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Rashmi M, Murmu S, Nagrale DT, Singh MK, Behera SK, Shankar R, Ranjan R, Jha GK, Chaurasia A, Kumar S. Dataset on double mutation in PGIP of Glycine max improves defense to PG of Sclerotinia sclerotiorum. Data Brief 2024; 54:110518. [PMID: 38827253 PMCID: PMC11141275 DOI: 10.1016/j.dib.2024.110518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/02/2024] [Indexed: 06/04/2024] Open
Abstract
The cell wall of the Glycine max altered by the polygalacturonases (PGs) secreted by the fungus Sclerotinia sclerotiorum, causes disease and quality losses. In soybeans, a resistance protein called polygalacturonases-inhibiting proteins (PGIPs) binds to the PG to block fungal infection. The active site residues of PGIP3, VAL170 and GLN242 are mutated naturally by various amino acids in different types of PGIPs. Therefore, the mutation of VAL170 to GLY is ineffective but the GLN242 amino acid mutation by LYS significantly alters the structure and is crucial for interacting with the PG protein. Docking and Molecular Dynamics simulation provide a comprehensive evaluation of the interactions between gmPGIP and ssPG. By elucidating the structural basis of the interaction between gmPGIP and ssPG, this investigation lays a foundation for the development of targeted strategies in-order to enhance soybean resistance against Sclerotinia sclerotiorum. By leveraging this knowledge, researchers can potentially engineer soybean varieties with improved resistance to the fungus, thereby reducing disease incidence and improving crop yields.
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Affiliation(s)
- Mayank Rashmi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sneha Murmu
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | | | | | - Raja Shankar
- ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | | | - Girish Kumar Jha
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Sunil Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Priyadarshinee M, Dehury B, Mishra S, Jena C, Patra M, Mishra NK, Samanta L, Mallick BC. Spectroscopic insights with molecular docking and molecular dynamic simulation studies of anticancer drug 5-Fluorouracil targeting human pyruvate kinase m2. J Biomol Struct Dyn 2024:1-13. [PMID: 38345048 DOI: 10.1080/07391102.2024.2313158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/27/2024] [Indexed: 02/22/2024]
Abstract
This study was conducted to test the efficacy of 5-fluorouracil (5-FU) as an anticancer drug against the human pyruvate kinase isozyme M2 (PKM2) using spectroscopic, molecular docking and molecular dynamic simulation studies. PKM2 fluorescence quenching studies in the presence of 5-FU performed at three different temperatures indicates dynamic quenching processes with single-set of binding (n ≈ 1) profile. The biomolecular quenching constants (kq) and the effective binding constants (Kb) obtained are shown to increase with temperature. The calculated enthalpy (ΔH) and entropy changes (ΔS) are estimated to be -118.06 kJ/mol and 146.14 kJ/mol/K respectively, which suggest the possible mode of interaction as electrostatic and hydrogen bonding. Further, these values were used to estimate the free energy changes (ΔG) and that increases with temperature. The negative ΔG values clearly indicates spontaneous binding process that stabilizes the complex formed between 5-FU and PKM2. Far-UV CD spectra of PKM2 in the presence of 5-FU shows decrease in α-helix contents which point towards the destabilization of secondary structure that weakens the biological activity of PKM2. The intrinsic fluorescence study and circular dichroism (CD) spectra showed minor conformational changes of PKM2 in the presence of 5-FU. Additionally, the results obtained from molecular docking and all-atom molecular dynamic simulation study supports the insight of the spectroscopic binding studies, and strengthens the dynamic stability of the complex between 5-FU and PKM2 through H-bonding. This study establishes a paradigm of 5-FU-PKM2 complexation and the efficacy of 5-FU that compromises the biological activity of the targeted PKM2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, India
| | | | | | - Neeraj K Mishra
- Department of Biotechnology, GITAM University, Vishakhapatnam, India
| | - Luna Samanta
- Department of Zoology, Ravenshaw University, Cuttack, India
| | - Bairagi C Mallick
- Department of Chemistry, Ravenshaw University, Cuttack, India
- Department of Chemistry, Central University of Jharkhand, Ranchi, India
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Pattnaik S, Murmu S, Prasad Rath B, Singh MK, Kumar S, Mohanty C. In silico screening of phytoconstituents as potential anti-inflammatory agents targeting NF-κB p65: an approach to promote burn wound healing. J Biomol Struct Dyn 2024:1-29. [PMID: 38287503 DOI: 10.1080/07391102.2024.2306199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/10/2024] [Indexed: 01/31/2024]
Abstract
Chronic burn wounds are frequently characterised by a prolonged and dysregulated inflammatory phase that is mediated by over-activation of NF-κB p65. Synthetic wound healing drugs used for treatment of inflammation are primarily associated with several shortcomings which reduce their therapeutic index. In this scenario, phytoconstituents that exhibit multifaceted biological activities including anti-inflammatory effects have emerged as a promising therapeutic alternative. However, identification and isolation of phytoconstituents from medicinal herbs is a cumbersome method that is linked to profound uncertainty. Hence, present study aimed to identify prospective phytoconstituents as inhibitors of RHD of NF-κB p65 by utilizing in silico approach. Virtual screening of 2821 phytoconstituents was performed against protein model. Out of 2821 phytoconstituents, 162 phytoconstituents displayed a higher binding affinity (≤ -8.0 kcal/mol). These 162 phytoconstituents were subjected to ADMET predictions, and 15 of them were found to satisfy Lipinski's rule of five and showed favorable pharmacokinetic properties. Among these 15 phytoconstituents, 5 phytoconstituents with high docking scores i.e. silibinin, bismurrayaquinone A, withafastuosin B, yuccagenin, (+)-catechin 3-gallate were selected for molecular dynamics (MD) simulation analysis. Results of MD simulation indicated that withafastuosin B, (+)-catechin 3-gallate and yuccagenin produced a compact and stable complex with protein without significant variations in conformation. Relative binding energy analysis of best hit molecules indicate that withafastuosin B, and (+)-catechin 3-gallate exhibit high binding affinity with target protein among other lead molecules. Findings of study suggest that these phytoconstituents could serve as promising anti-inflammatory agents for treatment of burn wounds by inhibiting the RHD of NF-κB p65.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saswati Pattnaik
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, Odisha, India
| | - Sneha Murmu
- ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, India
| | - Bibhu Prasad Rath
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, India
| | - Sunil Kumar
- ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, India
| | - Chandana Mohanty
- School of Applied Sciences, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, Odisha, India
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Zhao Y, Mao W, Tang W, Soares MA, Li H. Wild Rosa Endophyte M7SB41-Mediated Host Plant's Powdery Mildew Resistance. J Fungi (Basel) 2023; 9:620. [PMID: 37367556 DOI: 10.3390/jof9060620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Our previous studies indicated that endophyte M7SB41 (Seimatosporium sp.) can significantly enhance host plants powdery mildew (PM) resistance. To recover the mechanisms, differentially expressed genes (DEGs) were compared between E+ (endophte-inoculated) and E- (endophyte-free) plants by transcriptomics. A total of 4094, 1200 and 2319 DEGs between E+ and E- were identified at 0, 24, and 72 h after plants had been infected with PM pathogen Golovinomyces cichoracearum, respectively. Gene expression pattern analysis displayed a considerable difference and temporality in response to PM stress between the two groups. Transcriptional profiling analysis revealed that M7SB41 induced plant resistance to PM through Ca2+ signaling, salicylic acid (SA) signaling, and the phenylpropanoid biosynthesis pathway. In particular, we investigated the role and the timing of the SA and jasmonic acid (JA)-regulated defensive pathways. Both transcriptomes and pot experiments showed that SA-signaling may play a prominent role in PM resistance conferred by M7SB41. Additionally, the colonization of M7SB41 could effectively increase the activities and the expression of defense-related enzymes under PM pathogen stress. Meanwhile, our study revealed reliable candidate genes from TGA (TGACG motif-binding factor), WRKY, and pathogenesis-related genes related to M7SB41-mediate resistance. These findings offer a novel insight into the mechanisms of endophytes in activating plant defense responses.
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Affiliation(s)
- Yi Zhao
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, Yunnan Minzu University, Kunming 650500, China
| | - Wenqin Mao
- Life Science and Technology & Medical Faculty, Kunming University of Science and Technology, Kunming 650500, China
| | - Wenting Tang
- Life Science and Technology & Medical Faculty, Kunming University of Science and Technology, Kunming 650500, China
| | - Marcos Antônio Soares
- Department of Botany and Ecology, Federal University of Mato Grosso, Cuiabá 78060-900, Brazil
| | - Haiyan Li
- Life Science and Technology & Medical Faculty, Kunming University of Science and Technology, Kunming 650500, China
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Wu J, Gao T, Guo H, Zhao L, Lv S, Lv J, Yao R, Yu Y, Ma F. Application of molecular dynamics simulation for exploring the roles of plant biomolecules in promoting environmental health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161871. [PMID: 36708839 DOI: 10.1016/j.scitotenv.2023.161871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Understanding the dynamic changes of plant biomolecules is vital for exploring their mechanisms in the environment. Molecular dynamics (MD) simulation has been widely used to study structural evolution and corresponding properties of plant biomolecules at the microscopic scale. Here, this review (i) outlines structural properties of plant biomolecules, and the crucial role of MD simulation in advancing studies of the biomolecules; (ii) describes the development of MD simulation in plant biomolecules, determinants of simulation, and analysis parameters; (iii) introduces the applications of MD simulation in plant biomolecules, including the response of the biomolecules to multiple stresses, their roles in corrosive environments, and their contributions in improving environmental health; (iv) reviews techniques integrated with MD simulation, such as molecular biology, quantum mechanics, molecular docking, and machine learning modeling, which bridge gaps in MD simulation. Finally, we make suggestions on determination of force field types, investigation of plant biomolecule mechanisms, and use of MD simulation in combination with other techniques. This review provides comprehensive summaries of the mechanisms of plant biomolecules in the environment revealed by MD simulation and validates it as an applicable tool for bridging gaps between macroscopic and microscopic behavior, providing insights into the wide application of MD simulation in plant biomolecules.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China.
| | - Tian Gao
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Haijuan Guo
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Sidi Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Ruyi Yao
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Yanyi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
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Sharma M, Jabaji S. Transcriptional landscape of Brachypodium distachyon roots during interaction with Bacillus velezensis strain B26. Genomics 2023; 115:110583. [PMID: 36804269 DOI: 10.1016/j.ygeno.2023.110583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/02/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023]
Abstract
Plant growth promoting rhizobacteria (PGPR) communicate with plants through roots. The molecular mechanism by which plants and PGPR respond to each other is not very well known. In the current study, we did RNA sequence analysis of Brachypodium distachyon Bd21-3 roots inoculated with PGPR, Bacillus velezensis strain B26. From our list of differentially expressed genes, we concentrated on transcripts that have a high possibility of participating in plant-PGPR interaction. Transcripts associated to the hormone signalling pathway were differentially expressed. We identified the upregulation of various transcripts linked to ion transporters. Reduction in expression of defense signalling genes indicated that B26 suppresses the plant defense mechanisms to begin successful interaction with roots. Transcripts associated with lignin branch of the phenylpropanoid pathway were upregulated as well, leading to more accumulation of lignin in the cell wall which enhances mechanical strength of plants. Overall, this study is an excellent resource for investigating associations between plant-PGPR interactions.
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Affiliation(s)
- Meha Sharma
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, H9X 3V9 Quebec, Canada.
| | - Suha Jabaji
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, H9X 3V9 Quebec, Canada.
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Nagrale DT, Chaurasia A, Kumar S, Gawande SP, Hiremani NS, Shankar R, Gokte-Narkhedkar N, Renu, Prasad YG. PGPR: the treasure of multifarious beneficial microorganisms for nutrient mobilization, pest biocontrol and plant growth promotion in field crops. World J Microbiol Biotechnol 2023; 39:100. [PMID: 36792799 DOI: 10.1007/s11274-023-03536-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/30/2023] [Indexed: 02/17/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) have multifarious beneficial activities for plant growth promotion; act as source of metabolites, enzymes, nutrient mobilization, biological control of pests, induction of disease resistance vis-a-vis bioremediation potentials by phytoextraction and detoxification of heavy metals, pollutants and pesticides. Agrochemicals and synthetic pesticides are currently being utilized widely in all major field crops, thereby adversely affecting human and animal health, and posing serious threats to the environments. Beneficial microorganisms like PGPR could potentially substitute and supplement the toxic chemicals and pesticides with promising application in organic farming leading to sustainable agriculture practices and bioremediation of heavy metal contaminated sites. Among field crops limited bio-formulations have been prepared till now by utilization of PGPR strains having plant growth promotion, metabolites, enzymes, nutrient mobilization and biocontrol activities. The present review contributes comprehensive description of PGPR applications in field crops including commercial, oilseeds, leguminous and cereal crops to further extend the utilization of these potent groups of beneficial microorganisms so that even higher level of crop productivity and quality produce of field crops could be achieved. PGPR and bacteria based commercialized bio-formulations available worldwide for its application in the field crops have been compiled in this review which can be a substitute for the harmful synthetic chemicals. The current knowledge gap and potential target areas for future research have also been projected.
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Affiliation(s)
- D T Nagrale
- ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, 440010, India.
| | - A Chaurasia
- ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, 221305, India.
| | - S Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - S P Gawande
- ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, 440010, India
| | - N S Hiremani
- ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, 440010, India
| | - Raja Shankar
- ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru, 560089, India
| | - N Gokte-Narkhedkar
- ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, 440010, India
| | - Renu
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001, India
| | - Y G Prasad
- ICAR-Central Institute for Cotton Research, Nagpur, Maharashtra, 440010, India
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Sperotto RA, Hrmova M, Graether SP, Timmers LFSM. Editorial: Structural bioinformatics and biophysical approaches for understanding the plant responses to biotic and abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1012584. [PMID: 36161033 PMCID: PMC9507305 DOI: 10.3389/fpls.2022.1012584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Raul A. Sperotto
- Graduate Program in Biotechnology, University of Taquari Valley – Univates, Lajeado, Brazil
- Graduate Program in Plant Physiology, Federal University of Pelotas, Pelotas, Brazil
| | - Maria Hrmova
- Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, SA, Australia
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Steffen P. Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Luis Fernando S. M. Timmers
- Graduate Program in Biotechnology, University of Taquari Valley – Univates, Lajeado, Brazil
- Graduate Program in Medical Sciences, University of Taquari Valley – Univates, Lajeado, Brazil
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