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Yin Y, Wang X, Zhang P, Wang P, Wen J. Strategies for improving fengycin production: a review. Microb Cell Fact 2024; 23:144. [PMID: 38773450 PMCID: PMC11110267 DOI: 10.1186/s12934-024-02425-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/14/2024] [Indexed: 05/23/2024] Open
Abstract
Fengycin is an important member of the lipopeptide family with a wide range of applications in the agricultural, food, medical and cosmetic industries. However, its commercial application is severely hindered by low productivity and high cost. Therefore, numerous studies have been devoted to improving the production of fengycin. We summarize these studies in this review with the aim of providing a reference and guidance for future researchers. This review begins with an overview of the synthesis mechanism of fengycin via the non-ribosomal peptide synthetases (NRPS), and then delves into the strategies for improving the fengycin production in recent years. These strategies mainly include fermentation optimization and metabolic engineering, and the metabolic engineering encompasses enhancement of precursor supply, application of regulatory factors, promoter engineering, and application of genome-engineering (genome shuffling and genome-scale metabolic network model). Finally, we conclude this review with a prospect of fengycin production.
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Affiliation(s)
- Ying Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Xin Wang
- Coll Biol & Pharmaceut Sci, China Three Gorges Univ, Yichang, 443002, P. R. China
| | - Pengsheng Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Pan Wang
- Department of Nuclear Medicine, The First Hospital of Shanxi Medical University, Collaborative Innovation Center of Molecular Imaging Precision Medical, Shanxi Medical University, Taiyuan, 030001, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China.
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Medeot D, Sannazzaro A, Estrella MJ, Torres Tejerizo G, Contreras-Moreira B, Pistorio M, Jofré E. Unraveling the genome of Bacillus velezensis MEP 218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis. Sci Rep 2023; 13:22168. [PMID: 38092837 PMCID: PMC10719345 DOI: 10.1038/s41598-023-49194-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16-C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892 bp, with a total of 3474 coding sequences and a G + C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1-4 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16-C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.
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Affiliation(s)
- Daniela Medeot
- Instituto de Biotecnología Ambiental y Salud (INBIAS), CCT-CONICET-Córdoba, Universidad Nacional de Río Cuarto, 5800, Córdoba, Argentina
| | - Analía Sannazzaro
- Instituto Tecnológico de Chascomús (INTECH), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín (UNSAM), 7130, Chascomús, Argentina
| | - María Julia Estrella
- Instituto Tecnológico de Chascomús (INTECH), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín (UNSAM), 7130, Chascomús, Argentina
| | - Gonzalo Torres Tejerizo
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, 1900, La Plata, Argentina
| | | | - Mariano Pistorio
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, 1900, La Plata, Argentina
| | - Edgardo Jofré
- Instituto de Biotecnología Ambiental y Salud (INBIAS), CCT-CONICET-Córdoba, Universidad Nacional de Río Cuarto, 5800, Córdoba, Argentina.
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Akintayo SO, Hosseini B, Vahidinasab M, Messmer M, Pfannstiel J, Bertsche U, Hubel P, Henkel M, Hausmann R, Voegele RT, Lilge L. Characterization ofantifungal properties of lipopeptide-producing Bacillus velezensis strains and their proteome-based response to the phytopathogens, Diaporthe spp. Front Bioeng Biotechnol 2023; 11:1228386. [PMID: 37609113 PMCID: PMC10440741 DOI: 10.3389/fbioe.2023.1228386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/28/2023] [Indexed: 08/24/2023] Open
Abstract
Introduction: B. velezensis strains are of interest in agricultural applications due to their beneficial interactions with plants, notable through their antimicrobial activity. The biocontrol ability of two new lipopeptides-producing B. velezensis strains ES1-02 and EFSO2-04, against fungal phytopathogens of Diaporthe spp., was evaluated and compared with reference strains QST713 and FZB42. All strains were found to be effective against the plant pathogens, with the new strains showing comparable antifungal activity to QST713 and slightly lower activity than FZB42. Methods: Lipopeptides and their isoforms were identified by high-performance thin-layer chromatography (HPTLC) and mass spectrometric measurements. The associated antifungal influences were determined in direct in vitro antagonistic dual culture assays, and the inhibitory growth effects on Diaporthe spp. as representatives of phytopathogenic fungi were determined. The effects on bacterial physiology of selected B. velezensis strains were analyzed by mass spectrometric proteomic analyses using nano-LC-MS/MS. Results and Discussion: Lipopeptide production analysis revealed that all strains produced surfactin, and one lipopeptide of the iturin family, including bacillomycin L by ES1-02 and EFSO2-04, while QST713 and FZB42 produced iturin A and bacillomycin D, respectively. Fengycin production was however only detected in the reference strains. As a result of co-incubation of strain ES1-02 with the antagonistic phytopathogen D. longicolla, an increase in surfactin production of up to 10-fold was observed, making stress induction due to competitors an attractive strategy for surfactin bioproduction. An associated global proteome analysis showed a more detailed overview about the adaptation and response mechanisms of B. velezensis, including an increased abundance of proteins associated with the biosynthesis of antimicrobial compounds. Furthermore, higher abundance was determined for proteins associated with oxidative, nitrosative, and general stress response. In contrast, proteins involved in phosphate uptake, amino acid transport, and translation were decreased in abundance. Altogether, this study provides new insights into the physiological adaptation of lipopeptide-producing B. velezensis strains, which show the potential for use as biocontrol agents with respect to phytopathogenic fungi.
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Affiliation(s)
- Stephen Olusanmi Akintayo
- Department of Bioprocess Engineering, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
| | - Behnoush Hosseini
- Department of Phytopathology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Maliheh Vahidinasab
- Department of Bioprocess Engineering, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
| | - Marc Messmer
- Department of Bioprocess Engineering, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
| | - Jens Pfannstiel
- Core Facility Hohenheim, Mass Spectrometry Core Facility, University of Hohenheim, Stuttgart, Germany
| | - Ute Bertsche
- Core Facility Hohenheim, Mass Spectrometry Core Facility, University of Hohenheim, Stuttgart, Germany
| | - Philipp Hubel
- Core Facility Hohenheim, Mass Spectrometry Core Facility, University of Hohenheim, Stuttgart, Germany
| | - Marius Henkel
- Cellular Agriculture, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Rudolf Hausmann
- Department of Bioprocess Engineering, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
| | - Ralf T. Voegele
- Department of Phytopathology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Lars Lilge
- Department of Bioprocess Engineering, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands
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Théatre A, Hoste ACR, Rigolet A, Benneceur I, Bechet M, Ongena M, Deleu M, Jacques P. Bacillus sp.: A Remarkable Source of Bioactive Lipopeptides. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 181:123-179. [DOI: 10.1007/10_2021_182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Scaglione A, Fullone MR, Montemiglio LC, Parisi G, Zamparelli C, Vallone B, Savino C, Grgurina I. Structure of the adenylation domain Thr1 involved in the biosynthesis of 4-chlorothreonine in Streptomyces sp. OH-5093-protein flexibility and molecular bases of substrate specificity. FEBS J 2017; 284:2981-2999. [PMID: 28704585 DOI: 10.1111/febs.14163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 05/19/2017] [Accepted: 07/10/2017] [Indexed: 12/13/2022]
Abstract
We determined the crystal structure of Thr1, the self-standing adenylation domain involved in the nonribosomal-like biosynthesis of free 4-chlorothreonine in Streptomyces sp. OH-5093. Thr1 shows two monomers in the crystallographic asymmetric unit with different relative orientations of the C- and N-terminal subdomains both in the presence of substrates and in the unliganded form. Cocrystallization with substrates, adenosine 5'-triphosphate and l-threonine, yielded one monomer containing the two substrates and the other in complex with l-threonine adenylate, locked in a postadenylation state. Steady-state kinetics showed that Thr1 activates l-Thr and its stereoisomers, as well as d-Ala, l- and d-Ser, albeit with lower efficiency. Modeling of these substrates in the active site highlighted the molecular bases of substrate discrimination. This work provides the first crystal structure of a threonine-activating adenylation enzyme, a contribution to the studies on conformational rearrangement in adenylation domains and on substrate recognition in nonribosomal biosynthesis. DATABASE Structural data are available in the Protein Data Bank under the accession number 5N9W and 5N9X.
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Affiliation(s)
- Antonella Scaglione
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, Rome, Italy
| | - Maria Rosaria Fullone
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Giacomo Parisi
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, Rome, Italy
| | - Carlotta Zamparelli
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, Rome, Italy
| | - Ingeborg Grgurina
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
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Blacutt AA, Mitchell TR, Bacon CW, Gold SE. Bacillus mojavensis RRC101 Lipopeptides Provoke Physiological and Metabolic Changes During Antagonism Against Fusarium verticilliodes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016. [PMID: 29775248 DOI: 10.1094/mpmi-05-16-0093-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The mycotoxigenic pathogen Fusarium verticillioides threatens the quality and utility of maize across industrial and agricultural purposes. Chemical control is complicated by the intimate endophytic lifestyle of the pathogen with its host. Bacillus mojavensis RRC101, a maize-endophytic bacterium, has been observed to reduce F. verticillioides disease severity and fumonisin accumulation when coinoculated to maize. Genome sequencing and annotation identified a number of biocontrol-relevant pathways in RRC101. Biochemical assays confirmed the presence and activity of surfactin- and fengycin-type lipopeptides, with fengycins responsible for antifungal activity against F. verticillioides. This antagonism manifests as inhibition of filamentous growth, with microscopy revealing hyphal distortions, vacuolization, and lysis. F. verticillioides secondary metabolism also responds to antagonism, with lipopeptide challenge inducing greater fumonisin production and, in the case of fengycins, eliciting pigment accumulation at sites of inhibition. Together, these data suggest that antibiotic and toxin production are components of a complex biochemical interaction among maize endophytes, one pathogenic and one beneficial.
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Cheng YC, Ke WJ, Liu ST. Regions involved in fengycin synthetases enzyme complex formation. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2016; 50:755-762. [PMID: 26857334 DOI: 10.1016/j.jmii.2015.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/14/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND Fengycin is a lipopeptide antibiotic synthesized nonribosomally by five fengycin synthetases. These enzymes are linked in a specific order to form the complex. This study investigates how these enzymes interact in the complex and analyzes the regions in the enzymes that are critical to the interactions. METHODS Deletions were generated in the fengycin synthetases. The interaction of these mutant proteins with their partner enzymes in the complex was analyzed in vitro by a glutathione S-transferase (GST) or nickel pulldown assay. RESULTS The communication-mediating donor (COM-D) domains of the fengycin synthetases, when fused to GST, specifically pulled down their downstream partner enzymes in the GST-pulldown assays. The communication-mediating acceptor (COM-A) domains were required for binding between two partner enzymes, although the domains alone did not confer specificity of the binding to their upstream partner enzymes. This study found that the COM-A domain, the condensation domain, and a portion of the adenylation domain in fengycin synthetase B (FenB) were required for specific binding to fengycin synthetase A (FenA). CONCLUSION The interaction between the COM-D and COM-A domains in two partner enzymes is critical for nonribosomal peptide synthesis. The COM-A domain alone is insufficient for interacting with its upstream partner enzyme in the enzyme complex with specificity; a region that contains COM-A, condensation, and a portion of adenylation domains in the downstream partner enzyme is required.
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Affiliation(s)
- Yu-Chieh Cheng
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Ju Ke
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Microbiology and Immunology, Research Center for Bacterial Pathogenesis, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shih-Tung Liu
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Medical Research and Development Chiayi Branch, Chang Gung Memorial Hospital, Chiayi, Taiwan.
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Płaza G, Chojniak J, Rudnicka K, Paraszkiewicz K, Bernat P. Detection of biosurfactants in Bacillus species: genes and products identification. J Appl Microbiol 2015; 119:1023-34. [PMID: 26171834 DOI: 10.1111/jam.12893] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/15/2015] [Accepted: 06/22/2015] [Indexed: 11/30/2022]
Abstract
AIM To screen environmental Bacillus strains for detection of genes encoding the enzymes involved in biosurfactant synthesis and to evaluate their products e.g. surfactin, iturin and fengycin. MATERIALS AND RESULTS The taxonomic identification of isolated from the environment Bacillus strains was performed by Microgene ID Bacillus panel and GEN III Biolog system. The polymerase chain reaction (PCR) strategy for screening of genes in Bacillus strains was set up. Liquid chromatography-mass spectrometry (LC-MS/MS) method was used for the identification of lipopeptides (LPs). All studied strains exhibited the presence of srfAA gene and produced surfactin mostly as four homologues (C13 to C16). Moreover, in 2 strains (KP7, T'-1) simultaneous co-production of 3 biosurfactants: surfactin, iturin and fengycin was observed. Additionally, it was found out that isolate identified as Bacillus subtilis ssp. subtilis (KP7), beside LPs co-production, synthesizes surfactin with the efficiency much higher than other studied strains (40·2 mg l(-1) ) and with the yield ranging from 0·8 to 8·3 mg l(-1) . CONCLUSION We showed that the combined methodology based on PCR and LC-MS/MS technique is an optimal tool for the detection of genes encoding enzymes involved in biosurfactant synthesis as well as their products, e.g. surfactin, iturin and fengycin. This approach improves the screening and the identification of environmental Bacillus co-producing biosurfactants-stimulating and facilitating the development of this area of science. SIGNIFICANCE AND IMPACT OF THE STUDY The findings of this work will help to improve screening of biosurfactant producers. Discovery of novel biosurfactants and biosurfactants co-production ability has shed light on their new application fields and for the understanding of their interactions and properties.
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Affiliation(s)
- G Płaza
- Department of Environmental Microbiology, Institute for Ecology of Industrial Areas, Katowice, Poland
| | - J Chojniak
- Department of Environmental Microbiology, Institute for Ecology of Industrial Areas, Katowice, Poland
| | - K Rudnicka
- Laboratory of Gastroimmunology, Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - K Paraszkiewicz
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - P Bernat
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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10
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Honma M, Tanaka K, Konno K, Tsuge K, Okuno T, Hashimoto M. Termination of the structural confusion between plipastatin A1 and fengycin IX. Bioorg Med Chem 2012; 20:3793-8. [PMID: 22609073 DOI: 10.1016/j.bmc.2012.04.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 11/30/2022]
Abstract
Plipastatin A1 and fengycin IX were experimentally proven to be identical compounds, while these had been considered as diastereomers due to the permutation of the enantiomeric pair of Tyr in most papers. The (1)H NMR spectrum changed to become quite similar to that of plipastatin A1, when the sample which provided resembled spectrum of fengycin IX was treated with KOAc followed by LH-20 gel filtration. Our structural investigations disclosed that the structures of these molecules should be settled into that of plipastatin A1 by Umezawa (L-Tyr4 and D-Tyr10).
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Affiliation(s)
- Miho Honma
- Department of Agriculture and Bioscience, Hirosaki University, 3-Bunkyo-cho, Hirosaki 036-8561, Japan
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Batool M, Khalid MH, Hassan MN, Fauzia Yusuf H. Homology modeling of an antifungal metabolite plipastatin synthase from the Bacillus subtilis 168. Bioinformation 2011; 7:384-7. [PMID: 22347779 PMCID: PMC3280437 DOI: 10.6026/97320630007384] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 12/06/2011] [Indexed: 12/02/2022] Open
Abstract
Lipopeptides have a widespread role in different pathways of Bacillus subtilis; they can act as antagonists, spreader and immunostimulators. Plipastatin, an antifungal antibiotic, is one of the most important lipopeptide nonribosomly produced by Bacillus subtilis. Plipastatin has strong fungitoxic activity and involve in inhibition of phospholipase A2 and biofilm formation. For better understanding of the molecule and pathway by which lipopeptide plipastatin is synthesized, we present a computationally predicted structure of plipastatin using homology modeling. Primary and secondary structure analysis suggested that ppsD is a hydrophilic protein containing a significant proportion of alpha helices, and subcellular localization predictions suggested it is a cytoplasmic protein. The tertiary structure of protein (plipastatin synthase subunit D) was predicted by homology modeling. The results suggest a flexible structure which is also an important characteristic of active enzymes enabling them to bind various cofactors and substrates for proper functioning. Validation of 3D structure was done using Ramachandran plot ProsA-web and QMEAN score.This predicted information will help in better understanding of mechanisms underlying plipastatin synthase subunit D synthesis. Plipastatin can be used as an inhibitor of various fungal diseases in plants.
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Affiliation(s)
- Maria Batool
- Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Islamabad, Pakistan
- Department of Bioinformatics & Biotechnology, Government College University, Faisalabad, Pakistan
| | - Mohammad Hassan Khalid
- Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Islamabad, Pakistan
| | - Muhammad Nadeem Hassan
- Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Islamabad, Pakistan
| | - Hafeez Fauzia Yusuf
- Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Islamabad, Pakistan
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Production and characterization of fengycin by indigenous Bacillus subtilis F29-3 originating from a potato farm. Int J Mol Sci 2010; 11:4526-38. [PMID: 21151454 PMCID: PMC3000098 DOI: 10.3390/ijms11114526] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 10/24/2010] [Accepted: 11/10/2010] [Indexed: 11/30/2022] Open
Abstract
Fengycin, a lipopeptide biosurfactant, was produced by indigenous Bacillus subtilis F29-3 isolated from a potato farm. Although inhibiting the growth of filamentous fungi, the fengycin is ineffective against yeast and bacteria. In this study, fengycin was isolated from fermentation broth of B. subtilis F29-3 via acidic precipitation (pH 2.0 with 5 N HCl) followed by purification using ultrafiltration and nanofiltration. The purified fengycin product was characterized qualitatively by using fast atom bombardment-mass spectrometer, Fourier transform infrared spectrometer, ultraviolet-visible spectrophotometer, 13C-nuclear magnetic resonance spectrometer and matrix assisted laser desorption ionization-time of flight, followed by quantitative analysis using reversed-phase HPLC system. This study also attempted to increase fengycin production by B. subtilis F29-3 in order to optimize the fermentation medium constituents. The fermentation medium composition was optimized using response surface methodology (RSM) to increase fengycin production from B. subtilis F29-3. According to results of the five-level four-factor central composite design, the composition of soybean meal, NaNO3, MnSO4·4H2O, mannitol-mannitol, soybean meal-mannitol, soybean meal-soybean meal, NaNO3-NaNO3 and MnSO4·4H2O-MnSO4·4H2O significantly affected production. The simulation model produced a coefficient of determination (R2) of 0.9043, capable of accounting for 90.43% variability of the data. Results of the steepest ascent and central composite design indicated that 26.2 g/L of mannitol, 21.9 g/L of soybean meal, 3.1 g/L of NaNO3 and 0.2 g/L of MnSO4·4H2O represented the optimal medium composition, leading to the highest production of fengycin. Furthermore, the optimization strategy increased the fengycin production from 1.2 g/L to 3.5 g/L.
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Activation of the promoter of the fengycin synthetase operon by the UP element. J Bacteriol 2009; 191:4615-23. [PMID: 19447911 DOI: 10.1128/jb.00255-09] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis F29-3 produces an antifungal peptidic antibiotic that is synthesized nonribosomally by fengycin synthetases. Our previous work established that the promoter of the fengycin synthetase operon is located 86 nucleotides upstream of the translational initiation codon of fenC. This investigation involved transcriptional fusions with a DNA fragment that contains the region between positions -105 and +80 and determined that deleting the region between positions -55 and -42 reduces the promoter activity by 64.5%. Transcriptional fusions in the B. subtilis DB2 chromosome also indicated that mutating the sequence markedly reduces the promoter activity. An in vitro transcription analysis confirmed that the transcription is inefficient when the sequence in this region is mutated. Electrophoretic mobility shift and footprinting analyses demonstrated that the C-terminal domain of the RNA polymerase alpha subunit binds to the region between positions -55 and -39. These results indicated that the sequence is an UP element. Finally, this UP element is critical for the production of fengycin, since mutating the UP sequence in the chromosome of B. subtilis F29-3 reduces the transcription of the fen operon by 85% and prevents the cells from producing enough fengycin to suppress the germination of Paecilomyces variotii spores on agar plates.
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Abstract
This review describes secondary metabolites that have been shown to be synthesized by symbiotic bacteria, or for which this possibility has been discussed. It includes 365 references.
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Affiliation(s)
- Jörn Piel
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany.
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Ramarathnam R, Bo S, Chen Y, Fernando WGD, Xuewen G, de Kievit T. Molecular and biochemical detection of fengycin- and bacillomycin D-producing Bacillus spp., antagonistic to fungal pathogens of canola and wheat. Can J Microbiol 2007; 53:901-11. [PMID: 17898845 DOI: 10.1139/w07-049] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacillus species are well known for their ability to control plant diseases through various mechanisms, including the production of secondary metabolites. Bacillus subtilis DFH08, an antagonist of Fusarium graminearum , and other Bacillus spp. that are antagonists of common fungal pathogens of canola were screened for peptide synthetase biosynthetic genes of fengycin and bacillomycin D. Specific polymerase chain reaction (PCR) primers identified B. subtilis strains DFH08 and 49 for the presence of the fenD gene of the fengycin operon. Bacillus cereus DFE4, Bacillus amyloliquefaciens strains DFE16 and BS6, and B. subtilis 49 were identified for the presence of the bamC gene of the bacillomycin D synthetase biosynthetic operon. Both fengycin and bacillomycin D were detected in the culture extract of strain Bs49, characterized through MALDI–TOF–MS (matrix-assisted laser desorption ionization – time of flight – mass spectrometry), and their antifungal activities demonstrated against F. graminearum and Sclerotinia sclerotiorum . This study designed and used specific PCR primers for the detection of potential fengycin- and bacillomycin D-producing bacterial antagonists and confirmed the molecular detection with the biochemical detection of the corresponding antibiotic produced. This is also the first report of a B. cereus strain (DFE4) to have bacillomycin D biosynthetic genes. Bacteria that synthesize these lipopeptides could act as natural genetic sources for genetic engineering of the peptide synthetases for production of novel peptides.
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Affiliation(s)
- Rajesh Ramarathnam
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Wu CY, Chen CL, Lee YH, Cheng YC, Wu YC, Shu HY, Götz F, Liu ST. Nonribosomal Synthesis of Fengycin on an Enzyme Complex Formed by Fengycin Synthetases. J Biol Chem 2007; 282:5608-16. [PMID: 17182617 DOI: 10.1074/jbc.m609726200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fengycin, a lipopeptidic antibiotic, is synthesized nonribosomally by five fengycin synthetases (FenC, FenD, FenE, FenA, and FenB) in Bacillus subtilis F29-3. This work demonstrates that these fengycin synthetases interlock to form a chain, which coils into a 14.5-nm structure. In this chain, fengycin synthetases are linked in the order FenC-FenD-FenE-FenA-FenB by interactions between the C-terminal region of an upstream enzyme and the N-terminal region of its downstream partner enzyme, with their amino acid activation modules arranged colinearly with the amino acids in fengycin. This work also reveals that fengycin is synthesized on this fengycin synthetase chain, explaining how fengycin is synthesized efficiently and accurately. The results from this investigation demonstrate that forming a peptide synthetase complex is crucial to nonribosomal peptide synthesis.
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Affiliation(s)
- Cheng-Yeu Wu
- Molecular Genetics Laboratory, Department of Microbiology and Immunology, Chang-Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan 333, Taiwan
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