrient stress and disease resistance. The main goal of the current review is to provide insights into the interconnected regulation between nutrient signaling and immune signaling pathways in rice, focusing on phosphate, potassium and iron signaling. The underpinnings of plant/pathogen/AM fungus interaction concerning rice/M. oryzae/R. irregularis is highlighted. The role of microRNAs (miRNAs) involved in Pi (miR399, miR827) and Fe (miR7695) homeostasis in pathogenic/symbiotic interactions in rice is discussed. The intracellular dynamics of membrane proteins that function in nutrient transport transgenic rice lines expressing fluorescent protein fusion genes are outlined. Integrating functional genomic, nutritional and metal content, molecular and cell biology approaches to understand how disease resistance is regulated by nutrient status leading to novel concepts in fundamental processes underlying plant disease resistance will help to devise novel strategies for crop protection with less input of pesticides and fertilizers. � 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.Item Soil Diseases Suppressiveness Conferred by Organic Farming, Practices and Microbial Metabolites(Taylor and Francis Ltd., 2023-05-08T00:00:00) Yadav, Radheshyam; Beniwal, Rahul; Ramakrishna, WusirikaA major obstacle to the creation of efficient biobased disease management practices continues to be the poor integration of traditional agricultural practices and cutting-edge technical approaches. The present review will expand the understanding of organic amendments and metabolites-mediated microbial community metabolism and their mechanistic aspects in disease-suppressive soil (DSS). Organic amendments have been shown to promote the biocontrol potential of resident soil microbiota. Organic amendments positively affect the labile carbon, cation exchange content (CEC) and microbial enzymatic activity. DSS is considered a rich source of beneficial soil microbial community that produces a plethora of antibacterial metabolites. Multiple gene clusters associated with known metabolites offer mechanistic insights associated with disease-suppressive phenotypes. Organic amended soil has higher abundance of chemotaxis genes. Several strains of Bacillus and Pseudomonas produce key metabolites, phenazines, 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, cyclic lipopeptides and volatile organic compounds in DSS. High-resolution metagenomics combined with bioinformatics tools would be instrumental in the identification of biomarkers associated with suppressive soils. The integration of traditional and genomic approaches can be employed to infer the untapped potential of resident soil microbiomes. � 2023 Informa UK Limited, trading as Taylor & Francis Group.Item Multifarious Effects of Arsenic on Plants and Strategies for Mitigation(MDPI, 2023-02-09T00:00:00) Beniwal, Rahul; Yadav, Radheshyam; Ramakrishna, WusirikaArsenic contamination in soil and water is a major problem worldwide. Inorganic arsenic is widely present as arsenate and arsenite. Arsenic is transferred to crops through the soil and irrigation water. It is reported to reduce crop production in plants and can cause a wide array of diseases in humans, including different types of cancers, premature delivery, stillbirth, and spontaneous abortion. Arsenic methyltransferase (AS3MT) in the human body converts inorganic arsenic into monomethylarsonic acid and dimethylarsinic acid, which are later excreted from the body. Arsenic transfer from the soil to grains of rice involves different transporters such as Lsi1, Lsi2, and Lsi6. These transporters are also required for the transfer of silicate, which makes them important for the plant. Different mitigation strategies have been used to mitigate arsenic from crops, such as plant growth-promoting bacteria, fungi, and nanoparticles, as well as using different plant genotypes and plant extracts. Different factors such as nitric oxide, Fe, and jasmonate also affect the response of a plant to the oxidative stress caused by arsenic. This review highlights the various effects of arsenic on plants with respect to their biochemical, molecular, and physiological aspects and the employment of classical and innovative methods for their mitigation. The current review is expected to initiate further research to improve As remediation to mitigate the effect of heavy metal pollution on the environment. � 2023 by the authors.Item Antileukemic Activity of hsa-miR-203a-5p by Limiting Glutathione Metabolism in Imatinib-Resistant K562 Cells(MDPI, 2022-12-19T00:00:00) Singh, Priyanka; Yadav, Radheshyam; Verma, Malkhey; Chhabra, RavindreshImatinib has been the first and most successful tyrosine kinase inhibitor (TKI) for chronic myeloid leukemia (CML), but many patients develop resistance to it after a satisfactory response. Glutathione (GSH) metabolism is thought to be one of the factors causing the emergence of imatinib resistance. Since hsa-miR-203a-5p was found to downregulate Bcr-Abl1 oncogene and also a link between this oncogene and GSH metabolism is reported, the present study aimed to investigate whether hsa-miR-203a-5p could overcome imatinib resistance by targeting GSH metabolism in imatinib-resistant CML cells. After the development of imatinib-resistant K562 (IR-K562) cells by gradually exposing K562 (C) cells to increasing doses of imatinib, resistant cells were transfected with hsa-miR-203a-5p (R+203). Thereafter, cell lysates from various K562 cell sets (imatinib-sensitive, imatinib-resistant, and miR-transfected imatinib-resistant K562 cells) were used for GC-MS-based metabolic profiling. L-alanine, 5-oxoproline (also known as pyroglutamic acid), L-glutamic acid, glycine, and phosphoric acid (Pi)�five metabolites from our data, matched with the enumerated 28 metabolites of the MetaboAnalyst 5.0 for the GSH metabolism. All of these metabolites were present in higher concentrations in IR-K562 cells, but intriguingly, they were all reduced in R+203 and equated to imatinib-sensitive K562 cells (C). Concludingly, the identified metabolites associated with GSH metabolism could be used as diagnostic markers. � 2022 by the authors.Item Wheat grain proteomic and protein�metabolite interactions analyses provide insights into plant growth promoting bacteria�arbuscular mycorrhizal fungi�wheat interactions(Springer Science and Business Media Deutschland GmbH, 2022-04-09T00:00:00) Yadav, Radheshyam; Chakraborty, Sudip; Ramakrishna, WusirikaKey message: Proteomic, protein�protein and protein�metabolite interaction analyses in wheat inoculated with PGPB and AMF identified key proteins and metabolites that may have a role in enhancing yield and biofortification. Plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) have an impact on grain yield and nutrition. This dynamic yet complex interaction implies a broad reprogramming of the plant�s metabolic and proteomic activities. However, little information is available regarding the role of native PGPB and AMF and how they affect the plant proteome, especially under field conditions. Here, proteomic, protein�protein and protein�metabolite interaction studies in wheat triggered by PGPB, Bacillus subtilis CP4 either alone or together with AMF under field conditions was carried out. The dual inoculation with native PGPB (CP4) and AMF promoted the differential abundance of many proteins, such as histones, glutenin, avenin and ATP synthase compared to the control and single inoculation. Interaction study of these differentially expressed proteins using STRING revealed that they interact with other proteins involved in seed development and abiotic stress tolerance. Furthermore, these interacting proteins are involved in carbon fixation, sugar metabolism and biosynthesis of amino acids. Molecular docking predicted that wheat seed storage proteins, avenin and glutenin interact with secondary metabolites, such as trehalose, and sugars, such as xylitol. Mapping of differentially expressed proteins to KEGG pathways showed their involvement in sugar metabolism, biosynthesis of secondary metabolites and modulation of histones. These proteins and metabolites can serve as markers for improving wheat�PGPB�AMF interactions leading to higher yield and biofortification. � 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.Item Bacillus subtilis impact on plant growth, soil health and environment: Dr. Jekyll and Mr. Hyde(John Wiley and Sons Inc, 2022-02-09T00:00:00) Mahapatra, Subhasmita; Yadav, Radheshyam; Ramakrishna, WusirikaThe increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbours several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant�microbe interactions could be decoded using transcriptomics, proteomics, metabolomics and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health and the environment akin to the character of Mr. Hyde. � 2022 Society for Applied Microbiology.Item Co-occurrence and patterns of phosphate solubilizing, salt and metal tolerant and antibiotic-resistant bacteria in diverse soils(Springer Science and Business Media Deutschland GmbH, 2021-06-24T00:00:00) Rathore, Parikshita; Joy, Sherina Sara; Yadav, Radheshyam; Ramakrishna, WusirikaSoil is a treasure chest for beneficial bacteria with applications in diverse fields, which include agriculture, rhizoremediation, and medicine. Metagenomic analysis of four soil samples identified Proteobacteria as the dominant phylum (32�52%) followed by the phylum Acidobacteria (11�21% in three out of four soils). Bacteria that were prevalent at the highest level belong to the genus Kaistobacter (8�19%). PICRUSt analysis predicted KEGG functional pathways associated with the metagenomes of the four soils. The identified pathways could be attributed to metal tolerance, antibiotic resistance and plant growth promotion. The prevalence of phosphate solubilizing bacteria (PSB) was investigated in four soil samples, ranging from 26 to 59% of the total culturable bacteria. The abundance of salt-tolerant and metal-tolerant bacteria showed considerable variation ranging from 1 to 62% and 4�69%, respectively. In comparison, the soil with the maximum prevalence of temperature-tolerant and antibiotic-resistant bacteria was close 30%. In this study, the common pattern observed was that PSB were the most abundant in all types of soils compared to other traits. Conversely, most of the isolates, which are salt-tolerant, copper-tolerant, and ampicillin-resistant, showed phosphate solubilization activity. The sequencing of the partial 16S-rRNA gene revealed that PSB belonged to Bacillus genera. � 2021, King Abdulaziz City for Science and Technology.