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Paulo BS, Recchia MJJ, Lee S, Fergusson CH, Romanowski SB, Hernandez A, Krull N, Liu DY, Cavanagh H, Bos A, Gray CA, Murphy BT, Linington RG, Eustaquio AS. Discovery of megapolipeptins by genome mining of a Burkholderiales bacteria collection. Chem Sci 2024; 15:d4sc03594a. [PMID: 39309087 PMCID: PMC11411415 DOI: 10.1039/d4sc03594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 09/11/2024] [Indexed: 09/25/2024] Open
Abstract
Burkholderiales bacteria have emerged as a promising source of structurally diverse natural products that are expected to play important ecological and industrial roles. This order ranks in the top three in terms of predicted natural product diversity from available genomes, warranting further genome sequencing efforts. However, a major hurdle in obtaining the predicted products is that biosynthetic genes are often 'silent' or poorly expressed. Here we report complementary strain isolation, genomics, metabolomics, and synthetic biology approaches to enable natural product discovery. First, we built a collection of 316 rhizosphere-derived Burkholderiales strains over the course of five years. We then selected 115 strains for sequencing using the mass spectrometry pipeline IDBac to avoid strain redundancy. After predicting and comparing the biosynthetic potential of each strain, a biosynthetic gene cluster that was silent in the native Paraburkholderia megapolitana and Paraburkholderia acidicola producers was cloned and activated by heterologous expression in a Burkholderia sp. host, yielding megapolipeptins A and B. Megapolipeptins are unusual polyketide, nonribosomal peptide, and polyunsaturated fatty acid hybrids that show low structural similarity to known natural products, highlighting the advantage of our Burkholderiales genomics-driven and synthetic biology-enabled pipeline to discover novel natural products.
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Affiliation(s)
- Bruno S Paulo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | | | - Sanghoon Lee
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Claire H Fergusson
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Sean B Romanowski
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Antonio Hernandez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Nyssa Krull
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Dennis Y Liu
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Hannah Cavanagh
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Allyson Bos
- Department of Biological Sciences, University of New Brunswick Saint John New Brunswick E2L 4L5 Canada
| | - Christopher A Gray
- Department of Biological Sciences, University of New Brunswick Saint John New Brunswick E2L 4L5 Canada
| | - Brian T Murphy
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University Burnaby BC V5H 1S6 Canada
| | - Alessandra S Eustaquio
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
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2
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Liu A, Phillips K, Jia J, Deng P, Zhang D, Chang S, Lu SE. Development of a qPCR detection approach for pathogenic Burkholderia cenocepacia associated with fresh vegetables. Food Microbiol 2023; 115:104333. [PMID: 37567623 DOI: 10.1016/j.fm.2023.104333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 08/13/2023]
Abstract
Natural environment serves as a reservoir for Burkholderia cepacia complex organisms, including the highly transmissible opportunistic human pathogen B. cenocepacia. Currently, there is a lack of an effective and quantitative method for B. cenocepacia detection in fresh food and other environmental niches. A quantitative real-time PCR (qPCR) detection method for B. cenocepacia bacteria was established in this study and validated using artificially inoculated fresh vegetable samples. Genome-wide comparative methods were applied to identify target regions for the design of species-specific primers. Assay specificity was measured with 12 strains of closely related Burkholderia bacteria and demonstrated the primer pair BCF6/R6 were 100% specific for detection of B. cenocepacia. The described qPCR assay evaluated B. cenocepacia with a 2 pg μl-1 limit of detection and appropriate linearity (R2 = 0.999). In 50 samples of experimentally infected produce (lettuce, onion, and celery), the assay could detect B. cenocepacia as low as 2.6 × 102 cells in each sample equal to 1 g. The established qPCR method quantitatively detects B. cenocepacia with high sensitivity and specificity, making it a promising technique for B. cenocepacia detection and epidemiological research on B. cepacia complex organisms from fresh vegetables.
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Affiliation(s)
- Aixin Liu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA; College of Plant Protection, Shandong Agricultural University, Shandong, 271018, China
| | - Kate Phillips
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Jiayuan Jia
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Peng Deng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Dunhua Zhang
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Sam Chang
- Coastal Research and Extension Center, Seafood Processing Laboratory, Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Pascagoula, MS, 39567, USA
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA.
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3
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Wang D, Luo WZ, Zhang DD, Li R, Kong ZQ, Song J, Dai XF, Alkan N, Chen JY. Insights into the Biocontrol Function of a Burkholderia gladioli Strain against Botrytis cinerea. Microbiol Spectr 2023; 11:e0480522. [PMID: 36861984 PMCID: PMC10101029 DOI: 10.1128/spectrum.04805-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/10/2023] [Indexed: 03/03/2023] Open
Abstract
Pathogenic fungi are the main cause of yield loss and postharvest loss of crops. In recent years, some antifungal microorganisms have been exploited and applied to prevent and control pathogenic fungi. In this study, an antagonistic bacteria KRS027 isolated from the soil rhizosphere of a healthy cotton plant from an infected field was identified as Burkholderia gladioli by morphological identification, multilocus sequence analysis, and typing (MLSA-MLST) and physiobiochemical examinations. KRS027 showed broad spectrum antifungal activity against various phytopathogenic fungi by secreting soluble and volatile compounds. KRS027 also has the characteristics of plant growth promotion (PGP) including nitrogen fixation, phosphate, and potassium solubilization, production of siderophores, and various enzymes. KRS027 is not only proven safe by inoculation of tobacco leaves and hemolysis test but also could effectively protect tobacco and table grapes against gray mold disease caused by Botrytis cinerea. Furthermore, KRS027 can trigger plant immunity by inducing systemic resistance (ISR) activated by salicylic acid- (SA), jasmonic acid- (JA), and ethylene (ET)-dependent signaling pathways. The extracellular metabolites and volatile organic compounds (VOCs) of KRS027 affected the colony extension and hyphal development by downregulation of melanin biosynthesis and upregulation of vesicle transport, G protein subunit 1, mitochondrial oxidative phosphorylation, disturbance of autophagy process, and degrading the cell wall of B. cinerea. These results demonstrated that B. gladioli KRS027 would likely become a promising biocontrol and biofertilizer agent against fungal diseases, including B. cinerea, and would promote plant growth. IMPORTANCE Searching the economical, eco-friendly and efficient biological control measures is the key to protecting crops from pathogenic fungi. The species of Burkholderia genus are widespread in the natural environment, of which nonpathogenic members have been reported to have great potential for biological control agents and biofertilizers for agricultural application. Burkholderia gladioli strains, however, need more study and application in the control of pathogenic fungi, plant growth promotion, and induced systemic resistance (ISR). In this study, we found that a B. gladioli strain KRS027 has broad spectrum antifungal activity, especially in suppressing the incidence of gray mold disease caused by Botrytis cinerea, and can stimulate plant immunity response via ISR activated by salicylic acid- (SA), jasmonic acid- (JA), and ethylene (ET)-dependent signaling pathways. These results indicate that B. gladioli KRS027 may be a promising biocontrol and biofertilizer microorganism resource in agricultural applications.
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Affiliation(s)
- Dan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, China
| | - Wan-Zhen Luo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Xinjiang Agricultural University, Urumqi, China
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, China
| | - Zhi-Qiang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, China
| | - Noam Alkan
- Department of Postharvest Science, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, China
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Rodríguez-Cisneros M, Morales-Ruíz LM, Salazar-Gómez A, Rojas-Rojas FU, Estrada-de los Santos P. Compilation of the Antimicrobial Compounds Produced by Burkholderia Sensu Stricto. Molecules 2023; 28:1646. [PMID: 36838633 PMCID: PMC9958762 DOI: 10.3390/molecules28041646] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
Due to the increase in multidrug-resistant microorganisms, the investigation of novel or more efficient antimicrobial compounds is essential. The World Health Organization issued a list of priority multidrug-resistant bacteria whose eradication will require new antibiotics. Among them, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae are in the "critical" (most urgent) category. As a result, major investigations are ongoing worldwide to discover new antimicrobial compounds. Burkholderia, specifically Burkholderia sensu stricto, is recognized as an antimicrobial-producing group of species. Highly dissimilar compounds are among the molecules produced by this genus, such as those that are unique to a particular strain (like compound CF66I produced by Burkholderia cepacia CF-66) or antimicrobials found in a number of species, e.g., phenazines or ornibactins. The compounds produced by Burkholderia include N-containing heterocycles, volatile organic compounds, polyenes, polyynes, siderophores, macrolides, bacteriocins, quinolones, and other not classified antimicrobials. Some of them might be candidates not only for antimicrobials for both bacteria and fungi, but also as anticancer or antitumor agents. Therefore, in this review, the wide range of antimicrobial compounds produced by Burkholderia is explored, focusing especially on those compounds that were tested in vitro for antimicrobial activity. In addition, information was gathered regarding novel compounds discovered by genome-guided approaches.
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Affiliation(s)
- Mariana Rodríguez-Cisneros
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala S/N Col. Santo Tomás Alc. Miguel Hidalgo, Ciudad de México 11340, Mexico
| | - Leslie Mariana Morales-Ruíz
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala S/N Col. Santo Tomás Alc. Miguel Hidalgo, Ciudad de México 11340, Mexico
| | - Anuar Salazar-Gómez
- Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León UNAM), Blvd. UNAM 2011, León, Guanajuato 37684, Mexico
| | - Fernando Uriel Rojas-Rojas
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León UNAM), Blvd. UNAM 2011, León, Guanajuato 37684, Mexico
- Laboratorio Nacional PlanTECC, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León UNAM), Blvd. UNAM 2011, León, Guanajuato 37684, Mexico
| | - Paulina Estrada-de los Santos
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala S/N Col. Santo Tomás Alc. Miguel Hidalgo, Ciudad de México 11340, Mexico
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Doty SL, Joubert PM, Firrincieli A, Sher AW, Tournay R, Kill C, Parikh SS, Okubara P. Potential Biocontrol Activities of Populus Endophytes against Several Plant Pathogens Using Different Inhibitory Mechanisms. Pathogens 2022; 12:pathogens12010013. [PMID: 36678361 PMCID: PMC9862643 DOI: 10.3390/pathogens12010013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The plant microbiome can be used to bolster plant defense against abiotic and biotic stresses. Some strains of endophytes, the microorganisms within plants, can directly inhibit the growth of plant fungal pathogens. A previously isolated endophyte from wild Populus (poplar), WPB of the species Burkholderia vietnamiensis, had robust in vitro antifungal activity against pathogen strains that are highly virulent and of concern to Pacific Northwest agriculture: Rhizoctonia solani AG-8, Fusarium culmorum 70110023, and Gaemannomyces graminis var. tritici (Ggt) ARS-A1, as well as activity against the oomycete, Pythium ultimum 217. A direct screening method was developed for isolation of additional anti-fungal endophytes from wild poplar extracts. By challenging pathogens directly with dilute extracts, eleven isolates were found to be inhibitory to at least two plant pathogen strains and were therefore chosen for further characterization. Genomic analysis was conducted to determine if these endophyte strains harbored genes known to be involved in antimicrobial activities. The newly isolated Bacillus strains had gene clusters for production of bacillomycin, fengicyn, and bacillibactin, while the gene cluster for the synthesis of sessilin, viscosin and tolaasin were found in the Pseudomonas strains. The biosynthesis gene cluster for occidiofungin (ocf) was present in the Burkholderia vietnamiensis WPB genome, and an ocf deletion mutant lost inhibitory activity against 3 of the 4 pathogens. The new isolates lacked the gene cluster for occidiofungin implying they employ different modes of action. Other symbiotic traits including nitrogen fixation, phosphate solubilization, and the production of auxins and siderophores were investigated. Although it will be necessary to conduct in vivo tests of the candidates with pathogen-infected agricultural crops, the wild poplar tree microbiome may be a rich source of beneficial endophyte strains with potential for biocontrol applications against a variety of pathogens and utilizing varying modes of action.
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Affiliation(s)
- Sharon L. Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Correspondence:
| | - Pierre M. Joubert
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Andrea Firrincieli
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy
| | - Andrew W. Sher
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
| | - Robert Tournay
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
| | - Carina Kill
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Native Roots School, Taos, NM 87571, USA
| | - Shruti S. Parikh
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Department of Food Science and Technology, University of California, Davis, CA 95616, USA
| | - Patricia Okubara
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
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Chen X, Qu S, Luo X, Lu SE, Liu Y, Li H, Hou L, Lin J, Jiang N, Ma L. PafS Containing GGDEF-Domain Regulates Life Activities of Pseudomonas glycinae MS82. Microorganisms 2022; 10:microorganisms10122342. [PMID: 36557595 PMCID: PMC9781394 DOI: 10.3390/microorganisms10122342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Cyclic dimeric guanosine monophosphate (c-di-GMP) is synthesized by diguanylate cyclase (DGC) with the GGDEF domain. As a ubiquitous bacterial second messenger, it regulates diverse life-activity phenotypes in some bacteria. Although 38 genes encoding GGDEF-domain-containing proteins have been identified in the genome of the Pseudomonas glycinae strain MS82, whether c-di-GMP functions as a facilitator or repressor of life-activity phenotypes is poorly understood. In this study, one of the 38 genes containing a GGDEF domain in MS82, PafS was investigated to explore its regulatory function in bacterial life activities. The PafS-deletion mutant ΔPafS and reversion mutant PafS-comp were constructed by the method of biparental conjugation and homologous recombination. The life activities of the mutants, such as antifungal activity, biofilm formation ability, polysaccharide content, and motor behavior, were explored. The results showed that all life-activity phenotypes were significantly reduced after knocking out PafS, whereas all were significantly restored to a similar level to that of MS82 after the complementation of PafS. These results suggested that PafS plays an important role in the regulation of a range of cellular activities by c-di-GMP in P. glycinae MS82.
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Affiliation(s)
- Xianyi Chen
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Shaoxuan Qu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xin Luo
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA
| | - Youzhou Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Huiping Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Lijuan Hou
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jinsheng Lin
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Ning Jiang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Lin Ma
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Correspondence: ; Tel.: +86-25-84390875
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Genome mining of Burkholderia ambifaria strain T16, a rhizobacterium able to produce antimicrobial compounds and degrade the mycotoxin fusaric acid. World J Microbiol Biotechnol 2022; 38:114. [PMID: 35578144 DOI: 10.1007/s11274-022-03299-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
Burkholderia ambifaria T16 is a bacterium isolated from the rhizosphere of barley plants that showed a remarkable antifungal activity. This strain was also able to degrade fusaric acid (5-Butylpyridine-2-carboxylic acid) and detoxify this mycotoxin in inoculated barley seedlings. Genes and enzymes responsible for fusaric acid degradation have an important biotechnological potential in the control of fungal diseases caused by fusaric acid producers, or in the biodegradation/bio catalysis processes of pyridine derivatives. In this study, the complete genome of B. ambifaria T16 was sequenced and analyzed to identify genes involved in survival and competition in the rhizosphere, plant growth promotion, fungal growth inhibition, and degradation of aromatic compounds. The genomic analysis revealed the presence of several operons for the biosynthesis of antimicrobial compounds, such as pyrrolnitrin, ornibactin, occidiofungin and the membrane-associated AFC-BC11. These compounds were also detected in bacterial culture supernatants by mass spectrometry analysis. In addition, this strain has multiple genes contributing to its plant growth-promoting profile, including those for acetoin, 2,3-butanediol and indole-3-acetic acid production, siderophores biosynthesis, and solubilisation of organic and inorganic phosphate. A pan-genomic analysis demonstrated that the genome of strain T16 possesses large gene clusters that are absent in the genomes of B. ambifaria reference strains. According to predictions, most of these clusters would be involved in aromatic compounds degradation. One genomic region, encoding flavin-dependent monooxygenases of unknown function, is proposed as a candidate responsible for fusaric acid degradation.
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Xue L, Yang C, Jihong W, Lin L, Yuqiang Z, Zhitong J, Yanxin W, Zhoukun L, Lei F, Cui Z. Biocontrol potential of
Burkholderia
sp.
BV6
against the rice blast fungus
Magnaporthe oryzae. J Appl Microbiol 2022; 133:883-897. [DOI: 10.1111/jam.15605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/28/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Luo Xue
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences Nanjing Agricultural University Nanjing China
| | - Chen Yang
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences Nanjing Agricultural University Nanjing China
| | - Wang Jihong
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences Nanjing Agricultural University Nanjing China
| | - Liu Lin
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences Nanjing Agricultural University Nanjing China
| | - Zhao Yuqiang
- Institute of Botany Jiangsu Province and Chinese Academy of Sciences China
| | - Jiang Zhitong
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences Nanjing Agricultural University Nanjing China
| | - Wang Yanxin
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences Nanjing Agricultural University Nanjing China
| | - Li Zhoukun
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences Nanjing Agricultural University Nanjing China
| | - Fu Lei
- Nanjing Institute for Comprehensive Utilization of Wild Plants Nanjing China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences Nanjing Agricultural University Nanjing China
- Key Laboratory of Biological Interactions and Crop Health Nanjing Agricultural University Nanjing China
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9
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Chu D, Ilyas N, Peng L, Wang X, Wang D, Xu Z, Gao Q, Tan X, Zhang C, Li Y, Yuan Y. Genomic insights on fighting bacterial wilt by a novel Bacillus amyloliquefaciens strain Cas02. Microb Biotechnol 2022; 15:1152-1167. [PMID: 34570959 PMCID: PMC8966013 DOI: 10.1111/1751-7915.13925] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 11/28/2022] Open
Abstract
Bacterial wilt, caused by the Ralstonia solanacearum, can infect several economically important crops. However, the management strategies available to control this disease are limited. Plant growth-promoting rhizobacteria (PGPR) have been considered promising biocontrol agents. In this study, Bacillus amyloliquefaciens strain Cas02 was isolated from the rhizosphere soil of healthy tobacco plants and evaluated for its effect on plant growth promotion and bacterial wilt suppression. Strain Cas02 exhibited several growth-promoting-related features including siderophore production, cellulase activity, protease activity, ammonia production and catalase activity. Moreover, strain Cas02 showed a significant inhibitory growth effect on R. solanacearum, and its active substances were separated and identified to be macrolactin A and macrolactin W by HPLC-DAD-ESI-MS/MS. Both greenhouse and field experiments demonstrated a good performance of Cas02 in plant growth promotion and bacterial wilt suppression. To explore the underlying genetic mechanisms, complete genome sequencing was performed and the gene clusters responsible for antibacterial metabolites expression were identified. Overall, these findings suggest that the strain Cas02 could be a potential biocontrol agent in bacterial wilt management and a source of antimicrobial compounds for further exploitation.
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Affiliation(s)
- Depeng Chu
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Naila Ilyas
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Lijuan Peng
- Yunnan Tobacco Quality Supervision and Test StationKunming650106China
| | - Xiaoqiang Wang
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Dongkun Wang
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Zongchang Xu
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Qiang Gao
- Yishui Agricultural Technology Demonstration ParkLinyi276400China
| | - Xiaolei Tan
- Yishui Agricultural Technology Demonstration ParkLinyi276400China
| | - Chengsheng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Yiqiang Li
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
| | - Yuan Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao266101China
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Jia J, Ford E, Hobbs SM, Baird SM, Lu SE. Occidiofungin Is the Key Metabolite for Antifungal Activity of the Endophytic Bacterium Burkholderia sp. MS455 Against Aspergillus flavus. PHYTOPATHOLOGY 2022; 112:481-491. [PMID: 34433293 DOI: 10.1094/phyto-06-21-0225-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Aflatoxin is a secondary metabolite produced by Aspergillus fungi and presents a major food safety concern globally. Among the available methods for prevention and control of aflatoxin, the application of antifungal bacteria has gained favor in recent years. An endophytic bacterium MS455, isolated from soybean, exhibited broad-spectrum antifungal activity against economically important pathogens, including Aspergillus flavus. MS455 was identified as a strain of Burkholderia based on genomic analysis. Random and site-specific mutations were used in discovery of the genes that share high homology to the ocf gene cluster of Burkholderia contaminans strain MS14, which is responsible for production of the antifungal compound occidiofungin. RNA sequencing analysis demonstrated that ORF1, a homolog to the ambR1 LuxR-type regulatory gene, regulates occidiofungin biosynthesis in MS455. Additionally, 284 differentially expressed genes, including 138 upregulated and 146 downregulated genes, suggesting that, in addition to its role in occidiofungin production, ORF1 is involved in expression of multiple genes, especially those involved in ornibactin biosynthesis. Plate bioassays showed the growth of A. flavus was significantly inhibited by the wild-type strain MS455 as compared with the ORF1 mutant. Similarly, corn kernel assays showed that growth of A. flavus and aflatoxin production were reduced significantly by MS455 as compared with buffer control and the ORF1 mutant. Collectively, the results demonstrated that production of occidiofungin is essential for antifungal activity of the endophytic bacterium MS455. This research has provided insights about antifungal mechanisms of MS455 and development of biological approaches to prevent aflatoxin contamination in plant production.
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Affiliation(s)
- Jiayuan Jia
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Emerald Ford
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Sarah M Hobbs
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Sonya M Baird
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
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Alam K, Islam MM, Gong K, Abbasi MN, Li R, Zhang Y, Li A. In silico genome mining of potential novel biosynthetic gene clusters for drug discovery from Burkholderia bacteria. Comput Biol Med 2022; 140:105046. [PMID: 34864585 DOI: 10.1016/j.compbiomed.2021.105046] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022]
Abstract
As an emerging resource, Gram-negative Burkholderia bacteria were able to produce a wide range of bioactive secondary metabolites with potential therapeutic and biotechnological applications. Genome mining has emerged as an influential platform for screening and pinpointing natural product diversity with the increasing number of Burkholderia genome sequences. Here, for genome mining of potential biosynthetic gene clusters (BGCs) and prioritizing prolific producing Burkholderia strains, we investigated the relationship between species evolution and distribution of main BGC groups using computational analysis of complete genome sequences of 248 Burkholderia species publicly available. We uncovered significantly differential distribution patterns of BGCs in the Burkholderia phyla, even among strains that are genetically very similar. We found various types of BGCs in Burkholderia, including some representative and most common BGCs for biosynthesis of encrypted or known terpenes, non-ribosomal peptides (NRPs) and some hybrid BGCs for cryptic products. We also observed that Burkholderia contain a lot of unspecified BGCs, representing high potentials to produce novel compounds. Analysis of BGCs for RiPPs (Ribosomally synthesized and posttranslationally modified peptides) and a texobactin-like BGC as examples showed wide classification and diversity of RiPP BGCs in Burkholderia at species level and metabolite predication. In conclusion, as the biggest investigation in silico by far on BGCs of the particular genus Burkholderia, our data implied a great diversity of natural products in Burkholderia and BGC distributions closely related to phylogenetic variation, and suggested different or concurrent strategies used to identify new drug molecules from these microorganisms will be important for the selection of potential BGCs and prolific producing strains for drug discovery.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Md Mahmudul Islam
- Department of Microbiology, Rajshahi Institute of Biosciences (RIB), Affi. University of Rajshahi, Rajshahi, 6212, Bangladesh.
| | - Kai Gong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Muhammad Nazeer Abbasi
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Ruijuan Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
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12
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Barrera-Galicia GC, Peniche-Pavía HA, Peña-Cabriales JJ, Covarrubias SA, Vera-Núñez JA, Délano-Frier JP. Metabolic Footprints of Burkholderia Sensu Lato Rhizosphere Bacteria Active against Maize Fusarium Pathogens. Microorganisms 2021; 9:microorganisms9102061. [PMID: 34683382 PMCID: PMC8538949 DOI: 10.3390/microorganisms9102061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Consistent with their reported abundance in soils, several Burkholderia sensu lato strains were isolated from the rhizosphere of maize plants cultivated at different sites in central México. Comparative analysis of their 16S rRNA gene sequences permitted their separation into three distinctive clades, which were further subdivided into six other clusters by their close resemblance to (1) Trinickia dinghuensis; (2) Paraburkholderia kirstenboschensis, P. graminis, P. dilworthii and P. rhynchosiae; (3) B. gladioli; (4) B. arboris; (5) B. contaminans, or (6) B. metallica representative species. Direct confrontation assays revealed that these strains inhibited the growth of pathogenic Fusarium oxysporum f. sp. radicis-lycopersici, and F. verticillioides within a roughly 3-55% inhibition range. The use of a DIESI-based non-targeted mass spectroscopy experimental strategy further indicated that this method is an option for rapid determination of the pathogen inhibitory capacity of Burkholderia sensu lato strains based solely on the analysis of their exometabolome. Furthermore, it showed that the highest anti-fungal activity observed in B. contaminans and B. arboris was associated with a distinctive abundance of certain m/z ions, some of which were identified as components of the ornbactin and pyochelin siderophores. These results highlight the chemical diversity of Burkholderia sensu lato bacteria and suggest that their capacity to inhibit the Fusarium-related infection of maize in suppressive soils is associated with siderophore synthesis.
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Affiliation(s)
- Guadalupe C. Barrera-Galicia
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Héctor A. Peniche-Pavía
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Juan José Peña-Cabriales
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Sergio A. Covarrubias
- Área de Ciencias de la Salud, Ciudad Universitaria Campus Siglo XXI, Universidad Autónoma de Zacatecas, Zacatecas 98160, Zacatecas, Mexico; (S.A.C.); (J.A.V.-N.)
| | - José A. Vera-Núñez
- Área de Ciencias de la Salud, Ciudad Universitaria Campus Siglo XXI, Universidad Autónoma de Zacatecas, Zacatecas 98160, Zacatecas, Mexico; (S.A.C.); (J.A.V.-N.)
| | - John P. Délano-Frier
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
- Correspondence: ; Tel.: +52-462-623-9600
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Bach E, Passaglia LMP, Jiao J, Gross H. Burkholderia in the genomic era: from taxonomy to the discovery of new antimicrobial secondary metabolites. Crit Rev Microbiol 2021; 48:121-160. [PMID: 34346791 DOI: 10.1080/1040841x.2021.1946009] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Species of Burkholderia are highly versatile being found not only abundantly in soil, but also as plants and animals' commensals or pathogens. Their complex multireplicon genomes harbour an impressive number of polyketide synthase (PKS) and nonribosomal peptide-synthetase (NRPS) genes coding for the production of antimicrobial secondary metabolites (SMs), which have been successfully deciphered by genome-guided tools. Moreover, genome metrics supported the split of this genus into Burkholderia sensu stricto (s.s.) and five new other genera. Here, we show that the successful antimicrobial SMs producers belong to Burkholderia s.s. Additionally, we reviewed the occurrence, bioactivities, modes of action, structural, and biosynthetic information of thirty-eight Burkholderia antimicrobial SMs shedding light on their diversity, complexity, and uniqueness as well as the importance of genome-guided strategies to facilitate their discovery. Several Burkholderia NRPS and PKS display unusual features, which are reflected in their structural diversity, important bioactivities, and varied modes of action. Up to now, it is possible to observe a general tendency of Burkholderia SMs being more active against fungi. Although the modes of action and biosynthetic gene clusters of many SMs remain unknown, we highlight the potential of Burkholderia SMs as alternatives to fight against new diseases and antibiotic resistance.
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Affiliation(s)
- Evelise Bach
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Junjing Jiao
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Harald Gross
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
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Biological characteristics and salt-tolerant plant growth-promoting effects of an ACC deaminase-producing Burkholderia pyrrocinia strain isolated from the tea rhizosphere. Arch Microbiol 2021; 203:2279-2290. [PMID: 33644819 DOI: 10.1007/s00203-021-02204-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/30/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
Plant growth-promoting rhizobacteria that produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase can promote plant growth and enhance abiotic stress tolerance. In this study, Burkholderia pyrrocinia strain P10, with an ACC deaminase activity of 33.01-µmol/h/mg protein, was isolated from the tea rhizosphere and identified based on morphological, biochemical, and molecular characteristics. In addition to its ACC deaminase activity at pH 5.0-9.0 and in response to 5% NaCl and 20% polyethylene glycol, strain P10 can also solubilize phosphorus compounds, produce indole-3-acetic acid, and secrete siderophores. Pot experiments revealed that strain P10 can significantly enhance peanut seedling growth under saline conditions (100- and 170-mmol/L NaCl). Specifically, it increased the fresh weight and root length of plants by 90.12% and 79.22%, respectively, compared with high-salt stress. These results provide new insights into the biological characteristics of Burkholderia pyrrocinia, which may be useful as a bio-fertilizer.
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15
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Depoorter E, De Canck E, Coenye T, Vandamme P. Burkholderia Bacteria Produce Multiple Potentially Novel Molecules that Inhibit Carbapenem-Resistant Gram-Negative Bacterial Pathogens. Antibiotics (Basel) 2021; 10:antibiotics10020147. [PMID: 33540653 PMCID: PMC7912996 DOI: 10.3390/antibiotics10020147] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 01/12/2023] Open
Abstract
Antimicrobial resistance in Gram-negative pathogens represents a global threat to human health. This study determines the antimicrobial potential of a taxonomically and geographically diverse collection of 263 Burkholderia (sensu lato) isolates and applies natural product dereplication strategies to identify potentially novel molecules. Antimicrobial activity is almost exclusively present in Burkholderia sensu stricto bacteria and rarely observed in the novel genera Paraburkholderia, Caballeronia, Robbsia, Trinickia, and Mycetohabitans. Fourteen isolates show a unique spectrum of antimicrobial activity and inhibited carbapenem-resistant Gram-negative bacterial pathogens. Dereplication of the molecules present in crude spent agar extracts identifies 42 specialized metabolites, 19 of which represented potentially novel molecules. The known identified Burkholderia metabolites include toxoflavin, reumycin, pyrrolnitrin, enacyloxin, bactobolin, cepacidin, ditropolonyl sulfide, and antibiotics BN-227-F and SF 2420B, as well as the siderophores ornibactin, pyochelin, and cepabactin. Following semipreparative fractionation and activity testing, a total of five potentially novel molecules are detected in active fractions. Given the molecular formula and UV spectrum, two of those putative novel molecules are likely related to bactobolins, and another is likely related to enacyloxins. The results from this study confirm and extend the observation that Burkholderia bacteria present exciting opportunities for the discovery of potentially novel bioactive molecules.
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Affiliation(s)
- Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium; (E.D.); (E.D.C.)
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium; (E.D.); (E.D.C.)
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Department of Pharmaceutical Analysis, Ghent University, 9000 Ghent, Belgium;
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium; (E.D.); (E.D.C.)
- Correspondence: ; Tel.: +32-9264-5113
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16
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Influence of relevant cystic fibrosis bacteria on Scedosporium apiospermum and Scedosporium boydii growth and viability. Braz J Microbiol 2021; 52:185-193. [PMID: 33442865 DOI: 10.1007/s42770-020-00415-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022] Open
Abstract
Cystic fibrosis (CF) causes a variety of symptoms in different organs, but the majority of the morbidity and mortality of CF is related with pulmonary conditions. Primary infections are usually bacterial, and when treated with antibiotics, yeast infections appear or become more evident. Studies show that different microorganisms can co-inhabit the same environment and the interactions could be synergistic or antagonistic. Using techniques including viable and non-viable cell-to-cell interactions, mixed culture in liquid, and solid media sharing or not the supernatant, this study has evaluated interactions between the fungal species Scedosporium apiospermum and Scedosporium boydii with the bacterial species Staphylococcus aureus, Pseudomonas aeruginosa, and Burkholderia cepacia. Cell-to-cell interactions in liquid medium showed that P. aeruginosa and B. cepacia were able to reduce fungal viability but only in the presence of alive bacteria. Interactions without cell contact using a semi-permeable membrane showed that all bacteria were able to inhibit both fungal growths/viabilities. Cell-free supernatants from bacterial growth reduced fungal viability in planktonic fungal cells as well as in some conditions for preformed fungal biomass. According to the chemical analysis of the bacterial supernatants, the predominant component is protein. In this work, we verified that bacterial cells and their metabolites, present in the supernatants, can play anti-S. apiospermum and anti-S. boydii roles on fungal growth and viability.
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17
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Wang X, Chen D, Wang J, Feng C, Wang W, Zhang W, Li B, Yu J, Xia B. Cloning and Analysis of Genes Controlling Antibacterial Activities of Burkholderia pyrrocinia Strain Lyc2. Curr Microbiol 2019; 76:1003-1009. [PMID: 31183516 DOI: 10.1007/s00284-019-01690-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 04/15/2019] [Indexed: 01/07/2023]
Abstract
The Burkholderia pyrrocinia Lyc2 strain isolated from healthy plant rhizosphere showed significant antimicrobial activities against a variety of plant pathogens. In this study, a random mutation library was constructed using an EZ-Tn5 transposome kit and Erwinia amylovora was used as an indicator to screen for mutants with defective antibacterial activity. The transposon gene was verified in the chromosome of the Lyc2 strain using polymerase chain reaction (PCR). The gene that was disrupted by transposon was amplified by rescue cloning for functional and bioinformatics analyses. Antibacterial analysis indicated that the mutant Lyc2-MT2918 was defective in antibacterial activity. Sequence alignment of the mutant suggested that the disrupted gene Glu-2918 was homologous to the glutathione (GSH) synthase gene Bamb-2918 of strain B. ambifaria AMMD. Genetic functional analysis and complementary assay of the disrupted gene, which was predicted to encode GSH synthase, indicated the essential role of the Glu-2918 gene in the antibacterial activity of strain Lyc2.
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Affiliation(s)
- Xiaoqiang Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao, 266101, Shandong, People's Republic of China
| | - Dexin Chen
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao, 266101, Shandong, People's Republic of China.
| | - Jing Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao, 266101, Shandong, People's Republic of China
| | - Chao Feng
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao, 266101, Shandong, People's Republic of China
| | - Wenjing Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao, 266101, Shandong, People's Republic of China
| | - Wei Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao, 266101, Shandong, People's Republic of China
| | - Bin Li
- China National Tobacco Corporation, Sichuan Company, Chengdu, 610017, People's Republic of China
| | - Jiamin Yu
- China National Tobacco Corporation, Sichuan Company, Chengdu, 610017, People's Republic of China
| | - Bo Xia
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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The Siderophore Product Ornibactin Is Required for the Bactericidal Activity of Burkholderia contaminans MS14. Appl Environ Microbiol 2017; 83:AEM.00051-17. [PMID: 28188204 DOI: 10.1128/aem.00051-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/06/2017] [Indexed: 11/20/2022] Open
Abstract
Burkholderia contaminans MS14 was isolated from soil in Mississippi. When it is cultivated on nutrient broth-yeast extract agar, the colonies exhibit bactericidal activity against a wide range of plant-pathogenic bacteria. A bacteriostatic compound with siderophore activity was successfully purified and was determined by nuclear magnetic resonance spectroscopy to be ornibactin. Isolation of the bactericidal compound has not yet been achieved; therefore, the exact nature of the bactericidal compound is still unknown. During an attempt to isolate the bactericidal compound, an interesting relationship between the production of ornibactin and the bactericidal activity of MS14 was characterized. Transposon mutagenesis resulted in two strains that lost bactericidal activity, with insertional mutations in a nonribosomal peptide synthetase (NRPS) gene for ornibactin biosynthesis and a luxR family transcriptional regulatory gene. Coculture of these two mutant strains resulted in restoration of the bactericidal activity. Furthermore, the addition of ornibactin to the NRPS mutant restored the bactericidal phenotype. It has been demonstrated that, in MS14, ornibactin has an alternative function, aside from iron sequestration. Comparison of the ornibactin biosynthesis genes in Burkholderia species shows diversity among the regulatory elements, while the gene products for ornibactin synthesis are conserved. This is an interesting observation, given that ornibactin is thought to have the same defined function within Burkholderia species. Ornibactin is produced by most Burkholderia species, and its role in regulating the production of secondary metabolites should be investigated.IMPORTANCE Identification of the antibacterial product from strain MS14 is not the key feature of this study. We present a series of experiments that demonstrate that ornibactin is directly involved in the bactericidal phenotype of MS14. This observation provides evidence for an alternative function for ornibactin, aside from iron sequestration. Ornibactin should be further evaluated for its role in regulating the biosynthesis of secondary metabolites in other Burkholderia species.
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