1
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Kaneko K, Mieda M, Jiang Y, Takahashi N, Kakeya H. Tumescenamide C, a cyclic lipodepsipeptide from Streptomyces sp. KUSC_F05, exerts antimicrobial activity against the scab-forming actinomycete Streptomyces scabiei. J Antibiot (Tokyo) 2024; 77:353-364. [PMID: 38523145 DOI: 10.1038/s41429-024-00716-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/08/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024]
Abstract
The antimicrobial activity of tumescenamide C against the scab-forming S. scabiei NBRC13768 was confirmed with a potent IC50 value (1.5 μg/mL). Three tumescenamide C-resistant S. scabiei strains were generated to compare their gene variants. All three resistant strains contained nonsynonymous variants in genes related to cellobiose/cellotriose transport system components; cebF1, cebF2, and cebG2, which are responsible for the production of the phytotoxin thaxtomin A. Decrease in thaxtomin A production and the virulence of the three resistant strains were revealed by the LC/MS analysis and necrosis assay, respectively. Although the nonsynonymous variants were insufficient for identifying the molecular target of tumescenamide C, the cell wall component wall teichoic acid (WTA) was observed to bind significantly to tumescenamide C. Moreover, changes in the WTA contents were detected in the tumescenamide C-resistant strains. These results imply that tumescenamide C targets the cell wall system to exert antimicrobial effects on S. scabiei.
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Affiliation(s)
- Kensuke Kaneko
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
- Hachinohe College of Technology, Aomori, 039-1192, Japan
| | - Marika Mieda
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Yulu Jiang
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Nobuaki Takahashi
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan.
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2
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Vincent CV, Bignell DRD. Regulation of virulence mechanisms in plant-pathogenic Streptomyces. Can J Microbiol 2024; 70:199-212. [PMID: 38190652 DOI: 10.1139/cjm-2023-0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Streptomyces have a uniquely complex developmental life cycle that involves the coordination of morphological differentiation with the production of numerous bioactive specialized metabolites. The majority of Streptomyces spp. are soil-dwelling saprophytes, while plant pathogenicity is a rare attribute among members of this genus. Phytopathogenic Streptomyces are responsible for economically important diseases such as common scab, which affects potato and other root crops. Following the acquisition of genes encoding virulence factors, Streptomyces pathogens are expected to have specifically adapted their regulatory pathways to enable transition from a primarily saprophytic to a pathogenic lifestyle. Investigations of the regulation of pathogenesis have primarily focused on Streptomyces scabiei and the principal pathogenicity determinant thaxtomin A. The coordination of growth and thaxtomin A production in this species is controlled in a hierarchical manner by cluster-situated regulators, pleiotropic regulators, signalling and plant-derived molecules, and nutrients. Although the majority of phytopathogenic Streptomyces produce thaxtomins, many also produce additional virulence factors, and there are scab-causing pathogens that do not produce thaxtomins. The development of effective control strategies for common scab and other Streptomyces plant diseases requires a more in-depth understanding of the genetic and environmental factors that modulate the plant pathogenic lifestyle of these organisms.
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Affiliation(s)
- Corrie V Vincent
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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3
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Hudec C, Biessy A, Léger G, Albert D, Novinscak A, Filion M. Seasonal Dynamics of Various Scab-Causing Streptomyces Genotypes Among Potato Fields on Prince Edward Island. PHYTOPATHOLOGY 2024; 114:146-154. [PMID: 37366579 DOI: 10.1094/phyto-05-23-0149-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Potato common scab is an important bacterial plant disease caused by numerous Streptomyces species and strains. A better understanding of the genetic diversity and population dynamics of these microorganisms in the field is crucial to develop effective control methods. Our research group previously studied the genetic diversity of scab-causing Streptomyces spp. in Prince Edward Island, one of Canada's most important potato-growing provinces. Fourteen distinct Streptomyces genotypes were identified and displayed contrasting aggressiveness toward potato tubers. To better understand the distribution and occurrence of these genotypes over time under field conditions, the population dynamics were studied in nine commercial potato fields throughout a growing season. A comparative genomic-driven approach was used to design genotype-specific primers and probes, allowing us to quantify, using quantitative polymerase chain reaction, the abundance of each of the 14 genotypes in field soil. Thirteen of the previously identified genotypes were detected in at least one soil sample, with various frequencies and population sizes across the different fields under study. Interestingly, weakly virulent genotypes dominated, independent of time or location. Among them, three genotypes accounted for more than 80% of the genotypes' combined population. Although the highly virulent genotypes were detected in lower relative abundance than the weakly virulent ones, an increase in the highly virulent genotypes' population size was observed over the growing season in most fields. The results will ultimately be useful for the development of targeted common scab control strategies.
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Affiliation(s)
- Cindy Hudec
- Department of Biology, Université de Moncton, Moncton, NB E1A 3E9, Canada
| | - Adrien Biessy
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
| | - Geneviève Léger
- Department of Biology, Université de Moncton, Moncton, NB E1A 3E9, Canada
| | - Daphné Albert
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
| | - Amy Novinscak
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, BC V0M 1A2, Canada
| | - Martin Filion
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
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4
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Kerff F, Jourdan S, Francis IM, Deflandre B, Ribeiro Monteiro S, Stulanovic N, Loria R, Rigali S. Common scab disease: structural basis of elicitor recognition in pathogenic Streptomyces species. Microbiol Spectr 2023; 11:e0197523. [PMID: 37791952 PMCID: PMC10714786 DOI: 10.1128/spectrum.01975-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/21/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Common scab is a disease caused by a few Streptomyces species that affects important root and tuber crops including potato, beet, radish, and parsnip, resulting in major economic losses worldwide. In this work, we unveiled the molecular basis of host recognition by these pathogens by solving the structure of the sugar-binding protein CebE of Streptomyces scabiei in complex with cellotriose, the main elicitor of the pathogenic lifestyle of these bacteria. We further revealed that the signaling pathway from CebE-mediated transport of cellotriose is conserved in all pathogenic species except Streptomyces ipomoeae, which causes soft rot disease in sweet potatoes. Our work also provides the structural basis of the uptake of cellobiose and cellotriose in saprophytic Streptomyces species, the first step activating the expression of the enzymatic system degrading the most abundant polysaccharide on earth, cellulose.
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Affiliation(s)
- Frédéric Kerff
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Samuel Jourdan
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Isolde M. Francis
- Department of Biology, California State University, Bakersfield, California, USA
| | - Benoit Deflandre
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Silvia Ribeiro Monteiro
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Nudzejma Stulanovic
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Rosemary Loria
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Sébastien Rigali
- InBioS–Center for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
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5
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Haq IU, Mukhtar Z, Anwar-Ul-Haq M, Liaqat S. Deciphering host-pathogen interaction during Streptomyces spp. infestation of potato. Arch Microbiol 2023; 205:222. [PMID: 37149838 DOI: 10.1007/s00203-023-03560-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023]
Abstract
Potato crop, currently, is the staple food crop of about 1.3 billion global population. Potato is attaining even more admiration globally day by day owing to its public acceptability. However, potato sustainable production is distinctly challenged by multiple factors like diseases, pests and climate change etc. Among diseases, common scab is one of the prime threats to potato crop due to its soil-borne nature and versatility in phytotoxins' secretion. Common scab is caused multiple number of phytopathogenic streptomyces strains. Despite extensive research programs, researchers are still unable to identify a significant solution to this threat that is proliferating exceptional rate across the globe. To develop feasible remedies, adequate information regarding host-pathogen interaction should be available. This review possesses insights on existing pathogenic species, the evolution of novel pathogenic streptomyces spp. and phytotoxins produced by the pathogenic strains. Furthermore, which type of physiological, biochemical and genetic activities occur during pathogen's infestation of the host are also canvassed.
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Affiliation(s)
- Ihtisham Ul Haq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.
- Ayub Agricultural Research Institute, Faisalabad, Pakistan.
| | - Zahid Mukhtar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | | | - Sana Liaqat
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
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6
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Serag A, Salem MA, Gong S, Wu JL, Farag MA. Decoding Metabolic Reprogramming in Plants under Pathogen Attacks, a Comprehensive Review of Emerging Metabolomics Technologies to Maximize Their Applications. Metabolites 2023; 13:424. [PMID: 36984864 PMCID: PMC10055942 DOI: 10.3390/metabo13030424] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
In their environment, plants interact with a multitude of living organisms and have to cope with a large variety of aggressions of biotic or abiotic origin. What has been known for several decades is that the extraordinary variety of chemical compounds the plants are capable of synthesizing may be estimated in the range of hundreds of thousands, but only a fraction has been fully characterized to be implicated in defense responses. Despite the vast importance of these metabolites for plants and also for human health, our knowledge about their biosynthetic pathways and functions is still fragmentary. Recent progress has been made particularly for the phenylpropanoids and oxylipids metabolism, which is more emphasized in this review. With an increasing interest in monitoring plant metabolic reprogramming, the development of advanced analysis methods should now follow. This review capitalizes on the advanced technologies used in metabolome mapping in planta, including different metabolomics approaches, imaging, flux analysis, and interpretation using bioinformatics tools. Advantages and limitations with regards to the application of each technique towards monitoring which metabolite class or type are highlighted, with special emphasis on the necessary future developments to better mirror such intricate metabolic interactions in planta.
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Affiliation(s)
- Ahmed Serag
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Cairo 11751, Egypt
| | - Mohamed A. Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr st., Shibin Elkom 32511, Menoufia, Egypt
| | - Shilin Gong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Mohamed A. Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr el Aini St., Cairo 11562, Egypt
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7
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Borba MP, Witusk JP, Cunha DM, de Lima-Morales D, Martins AF, Van Der Sand S. Whole-genome sequencing-based characterization of Streptomyces sp. 6(4): focus on natural product. Access Microbiol 2023; 5:000466.v3. [PMID: 37091737 PMCID: PMC10118248 DOI: 10.1099/acmi.0.000466.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/23/2022] [Indexed: 03/06/2023] Open
Abstract
We have sequenced the whole genome of
Streptomyces
sp. 6(4) isolated from tomato roots that presents antifungal activity against phytopathogenic fungi, mainly Bipolaris sorokiniana. The genome has almost 7 Mb and 3368 hypothetical proteins that were analysed and characterized in Uniprot with the emphasis on biological compounds. Multilocus sequence typing (MLST) analyses were performed in an effort to characterize and identify this isolate, resulting in a new sequence type (ST), classified as ST64. Phenetic and phylogenetic trees were constructed to investigate
Streptomyces
sp. 6(4) evolution and sequence similarity, and the isolate is a strain closer to
Streptomyces prasinus
and
Streptomyces viridosporus
. It is known that the genus
Streptomyces
possess huge metabolic capacity with the presence of cryptic genes. These genes are usually present in clusters, which are responsible for the production of diverse natural products, mainly antibiotics. In addition, 6(4) showed 11 biosynthetic gene clusters through antiSMASH, including 3 polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) type clusters.
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Affiliation(s)
- Marcela Proença Borba
- Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - João Paulo Witusk
- Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Débora Marchesan Cunha
- Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Daiana de Lima-Morales
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
- Núcleo de Bioinformática do Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Andreza Francisco Martins
- Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Sueli Van Der Sand
- Programa de Pós-graduação em Microbiologia Agrícola e do Ambiente, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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8
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Gomes PWP, de Tralia Medeiros TC, Maimone NM, Leão TF, de Moraes LAB, Bauermeister A. Microbial Metabolites Annotation by Mass Spectrometry-Based Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:225-248. [PMID: 37843811 DOI: 10.1007/978-3-031-41741-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Since the discovery of penicillin, microbial metabolites have been extensively investigated for drug discovery purposes. In the last decades, microbial derived compounds have gained increasing attention in different fields from pharmacognosy to industry and agriculture. Microbial metabolites in microbiomes present specific functions and can be associated with the maintenance of the natural ecosystems. These metabolites may exhibit a broad range of biological activities of great interest to human purposes. Samples from either microbial isolated cultures or microbiomes consist of complex mixtures of metabolites and their analysis are not a simple process. Mass spectrometry-based metabolomics encompass a set of analytical methods that have brought several improvements to the microbial natural products field. This analytical tool allows the comprehensively detection of metabolites, and therefore, the access of the chemical profile from those biological samples. These analyses generate thousands of mass spectra which is challenging to analyse. In this context, bioinformatic metabolomics tools have been successfully employed to accelerate and facilitate the investigation of specialized microbial metabolites. Herein, we describe metabolomics tools used to provide chemical information for the metabolites, and furthermore, we discuss how they can improve investigation of microbial cultures and interactions.
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Affiliation(s)
- Paulo Wender P Gomes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Talita Carla de Tralia Medeiros
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Naydja Moralles Maimone
- Departamento de Ciências Exatas, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Tiago F Leão
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Luiz Alberto Beraldo de Moraes
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.
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9
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Montecillo JAV, Bae H. In silico analysis of koranimine, a cyclic imine compound from Peribacillus frigoritolerans reveals potential nematicidal activity. Sci Rep 2022; 12:18883. [PMID: 36344604 PMCID: PMC9640594 DOI: 10.1038/s41598-022-20461-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Pine wilt disease (PWD) is a destructive vector-borne forest disease caused by the nematode Bursaphelenchus xylophilus. To date, several options are available for the management of pine wilt disease; however constant development and search for natural products with potential nematicidal activity are imperative to diversify management options and to cope with the possible future emergence of resistance in parasitic nematodes. Here, a combined metabolomics and genomics approach was employed to investigate the chemical repertoire and biosynthetic potential of the bacterial endophyte Peribacillus frigoritolerans BE93, previously characterized to exhibit nematicidal activity against B. xylophilus. Feature-based molecular networking revealed the presence of diverse secondary metabolites. A cyclic imine heptapeptide, koranimine, was found to be among the most abundant secondary metabolites produced. Genome mining displayed the presence of several putative biosynthetic gene clusters (BGCs), including a dedicated non-ribosomal peptide synthase (NRPS) BGC for koranimine. Given the non-ribosomal peptide nature of koranimine, in silico molecular docking analysis was conducted to investigate its potential nematicidal activity against the target receptor ivermectin-sensitive invertebrate α glutamate-gated chloride channel (GluCl). Results revealed the binding of koranimine at the allosteric site of the channel-the ivermectin binding site. Moreover, the ligand-receptor interactions observed were mostly shared between koranimine and ivermectin when bound to the α GluCl receptor thus, suggesting a possibly shared mechanism of potential nematicidal activity. This study highlights the efficiency of combined metabolomics and genomics approach in the identification of candidate compounds.
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Affiliation(s)
- Jake Adolf V Montecillo
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
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10
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Effect of Site and Phenological Status on the Potato Bacterial Rhizomicrobiota. Microorganisms 2022; 10:microorganisms10091743. [PMID: 36144345 PMCID: PMC9501399 DOI: 10.3390/microorganisms10091743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
The potato is the fourth major food crop in the world. Its cultivation can encounter problems, resulting in poor growth and reduced yield. Plant microbiota has shown an ability to increase growth and resistance. However, in the development of effective microbiota manipulation strategies, it is essential to know the effect of environmental variables on microbiota composition and function. Here, we aimed to identify the differential impact of the site of cultivation and plant growth stage on potato rhizosphere microbiota. We performed a 16S rRNA gene amplicon sequencing analysis of rhizospheric soil collected from potato plants grown at four sites in central Italy during two phenological stages. Rhizomicrobiota was mainly composed of members of phyla Acidobacteriota, Actinobacteriota, Chloroflexi, and Proteobacteria and was affected by both the site of cultivation and the plant stages. However, cultivation sites overcome the effect of plant phenological stages. The PiCRUST analysis suggested a high abundance of functions related to the biosynthesis of the siderophore enterobactin. The presence of site-specific taxa and functional profiling of the microbiota could be further exploited in long-term studies to evaluate the possibility of developing biomarkers for traceability of the products and to exploit plant growth-promoting abilities in the native potato microbiota.
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11
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Nigericin and Geldanamycin Are Phytotoxic Specialized Metabolites Produced by the Plant Pathogen
Streptomyces
sp. 11-1-2. Microbiol Spectr 2022; 10:e0231421. [PMID: 35225656 PMCID: PMC9045263 DOI: 10.1128/spectrum.02314-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plant pathogens use a variety of mechanisms, including the production of phytotoxic specialized metabolites, to establish an infection of host tissue. Although thaxtomin A is considered the key phytotoxin involved in the development of potato scab disease, there is increasing evidence that other phytotoxins can play a role in disease development in some instances.
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12
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Steglińska A, Bekhter A, Wawrzyniak P, Kunicka-Styczyńska A, Jastrząbek K, Fidler M, Śmigielski K, Gutarowska B. Antimicrobial Activities of Plant Extracts against Solanum tuberosum L. Phytopathogens. Molecules 2022; 27:1579. [PMID: 35268680 PMCID: PMC8911893 DOI: 10.3390/molecules27051579] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 02/05/2023] Open
Abstract
The purpose of the study was to select an environmentally friendly plant biopesticide to protect seed potatoes against phytopathogens. The scope included the evaluation of the antimicrobial activities of 22 plant water extracts, 22 water-glycol extracts, and 3 subcritical carbon dioxide extracts using the agar diffusion method against 10 potato phytopathogens. For the most effective extracts, minimal inhibitory concentration (MIC), chemical composition analysis by gas chromatography-mass spectrometry and in situ assays on seed potatoes were performed. Garlic water extract was finally selected as the most effective in phytopathogen growth inhibition, both in vitro and in situ, with MIC values ranging between 6.3-25 mg/mL. 5-Hydroxymethylfurfural was determined to be the main component of this extract (33.24%). Garlic water extract was proposed as a potential biopesticide against potato phytopathogens.
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Affiliation(s)
- Aleksandra Steglińska
- Department of Environmental Biotechnology, Lodz University of Technology, Wólczańska 171/173, 90-530 Łódź, Poland; (M.F.); (K.Ś.); (B.G.)
| | - Anastasiia Bekhter
- Institute of Natural Products and Cosmetics, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Łódź, Poland; (A.B.); (K.J.)
| | - Paweł Wawrzyniak
- Faculty of Process and Environmental Engineering, Lodz University of Technology, Wólczańska 213, 90-924 Łódź, Poland;
| | - Alina Kunicka-Styczyńska
- Department of Sugar Industry and Food Safety Management, Lodz University of Technology, Wólczańska 171/173, 90-530 Łódź, Poland;
| | - Konrad Jastrząbek
- Institute of Natural Products and Cosmetics, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Łódź, Poland; (A.B.); (K.J.)
| | - Michał Fidler
- Department of Environmental Biotechnology, Lodz University of Technology, Wólczańska 171/173, 90-530 Łódź, Poland; (M.F.); (K.Ś.); (B.G.)
| | - Krzysztof Śmigielski
- Department of Environmental Biotechnology, Lodz University of Technology, Wólczańska 171/173, 90-530 Łódź, Poland; (M.F.); (K.Ś.); (B.G.)
| | - Beata Gutarowska
- Department of Environmental Biotechnology, Lodz University of Technology, Wólczańska 171/173, 90-530 Łódź, Poland; (M.F.); (K.Ś.); (B.G.)
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13
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Gutierrez J, Bakke A, Vatta M, Merrill AR. Plant Natural Products as Antimicrobials for Control of Streptomyces scabies: A Causative Agent of the Common Scab Disease. Front Microbiol 2022; 12:833233. [PMID: 35154047 PMCID: PMC8828645 DOI: 10.3389/fmicb.2021.833233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
The common scab disease caused by Streptomyces scabies, a soil-dwelling Gram-positive bacterium, is an economically important disease of potatoes and other tuber crops. The lack of effective treatments against this disease accounts for large economic losses globally. Plant extracts were screened to find several that effectively inhibited Streptomyces scabies growth in culture. Seven tinctures showed the greatest inhibition of S. scabies growth by reducing pathogen growth in culture by 75% or more. These extracts were myrrh, garlic, cayenne, barberry, frankincense, wild indigo root, and lavender. Myrrh extract from Commiphora myrrha, a resin made from tree sap, showed strong antibacterial activity by reducing the growth of S. scabies to 13% of the control. Additionally, a flavonoid library was screened to identify several compounds that were effective to control the pathogen growth. The flavonoids that showed the greatest inhibition of Streptomyces scabies growth were sophoraflavanone G, jaceosidin, baicalein, and quercetin. Minimum inhibitory concentrations for the effective flavonoids were calculated to be 6.8 ± 0.4 μM, 100.0 ± 2.1 μM, 202.9 ± 5.3 μM, and 285.2 ± 6.8 μM, respectively. The mean lethal doses for these flavonoids against Streptomyces scabies were 2.0 ± 0.1 μM, 22.6 ± 0.5 μM, 52.9 ± 1.3 μM, and 37.8 ± 1.0 μM, respectively. A live/dead assay showed complete cell death in the presence of sophoraflavanone G indicative of a bactericidal mechanism for flavonoid action on Streptomyces scabies. Scanning electron and transmission electron microscopy imaging showed damaged cell membrane morphologies when Streptomyces scabies was exposed to these flavonoids. Mycelia appeared as flat and deflated structures with contents seen as spewing from branching hyphae with numerous holes and tears in the membrane structure indicative of cell death. Sophoraflavanone G showed the greatest potency and potential as a natural antibiotic from the library of tested flavonoids. These results suggest that these plant compounds act on the pathogen through a bactericidal mechanism involving cell membrane destabilization and disruption leading to cell death.
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Deflandre B, Stulanovic N, Planckaert S, Anderssen S, Bonometti B, Karim L, Coppieters W, Devreese B, Rigali S. The virulome of Streptomyces scabiei in response to cello-oligosaccharide elicitors. Microb Genom 2022; 8. [PMID: 35040428 PMCID: PMC8914351 DOI: 10.1099/mgen.0.000760] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The development of spots or lesions symptomatic of common scab on root and tuber crops is caused by few pathogenic Streptomyces with Streptomyces scabiei 87–22 as the model species. Thaxtomin phytotoxins are the primary virulence determinants, mainly acting by impairing cellulose synthesis, and their production in S. scabiei is in turn boosted by cello-oligosaccharides released from host plants. In this work we aimed to determine which molecules and which biosynthetic gene clusters (BGCs) of the specialized metabolism of S. scabiei 87–22 show a production and/or a transcriptional response to cello-oligosaccharides. Comparative metabolomic analyses revealed that molecules of the virulome of S. scabiei induced by cellobiose and cellotriose include (i) thaxtomin and concanamycin phytotoxins, (ii) desferrioxamines, scabichelin and turgichelin siderophores in order to acquire iron essential for housekeeping functions, (iii) ectoine for protection against osmotic shock once inside the host, and (iv) bottromycin and concanamycin antimicrobials possibly to prevent other microorganisms from colonizing the same niche. Importantly, both cello-oligosaccharides reduced the production of the spore germination inhibitors germicidins thereby giving the ‘green light’ to escape dormancy and trigger the onset of the pathogenic lifestyle. For most metabolites - either with induced or reduced production - cellotriose was revealed to be a slightly stronger elicitor compared to cellobiose, supporting an earlier hypothesis which suggested the trisaccharide was the real trigger for virulence released from the plant cell wall through the action of thaxtomins. Interestingly, except for thaxtomins, none of these BGCs’ expression seems to be under direct control of the cellulose utilization repressor CebR suggesting the existence of a yet unknown mechanism for switching on the virulome. Finally, a transcriptomic analysis revealed nine additional cryptic BGCs that have their expression awakened by cello-oligosaccharides, suggesting that other and yet to be discovered metabolites could be part of the virulome of S. scabiei.
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Affiliation(s)
- Benoit Deflandre
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Nudzejma Stulanovic
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Sören Planckaert
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Sinaeda Anderssen
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Beatrice Bonometti
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Latifa Karim
- Genomics Platform, GIGA, University of Liège, B-4000, Liège, Belgium
| | - Wouter Coppieters
- Genomics Platform, GIGA, University of Liège, B-4000, Liège, Belgium
| | - Bart Devreese
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Sébastien Rigali
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
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Hwang IS, Oh EJ, Song E, Park IW, Lee Y, Sohn KH, Choi D, Oh CS. An Apoplastic Effector Pat-1 Cm of the Gram-Positive Bacterium Clavibacter michiganensis Acts as Both a Pathogenicity Factor and an Immunity Elicitor in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:888290. [PMID: 35432427 PMCID: PMC9006514 DOI: 10.3389/fpls.2022.888290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 05/09/2023]
Abstract
Clavibacter michiganensis, a Gram-positive plant-pathogenic bacterium, utilizes apoplastic effectors for disease development in host plants. Here, we determine the roles of Pat-1Cm (a putative serine protease) in pathogenicity and plant immunity. Pat-1Cm was found to be a genuine secreted protein, and the secreted mature form did not carry the first 33 amino acids predicted to be a signal peptide (SP). The pat-1Cm mutant impaired to cause wilting, but still caused canker symptom in tomato. Moreover, this mutant failed to trigger the hypersensitive response (HR) in a nonhost Nicotiana tabacum. Among orthologs and paralogs of pat-1Cm , only chp-7Cs from Clavibacter sepedonicus, a potato pathogen, successfully complemented pat-1Cm function in pathogenicity in tomato, whereas all failed to complement pat-1Cm function in HR induction in N. tabacum. Based on the structural prediction, Pat-1Cm carried a catalytic triad for putative serine protease, and alanine substitution of any amino acids in the triad abolished both pathogenicity and HR-inducing activities of Pat-1Cm in C. michiganensis. Ectopic expression of pat-1Cm with an SP from tobacco secreted protein triggered HR in N. tabacum, but not in tomato, whereas a catalytic triad mutant failed to induce HR. Inoculation of the pat-1Cm mutant mixed with the mutant of another apoplastic effector CelA (cellulase) caused severe wilting in tomato, indicating that these two apoplastic effectors can functionally cooperate in pathogenicity. Overall, these results indicate that Pat-1Cm is a distinct secreted protein carrying a functional catalytic triad for serine protease and this enzymatic activity might be critical for both pathogenicity and HR-eliciting activities of Pat-1Cm in plants.
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Affiliation(s)
- In Sun Hwang
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Eom-Ji Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Eunbee Song
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - In Woong Park
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, South Korea
| | - Doil Choi
- Department of Plant Science, Plant Immunity Research Center, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
- *Correspondence: Chang-Sik Oh,
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Old Enzyme, New Role: The β-Glucosidase BglC of Streptomyces scabiei Interferes with the Plant Defense Mechanism by Hydrolyzing Scopolin. BIOPHYSICA 2021. [DOI: 10.3390/biophysica2010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The beta-glucosidase BglC fulfills multiple functions in both primary metabolism and induction of pathogenicity of Streptomyces scabiei, the causative agent of common scab in root and tuber crops. Indeed, this enzyme hydrolyzes cellobiose and cellotriose to feed glycolysis with glucose directly and modifies the intracellular concentration of these cello-oligosaccharides, which are the virulence elicitors. The inactivation of bglC led to unexpected phenotypes such as the constitutive overproduction of thaxtomin A, the main virulence determinant of S. scabiei. In this work, we reveal a new target substrate of BglC, the phytoalexin scopolin. Removal of the glucose moiety of scopolin generates scopoletin, a potent inhibitor of thaxtomin A production. The hydrolysis of scopolin by BglC displayed substrate inhibition kinetics, which contrasts with the typical Michaelis–Menten saturation curve previously observed for the degradation of its natural substrate cellobiose. Our work, therefore, reveals that BglC targets both cello-oligosaccharide elicitors emanating from the hosts of S. scabiei, and the scopolin phytoalexin generated by the host defense mechanisms, thereby occupying a key position to fine-tune the production of the main virulence determinant thaxtomin A.
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