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Khan A, Singh AV, Gautam SS, Agarwal A, Punetha A, Upadhayay VK, Kukreti B, Bundela V, Jugran AK, Goel R. Microbial bioformulation: a microbial assisted biostimulating fertilization technique for sustainable agriculture. FRONTIERS IN PLANT SCIENCE 2023; 14:1270039. [PMID: 38148858 PMCID: PMC10749938 DOI: 10.3389/fpls.2023.1270039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/03/2023] [Indexed: 12/28/2023]
Abstract
Addressing the pressing issues of increased food demand, declining crop productivity under varying agroclimatic conditions, and the deteriorating soil health resulting from the overuse of agricultural chemicals, requires innovative and effective strategies for the present era. Microbial bioformulation technology is a revolutionary, and eco-friendly alternative to agrochemicals that paves the way for sustainable agriculture. This technology harnesses the power of potential microbial strains and their cell-free filtrate possessing specific properties, such as phosphorus, potassium, and zinc solubilization, nitrogen fixation, siderophore production, and pathogen protection. The application of microbial bioformulations offers several remarkable advantages, including its sustainable nature, plant probiotic properties, and long-term viability, positioning it as a promising technology for the future of agriculture. To maintain the survival and viability of microbial strains, diverse carrier materials are employed to provide essential nourishment and support. Various carrier materials with their unique pros and cons are available, and choosing the most appropriate one is a key consideration, as it substantially extends the shelf life of microbial cells and maintains the overall quality of the bioinoculants. An exemplary modern bioformulation technology involves immobilizing microbial cells and utilizing cell-free filters to preserve the efficacy of bioinoculants, showcasing cutting-edge progress in this field. Moreover, the effective delivery of bioformulations in agricultural fields is another critical aspect to improve their overall efficiency. Proper and suitable application of microbial formulations is essential to boost soil fertility, preserve the soil's microbial ecology, enhance soil nutrition, and support crop physiological and biochemical processes, leading to increased yields in a sustainable manner while reducing reliance on expensive and toxic agrochemicals. This manuscript centers on exploring microbial bioformulations and their carrier materials, providing insights into the selection criteria, the development process of bioformulations, precautions, and best practices for various agricultural lands. The potential of bioformulations in promoting plant growth and defense against pathogens and diseases, while addressing biosafety concerns, is also a focal point of this study.
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Affiliation(s)
- Amir Khan
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Ajay Veer Singh
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Shiv Shanker Gautam
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Aparna Agarwal
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Arjita Punetha
- School of Environmental Science and Natural Resource, Dehradun, Uttarakhand, India
| | - Viabhav Kumar Upadhayay
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agriculture University, Samastipur, India
| | - Bharti Kukreti
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Vindhya Bundela
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Arun Kumar Jugran
- G. B. Pant National Institute of Himalayan Environment (GBPNIHE), Garhwal Regional Centre, Srinager, Uttarakhand, India
| | - Reeta Goel
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura, Uttar Pradesh, India
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2
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Mineyeva IV. α,β-Unsaturated β-Methyl-δ-lactones in Nitrile Oxide Cycloaddition Reactions. Synthesis of Saturated Lactones and Lactams. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1070428022060033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Yoon WS, Jang WJ, Yoon W, Yun H, Yun J. Copper-catalysed asymmetric reductive cross-coupling of prochiral alkenes. Nat Commun 2022; 13:2570. [PMID: 35545634 PMCID: PMC9095606 DOI: 10.1038/s41467-022-30286-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Asymmetric construction of C(sp3)-C(sp3) bond with good stereocontrol of the two connecting carbon centres retaining all carbon or hydrogen substituents is a challenging target in transition metal catalysis. Transition metal-catalysed reductive coupling of unsaturated π-substrates is considered as a potent tool to expediently develop the molecular complexity with high atom efficiency. However, such an asymmetric and intermolecular process has yet to be developed fully. Herein, we report an efficient strategy to reductively couple two prochiral conjugate alkenes using a copper-catalysed tandem protocol in the presence of diboron. Notably, this transformation incorporates a wide range of terminal and internal enynes as coupling partners and facilitates highly diastereo- and enantioselective synthesis of organoboron derivatives with multiple adjacent stereocentres in a single operation.
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Affiliation(s)
- Wan Seok Yoon
- Department of Chemistry and Institute of Basic Science, Sungkyunkwan University, Suwon, 16419, Korea
| | - Won Jun Jang
- Department of Chemistry and Institute of Basic Science, Sungkyunkwan University, Suwon, 16419, Korea
- Department of Chemistry, Dong-A University, Busan, 49315, Korea
| | - Woojin Yoon
- Department of Energy Systems Research and Department of Chemistry, Ajou University, Suwon, 16499, Korea
| | - Hoseop Yun
- Department of Energy Systems Research and Department of Chemistry, Ajou University, Suwon, 16499, Korea.
| | - Jaesook Yun
- Department of Chemistry and Institute of Basic Science, Sungkyunkwan University, Suwon, 16419, Korea.
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4
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El Kharrat S, Laurent P, Boiteau L. Diastereoselective Synthesis of Perfluoroalkylmethyl‐Substituted 1,2,3,4‐Tetrahydroquinolines Derivatives through 1‐Iodo‐1,3‐Bis(acetoxy) Synthons. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Salem El Kharrat
- Universite Saint-Joseph Faculte de pharmacie Faculty of Pharmacy Rue de Damas 1107 2180 Beirut LEBANON
| | - Philippe Laurent
- Université de Montpellier: Universite de Montpellier Institut des Biomolecules Max Mousseron 1919 route de Mende 34293 Montpellier FRANCE
| | - Laurent Boiteau
- University of Montpellier: Universite de Montpellier IBMM FRANCE
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5
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Li X, Zhang M, Qi D, Zhou D, Qi C, Li C, Liu S, Xiang D, Zhang L, Xie J, Wang W. Biocontrol Ability and Mechanism of a Broad-Spectrum Antifungal Strain Bacillus safensis sp. QN1NO-4 Against Strawberry Anthracnose Caused by Colletotrichum fragariae. Front Microbiol 2021; 12:735732. [PMID: 34603266 PMCID: PMC8486013 DOI: 10.3389/fmicb.2021.735732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/18/2021] [Indexed: 12/19/2022] Open
Abstract
Strawberry is a very popular fruit with a special taste, color, and nutritional value. Anthracnose caused by Colletotrichum fragariae severely limits fruit shelf life during post-harvest storage. Use of traditional chemical fungicides leads to serious environment pollution and threatens food safety. Biocontrol is considered as a promising strategy to manage the post-harvest fruit diseases. Here, strain QN1NO-4 isolated from noni (Morinda citrifolia L.) fruit exhibited a high antifungal activity against C. fragariae. Based on its physicochemical profiles and phylogenetic tree of the 16S rRNA sequence, strain QN1NO-4 belonged to the genus Bacillus. The average nucleotide identity (ANI) calculated by comparing two standard strain genomes was below 95-96%, suggesting that the strain might be a novel species of the genus Bacillus and named as Bacillus safensis sp. QN1NO-4. Its extract effectively reduced the incidence of strawberry anthracnose of harvested fruit. Fruit weight and TSS contents were also maintained significantly. The antifungal mechanism assays indicated that the extract of the test antagonist inhibited mycelial growth and spore germination of C. fragariae in vitro. Cells of strain QN1NO-4 demonstrated the cytoplasmic heterogeneity, disappeared organelles, and ruptured ultrastructure. Notably, the strain extract also had a broad-spectrum antifungal activity. Compared with the whole genome of strain QN1NO-4, several functional gene clusters involved in the biosynthesis of active secondary metabolites were observed. Fifteen compounds were identified by gas chromatography-mass spectrometry (GC-MS). Hence, the fruit endophyte B. safensis sp. QN1NO-4 is a potential bio-agent identified for the management of post-harvest disease of strawberry fruit.
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Affiliation(s)
- Xiaojuan Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.,Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Science, Hainan Normal University, Haikou, China.,College of Ecology and Environment, Hainan University, Haikou, China
| | - Miaoyi Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Dengfeng Qi
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Dengbo Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chunlin Qi
- College of Ecology and Environment, Hainan University, Haikou, China
| | - Chunyu Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Siwen Liu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dandan Xiang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Lu Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Science, Hainan Normal University, Haikou, China
| | - Jianghui Xie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wei Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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6
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Walker PD, Weir ANM, Willis CL, Crump MP. Polyketide β-branching: diversity, mechanism and selectivity. Nat Prod Rep 2021; 38:723-756. [PMID: 33057534 DOI: 10.1039/d0np00045k] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2008 to August 2020 Polyketides are a family of natural products constructed from simple building blocks to generate a diverse range of often complex chemical structures with biological activities of both pharmaceutical and agrochemical importance. Their biosynthesis is controlled by polyketide synthases (PKSs) which catalyse the condensation of thioesters to assemble a functionalised linear carbon chain. Alkyl-branches may be installed at the nucleophilic α- or electrophilic β-carbon of the growing chain. Polyketide β-branching is a fascinating biosynthetic modification that allows for the conversion of a β-ketone into a β-alkyl group or functionalised side-chain. The overall transformation is catalysed by a multi-protein 3-hydroxy-3-methylglutaryl synthase (HMGS) cassette and is reminiscent of the mevalonate pathway in terpene biosynthesis. The first step most commonly involves the aldol addition of acetate to the electrophilic carbon of the β-ketothioester catalysed by a 3-hydroxy-3-methylglutaryl synthase (HMGS). Subsequent dehydration and decarboxylation selectively generates either α,β- or β,γ-unsaturated β-alkyl branches which may be further modified. This review covers 2008 to August 2020 and summarises the diversity of β-branch incorporation and the mechanistic details of each catalytic step. This is extended to discussion of polyketides containing multiple β-branches and the selectivity exerted by the PKS to ensure β-branching fidelity. Finally, the application of HMGS in data mining, additional β-branching mechanisms and current knowledge of the role of β-branches in this important class of biologically active natural products is discussed.
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Affiliation(s)
- P D Walker
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - A N M Weir
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - C L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - M P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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7
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Davies JA, Bull FM, Walker PD, Weir ANM, Lavigne R, Masschelein J, Simpson TJ, Race PR, Crump MP, Willis CL. Total Synthesis of Kalimantacin A. Org Lett 2020; 22:6349-6353. [PMID: 32806153 DOI: 10.1021/acs.orglett.0c02190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The kalimantacins make up a family of hybrid polyketide-nonribosomal peptide-derived natural products that display potent and selective antibiotic activity against multidrug resistant strains of Staphylococcus aureus. Herein, we report the first total synthesis of kalimantacin A, in which three fragments are prepared and then united via Sonogashira and amide couplings. The enantioselective synthetic approach is convergent, unlocking routes to further kalimantacins and analogues for structure-activity relationship studies and clinical evaluation.
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Affiliation(s)
- Jonathan A Davies
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Freya M Bull
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Paul D Walker
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Angus N M Weir
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, P.O. Box 2462, 3001 Leuven, Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery and Engineering, KU Leuven, Kasteel Park, Ardenberg 31, P.O. Box 2438, 3001 Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium
| | - Thomas J Simpson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Paul R Race
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Christine L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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8
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Fage CD, Lathouwers T, Vanmeert M, Gao L, Vrancken K, Lammens E, Weir ANM, Degroote R, Cuppens H, Kosol S, Simpson TJ, Crump MP, Willis CL, Herdewijn P, Lescrinier E, Lavigne R, Anné J, Masschelein J. The Kalimantacin Polyketide Antibiotics Inhibit Fatty Acid Biosynthesis in
Staphylococcus aureus
by Targeting the Enoyl‐Acyl Carrier Protein Binding Site of FabI. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Thomas Lathouwers
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Michiel Vanmeert
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Ling‐Jie Gao
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Kristof Vrancken
- Laboratory of Molecular Bacteriology Rega Institute for Medical Research Herestraat 49, PO Box 1037 3000 Leuven Belgium
| | - Eveline‐Marie Lammens
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Angus N. M. Weir
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Ruben Degroote
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Harry Cuppens
- Department of Human Genetics KU Leuven Herestraat 49 3000 Leuven Belgium
| | - Simone Kosol
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
| | - Thomas J. Simpson
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Matthew P. Crump
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Christine L. Willis
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Eveline Lescrinier
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Jozef Anné
- Laboratory of Molecular Bacteriology Rega Institute for Medical Research Herestraat 49, PO Box 1037 3000 Leuven Belgium
| | - Joleen Masschelein
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
- Laboratory for Biomolecular Discovery and Engineering KU Leuven Kasteelpark Arenberg 31, box 2438 3001 Heverlee Belgium
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9
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Fage CD, Lathouwers T, Vanmeert M, Gao L, Vrancken K, Lammens E, Weir ANM, Degroote R, Cuppens H, Kosol S, Simpson TJ, Crump MP, Willis CL, Herdewijn P, Lescrinier E, Lavigne R, Anné J, Masschelein J. The Kalimantacin Polyketide Antibiotics Inhibit Fatty Acid Biosynthesis in
Staphylococcus aureus
by Targeting the Enoyl‐Acyl Carrier Protein Binding Site of FabI. Angew Chem Int Ed Engl 2020; 59:10549-10556. [DOI: 10.1002/anie.201915407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/17/2020] [Indexed: 01/07/2023]
Affiliation(s)
| | - Thomas Lathouwers
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Michiel Vanmeert
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Ling‐Jie Gao
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Kristof Vrancken
- Laboratory of Molecular Bacteriology Rega Institute for Medical Research Herestraat 49, PO Box 1037 3000 Leuven Belgium
| | - Eveline‐Marie Lammens
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Angus N. M. Weir
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Ruben Degroote
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Harry Cuppens
- Department of Human Genetics KU Leuven Herestraat 49 3000 Leuven Belgium
| | - Simone Kosol
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
| | - Thomas J. Simpson
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Matthew P. Crump
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Christine L. Willis
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Eveline Lescrinier
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Jozef Anné
- Laboratory of Molecular Bacteriology Rega Institute for Medical Research Herestraat 49, PO Box 1037 3000 Leuven Belgium
| | - Joleen Masschelein
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
- Laboratory for Biomolecular Discovery and Engineering KU Leuven Kasteelpark Arenberg 31, box 2438 3001 Heverlee Belgium
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Walker PD, Williams C, Weir ANM, Wang L, Crosby J, Race PR, Simpson TJ, Willis CL, Crump MP. Control of β‐Branching in Kalimantacin Biosynthesis: Application of13C NMR to Polyketide Programming. Angew Chem Int Ed Engl 2019; 58:12446-12450. [DOI: 10.1002/anie.201905482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/12/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Paul D. Walker
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Angus N. M. Weir
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Luoyi Wang
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - John Crosby
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Paul R. Race
- School of BiochemistryUniversity of Bristol University Walk Bristol BS8 1TD UK
| | - Thomas J. Simpson
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Matthew P. Crump
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
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11
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Walker PD, Williams C, Weir ANM, Wang L, Crosby J, Race PR, Simpson TJ, Willis CL, Crump MP. Control of β‐Branching in Kalimantacin Biosynthesis: Application of13C NMR to Polyketide Programming. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Paul D. Walker
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Angus N. M. Weir
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Luoyi Wang
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - John Crosby
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Paul R. Race
- School of BiochemistryUniversity of Bristol University Walk Bristol BS8 1TD UK
| | - Thomas J. Simpson
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Matthew P. Crump
- School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
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12
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Ding T, Li T, Li J. Virtual screening for quorum-sensing inhibitors of Pseudomonas fluorescens P07 from a food-derived compound database. J Appl Microbiol 2019; 127:763-777. [PMID: 31125995 DOI: 10.1111/jam.14333] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/09/2019] [Accepted: 05/18/2019] [Indexed: 01/15/2023]
Abstract
AIMS Pseudomonas fluorescens are important psychrotrophic food spoilage bacteria that are frequently detected in dairy, meat and aquatic products. Quorum sensing (QS) is an intercellular communication and gene regulation mechanism that enables bacteria to monitor their cell densities and regulate a variety of physiological processes. Hence, targeting the bacterial QS system might be a feasible approach to improve food quality and safety by regulating the spoilage caused by P. fluorescens. METHODS AND RESULTS In this study, we screened a food-derived three-dimensional (3D) compound database to search for potential QS inhibitors (QSIs) with higher security. The 3D structures of LuxI- and LuxR-type proteins of P. fluorescens P07 were used as targets to screen for QSIs. A total of 25 compounds with high docking scores were tested for their anti-QS activities by indicator strains. The results show that 19 compounds possessed anti-QS activities. Among them, (+)-catechin had the strongest anti-QS activity. The results show that (+)-catechin significantly inhibited the production of extracellular enzymes, swimming motility, biofilm formation, acyl-homoserine lactones and extracellular polymeric substances (EPSs) of P. fluorescens P07. The inhibitory mechanism of (+)-catechin on the QS system of P. fluorescens P07 was discussed in the context of molecular docking analysis and real-time quantitative PCR (RT-qPCR). CONCLUSIONS Virtual screening was useful in finding novel QSIs with high security of P. fluorescens P07 from a food-derived 3D compound database. The high hit rate suggested that foods are rich sources of QSIs, and have great potential for exploration. SIGNIFICANCE AND IMPACT OF THE STUDY The modelled LuxI- and LuxR-type proteins could be used as targets to discover P. fluorescens P07 QSIs. (+)-catechin, (-)-epicatechin, propyl gallate, hesperidin and lycopene which were identified as potent QSIs, and may be applied in food preservation and biofilm elimination.
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Affiliation(s)
- T Ding
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - T Li
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian, Liaoning, China
| | - J Li
- School of Food Science and Technology, Jiangnan University, Wuxi, China.,College of Food Science and Technology, Bohai University, Jinzhou,, Liaoning, China.,Food Safety Key Lab of Liaoning Province, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning, China
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Comparison of structures and cytotoxicity of mupirocin and batumin against melanoma and several other cancer cell lines. Future Med Chem 2019; 11:677-691. [PMID: 30947530 DOI: 10.4155/fmc-2018-0333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: To determine the computer-predicted anticancer activity of mupirocin and to compare its activities with those determined for another polyene antibiotic, batumin. Materials & methods: Molecular docking, cytotoxicity assays, cell microscopy and cell cycle progression were studied in cancer and nontumorigenic cell lines. Results & conclusion: Cytotoxicity of mupirocin against several cancerous cell lines was detected with the highest one (IC50 = 5.4 μg/ml) against melanoma cell line. The profile of cytotoxicity of mupirocin was similar to that reported for batumin. Nevertheless, the morphology of cells treated with these antibiotics and alterations in cell cycle progression suggested possible dissimilarity in their mechanisms of action. Selective cytotoxicity of mupirocin against melanoma cells potentiates further studies to discover nontoxic drugs for melanoma prevention.
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Promising anticancer activity of batumin: a natural polyene antibiotic produced by Pseudomonas batumici. Future Med Chem 2018; 10:2187-2199. [PMID: 30081676 DOI: 10.4155/fmc-2018-0062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
AIM To determine the computer-predicted anticancer activity of antibiotic batumin. MATERIALS & METHODS Cytotoxicity assays, cell morphology microscopy and cell cycle progression were studied in cancer and nontumorigenic cell lines. An in vivo experiment on Lewis lung carcinoma (3LL)-transplanted mice was conducted to evaluate potential antimetastatic. RESULTS & CONCLUSION Cytotoxicity against melanoma and lung carcinoma cells (IC50 ≈ 5 μg/ml) was detected. Hypercondensed chromatin and apoptotic body formation in batumin-treated cells suggested the induction of apoptosis supported also by an observed increase in the quantity of cells occupying the sub-G1 cell cycle phase. Twofold reduction in the number and volume of lung metastases in Lewis lung carcinoma (3LL)-bearing batumin-treated mice was demonstrated. Highly specific cytotoxicity of batumin against cancer cell lines potentiates further studies.
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Luo Y, Cheng Y, Yi J, Zhang Z, Luo Q, Zhang D, Li Y. Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism. Front Microbiol 2018; 9:1520. [PMID: 30050512 PMCID: PMC6052121 DOI: 10.3389/fmicb.2018.01520] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022] Open
Abstract
Paenibacillus polymyxa (formerly known as Bacillus polymyxa) has been extensively studied for agricultural applications as a plant-growth-promoting rhizobacterium and is also an important biocontrol agent. Our team has developed the P. polymyxa strain HY96-2 from the tomato rhizosphere as the first microbial biopesticide based on P. polymyxa for controlling plant diseases around the world, leading to the commercialization of this microbial biopesticide in China. However, further research is essential for understanding its precise biocontrol mechanisms. In this paper, we report the complete genome sequence of HY96-2 and the results of a comparative genomic analysis between different P. polymyxa strains. The complete genome size of HY96-2 was found to be 5.75 Mb and 5207 coding sequences were predicted. HY96-2 was compared with seven other P. polymyxa strains for which complete genome sequences have been published, using phylogenetic tree, pan-genome, and nucleic acid co-linearity analysis. In addition, the genes and gene clusters involved in biofilm formation, antibiotic synthesis, and systemic resistance inducer production were compared between strain HY96-2 and two other strains, namely, SC2 and E681. The results revealed that all three of the P. polymyxa strains have the ability to control plant diseases via the mechanisms of colonization (biofilm formation), antagonism (antibiotic production), and induced resistance (systemic resistance inducer production). However, the variation of the corresponding genes or gene clusters between the three strains may lead to different antimicrobial spectra and biocontrol efficacies. Two possible pathways of biofilm formation in P. polymyxa were reported for the first time after searching the KEGG database. This study provides a scientific basis for the further optimization of the field applications and quality standards of industrial microbial biopesticides based on HY96-2. It may also serve as a reference for studying the differences in antimicrobial spectra and biocontrol capability between different biocontrol agents.
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Affiliation(s)
| | | | | | | | | | - Daojing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuanguang Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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López G, Diaz-Cárdenas C, Shapiro N, Woyke T, Kyrpides NC, David Alzate J, González LN, Restrepo S, Baena S. Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes. Stand Genomic Sci 2017; 12:78. [PMID: 29255573 PMCID: PMC5731063 DOI: 10.1186/s40793-017-0292-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/24/2017] [Indexed: 12/22/2022] Open
Abstract
Here we present the physiological features of Pseudomonas extremaustralis strain USBA-GBX-515 (CMPUJU 515), isolated from soils in Superparamo ecosystems, > 4000 m.a.s.l, in the northern Andes of South America, as well as the thorough analysis of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium of 1.0–3.0 μm × 0.5–1 μm, motile and unable to form spores, it grows aerobically and cells show one single flagellum. Several genetic indices, the phylogenetic analysis of the 16S rRNA gene sequence and the phenotypic characterization confirmed that USBA-GBX-515 is a member of Pseudomonas genus and, the similarity of the 16S rDNA sequence was 100% with P. extremaustralis strain CT14–3T. The draft genome of P. extremaustralis strain USBA-GBX-515 consisted of 6,143,638 Mb with a G + C content of 60.9 mol%. A total of 5665 genes were predicted and of those, 5544 were protein coding genes and 121 were RNA genes. The distribution of genes into COG functional categories showed that most genes were classified in the category of amino acid transport and metabolism (10.5%) followed by transcription (8.4%) and signal transduction mechanisms (7.3%). We performed experimental analyses of the lipolytic activity and results showed activity mainly on short chain fatty acids. The genome analysis demonstrated the existence of two genes, lip515A and est515A, related to a triacylglycerol lipase and carboxylesterase, respectively. Ammonification genes were also observed, mainly nitrate reductase genes. Genes related with synthesis of poly-hydroxyalkanoates (PHAs), especially poly-hydroxybutyrates (PHBs), were detected. The phaABC and phbABC operons also appeared complete in the genome. P. extremaustralis strain USBA-GBX-515 conserves the same gene organization of the type strain CT14–3T. We also thoroughly analyzed the potential for production of secondary metabolites finding close to 400 genes in 32 biosynthetic gene clusters involved in their production.
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Affiliation(s)
- Gina López
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
| | - Carolina Diaz-Cárdenas
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - J David Alzate
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A - 12, Bogotá, DC Colombia
| | - Laura N González
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A - 12, Bogotá, DC Colombia
| | - Silvia Restrepo
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A - 12, Bogotá, DC Colombia
| | - Sandra Baena
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
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