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Chin WC, Zhou YZ, Wang HY, Feng YT, Yang RY, Huang ZF, Yang YL. Bacterial polyynes uncovered: a journey through their bioactive properties, biosynthetic mechanisms, and sustainable production strategies. Nat Prod Rep 2024; 41:977-989. [PMID: 38284321 DOI: 10.1039/d3np00059a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Covering: up to 2023Conjugated polyynes are natural compounds characterized by alternating single and triple carbon-carbon bonds, endowing them with distinct physicochemical traits and a range of biological activities. While traditionally sourced mainly from plants, recent investigations have revealed many compounds originating from bacterial strains. This review synthesizes current research on bacterial-derived conjugated polyynes, delving into their biosynthetic routes, underscoring the variety in their molecular structures, and examining their potential applications in biotechnology. Additionally, we outline future directions for metabolic and protein engineering to establish more robust and stable platforms for their production.
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Affiliation(s)
- Wei-Chih Chin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yang-Zhi Zhou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Hao-Yung Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Department of Wood Based Materials and Design, National Chiayi University, Chiayi, Taiwan
| | - Yu-Ting Feng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Ru-Yin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Zih-Fang Huang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
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Yang Y, Wang H, Tu J, Li Y, Guan H. Comprehensive genomic analysis of Burkholderia arboris PN-1 reveals its biocontrol potential against Fusarium solani-induced root rot in Panax notoginseng. Curr Genet 2024; 70:4. [PMID: 38555312 DOI: 10.1007/s00294-024-01288-4] [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: 12/19/2023] [Revised: 02/17/2024] [Accepted: 02/23/2024] [Indexed: 04/02/2024]
Abstract
Panax notoginseng (Burkill) F.H. Chen, a valuable traditional Chinese medicine, faces significant yield and quality challenges stemming from root rot primarily caused by Fusarium solani. Burkholderia arboris PN-1, isolated from the rhizosphere soil of P. notoginseng, demonstrated a remarkable ability to inhibit the growth of F. solani. This study integrates phenotypic, phylogenetic, and genomic analyses to enhance our understanding of the biocontrol mechanisms employed by B. arboris PN-1. Phenotype analysis reveals that B. arboris PN-1 effectively suppresses P. notoginseng root rot both in vitro and in vivo. The genome of B. arboris PN-1 comprises three circular chromosomes (contig 1: 3,651,544 bp, contig 2: 1,355,460 bp, and contig 3: 3,471,056 bp), with a 66.81% GC content, housing 7,550 protein-coding genes. Notably, no plasmids were detected. Phylogenetic analysis places PN-1 in close relation to B. arboris AU14372, B. arboris LMG24066, and B. arboris MEC_B345. Average nucleotide identity (ANI) values confirm the PN-1 classification as B. arboris. Comparative analysis with seven other B. arboris strains identified 4,628 core genes in B. arboris PN-1. The pan-genome of B. arboris appears open but may approach closure. Whole-genome sequencing revealed 265 carbohydrate-active enzymes and identified 9 gene clusters encoding secondary metabolites. This comprehensive investigation enhances our understanding of B. arboris genomes, paving the way for their potential as effective biocontrol agents against fungal plant pathogens in the future.
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Affiliation(s)
- Yun Yang
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Wenshan Academy of Agricultural Sciences, Wenshan, 663000, Yunnan, China
| | - Haoji Wang
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Jielei Tu
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Yan Li
- Yunnan Provincial Rural Energy Management Station, Kunming, 650233, Yunnan, China
| | - Huilin Guan
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China.
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China.
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Suenaga M, Katayama N, Kitamura K, Kai K. Structures and Biosynthesis of Caryoynencins, Unstable Bacterial Polyynes from Pseudomonas protegens Recombinant Expressing the cayG Gene. J Org Chem 2023; 88:16280-16291. [PMID: 37947517 DOI: 10.1021/acs.joc.3c01789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Bacteria in certain genera can produce "bacterial polyynes" that contain a conjugated C≡C bond starting from a terminal alkyne. Protegenin A is a derivative of octadecanoic acid that contains an ene-tetrayne moiety. It was discovered in Pseudomonas protegens Cab57 and exhibits strong antioomycete and moderate antifungal activity. By introducing cayG, a cytochrome P450 gene from Burkholderia caryophylli, into P. protegens Cab57, protegenin A was converted into more complex polyynes, caryoynencins A-E. A purification method that minimized the degradation and isomerization of caryoynencins was established. For the first time, as far as we know, the 1H and 13C{1H} NMR signals of caryoynencins were completely assigned by analyzing the NMR data of the isolated compounds and protegenin A enriched with [1-13C]- or [2-13C]-acetate. Through the structural analysis of caryoynencins D/E and bioconversion experiments, we observed that CayG constructs the allyl alcohol moiety of caryoynencins A-C through sequential hydroxylation, dehydration, and hydroxylation. The recombinant strain exhibited a stronger antioomycete activity compared to the wild-type strain. This paper proposes a stable purification and structural determination method for various bacterial polyynes, and P. protegens Cab57 holds promise as an engineering host for the production of biologically active polyynes.
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Affiliation(s)
- Mayuna Suenaga
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Naoka Katayama
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Kokoro Kitamura
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Kenji Kai
- Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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Bai X, Chen H, Ren X, Zhong L, Wang X, Ji X, Zhang Y, Wang Y, Bian X. Heterologous Biosynthesis of Complex Bacterial Natural Products in Burkholderia gladioli. ACS Synth Biol 2023; 12:3072-3081. [PMID: 37708405 DOI: 10.1021/acssynbio.3c00389] [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] [Indexed: 09/16/2023]
Abstract
Bacterial natural products (NPs) are an indispensable source of drugs and biopesticides. Heterologous expression is an essential method for discovering bacterial NPs and the efficient biosynthesis of valuable NPs, but the chassis for Gram-negative bacterial NPs remains inadequate. In this study, we built a Burkholderiales mutant Burkholderia gladioli Δgbn::attB by introducing an integrated site (attB) to inactivate the native gladiolin (gbn) biosynthetic gene cluster, which stabilizes large foreign gene clusters and reduces the native metabolite profile. The growth and successful heterologous production of high-value NPs such as phylogenetically close Burkholderiales-derived antitumor polyketides (PKs) rhizoxins, phylogenetically distant Gammaproteobacteria-derived anti-MRSA (methicillin-resistant Staphylococcus aureus) antibiotics WAP-8294As, and Deltaproteobacteria-derived antitumor PKs disorazols demonstrate that this strain is a potential chassis for Gram-negative bacterial NPs. We further improved the yields of WAP-8294As through promoter insertions and precursor pathway overexpression based on heterologous expression in this strain. This study provides a robust bacterial chassis for genome mining, efficient production, and molecular engineering of bacterial NPs.
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Affiliation(s)
- Xianping Bai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Hanna Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiangmei Ren
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lin Zhong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xingyan Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoqi Ji
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Yan Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266100, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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Webster G, Mullins AJ, Petrova YD, Mahenthiralingam E. Polyyne-producing Burkholderia suppress Globisporangium ultimum damping-off disease of Pisum sativum (pea). Front Microbiol 2023; 14:1240206. [PMID: 37692405 PMCID: PMC10485841 DOI: 10.3389/fmicb.2023.1240206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Extensive crop losses are caused by oomycete and fungal damping-off diseases. Agriculture relies heavily on chemical pesticides to control disease, but due to safety concerns multiple agents have been withdrawn. Burkholderia were successfully used as commercial biopesticides because of their fungicidal activity and plant protective traits. However, their potential for opportunistic pathogenicity led to a moratorium on their registration as biopesticides. Subsequently, Burkholderia were shown to produce multiple specialised metabolites including potent antimicrobial polyynes. Cepacin A, a polyyne produced by Burkholderia ambifaria biopesticide strains was shown to be an important metabolite for the protection of germinating peas against Globisporangium ultimum (formerly Pythium) damping-off disease. Recently, there has been an expansion in bacterial polyyne discovery, with the metabolites and their biosynthetic gene pathways found in several bacterial genera including Burkholderia, Collimonas, Trinickia, and Pseudomonas. To define the efficacy of these bacterial polyyne producers as biopesticidal agents, we systematically evaluated metabolite production, in vitro microbial antagonism, and G. ultimum biocontrol across a panel of 30 strains representing four bacterial genera. In vitro polyyne production and antimicrobial activity was demonstrated for most strains, but only Burkholderia polyyne producers were protective within the in vivo G. ultimum damping-off pea protection model. B. ambifaria was the most effective cepacin-expressing biopesticide, and despite their known potential for plant pathogenicity Burkholderia gladioli and Burkholderia plantarii were uniquely shown to be protective as caryoynencin-producing biopesticides. In summary, Burkholderia are effective biopesticides due to their suite of antimicrobials, but the ability to deploy polyyne metabolites, caryoynencin and cepacin, is strain and species dependent. Graphical Abstract.
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Roca A, Matilla MA. Microbial antibiotics take the lead in the fight against plant pathogens. Microb Biotechnol 2023; 16:28-33. [PMID: 36464960 PMCID: PMC9803328 DOI: 10.1111/1751-7915.14185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
The plant microbiome is essential for plant fitness and health. Antibiotics produced by plant-associated bacteria have been shown to play an important role in protecting plant hosts against phytopathogens. Here, we highlight the strong biotechnological potential of (i) antibiotic producing plant-associated bacteria as biocontrol agents and (ii) the heterologous expression of antibiotic biosynthetic gene clusters in non-pathogenic plant-associated bacteria. We also provide the complete list of the active substances based on bacteria, fungi, and viruses currently approved or pending approval in the European Union, as an indication of the significant emergence and biotechnological applicability of biopesticides. Further progress in this field of research will enable the development of novel biopesticides for the biocontrol of agricultural pests.
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Affiliation(s)
- Amalia Roca
- Department of Microbiology, Facultad de FarmaciaCampus Universitario de Cartuja, Universidad de GranadaGranadaSpain
| | - Miguel A. Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del ZaidínConsejo Superior de Investigaciones CientíficasGranadaSpain
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Matilla MA, Monson RE, Murphy A, Schicketanz M, Rawlinson A, Duncan C, Mata J, Leeper F, Salmond GPC. Solanimycin: Biosynthesis and Distribution of a New Antifungal Antibiotic Regulated by Two Quorum-Sensing Systems. mBio 2022; 13:e0247222. [PMID: 36214559 PMCID: PMC9765074 DOI: 10.1128/mbio.02472-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/20/2022] Open
Abstract
The increasing emergence of drug-resistant fungal infections has necessitated a search for new compounds capable of combating fungal pathogens of plants, animals, and humans. Microorganisms represent the main source of antibiotics with applicability in agriculture and in the clinic, but many aspects of their metabolic potential remain to be explored. This report describes the discovery and characterization of a new antifungal compound, solanimycin, produced by a hybrid polyketide/nonribosomal peptide (PKS/NRPS) system in Dickeya solani, the enterobacterial pathogen of potato. Solanimycin was active against a broad range of plant-pathogenic fungi of global economic concern and the human pathogen Candida albicans. The genomic cluster responsible for solanimycin production was defined and analyzed to identify the corresponding biosynthetic proteins, which include four multimodular PKS/NRPS proteins and several tailoring enzymes. Antifungal production in D. solani was enhanced in response to experimental conditions found in infected potato tubers and high-density fungal cultures. Solanimycin biosynthesis was cell density dependent in D. solani and was controlled by both the ExpIR acyl-homoserine lactone and Vfm quorum-sensing systems of the bacterial phytopathogen. The expression of the solanimycin cluster was also regulated at the post-transcriptional level, with the regulator RsmA playing a major role. The solanimycin biosynthetic cluster was conserved across phylogenetically distant bacterial genera, and multiple pieces of evidence support that the corresponding gene clusters were acquired by horizontal gene transfer. Given its potent broad-range antifungal properties, this study suggests that solanimycin and related molecules may have potential utility for agricultural and clinical exploitation. IMPORTANCE Fungal infections represent a major clinical, agricultural, and food security threat worldwide, which is accentuated due to the difficult treatment of these infections. Microorganisms represent a prolific source of antibiotics, and current data support that this enormous biosynthetic potential has been scarcely explored. To improve the performance in the discovery of novel antimicrobials, there is a need to diversify the isolation niches for new antibiotic-producing microorganisms as well as to scrutinize novel phylogenetic positions. With the identification of the antifungal antibiotic solanimycin in a broad diversity of phytopathogenic Dickeya spp., we provide further support for the potential of plant-associated bacteria for the biosynthesis of novel antimicrobials. The complex regulatory networks involved in solanimycin production reflect the high metabolic cost of bacterial secondary metabolism. This metabolic regulatory control makes many antibiotics cryptic under standard laboratory conditions, and mimicking environmental conditions, as shown here, is a strategy to activate cryptic antibiotic clusters.
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Affiliation(s)
- Miguel A. Matilla
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Rita E. Monson
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Annabel Murphy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Muriel Schicketanz
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alison Rawlinson
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Caia Duncan
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Finian Leeper
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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Petrova YD, Mahenthiralingam E. Discovery, mode of action and secretion of Burkholderia sensu lato key antimicrobial specialised metabolites. Cell Surf 2022; 8:100081. [PMID: 36277081 PMCID: PMC9579380 DOI: 10.1016/j.tcsw.2022.100081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Burkholderia sensu lato bacteria have genomes rich in biosynthetic gene clusters (BGCs) encoding for multiple bioactive specialised metabolites. Diverse classes of antimicrobial natural products have been isolated from Burkholderia, including polyynes, shikimate pathway derivatives, polyketides, non-ribosomal peptides and hybrid polyketide non-ribosomal peptides. We highlight examples of Burkholderia metabolites, overviewing their biosynthesis, bioactivity, mechanisms of action and secretion.
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