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Ran L, Wu H, Xia F, Xue Y, Wei W, Wang J, Wang J, Zhao S, Yan S, Shi H, Zheng S, Zhang Y, Qiu X. Effect of PGPR on growth and nutrient utilization of Elymus nutans Griseb at different temperatures. PLoS One 2025; 20:e0323613. [PMID: 40354404 PMCID: PMC12068589 DOI: 10.1371/journal.pone.0323613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2024] [Accepted: 04/11/2025] [Indexed: 05/14/2025] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) are beneficial bacteria that facilitate plant growth and can be used in the restoration of ecosystems. However, PGPR vary in their temperature tolerance, and few studies have investigated the effect of temperature on PGPR-mediated growth promotion or PGPR inoculum colonization. Therefore, we isolated and purified rhizosphere bacteria from the rhizosphere soil of Elymus nutans Griseb (EnG), collected from the Qinghai-Tibet Plateau. Selective culture media were used to assess whether these strains possess plant growth-promoting abilities and to measure the magnitude of their plant growth-promoting ability. Then screen out the strains (S1, S2, S3, S4, and S5) with strong plant growth-promoting ability for identification. To demonstrate the growth-promoting effects of the selected PGPR, we conducted a study. In this study, we simulated three temperature gradients (10°C, 15°C, and 20°C) during the growing season of EnG on the Tibetan Plateau. Furthermore, we established four incubation substrate treatments: T1(addition of PGPR but no addition of NPK fertilizers), T2 (neither PGPR nor NPK fertilizers addition), T3 (addition of PGPR both and NPK fertilizers), and T4 (addition of NPK fertilizers but not PGPR), to explore the effects of PGPR on the growth and nutrient (NPK) utilization efficiency of EnG at different temperatures. The results revealed that compared with those under T2, the plant height (PT) and dry weight under, T1 increased by 51.72% - 70.67% and 24.99-51.25%, respectively. The soluble sugar (SS) and soluble protein (SP) content significantly increased by 59.37% and 369.66%, respctively, at 10 °C (p < 0.05) and by 100.17% and 94.5%, respectively, at 15 °C (p < 0.05). Compared with those under T4, the physiological efficiencies of N (NPE) at 15 °C and 20 °C significantly decreased by 40.43% and 72.11%, respectively, under T3. In summary, these showed that this PGPR (S1, S2, S3, S4, and S5) promoted the growth of EnG on the Tibetan plateau and improved its nutrient utilization efficiency.
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Affiliation(s)
- Linling Ran
- Key Laboratory of Southwest China Wildlife Resource Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Haoyang Wu
- Key Laboratory of Southwest China Wildlife Resource Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Fei Xia
- State Key Laboratory of Highland Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Pratacultural Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
| | - Yunyin Xue
- School of Geography and Tourism, Shaanxi Normal University, Xi’an, China
| | - Wei Wei
- State Key Laboratory of Highland Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Pratacultural Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
| | - Junqiang Wang
- Key Laboratory of Southwest China Wildlife Resource Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Jinglong Wang
- State Key Laboratory of Highland Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
- Institute of Pratacultural Science, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, China
| | - Shanshan Zhao
- Key Laboratory of Southwest China Wildlife Resource Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Shuang Yan
- Key Laboratory of Southwest China Wildlife Resource Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Hao Shi
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Shaikun Zheng
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Yu Zhang
- Key Laboratory of Southwest China Wildlife Resource Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Xiaoqin Qiu
- Key Laboratory of Southwest China Wildlife Resource Conservation (Ministry of Education), China West Normal University, Nanchong, China
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Rico-Jiménez M, Udaondo Z, Krell T, Matilla MA. Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica. mSystems 2024; 9:e0016524. [PMID: 38837409 PMCID: PMC11264596 DOI: 10.1128/msystems.00165-24] [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: 02/02/2024] [Accepted: 04/26/2024] [Indexed: 06/07/2024] Open
Abstract
The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria. IMPORTANCE Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.
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Affiliation(s)
- Miriam Rico-Jiménez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Zulema Udaondo
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, Spain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A. Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Höing L, Sowa ST, Toplak M, Reinhardt JK, Jakob R, Maier T, Lill MA, Teufel R. Biosynthesis of the bacterial antibiotic 3,7-dihydroxytropolone through enzymatic salvaging of catabolic shunt products. Chem Sci 2024; 15:7749-7756. [PMID: 38784727 PMCID: PMC11110157 DOI: 10.1039/d4sc01715c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/21/2024] [Indexed: 05/25/2024] Open
Abstract
The non-benzenoid aromatic tropone ring is a structural motif of numerous microbial and plant natural products with potent bioactivities. In bacteria, tropone biosynthesis involves early steps of the widespread CoA-dependent phenylacetic acid (paa) catabolon, from which a shunt product is sequestered and surprisingly further utilized as a universal precursor for structurally and functionally diverse tropone derivatives such as tropodithietic acid or (hydroxy)tropolones. Here, we elucidate the biosynthesis of the antibiotic 3,7-dihydroxytropolone in Actinobacteria by in vitro pathway reconstitution using paa catabolic enzymes as well as dedicated downstream tailoring enzymes, including a thioesterase (TrlF) and two flavoprotein monooxygenases (TrlCD and TrlE). We furthermore mechanistically and structurally characterize the multifunctional key enzyme TrlE, which mediates an unanticipated ipso-substitution involving a hydroxylation and subsequent decarboxylation of the CoA-freed side chain, followed by ring oxidation to afford tropolone. This study showcases a remarkably efficient strategy for 3,7-dihydroxytropolone biosynthesis and illuminates the functions of the involved biosynthetic enzymes.
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Affiliation(s)
- Lars Höing
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Sven T Sowa
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Marina Toplak
- Hilde-Mangold-Haus (CIBSS), University of Freiburg Habsburgerstrasse 49 79104 Freiburg im Breisgau Germany
| | - Jakob K Reinhardt
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Roman Jakob
- Biozentrum, University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Timm Maier
- Biozentrum, University of Basel Spitalstrasse 41 4056 Basel Switzerland
| | - Markus A Lill
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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Kim B, Han SR, Lee H, Oh TJ. Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus. Front Microbiol 2024; 14:1302236. [PMID: 38293557 PMCID: PMC10826400 DOI: 10.3389/fmicb.2023.1302236] [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: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
Burkholderia is a versatile strain that has expanded into several genera. It has been steadily reported that the genome features of Burkholderia exhibit activities ranging from plant growth promotion to pathogenicity across various isolation areas. The objective of this study was to investigate the secondary metabolite patterns of 366 Burkholderia species through comparative genomics. Samples were selected based on assembly quality assessment and similarity below 80% in average nucleotide identity. Duplicate samples were excluded. Samples were divided into two groups using FastANI analysis. Group A included B. pseudomallei complex. Group B included B. cepacia complex. The limitations of MLST were proposed. The detection of genes was performed, including environmental and virulence-related genes. In the pan-genome analysis, each complex possessed a similar pattern of cluster for orthologous groups. Group A (n = 185) had 14,066 cloud genes, 2,465 shell genes, 682 soft-core genes, and 2,553 strict-core genes. Group B (n = 181) had 39,867 cloud genes, 4,986 shell genes, 324 soft-core genes, 222 core genes, and 2,949 strict-core genes. AntiSMASH was employed to analyze the biosynthetic gene cluster (BGC). The results were then utilized for network analysis using BiG-SCAPE and CORASON. Principal component analysis was conducted and a table was constructed using the results obtained from antiSMASH. The results were divided into Group A and Group B. We expected the various species to show similar patterns of secondary metabolite gene clusters. For in-depth analysis, a network analysis of secondary metabolite gene clusters was conducted, exemplified by BiG-SCAPE analysis. Depending on the species and complex, Burkholderia possessed several kinds of siderophore. Among them, ornibactin was possessed in most Burkholderia and was clustered into 4,062 clans. There was a similar pattern of gene clusters depending on the species. NRPS_04014 belonged to siderophore BGCs including ornibactin and indigoidine. However, it was observed that each family included a similar species. This suggests that, besides siderophores being species-specific, the ornibactin gene cluster itself might also be species-specific. The results suggest that siderophores are associated with environmental adaptation, possessing a similar pattern of siderophore gene clusters among species, which could provide another perspective on species-specific environmental adaptation mechanisms.
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Affiliation(s)
- Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
| | - So-Ra Han
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
| | - Hyun Lee
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Division of Computer Science and Engineering, SunMoon University, Asan, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Republic of Korea
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Lv T, Zhan C, Pan Q, Xu H, Fang H, Wang M, Matsumoto H. Plant pathogenesis: Toward multidimensional understanding of the microbiome. IMETA 2023; 2:e129. [PMID: 38867927 PMCID: PMC10989765 DOI: 10.1002/imt2.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 06/14/2024]
Abstract
Single pathogen-targeted disease management measure has shown drawbacks in field efficacy under the scenario of global change. An in-depth understanding of plant pathogenesis will provide a promising solution but faces the challenges of the emerging paradigm involving the plant microbiome. While the beneficial impact of the plant microbiome is well characterized, their potential role in facilitating pathological processes has so far remained largely overlooked. To address these unsolved controversies and emerging challenges, we hereby highlight the pathobiome, the disease-assisting portion hidden in the plant microbiome, in the plant pathogenesis paradigm. We review the detrimental actions mediated by the pathobiome at multiple scales and further discuss how natural and human triggers result in the prevalence of the plant pathobiome, which would probably provide a clue to the mitigation of plant disease epidemics. Collectively, the article would advance the current insight into plant pathogenesis and also pave a new way to cope with the upward trends of plant disease by designing the pathobiome-targeted measure.
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Affiliation(s)
- Tianxing Lv
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Chengfang Zhan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Qianqian Pan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Haorong Xu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hongda Fang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Global Education Program for AgriScience Frontiers, Graduate School of AgricultureHokkaido UniversitySapporoJapan
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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Pantoja-Guerra M, Burkett-Cadena M, Cadena J, Dunlap CA, Ramírez CA. Lysinibacillus spp.: an IAA-producing endospore forming-bacteria that promotes plant growth. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01828-x. [PMID: 37138159 DOI: 10.1007/s10482-023-01828-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/29/2023] [Indexed: 05/05/2023]
Abstract
Lysinibacillus is a bacterial genus that has generated recent interest for its biotechnological potential in agriculture. Strains belonging to this group are recognized for their mosquitocidal and bioremediation activity. However, in recent years some reports indicate its importance as plant growth promoting rhizobacteria (PGPR). This research sought to provide evidence of the PGP activity of Lysinibacillus spp. and the role of the indole-3-acetic acid (IAA) production associated with this activity. Twelve Lysinibacillus spp. strains were evaluated under greenhouse conditions, six of which increased the biomass and root architecture of corn plants. In most cases, growth stimulation was evident at 108 CFU/mL inoculum concentration. All strains produced IAA with high variation between them (20-70 µg/mL). The bioinformatic identification of predicted genes associated with IAA production allowed the detection of the indole pyruvic acid pathway to synthesize IAA in all strains; additionally, genes for a tryptamine pathway were detected in two strains. Extracellular filtrates from all strain's cultures increased the corn coleoptile length in an IAA-similar concentration pattern, which demonstrates the filtrates had an auxin-like effect on plant tissue. Five of the six strains that previously showed PGPR activity in corn also promoted the growth of Arabidopsis thaliana (col 0). These strains induced changes in root architecture of Arabidopsis mutant plants (aux1-7/axr4-2), the partial reversion of mutant phenotype indicated the role of IAA on plant growth. This work provided solid evidence of the association of Lysinibacillus spp. IAA production with their PGP activity, which constitutes a new approach for this genus. These elements contribute to the biotechnological exploration of this bacterial genus for agricultural biotechnology.
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Affiliation(s)
- Manuel Pantoja-Guerra
- Universidad de Antioquia, Instituto de Biología, Medellín, Colombia.
- Facultad de Ciencias Agropecuarias, Unilasallista Corporación Universitaria, Caldas - Antioquia, Colombia.
| | | | | | - Christopher A Dunlap
- United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, 1815 N University, Peoria, IL, USA
| | - Camilo A Ramírez
- Universidad de Antioquia, Instituto de Biología, Medellín, Colombia
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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: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [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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Machino K, Sakakibara Y, Osada K, Ochiai T, Uraki Y, Shigetomi K. Pseudomonas bohemica strain ins3 eliminates antibacterial hinokitiol from its culture broth. Biosci Biotechnol Biochem 2023; 87:236-239. [PMID: 36367540 DOI: 10.1093/bbb/zbac180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
A bacterial strain, Pseudomonas bohemica strain ins3 was newly isolated as a resistant strain against high concentrations of hinokitiol. This strain was revealed not only to show resistance but also completely remove this compound from its culture broth. In addition, its mechanism was revealed to be independent of conventional aromatic dioxygenases, ie catechol-1,2- or 2,3-dioxygenases.
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Affiliation(s)
- Ken Machino
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | | | - Kota Osada
- School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Takahiro Ochiai
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yasumitsu Uraki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kengo Shigetomi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Xu P, Fan X, Mao Y, Cheng H, Xu A, Lai W, Lv T, Hu Y, Nie Y, Zheng X, Meng Q, Wang Y, Cernava T, Wang M. Temporal metabolite responsiveness of microbiota in the tea plant phyllosphere promotes continuous suppression of fungal pathogens. J Adv Res 2022; 39:49-60. [PMID: 35777916 PMCID: PMC9263646 DOI: 10.1016/j.jare.2021.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION A broad spectrum of rhizosphere bacteria and fungi were shown to play a central role for health, fitness and productivity of their host plants. However, implications of host metabolism on microbiota assembly in the phyllosphere and potential consequences for holobiont functioning were sparsely addressed. Previous observations indicated that tea plants might reduce disease occurrence in various forests located in their proximity; the underlying mechanisms and potential implications of the phyllosphere microbiota remained elusive. OBJECTIVES This study aimed atdeciphering microbiome assembly in the tea plant phyllosphere throughout shoot development as well as elucidating potential implications of host metabolites in this process. The main focus was to explore hidden interconnections between the homeostasis of the phyllosphere microbiome and resistance to fungal pathogens. METHODS Profiling of host metabolites and microbiome analyses based on high-throughput sequencing were integrated to identify drivers of microbiome assembly throughout shoot development in the phyllosphere of tea plants. This was complemented by tracking of beneficial microorganisms in all compartments of the plant. Synthetic assemblages (SynAss), bioassays and field surveys were implemented to verify functioning of the phyllosphere microbiota. RESULTS Theophylline and epigallocatechin gallate, two prevalent metabolites at the early and late shoot development stage respectively, were identified as the main drivers of microbial community assembly. Flavobacterium and Myriangium were distinct microbial responders at the early stage, while Parabacteroides and Mortierella were more enriched at the late stage. Reconstructed, stage-specific SynAss suppressed various tree phytopathogens by 13.0%-69.3% in vitro and reduced disease incidence by 8.24%-41.3% in vivo. CONCLUSION The findings indicate that a functional phyllosphere microbiota was assembled along with development-specific metabolites in tea plants, which continuously suppressed prevalent fungal pathogens. The insights gained into the temporally resolved metabolite response of the tea plant microbiota could provide novel solutions for disease management.
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Affiliation(s)
- Ping Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyan Fan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China; Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Yuxiao Mao
- Hangzhou Academy of Agricultural Sciences, Hangzhou 310000, China
| | - Haiyan Cheng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Anan Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Wanyi Lai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Tianxing Lv
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Yang Hu
- Zhejiang Provincial Key Laboratory of Biological and Chemical Utilization of Forest Resources, Zhejiang Academy of Forestry, Hangzhou 310023, Zhejiang, China
| | - Yanxia Nie
- Ecology and Environmental Sciences Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuxia Zheng
- Hangzhou Academy of Agricultural Sciences, Hangzhou 310000, China
| | - Qing Meng
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yuefei Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria.
| | - Mengcen Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China.
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10
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Matsumoto H, Qian Y, Fan X, Chen S, Nie Y, Qiao K, Xiang D, Zhang X, Li M, Guo B, Shen P, Wang Q, Yu Y, Cernava T, Wang M. Reprogramming of phytopathogen transcriptome by a non-bactericidal pesticide residue alleviates its virulence in rice. FUNDAMENTAL RESEARCH 2022; 2:198-207. [PMID: 38933150 PMCID: PMC11197535 DOI: 10.1016/j.fmre.2021.12.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 11/23/2022] Open
Abstract
Bacteria equipped with virulence systems based on highly bioactive small molecules can circumvent their host's defense mechanisms. Pathogens employing this strategy are currently threatening global rice production. In the present study, variations in the virulence of the highly destructive Burkholderia plantarii were observed in different rice-producing regions. The environment-linked variation was not attributable to any known host-related or external factors. Co-occurrence analyses indicated a connection between reduced virulence and 5-Amino-1,3,4-thiadiazole-2-thiol (ATT), a non-bactericidal organic compound. ATT, which accumulates in rice plants during metabolization of specific agrochemicals, was found to reduce virulence factor secretion by B. plantarii up to 88.8% and inhibit pathogen virulence by hijacking an upstream signaling cascade. Detailed assessment of the newly discovered virulence inhibitor resulted in mechanistic insights into positive effects of ATT accumulation in plant tissues. Mechanisms of virulence alleviation were deciphered by integrating high-throughput data, gene knockout mutants, and molecular interaction assays. TroK, a histidine protein kinase in a two-component system that regulates virulence factor secretion, is likely the molecular target antagonized by ATT. Our findings provide novel insights into virulence modulation in an important plant-pathogen system that relies on the host's metabolic activity and subsequent signaling interference.
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Affiliation(s)
- Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuan Qian
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyan Fan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanxia Nie
- Ecology and Environmental Sciences Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Kun Qiao
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
| | - Dandan Xiang
- Key laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xinzhong Zhang
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Meng Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
| | - Bo Guo
- Shanghai International Studies University, Shanghai 200083, China
| | - Peilin Shen
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Xiaoshan Agricultural Comprehensive Development Zone & Management Committee, Hangzhou 311200, China
| | - Qiangwei Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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11
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Toplak M, Teufel R. Three Rings to Rule Them All: How Versatile Flavoenzymes Orchestrate the Structural Diversification of Natural Products. Biochemistry 2021; 61:47-56. [PMID: 34962769 PMCID: PMC8772269 DOI: 10.1021/acs.biochem.1c00763] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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The structural diversification
of natural products is instrumental
to their versatile bioactivities. In this context, redox tailoring
enzymes are commonly involved in the modification and functionalization
of advanced pathway intermediates en route to the mature natural products.
In recent years, flavoprotein monooxygenases have been shown to mediate
numerous redox tailoring reactions that include not only (aromatic)
hydroxylation, Baeyer–Villiger oxidation, or epoxidation reactions
but also oxygenations that are coupled to extensive remodeling of
the carbon backbone, which are often central to the installment of
the respective pharmacophores. In this Perspective, we will highlight
recent developments and discoveries in the field of flavoenzyme catalysis
in bacterial natural product biosynthesis and illustrate how the flavin
cofactor can be fine-tuned to enable chemo-, regio-, and stereospecific
oxygenations via distinct flavin-C4a-peroxide and flavin-N5-(per)oxide
species. Open questions remain, e.g., regarding the breadth of chemical
reactions enabled particularly by the newly discovered flavin-N5-oxygen
adducts and the role of the protein environment in steering such cascade-like
reactions. Outstanding cases involving different flavin oxygenating
species will be exemplified by the tailoring of bacterial aromatic
polyketides, including enterocin, rubromycins, rishirilides, mithramycin,
anthracyclins, chartreusin, jadomycin, and xantholipin. In addition,
the biosynthesis of tropone natural products, including tropolone
and tropodithietic acid, will be presented, which features a recently
described prototypical flavoprotein dioxygenase that may combine flavin-N5-peroxide
and flavin-N5-oxide chemistry. Finally, structural and mechanistic
features of selected enzymes will be discussed as well as hurdles
for their application in the formation of natural product derivatives
via bioengineering.
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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12
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Li M, Wang J, Yao T, Wang Z, Zhang H, Li C. Isolation and Characterization of Cold-Adapted PGPB and Their Effect on Plant Growth Promotion. J Microbiol Biotechnol 2021; 31:1218-1230. [PMID: 34261854 PMCID: PMC9705895 DOI: 10.4014/jmb.2105.05012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/15/2022]
Abstract
Cold-adapted plant growth-promoting bacteria (PGPB) with multiple functions are an important resource for microbial fertilizers with low-temperature application. In this study, culturable cold-adapted PGPB strains with nitrogen fixation and phosphorus solubilization abilities were isolated. They were screened from root and rhizosphere of four dominant grass species in nondegraded alpine grasslands of the Qilian Mountains, China. Their other growth-promoting characteristics, including secretion of indole-3-acetic acid (IAA), production of siderophores and ACC deaminase, and antifungal activity, were further studied by qualitative and quantitative methods. In addition, whether the PGPB strains could still exert plant growth-promoting activity at 4°C was verified. The results showed that 67 isolates could maintain one or more growth-promoting traits at 4°C, and these isolates were defined as cold-adapted PGPB. They were divided into 8 genera by 16S rRNA gene sequencing and phylogenetic analysis, of which Pseudomonas (64.2%) and Serratia (13.4%) were the common dominant genera, and a few specific genera varied among the plant species. A test-tube culture showed that inoculation of Elymus nutans seedlings with cold-adapted PGPB possessing different functional characteristics had a significant growth-promoting effect under controlled low-temperature conditions, including the development of the roots and aboveground parts. Pearson correlation analysis revealed that different growth-promoting characteristics made different contributions to the development of the roots and aboveground parts. These cold-adapted PGPB can be used as excellent strain resources suitable for the near-natural restoration of degraded alpine grasslands or agriculture stock production in cold areas.
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Affiliation(s)
- Mingyuan Li
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730000, P.R. China,College of Biologic and Geographic Sciences, Kashi University, Kashi 844000, P.R. China,Key Laboratory of Ecology and Biological Resources in Yarkand Oasis of Education of Xinjiang Uygur Autonomous Region, Kashi 844000, P.R. China
| | - Jilian Wang
- College of Biologic and Geographic Sciences, Kashi University, Kashi 844000, P.R. China,Key Laboratory of Ecology and Biological Resources in Yarkand Oasis of Education of Xinjiang Uygur Autonomous Region, Kashi 844000, P.R. China
| | - Tuo Yao
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730000, P.R. China,Corresponding author Phone: +86-0931-7631227 E-mail:
| | - Zhenlong Wang
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730000, P.R. China
| | - Huirong Zhang
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730000, P.R. China
| | - Changning Li
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730000, P.R. China
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13
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Fan X, Fu Y, Nie Y, Matsumoto H, Wang Y, Hu T, Pan Q, Lv T, Fang H, Xu H, Wang Y, Ge H, Zhu G, Liu Y, Wang Q, Wang M. Keystone taxa-mediated bacteriome response shapes the resilience of the paddy ecosystem to fungicide triadimefon contamination. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126061. [PMID: 34229385 DOI: 10.1016/j.jhazmat.2021.126061] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/18/2021] [Accepted: 05/04/2021] [Indexed: 05/22/2023]
Abstract
The increasing input of fungicides has emerged as a global concern for agroecosystem stability and sustainability. Agroecosystem resilience has been linked to microbiome response, however, is not well understood. Focusing on a widespread triazole-class fungicide triadimefon in the paddy ecosystem, we characterized that the soils and sediments were dominant triadimefon reservoirs with the peak level at 195 μg kg-1 and 31.3 μg kg-1, respectively, but essential for the resilience of paddy ecosystem to triadimefon. In paddy simulation models, the half-life of triadimefon in soil-sediment was 8.4-28.9 days, while it was prolonged to 86.6-115.5 days after elimination of resident microbial community. Phospholipid fatty acid profiling and high-throughput sequencing showed that the distinctive bacterial community responses contributed to variable degradation of triadimefon in paddy soils and sediments. Sphingomonas and Xanthomonas were identified as positive responders of the keystone taxa in the responsive bacteriome, whereas Enterobacter were negative responders that declined over time. Synthetic assemblages combined with quantitative polymerase chain reaction further validated that Sphingomonas and Xanthomonas were involved in sustaining soil-sediment resilience to triadimefon contamination. Collectively, our results revealed that the shaping of soil and sediment bacteriomes was responsible for the resilience of the paddy agroecosystem to fungicide contamination.
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Affiliation(s)
- Xiaoyan Fan
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yan Fu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; Ningbo Academy of Agricultural Sciences, Ningbo 315040, China
| | - Yanxia Nie
- Ecology and Environmental Sciences Center, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Haruna Matsumoto
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yue Wang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tingting Hu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qianqian Pan
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tianxing Lv
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hongda Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Haorong Xu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yi Wang
- Jinhua Academy of Agricultural Sciences, Jinhua 321017, China
| | - Hang Ge
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Guonian Zhu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yihua Liu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Qiangwei Wang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengcen Wang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
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14
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Duan Y, Toplak M, Hou A, Brock NL, Dickschat JS, Teufel R. A Flavoprotein Dioxygenase Steers Bacterial Tropone Biosynthesis via Coenzyme A-Ester Oxygenolysis and Ring Epoxidation. J Am Chem Soc 2021; 143:10413-10421. [PMID: 34196542 PMCID: PMC8283759 DOI: 10.1021/jacs.1c04996] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Bacterial tropone
natural products such as tropolone, tropodithietic
acid, or the roseobacticides play crucial roles in various terrestrial
and marine symbiotic interactions as virulence factors, antibiotics,
algaecides, or quorum sensing signals. We now show that their poorly
understood biosynthesis depends on a shunt product from aerobic CoA-dependent
phenylacetic acid catabolism that is salvaged by the dedicated acyl-CoA
dehydrogenase-like flavoenzyme TdaE. Further characterization of TdaE
revealed an unanticipated complex catalysis, comprising substrate
dehydrogenation, noncanonical CoA-ester oxygenolysis, and final ring
epoxidation. The enzyme thereby functions as an archetypal flavoprotein
dioxygenase that incorporates both oxygen atoms from O2 into the substrate, most likely involving flavin-N5-peroxide and
flavin-N5-oxide species for consecutive CoA-ester cleavage and epoxidation,
respectively. The subsequent spontaneous decarboxylation of the reactive
enzyme product yields tropolone, which serves as a key virulence factor
in rice panicle blight caused by pathogenic edaphic Burkholderia
plantarii. Alternatively, the TdaE product is most likely
converted to more complex sulfur-containing secondary metabolites
such as tropodithietic acid from predominant marine Rhodobacteraceae (e.g., Phaeobacter inhibens).
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Affiliation(s)
- Ying Duan
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Anwei Hou
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Nelson L Brock
- Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.,Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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15
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Sakakibara Y, Osada K, Uraki Y, Ubukata M, Shigetomi K. Direct deuteration of hinokitiol and its mechanistic study. Biosci Biotechnol Biochem 2021; 85:215-222. [PMID: 33590006 DOI: 10.1093/bbb/zbaa031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/05/2020] [Indexed: 11/14/2022]
Abstract
Hinokitiol has a broad antibacterial activity against bacteria and fungi. While its biosynthetic pathway has been intensively studied, its dynamics in natural environments, such as biodegradation pathway, remain unclear. In this study, the authors report a direct deuterium labeling of hinokitiol as a traceable molecular probe to serve those studies. Hinokitiol was subjected to the H2-Pd/C-D2O conditions and deuterated hinokitiol was obtained with excellent deuteration efficiencies and in moderate yield. The 1H and 2H NMR spectra indicated that all ring- and aliphatic hydrogens except that on C-6 were substituted by deuterium. According to the substrate scope and computational chemistry, deuteration on tropolone ring was suggested to proceed via D+-mediated process, and which was supported by the results of the experiment with trifluoroacetic acid and Pd(TPP)4. On the other hand, the deuteration on aliphatic group was predicted to be catalyzed by Pd(II) species.
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Affiliation(s)
| | - Kota Osada
- School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yasumitsu Uraki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Makoto Ubukata
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kengo Shigetomi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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16
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Hashimoto M. In Memory of Professor Yasuyuki Hashidoko. Biosci Biotechnol Biochem 2021. [DOI: 10.1093/bbb/zbaa074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Matsumoto H, Fan X, Wang Y, Kusstatscher P, Duan J, Wu S, Chen S, Qiao K, Wang Y, Ma B, Zhu G, Hashidoko Y, Berg G, Cernava T, Wang M. Bacterial seed endophyte shapes disease resistance in rice. NATURE PLANTS 2021; 7:60-72. [PMID: 33398157 DOI: 10.1038/s41477-020-00826-5] [Citation(s) in RCA: 204] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 11/24/2020] [Indexed: 05/20/2023]
Abstract
Cereal crop production is severely affected by seed-borne bacterial diseases across the world. Locally occurring disease resistance in various crops remains elusive. Here, we have observed that rice plants of the same cultivar can be differentiated into disease-resistant and susceptible phenotypes under the same pathogen pressure. Following the identification of a seed-endophytic bacterium as the resistance-conferring agent, integration of high-throughput data, gene mutagenesis and molecular interaction assays facilitated the discovery of the underlying mode of action. Sphingomonas melonis that is accumulated and transmitted across generations in disease-resistant rice seeds confers resistance to disease-susceptible phenotypes by producing anthranilic acid. Without affecting cell growth, anthranilic acid interferes with the sigma factor RpoS of the seed-borne pathogen Burkholderia plantarii, probably leading to impairment of upstream cascades that are required for virulence factor biosynthesis. The overall findings highlight the hidden role of seed endophytes in the phytopathology paradigm of 'disease triangles', which encompass the plant, pathogens and environmental conditions. These insights are potentially exploitable for modern crop cultivation threatened by globally widespread bacterial diseases.
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Affiliation(s)
- Haruna Matsumoto
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Xiaoyan Fan
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Yue Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Jie Duan
- Laboratory of Molecular and Ecological Chemistry, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sanling Wu
- Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environment Sciences, Zhejiang University, Hangzhou, China
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kun Qiao
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Yiling Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Guonian Zhu
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Yasuyuki Hashidoko
- Laboratory of Molecular and Ecological Chemistry, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Mengcen Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China.
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18
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Laird TS, Flores N, Leveau JHJ. Bacterial catabolism of indole-3-acetic acid. Appl Microbiol Biotechnol 2020; 104:9535-9550. [PMID: 33037916 DOI: 10.1007/s00253-020-10938-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/21/2020] [Accepted: 09/27/2020] [Indexed: 12/18/2022]
Abstract
Indole-3-acetic acid (IAA) is a molecule with the chemical formula C10H9NO2, with a demonstrated presence in various environments and organisms, and with a biological function in several of these organisms, most notably in plants where it acts as a growth hormone. The existence of microorganisms with the ability to catabolize or assimilate IAA has long been recognized. To date, two sets of gene clusters underlying this property in bacteria have been identified and characterized: one (iac) is responsible for the aerobic degradation of IAA into catechol, and another (iaa) for the anaerobic conversion of IAA to 2-aminobenzoyl-CoA. Here, we summarize the literature on the products, reactions, and pathways that these gene clusters encode. We explore two hypotheses about the benefit that iac/iaa gene clusters confer upon their bacterial hosts: (1) exploitation of IAA as a source of carbon, nitrogen, and energy; and (2) interference with IAA-dependent processes and functions in other organisms, including plants. The evidence for both hypotheses will be reviewed for iac/iaa-carrying model strains of Pseudomonas putida, Enterobacter soli, Acinetobacter baumannii, Paraburkholderia phytofirmans, Caballeronia glathei, Aromatoleum evansii, and Aromatoleum aromaticum, more specifically in the context of access to IAA in the environments from which these bacteria were originally isolated, which include not only plants, but also soils and sediment, as well as patients in hospital environments. We end the mini-review with an outlook for iac/iaa-inspired research that addresses current gaps in knowledge, biotechnological applications of iac/iaa-encoded enzymology, and the use of IAA-destroying bacteria to treat pathologies related to IAA excess in plants and humans. KEY POINTS: • The iac/iaa gene clusters encode bacterial catabolism of the plant growth hormone IAA. • Plants are not the only environment where IAA or IAA-degrading bacteria can be found. • The iac/iaa genes allow growth at the expense of IAA; other benefits remain unknown.
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Affiliation(s)
- Tyler S Laird
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Neptali Flores
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Johan H J Leveau
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA.
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Jenab A, Roghanian R, Emtiazi G. Bacterial Natural Compounds with Anti-Inflammatory and Immunomodulatory Properties (Mini Review). Drug Des Devel Ther 2020; 14:3787-3801. [PMID: 32982183 PMCID: PMC7509312 DOI: 10.2147/dddt.s261283] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/26/2020] [Indexed: 12/31/2022] Open
Abstract
Inflammation is part of the body's complex biological response to harmful stimuli such as damaged cells, pathogens, or irritants. It is a protective response involving blood cells, immune cells, and molecular mediators. The inflammation not only can eliminate the primary cause of cell injury but also clears out necrotic cells, tissue damaged from the original insults and inflammatory process. Furthermore, it can initiate tissue repair. Pro-inflammatory cytokines are produced predominantly by activated macrophages and are involved in the up-regulation of inflammatory reactions. They are involved in further regulating inflammatory reactions. There is ample evidence that some pro-inflammatory cytokines, such as interleukin 1β (IL-1β), IL-6, and tumor necrosis factor-α (TNF-α), are involved in the pathological pain process. Some of the natural compounds promote cytokines production and inhibit inflammatory responses. The natural compounds which are produced from microorganisms such as omega-3 fatty acid, cyclic peptide, antimicrobial peptide, oligosaccharides, and polysaccharides can reduce inflammation and could be easily incorporated into the diet without any adverse effects. For example, SCFA (short-chain fatty acids), peptide bacteriocin, and polycyclic peptide bacteriocin (nisin) could be used in the treatment of atherosclerosis, orthopedic postoperative infections, and mycobacterium tuberculosis infection, respectively. Also, fatty acids (saturated and unsaturated fatty acids) can be introduced as anti-inflammatory drugs. This review article summarizes bacterial natural compounds with modulating effects on cytokines that are surveyed which may have potential anti-inflammatory drug-like activity.
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Affiliation(s)
- Anahita Jenab
- Biological Science and Technology, Department of Cellular and Microbiology, University of Isfahan, Hezar Jerib, Isfahan, Iran
| | - Rasoul Roghanian
- Biological Science and Technology, Department of Cellular and Microbiology, University of Isfahan, Hezar Jerib, Isfahan, Iran
| | - Giti Emtiazi
- Biological Science and Technology, Department of Cellular and Microbiology, University of Isfahan, Hezar Jerib, Isfahan, Iran
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20
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Duan Y, Petzold M, Saleem‐Batcha R, Teufel R. Bacterial Tropone Natural Products and Derivatives: Overview of their Biosynthesis, Bioactivities, Ecological Role and Biotechnological Potential. Chembiochem 2020; 21:2384-2407. [PMID: 32239689 PMCID: PMC7497051 DOI: 10.1002/cbic.201900786] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/02/2020] [Indexed: 12/05/2022]
Abstract
Tropone natural products are non-benzene aromatic compounds of significant ecological and pharmaceutical interest. Herein, we highlight current knowledge on bacterial tropones and their derivatives such as tropolones, tropodithietic acid, and roseobacticides. Their unusual biosynthesis depends on a universal CoA-bound precursor featuring a seven-membered carbon ring as backbone, which is generated by a side reaction of the phenylacetic acid catabolic pathway. Enzymes encoded by separate gene clusters then further modify this key intermediate by oxidation, CoA-release, or incorporation of sulfur among other reactions. Tropones play important roles in the terrestrial and marine environment where they act as antibiotics, algaecides, or quorum sensing signals, while their bacterial producers are often involved in symbiotic interactions with plants and marine invertebrates (e. g., algae, corals, sponges, or mollusks). Because of their potent bioactivities and of slowly developing bacterial resistance, tropones and their derivatives hold great promise for biomedical or biotechnological applications, for instance as antibiotics in (shell)fish aquaculture.
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Affiliation(s)
- Ying Duan
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | - Melanie Petzold
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | | | - Robin Teufel
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
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21
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Abstract
Burkholderia bacteria are multifaceted organisms that are ecologically and metabolically diverse. The Burkholderia genus has gained prominence because it includes human pathogens; however, many strains are nonpathogenic and have desirable characteristics such as beneficial plant associations and degradation of pollutants. The diversity of the Burkholderia genus is reflected within the large genomes that feature multiple replicons. Burkholderia genomes encode a plethora of natural products with potential therapeutic relevance and biotechnological applications. This review highlights Burkholderia as an emerging source of natural products. An overview of the taxonomy of the Burkholderia genus, which is currently being revised, is provided. We then present a curated compilation of natural products isolated from Burkholderia sensu lato and analyze their characteristics in terms of biosynthetic class, discovery method, and bioactivity. Finally, we describe and discuss genome characteristics and highlight the biosynthesis of a select number of natural products that are encoded in unusual biosynthetic gene clusters. The availability of >1000 Burkholderia genomes in public databases provides an opportunity to realize the genetic potential of this underexplored taxon for natural product discovery.
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Affiliation(s)
- Sylvia Kunakom
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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22
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Matilla MA, Daddaoua A, Chini A, Morel B, Krell T. An auxin controls bacterial antibiotics production. Nucleic Acids Res 2019; 46:11229-11238. [PMID: 30500953 PMCID: PMC6265452 DOI: 10.1093/nar/gky766] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/21/2018] [Indexed: 01/02/2023] Open
Abstract
The majority of clinically used antibiotics originate from bacteria. As the need for new antibiotics grows, large-scale genome sequencing and mining approaches are being used to identify novel antibiotics. However, this task is hampered by the fact that many antibiotic biosynthetic clusters are not expressed under laboratory conditions. One strategy to overcome this limitation is the identification of signals that activate the expression of silent biosynthetic pathways. Here, we report the use of high-throughput screening to identify signals that control the biosynthesis of the acetyl-CoA carboxylase inhibitor antibiotic andrimid in the broad-range antibiotic-producing rhizobacterium Serratia plymuthica A153. We reveal that the pathway-specific transcriptional activator AdmX recognizes the auxin indole-3-acetic acid (IAA). IAA binding causes conformational changes in AdmX that result in the inhibition of the expression of the andrimid cluster and the suppression of antibiotic production. We also show that IAA synthesis by pathogenic and beneficial plant-associated bacteria inhibits andrimid production in A153. Because IAA is a signalling molecule that is present across all domains of life, this study highlights the importance of intra- and inter-kingdom signalling in the regulation of antibiotic synthesis. Our discovery unravels, for the first time, an IAA-dependent molecular mechanism for the regulation of antibiotic synthesis.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | | | - Andrea Chini
- Department of Plant Molecular Genetics, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Bertrand Morel
- Departament of Physical Chemistry and Institute for Biotechnology, Science Faculty, Granada University, 18071 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
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23
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Abstract
This review on natural products containing a tropolonoid motif highlights analytical methods applied for structural identification and biosynthetic pathway analysis, the ecological context and the pharmacological potential of this compound class.
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Affiliation(s)
- Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute
- 07745 Jena
- Germany
| | - David Roman
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute
- 07745 Jena
- Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute
- 07745 Jena
- Germany
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24
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Sumayo MS, Son JS, Ghim SY. Exogenous application of phenylacetic acid promotes root hair growth and induces the systemic resistance of tobacco against bacterial soft-rot pathogen Pectobacterium carotovorum subsp. carotovorum. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:1119-1127. [PMID: 32290973 DOI: 10.1071/fp17332] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/14/2018] [Indexed: 06/11/2023]
Abstract
Phenylacetic acid (PAA) was evaluated for its capability to promote plant growth and induce systemic resistance in tobacco (Nicotianum tabacum L cv. Xanthi) against the bacterial soft rot pathogen Pectobacterium carotovorum subsp. carotovorum (PCC). Exogenous application of PAA influenced root formation, the activities of defence-related enzymes and the expression of defence and growth-related genes. Increased formation of lateral roots can be observed in tobacco treated with higher PAA concentrations. The highest elicitation of induced systemic resistance (ISR) was found in plants treated with 0.5mM PAA, where the phytotoxic effect was minimal. The activities of the defence enzymes phenylalanine ammonia-lyase (PAL), peroxidase (POD) and polyphnenoloxidase (PPO) were modulated upon treatment with different PAA concentrations. Reverse transcription-PCR analyses showed that 0.5mM PAA modulated the expression of the growth-related genes NtEXP2 and NtEXP6, and the defence-related genes Coi1, NPR1, PR-1a and PR-1b. These results showed that different concentrations of PAA can elicit different responses and effects on tobacco growth and resistance. This study presents the important role of PAA not only on plant growth but also for plant immunity against phytopathogens.
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Affiliation(s)
- Marilyn S Sumayo
- School of Life Sciences, BK21 Plus Kyungpook National University Creative BioResearch Group and Research Institute for Dokdo and Ulleung-do Island, Kyungpook National University, 80 Daehakru, Bukgu, Daegu 41566, Korea
| | - Jin-Soo Son
- School of Life Sciences, BK21 Plus Kyungpook National University Creative BioResearch Group and Research Institute for Dokdo and Ulleung-do Island, Kyungpook National University, 80 Daehakru, Bukgu, Daegu 41566, Korea
| | - Sa-Youl Ghim
- School of Life Sciences, BK21 Plus Kyungpook National University Creative BioResearch Group and Research Institute for Dokdo and Ulleung-do Island, Kyungpook National University, 80 Daehakru, Bukgu, Daegu 41566, Korea
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25
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Liu X, Fan X, Matsumoto H, Nie Y, Sha Z, Yi K, Pan J, Qian Y, Cao M, Wang Y, Zhu G, Wang M. Biotoxin Tropolone Contamination Associated with Nationwide Occurrence of Pathogen Burkholderia plantarii in Agricultural Environments in China. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5105-5114. [PMID: 29589436 DOI: 10.1021/acs.est.7b05915] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Tropolone, a biotoxin produced by the agricultural pathogen Burkholderia plantarii, exerts cytotoxicity toward a wide array of biota. However, due to the lack of quantitative and qualitative approach, both B. plantarii occurrence and tropolone contamination in agricultural environments remain poorly understood. Here, we presented a sensitive and reliable method for detection of B. plantarii in artificial, plant, and environmental matrices by tropolone-targeted gas chromatography-triple-quadrupole tandem mass spectrometry analysis. Limits of detection for B. plantarii and tropolone were 10 colony-forming units (CFU)/mL and 0.017 μg/kg, respectively. In a series of simulation trials, we found that B. plantarii from 10 to 108 CFU/mL produced tropolone between 0.006 and 107.8 mg/kg in a cell-population-dependent manner, regardless of habitat. Correlation analysis clarified a reliable reflection of B. plantarii density by tropolone level with R2 values from 0.9201 to 0.9756 ( p < 0.01). Through a nationwide pilot study conducted in China, tropolone contamination was observed at 0.014-0.157 mg/kg in paddy soil and rice grains, and subsequent redundancy analysis revealed soil organic matter to be a dominant environmental factor, having a positive correlation with tropolone contamination. In this context, our results imply that potential ecological and dietary risks posed by long-term exposure to trace levels of tropolone contamination are of concern.
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Affiliation(s)
- Xiaoyu Liu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology , Zhejiang University , Hangzhou 310058 , China
| | - Xiaoyan Fan
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology , Zhejiang University , Hangzhou 310058 , China
| | - Haruna Matsumoto
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology , Zhejiang University , Hangzhou 310058 , China
| | - Yanxia Nie
- Ecology and Environmental Sciences Center, South China Botanical Garden , Chinese Academy of Sciences , Guangzhou 510650 , China
| | - Zhimin Sha
- School of Agriculture and Biology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Kunpeng Yi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , China
| | - Jiuyue Pan
- College of Plant Protection , Hunan Agricultural University , Changsha 410128 , China
| | - Yuan Qian
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology , Zhejiang University , Hangzhou 310058 , China
| | - Mengchao Cao
- Patent Examination Cooperation Jiangsu Center of the Patent Office, State Intellectual Property Office of the PRC , Suzhou 215163 , China
| | - Yihu Wang
- Solution Department , Jiangsu Rotam Chemistry Co., Ltd. , Suzhou 215301 , China
| | - Guonian Zhu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology , Zhejiang University , Hangzhou 310058 , China
| | - Mengcen Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology , Zhejiang University , Hangzhou 310058 , China
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26
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Hashidoko Y. Studies on the metabolic regulation of denitrifying bacteria and phytopathogenic microorganisms using chemical agents found in chemical ecology-based phenomena. JOURNAL OF PESTICIDE SCIENCE 2018; 43:47-54. [PMID: 30363125 PMCID: PMC6140671 DOI: 10.1584/jpestics.j17-04] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/16/2017] [Indexed: 05/27/2023]
Abstract
An interaction between two different living creatures is often mediated by a chemical substance, along with metabolic or morphological differentiation. Such phenomenon-based investigation of chemical substances sometimes leads to the discovery of a novel signaling substance associated with biological pest control, including pinpoint regulation of fundamental metabolisms. In studies on the metabolic regulation of denitrifying bacteria and phytopathogenic microorganisms, such chemicals linked to the introduction of new ideas and unique approaches for biorational pest controls are described.
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Affiliation(s)
- Yasuyuki Hashidoko
- Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo 060–8589, Japan
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27
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Simonetti E, Roberts IN, Montecchia MS, Gutierrez-Boem FH, Gomez FM, Ruiz JA. A novel Burkholderia ambifaria strain able to degrade the mycotoxin fusaric acid and to inhibit Fusarium spp. growth. Microbiol Res 2017; 206:50-59. [PMID: 29146260 DOI: 10.1016/j.micres.2017.09.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 09/07/2017] [Accepted: 09/20/2017] [Indexed: 02/05/2023]
Abstract
Fusaric acid (FA) is a fungal metabolite produced by several Fusarium species responsible for wilts and root rot diseases of a great variety of plants. Bacillus spp. and Pseudomonas spp. have been considered as promising biocontrol agents against phytopathogenic Fusarium spp., however it has been demonstrated that FA negatively affects growth and production of some antibiotics in these bacteria. Thus, the capability to degrade FA would be a desirable characteristic in bacterial biocontrol agents of Fusarium wilt. Taking this into account, bacteria isolated from the rhizosphere of barley were screened for their ability to use FA as sole carbon and energy source. One strain that fulfilled this requirement was identified according to sequence analysis of 16S rRNA, gyrB and recA genes as Burkholderia ambifaria. This strain, designated T16, was able to grow with FA as sole carbon, nitrogen and energy source and also showed the ability to detoxify FA in barley seedlings. This bacterium also exhibited higher growth rate, higher cell densities, longer survival, higher levels of indole-3-acetic acid (IAA) production, enhanced biofilm formation and increased resistance to different antibiotics when cultivated in Luria Bertani medium at pH 5.3 compared to pH 7.3. Furthermore, B. ambifaria T16 showed distinctive plant growth-promoting features, such as siderophore production, phosphate-solubilization, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, in vitro antagonism against Fusarium spp. and improvement of grain yield when inoculated to barley plants grown under greenhouse conditions. This strain might serve as a new source of metabolites or genes for the development of novel FA-detoxification systems.
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Affiliation(s)
- Ester Simonetti
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Irma N Roberts
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Marcela S Montecchia
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Flavio H Gutierrez-Boem
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Federico M Gomez
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina
| | - Jimena A Ruiz
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales, Universidad de Buenos Aires, CONICET, FAUBA. Av. San Martín 4453, C1417DSE, Ciudad Autónoma de Buenos Aires, Argentina.
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28
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Genome Sequence of Burkholderia plantarii ZJ171, a Tropolone-Producing Bacterial Pathogen Responsible for Rice Seedling Blight. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01318-16. [PMID: 27932643 PMCID: PMC5146435 DOI: 10.1128/genomea.01318-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Burkholderia plantarii is the causal agent of rice seedling blight. Here, we report the draft genome sequence of B. plantarii, which contains 8,020,831 bp, with a G+C content of 68.66% and a predicted 7,688 coding sequences. The annotated genome sequence will provide further insight into its pathogenicity.
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