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Wang CY, Hu JQ, Wang DG, Li YZ, Wu C. Recent advances in discovery and biosynthesis of natural products from myxobacteria: an overview from 2017 to 2023. Nat Prod Rep 2024; 41:905-934. [PMID: 38390645 DOI: 10.1039/d3np00062a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Covering: 2017.01 to 2023.11Natural products biosynthesized by myxobacteria are appealing due to their sophisticated chemical skeletons, remarkable biological activities, and intriguing biosynthetic enzymology. This review aims to systematically summarize the advances in the discovery methods, new structures, and bioactivities of myxobacterial NPs reported in the period of 2017-2023. In addition, the peculiar biosynthetic pathways of several structural families are also highlighted.
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Affiliation(s)
- Chao-Yi Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
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Ahearne A, Phillips KE, Knehans T, Hoing M, Dowd SE, Stevens DC. Chromosomal organization of biosynthetic gene clusters, including those of nine novel species, suggests plasticity of myxobacterial specialized metabolism. Front Microbiol 2023; 14:1227206. [PMID: 37601375 PMCID: PMC10435759 DOI: 10.3389/fmicb.2023.1227206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Natural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism. Methods In this study, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America. Results Nine isolates were determined to be novel species of myxobacteria including representatives from the genera Archangium, Myxococcus, Nannocystis, Polyangium, Pyxidicoccus, Sorangium, and Stigmatella. Growth profiles, biochemical assays, and descriptions were provided for all proposed novel species. We assess the BGC content of all isolates and observe differences between Myxococcia and Polyangiia clusters. Discussion Continued discovery and sequencing of novel myxobacteria from the environment provide BGCs for the genome mining pipeline. Utilizing complete or near-complete genome sequences, we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest that the spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Kayleigh E. Phillips
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Thomas Knehans
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Miranda Hoing
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Scot E. Dowd
- Molecular Research LP (MR DNA), Shallowater, TX, United States
| | - David Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
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Ahearne A, Phillips K, Knehans T, Hoing M, Dowd SE, Stevens DC. Chromosomal organization of biosynthetic gene clusters suggests plasticity of myxobacterial specialized metabolism including descriptions for nine novel species: Archangium lansinium sp. nov., Myxococcus landrumus sp. nov., Nannocystis bainbridgea sp. nov., Nannocystis poenicansa sp. nov., Nannocystis radixulma sp. nov., Polyangium mundeleinium sp. nov., Pyxidicoccus parkwaysis sp. nov., Sorangium aterium sp. nov., Stigmatella ashevillena sp. nov. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531766. [PMID: 36945379 PMCID: PMC10028903 DOI: 10.1101/2023.03.08.531766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Natural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism. Continued discovery and sequencing of novel myxobacteria from the environment provides BGCs for the genome mining pipeline. Herein, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America. Nine isolates where determined to be novel species of myxobacteria including representatives from the genera Archangium, Myxococcus, Nannocystis, Polyangium, Pyxidicoccus, Sorangium, and Stigmatella. Growth profiles, biochemical assays, and descriptions are provided for all proposed novel species. We assess the BGC content of all isolates and observe differences between Myxococcia and Polyangiia clusters. Utilizing complete or near complete genome sequences we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Kayleigh Phillips
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Thomas Knehans
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Miranda Hoing
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Scot E. Dowd
- MR DNA, Molecular Research LP, Shallowater, TX 79363, USA
| | - D. Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
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Synthesis and Antifungal Activity of New butenolide Containing Methoxyacrylate Scaffold. Molecules 2022; 27:molecules27196541. [PMID: 36235077 PMCID: PMC9573425 DOI: 10.3390/molecules27196541] [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: 09/13/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
In order to improve the antifungal activity of new butenolides containing oxime ether moiety, a series of new butenolide compounds containing methoxyacrylate scaffold were designed and synthesized, based on the previous reports. Their structures were characterized by 1H NMR, 13C NMR, HR-MS spectra, and X-ray diffraction analysis. The in vitro antifungal activities were evaluated by the mycelium growth rate method. The results showed that the inhibitory activities of these new compounds against Sclerotinia sclerotiorum were significantly improved, in comparison with that of the lead compound 3-8; the EC50 values of V-6 and VI-7 against S. sclerotiorum were 1.51 and 1.81 mg/L, nearly seven times that of 3-8 (EC50 10.62 mg/L). Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observation indicated that compound VI-3 had a significant impact on the structure and function of the hyphal cell of S. sclerotiorum mycelium and the positive control trifloxystrobin. Molecular simulation docking results indicated that the introduction of methoxyacrylate scaffold is beneficial to improving the antifungal activity of these compounds against S. sclerotiorum, which can be used as the lead for further structure optimization.
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Panter F, Popoff A, Garcia R, Krug D, Müller R. Myxobacteria of the Cystobacterineae Suborder Are Producers of New Vitamin K 2 Derived Myxoquinones. Microorganisms 2022; 10:microorganisms10030534. [PMID: 35336107 PMCID: PMC8955186 DOI: 10.3390/microorganisms10030534] [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: 01/05/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Vitamin K is an essential, lipid soluble vitamin that plays an important role in the human blood coagulation cascade as well as in the life cycle of bacteria and plants. In this study, we report the isolation and structure elucidation of unprecedented polyhydroxylated menaquinone variants named myxoquinones that are produced by myxobacteria and structurally belong to the Vitamin K family. We analyze the occurrence of myxoquinones across an LC-MS data collection from myxobacterial extracts and shed light on the distribution of myxoquinone-type biosynthetic gene clusters among publicly available myxobacterial genomes. Our findings indicate that myxoquinones are specifically produced by strains of the Cystobacterineae suborder within myxobacteria. Furthermore, bioinformatic analysis of the matching gene clusters allowed us to propose a biosynthetic model for myxoquinone formation. Due to their increased water-solubility, the myxoquinones could be a suitable starting point for the development of a better bioavailable treatment of vitamin K deficiency.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (F.P.); (A.P.); (R.G.); (D.K.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Alexander Popoff
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (F.P.); (A.P.); (R.G.); (D.K.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Ronald Garcia
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (F.P.); (A.P.); (R.G.); (D.K.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Daniel Krug
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (F.P.); (A.P.); (R.G.); (D.K.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (F.P.); (A.P.); (R.G.); (D.K.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8 1, 66123 Saarbrücken, Germany
- Correspondence:
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Shen Q, Zhou H, Dai G, Zhong G, Huo L, Li A, Liu Y, Yang M, Ravichandran V, Zheng Z, Tang YJ, Jiao N, Zhang Y, Bian X. Characterization of a Cryptic NRPS Gene Cluster in Bacillus velezensis FZB42 Reveals a Discrete Oxidase Involved in Multithiazole Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05131] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Qiyao Shen
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Guannan Zhong
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Liujie Huo
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Aiying Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yang Liu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Ming Yang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Vinothkannan Ravichandran
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhihui Zheng
- New Drug Research and Development Center, North China Pharmaceutical Group Corporation, Shijiazhuang 050015, China
| | - Ya-Jie Tang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Nianzhi Jiao
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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Back D, Shaffer BT, Loper JE, Philmus B. Untargeted Identification of Alkyne-Containing Natural Products Using Ruthenium-Catalyzed Azide Alkyne Cycloaddition Reactions Coupled to LC-MS/MS. JOURNAL OF NATURAL PRODUCTS 2022; 85:105-114. [PMID: 35044192 PMCID: PMC8853637 DOI: 10.1021/acs.jnatprod.1c00798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Alkyne-containing natural products have been identified from plants, insects, algae, fungi, and bacteria. This class of natural products has been characterized as having a variety of biological activities. Polyynes are a subclass of acetylenic natural products that contain conjugated alkynes and are underrepresented in natural product databases due to the fact that they decompose during purification. Here we report a workflow that utilizes alkyne azide cycloaddition (AAC) reactions followed by LC-MS/MS analysis to identify acetylenic natural products. In this report, we demonstrate that alkyne azide cycloaddition reactions with p-bromobenzyl azide result in p-bromobenzyl-substituted triazole products that fragment to a common brominated tropylium ion. We were able to identify a synthetic alkyne spiked into the extract of Anabaena sp. PCC 7120 at a concentration of 10 μg/mL after optimization of MS/MS conditions. We then successfully identified the known natural product fischerellin A in the extract of Fischerella muscicola PCC 9339. Lastly, we identified the recently identified natural products protegenins A and C from Pseudomonas protegens Pf-5 through a combination of genome mining and RuAAC reactions. This is the first report of RuAAC reactions to detect acetylenic natural products. We also compare CuAAC and RuAAC reactions and find that CuAAC reactions produce fewer byproducts compared to RuAAC but is limited to terminal-alkyne-containing compounds. In contrast, RuAAC is capable of identification of both terminal and internal acetylenic natural products, but byproducts need to be eliminated from analysis by creation of an exclusion list. We believe that both CuAAC and RuAAC reactions coupled to LC-MS/MS represent a method for the untargeted identification of acetylenic natural products, but each method has strengths and weaknesses.
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Affiliation(s)
- Daniel Back
- Department of Pharmaceutical Sciences, 203 Pharmacy Bldg., Oregon State University, Corvallis, OR 97331
| | - Brenda T. Shaffer
- Agricultural Research Service, US Department of Agriculture, 3420 N.W. Orchard Avenue, Corvallis, OR 97330
| | - Joyce E. Loper
- Agricultural Research Service, US Department of Agriculture, 3420 N.W. Orchard Avenue, Corvallis, OR 97330
- College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, 203 Pharmacy Bldg., Oregon State University, Corvallis, OR 97331
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Ahearne A, Albataineh H, Dowd SE, Stevens DC. Assessment of Evolutionary Relationships for Prioritization of Myxobacteria for Natural Product Discovery. Microorganisms 2021; 9:microorganisms9071376. [PMID: 34202719 PMCID: PMC8307915 DOI: 10.3390/microorganisms9071376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
Discoveries of novel myxobacteria have started to unveil the potentially vast phylogenetic diversity within the family Myxococcaceae and have brought about an updated approach to myxobacterial classification. While traditional approaches focused on morphology, 16S gene sequences, and biochemistry, modern methods including comparative genomics have provided a more thorough assessment of myxobacterial taxonomy. Herein, we utilize long-read genome sequencing for two myxobacteria previously classified as Archangium primigenium and Chondrococcus macrosporus, as well as four environmental myxobacteria newly isolated for this study. Average nucleotide identity and digital DNA-DNA hybridization scores from comparative genomics suggest previously classified as A. primigenium to instead be a novel member of the genus Melittangium, C. macrosporus to be a potentially novel member of the genus Corallococcus with high similarity to Corallococcus exercitus, and the four isolated myxobacteria to include another novel Corallococcus species, a novel Pyxidicoccus species, a strain of Corallococcus exiguus, and a potentially novel Myxococcus species with high similarity to Myxococcus stipitatus. We assess the biosynthetic potential of each sequenced myxobacterium and suggest that genus-level conservation of biosynthetic pathways support our preliminary taxonomic assignment. Altogether, we suggest that long-read genome sequencing benefits the classification of myxobacteria and improves determination of biosynthetic potential for prioritization of natural product discovery.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
| | - Hanan Albataineh
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
| | - Scot E. Dowd
- MR DNA, Molecular Research LP, Shallowater, TX 79363, USA;
| | - D. Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
- Correspondence: ; Tel.: +1-662-915-5730
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Okoth DA, Hug JJ, Mándi A, Kurtán T, Garcia R, Müller R. Structure and biosynthesis of sorangipyranone — a new γ-dihydropyrone from the myxobacterial strain MSr12020. J Ind Microbiol Biotechnol 2021; 48:6277809. [DOI: 10.1093/jimb/kuab029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/13/2021] [Indexed: 12/26/2022]
Abstract
Abstract
Sorangipyranone was isolated as a novel natural product featuring a unique 2,3-dihydro-γ-4H-pyrone scaffold from cultures of the myxobacterial strain MSr12020. We report here the full structure elucidation of sorangipyranone by spectroscopic techniques including 2D NMR and high-resolution mass spectrometry together with the analysis of the biosynthetic pathway. Determination of the absolute configuration was performed by time-dependent density functional theory–electronic circular dichroism calculations and determination of the applicability of the Snatzke's helicity rule, to correlate the high-wavelength n→π* electronic circular dichroism (ECD) transition and the absolute configuration of the 2,3-dihydro-4H-γ-pyrone, was done by the analysis of low-energy conformers and the Kohn-Sham orbitals. Sorangipyranone outlines a new class of a γ-dihydropyrone-containing natural product comprised of malonyl-CoA-derived building blocks and features a unique polyketide scaffold. In silico analysis of the genome sequence of the myxobacterial strain MSr12020 complemented with feeding experiments employing stable isotope-labeled precursors allowed the identification and annotation of a candidate biosynthetic gene cluster that encodes a modular polyketide synthase assembly line. A model for the biosynthetic pathway leading to the formation of the γ-dihydropyrone scaffold is presented in this study.
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Affiliation(s)
- Dorothy A Okoth
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Joachim J Hug
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Attila Mándi
- Department of Organic Chemistry, University of Debrecen, P. O. Box 400, 4002 Debrecen, Hungary
| | - Tibor Kurtán
- Department of Organic Chemistry, University of Debrecen, P. O. Box 400, 4002 Debrecen, Hungary
| | - Ronald Garcia
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig Inhoffenstraße 7, 38124 Braunschweig, Germany
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Panter F, Bader CD, Müller R. The Sandarazols are Cryptic and Structurally Unique Plasmid-Encoded Toxins from a Rare Myxobacterium*. Angew Chem Int Ed Engl 2021; 60:8081-8088. [PMID: 33534143 PMCID: PMC8048970 DOI: 10.1002/anie.202014671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/12/2021] [Indexed: 11/20/2022]
Abstract
Herein, we describe a new plasmid found in Sandaracinus sp. MSr10575 named pSa001 spanning 209.7 kbp that harbors a cryptic secondary metabolite biosynthesis gene cluster (BGC). Activation of this BGC by homologous-recombination-mediated exchange of the native promoter sequence against a vanillate inducible system led to the production and subsequent isolation and structure elucidation of novel secondary metabolites, the sandarazols A-G. The sandarazols contain intriguing structural features and very reactive functional groups such as an α-chlorinated ketone, an epoxyketone, and a (2R)-2-amino-3-(N,N-dimethylamino)-propionic acid building block. In-depth investigation of the underlying biosynthetic machinery led to a concise biosynthetic model for the new compound family, including several uncommon biosynthetic steps. The chlorinated congener sandarazol C shows an IC50 value of 0.5 μm against HCT 116 cells and a MIC of 14 μm against Mycobacterium smegmatis, which points at the sandarazols' potential function as defensive secondary metabolites or toxins.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
- Helmholtz International Lab for Anti-Infectives, Campus E8 166123SaarbrückenGermany
| | - Chantal D. Bader
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
| | - Rolf Müller
- Department of Microbial Natural ProductsHelmholtz-Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University, Campus E8 166123SaarbrückenGermany
- German Centre for Infection Research (DZIF), Partner SiteHannover-BraunschweigGermany
- Helmholtz International Lab for Anti-Infectives, Campus E8 166123SaarbrückenGermany
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Panter F, Bader CD, Müller R. Die Sandarazole sind kryptische und strukturell einzigartige, Plasmid‐codierte Toxine aus einem seltenen Myxobakterium**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fabian Panter
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
- Helmholtz International Lab for Anti-Infectives, Campus E8 1 66123 Saarbrücken Deutschland
| | - Chantal D. Bader
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
| | - Rolf Müller
- Abteilung Mikrobielle Naturstoffe Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz Zentrum für Infektionsforschung (HZI) und Fachbereich Pharmazie Universität des Saarlandes, Campus E8 1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hannover-Braunschweig Deutschland
- Helmholtz International Lab for Anti-Infectives, Campus E8 1 66123 Saarbrücken Deutschland
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Panter F, Bader CD, Müller R. Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics. Chem Sci 2021; 12:5994-6010. [PMID: 33995996 PMCID: PMC8098685 DOI: 10.1039/d0sc06919a] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development based on natural products has faced a long lasting decline since the 1970s, while both the speed and the extent of antimicrobial resistance (AMR) development have been severely underestimated. The discovery of antimicrobial natural products of bacterial and fungal origin featuring new chemistry and previously unknown mode of actions is increasingly challenged by rediscovery issues. Natural products that are abundantly produced by the corresponding wild type organisms often featuring strong UV signals have been extensively characterized, especially the ones produced by extensively screened microbial genera such as streptomycetes. Purely synthetic chemistry approaches aiming to replace the declining supply from natural products as starting materials to develop novel antibiotics largely failed to provide significant numbers of antibiotic drug leads. To cope with this fundamental issue, microbial natural products science is being transformed from a 'grind-and-find' study to an integrated approach based on bacterial genomics and metabolomics. Novel technologies in instrumental analytics are increasingly employed to lower detection limits and expand the space of detectable substance classes, while broadening the scope of accessible and potentially bioactive natural products. Furthermore, the almost exponential increase in publicly available bacterial genome data has shown that the biosynthetic potential of the investigated strains by far exceeds the amount of detected metabolites. This can be judged by the discrepancy between the number of biosynthetic gene clusters (BGC) encoded in the genome of each microbial strain and the number of secondary metabolites actually detected, even when considering the increased sensitivity provided by novel analytical instrumentation. In silico annotation tools for biosynthetic gene cluster classification and analysis allow fast prioritization in BGC-to-compound workflows, which is highly important to be able to process the enormous underlying data volumes. BGC prioritization is currently accompanied by novel molecular biology-based approaches to access the so-called orphan BGCs not yet correlated with a secondary metabolite. Integration of metabolomics, in silico genomics and molecular biology approaches into the mainstream of natural product research will critically influence future success and impact the natural product field in pharmaceutical, nutritional and agrochemical applications and especially in anti-infective research.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
| | - Chantal D Bader
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
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13
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Bader CD, Haack PA, Panter F, Krug D, Müller R. Expanding the Scope of Detectable Microbial Natural Products by Complementary Analytical Methods and Cultivation Systems. JOURNAL OF NATURAL PRODUCTS 2021; 84:268-277. [PMID: 33449690 DOI: 10.1021/acs.jnatprod.0c00942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent advances in genome sequencing have unveiled a large discrepancy between the genome-encoded capacity of microorganisms to produce secondary metabolites and the number detected. In this work, a two-platform mass spectrometry analysis for the comprehensive secondary metabolomics characterization of nine myxobacterial strains, focusing on extending the range of detectable secondary metabolites by diversifying analytical methods and cultivation conditions, is presented. Direct infusion measurements of crude extracts on a Fourier transform ion cyclotron resonance mass spectrometer are compared to a time-of-flight device coupled to liquid chromatography measurements. Both methods are successful in detecting known metabolites, whereas statistical analysis of unknowns highlights their complementarity: Strikingly, 82-99% of molecular features detected with one setup were not detectable with the other. Metabolite profile differences from our set of strains grown in liquid culture versus their swarming colonies on agar plates were evaluated. The detection of up to 96% more molecular features when both liquid and plate cultures were analyzed translates into increased chances to identify new secondary metabolites. Discrimination between primary and secondary metabolism in combination with GNPS molecular networking revealed strain Mx3 as particularly promising for the isolation of novel secondary metabolites among the nine strains investigated in this study.
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Affiliation(s)
- Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Patrick A Haack
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Fabian Panter
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Daniel Krug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig), and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
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14
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Omoke D, Kipsum M, Otieno S, Esalimba E, Sheth M, Lenhart A, Njeru EM, Ochomo E, Dada N. Western Kenyan Anopheles gambiae showing intense permethrin resistance harbour distinct microbiota. Malar J 2021; 20:77. [PMID: 33557825 PMCID: PMC7869237 DOI: 10.1186/s12936-021-03606-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/22/2021] [Indexed: 12/11/2022] Open
Abstract
Background Insecticide resistance poses a growing challenge to malaria vector control in Kenya and around the world. Following evidence of associations between the mosquito microbiota and insecticide resistance, the microbiota of Anopheles gambiae sensu stricto (s.s.) from Tulukuyi village, Bungoma, Kenya, with differing permethrin resistance profiles were comparatively characterized. Methods Using the CDC bottle bioassay, 133 2–3 day-old, virgin, non-blood fed female F1 progeny of field-caught An. gambiae s.s. were exposed to five times (107.5 µg/ml) the discriminating dose of permethrin. Post bioassay, 50 resistant and 50 susceptible mosquitoes were subsequently screened for kdr East and West mutations, and individually processed for microbial analysis using high throughput sequencing targeting the universal bacterial and archaeal 16S rRNA gene. Results 47 % of the samples tested (n = 133) were resistant, and of the 100 selected for further processing, 99 % were positive for kdr East and 1 % for kdr West. Overall, 84 bacterial taxa were detected across all mosquito samples, with 36 of these shared between resistant and susceptible mosquitoes. A total of 20 bacterial taxa were unique to the resistant mosquitoes and 28 were unique to the susceptible mosquitoes. There were significant differences in bacterial composition between resistant and susceptible individuals (PERMANOVA, pseudo-F = 2.33, P = 0.001), with presence of Sphingobacterium, Lysinibacillus and Streptococcus (all known pyrethroid-degrading taxa), and the radiotolerant Rubrobacter, being significantly associated with resistant mosquitoes. On the other hand, the presence of Myxococcus, was significantly associated with susceptible mosquitoes. Conclusions This is the first report of distinct microbiota in An. gambiae s.s. associated with intense pyrethroid resistance. The findings highlight differentially abundant bacterial taxa between resistant and susceptible mosquitoes, and further suggest a microbe-mediated mechanism of insecticide resistance in mosquitoes. These results also indicate fixation of the kdr East mutation in this mosquito population, precluding further analysis of its associations with the mosquito microbiota, but presenting the hypothesis that any microbe-mediated mechanism of insecticide resistance would be likely of a metabolic nature. Overall, this study lays initial groundwork for understanding microbe-mediated mechanisms of insecticide resistance in African mosquito vectors of malaria, and potentially identifying novel microbial markers of insecticide resistance that could supplement existing vector surveillance tools.
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Affiliation(s)
- Diana Omoke
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya.,Entomology Section, Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Mathew Kipsum
- Entomology Section, Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Samson Otieno
- Entomology Section, Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Edward Esalimba
- Entomology Section, Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Mili Sheth
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging & Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Audrey Lenhart
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Diseases Control and Prevention, Atlanta, GA, USA
| | - Ezekiel Mugendi Njeru
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Eric Ochomo
- Entomology Section, Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Nsa Dada
- Faculty of Science and Technology, Norwegian University of Life Science, Aas, Norway. .,Public Health and Epidemiology Department, Nigerian Institute of Medical Research, Lagos, Nigeria.
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15
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Bader CD, Neuber M, Panter F, Krug D, Müller R. Supercritical Fluid Extraction Enhances Discovery of Secondary Metabolites from Myxobacteria. Anal Chem 2020; 92:15403-15411. [DOI: 10.1021/acs.analchem.0c02995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Chantal D. Bader
- Department Microbial Natural Products, Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig) and Department of Pharmacy, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus E8.1, 66123 Saarbrücken, Germany
| | - Markus Neuber
- Department Microbial Natural Products, Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig) and Department of Pharmacy, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus E8.1, 66123 Saarbrücken, Germany
| | - Fabian Panter
- Department Microbial Natural Products, Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig) and Department of Pharmacy, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus E8.1, 66123 Saarbrücken, Germany
| | - Daniel Krug
- Department Microbial Natural Products, Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig) and Department of Pharmacy, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partnersite Hannover-Braunschweig) and Department of Pharmacy, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus E8.1, 66123 Saarbrücken, Germany
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Natural Compound-derived Cytochrome bc1 Complex Inhibitors as Antifungal Agents. Molecules 2020; 25:molecules25194582. [PMID: 33036496 PMCID: PMC7583968 DOI: 10.3390/molecules25194582] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/25/2020] [Accepted: 10/06/2020] [Indexed: 01/09/2023] Open
Abstract
The high incidence of fungal pathogens has become a global issue for crop protection. A promising strategy to control fungal plant infections is based on the use of nature-inspired compounds. The cytochrome bc1 complex is an essential component of the cellular respiratory chain and is one of the most important fungicidal targets. Natural products have played a crucial role in the discovery of cytochrome bc1 inhibitors, as proven by the development of strobilurins, one of the most important classes of crop-protection agents, over the past two decades. In this review, we summarize advances in the exploration of natural product scaffolds for the design and development of new bc1 complex inhibitors. Particular emphasis is given to molecular modeling-based approaches and structure-activity relationship (SAR) studies performed to improve the stability and increase the potency of natural precursors. The collected results highlight the versatility of natural compounds and provide an insight into the potential development of nature-inspired derivatives as antifungal agents.
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17
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Microbiotal characteristics colonized in intestinal mucosa of mice with diarrhoea and repeated stress. 3 Biotech 2020; 10:372. [PMID: 32832332 DOI: 10.1007/s13205-020-02368-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/27/2020] [Indexed: 12/27/2022] Open
Abstract
To understand the role of intestinal mucosal microbiota on mental stress-related diarrhoea, we collected the intestinal mucosa of mice treated with Folium senna extract gavage combined with restraint and tail pinch stress for 7 days; and intestinal mucosal microbiota characteristics were analyzed by 16S rRNA Pacbio SMRT gene full-length sequencing. The results showed that the diversity (i.e., alpha diversity including the Chao1, Simpson, ACE, and Shannon indices and beta diversity including the NMDS of weighted UniFrac distances) and composition of the microbial community in the intestinal mucosa of mice with diarrhoea and repeated stress changed significantly (P < 0.05). In the co-occurrence network, Staphylococcus sciuri and Escherichia fergusonii was identified as putative keystone species. Moreover, the characteristics of the intestinal microbial species was analyzed by LEfSe, Metastats, and group difference, and ten altered gut microbiota species can be used as characteristic microbes in the mice with diarrhoea and repeated stress: the abundances of Stigmatella aurantiaca, Candidatus arthromitus sp. SFB-mouse, Erythrobacter gaetbuli, Desulfitobacterium hafniense, Ochrobactrum pituitosum, and Candidatus arthromitus sp. SFB-mouse-NL in the model group were significantly lower than those in the control group (P < 0.05); whereas Microbacterium dextranolyticum, Klebsiella pneumoniae, Escherichia sp. BBDP27, and Streptococcus danieliae were enriched in the control group (P < 0.05). Collectively, mental stress-related diarrhoea increased the intestinal microbiota diversity. The species associated with mental stress-related diarrhoea including Microbacterium dextranolyticum, Klebsiella pneumoniae, Escherichia sp. BBDP27, and Streptococcus danieliae were significantly enriched; while the species which are beneficial to mental stress-related diarrhoea are Stigmatella aurantiaca, Candidatus arthromitus sp. SFB-mouse, Erythrobacter gaetbuli, Desulfitobacterium hafniense, Ochrobactrum pituitosum, and Candidatus arthromitus sp. SFB-mouse-NL for its significantly depleted.
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Soldatou S, Eldjarn GH, Huerta-Uribe A, Rogers S, Duncan KR. Linking biosynthetic and chemical space to accelerate microbial secondary metabolite discovery. FEMS Microbiol Lett 2020; 366:5525086. [PMID: 31252431 PMCID: PMC6697067 DOI: 10.1093/femsle/fnz142] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/19/2019] [Indexed: 12/17/2022] Open
Abstract
Secondary metabolites can be viewed as a chemical language, facilitating communication between microorganisms. From an ecological point of view, this metabolite exchange is in constant flux due to evolutionary and environmental pressures. From a biomedical perspective, the chemistry is unsurpassed for its antibiotic properties. Genome sequencing of microorganisms has revealed a large reservoir of Biosynthetic Gene Clusters (BGCs); however, linking these to the secondary metabolites they encode is currently a major bottleneck to chemical discovery. This linking of genes to metabolites with experimental validation will aid the elicitation of silent or cryptic (not expressed under normal laboratory conditions) BGCs. As a result, this will accelerate chemical dereplication, our understanding of gene transcription and provide a comprehensive resource for synthetic biology. This will ultimately provide an improved understanding of both the biosynthetic and chemical space. In recent years, integrating these complex metabolomic and genomic data sets has been achieved using a spectrum of manual and automated approaches. In this review, we cover examples of these approaches, while addressing current challenges and future directions in linking these data sets.
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Affiliation(s)
- Sylvia Soldatou
- Department of Chemistry, University of Aberdeen, Aberdeen, UK. AB24 3UE
| | | | - Alejandro Huerta-Uribe
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK. G4 0RE
| | - Simon Rogers
- School of Computing Science, University of Glasgow, Glasgow, UK. G12 8RZ
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK. G4 0RE
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Bader CD, Panter F, Müller R. In depth natural product discovery - Myxobacterial strains that provided multiple secondary metabolites. Biotechnol Adv 2019; 39:107480. [PMID: 31707075 DOI: 10.1016/j.biotechadv.2019.107480] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/28/2022]
Abstract
In recognition of many microorganisms ability to produce a variety of secondary metabolites in parallel, Zeeck and coworkers introduced the term "OSMAC" (one strain many compounds) around the turn of the century. Since then, additional efforts focused on the systematic characterization of a single bacterial species ability to form multiple secondary metabolite scaffolds. With the beginning of the genomic era mainly initiated by a dramatic reduction of sequencing costs, investigations of the genome encoded biosynthetic potential and especially the exploitation of biosynthetic gene clusters of undefined function gained attention. This was seen as a novel means to extend range and diversity of bacterial secondary metabolites. Genome analyses showed that even for well-studied bacterial strains, like the myxobacterium Myxococcus xanthus DK1622, many biosynthetic gene clusters are not yet assigned to their corresponding hypothetical secondary metabolites. In contrast to the results from emerging genome and metabolome mining techniques that show the large untapped biosynthetic potential per strain, many newly isolated bacterial species are still used for the isolation of only one target compound class and successively abandoned in the sense that no follow up studies are published from the same species. This work provides an overview about myxobacterial bacterial strains, from which not just one but multiple different secondary metabolite classes were successfully isolated. The underlying methods used for strain prioritization and natural product discovery such as biological characterization of crude extracts against a panel of pathogens, in-silico prediction of secondary metabolite abundance from genome data and state of the art instrumental analytics required for new natural product scaffold discovery in comparative settings are summarized and classified according to their output. Furthermore, for each approach selected studies performed with actinobacteria are shown to underline especially innovative methods used for natural product discovery.
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Affiliation(s)
- Chantal D Bader
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Fabian Panter
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany.
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20
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Hill RA, Sutherland A. Hot off the Press. Nat Prod Rep 2019. [DOI: 10.1039/c9np90010a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as preuisolactone A from Preussia isomera.
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