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Burguet P, La Rocca R, Kune C, Tellatin D, Stulanovic N, Rigolet A, Far J, Ongena M, Rigali S, Quinton L. Exploiting Differential Signal Filtering (DSF) and Image Structure Filtering (ISF) Methods for Untargeted Mass Spectrometry Imaging of Bacterial Metabolites. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1743-1755. [PMID: 39007645 DOI: 10.1021/jasms.4c00129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is a label-free technique, producing images where pixels contain mass spectra. The technique allows the visualization of the spatial distribution of (bio)molecules from metabolites to proteins, on surfaces such as tissues sections or bacteria culture media. One particularly exciting example of MALDI-MSI use rests on its potential to localize ionized compounds produced during microbial interactions and chemical communication, offering a molecular snapshot of metabolomes at a given time. The huge size and the complexity of generated MSI data make the processing of the data challenging, which requires the use of computational methods. Despite recent advances, currently available commercial software relies mainly on statistical tools to identify patterns, similarities, and differences within data sets. However, grouping m/z values unique to a given data set according to microbiological contexts, such as coculture experiments, still requires tedious manual analysis. Here we propose a nontargeted method exploiting the differential signals between negative controls and tested experimental conditions, i.e., differential signal filtering (DSF), and a scoring of the ion images using image structure filtering (ISF) coupled with a fold change score between the controls and the conditions of interest. These methods were first applied to coculture experiments involving Escherichia coli and Streptomyces coelicolor, revealing specific MS signals during bacterial interaction. Two case studies were also investigated: (i) cellobiose-mediated induction for the pathogenicity of Streptomyces scabiei, the causative agent of common scab on root and tuber crops, and (ii) iron-repressed production of siderophores of S. scabiei. This report proposes guidelines for MALDI-MSI data treatment applied in the case of microbiology contexts, with enhanced ion peak annotation in specific culture conditions. The strengths and weaknesses of the methods are discussed.
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Affiliation(s)
- Pierre Burguet
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Raphaël La Rocca
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Déborah Tellatin
- InBioS - Center for Protein Engineering, University of Liège, 4000 Liège, Belgium
| | - Nudzejma Stulanovic
- InBioS - Center for Protein Engineering, University of Liège, 4000 Liège, Belgium
| | - Augustin Rigolet
- Gembloux Agro-Bio Tech, University of Liege, 5030 Gembloux, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Marc Ongena
- Gembloux Agro-Bio Tech, University of Liege, 5030 Gembloux, Belgium
| | - Sébastien Rigali
- InBioS - Center for Protein Engineering, University of Liège, 4000 Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
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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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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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Yasawong M, Pana W, Chanthasena P, Santapan N, Songngamsuk T, Phatcharaharikarn M, Ganta P, Kerdtoob S, Nantapong N. Draft genome sequence data of the endophytic actinobacterium Streptomyces justiciae WPN32, a potential bioactive compounds producer. Data Brief 2024; 52:109844. [PMID: 38146286 PMCID: PMC10749237 DOI: 10.1016/j.dib.2023.109844] [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: 10/17/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023] Open
Abstract
Streptomyces justiciae WPN32 is an endophytic actinobacterium isolated from the rhizosphere of turmeric field soil at the Botanical Garden of Suranaree University of Technology (Nakhon Ratchasima Province, Thailand). Here we present the draft genome sequence of S. justiciae WPN32. It was sequenced on the Illumina NextSeq 550 sequencer. The draft genome consisted of 123 contigs with a total size of 9,832,147 base pairs, an N50 of 237,572 base pairs and a GC content of 70.87%. The dDDH between WPN32 and Streptomyces justiciae 3R004T was 80.1%, identifying the strain as Streptomyces justiciae. The data presented here may aid microbial taxonomy, comparative genomics and identification of gene clusters associated with the synthesis of bioactive compounds. The draft genome sequence data has been deposited at NCBI under Bioproject accession number PRJNA680432.
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Affiliation(s)
- Montri Yasawong
- Programme on Environmental Toxicology, Chulabhorn Graduate Institute, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Wannika Pana
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Panjamaphon Chanthasena
- Faculty of Allied Health Sciences, Nakhon Ratchasima College, Nakhon Ratchasima 30000, Thailand
| | - Napatsorn Santapan
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Thunwarat Songngamsuk
- Programme on Environmental Toxicology, Chulabhorn Graduate Institute, Bangkok 10210, Thailand
| | | | - Phongsakorn Ganta
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Supavadee Kerdtoob
- Faculty of Allied Health Sciences, Nakhon Ratchasima College, Nakhon Ratchasima 30000, Thailand
| | - Nawarat Nantapong
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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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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Pang F, Solanki MK, Wang Z. Streptomyces can be an excellent plant growth manager. World J Microbiol Biotechnol 2022; 38:193. [PMID: 35980475 DOI: 10.1007/s11274-022-03380-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/07/2022] [Indexed: 11/27/2022]
Abstract
Streptomyces, the most abundant and arguably the most important genus of actinomycetes, is an important source of biologically active compounds such as antibiotics, and extracellular hydrolytic enzymes. Since Streptomyces can have a beneficial symbiotic relationship with plants they can contribute to nutrition, health and fitness of the latter. This review article summarizes recent research contributions on the ability of Streptomyces to promote plant growth and improve plant tolerance to biotic and abiotic stress responses, as well as on the consequences, on plant health, of the enrichment of rhizospheric soils in Streptomyces species. This review summarizes the most recent reports of the contribution of Streptomyces to plant growth, health and fitness and suggests future research directions to promote the use of these bacteria for the development of a cleaner agriculture.
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Affiliation(s)
- Fei Pang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Biology and Pharmacy, Yulin Normal University, Yulin, 537000, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-701, Katowice, Poland.
| | - Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Biology and Pharmacy, Yulin Normal University, Yulin, 537000, China.
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Structure and Function of BcpE2, the Most Promiscuous GH3-Family Glucose Scavenging Beta-Glucosidase. mBio 2022; 13:e0093522. [PMID: 35913158 PMCID: PMC9426481 DOI: 10.1128/mbio.00935-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellulose being the most abundant polysaccharide on earth, beta-glucosidases hydrolyzing cello-oligosaccharides are key enzymes to fuel glycolysis in microorganisms developing on plant material. In Streptomyces scabiei, the causative agent of common scab in root and tuber crops, a genetic compensation phenomenon safeguards the loss of the gene encoding the cello-oligosaccharide hydrolase BglC by awakening the expression of alternative beta-glucosidases. Here, we revealed that the BglC compensating enzyme BcpE2 was the GH3-family beta-glucosidase that displayed the highest reported substrate promiscuity and was able to release the glucose moiety of all tested types of plant-derived heterosides (aryl β-glucosides, monolignol glucosides, cyanogenic glucosides, anthocyanosides, and coumarin heterosides). BcpE2 structure analysis highlighted a large cavity in the PA14 domain that covered the active site, and the high flexibility of this domain would allow proper adjustment of this cavity for disparate heterosides. The exceptional substrate promiscuity of BcpE2 provides microorganisms a versatile tool for scavenging glucose from plant-derived nutrients that widely vary in size and structure. Importantly, scopolin was the only substrate commonly hydrolyzed by both BglC and BcpE2, thereby generating the potent virulence inhibitor scopoletin. Next to fueling glycolysis, both enzymes would also fine-tune the strength of virulence. IMPORTANCE Plant decaying biomass is the most abundant provider of carbon sources for soil-dwelling microorganisms. To optimally evolve in such environmental niches, microorganisms possess an arsenal of hydrolytic enzymatic complexes to feed on the various types of polysaccharides, oligosaccharides, and monosaccharides. In this work, structural, enzymatic, and expression studies revealed the existence of a "swiss-army knife" enzyme, BcpE2, that was able to retrieve the glucose moiety of a multitude of plant-derived substrates that vary in size, structure, and origin. This enzyme would provide the microorganisms with a tool that would allow them to find nutrients from any type of plant-derived material.
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