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Thaker K, Patoliya J, Rabadiya K, Patel D, Ponnuchamy M, Rama Reddy NR, Joshi R. An in-silico approach to unravel the structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS): a critical enzyme for sennoside biosynthesis in Cassia angustifolia Vahl. J Biomol Struct Dyn 2024; 42:3848-3861. [PMID: 37243697 DOI: 10.1080/07391102.2023.2216300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/13/2023] [Indexed: 05/29/2023]
Abstract
The laxative properties of senna are attributed to the presence of sennosides produced in the plant. The low production level of sennosides in the plant is an important impediment to their growing demand and utilization. Understanding biosynthetic pathways helps to engineer them in terms of enhanced production. The biosynthetic pathways of sennoside production in plants are not completely known yet. However, attempts to get information on genes and proteins engaged in it have been made which decode involvement of various pathways including shikimate pathway. 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS) is a key enzyme involved in sennosides production through the shikimate pathway. Unfortunately, there is no information available on proteomic characterization of DAHPS enzyme of senna (caDAHPS) resulting in lack of knowledge about its role. We for the first time characterized DAHPS enzyme of senna using in-silico analysis. To the best of our knowledge this is the first attempt to identify the coding sequence of caDAHPS by cloning and sequencing. We found Gln179, Arg175, Glu462, Glu302, Lys357 and His420 amino acids in the active site of caDAHPS through molecular docking. followed by molecular dynamic simulation. The amino acid residues, Lys182, Cys136, His460, Leu304, Gly333, Glu334, Pro183, Asp492 and Arg433 at the surface interact with PEP by van der Waals bonds imparting stability to the enzyme-substrate complex. Docking results were further validated by molecular dynamics. The presented in-silico analysis of caDAHPS will generate opportunities to engineer the sennoside biosynthesis in plants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khushali Thaker
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Jaimini Patoliya
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Khushbu Rabadiya
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Dhaval Patel
- Gujarat Biotechnology University, Gandhinagar, Gujarat, India
| | - Manivel Ponnuchamy
- ICAR-Directorate of Medicinal and Aromatic Plants Research (DMAPR), Anand, Gujarat, India
| | | | - Rushikesh Joshi
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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Rode S, Kaur H, Sharma M, Shah V, Singh SS, Gubyad M, Ghosh DK, Sircar D, Kumar P, Roy P, Sharma AK. Characterization of Type1 Lipid Transfer Protein from Citrus sinensis: Unraveling its potential as an antimicrobial and insecticidal agent. Int J Biol Macromol 2024; 265:130811. [PMID: 38490399 DOI: 10.1016/j.ijbiomac.2024.130811] [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: 09/30/2023] [Revised: 12/27/2023] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
Lipid Transfer Protein1 (LTP1) is a cationic, multifaceted protein belonging to the pathogenesis-related protein (PR14) family. Despite being involved in diverse physiological processes and defense mechanisms, the precise in-vivo role of LTP1 remains undiscovered. This work presents the characterization of recombinant Citrus sinensis LTP1 (CsLTP1) along with lipid binding studies through in-silico and in-vitro approaches. CsLTP1 demonstrated great thermal and pH stability with a huge biotechnological potential. It showed in-vitro binding capacity with jasmonic acid and lipids involved in regulating plant immune responses. Gene expression profiling indicated a significant upregulation of CsLTP1 in Candidatus-infected Citrus plants. CsLTP1 disrupted the cell membrane integrity of various pathogens, making it a potent antimicrobial agent. Further, in-vivo antimicrobial and insecticidal properties of CsLTP1 have been explored. The impact of exogenous CsLTP1 treatment on rice crop metabolism for managing blight disease has been studied using GC-MS. CsLTP1 triggered crucial metabolic pathways in rice plants while controlling the blight disease. CsLTP1 effectively inhibited Helicoverpa armigera larvae by impeding mid-gut α-amylase activity and obstructing its developmental stages. This study highlights the pivotal role of CsLTP1 in plant defense by offering insights for developing multi-target therapeutic agent or disease-resistant varieties to comprehensively tackle the challenges towards crop protection.
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Affiliation(s)
- Surabhi Rode
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Harry Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Monica Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Vivek Shah
- Division of Crop Protection, ICAR Central Institute for Cotton Research, Nagpur, India
| | - Shiv Shakti Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Mrugendra Gubyad
- Plant Virology Laboratory, Central Citrus Research Institute, Nagpur, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, Central Citrus Research Institute, Nagpur, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Partha Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India.
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Gupta DN, Lonare S, Rani R, Singh A, Ghosh DK, Tomar S, Sharma AK. Comparative Analysis of Inhibitor Binding to Peroxiredoxins from Candidatus Liberibacter asiaticus and Its Host Citrus sinensis. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04798-y. [PMID: 38157153 DOI: 10.1007/s12010-023-04798-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
The peroxiredoxins (Prxs), potential drug targets, constitute an important class of antioxidant enzymes present in both pathogen and their host. The comparative binding potential of inhibitors to Prxs from pathogen and host could be an important step in drug development against pathogens. Huanglongbing (HLB) is a most devastating disease of citrus caused by Candidatus Liberibacter asiaticus (CLa). In this study, the binding of conoidin-A (conoidin) and celastrol inhibitor molecules to peroxiredoxin of bacterioferritin comigratory protein family from CLa (CLaBCP) and its host plant peroxiredoxin from Citrus sinensis (CsPrx) was assessed. The CLaBCP has a lower specific activity than CsPrx and is efficiently inhibited by conoidin and celastrol molecules. The biophysical studies showed conformational changes and significant thermal stability of CLaBCP in the presence of inhibitor molecules as compared to CsPrx. The surface plasmon resonance (SPR) studies revealed that the conoidin and celastrol inhibitor molecules have a strong binding affinity (KD) with CLaBCP at 33.0 µM, and 18.5 µM as compared to CsPrx at 52.0 µM and 61.6 µM, respectively. The docked complexes of inhibitor molecules showed more structural stability of CLaBCP as compared to CsPrx during the run of molecular dynamics-based simulations for 100 ns. The present study suggests that the conoidin and celastrol molecules can be exploited as potential inhibitor molecules against the CLa to manage the HLB disease.
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Affiliation(s)
- Deena Nath Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Sapna Lonare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ruchi Rani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR Central Citrus Research Institute, Nagpur, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
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Saeed Q, Ahmad F, Yousaf N, Ali H, Tirmazi SAAS, Alshammari A, Kausar N, Ahmed M, Imran M, Jamshed M, Alharbi M, Muddassar M. In Silico and In Vivo Evaluation of Synthesized SCP-2 Inhibiting Compounds on Life Table Parameters of Helicoverpa armigera (Hübner). INSECTS 2022; 13:1169. [PMID: 36555079 PMCID: PMC9782802 DOI: 10.3390/insects13121169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
For environment-friendly, safe and nonpersistent chemical control of a significant polyphagous insect pest, Helicoverpa armigera, discovery of growth-regulating xenobiotics can offer a sustainable alternative to conventional insecticides. For this purpose, chemically synthesized compounds to inhibit sterol carrier protein (SCP-2) function using in silico and in vivo assays were evaluated to estimate their impact on the survivals and lifetable indices of H. armigera. From nine chemically synthesized compounds, OA-02, OA-06 and OA-09 were selected for this study based on binding poses mimicking cholesterol, a natural substrate of sterol carrier protein and molecular dynamics simulations. In vivo bioassays revealed that all compounds significantly reduced the larval and pupal weight accumulations and stadia lengths. Subsequently, the pupal periods were prolonged upon treatment with higher doses of the selected compounds. Moreover, OA-09 significantly reduced pupation and adult emergence rates as well as the fertility of female moths; however, fecundity remained unaffected, in general. The life table parameters of H. armigera were significantly reduced when treated with OA-09 at higher doses. The population treated with 450 μM of OA-09 had the least net reproductive rates (Ro) and gross reproductive rate (GRR) compared to the control population. The same compound resulted in a declining survival during the early stages of development coupled with reduced larval and pupal durations, and fertility. These results have a significant implication for developing an effective and sustainable chemical treatment against H. armigera infestation.
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Affiliation(s)
- Qamar Saeed
- Department of Entomology, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Faheem Ahmad
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad 45550, Pakistan
| | - Numan Yousaf
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad 45550, Pakistan
| | - Haider Ali
- Department of Entomology, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | | | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Ryadh 11451, Saudi Arabia
| | - Naeema Kausar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad 45550, Pakistan
| | - Mahmood Ahmed
- Department of Chemistry, Division of Science and Technology, University of Education, College Road, Lahore 54000, Pakistan
| | - Muhammad Imran
- KAM-School of Life Sciences, FC College (A Chartered University), Lahore 54000, Pakistan
| | - Muhammad Jamshed
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Ryadh 11451, Saudi Arabia
| | - Muhammad Muddassar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad 45550, Pakistan
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