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Präve L, Seyfert CE, Bozhüyük KAJ, Racine E, Müller R, Bode HB. Investigation of the Odilorhabdin Biosynthetic Gene Cluster Using NRPS Engineering. Angew Chem Int Ed Engl 2024; 63:e202406389. [PMID: 38801753 DOI: 10.1002/anie.202406389] [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: 04/03/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
The recently identified natural product NOSO-95A from entomopathogenic Xenorhabdus bacteria, derived from a biosynthetic gene cluster (BGC) encoding a non-ribosomal peptide synthetase (NRPS), was the first member of the odilorhabdin class of antibiotics. This class exhibits broad-spectrum antibiotic activity and inspired the development of the synthetic derivative NOSO-502, which holds potential as a new clinical drug by breaking antibiotic resistance. While the mode of action of odilorhabdins was broadly investigated, their biosynthesis pathway remained poorly understood. Here we describe the heterologous production of NOSO-95A in Escherichia coli after refactoring the complete BGC. Since the production titer was low, NRPS engineering was applied to uncover the underlying biosynthetic principles. For this, modules of the odilorhabdin NRPS fused to other synthetases were co-expressed with candidate hydroxylases encoded in the BGC allowing the characterization of the biosynthesis of three unusual amino acids and leading to the identification of a prodrug-activation mechanism by deacylation. Our work demonstrates the application of NRPS engineering as a blueprint to mechanistically elucidate large or toxic NRPS and provides the basis to generate novel odilorhabdin analogues with improved properties in the future.
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Affiliation(s)
- Leonard Präve
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Carsten E Seyfert
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Department of Pharmacy, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Hannover-Braunschweig, Germany
| | - Kenan A J Bozhüyük
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438, Frankfurt, Germany
- Myria Biosciences AG, Hochbergerstrasse 60 C, 4057, Basel, Switzerland
- Present address: Synthetic Biology of Microbial Natural Products (SIMS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123, Saarbrücken, Germany
| | - Emilie Racine
- Nosopharm, 226 rue Georges Besse, 30000, Nîmes, France
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Department of Pharmacy, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Hannover-Braunschweig, Germany
| | - Helge B Bode
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438, Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043, Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043, Marburg, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt, Germany
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2
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Lam YC, Hamchand R, Mucci NC, Kauffman SJ, Dudkina N, Reagle EV, Casanova-Torres ÁM, DeCuyper J, Chen H, Song D, Thomas MG, Palm NW, Goodrich-Blair H, Crawford JM. The Xenorhabdus nematophila LrhA transcriptional regulator modulates production of γ-keto- N-acyl amides with inhibitory activity against mutualistic host nematode egg hatching. Appl Environ Microbiol 2024; 90:e0052824. [PMID: 38916293 PMCID: PMC11267870 DOI: 10.1128/aem.00528-24] [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: 03/21/2024] [Accepted: 06/01/2024] [Indexed: 06/26/2024] Open
Abstract
Xenorhabdus nematophila is a symbiotic Gammaproteobacterium that produces diverse natural products that facilitate mutualistic and pathogenic interactions in their nematode and insect hosts, respectively. The interplay between X. nematophila secondary metabolism and symbiosis stage is tuned by various global regulators. An example of such a regulator is the LysR-type protein transcription factor LrhA, which regulates amino acid metabolism and is necessary for virulence in insects and normal nematode progeny production. Here, we utilized comparative metabolomics and molecular networking to identify small molecule factors regulated by LrhA and characterized a rare γ-ketoacid (GKA) and two new N-acyl amides, GKA-Arg (1) and GKA-Pro (2) which harbor a γ-keto acyl appendage. A lrhA null mutant produced elevated levels of compound 1 and reduced levels of compound 2 relative to wild type. N-acyl amides 1 and 2 were shown to be selective agonists for the human G-protein-coupled receptors (GPCRs) C3AR1 and CHRM2, respectively. The CHRM2 agonist 2 deleteriously affected the hatch rate and length of Steinernema nematodes. This work further highlights the utility of exploiting regulators of host-bacteria interactions for the identification of the bioactive small molecule signals that they control. IMPORTANCE Xenorhabdus bacteria are of interest due to their symbiotic relationship with Steinernema nematodes and their ability to produce a variety of natural bioactive compounds. Despite their importance, the regulatory hierarchy connecting specific natural products and their regulators is poorly understood. In this study, comparative metabolomic profiling was utilized to identify the secondary metabolites modulated by the X. nematophila global regulator LrhA. This analysis led to the discovery of three metabolites, including an N-acyl amide that inhibited the egg hatching rate and length of Steinernema carpocapsae nematodes. These findings support the notion that X. nematophila LrhA influences the symbiosis between X. nematophila and S. carpocapsae through N-acyl amide signaling. A deeper understanding of the regulatory hierarchy of these natural products could contribute to a better comprehension of the symbiotic relationship between X. nematophila and S. carpocapsae.
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Affiliation(s)
- Yick Chong Lam
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
| | - Randy Hamchand
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
| | - Nicholas C. Mucci
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Sarah J. Kauffman
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Natavan Dudkina
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
| | - Emily V. Reagle
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Jessica DeCuyper
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Haiwei Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Deguang Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael G. Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Noah W. Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Heidi Goodrich-Blair
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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3
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Li J, Wang K, Luo S, Tian Y, Li Y, Hu S, Tan H, Zhang J, Li J. Co-expression of a pair of interdependent regulators coding genes ovmZ and ovmW awakens the production of angucyclinones antibiotics in Streptomyces neyagawaensis. Microb Cell Fact 2024; 23:202. [PMID: 39026365 PMCID: PMC11264864 DOI: 10.1186/s12934-024-02478-y] [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: 05/20/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Microbial genome sequencing and analysis revealed the presence of abundant silent secondary metabolites biosynthetic gene clusters (BGCs) in streptomycetes. Activating these BGCs has great significance for discovering new compounds and novel biosynthetic pathways. RESULTS In this study, we found that ovmZ and ovmW homologs, a pair of interdependent transcriptional regulators coding genes, are widespread in actinobacteria and closely associated with the biosynthesis of secondary metabolites. Through co-overexpression of native ovmZ and ovmW in Streptomyces neyagawaensis NRRL B-3092, a silent type II polyketide synthase (PKS) gene cluster was activated to produce gephyromycin A, tetrangomycin and fridamycin E with the yields of 22.3 ± 8.0 mg/L, 4.8 ± 0.5 mg/L and 20.3 ± 4.1 mg/L respectively in the recombinant strain of S.ne/pZnWn. However, expression of either ovmZ or ovmW failed to activate this gene cluster. Interestingly, overexpression of the heterologous ovmZ and ovmW pair from oviedomycin BGC of S. ansochromogenes 7100 also led to awakening of this silent angucyclinone BGC in S. neyagawaensis. CONCLUSION A silent angucyclinone BGC was activated by overexpressing both ovmZ and ovmW in S. neyagawaensis. Due to the wide distribution of ovmZ and ovmW in the BGCs of actinobacteria, co-overexpression of ovmZ and ovmW could be a strategy for activating silent BGCs, thus stimulating the biosynthesis of secondary metabolites.
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Affiliation(s)
- Junyue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sainan Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuqing Tian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jine Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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Chandrakasan G, García-Trejo JF, Feregrino-Pérez AA, Aguirre-Becerra H, García ER, Nieto-Ramírez MI. Preliminary Screening on Antibacterial Crude Secondary Metabolites Extracted from Bacterial Symbionts and Identification of Functional Bioactive Compounds by FTIR, HPLC and Gas Chromatography-Mass Spectrometry. Molecules 2024; 29:2914. [PMID: 38930979 PMCID: PMC11206551 DOI: 10.3390/molecules29122914] [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] [Received: 04/30/2024] [Revised: 06/02/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Secondary metabolites, bioactive compounds produced by living organisms, can unveil symbiotic relationships in nature. In this study, soilborne entomopathogenic nematodes associated with symbiotic bacteria (Xenorhabdus stockiae and Photorhabdus luminescens) were extracted from solvent supernatant containing secondary metabolites, demonstrating significant inhibitory effects against E. coli, S. aureus, B. subtilus, P. mirabilis, E. faecalis, and P. stutzeri. The characterization of these secondary metabolites by Fourier transforms infrared spectroscopy revealed amine groups of proteins, hydroxyl and carboxyl groups of polyphenols, hydroxyl groups of polysaccharides, and carboxyl groups of organic acids. Furthermore, the obtained crude extracts were analyzed by high-performance liquid chromatography for the basic identification of potential bioactive peptides. Gas chromatography-mass spectrometry analysis of ethyl acetate extracts from Xenorhabdus stockiae identified major compounds including nonanoic acid derivatives, proline, paromycin, octodecanal derivatives, trioxa-5-aza-1-silabicyclo, 4-octadecenal, methyl ester, oleic acid, and 1,2-benzenedicarboxylicacid. Additional extraction from Photorhabdus luminescens yielded functional compounds such as indole-3-acetic acid, phthalic acid, 1-tetradecanol, nemorosonol, 1-eicosanol, and unsaturated fatty acids. These findings support the potential development of novel natural antimicrobial agents for future pathogen suppression.
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Affiliation(s)
- Gobinath Chandrakasan
- División de Estudios de Posgrado, Facultad de Ingeniería, Universidad Autónoma de Querétaro, Santiago de Querétaro 76010, Querétaro, Mexico; (A.A.F.-P.); (H.A.-B.); (E.R.G.); (M.I.N.-R.)
| | - Juan Fernando García-Trejo
- División de Estudios de Posgrado, Facultad de Ingeniería, Universidad Autónoma de Querétaro, Santiago de Querétaro 76010, Querétaro, Mexico; (A.A.F.-P.); (H.A.-B.); (E.R.G.); (M.I.N.-R.)
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5
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Nuhamunada M, Mohite OS, Phaneuf P, Palsson B, Weber T. BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets. Nucleic Acids Res 2024; 52:5478-5495. [PMID: 38686794 PMCID: PMC11162802 DOI: 10.1093/nar/gkae314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome mining of bacterial pangenomes. BGCFlow incorporates several genome analytics and mining tools grouped into five common stages of analysis such as: (i) data selection, (ii) functional annotation, (iii) phylogenetic analysis, (iv) genome mining, and (v) comparative analysis. Furthermore, BGCFlow provides easy configuration of different projects, parallel distribution, scheduled job monitoring, an interactive database to visualize tables, exploratory Jupyter Notebooks, and customized reports. Here, we demonstrate the application of BGCFlow by investigating the phylogenetic distribution of various biosynthetic gene clusters detected across 42 genomes of the Saccharopolyspora genus, known to produce industrially important secondary/specialized metabolites. The BGCFlow-guided analysis predicted more accurate dereplication of BGCs and guided the targeted comparative analysis of selected RiPPs. The scalable, interoperable, adaptable, re-entrant, and reproducible nature of the BGCFlow will provide an effective novel way to extract the biosynthetic knowledge from the ever-growing genomic datasets of biotechnologically relevant bacterial species.
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Affiliation(s)
- Matin Nuhamunada
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Omkar S Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Patrick V Phaneuf
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Bernhard O Palsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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6
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Shende VV, Bauman KD, Moore BS. The shikimate pathway: gateway to metabolic diversity. Nat Prod Rep 2024; 41:604-648. [PMID: 38170905 PMCID: PMC11043010 DOI: 10.1039/d3np00037k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Covering: 1997 to 2023The shikimate pathway is the metabolic process responsible for the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Seven metabolic steps convert phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) into shikimate and ultimately chorismate, which serves as the branch point for dedicated aromatic amino acid biosynthesis. Bacteria, fungi, algae, and plants (yet not animals) biosynthesize chorismate and exploit its intermediates in their specialized metabolism. This review highlights the metabolic diversity derived from intermediates of the shikimate pathway along the seven steps from PEP and E4P to chorismate, as well as additional sections on compounds derived from prephenate, anthranilate and the synonymous aminoshikimate pathway. We discuss the genomic basis and biochemical support leading to shikimate-derived antibiotics, lipids, pigments, cofactors, and other metabolites across the tree of life.
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Affiliation(s)
- Vikram V Shende
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Katherine D Bauman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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Buedenbender L, Ageitos L, Lages MA, Platas-Iglesias C, Balado M, Lemos ML, Rodríguez J, Jiménez C. O-versus S-Metal Coordination of the Thiocarboxylate Group: An NMR Study of the Two Tautomeric Forms of the Ga(III)-Photoxenobactin E Complex. Inorg Chem 2024; 63:4176-4184. [PMID: 38387064 PMCID: PMC10915793 DOI: 10.1021/acs.inorgchem.3c04076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024]
Abstract
Photoxenobactin E (1) is a natural product with an unusual thiocarboxylic acid terminus recently isolated from an entomopathogenic bacterium. The biosynthetic gene cluster associated with photoxenobactin E, and other reported derivatives, is very similar to that of piscibactin, the siderophore responsible for the iron uptake among bacteria of the Vibrionaceae family, including potential human pathogens. Here, the reisolation of 1 from the fish pathogen Vibrio anguillarum RV22 cultured under iron deprivation, its ability to chelate Ga(III), and the full NMR spectroscopic characterization of the Ga(III)-photoxenobactin E complex are presented. Our results show that Ga(III)-photoxenobactin E in solution exists in a thiol-thione tautomeric equilibrium, where Ga(III) is coordinated through the sulfur (thiol form) or oxygen (thione form) atoms of the thiocarboxylate group. This report represents the first NMR study of the chemical exchange between the thiol and thione forms associated with thiocarboxylate-Ga(III) coordination, including the kinetics of the interconversion process associated with this tautomeric exchange. These findings show significant implications for ligand design as they illustrate the potential of the thiocarboxylate group as a versatile donor for hard metal ions such as Ga(III).
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Affiliation(s)
- Larissa Buedenbender
- CICA
− Centro Interdisciplinar de Química e Bioloxía
e Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Lucía Ageitos
- CICA
− Centro Interdisciplinar de Química e Bioloxía
e Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Marta A. Lages
- Departamento
de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Carlos Platas-Iglesias
- CICA
− Centro Interdisciplinar de Química e Bioloxía
e Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Miguel Balado
- Departamento
de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Manuel L. Lemos
- Departamento
de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Jaime Rodríguez
- CICA
− Centro Interdisciplinar de Química e Bioloxía
e Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Carlos Jiménez
- CICA
− Centro Interdisciplinar de Química e Bioloxía
e Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
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Ogaya C, Huong N, Touceda-González M, Barg M, Dörfler V, Ehlers RU, Molina C. Monitoring the Photorhabdus spp. bacterial load in Heterorhabditis bacteriophora dauer juveniles over different storage times and temperatures: A molecular approach. J Invertebr Pathol 2024; 203:108048. [PMID: 38159796 DOI: 10.1016/j.jip.2023.108048] [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] [Received: 10/06/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Biological control products based on the entomopathogenic nematode Heterorhabditis bacteriophora can vary in virulence (quality). The influence of their symbiotic bacteria Photorhabdus spp. inside the infective dauer juvenile (DJ) on DJ quality has not received much attention in the past. The presence of the bacteria in the DJ is crucial for its biocontrol potential. This investigation provides a method to quantify the bacterial load inside the DJ based on a qPCR technique. Information from the genome of Photorhabdus laumondii strain DE2 was used to identify single copy genes with no homology to any other bacterial accessions. One gene (hereby named CG2) was selected for primers design and for further qPCR experiments. Cross-amplification tests with P. thracensis and P. kayaii, also symbionts of H. bacteriophora, were positive, whereas no amplicons were produced for P. temperata or Xenorhabdus nematophila. We tested our qPCR system in DJ populations carrying defined proportions of bacteria-free (axenic) vs bacteria-carrying nematodes. With an increasing proportion of axenic DJ in a population, virulence declined, and the virulence was proportional to the amount of bacterial DNA detected in the population by qPCR. Along liquid storage over long time, virulence also decreased, and this factor correlated with the reduction of bacterial DNA on the respective DJ population. We observed that stored DJ kept virulent up to 90 days and thereafter the virulence as well as the amount of bacterial DNA drastically decreased. Storage temperature also influenced the bacterial survival. Inside formulated DJ, the loss of bacterial DNA on the DJ population was accelerated under storage temperatures below 7.5 °C, suggesting that reproduction of the bacterial cells takes place when growth temperature is favorable. The role of bacterial survival inside stored DJ can now be adequately addressed using this molecular quality-control technique.
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Affiliation(s)
- Christopher Ogaya
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118 Kiel, Germany; e-nema GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany
| | - Nontarak Huong
- Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | | | - Mike Barg
- e-nema GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany
| | - Verena Dörfler
- e-nema GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany
| | - Ralf-Udo Ehlers
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118 Kiel, Germany; Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Carlos Molina
- e-nema GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany.
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9
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Huang X, Tang Q, Liu S, Li C, Li Y, Sun Y, Ding X, Xia L, Hu S. Discovery of an antitumor compound from xenorhabdus stockiae HN_xs01. World J Microbiol Biotechnol 2024; 40:101. [PMID: 38366186 DOI: 10.1007/s11274-024-03915-1] [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: 04/25/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024]
Abstract
Xenorhabdus, known for its symbiotic relationship with Entomopathogenic nematodes (EPNs), belongs to the Enterobacteriaceae family. This dual-host symbiotic nematode exhibits pathogenic traits, rendering it a promising biocontrol agent against insects. Our prior investigations revealed that Xenorhabdus stockiae HN_xs01, isolated in our laboratory, demonstrates exceptional potential in halting bacterial growth and displaying anti-tumor activity. Subsequently, we separated and purified the supernatant of the HN_xs01 strain and obtained a new compound with significant inhibitory activity on tumor cells, which we named XNAE. Through LC-MS analysis, the mass-to-nucleus ratio of XNAE was determined to be 254.24. Our findings indicated that XNAE exerts a time- and dose-dependent inhibition on B16 and HeLa cells. After 24 h, its IC50 for B16 and HeLa cells was 30.178 µg/mL and 33.015 µg/mL, respectively. Electron microscopy revealed conspicuous damage to subcellular structures, notably mitochondria and the cytoskeleton, resulting in a notable reduction in cell numbers among treated tumor cells. Interestingly, while XNAE exerted a more pronounced inhibitory effect on B16 cells compared to HeLa cells, it showed no discernible impact on HUVEC cells. Treatment of B16 cells with XNAE induced early apoptosis and led to cell cycle arrest in the G2 phase, as evidenced by flow cytometry analysis. The impressive capability of X. stockiae HN_xs01 in synthesizing bioactive secondary metabolites promises to significantly expand the reservoir of natural products. Further exploration to identify the bioactivity of these compounds holds the potential to shed light on their roles in bacteria-host interaction. Overall, these outcomes underscore the promising potential of XNAE as a bioactive compound for tumor treatment.
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Affiliation(s)
- Xiyin Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Qiong Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Siqin Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Chen Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Yaoguang Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Yunjun Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Xuezhi Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Shengbiao Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China.
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10
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Palma L, Frizzo L, Kaiser S, Berry C, Caballero P, Bode HB, Del Valle EE. Genome Sequence Analysis of Native Xenorhabdus Strains Isolated from Entomopathogenic Nematodes in Argentina. Toxins (Basel) 2024; 16:108. [PMID: 38393187 PMCID: PMC10892061 DOI: 10.3390/toxins16020108] [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: 01/02/2024] [Revised: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Entomopathogenic nematodes from the genus Steinernema (Nematoda: Steinernematidae) are capable of causing the rapid killing of insect hosts, facilitated by their association with symbiotic Gram-negative bacteria in the genus Xenorhabdus (Enterobacterales: Morganellaceae), positioning them as interesting candidate tools for the control of insect pests. In spite of this, only a limited number of species from this bacterial genus have been identified from their nematode hosts and their insecticidal properties documented. This study aimed to perform the genome sequence analysis of fourteen Xenorhabdus strains that were isolated from Steinernema nematodes in Argentina. All of the strains were found to be able of killing 7th instar larvae of Galleria mellonella (L.) (Lepidoptera: Pyralidae). Their sequenced genomes harbour 110 putative insecticidal proteins including Tc, Txp, Mcf, Pra/Prb and App homologs, plus other virulence factors such as putative nematocidal proteins, chitinases and secondary metabolite gene clusters for the synthesis of different bioactive compounds. Maximum-likelihood phylogenetic analysis plus average nucleotide identity calculations strongly suggested that three strains should be considered novel species. The species name for strains PSL and Reich (same species according to % ANI) is proposed as Xenorhabdus littoralis sp. nov., whereas strain 12 is proposed as Xenorhabdus santafensis sp. nov. In this work, we present a dual insight into the biocidal potential and diversity of the Xenorhabdus genus, demonstrated by different numbers of putative insecticidal genes and biosynthetic gene clusters, along with a fresh exploration of the species within this genus.
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Affiliation(s)
- Leopoldo Palma
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Departamento de Genética, Universitat de València, 46100 Burjassot, Spain
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
- Instituto Multidisciplinario de Investigación y Transferencia Agroalimentaria y Biotecnológica (IMITAB), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Villa María (UNVM), Villa María 1555, Argentina
| | - Laureano Frizzo
- ICIVET Litoral, CONICET-UNL, Departamento de Salud Pública, Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, Esperanza S3080, Argentina;
| | - Sebastian Kaiser
- Department of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany; (S.K.); (H.B.B.)
- Evolutionary Biochemistry Group, Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Colin Berry
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK;
| | - Primitivo Caballero
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra, 31006 Pamplona, Spain;
- Departamento de Investigación y Desarrollo, Bioinsectis SL, Polígono Industrial Mocholi Plaza Cein 5, Nave A14, 31110 Noain, Spain
| | - Helge B. Bode
- Department of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany; (S.K.); (H.B.B.)
- Molecular Biotechnology, Department of Biosciences, Goethe Universität Frankfurt, 60438 Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt, Germany
| | - Eleodoro Eduardo Del Valle
- ICiagro Litoral, CONICET, Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Kreder 2805, Esperanza S3080, Argentina
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11
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Jin G, Kim IH, Kim Y. The Lrp transcriptional factor of an entomopathogenic bacterium, Xenorhabdus hominickii, activates non-ribosomal peptide synthetases to suppress insect immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 151:105101. [PMID: 38000489 DOI: 10.1016/j.dci.2023.105101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/11/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Two bacterial genera, Xenorhabdus and Photorhabdus, are mutually symbiotic to the entomopathogenic nematodes, Steinernema and Heterorhabditis, respectively. The infective juveniles deliver the symbiotic bacteria to the hemocoel of target insects, in which the bacteria proliferate and help the development of the host nematode. The successful parasitism of the nematode-bacterial complex depends on host immunosuppression by the bacteria via their secondary metabolites. Leucine-responsive regulatory protein (Lrp) is a global bacterial transcriptional factor that plays a crucial role in parasitism. However, its regulatory targets to suppress insect immunity are not clearly understood. This study investigated the bacterial genes regulated by Lrp and the subsequent production of secondary metabolites in Xenorhabdus hominickii. Lrp expression occurred at the early infection stage of the bacteria in a target insect, Spodoptera exigua. A preliminary in silico screening indicated that 3.7% genes among 4075 predicted genes encoded in X. hominickii had the Lrp-response element on their promoters, including two non-ribosomal peptide synthetases (NRPSs). Eight NRPS (NRPS1-NRPS8) genes were predicted in the bacterial genome, in which six NRPS (NRPS3-NRPS8) expressions were positively correlated with Lrp expression in the infected larvae of S. exigua. Exchange of the Lrp promoter with an inducible promoter altered the production of the secondary metabolites and the NRPS expression levels. The immunosuppressive activities of X. hominickii were dependent on the Lrp expression level. The metabolites produced by Lrp expression included the eicosanoid-biosynthesis inhibitors and hemolytic factors. A cyclic dipeptide (=cPF) was produced by the bacteria at high Lrp expression and inhibited the phospholipase A2 activity of S. exigua in a competitive inhibitory manner. These results suggest that Lrp is a global transcriptional factor of X. hominickii and plays a crucial role in insect immunosuppression by modulating NRPS expression.
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Affiliation(s)
- Gahyeon Jin
- Department of Plant Medicals, Andong National University, Andong, 36729, South Korea
| | - Il-Hwan Kim
- Korea Research Institute of Standards and Science, Daejeon, 34113, South Korea
| | - Yonggyun Kim
- Department of Plant Medicals, Andong National University, Andong, 36729, South Korea.
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12
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Jin G, Kim Y. Screening of insect immune suppressors using a recombinant phospholipase A2 of a lepidopteran insect. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22081. [PMID: 38288493 DOI: 10.1002/arch.22081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 02/01/2024]
Abstract
Phospholipase A2 (PLA2 ) catalyzes phospholipids at the sn-2 position to release free fatty acids, including arachidonic acid (AA) or its precursor. The free AA is then oxygenated into different eicosanoids, which mediate the diverse physiological processes in insects. Any inhibition of the PLA2 catalysis would give rise to serious malfunctioning in insect growth and development. An onion moth, Acrolepiopsis sapporensis, encodes four different PLA2 genes (As-PLA2 A-As-PLA2 D), in which As-PLA2 A is dominantly expressed at all developmental stages and in different larval tissues. RNA interference of the As-PLA2 A expression significantly reduced the PLA2 activity of A. sapporensis, which suffered from immunosuppression. A recombinant As-PLA2 A protein was purified from a bacterial expression system, which exhibited a typical Michaelis-Menten kinetics and hence susceptible to a specific inhibitor to sPLA2 and dithiothreitol. A total of 19 bacterial metabolites derived from Xenorhabdus and Photorhabdus were screened against the recombinant As-PLA2 A. Five potent metabolites were highly inhibitory and followed a competitive enzyme inhibition. These five inhibitors suppressed the immune responses of A. sapporensis by inhibiting hemocyte-spreading behavior and phenoloxidase activity. However, an addition of AA could significantly rescue the immunosuppression induced by the selected inhibitors. These studies suggest that the recombinant As-PLA2 A protein can be applied for high-throughput screening of insect immunosuppressive compounds.
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Affiliation(s)
- Gahyeon Jin
- Department of Plant Medicals, Andong National University, Andong, Korea
| | - Yonggyun Kim
- Department of Plant Medicals, Andong National University, Andong, Korea
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13
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Jin G, Hrithik MTH, Lee DH, Kim IH, Jung JS, Bode HB, Kim Y. Manipulation of GameXPeptide synthetase gene expression by a promoter exchange alters the virulence of an entomopathogenic bacterium, Photorhabdus temperata temperata, by modulating insect immune responses. Front Microbiol 2023; 14:1271764. [PMID: 38173677 PMCID: PMC10764021 DOI: 10.3389/fmicb.2023.1271764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/23/2023] [Indexed: 01/05/2024] Open
Abstract
An entomopathogenic bacterium, Photorhabdus temperata subsp. temperata, is mutualistic to its host nematode, Heterorhabditis megidis. The infective juvenile nematodes enter target insects through natural openings and release the symbiotic bacteria into the insect hemocoel. The released bacteria suppress the insect immune responses and cause septicemia through their secondary metabolites. GameXPeptide (GXP) is one of the common secondary metabolites of most Photorhabdus species and is produced by the catalytic activity of a specific non-ribosomal peptide synthetase called GxpS encoded by the gxpS gene. This study confirmed gxpS to be encoded in the P. temperata temperata genome and analyzed its expression during bacterial growth. LC-MS/MS analysis of the bacterial culture broth contained at least four different GXPs (GXP-A to GXP-D), in which GXP-A was the most abundant. To investigate GXP synthesis following gxpS expression, the gxpS promoter of P. temperata temperata was replaced with an inducible arabinose promoter by homologous recombination. The gxpS transcript levels in the mutant were altered by the addition of l-arabinose. Without the inducer, the gxpS transcript level was significantly lower compared to the wild type and produced significantly lower amounts of the four GXPs. The addition of the inducer to the mutant significantly increased gxpS expression and produced significantly higher levels of the four GXPs compared to the wild type. The metabolite extracts obtained from wild-type and mutant bacteria showed differential immunosuppressive activities according to their GXP contents against the cellular and humoral immune responses of a lepidopteran insect, Spodoptera exigua. Interestingly, the gxpS-mutant bacteria showed less insecticidal activity compared to the wild type, whereas the addition of GXP to the mutant significantly restored insecticidal activity. These results suggest that the gxpS gene encoded in P. temperata temperata is responsible for the production of at least four different GXPs, which play crucial roles in bacterial virulence.
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Affiliation(s)
- Gahyeon Jin
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
| | | | - Dong-Hee Lee
- Industry Academy Cooperation Foundation, Andong National University, Andong, Republic of Korea
| | - Il-Hwan Kim
- Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Ji-Seon Jung
- Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Helge B. Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe Universität Frankfurt, Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips Universität Marburg, Marburg, Germany
- Department of Chemistry, Phillips Universität Marburg, Marburg, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
| | - Yonggyun Kim
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
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14
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Gouda NA, Alshammari SO, Abourehab MAS, Alshammari QA, Elkamhawy A. Therapeutic potential of natural products in inflammation: underlying molecular mechanisms, clinical outcomes, technological advances, and future perspectives. Inflammopharmacology 2023; 31:2857-2883. [PMID: 37950803 DOI: 10.1007/s10787-023-01366-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/06/2023] [Indexed: 11/13/2023]
Abstract
Chronic inflammation is a common underlying factor in many major diseases, including heart disease, diabetes, cancer, and autoimmune disorders, and is responsible for up to 60% of all deaths worldwide. Metformin, statins, and corticosteroids, and NSAIDs (non-steroidal anti-inflammatory drugs) are often given as anti-inflammatory pharmaceuticals, however, often have even more debilitating side effects than the illness itself. The natural product-based therapy of inflammation-related diseases has no adverse effects and good beneficial results compared to substitute conventional anti-inflammatory medications. In this review article, we provide a concise overview of present pharmacological treatments, the pathophysiology of inflammation, and the signaling pathways that underlie it. In addition, we focus on the most promising natural products identified as potential anti-inflammatory therapeutic agents. Moreover, preclinical studies and clinical trials evaluating the efficacy of natural products as anti-inflammatory therapeutic agents and their pragmatic applications with promising outcomes are reviewed. In addition, the safety, side effects and technical barriers of natural products are discussed. Furthermore, we also summarized the latest technological advances in the discovery and scientific development of natural products-based medicine.
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Affiliation(s)
- Noha A Gouda
- College of Pharmacy, Dongguk University-Seoul, Goyang, Gyeonggi, 10326, Republic of Korea
| | - Saud O Alshammari
- Department of Pharmacognosy and Alternative Medicine, Faculty of Pharmacy, Northern Border University, Rafha, 76321, Saudi Arabia
| | - Mohammed A S Abourehab
- Department of Pharmaceutics, College of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Qamar A Alshammari
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Northern Border University, Rafha, 76321, Saudi Arabia
| | - Ahmed Elkamhawy
- College of Pharmacy, Dongguk University-Seoul, Goyang, Gyeonggi, 10326, Republic of Korea.
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
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15
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Meesil W, Muangpat P, Sitthisak S, Rattanarojpong T, Chantratita N, Machado RAR, Shi YM, Bode HB, Vitta A, Thanwisai A. Genome mining reveals novel biosynthetic gene clusters in entomopathogenic bacteria. Sci Rep 2023; 13:20764. [PMID: 38007490 PMCID: PMC10676414 DOI: 10.1038/s41598-023-47121-9] [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: 08/07/2023] [Accepted: 11/09/2023] [Indexed: 11/27/2023] Open
Abstract
The discovery of novel bioactive compounds produced by microorganisms holds significant potential for the development of therapeutics and agrochemicals. In this study, we conducted genome mining to explore the biosynthetic potential of entomopathogenic bacteria belonging to the genera Xenorhabdus and Photorhabdus. By utilizing next-generation sequencing and bioinformatics tools, we identified novel biosynthetic gene clusters (BGCs) in the genomes of the bacteria, specifically plu00736 and plu00747. These clusters were identified as unidentified non-ribosomal peptide synthetase (NRPS) and unidentified type I polyketide synthase (T1PKS) clusters. These BGCs exhibited unique genetic architecture and encoded several putative enzymes and regulatory elements, suggesting its involvement in the synthesis of bioactive secondary metabolites. Furthermore, comparative genome analysis revealed that these BGCs were distinct from previously characterized gene clusters, indicating the potential for the production of novel compounds. Our findings highlighted the importance of genome mining as a powerful approach for the discovery of biosynthetic gene clusters and the identification of novel bioactive compounds. Further investigations involving expression studies and functional characterization of the identified BGCs will provide valuable insights into the biosynthesis and potential applications of these bioactive compounds.
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Affiliation(s)
- Wipanee Meesil
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Paramaporn Muangpat
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Sutthirat Sitthisak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
- Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Triwit Rattanarojpong
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10400, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Yi-Ming Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe University, Frankfurt, 60438, Frankfurt am Main, Germany
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe University, Frankfurt, 60438, Frankfurt am Main, Germany
- Chemical Biology, Department of Chemistry, Philipps University Marburg, 35032, Marburg, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- SYNMIKRO (Zentrum für Synthetische Mikrobiologie), 35032, Marburg, Germany
| | - Apichat Vitta
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
- Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
- Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok, 65000, Thailand
| | - Aunchalee Thanwisai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.
- Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.
- Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok, 65000, Thailand.
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16
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Zhang S, Yang W, Chen J, Zhang C, Zhang S, Gao L. Whole genome sequencing and annotation of Scleroderma yunnanense, the only edible Scleroderma species. Genomics 2023; 115:110727. [PMID: 37839651 DOI: 10.1016/j.ygeno.2023.110727] [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] [Received: 05/30/2023] [Revised: 09/18/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
Scleroderma yunnanense, an ectomycorrhizal fungus, is a popular edible mushroom within the Yunnan Province of Southwest China that holds great ecological and economic implications. However, despite its significance, there remains limited information about this species. Therefore, we sequenced S. yunnanense genome to identify the functional genes of S. yunnanense involved in secondary metabolite and carbohydrate production pathways. First, we present the 40.43 Mb high-quality reference genome for S. yunnanense, distributed across 35 contigs; moreover, the N50 contig size was found to reach 3.31 Mb and contained 8877 functional genes. Finally, genome annotation was conducted to compare the functional genes of S. yunnanense with protein sequences from different publicly available databases. Taken together, we identified 12 biosynthetic gene clusters across 10 contigs; among these were 13 key mevalonate (MVA) pathway enzymes, a key tyrosinase enzyme in the 3,4-dihydroxyphenylalanine (DOPA) pathway that is responsible for producing DOPA melanins, and 16 enzymes involved in uridine diphosphate glucose biosynthesis. Overall, this study presents the first genome assembly and annotation of S. yunnanense; ultimately, this information will be important in the elucidation of the biological activities and artificial domestication of this fungus.
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Affiliation(s)
- Shanshan Zhang
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China.
| | - Wenzhong Yang
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China
| | - Jian Chen
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China.
| | - Chuanguang Zhang
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China.
| | - Siqi Zhang
- Wenshan Prefecture Central Blood Station, Yunnan 663099, China
| | - Lanjing Gao
- College of Forestry, Beijing Forestry University, Beijing 100083, China
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17
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Zhong W, Aiosa N, Deutsch JM, Garg N, Agarwal V. Pseudobulbiferamides: Plasmid-Encoded Ureidopeptide Natural Products with Biosynthetic Gene Clusters Shared Among Marine Bacteria of Different Genera. JOURNAL OF NATURAL PRODUCTS 2023; 86:2414-2420. [PMID: 37713418 PMCID: PMC10616845 DOI: 10.1021/acs.jnatprod.3c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Indexed: 09/17/2023]
Abstract
Ureidopeptidic natural products possess a wide variety of favorable pharmacological properties. In addition, they have been shown to mediate core physiological functions in producer bacteria. Here, we report that similar ureidopeptidic natural products with conserved biosynthetic gene clusters are produced by different bacterial genera that coinhabit marine invertebrate microbiomes. We demonstrate that a Microbulbifer strain isolated from a marine sponge can produce two different classes of ureidopeptide natural products encoded by two different biosynthetic gene clusters that are positioned on the bacterial chromosome and on a plasmid. The plasmid encoded ureidopeptide natural products, which we term the pseudobulbiferamides (5-8), resemble the ureidopeptide natural products produced by Pseudovibrio, a different marine bacterial genus that is likewise present in marine sponge commensal microbiomes. Using imaging mass spectrometry, we find that the two classes of Microbulbifer-derived ureidopeptides occupy different physical spaces relative to the bacterial colony, perhaps implying different roles for these two compound classes in Microbulbifer physiology and environmental interactions.
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Affiliation(s)
- Weimao Zhong
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Nicole Aiosa
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Jessica M. Deutsch
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Neha Garg
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- Center
for Microbial Dynamics and Infection, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vinayak Agarwal
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
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18
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Yoshimura A, Saeki R, Nakada R, Tomimoto S, Jomori T, Suganuma K, Wakimoto T. Membrane-Vesicle-Mediated Interbacterial Communication Activates Silent Secondary Metabolite Production. Angew Chem Int Ed Engl 2023; 62:e202307304. [PMID: 37449463 DOI: 10.1002/anie.202307304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Most bacterial biosynthetic gene clusters (BGCs) are "silent BGCs" that are expressed poorly or not at all under normal culture conditions. However, silent BGCs, even in part, may be conditionally expressed in response to external stimuli in the original bacterial habitats. The growing knowledge of bacterial membrane vesicles (MVs) suggests that they could be promising imitators of the exogenous stimulants, especially given their functions as signaling mediators in bacterial cell-to-cell communication. Therefore, we envisioned that MVs added to bacterial cultures could activate diverse silent BGCs. Herein, we employed Burkholderia multivorans MVs, which induced silent metabolites in a wide range of bacteria in Actinobacteria, Bacteroidetes and Proteobacteria phyla. A mechanistic analysis of MV-induced metabolite production in Xenorhabdus innexi suggested that the B. multivorans MVs activate silent metabolite production by inhibiting quorum sensing in X. innexi. In turn, the X. innexi MVs carrying some MV-induced peptides suppressed the growth of B. multivorans, highlighting the interspecies communication between B. multivorans and X. innexi through MV exchange.
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Affiliation(s)
- Aya Yoshimura
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Rio Saeki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Ryusuke Nakada
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Shota Tomimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Takahiro Jomori
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
- Faculty of Science, University of the Ryukyus, 1-Senbaru, Nishihara, Nakagami, Okinawa, 903-0213, Japan
| | - Keisuke Suganuma
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, 080-8555, Japan
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine Inada, Obihiro, 080-8555, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
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19
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Bode E, Assmann D, Happel P, Meyer E, Münch K, Rössel N, Bode HB. easyPACId, a Simple Method for Induced Production, Isolation, Identification, and Testing of Natural Products from Proteobacteria. Bio Protoc 2023; 13:e4709. [PMID: 37449040 PMCID: PMC10336570 DOI: 10.21769/bioprotoc.4709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/21/2023] [Accepted: 04/21/2023] [Indexed: 07/18/2023] Open
Abstract
The easyPACId (easy Promoter Activation and Compound Identification) approach is focused on the targeted activation of natural product biosynthetic gene clusters (BGCs) encoding non-ribosomal peptide synthetases (NRPS), polyketide synthases (PKS), NRPS-PKS hybrids, or other BGC classes. It was applied to entomopathogenic bacteria of the genera Xenorhabdus and Photorhabdus by exchanging the natural promoter of desired BGCs against the L-arabinose inducible PBAD promoter in ∆hfq mutants of the respective strains. The crude (culture) extracts of the cultivated easyPACId mutants are enriched with the single compound or compound class and can be tested directly against various target organisms without further purification of the produced natural products. Furthermore, isolation and identification of compounds from these mutants is simplified due to the reduced background in the ∆hfq strains. The approach avoids problems often encountered in heterologous expression hosts, chemical synthesis, or tedious extraction of desired compounds from wild-type crude extracts. This protocol describes easyPACId for Xenorhabdus and Photorhabdus, but it was also successfully adapted to Pseudomonas entomophila and might be suitable for other proteobacteria that carry hfq.
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Affiliation(s)
- Edna Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniela Assmann
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Petra Happel
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Elmar Meyer
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Karin Münch
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Rössel
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Helge B. Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Molecular Biotechnology, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Chemical Biology, Department of Chemistry, Philipps University Marburg, Marburg, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- SYNMIKRO (Zentrum für Synthetische Mikrobiologie), Marburg, Germany
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20
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Steinmetz T, Lombe BK, Nett M. Intermediates and shunt products of massiliachelin biosynthesis in Massilia sp. NR 4-1. Beilstein J Org Chem 2023; 19:909-917. [PMID: 37377775 PMCID: PMC10291242 DOI: 10.3762/bjoc.19.69] [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: 04/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Siderophores are small molecules secreted by microorganisms in order to scavenge iron from the environment. An example is the thiazoline-containing natural product massiliachelin, which is produced by Massilia sp. NR 4-1 under iron-deficient conditions. Based on experimental evidence and genome analysis, it was suspected that this bacterium synthesizes further iron-chelating molecules. After a thorough inspection of its metabolic profile, six previously overlooked compounds were isolated that were active in the chrome azurol S (CAS) assay. Mass spectrometric measurements and nuclear magnetic resonance spectroscopic analyses identified these compounds as possible biosynthetic intermediates or shunt products of massiliachelin. Their bioactivity was tested against one Gram-positive and three Gram-negative bacteria.
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Affiliation(s)
- Till Steinmetz
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
| | - Blaise Kimbadi Lombe
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
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21
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Awori RM, Waturu CN, Pidot SJ, Amugune NO, Bode HB. Draft genomes, phylogenomic reconstruction and comparative genome analysis of three Xenorhabdus strains isolated from soil-dwelling nematodes in Kenya. Access Microbiol 2023; 5:acmi000531.v4. [PMID: 37323942 PMCID: PMC10267655 DOI: 10.1099/acmi.0.000531.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/27/2023] [Indexed: 06/17/2023] Open
Abstract
As a proven source of potent and selective antimicrobials, Xenorhabdus bacteria are important to an age plagued with difficult-to-treat microbial infections. Yet, only 27 species have been described to date. In this study, a novel Xenorhabdus species was discovered through genomic studies on three isolates from Kenyan soils. Soils in Western Kenya were surveyed for steinernematids and Steinernema isolates VH1 and BG5 were recovered from red volcanic loam soils from cultivated land in Vihiga and clay soils from riverine land in Bungoma respectively. From the two nematode isolates, Xenorhabdus sp. BG5 and Xenorhabdus sp. VH1 were isolated. The genomes of these two, plus that of X. griffiniae XN45 - this was previously isolated from Steinernema sp. scarpo that also originated from Kenyan soils - were sequenced and assembled. Nascent genome assemblies of the three isolates were of good quality with over 70 % of their proteome having known functions. These three isolates formed the X. griffiniae clade in a phylogenomic reconstruction of the genus. Their species were delineated using three overall genome relatedness indices: an unnamed species of the genus, Xenorhabdus sp. BG5, X. griffiniae VH1 and X. griffiniae XN45. A pangenome analysis of this clade revealed that over 70 % of species-specific genes encoded unknown functions. Transposases were linked to genomic islands in Xenorhabdus sp. BG5. Thus, overall genome-related indices sufficiently delineated species of two new Xenorhabdus isolates from Kenya, both of which were closely related to X. griffiniae . The functions encoded by most species-specific genes in the X. griffiniae clade remain unknown.
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Affiliation(s)
- Ryan Musumba Awori
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Elakistos Biosciences, PO Box 19301-00100, Nairobi, Kenya
| | - Charles N. Waturu
- Horticulture Research Institute, Kenya Agricultural and Livestock Research Organisation, PO Box 220 Thika
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Nelson O. Amugune
- Department of Biology, University of Nairobi, PO Box 30197-00100, Nairobi, Kenya
| | - Helge B. Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Chemical Biology, Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
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22
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Gaudêncio SP, Bayram E, Lukić Bilela L, Cueto M, Díaz-Marrero AR, Haznedaroglu BZ, Jimenez C, Mandalakis M, Pereira F, Reyes F, Tasdemir D. Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation. Mar Drugs 2023; 21:md21050308. [PMID: 37233502 DOI: 10.3390/md21050308] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.
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Affiliation(s)
- Susana P Gaudêncio
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Engin Bayram
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Lada Lukić Bilela
- Department of Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Mercedes Cueto
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
| | - Ana R Díaz-Marrero
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
- Instituto Universitario de Bio-Orgánica (IUBO), Universidad de La Laguna, 38206 La Laguna, Spain
| | - Berat Z Haznedaroglu
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Carlos Jimenez
- CICA- Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, HCMR Thalassocosmos, 71500 Gournes, Crete, Greece
| | - Florbela Pereira
- LAQV, REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Fernando Reyes
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Armilla, Spain
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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23
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de la Fuente MC, Ageitos L, Lages MA, Martínez-Matamoros D, Forero AM, Balado M, Lemos ML, Rodríguez J, Jiménez C. Structural Requirements for Ga 3+ Coordination in Synthetic Analogues of the Siderophore Piscibactin Deduced by Chemical Synthesis and Density Functional Theory Calculations. Inorg Chem 2023; 62:7503-7514. [PMID: 37140938 DOI: 10.1021/acs.inorgchem.3c00787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Stereoselective total synthesis of several analogues of piscibactin (Pcb), the siderophore produced by different pathogenic Gram-negative bacteria, was performed. The acid-sensitive α-methylthiazoline moiety was replaced by a more stable thiazole ring, differing in the configuration of the OH group at the C-13 position. The ability of these Pcb analogues to form complexes with Ga3+ as a mimic of Fe3+ showed that the configuration of the hydroxyl group at C-13 as 13S is crucial for the chelation of Ga3+ to preserve the metal coordination, while the presence of a thiazole ring instead of the α-methylthiazoline moiety does not affect such coordination. A complete 1H and 13C NMR chemical shift assignment of the diastereoisomer mixtures around C9/C10 was done for diagnostic stereochemical disposition. Additionally, density functional theory calculations were performed not only for confirming the stereochemistry of the Ga3+ complex among the six possible diastereoisomers but also for deducing the ability of these to form octahedral coordination spheres with gallium. Finally, the lack of antimicrobial activity of Pcb and Pcb thiazole analogue Ga3+ complexes against Vibrio anguillarum agrees with one of the roles of siderophores in protecting pathogens from metal ion toxicity. The efficient metal coordination shown by this scaffold suggests its possible use as a starting point for the design of new chelating agents or vectors for the development of new antibacterials that exploit the "Trojan horse" strategy using the microbial iron uptake mechanisms. The results obtained will be of great help in the development of biotechnological applications for these types of compounds.
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Affiliation(s)
- M Carmen de la Fuente
- CICA─Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, A Coruña 15071, Spain
| | - Lucía Ageitos
- CICA─Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, A Coruña 15071, Spain
| | - Marta A Lages
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Diana Martínez-Matamoros
- CICA─Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, A Coruña 15071, Spain
| | - Abel M Forero
- CICA─Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, A Coruña 15071, Spain
| | - Miguel Balado
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Manuel L Lemos
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Jaime Rodríguez
- CICA─Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, A Coruña 15071, Spain
| | - Carlos Jiménez
- CICA─Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, A Coruña 15071, Spain
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24
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Xue D, Shang Z, Older EA, Zhong Z, Pulliam C, Peter K, Nagarkatti M, Nagarkatti P, Li YX, Li J. Refactoring and Heterologous Expression of Class III Lanthipeptide Biosynthetic Gene Clusters Lead to the Discovery of N, N-Dimethylated Lantibiotics from Firmicutes. ACS Chem Biol 2023; 18:508-517. [PMID: 36926816 PMCID: PMC10069475 DOI: 10.1021/acschembio.2c00849] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Class III lanthipeptides are an emerging subclass of lanthipeptides, representing an underexplored trove of new natural products with potentially broad chemical diversity and important biological activity. Bioinformatic analysis of class III lanthipeptide biosynthetic gene cluster (BGC) distribution has revealed their high abundance in the phylum Firmicutes. Many of these clusters also feature methyltransferase (MT) genes, which likely encode uncommon class III lanthipeptides. However, two hurdles, silent BGCs and low-yielding pathways, have hindered the discovery of class III lanthipeptides from Firmicutes. Here, we report the design and construction of a biosynthetic pathway refactoring and heterologous overexpression strategy which seeks to overcome these hurdles, simultaneously activating and increasing the production of these Firmicutes class III lanthipeptides. Applying our strategy to MT-containing BGCs, we report the discovery of new class III lanthipeptides from Firmicutes bearing rare N,N-dimethylations. We reveal the importance of the first two amino acids in the N-terminus of the core peptide in controlling the MT dimethylation activity. Leveraging this feature, we engineer class III lanthipeptides to enable N,N-dimethylation, resulting in significantly increased antibacterial activity. Furthermore, the refactoring and heterologous overexpression strategy showcased in this study is potentially applicable to other ribosomally synthesized and post-translationally modified peptide BGCs from Firmicutes, unlocking the genetic potential of Firmicutes for producing peptide natural products.
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Affiliation(s)
- Dan Xue
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Zhuo Shang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ethan A Older
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Zheng Zhong
- Department of Chemistry and the Swire Institute of Marine Science, The University of Hong Kong, Hong Kong 999077, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 519000, China
| | - Conor Pulliam
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Kyle Peter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Yong-Xin Li
- Department of Chemistry and the Swire Institute of Marine Science, The University of Hong Kong, Hong Kong 999077, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 519000, China
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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25
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Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity. Int J Mol Sci 2023; 24:ijms24044158. [PMID: 36835570 PMCID: PMC9966250 DOI: 10.3390/ijms24044158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa and to predict phenotypes, secondary metabolites, host-associated interactions, survivability, and biochemical productivity under proposed environmental conditions. The significantly distinctive phenotypes of members of the marine bacterial species Pseudoalteromonas distincta and an inability to use common molecular markers make their identification within the genus Pseudoalteromonas and prediction of their biotechnology potential impossible without genome-scale analysis and metabolic reconstruction. A new strain, KMM 6257, of a carotenoid-like phenotype, isolated from a deep-habituating starfish, emended the description of P. distincta, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics. P. distincta possesses putative methylerythritol phosphate pathway II and 4,4'-diapolycopenedioate biosynthesis, related to C30 carotenoids, and their functional analogues, aryl polyene biosynthetic gene clusters (BGC). However, the yellow-orange pigmentation phenotypes in some strains coincide with the presence of a hybrid BGC encoding for aryl polyene esterified with resorcinol. The alginate degradation and glycosylated immunosuppressant production, similar to brasilicardin, streptorubin, and nucleocidines, are the common predicted features. Starch, agar, carrageenan, xylose, lignin-derived compound degradation, polysaccharide, folate, and cobalamin biosynthesis are all strain-specific.
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26
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Shi YM, Crames JJ, Czech L, Bozhüyük KAJ, Shi YN, Hirschmann M, Lamberth S, Claus P, Paczia N, Rückert C, Kalinowski J, Bange G, Bode HB. Genome Mining Enabled by Biosynthetic Characterization Uncovers a Class of Benzoxazolinate-Containing Natural Products in Diverse Bacteria. Angew Chem Int Ed Engl 2022; 61:e202206106. [PMID: 36198080 PMCID: PMC10098953 DOI: 10.1002/anie.202206106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 11/18/2022]
Abstract
Benzoxazolinate is a rare bis-heterocyclic moiety that interacts with proteins and DNA and confers extraordinary bioactivities on natural products, such as C-1027. However, the biosynthetic gene responsible for the key cyclization step of benzoxazolinate remains unclear. Herein, we show a putative acyl AMP-ligase responsible for the last cyclization step. We used the enzyme as a probe for genome mining and discovered that the orphan benzobactin gene cluster in entomopathogenic bacteria prevails across Proteobacteria and Firmicutes. It turns out that Pseudomonas chlororaphis produces various benzobactins, whose biosynthesis is highlighted by a synergistic effect of two unclustered genes encoding enzymes on boosting benzobactin production; the formation of non-proteinogenic 2-hydroxymethylserine by a serine hydroxymethyltransferase; and the types I and II NRPS architecture for structural diversity. Our findings reveal the biosynthetic potential of a widespread benzobactin gene cluster.
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Affiliation(s)
- Yi-Ming Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jan J Crames
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Laura Czech
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Kenan A J Bozhüyük
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Yan-Ni Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Merle Hirschmann
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Stefanie Lamberth
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Peter Claus
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615, Bielefeld, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany.,Chemical Biology, Department of Chemistry, Philipps University of Marburg, 35043, Marburg, Germany
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27
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Du AQ, Ying TT, Zhou ZY, Yu WC, Hu GA, Luo X, Ma MJ, Yu YL, Wang H, Wei B. Non-ribosomal peptide biosynthetic potential of the nematode symbiont Photorhabdus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:917-925. [PMID: 35998886 DOI: 10.1111/1758-2229.13118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Photorhabdus, the symbiotic bacteria of Heterorhabditis nematodes, has been reported to possess many non-ribosomal peptide synthetase (NRPS) biosynthesis gene clusters (BGCs). To provide an in-depth assessment of the non-ribosomal peptide biosynthetic potential of Photorhabdus, we compared the distribution of BGCs in 81 Photorhabdus strains, confirming the predominant presence (44.80%) of NRPS BGCs in Photorhabdus. All 990 NRPS BGCs were clustered into 275 gene cluster families (GCFs) and only 13 GCFs could be annotated with known BGCs, suggesting their great diversity and novelty. These NRPS BGCs encoded 351 novel peptides containing more than four amino acids, and 173 of them showed high sequence similarity to known BGCs encoding bioactive peptides, implying the promising potential of Photorhabdus to produce valuable peptides. Sequence similarity networking of adenylation (A-) domains suggested that the substrate specificity of A-domains was not directly correlated with the sequence similarity. The molecular similarity network of predicted metabolite scaffolds of NRPS BGCs and reported peptides from Photorhabdus and a relevant database demonstrated that the non-ribosomal peptide biosynthetic potential of Photorhabdus was largely untapped and revealed the core peptides deserving intensive studies. Our present study provides valuable information for the targeted discovery of novel non-ribosomal peptides from Photorhabdus.
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Affiliation(s)
- Ao-Qi Du
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Ti-Ti Ying
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Zhen-Yi Zhou
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Wen-Chao Yu
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Gang-Ao Hu
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Xian Luo
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Man-Jing Ma
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Yan-Lei Yu
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Hong Wang
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Bin Wei
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
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28
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Zhao H, Yang Y, Wang S, Yang X, Zhou K, Xu C, Zhang X, Fan J, Hou D, Li X, Lin H, Tan Y, Wang S, Chu XY, Zhuoma D, Zhang F, Ju D, Zeng X, Chen YZ. NPASS database update 2023: quantitative natural product activity and species source database for biomedical research. Nucleic Acids Res 2022; 51:D621-D628. [PMID: 36624664 PMCID: PMC9825494 DOI: 10.1093/nar/gkac1069] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/16/2022] [Accepted: 10/26/2022] [Indexed: 11/30/2022] Open
Abstract
Quantitative activity and species source data of natural products (NPs) are important for drug discovery, medicinal plant research, and microbial investigations. Activity values of NPs against specific targets are useful for discovering targeted therapeutic agents and investigating the mechanism of medicinal plants. Composition/concentration values of NPs in individual species facilitate the assessments and investigations of the therapeutic quality of herbs and phenotypes of microbes. Here, we describe an update of the NPASS natural product activity and species source database previously featured in NAR. This update includes: (i) new data of ∼95 000 records of the composition/concentration values of ∼1 490 NPs/NP clusters in ∼390 species, (ii) extended data of activity values of ∼43 200 NPs against ∼7 700 targets (∼40% and ∼32% increase, respectively), (iii) extended data of ∼31 600 species sources of ∼94 400 NPs (∼26% and ∼32% increase, respectively), (iv) new species types of ∼440 co-cultured microbes and ∼420 engineered microbes, (v) new data of ∼66 600 NPs without experimental activity values but with estimated activity profiles from the established chemical similarity tool Chemical Checker, (vi) new data of the computed drug-likeness properties and the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties for all NPs. NPASS update version is freely accessible at http://bidd.group/NPASS.
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Affiliation(s)
| | | | | | | | - Kaicheng Zhou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Caili Xu
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xuyao Zhang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Jiajun Fan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Dongyue Hou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xingxiu Li
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Hanbo Lin
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Ying Tan
- The State Key Laboratory of Chemical Oncogenomics & Key Laboratory of Chemical Biology, Tsinghua University Shenzhen Graduate School, Shenzhen Kivita Innovative Drug Discovery Institute, China
| | - Shanshan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Xin-Yi Chu
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | | | - Fengying Zhang
- Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University, Nanchang 330045, China
| | - Dianwen Ju
- Correspondence may also be addressed to Dianwen Ju. Tel: +86 51980037;
| | - Xian Zeng
- Correspondence may also be addressed to Xian Zeng. Tel: +86 51980035;
| | - Yu Zong Chen
- To whom correspondence should be addressed. Tel: +86 755 26032094;
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Structural diversity, bioactivity, and biosynthesis of phosphoglycolipid family antibiotics: recent advances. BBA ADVANCES 2022; 2:100065. [PMID: 37082588 PMCID: PMC10074958 DOI: 10.1016/j.bbadva.2022.100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Moenomycins, such as moenomycin A, are phosphoglycolipid specialized metabolites produced by a number of actinobacterial species. They are among the most potent antibacterial compounds known to date, which drew numerous studies directed at various aspects of the chemistry and biology of moenomycins. In this review, we outline the advances in moenomycin research over the last decade. We focus on biological aspects, highlighting the contribution of the novel methods of genomics and molecular biology to the deciphering of the biosynthesis and activity of moenomycins. Specifically, we describe the structural diversity of moenomycins as well as the underlying genomic variations in moenomycin biosynthetic gene clusters. We also describe the most recent data on the mechanism of action and assembly of complicated phosphoglycolipid scaffold. We conclude with the description of the genetic control of moenomycin production by Streptomyces bacteria and a brief outlook on future developments.
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30
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Hrithik MTH, Park Y, Park H, Kim Y. Integrated Biological Control Using a Mixture of Two Entomopathogenic Bacteria, Bacillus thuringiensis and Xenorhabdus hominickii, against Spodoptera exigua and Other Congeners. INSECTS 2022; 13:860. [PMID: 36292808 PMCID: PMC9604179 DOI: 10.3390/insects13100860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Insect immunity defends against the virulence of various entomopathogens, including Bacillus thuringiensis (Bt). This study tested a hypothesis that any suppression of immune responses enhances Bt virulence. In a previous study, the entomopathogenic bacterium, Xenorhabdus hominickii (Xh), was shown to produce secondary metabolites to suppress insect immune responses. Indeed, the addition of Xh culture broth (XhE) significantly enhanced the insecticidal activity of Bt against S. exigua. To analyze the virulence enhanced by the addition of Xh metabolites, four bacterial secondary metabolites were individually added to the Bt treatment. Each metabolite significantly enhanced the Bt insecticidal activity, along with significant suppression of the induced immune responses. A bacterial mixture was prepared by adding freeze-dried XhE to Bt spores, and the optimal mixture ratio to kill the insects was determined. The formulated bacterial mixture was applied to S. exigua larvae infesting Welsh onions in a greenhouse and showed enhanced control efficacy compared to Bt alone. The bacterial mixture was also effective in controlling other Spodopteran species such as S. litura and S. frugiperda but not other insect genera or orders. This suggests that Bt+XhE can effectively control Spodoptera-associated pests by suppressing the immune defenses.
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Affiliation(s)
- Md Tafim Hossain Hrithik
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong 36729, Korea
| | - Youngjin Park
- Animal and Plant Quarantine Agency, 167, Yongjeon-ro, Gimcheon 39660, Korea
| | - Hyemi Park
- Animal and Plant Quarantine Agency, 167, Yongjeon-ro, Gimcheon 39660, Korea
| | - Yonggyun Kim
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong 36729, Korea
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31
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Awori RM. Nematophilic bacteria associated with entomopathogenic nematodes and drug development of their biomolecules. Front Microbiol 2022; 13:993688. [PMID: 36187939 PMCID: PMC9520725 DOI: 10.3389/fmicb.2022.993688] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022] Open
Abstract
The importance of Xenorhabdus and Photorhabdus symbionts to their respective Steinernema and Heterorhabditis nematode hosts is that they not only contribute to their entomopathogenicity but also to their fecundity through the production of small molecules. Thus, this mini-review gives a brief introductory overview of these nematophilic bacteria. Specifically, their type species, nematode hosts, and geographic region of isolations are tabulated. The use of nucleotide sequence-based techniques for their species delineation and how pangenomes can improve this are highlighted. Using the Steinernema–Xenorhabdus association as an example, the bacterium-nematode lifecycle is visualized with an emphasis on the role of bacterial biomolecules. Those currently in drug development are discussed, and two potential antimalarial lead compounds are highlighted. Thus, this mini-review tabulates forty-eight significant nematophilic bacteria and visualizes the ecological importance of their biomolecules. It further discusses three of these biomolecules that are currently in drug development. Through it, one is introduced to Xenorhabdus and Photorhabdus bacteria, their natural production of biomolecules in the nematode-bacterium lifecycle, and how these molecules are useful in developing novel therapies.
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Affiliation(s)
- Ryan Musumba Awori
- Department of Biology, University of Nairobi, Nairobi, Kenya
- Elakistos Biosciences, Nairobi, Kenya
- *Correspondence: Ryan Musumba Awori,
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32
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Identification of Key Functions Required for Production and Utilization of the Siderophore Piscibactin Encoded by the High-Pathogenicity Island irp-HPI in Vibrionaceae. Int J Mol Sci 2022; 23:ijms23168865. [PMID: 36012135 PMCID: PMC9408133 DOI: 10.3390/ijms23168865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/27/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022] Open
Abstract
Piscibactin is a widespread siderophore system present in many different bacteria, especially within the Vibrionaceae family. Previous works showed that most functions required for biosynthesis and transport of this siderophore are encoded by the high-pathogenicity island irp-HPI. In the present work, using Vibrio anguillarum as a model, we could identify additional key functions encoded by irp-HPI that are necessary for piscibactin production and transport and that have remained unknown. Allelic exchange mutagenesis, combined with cross-feeding bioassays and LC-MS analysis, were used to demonstrate that Irp4 protein is an essential component for piscibactin synthesis since it is the thioesterase required for nascent piscibactin be released from the NRPS Irp1. We also show that Irp8 is a MFS-type protein essential for piscibactin secretion. In addition, after passage through the outer membrane transporter FrpA, the completion of ferri-piscibactin internalization through the inner membrane would be achieved by the ABC-type transporter FrpBC. The expression of this transporter is coordinated with the expression of FrpA and with the genes encoding biosynthetic functions. Since piscibactin is a major virulence factor of some pathogenic vibrios, the elements of biosynthesis and transport described here could be additional interesting targets for the design of novel antimicrobials against these bacterial pathogens.
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Reitz ZL, Medema MH. Genome mining strategies for metallophore discovery. Curr Opin Biotechnol 2022; 77:102757. [PMID: 35914390 DOI: 10.1016/j.copbio.2022.102757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 11/03/2022]
Abstract
Many bacteria use small-molecule chelators called metallophores to acquire trace metals from their environment. These molecules play a central role in interactions between bacteria, plants, and animals. Hence, knowing their full diversity is key to combatting infectious diseases as well as harnessing beneficial microbial communities. Metallophore discovery has been streamlined by advances in genome mining, where genomes are scanned for genes involved in metallophore biosynthesis. This review highlights recent trends and advances in predicting the presence and structure of metallophores based solely on genomic information. Recent work suggests new families of metallophores remain hidden from current homology-based approaches. Their discovery will require new genome mining approaches that move beyond biosynthesis to consider metallophore transporters, regulation, and evolution.
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Affiliation(s)
- Zachary L Reitz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
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34
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Shi YM, Hirschmann M, Shi YN, Bode HB. Cleavage Off-Loading and Post-assembly-Line Conversions Yield Products with Unusual Termini during Biosynthesis. ACS Chem Biol 2022; 17:2221-2228. [PMID: 35860925 PMCID: PMC9396620 DOI: 10.1021/acschembio.2c00367] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Piscibactins and photoxenobactins are metallophores and
virulence
factors, whose biosynthetic gene cluster, termed pxb, is the most prevalent polyketide synthase/non-ribosomal peptide
synthetase hybrid cluster across entomopathogenic bacteria. They are
structurally similar to yersiniabactin, which contributes to the virulence
of the human pathogen Yersinia pestis. However, the pxb-derived products feature various
chain lengths and unusual carboxamide, thiocarboxylic acid, and dithioperoxoate
termini, which are rarely found in thiotemplated biosyntheses. Here,
we characterize the pxb biosynthetic logic by gene
deletions, site-directed mutagenesis, and isotope labeling experiments.
Notably, we propose that it involves (1) heterocyclization domains
with various catalytic efficiencies catalyzing thiazoline and amide/thioester
bond formation and (2) putative C–N and C–S bond cleavage
off-loading manners, which lead to products with different chain lengths
and usual termini. Additionally, the post-assembly-line spontaneous
conversions of the biosynthetic end product contribute to production
titers of the other products in the culture medium. This study broadens
our knowledge of thiotemplated biosynthesis and how bacterial host
generate a chemical arsenal.
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Affiliation(s)
- Yi-Ming Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Merle Hirschmann
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Yan-Ni Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.,Chemical Biology, Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
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35
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Phurealipids, produced by the entomopathogenic bacteria, Photorhabdus, mimic juvenile hormone to suppress insect immunity and immature development. J Invertebr Pathol 2022; 193:107799. [PMID: 35850258 DOI: 10.1016/j.jip.2022.107799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 11/23/2022]
Abstract
Phurealipids (Photorhabdus urea lipids) are synthesized from Photorhabdus bacteria that are symbiotic to entomopathogenic nematodes. Their chemical structures are similar to that of juvenile hormone (JH) and have been suspected to mimic JH signaling in immunity and the development of insects. This study investigated the physiological roles of phurealipids with respect to their contribution to bacterial pathogenicity using four natural (HB13, HB69, HB416, and HB421) and one derivative (HB27) compound. First, phurealipids like JH suppressed insect immune responses. Overall, phurealipids showed JH like immunosuppressive behavior in a lepidopteran insect Spodoptera exigua larvae. More specifically, phurealipids significantly suppressed the hemocyte spreading behavior which is a key immune response upon immune challenge. Interestingly, the methyl urea derivatives (HB13, HB27, and HB69) were more potent than the unmethylated forms (HB416 and HB421). The inhibitory activity of phurealipids prevented the cellular immune response measured by hemocytic nodule formation in response to the bacterial challenge. Phurealipids also suppressed the expression of cecropin and gallerimycin, which are two highly inducible antimicrobial peptides, in S. exigua upon immune challenge. The immunosuppressive activity of the phurealipids significantly enhanced the bacterial pathogenicity of Bacillus thuringiensis against S. exigua. Second, phurealipids like JH prevented insect metamorphosis. Especially, the methylated urea derivatives of the phurealipids showed the JH-like function by inducing the expression of S. exigua Kr-h1, a transcriptional factor. At the pupal stage, exhibiting the lowest expression of Kr-h1, phurealipid treatments elevated the expression level of Kr-h1 and delayed the pupa-to-adult metamorphosis. These results suggest that phurealipids play crucial roles in Photorhabdus pathogenicity by suppressing host immune defenses and delaying host metamorphosis.
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36
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Gulsen SH, Tileklioglu E, Bode E, Cimen H, Ertabaklar H, Ulug D, Ertug S, Wenski SL, Touray M, Hazir C, Bilecenoglu DK, Yildiz I, Bode HB, Hazir S. Antiprotozoal activity of different Xenorhabdus and Photorhabdus bacterial secondary metabolites and identification of bioactive compounds using the easyPACId approach. Sci Rep 2022; 12:10779. [PMID: 35750682 PMCID: PMC9232601 DOI: 10.1038/s41598-022-13722-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/26/2022] [Indexed: 12/20/2022] Open
Abstract
Natural products have been proven to be important starting points for the development of new drugs. Bacteria in the genera Photorhabdus and Xenorhabdus produce antimicrobial compounds as secondary metabolites to compete with other organisms. Our study is the first comprehensive study screening the anti-protozoal activity of supernatants containing secondary metabolites produced by 5 Photorhabdus and 22 Xenorhabdus species against human parasitic protozoa, Acanthamoeba castellanii, Entamoeba histolytica, Trichomonas vaginalis, Leishmania tropica and Trypanosoma cruzi, and the identification of novel bioactive antiprotozoal compounds using the easyPACId approach (easy Promoter Activated Compound Identification) method. Though not in all species, both bacterial genera produce antiprotozoal compounds effective on human pathogenic protozoa. The promoter exchange mutants revealed that antiprotozoal bioactive compounds produced by Xenorhabdus bacteria were fabclavines, xenocoumacins, xenorhabdins and PAX peptides. Among the bacteria assessed, only P. namnaoensis appears to have acquired amoebicidal property which is effective on E. histolytica trophozoites. These discovered antiprotozoal compounds might serve as starting points for the development of alternative and novel pharmaceutical agents against human parasitic protozoa in the future.
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Affiliation(s)
- Sebnem Hazal Gulsen
- Department of Biology, Faculty of Arts and Science, Aydin Adnan Menderes University, Aydin, Türkiye
| | - Evren Tileklioglu
- Department of Parasitology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin, Türkiye
| | - Edna Bode
- Max-Planck-Institute for Terrestrial Microbiology Department, Natural Products in Organismic Interactions, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Harun Cimen
- Department of Biology, Faculty of Arts and Science, Aydin Adnan Menderes University, Aydin, Türkiye
| | - Hatice Ertabaklar
- Department of Parasitology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin, Türkiye
| | - Derya Ulug
- Department of Biology, Faculty of Arts and Science, Aydin Adnan Menderes University, Aydin, Türkiye
| | - Sema Ertug
- Department of Parasitology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin, Türkiye
| | - Sebastian L Wenski
- Max-Planck-Institute for Terrestrial Microbiology Department, Natural Products in Organismic Interactions, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Mustapha Touray
- Department of Biology, Faculty of Arts and Science, Aydin Adnan Menderes University, Aydin, Türkiye
| | - Canan Hazir
- Aydin Health Services Vocational School, Aydin Adnan Menderes University, 09100, Aydin, Türkiye
| | | | - Ibrahim Yildiz
- Department of Parasitology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin, Türkiye
| | - Helge B Bode
- Max-Planck-Institute for Terrestrial Microbiology Department, Natural Products in Organismic Interactions, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany. .,Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany. .,Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt, Germany.
| | - Selcuk Hazir
- Department of Biology, Faculty of Arts and Science, Aydin Adnan Menderes University, Aydin, Türkiye.
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37
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Mohite OS, Lloyd CJ, Monk JM, Weber T, Palsson BO. Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets. Synth Syst Biotechnol 2022; 7:900-910. [PMID: 35647330 PMCID: PMC9125672 DOI: 10.1016/j.synbio.2022.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 11/25/2022] Open
Abstract
In silico genome mining provides easy access to secondary metabolite biosynthetic gene clusters (BGCs) encoding the biosynthesis of many bioactive compounds, which are the basis for many important drugs used in human medicine. However, the association between BGCs and other functions encoded in the genomes of producers have remained elusive. Here, we present a systems biology workflow that integrates genome mining with a detailed pangenome analysis for detecting genes associated with a particular BGC. We analyzed 3,889 enterobacterial genomes and found 13,266 BGCs, represented by 252 distinct BGC families and 347 additional singletons. A pangenome analysis revealed 88 genes putatively associated with a specific BGC coding for the colon cancer-related colibactin that code for diverse metabolic and regulatory functions. The presented workflow opens up the possibility to discover novel secondary metabolites, better understand their physiological roles, and provides a guide to identify and analyze BGC associated gene sets.
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