1
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Hu WF, Yang JY, Wang JJ, Yuan SF, Yue XJ, Zhang Z, Zhang YQ, Meng JY, Li YZ. Characteristics and immune functions of the endogenous CRISPR-Cas systems in myxobacteria. mSystems 2024; 9:e0121023. [PMID: 38747603 PMCID: PMC11237760 DOI: 10.1128/msystems.01210-23] [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: 11/13/2023] [Accepted: 04/15/2024] [Indexed: 06/19/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) system widely occurs in prokaryotic organisms to recognize and destruct genetic invaders. Systematic collation and characterization of endogenous CRISPR-Cas systems are conducive to our understanding and potential utilization of this natural genetic machinery. In this study, we screened 39 complete and 692 incomplete genomes of myxobacteria using a combined strategy to dispose of the abridged genome information and revealed at least 19 CRISPR-Cas subtypes, which were distributed with a taxonomic difference and often lost stochastically in intraspecies strains. The cas genes in each subtype were evolutionarily clustered but deeply separated, while most of the CRISPRs were divided into four types based on the motif characteristics of repeat sequences. The spacers recorded in myxobacterial CRISPRs were in high G+C content, matching lots of phages, tiny amounts of plasmids, and, surprisingly, massive organismic genomes. We experimentally demonstrated the immune and self-target immune activities of three endogenous systems in Myxococcus xanthus DK1622 against artificial genetic invaders and revealed the microhomology-mediated end-joining mechanism for the immunity-induced DNA repair but not homology-directed repair. The panoramic view and immune activities imply potential omnipotent immune functions and applications of the endogenous CRISPR-Cas machinery. IMPORTANCE Serving as an adaptive immune system, clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) empower prokaryotes to fend off the intrusion of external genetic materials. Myxobacteria are a collective of swarming Gram-stain-negative predatory bacteria distinguished by intricate multicellular social behavior. An in-depth analysis of their intrinsic CRISPR-Cas systems is beneficial for our understanding of the survival strategies employed by host cells within their environmental niches. Moreover, the experimental findings presented in this study not only suggest the robust immune functions of CRISPR-Cas in myxobacteria but also their potential applications.
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Affiliation(s)
- Wei-Feng Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jiang-Yu Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jing-Jing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Shu-Fei Yuan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xin-Jing Yue
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Ya-Qi Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jun-Yan Meng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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2
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Zang Y, Zhang X, Wang Z, Tong Q, Zhou Y, Yao Q, Zhu H. Hyalangiumruber sp. nov, characterization of a novel myxobacterium strain s54d21 and their secondary metabolites. Front Microbiol 2024; 15:1369499. [PMID: 38525079 PMCID: PMC10959286 DOI: 10.3389/fmicb.2024.1369499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/22/2024] [Indexed: 03/26/2024] Open
Abstract
Myxobacteria are special bacteria with wide adaptability, which are rich sources of structurally diverse natural products with intriguing biological properties. Here, a gram-negative myxobacterium strain s54d21T was isolated from the sediment of a wetland park in China using the Escherichia coli baiting method. Based on 16S rRNA gene sequence and genomic data, the strain was demonstrated to be a novel species of a rare genus Hyalangium, designated Hyalangium ruber sp. nov (type strain s54d21T = GDMCC 1.1945T = JCM 39263T). The subsequent chemical investigation of the strain s54d21T led to the isolation of three rare 3,5,6-trisubstituted 2(1H)-pyrazinones, namely, hyalanones A-C (1-3), together with a known macrolactin A (4). Those new structures and their absolute configurations were unambiguously assigned by extensive analyses of spectroscopic data and density functional theory (DFT) calculations. In biological assays, compound 4 exhibited moderate cytotoxic activities against human cell lines RKO, A549, and NCM460 with IC50 values ranging from 27.21 to 32.14 μM.
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Affiliation(s)
- Yi Zang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xianjiao Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Zhe Wang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingyi Tong
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Zhou
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qing Yao
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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3
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Buntine J, Dasgupta S, Dorney K, Rubinstein O, Salimimarand M, White JM, Rizzacasa MA. Total Synthesis of Icumazole A Using a Modified Cadiot-Chodkiewicz Coupling. Org Lett 2024; 26:1062-1066. [PMID: 38285532 DOI: 10.1021/acs.orglett.3c04268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
The first total synthesis of myxobacteria metabolite icumazole A (1) is reported. Key steps in the route include an organocatalyzed asymmetric self-aldol reaction followed by an acetate aldol reaction to form the stereotriad present in the oxazole moiety, an intramolecular Diels-Alder reaction to form the isochromanone, and an acetylide addition and selective methylation. The final steps involved a high-yielding modified Cadiot-Chodkiewicz coupling and stereoselective reduction to secure the Z,Z-diene and afford 1.
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Affiliation(s)
- Jack Buntine
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Samrat Dasgupta
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Keely Dorney
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Oscar Rubinstein
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Mina Salimimarand
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jonathan M White
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Mark A Rizzacasa
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
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4
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Ali Y, Khan AA, Alanazi AM, Abdikakharovich SA, Shah JA, Ren ZG, Khattak S. Identification of the myxobacterial secondary metabolites Aurachin A and Soraphinol A as promising inhibitors of thymidylate kinase of the Monkeypox virus. Mol Divers 2024:10.1007/s11030-023-10764-x. [PMID: 38183513 DOI: 10.1007/s11030-023-10764-x] [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: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 01/08/2024]
Abstract
Thymidylate kinase (TMPK) of monkeypox virus (MPXV) has emerged as a promising target for potential therapeutics due to its significant role in pyrimidine metabolism. While smallpox drugs are advised for treating monkeypox, the European Medicine Agency has sanctioned Tecovirimat due to its potent nanomolar activity. Nonetheless, there is a need for monkeypox-specific therapeutic options. In this work, we employed docking-based virtual screening and molecular dynamics (MD) simulations to identify myxobacterial secondary metabolites as promising anti-viral natural compounds capable of inhibiting thymidylate kinase. The computational pharmacokinetics and manual curation of top-scoring compounds identified six lead compounds that were compared in terms of protein-ligand contacts and protein-essential dynamics. The study shows that among the six candidates, Aurachin A and the Soraphinol analogues such as Soraphinol A and Soraphinol C remain very stable compared to other compounds, enabling the active site integrity via a stable dynamics pattern. We also show that other compounds such as Phenoxan, Phenylnannolone C, and 8E-Aurafuron B remain unstable and have a negative impact on the active site integrity and may not be suitable binders for TMPK protein. Analyzing the Aurachin A and Soraphinol A binding, the established hydrogen bonds with Arg93 and the conserved hydrophobic interaction with Tyr101 are consistent with previous experimental interactions. Additionally, a deeper insight into the indole and the aromatic ring interaction through π-π stacking and π-cation interactions, as well as the background of Aurachin A and Soraphinol A as a bioactive compound, has significant implications not only for its potential as a promising drug but also for directing future drug discovery efforts targeting the TMPK protein.
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Affiliation(s)
- Yasir Ali
- Institute of Chemistry, Slovak Academy of Sciences, 845 38, Bratislava, Slovakia
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Amer M Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | | | - Junaid Ali Shah
- Ferghana Medical Institute of Public Health, 104100, Ferghana, Uzbekistan
| | - Zhi-Guang Ren
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University College of Medicine, Kaifeng, 475004, Henan, China.
| | - Saadullah Khattak
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University College of Medicine, Kaifeng, 475004, Henan, China.
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5
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Hertrampf G, Vojnovic S, Müller JI, Merten C, Nikodinovic-Runic J, Gulder TAM. Synthesis, Stereochemical Determination, and Antimicrobial Evaluation of Myxocoumarin A. J Org Chem 2023; 88:14184-14188. [PMID: 37708429 DOI: 10.1021/acs.joc.3c01285] [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: 09/16/2023]
Abstract
The myxobacterial natural product myxocoumarin A from Stigmatella aurantiaca MYX-030 has remarkable antifungal activity against agriculturally relevant pathogens. To broaden the initial evaluation of its biological potential, we herein completed the first total synthesis of myxocoumarin A. This synthetic access facilitated stereochemical investigations on the natural product structure, revealing its (R)-configuration. Biological activity profiling showed a lack of activity against Candida spp. and Gram-negative bacteria but revealed strong antibiotic activities against Bacillus subtilis and Staphylococcus aureus, including MRSA.
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Affiliation(s)
- Gesa Hertrampf
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069 Dresden, Germany
| | - Sandra Vojnovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, Belgrade, 11000, Serbia
| | - Jonas I Müller
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069 Dresden, Germany
| | - Christian Merten
- Organic Chemistry II, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Jasmina Nikodinovic-Runic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, Belgrade, 11000, Serbia
| | - Tobias A M Gulder
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069 Dresden, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Natural Product Biotechnology, Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
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6
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Saggu SK, Nath A, Kumar S. Myxobacteria: biology and bioactive secondary metabolites. Res Microbiol 2023; 174:104079. [PMID: 37169232 DOI: 10.1016/j.resmic.2023.104079] [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: 01/19/2023] [Revised: 04/22/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Myxobacteria are Gram-negative eubacteria and they thrive in a variety of habitats including soil rich in organic matter, rotting wood, animal dung and marine environment. Myxobacteria are a promising source of new compounds associated with diverse bioactive spectrum and unique mode of action. The genome information of myxobacteria has revealed many orphan biosynthetic pathways indicating that these bacteria can be the source of several novel natural products. In this review, we highlight the biology of myxobacteria with emphasis on their habitat, life cycle, isolation methods and enlist all the bioactive secondary metabolites purified till date and their mode of action.
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Affiliation(s)
- Sandeep Kaur Saggu
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, India - 144004.
| | - Amar Nath
- University Centre of Excellence in Research, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
| | - Shiv Kumar
- Guru Gobind Singh Medical College, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
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7
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Gao Y, Birkelbach J, Fu C, Herrmann J, Irschik H, Morgenstern B, Hirschfelder K, Li R, Zhang Y, Jansen R, Müller R. The Disorazole Z Family of Highly Potent Anticancer Natural Products from Sorangium cellulosum: Structure, Bioactivity, Biosynthesis, and Heterologous Expression. Microbiol Spectr 2023; 11:e0073023. [PMID: 37318329 PMCID: PMC10434194 DOI: 10.1128/spectrum.00730-23] [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: 02/16/2023] [Accepted: 03/24/2023] [Indexed: 06/16/2023] Open
Abstract
Myxobacteria serve as a treasure trove of secondary metabolites. During our ongoing search for bioactive natural products, a novel subclass of disorazoles termed disorazole Z was discovered. Ten disorazole Z family members were purified from a large-scale fermentation of the myxobacterium Sorangium cellulosum So ce1875 and characterized by electrospray ionization-high-resolution mass spectrometry (ESI-HRMS), X-ray, nuclear magnetic resonance (NMR), and Mosher ester analysis. Disorazole Z compounds are characterized by the lack of one polyketide extension cycle, resulting in a shortened monomer in comparison to disorazole A, which finally forms a dimer in the bis-lactone core structure. In addition, an unprecedented modification of a geminal dimethyl group takes place to form a carboxylic acid methyl ester. The main component disorazole Z1 shows comparable activity in effectively killing cancer cells to disorazole A1 via binding to tubulin, which we show induces microtubule depolymerization, endoplasmic reticulum delocalization, and eventually apoptosis. The disorazole Z biosynthetic gene cluster (BGC) was identified and characterized from the alternative producer S. cellulosum So ce427 and compared to the known disorazole A BGC, followed by heterologous expression in the host Myxococcus xanthus DK1622. Pathway engineering by promoter substitution and gene deletion paves the way for detailed biosynthesis studies and efficient heterologous production of disorazole Z congeners. IMPORTANCE Microbial secondary metabolites are a prolific reservoir for the discovery of bioactive compounds, which prove to be privileged scaffolds for the development of new drugs such as antibacterial and small-molecule anticancer drugs. Consequently, the continuous discovery of novel bioactive natural products is of great importance for pharmaceutical research. Myxobacteria, especially Sorangium spp., which are known for their large genomes with yet-underexploited biosynthetic potential, are proficient producers of such secondary metabolites. From the fermentation broth of Sorangium cellulosum strain So ce1875, we isolated and characterized a family of natural products named disorazole Z, which showed potent anticancer activity. Further, we report on the biosynthesis and heterologous production of disorazole Z. These results can be stepping stones toward pharmaceutical development of the disorazole family of anticancer natural products for (pre)clinical studies.
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Affiliation(s)
- Yunsheng Gao
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Joy Birkelbach
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
| | - Chengzhang Fu
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
| | - Herbert Irschik
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Bernd Morgenstern
- Department of Inorganic Chemistry, Saarland University, Saarbrücken, Germany
| | - Kerstin Hirschfelder
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
| | - Ruijuan Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rolf Jansen
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University, Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, Braunschweig, Germany
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8
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Wang X, Chen X, Wang ZJ, Zhuang M, Zhong L, Fu C, Garcia R, Müller R, Zhang Y, Yan J, Wu D, Huo L. Discovery and Characterization of a Myxobacterial Lanthipeptide with Unique Biosynthetic Features and Anti-inflammatory Activity. J Am Chem Soc 2023. [PMID: 37466996 DOI: 10.1021/jacs.3c06014] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The genomes of myxobacteria harbor a variety of biosynthetic gene clusters encoding numerous secondary metabolites, including ribosomally synthesized and post-translationally modified peptides (RiPPs) with diverse chemical structures and biological activities. However, the biosynthetic potential of RiPPs from myxobacteria remains barely explored. Herein, we report a novel myxobacteria lanthipeptide myxococin identified from Myxococcus fulvus. Myxococins represent the first example of lanthipeptides, of which the characteristic multiple thioether rings are installed by employing a Class II lanthipeptide synthetase MfuM and a Class I lanthipeptide cyclase MfuC in a cascaded way. Unprecedentedly, we biochemically characterized the first M61 family aminopeptidase MfuP involved in RiPP biosynthesis, demonstrating that MfuP showed the activity of an endopeptidase activity. MfuP is leader-independent but strictly selective for the multibridge structure of myxococin A and responsible for unwrapping two rings via amide bond hydrolysis, yielding myxococin B. Furthermore, the X-ray crystal structure of MfuP and structural analysis, including active-site mutations, are reported. Finally, myxococins are evaluated to exhibit anti-inflammatory activity in lipopolysaccharide-induced macrophages without detectable cytotoxicity.
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Affiliation(s)
- Xiaotong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Xiaoyu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Zong-Jie Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Mengwei Zhuang
- Department of Diagnostics, Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Lin Zhong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Chin
| | - Chengzhang Fu
- Helmholtz International Laboratory, Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Ronald Garcia
- Helmholtz International Laboratory, Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz International Laboratory, Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- Helmholtz International Lab for Anti-Infectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Jie Yan
- Department of Diagnostics, Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dalei Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Liujie Huo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
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9
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Liu Y, Yamazaki S, Ojika M. Heterologous Biosynthesis of Myxobacterial Antibiotic Miuraenamide A. Molecules 2023; 28:molecules28062815. [PMID: 36985787 PMCID: PMC10051162 DOI: 10.3390/molecules28062815] [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: 02/15/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
The hard-to-culture slightly halophilic myxobacterium "Paraliomyxa miuraensis" SMH-27-4 produces antifungal cyclodepsipeptide miuraenamide A (1). Herein, the region (85.9 kbp) containing the biosynthetic gene cluster (BGC) coding the assembly of 1 was identified and heterologously expressed in Myxococcus xanthus. A biosynthetic pathway proposed using in silico analysis was verified through the gene disruption of the heterologous transformant. In addition to the core polyketide synthase (PKS) and nonribosomal peptide synthase (NRPS) genes, tyrosine halogenase and O-methyltransferase genes participated in the biosynthesis of 1 as their gene-disrupted mutants produced a new congener, debromomiuraenamide A (4), and a previously isolated congener, miuraenamide E (3), respectively. Multigene disruption provided a heterologous mutant that produced 1 with the highest yield among the prepared mutants. When fed on 3-bromo-L-tyrosine, this mutant produced more 1 in the yield of 1.21 mg/L, which was 20 times higher than that produced by the initially prepared heterologous transformant. Although this yield was comparable to that of the original producer SMH-27-4 (1 mg/L), the culture time was 4.5 times shorter than that of SMH-27-4, indicating a five-fold efficiency in productivity. The results indicate the great potential of the miuraenamide BGC for the future contribution to drug development through logical gene manipulation.
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Affiliation(s)
- Ying Liu
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Satoshi Yamazaki
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Makoto Ojika
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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10
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Wang DG, Wang CY, Hu JQ, Wang JJ, Liu WC, Zhang WJ, Du XR, Wang H, Zhu LL, Sui HY, Li YZ, Wu C. Constructing a Myxobacterial Natural Product Database to Facilitate NMR-Based Metabolomics Bioprospecting of Myxobacteria. Anal Chem 2023; 95:5256-5266. [PMID: 36917632 DOI: 10.1021/acs.analchem.2c05145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Myxobacteria are fascinating prokaryotes featuring a potent capacity for producing a wealth of bioactive molecules with intricate chemical topology as well as intriguing enzymology, and thus it is critical to developing an efficient pipeline for bioprospecting. Herein, we construct the database MyxoDB, the first public compendium solely dedicated to myxobacteria, which enabled us to provide an overview of the structural diversity and taxonomic distribution of known myxobacterial natural products. Moreover, we demonstrated that the cutting-edge NMR-based metabolomics was effective to differentiate the biosynthetic priority of myxobacteria, whereby MyxoDB could greatly streamline the dereplication of multifarious known compounds and accordingly speed up the discovery of new compounds. This led to the rapid identification of a class of linear di-lipopeptides (archangimins) and a rare rearranged sterol (corasterol) that were endowed with unique chemical architectures and/or biosynthetic enzymology. We also showcased that NMR-based metabolomics, MyxoDB, and genomics can also work concertedly to accelerate the targeted discovery of a polyketidic compound pyxipyrrolone C. All in all, this study sets the stage for the discovery of many more novel natural products from underexplored myxobacterial resources.
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Affiliation(s)
- De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Chao-Yi Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jing-Jing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Wen-Chao Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Wen-Juan Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xin-Ran Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Han Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Le-Le Zhu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hai-Yan Sui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
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A Diverged Transcriptional Network for Usage of Two Fe-S Cluster Biogenesis Machineries in the Delta-Proteobacterium Myxococcus xanthus. mBio 2023; 14:e0300122. [PMID: 36656032 PMCID: PMC9973013 DOI: 10.1128/mbio.03001-22] [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] [Indexed: 01/20/2023] Open
Abstract
Myxococcus xanthus possesses two Fe-S cluster biogenesis machineries, ISC (iron-sulfur cluster) and SUF (sulfur mobilization). Here, we show that in comparison to the phylogenetically distant Enterobacteria, which also have both machineries, M. xanthus evolved an independent transcriptional scheme to coordinately regulate the expression of these machineries. This transcriptional response is directed by RisR, which we show to belong to a phylogenetically distant and biochemically distinct subgroup of the Rrf2 transcription factor family, in comparison to IscR that regulates the isc and suf operons in Enterobacteria. We report that RisR harbors an Fe-S cluster and that holo-RisR acts as a repressor of both the isc and suf operons, in contrast to Escherichia coli, where holo-IscR represses the isc operon whereas apo-IscR activates the suf operon. In addition, we establish that the nature of the cluster and the DNA binding sites of RisR, in the isc and suf operons, diverge from those of IscR. We further show that in M. xanthus, the two machineries appear to be fully interchangeable in maintaining housekeeping levels of Fe-S cluster biogenesis and in synthesizing the Fe-S cluster for their common regulator, RisR. We also demonstrate that in response to oxidative stress and iron limitation, transcriptional upregulation of the M. xanthus isc and suf operons was mediated solely by RisR and that the contribution of the SUF machinery was greater than the ISC machinery. Altogether, these findings shed light on the diversity of homeostatic mechanisms exploited by bacteria to coordinately use two Fe-S cluster biogenesis machineries. IMPORTANCE Fe-S proteins are ubiquitous and control a wide variety of key biological processes; therefore, maintaining Fe-S cluster homeostasis is an essential task for all organisms. Here, we provide the first example of how a bacterium from the Deltaproteobacteria branch coordinates expression of two Fe-S cluster biogenesis machineries. The results revealed a new model of coordination, highlighting the unique and common features that have independently emerged in phylogenetically distant bacteria to maintain Fe-S cluster homeostasis in response to environmental changes. Regulation is orchestrated by a previously uncharacterized transcriptional regulator, RisR, belonging to the Rrf2 superfamily, whose members are known to sense diverse environmental stresses frequently encountered by bacteria. Understanding how M. xanthus maintains Fe-S cluster homeostasis via RisR regulation revealed a strategy reflective of the aerobic lifestyle of this organsim. This new knowledge also paves the way to improve production of Fe-S-dependent secondary metabolites using M. xanthus as a chassis.
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12
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Liu Y, Ojika M. Genomic Analysis of the Rare Slightly Halophilic Myxobacterium " Paraliomyxa miuraensis" SMH-27-4, the Producer of the Antibiotic Miuraenamide A. Microorganisms 2023; 11:microorganisms11020371. [PMID: 36838335 PMCID: PMC9960870 DOI: 10.3390/microorganisms11020371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023] Open
Abstract
Halophilic/halotolerant myxobacteria are extremely rare bacteria but an important source of novel bioactive secondary metabolites as drug leads. A slightly halophilic myxobacterium, "Paraliomyxa miuraensis" SMH-27-4, the producer of the antifungal antibiotic miuraenamide A, was considered to represent a novel genus. This study aimed to use the whole-genome sequence of this difficult-to-culture bacterium to provide genomic evidence supporting its taxonomy and to explore its potential as a novel secondary metabolite producer and its predicted gene functions. The draft genome was sequenced and de novo assembled into 164 contigs (11.8 Mbp). The 16S rRNA gene sequence-based and genome sequence-based phylogenetic analyses supported that this strain represents a novel genus of the family Nannocystaceae. Seventeen biosynthetic gene clusters (BGCs) were identified, and only five of them show some degree of similarity with the previously annotated BGCs, suggesting the great potential of producing novel secondary metabolites. The comparative genomic analysis within the family Nannocystaceae revealed the distribution of its members' gene functions. This study unveiled the novel genomic features and potential of the secondary metabolite production of this myxobacterium.
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13
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Ibrahimi M, Loqman S, Jemo M, Hafidi M, Lemee L, Ouhdouch Y. The potential of facultative predatory Actinomycetota spp. and prospects in agricultural sustainability. Front Microbiol 2023; 13:1081815. [PMID: 36762097 PMCID: PMC9905845 DOI: 10.3389/fmicb.2022.1081815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023] Open
Abstract
Actinomycetota in the phylum of bacteria has been explored extensively as a source of antibiotics and secondary metabolites. In addition to acting as plant growth-promoting agents, they also possess the potential to control various plant pathogens; however, there are limited studies that report the facultative predatory ability of Actinomycetota spp. Furthermore, the mechanisms that underline predation are poorly understood. We assessed the diversity of strategies employed by predatory bacteria to attack and subsequently induce the cell lysing of their prey. We revisited the diversity and abundance of secondary metabolite molecules linked to the different predation strategies by bacteria species. We analyzed the pros and cons of the distinctive predation mechanisms and explored their potential for the development of new biocontrol agents. The facultative predatory behaviors diverge from group attack "wolfpack," cell-to-cell proximity "epibiotic," periplasmic penetration, and endobiotic invasion to degrade host-cellular content. The epibiotic represents the dominant facultative mode of predation, irrespective of the habitat origins. The wolfpack is the second-used approach among the Actinomycetota harboring predatory traits. The secondary molecules as chemical weapons engaged in the respective attacks were reviewed. We finally explored the use of predatory Actinomycetota as a new cost-effective and sustainable biocontrol agent against plant pathogens.
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Affiliation(s)
- Manar Ibrahimi
- Laboratory of Molecular Chemistry, Materials and Catalysis, Faculty of Sciences and Technics, Sultan Moulay Slimane University, Beni-Mellal, Morocco,Higher School of Technology Fkih Ben Salah, Sultan Moulay Slimane University, Fkih Ben Salah, Morocco
| | - Souad Loqman
- Laboratory of Microbiology and Virology, Faculty of Medicine and Pharmacy, Cadi Ayyad University, Marrakesh, Morocco
| | - Martin Jemo
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Mohamed Hafidi
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco,Labelled Research Unit N°4 CNRST, Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco
| | - Laurent Lemee
- Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP–CNRS UMR 7285), Université de Poitiers, Poitiers, France
| | - Yedir Ouhdouch
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco,Labelled Research Unit N°4 CNRST, Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco,*Correspondence: Yedir Ouhdouch,
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14
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Octaviana S, Primahana G, Mozef T, Borges LGA, Pieper DH, Wink J. Diversity of Myxobacteria Isolated from Indonesian Mangroves and Their Potential for New Antimicrobial Sources. Curr Microbiol 2023; 80:46. [PMID: 36538090 PMCID: PMC9768008 DOI: 10.1007/s00284-022-03066-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
Abstract
Mangroves are unique intertidal ecosystems that provide ecological niches to different microbes, which play various roles in nutrient recycling and diverse environmental activities. The association between myxobacteria and mangroves are hitherto poorly understood. The aim of our study was to evaluate the myxobacterial community composition as well as isolate myxobacteria and to characterize the antimicrobial activity of myxobacteria isolates from Indonesian mangroves. Twenty-five cultivable myxobacteria were affiliated in six genera: Myxococcus, Corallococcus, Archangium, Chondromyces, Racemicystis and Nannocystis of the order Myxococcales based on partial 16S rRNA gene sequences. Thirteen crude extracts showed moderate activities against at least one of human pathogenic microorganisms. The crude extract of Racemicystis sp. strain 503MSO indicated a novel compound, which has not been reported in the database yet and the identification of this compound needs further study. The myxobacterial communities of three different sampling sites were analyzed using primers adapted for the myxobacteria group identification. The results showed that myxobacterial communities are more diverse than assumed. Therefore, our study has highlighted the importance of the mangrove habitat as promising harbor of myxobacteria as well as novel antimicrobial compounds with activity against pathogenic microorganisms.
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Affiliation(s)
- Senlie Octaviana
- Helmholtz Center for Infection Research, Microbial Strain Collection, Braunschweig, Germany ,Research Center for Applied Microbiology BRIN, Cibinong, Jawa Barat Indonesia
| | - Gian Primahana
- Microbial Drug, Helmholtz Center for Infection Research, Braunschweig, Germany ,Research Center for Pharmaceutical Ingredients and Traditional Medicines BRIN, Cibinong, Jawa Barat Indonesia
| | - Tjandrawati Mozef
- Research Center for Pharmaceutical Ingredients and Traditional Medicines BRIN, Cibinong, Jawa Barat Indonesia
| | - Luiz G. A. Borges
- Microbial Interactions and Processes, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Dietmar H. Pieper
- Microbial Interactions and Processes, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Joachim Wink
- Helmholtz Center for Infection Research, Microbial Strain Collection, Braunschweig, Germany
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15
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Wang W, Liu H, Yan J, Jiang Y, Cheng H, Wang D. Research progress on the synthesis, structural modification and biological activity of stigmatellin A. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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A Dual-Functional Orphan Response Regulator Negatively Controls the Differential Transcription of Duplicate groELs and Plays a Global Regulatory Role in Myxococcus. mSystems 2022; 7:e0105621. [PMID: 35353010 PMCID: PMC9040617 DOI: 10.1128/msystems.01056-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Differential transcription of functionally divergent duplicate genes is critical for bacterial cells to properly and competitively function in the environment, but the transcriptional regulation mechanisms remain in mystery. Myxococcus xanthus DK1622 possesses two duplicate groELs with divergent functions. Here, we report that MXAN_4468, an orphan gene located upstream of groEL2, encodes a response regulator (RR) and is responsible for the differential expression regulation of duplicate groELs. This RR protein realizes its negative regulatory role via a novel dual-mode functioning manner: binding to the transcription repressor HrcA to enhance its transcriptional inhibition of duplicate groELs and binding to the 3′ end of the MXAN_4468 sequence to specifically decrease the transcription of the following groEL2. Phosphorylation at the conserved 61st aspartic acid is required to trigger the regulatory functions of MXAN_4468. Pull-down experiment and mutation demonstrated that two noncognate CheA proteins, respectively belonging to the Che8 and Che7 chemosensory pathways, are involved in the protein phosphorylation. A transcriptome analysis, as well as the pull-down experiment, suggested that MXAN_4468 plays a global negative regulatory role in M. xanthus. This study elucidates, for the first time, the regulatory mechanism of differential transcription of bacterial duplicate groELs and suggests a global regulatory role of a dual-functional orphan RR. IMPORTANCE Multiply copied groELs require precise regulation of transcriptions for their divergent cellular functions. Here, we reported that an orphan response regulator (RR) tunes the transcriptional discrepancy of the duplicate groELs in Myxococcus xanthus DK1622 in a dual-functional mode. This RR protein has a conserved phosphorylation site, and the phosphorylation is required for the regulatory functions. Transcriptomic analysis, as well as a pull-down experiment, suggests that the RR plays a global regulatory role in M. xanthus. This study highlights that the dual-functional orphan RR might be involved in conducting the transcriptional symphony to stabilize the complex biological functions in cells.
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Wang Z, Forelli N, Hernandez Y, Ternei M, Brady SF. Lapcin, a potent dual topoisomerase I/II inhibitor discovered by soil metagenome guided total chemical synthesis. Nat Commun 2022; 13:842. [PMID: 35149673 PMCID: PMC8837603 DOI: 10.1038/s41467-022-28292-x] [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: 10/14/2021] [Accepted: 01/11/2022] [Indexed: 01/21/2023] Open
Abstract
In natural product discovery programs, the power of synthetic chemistry is often leveraged for the total synthesis and diversification of characterized metabolites. The synthesis of structures that are bioinformatically predicted to arise from uncharacterized biosynthetic gene clusters (BGCs) provides a means for synthetic chemistry to enter this process at an early stage. The recent identification of non-ribosomal peptides (NRPs) containing multiple ρ-aminobenzoic acids (PABAs) led us to search soil metagenomes for BGCs that polymerize PABA. Here, we use PABA-specific adenylation-domain sequences to guide the cloning of the lap BGC directly from soil. This BGC was predicted to encode a unique N-acylated PABA and thiazole containing structure. Chemical synthesis of this structure gave lapcin, a dual topoisomerase I/II inhibitor with nM to pM IC50s against diverse cancer cell lines. The discovery of lapcin highlights the power of coupling metagenomics, bioinformatics and total chemical synthesis to unlock the biosynthetic potential contained in even complex uncharacterized BGCs. Chemical synthesis of secondary metabolites isolated from nature, and derivatives thereof, is still a paradigm of significance to drug development. Here the authors instead use bioinformatics to analyze a biosynthetic gene cluster found in the soil metagenome, and chemical synthesis of its predict product to produce lapcin, a dual topoisomerase I/II inhibitor with promising activity against cancer cell lines.
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Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Nicholas Forelli
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Yozen Hernandez
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA.
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Genome-Guided Discovery of the First Myxobacterial Biarylitide Myxarylin Reveals Distinct C-N Biaryl Crosslinking in RiPP Biosynthesis. Molecules 2021; 26:molecules26247483. [PMID: 34946566 PMCID: PMC8708641 DOI: 10.3390/molecules26247483] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse group of natural products. They feature a wide range of intriguing post-translational modifications, as exemplified by the biarylitides. These are a family of cyclic tripeptides found in Planomonospora, carrying a biaryl linkage between two aromatic amino acids. Recent genomic analyses revealed that the minimal biosynthetic prerequisite of biarylitide biosynthesis consists of only one ribosomally synthesized pentapeptide precursor as the substrate and a modifying cytochrome-P450-dependent enzyme. In silico analyses revealed that minimal biarylitide RiPP clusters are widespread among natural product producers across phylogenetic borders, including myxobacteria. We report here the genome-guided discovery of the first myxobacterial biarylitide MeYLH, termed Myxarylin, from Pyxidicoccus fallax An d48. Myxarylin was found to be an N-methylated tripeptide that surprisingly exhibits a C–N biaryl crosslink. In contrast to Myxarylin, previously isolated biarylitides are N-acetylated tripeptides that feature a C–C biaryl crosslink. Furthermore, the formation of Myxarylin was confirmed by the heterologous expression of the identified biosynthetic genes in Myxococcus xanthus DK1622. These findings expand the structural and biosynthetic scope of biarylitide-type RiPPs and emphasize the distinct biochemistry found in the myxobacterial realm.
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Bhat MA, Mishra AK, Bhat MA, Banday MI, Bashir O, Rather IA, Rahman S, Shah AA, Jan AT. Myxobacteria as a Source of New Bioactive Compounds: A Perspective Study. Pharmaceutics 2021; 13:1265. [PMID: 34452226 PMCID: PMC8401837 DOI: 10.3390/pharmaceutics13081265] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
Myxobacteria are unicellular, Gram-negative, soil-dwelling, gliding bacteria that belong to class δ-proteobacteria and order Myxococcales. They grow and proliferate by transverse fission under normal conditions, but form fruiting bodies which contain myxospores during unfavorable conditions. In view of the escalating problem of antibiotic resistance among disease-causing pathogens, it becomes mandatory to search for new antibiotics effective against such pathogens from natural sources. Among the different approaches, Myxobacteria, having a rich armor of secondary metabolites, preferably derivatives of polyketide synthases (PKSs) along with non-ribosomal peptide synthases (NRPSs) and their hybrids, are currently being explored as producers of new antibiotics. The Myxobacterial species are functionally characterized to assess their ability to produce antibacterial, antifungal, anticancer, antimalarial, immunosuppressive, cytotoxic and antioxidative bioactive compounds. In our study, we have found their compounds to be effective against a wide range of pathogens associated with the concurrence of different infectious diseases.
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Affiliation(s)
- Mudasir Ahmad Bhat
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | | | - Mujtaba Aamir Bhat
- Department of Botany, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | - Mohammad Iqbal Banday
- Department of Microbiology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | - Ommer Bashir
- Department of School Education, Jammu 181205, Jammu and Kashmir, India;
| | - Irfan A. Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia;
| | - Safikur Rahman
- Department of Botany, MS College, BR Ambedkar Bihar University, Muzaffarpur 845401, Bihar, India;
| | - Ali Asghar Shah
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | - Arif Tasleem Jan
- Department of Botany, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
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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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21
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Wu Z, Cui H, Sun Z, Liu H. Biocontrol mechanism of Myxococcus xanthus B25-I-1 against Phytophthora infestans. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 175:104832. [PMID: 33993957 DOI: 10.1016/j.pestbp.2021.104832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Phytophthora infestans is the pathogen causing potato late blight, one of the most serious diseases of potato. Myxobacteria have become a valuable biological control resource due to their preponderant abilities to produce various secondary metabolites with novel structure and remarkable biological activity. In this study, Myxococcus xanthus strain B25-I-1, which exhibited strong antagonistic activity against P. infestans, was isolated from soil sample and identified by 16S rRNA sequence analysis. The strain exhibited antagonistic activity against several species of fungus and bacteria. Analysis of the biocontrol mechanism showed that the active extract produced by strain B25-I-1 had strong inhibitory effects on mycelium and the asexual and sexual reproductive structures of P. infestans. Furthermore, these active extract decreased the content of soluble proteins and activity of the protective enzymes (PPO, POD, PAL, and SOD), increased the oxidative damage and the permeability of the cell membrane in P. infestans. All of these mechanisms might be the biocontrol mechanism of B25-I-1 against P. infestans. The active extract of strain B25-I-1 was separated by TLC and HPLC, and the components with antibiotic activity were detected by HPLC-MS. It was found that the antagonistic components of B25-I-1 contained methyl (2R)-2-azido-3-hydroxyl-2-methylpropanoate and N-(3-Amino-2-hydroxypropyl)-N-methylsulfuric diamide. The active extract significantly inhibited the infection on detached potato leaves by P. infestans, and these substances did not cause damage to the potato leaves. In conclusion, M. xanthus B25-I-1 produced active extract against P. infestans and might potentially be a candidate to develop into biological pesticides for the control of potato late blight. This study adds to the literature on the isolation and identification of active extracts from myxobacteria, and B25-I-1 in particular, for cures or treatments to potato late blight.
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Affiliation(s)
- Zhihua Wu
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China; Baotou Teachers' College, Baotou, Inner Mongolia 014030, China; The Second Affiliated Hospital of Baotou Medical College, lnner Mongolia University of Science and Technology, Baotou, Inner Mongolia 014040, China
| | - Haichen Cui
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Zhining Sun
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Huirong Liu
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China.
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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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Wu ZH, Ma Q, Sun ZN, Cui HC, Liu HR. Biocontrol mechanism of Myxococcus fulvus B25-I-3 against Phytophthora infestans and its control efficiency on potato late blight. Folia Microbiol (Praha) 2021; 66:555-567. [PMID: 33788146 DOI: 10.1007/s12223-021-00865-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/23/2021] [Indexed: 12/16/2022]
Abstract
Phytophthora infestans is the pathogen of potato late blight, which is one of the most serious diseases of the potato. Myxobacteria, especially Myxococcus, become a valuable biological control resource due to their preponderant abilities to produce various secondary metabolites with novel structure and remarkable biological activity. In a previous study, Myxococcus fulvus B25-I-3 with antagonistic activity against P. infestans was isolated from an environmental sample by rabbit fecal induction method. The biocontrol mechanism of M. fulvus B25-I-3 against P. infestans and its control efficiency on potato late blight were studied. The results showed that the active substances produced by strain B25-I-3 had strong inhibitory effect on the asexual reproduction and sexual reproduction of P. infestans. In addition, the active substances could reduce the content of soluble proteins and the activity of the protective enzymes (polyphenol oxidase, peroxidase, phenylalanine ammonia lyase, superoxide dismutase) in P. infestans and increase the oxidative damage and permeability of cell membrane. And the active substances could inhibit the infection of the detached potato leaves by P. infestans significantly. In conclusion, M. fulvus B25-I-3 can produce active substances against P. infestans and has potential value to develop into biological pesticides for the control of potato late blight. The completion of this work may provide basic data for the isolation and identification of active substances and the development of pesticides against potato late blight.
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Affiliation(s)
- Zhi Hua Wu
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010010, China
- Baotou Teachers' College, Baotou, 014030, China
- The Second Affiliated Hospital of Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, 014040, China
| | - Qiang Ma
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010010, China
| | - Zhi Ning Sun
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010010, China
| | - Hai Chen Cui
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010010, China
| | - Hui Rong Liu
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010010, China.
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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: 21] [Impact Index Per Article: 7.0] [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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Kappler S, Siebert A, Kazmaier U. Synthesis of New Cyclopeptide Analogues of the Miuraenamides. Curr Org Synth 2021; 18:418-424. [PMID: 33441075 DOI: 10.2174/1570179418666210113161550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/05/2020] [Accepted: 11/21/2020] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Miuraenamides belong to natural marine compounds with interesting biological properties. MATERIALS AND METHODS Miuraenamides initiate polymerization of monomeric actin and therefore show high cytotoxicity by influencing the cytoskeleton. New derivatives of the miuraenamides have been synthesized containing an N-methylated amide bond instead of the more easily hydrolysable ester in the natural products. RESULTS Incorporation of an aromatic side chain onto the C-terminal amino acid of the tripeptide fragment also led to highly active new miuraenamides. CONCLUSION In this study, we showed that the ester bond of the natural product miuraenamide can be replaced by an N-methyl amide. The yields in the cyclization step were high and generally much better than with the corresponding esters. On the other hand, the biological activity of the new amide analogs was lower compared to the natural products, but the activity could significantly be increased by incorporation of a p-nitrophenyl group at the C-terminus of the peptide fragment.
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Affiliation(s)
- Sarah Kappler
- Institute of Organic Chemistry, Saarland University, P.O. Box 151150, 66041 Saarbrücken, Germany
| | - Andreas Siebert
- Institute of Organic Chemistry, Saarland University, P.O. Box 151150, 66041 Saarbrücken, Germany
| | - Uli Kazmaier
- Institute of Organic Chemistry, Saarland University, P.O. Box 151150, 66041 Saarbrücken, Germany
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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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Hug JJ, Dastbaz J, Adam S, Revermann O, Koehnke J, Krug D, Müller R. Biosynthesis of Cittilins, Unusual Ribosomally Synthesized and Post-translationally Modified Peptides from Myxococcus xanthus. ACS Chem Biol 2020; 15:2221-2231. [PMID: 32639716 DOI: 10.1021/acschembio.0c00430] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cittilins are secondary metabolites from myxobacteria comprised of three l-tyrosines and one l-isoleucine forming a bicyclic tetrapeptide scaffold with biaryl and aryl-oxygen-aryl ether bonds. Here we reveal that cittilins belong to the ribosomally synthesized and post-translationally modified peptide (RiPP) family of natural products, for which only the crocagins have been reported from myxobacteria. A 27 amino acid precursor peptide harbors a C-terminal four amino acid core peptide, which is enzymatically modified and finally exported to yield cittilins. The small biosynthetic gene cluster responsible for cittilin biosynthesis also encodes a cytochrome P450 enzyme and a methyltransferase, whereas a gene encoding a prolyl endopeptidase for the cleavage of the precursor peptide is located outside of the cittilin biosynthetic gene cluster. We confirm the roles of the biosynthetic genes responsible for the formation of cittilins using targeted gene inactivation and heterologous expression in Streptomyces ssp. We also report first steps toward the biochemical characterization of the proposed biosynthetic pathway in vitro. An investigation of the cellular uptake properties of cittilin A connected it to a potential biological function as an inhibitor of the prokaryotic carbon storage regulator A (CsrA).
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Affiliation(s)
- Joachim J. Hug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Jan Dastbaz
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Sebastian Adam
- Department Structural Biology of Biosynthetic Enzymes, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Ole Revermann
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Jesko Koehnke
- Department Structural Biology of Biosynthetic Enzymes, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, 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) and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
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Martínez-Núñez MA, Rodríguez-Escamilla Z. Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes. Toxins (Basel) 2020; 12:toxins12060349. [PMID: 32466531 PMCID: PMC7354552 DOI: 10.3390/toxins12060349] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/02/2020] [Accepted: 04/16/2020] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes represent a source of both biotechnological and pharmaceutical molecules of importance, such as nonribosomal peptides (NRPs). NRPs are secondary metabolites which their synthesis is independent of ribosomes. Traditionally, obtaining NRPs had focused on organisms from terrestrial environments, but in recent years marine and coastal environments have emerged as an important source for the search and obtaining of nonribosomal compounds. In this study, we carried out a metataxonomic analysis of sediment of the coast of Yucatan in order to evaluate the potential of the microbial communities to contain bacteria involved in the synthesis of NRPs in two sites: one contaminated and the other conserved. As well as a metatranscriptomic analysis to discover nonribosomal peptide synthetases (NRPSs) genes. We found that the phyla with the highest representation of NRPs producing organisms were the Proteobacteria and Firmicutes present in the sediments of the conserved site. Similarly, the metatranscriptomic analysis showed that 52% of the sequences identified as catalytic domains of NRPSs were found in the conserved site sample, mostly (82%) belonging to Proteobacteria and Firmicutes; while the representation of Actinobacteria traditionally described as the major producers of secondary metabolites was low. It is important to highlight the prediction of metabolic pathways for siderophores production, as well as the identification of NRPS's condensation domain in organisms of the Archaea domain. Because this opens the possibility to the search for new nonribosomal structures in these organisms. This is the first mining study using high throughput sequencing technologies conducted in the sediments of the Yucatan coast to search for bacteria producing NRPs, and genes that encode NRPSs enzymes.
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Izzat S, Rachid S, Ajdidi A, El-Nakady YA, Liu XX, Ye BC, Müller R. The ROK like protein of Myxococcus xanthus DK1622 acts as a pleiotropic transcriptional regulator for secondary metabolism. J Biotechnol 2020; 311:25-34. [PMID: 32057784 DOI: 10.1016/j.jbiotec.2020.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 11/17/2022]
Abstract
Myxococcus xanthus DK1622 is known as a proficient producer of different kinds of secondary metabolites (SM) with various biological activities, including myxovirescin A, myxalamide A, myxochromide A and DKxanthene. Low production of SM in the wild type bacteria makes searching for production optimization methods highly desirable. Identification and induction of endogenous key molecular feature(s) regulating the production level of the metabolites remain promising, while heterologous expression of the biosynthetic genes is not always efficient because of various complicating factors including codon usage bias. This study established proteomic and molecular approaches to elucidate the regulatory roles of the ROK regulatory protein in the modification of secondary metabolite biosynthesis. Interestingly, the results revealed that rok inactivation significantly reduced the production of the SM and also changed the motility in the bacteria. Electrophoretic mobility shift assay using purified ROK protein indicated a direct enhancement of the promoters encoding transcription of the DKxanthene, myxochelin A, and myxalamide A biosynthesis machinery. Comparative proteomic analysis by two-dimensional fluorescence difference in-gel electrophoresis (2D-DIGE) was employed to identify the protein profiles of the wild type and rok mutant strains during early and late logarithmic growth phases of the bacterial culture. Resulting data demonstrated overall 130 differently altered proteins by the effect of the rok gene mutation, including putative proteins suspected to be involved in transcriptional regulation, carbohydrate metabolism, development, spore formation, and motility. Except for a slight induction seen in the production of myxovirescin A in a rok over-expression background, no changes were found in the formation of the other SM. From the outcome of our investigation, it is possible to conclude that ROK acts as a pleiotropic regulator of secondary metabolite formation and development in M. xanthus, while its direct effects still remain speculative. More experiments are required to elucidate in detail the variable regulation effects of the protein and to explore applicable approaches for generating valuable SM in this bacterium.
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Affiliation(s)
- Selar Izzat
- Department of Biology, School of Science and Health, Koya University, Koysinjaq, Kurdistan Region, Iraq
| | - Shwan Rachid
- Charmo Research Center, Charmo University, 46023 Chamchamal-Sulaimani, Iraq; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
| | - Ahmad Ajdidi
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Yasser A El-Nakady
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; Zoology Department, College of Science, King Saud University, P.O. Box 2455, 11415 Riyadh - Saudi Arabia
| | - Xin-Xin Liu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
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31
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Panter F, Garcia R, Thewes A, Zaburannyi N, Bunk B, Overmann J, Gutierrez MV, Krug D, Müller R. Production of a Dibrominated Aromatic Secondary Metabolite by a Planctomycete Implies Complex Interaction with a Macroalgal Host. ACS Chem Biol 2019; 14:2713-2719. [PMID: 31644258 DOI: 10.1021/acschembio.9b00641] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The roles of the majority of bacterial secondary metabolites, especially those from uncommon sources, are still elusive even though many of these compounds show striking biological activities. To further investigate the secondary metabolite repertoire of underexploited bacterial families, we chose to analyze a novel representative of the yet untapped bacterial phylum Planctomycetes for the production of secondary metabolites under laboratory culture conditions. Development of a planctomycetal high density cultivation technique in combination with high resolution mass spectrometric analysis revealed Planctomycetales strain 10988 to produce the plant toxin 3,5-dibromo-p-anisic acid. This molecule represents the first secondary metabolite reported from any planctomycete. Genome mining revealed the biosynthetic origin of this doubly brominated secondary metabolite, and a biosynthesis model for the compound was devised. Comparison of the biosynthetic route to biosynthetic gene clusters responsible for formation of polybrominated small aromatic compounds reveals evidence of an evolutionary link, while the compound's herbicidal activity points toward a complex interaction of planctomycetes with their macroalgal host.
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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) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF),
Partner Site Hannover−Braunschweig, Braunschweig, Germany
| | - Ronald Garcia
- Department of 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 Centre for Infection Research (DZIF),
Partner Site Hannover−Braunschweig, Braunschweig, Germany
| | - Angela Thewes
- Department of 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 Centre for Infection Research (DZIF),
Partner Site Hannover−Braunschweig, Braunschweig, Germany
| | - Nestor Zaburannyi
- Department of 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 Centre for Infection Research (DZIF),
Partner Site Hannover−Braunschweig, Braunschweig, Germany
| | - Boyke Bunk
- German Centre for Infection Research (DZIF),
Partner Site Hannover−Braunschweig, Braunschweig, Germany
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124 Braunschweig, Germany
| | - Jörg Overmann
- German Centre for Infection Research (DZIF),
Partner Site Hannover−Braunschweig, Braunschweig, Germany
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124 Braunschweig, Germany
| | - Mary V. Gutierrez
- Biology Department, Far Eastern University, Nicanor Reyes Street, Sampaloc, Manila, 1008 Metro Manila, Philippines
| | - Daniel Krug
- Department of 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 Centre for Infection Research (DZIF),
Partner Site Hannover−Braunschweig, Braunschweig, Germany
| | - Rolf Müller
- Department of 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 Centre for Infection Research (DZIF),
Partner Site Hannover−Braunschweig, Braunschweig, Germany
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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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Ahn S, Li FN, Han YT. Concise Synthesis of Nannozinone A: An Unusual Dihydropyrrolopyrazinone Metabolite From Myxobacteria. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19857493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Nannozinone A is an unprecedented dihydropyrrolopyrazinone metabolite derived from myxobacterial Nannocystis pusilla strain MNa10913. In this paper, the synthesis of nannozinone A was disclosed for the first time. Nannozinone A was readily obtained in 6 steps and in 36% overall yield from commercially available N-Boc-propinal. Key feature of the synthesis includes intramolecular imine formation and subsequent spontaneous oxidation toward the unique dihydropyrrolopyrazinone skeleton. This concise synthetic route would be helpful to prepare natural dihydropyrrolopyrazinones and their derivatives.
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Affiliation(s)
- Sungwan Ahn
- College of Pharmacy, Dankook University, Chenan, Republic of Korea
| | - Fu-nan Li
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Young Taek Han
- College of Pharmacy, Dankook University, Chenan, Republic of Korea
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Beule L, Chen KH, Hsu CM, Mackowiak C, Dubeux Jr. JC, Blount A, Liao HL. Soil bacterial and fungal communities of six bahiagrass cultivars. PeerJ 2019; 7:e7014. [PMID: 31179193 PMCID: PMC6545100 DOI: 10.7717/peerj.7014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/19/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Cultivars of bahiagrass (Paspalum notatum Flüggé) are widely used for pasture in the Southeastern USA. Soil microbial communities are unexplored in bahiagrass and they may be cultivar-dependent, as previously proven for other grass species. Understanding the influence of cultivar selection on soil microbial communities is crucial as microbiome taxa have repeatedly been shown to be directly linked to plant performance. OBJECTIVES This study aimed to determine whether different bahiagrass cultivars interactively influence soil bacterial and fungal communities. METHODS Six bahiagrass cultivars ('Argentine', 'Pensacola', 'Sand Mountain', 'Tifton 9', 'TifQuik', and 'UF-Riata') were grown in a randomized complete block design with four replicate plots of 4.6 × 1.8 m per cultivar in a Rhodic Kandiudults soil in Northwest Florida, USA. Three soil subsamples per replicate plot were randomly collected. Soil DNA was extracted and bacterial 16S ribosomal RNA and fungal ribosomal internal transcribed spacer 1 genes were amplified and sequenced with one Illumina Miseq Nano. RESULTS The soil bacterial and fungal community across bahiagrass cultivars showed similarities with communities recovered from other grassland ecosystems. Few differences in community composition and diversity of soil bacteria among cultivars were detected; none were detected for soil fungi. The relative abundance of sequences assigned to nitrite-oxidizing Nitrospira was greater under 'Sand Mountain' than 'UF-Riata'. Indicator species analysis revealed that several bacterial and fungal indicators associated with either a single cultivar or a combination of cultivars are likely to be plant pathogens or antagonists. CONCLUSIONS Our results suggest a low impact of plant cultivar choice on the soil bacterial community composition, whereas the soil fungal community was unaffected. Shifts in the relative abundance of Nitrospira members in response to cultivar choice may have implications for soil N dynamics. The cultivars associated with presumptive plant pathogens or antagonists indicates that the ability of bahiagrass to control plant pathogens may be cultivar-dependent, however, physiological studies on plant-microbe interactions are required to confirm this presumption. We therefore suggest that future studies should explore the potential of different bahiagrass cultivars on plant pathogen control, particularly in sod-based crop rotation.
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Affiliation(s)
- Lukas Beule
- Molecular Phytopathology and Mycotoxin Research, Georg-August Universität Göttingen, Goettingen, Germany
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Ko-Hsuan Chen
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Chih-Ming Hsu
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Cheryl Mackowiak
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Jose C.B. Dubeux Jr.
- North Florida Research and Education Center, University of Florida, Marianna, FL, United States of America
| | - Ann Blount
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
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Müller JI, Kusserow K, Hertrampf G, Pavic A, Nikodinovic-Runic J, Gulder TAM. Synthesis and initial biological evaluation of myxocoumarin B. Org Biomol Chem 2019; 17:1966-1969. [PMID: 30357251 DOI: 10.1039/c8ob02273a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The myxocoumarins A and B from Stigmatella aurantiaca MYX-030 are natural products featuring unusual nitro- and long-chain alkyl substitution. While myxocoumarin A was shown to exhibit strong antifungal properties, the antifungal potential of myxocoumarin B was not yet assessed due to low production titers during initial isolation. We therefore developed a total synthesis of myxocoumarin B that involves a late-stage Pd-catalyzed nitration of the coumarin core. The availability of synthetic material facilitated the initial evaluation of the bioactivity of myxocoumarin B, which revealed a lack of activity against medically relevant Candida sp. and low cytotoxicity in vitro against human fibroblasts (MRC-5) and in vivo (zebrafish).
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Affiliation(s)
- Jonas I Müller
- Biosystems Chemistry, Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM), Technical University of Munich, Germany.
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Panter F, Krug D, Müller R. Novel Methoxymethacrylate Natural Products Uncovered by Statistics-Based Mining of the Myxococcus fulvus Secondary Metabolome. ACS Chem Biol 2019; 14:88-98. [PMID: 30543288 DOI: 10.1021/acschembio.8b00948] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This study reports the uncovering of new myxobacterial natural products through comprehensive analysis of the Myxococcus fulvus secondary metabolome. Statistics-based mining of mass spectrometry data paved the way for full structure elucidation of two new secondary metabolites named fulvuthiacene A and B, and investigation of the underlying biosynthetic pathway revealed an evolutionary link between the fulvuthiacene hybrid polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene cluster and the related myxothiazol and melithiazol assembly lines. Detailed characterization of the post-PKS modification enzyme cascade responsible for the fulvuthiacenes' terminal β-methoxy-methyl acrylate moiety was pursued by heterologous expression of these enzymes in the myxothiazol producer Stigmatella aurantiaca DW4/3-1. The discovery of fulvuthiacenes provides new insights into the overall structure-activity relationship picture for the β-methoxyacrylate class of respiratory chain inhibitors and might thus serve as starting point for the development of next-generation β-methoxymethacrylate fungicides.
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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) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover−Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Daniel Krug
- Department of 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 Centre for Infection Research (DZIF), Partner Site Hannover−Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Rolf Müller
- Department of 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 Centre for Infection Research (DZIF), Partner Site Hannover−Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany
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Kappler S, Karmann L, Prudel C, Herrmann J, Caddeu G, Müller R, Vollmar AM, Zahler S, Kazmaier U. Synthesis and Biological Evaluation of Modified Miuraenamides. European J Org Chem 2018. [DOI: 10.1002/ejoc.201801391] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sarah Kappler
- Organic Chemistry; Saarland University; Campus C4.2 66123 Saarbrücken Germany
| | - Lisa Karmann
- Organic Chemistry; Saarland University; Campus C4.2 66123 Saarbrücken Germany
| | - Cynthia Prudel
- Organic Chemistry; Saarland University; Campus C4.2 66123 Saarbrücken Germany
| | - Jennifer Herrmann
- Department Microbial Natural Products; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS); Saarland University; Campus E8.1 66123 Saarbrücken Germany
| | - Giulia Caddeu
- Department of Pharmacy, Pharmaceutical Biology; Ludwig-Maximilians-University Munich); Butenandtstr. 5-13 81377 München Germany
| | - Rolf Müller
- Department Microbial Natural Products; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS); Saarland University; Campus E8.1 66123 Saarbrücken Germany
| | - Angelika M. Vollmar
- Department of Pharmacy, Pharmaceutical Biology; Ludwig-Maximilians-University Munich); Butenandtstr. 5-13 81377 München Germany
| | - Stefan Zahler
- Department of Pharmacy, Pharmaceutical Biology; Ludwig-Maximilians-University Munich); Butenandtstr. 5-13 81377 München Germany
| | - Uli Kazmaier
- Organic Chemistry; Saarland University; Campus C4.2 66123 Saarbrücken Germany
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Yang YJ, Singh RP, Lan X, Zhang CS, Li YZ, Li YQ, Sheng DH. Genome Editing in Model Strain Myxococcus xanthus DK1622 by a Site-Specific Cre/loxP Recombination System. Biomolecules 2018; 8:biom8040137. [PMID: 30404219 PMCID: PMC6316027 DOI: 10.3390/biom8040137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 11/17/2022] Open
Abstract
Myxococcus xanthus DK1622 is a rich source of novel secondary metabolites, and it is often used as an expression host of exogenous biosynthetic gene clusters. However, the frequency of obtaining large genome-deletion variants by using traditional strategies is low, and progenies generated by homologous recombination contain irregular deletions. The present study aims to develop an efficient genome-engineering system for this bacterium based on the Cre/loxP system. We first verified the functionality of the native cre system that was integrated into the chromosome with an inducible promoter PcuoA. Then we assayed the deletion frequency of 8-bp-spacer-sequence mutants in loxP by Cre recombinase which was expressed by suicide vector pBJ113 or self-replicative vector pZJY41. It was found that higher guanine content in a spacer sequence had higher deletion frequency, and the self-replicative vector was more suitable for the Cre/loxP system, probably due to the leaky expression of inducible promoter PcuoA. We also inspected the effects of different antibiotics and the native or synthetic cre gene. Polymerase chain reaction (PCR) and sequencing of new genome joints confirmed that the Cre/loxP system was able to delete a 466 kb fragment in M. xanthus. This Cre/loxP-mediated recombination could serve as an alternative genetic manipulation method.
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Affiliation(s)
- Ying-Jie Yang
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, Qingdao 266237, China.
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Raghvendra Pratap Singh
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, Qingdao 266237, China.
- Research and Development Department, Biotechnology, Uttaranchal University, Dehradun 248007, India.
| | - Xin Lan
- Department of Bio-Chemistry, Qingdao Technical College, Qingdao 266555, China.
| | - Cheng-Sheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, Qingdao 266237, China.
| | - Yi-Qiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Duo-Hong Sheng
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, Qingdao 266237, China.
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Engineering Pseudochelin Production in Myxococcus xanthus. Appl Environ Microbiol 2018; 84:AEM.01789-18. [PMID: 30217842 DOI: 10.1128/aem.01789-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/01/2018] [Indexed: 12/15/2022] Open
Abstract
Myxobacteria utilize the catechol natural products myxochelin A and B in order to maintain their iron homeostasis. Recently, the production of these siderophores, along with a new myxochelin derivative named pseudochelin A, was reported for the marine bacterium Pseudoalteromonas piscicida S2040. The latter derivative features a characteristic imidazoline moiety, which was proposed to originate from an intramolecular condensation reaction of the β-aminoethyl amide group in myxochelin B. To identify the enzyme catalyzing this conversion, we compared the myxochelin regulons of two myxobacterial strains that produce solely myxochelin A and B with those of P. piscicida S2040. This approach revealed a gene exclusive to the myxochelin regulon in P. piscicida S2040, coding for an enzyme of the amidohydrolase superfamily. To prove that this enzyme is indeed responsible for the postulated conversion, the reaction was reconstituted in vitro using a hexahistidine-tagged recombinant protein made in Escherichia coli, with myxochelin B as the substrate. To test the production of pseudochelin A under in vivo conditions, the amidohydrolase gene was cloned into the myxobacterial plasmid pZJY156 and placed under the control of a copper-inducible promoter. The resulting vector was introduced into the myxobacterium Myxococcus xanthus DSM 16526, a native producer of myxochelin A and B. Following induction with copper, the myxobacterial expression strain was found to synthesize small quantities of pseudochelin A. Replacement of the copper-inducible promoter with the constitutive pilA promoter led to increased production levels in M. xanthus, which facilitated the isolation and subsequent structural verification of the heterologously produced compound.IMPORTANCE In this study, an enzyme for imidazoline formation in pseudochelin biosynthesis was identified. Evidence for the involvement of this enzyme in the postulated reaction was obtained after in vitro reconstitution. Furthermore, the function of this enzyme was demonstrated in vivo by transferring the corresponding gene into the bacterium Myxococcus xanthus, which thereby became a producer of pseudochelin A. In addition to clarifying the molecular basis of imidazoline formation in siderophore biosynthesis, we describe the heterologous expression of a gene in a myxobacterium without chromosomal integration. Due to its metabolic proficiency, M. xanthus represents an interesting alternative to established host systems for the reconstitution and manipulation of biosynthetic pathways. Since the plasmid used in this study is easily adaptable for the expression of other enzymes as well, we expand the conventional expression strategy for myxobacteria, which is based on the integration of biosynthetic genes into the host genome.
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Mulwa LS, Stadler M. Antiviral Compounds from Myxobacteria. Microorganisms 2018; 6:microorganisms6030073. [PMID: 30029487 PMCID: PMC6163824 DOI: 10.3390/microorganisms6030073] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 02/07/2023] Open
Abstract
Viral infections including human immunodeficiency virus (HIV), cytomegalovirus (CMV), hepatitis B virus (HBV), and hepatitis C virus (HCV) pose an ongoing threat to human health due to the lack of effective therapeutic agents. The re-emergence of old viral diseases such as the recent Ebola outbreaks in West Africa represents a global public health issue. Drug resistance and toxicity to target cells are the major challenges for the current antiviral agents. Therefore, there is a need for identifying agents with novel modes of action and improved efficacy. Viral-based illnesses are further aggravated by co-infections, such as an HIV patient co-infected with HBV or HCV. The drugs used to treat or manage HIV tend to increase the pathogenesis of HBV and HCV. Hence, novel antiviral drug candidates should ideally have broad-spectrum activity and no negative drug-drug interactions. Myxobacteria are in the focus of this review since they produce numerous structurally and functionally unique bioactive compounds, which have only recently been screened for antiviral effects. This research has already led to some interesting findings, including the discovery of several candidate compounds with broad-spectrum antiviral activity. The present review looks at myxobacteria-derived antiviral secondary metabolites.
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Affiliation(s)
- Lucky S Mulwa
- Department of Microbial Drugs, Helmholtz Centre for Infection Research and German Centre for Infectio Research (DZIF), Partner Site Hannover/Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany.
- Department of Microbial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany.
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research and German Centre for Infectio Research (DZIF), Partner Site Hannover/Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany.
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Panter F, Krug D, Baumann S, Müller R. Self-resistance guided genome mining uncovers new topoisomerase inhibitors from myxobacteria. Chem Sci 2018; 9:4898-4908. [PMID: 29910943 PMCID: PMC5982219 DOI: 10.1039/c8sc01325j] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/01/2018] [Indexed: 01/14/2023] Open
Abstract
There is astounding discrepancy between the genome-inscribed production capacity and the set of known secondary metabolite classes from many microorganisms as detected under laboratory cultivation conditions. Genome-mining techniques are meant to fill this gap, but in order to favor discovery of structurally novel as well as bioactive compounds it is crucial to amend genomics-based strategies with selective filtering principles. In this study, we followed a self-resistance guided approach aiming at the discovery of inhibitors of topoisomerase, known as valid target in both cancer and antibiotic therapy. A common host self-defense mechanism against such inhibitors in bacteria is mediated by so-called pentapeptide repeat proteins (PRP). Genes encoding the biosynthetic machinery for production of an alleged topoisomerase inhibitor were found on the basis of their collocation adjacent to a predicted PRP in the genome of the myxobacterium Pyxidicoccus fallax An d48, but to date no matching compound has been reported from this bacterium. Activation of this peculiar polyketide synthase type-II gene cluster in the native host as well as its heterologous expression led to the structure elucidation of new natural products that were named pyxidicyclines and provided an insight into their biosynthesis. Subsequent topoisomerase inhibition assays showed strong affinity to - and inhibition of - unwinding topoisomerases such as E. coli topoisomerase IV and human topoisomerase I by pyxidicyclines as well as precise selectivity, since E. coli topoisomerase II (gyrase) was not inhibited at concentrations up to 50 μg ml-1.
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Affiliation(s)
- Fabian Panter
- Department Microbial Natural Products , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research (HZI) , Department of Pharmaceutical Biotechnology , 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) , Department of Pharmaceutical Biotechnology , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany .
| | - Sascha Baumann
- Department Microbial Natural Products , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research (HZI) , Department of Pharmaceutical Biotechnology , 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) , Department of Pharmaceutical Biotechnology , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany .
- German Centre for Infection Research , partner-site Hannover/Braunschweig , Germany
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Hoffmann M, Auerbach D, Panter F, Hoffmann T, Dorrestein PC, Müller R. Homospermidine Lipids: A Compound Class Specifically Formed during Fruiting Body Formation of Myxococcus xanthus DK1622. ACS Chem Biol 2018; 13:273-280. [PMID: 29185703 DOI: 10.1021/acschembio.7b00816] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The fascinating ability of myxobacteria to form multicellular spore filled fruiting bodies under starvation conditions was widely studied as a model for cooperative microbial behavior. The potential of a life cycle induced change of secondary metabolism, as a means to discover novel natural products, remains largely underexplored. We therefore studied the model organism Myxococcus xanthus DK1622 under submersed and solid cultivation conditions to find putatively life-cycle related compounds by applying statistical analysis on analytical data. Utilizing the advantageous characteristics of LC-MS, LC-MS/MS, and MALDI-MSI allowed the identification of compounds unambiguously associated with myxobacterial fruiting bodies. Our screening effort resulted in the purification and structure elucidation of a novel compound, the homospermidine lipid, from cultures that had undergone the fruiting process. A combination of molecular networking and targeted LC-MS/MS in conjunction with our in-house metabolomics database subsequently revealed alternative producers of the respective compound as well as a number of compounds belonging to the same structural class. Three further members of this compound class were isolated from an alternative producer and structurally elucidated by NMR. Insights into the biosynthesis of this novel compound class was gained by feeding of isotopically labeled substrates and in silico analysis.
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Affiliation(s)
- Michael Hoffmann
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - David Auerbach
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Panter
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Thomas Hoffmann
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
- Collaborative Mass Spectrometry Innovation Center, Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States
| | - Rolf Müller
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
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Yang YJ, Wang Y, Li ZF, Gong Y, Zhang P, Hu WC, Sheng DH, Li YZ. Increasing on-target cleavage efficiency for CRISPR/Cas9-induced large fragment deletion in Myxococcus xanthus. Microb Cell Fact 2017; 16:142. [PMID: 28814300 PMCID: PMC5559782 DOI: 10.1186/s12934-017-0758-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/09/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The CRISPR/Cas9 system is a powerful tool for genome editing, in which the sgRNA binds and guides the Cas9 protein for the sequence-specific cleavage. The protocol is employable in different organisms, but is often limited by cell damage due to the endonuclease activity of the introduced Cas9 and the potential off-target DNA cleavage from incorrect guide by the 20 nt spacer. RESULTS In this study, after resolving some critical limits, we have established an efficient CRISPR/Cas9 system for the deletion of large genome fragments related to the biosynthesis of secondary metabolites in Myxococcus xanthus cells. We revealed that the high expression of a codon-optimized cas9 gene in M. xanthus was cytotoxic, and developed a temporally high expression strategy to reduce the cell damage from high expressions of Cas9. We optimized the deletion protocol by using the tRNA-sgRNA-tRNA chimeric structure to ensure correct sgRNA sequence. We found that, in addition to the position-dependent nucleotide preference, the free energy of a 20 nt spacer was a key factor for the deletion efficiency. CONCLUSIONS By using the developed protocol, we achieved the CRISPR/Cas9-induced deletion of large biosynthetic gene clusters for secondary metabolites in M. xanthus DK1622 and its epothilone-producing mutant. The findings and the proposals described in this paper were suggested to be workable in other organisms, for example, other Gram negative bacteria with high GC content.
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Affiliation(s)
- Ying-jie Yang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Ye Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Zhi-feng Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Ya Gong
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Wen-chao Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Duo-hong Sheng
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
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Bian X, Tang B, Yu Y, Tu Q, Gross F, Wang H, Li A, Fu J, Shen Y, Li YZ, Stewart AF, Zhao G, Ding X, Müller R, Zhang Y. Heterologous Production and Yield Improvement of Epothilones in Burkholderiales Strain DSM 7029. ACS Chem Biol 2017; 12:1805-1812. [PMID: 28467833 DOI: 10.1021/acschembio.7b00097] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cloning of microbial natural product biosynthetic gene clusters and their heterologous expression in a suitable host have proven to be a feasible approach to improve the yield of valuable natural products and to begin mining cryptic natural products in microorganisms. Myxobacteria are a prolific source of novel bioactive natural products with only limited choices of heterologous hosts that have been exploited. Here, we describe the use of Burkholderiales strain DSM 7029 as a potential heterologous host for the functional expression of myxobacterial secondary metabolites. Using a newly established electroporation procedure, the 56 kb epothilone biosynthetic gene cluster from the myxobacterium Sorangium cellulosum was introduced into the chromosome of strain DSM 7029 by transposition. Production of epothilones A, B, C, and D was detected despite their yields being low. Optimization of the medium, introduction of the exogenous methylmalonyl-CoA biosynthetic pathway, and overexpression of rare tRNA genes resulted in an approximately 75-fold increase in the total yields of epothilones to 307 μg L-1. These results show that strain DSM 7029 has the potential to produce epothilones with reasonable titers and might be a broadly applicable host for the heterologous expression of other myxobacterial polyketide synthases and nonribosomal peptide synthetases, expediting the process of genome mining.
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Affiliation(s)
- Xiaoying Bian
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, 66123 Saarbrücken, Germany
| | - Biao Tang
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
| | - Yucong Yu
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
| | - Qiang Tu
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, 66123 Saarbrücken, Germany
| | - Frank Gross
- Genomics,
Biotechnology Center, Technische Universität Dresden, Dresden 01062, Germany
| | - Hailong Wang
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - Aiying Li
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - Jun Fu
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
- Genomics,
Biotechnology Center, Technische Universität Dresden, Dresden 01062, Germany
| | - Yuemao Shen
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - Yue-zhong Li
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
| | - A. Francis Stewart
- Genomics,
Biotechnology Center, Technische Universität Dresden, Dresden 01062, Germany
| | - Guoping Zhao
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
- CAS
Key Laboratory of Synthetic Biology, Institute of Plant Physiology
and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaoming Ding
- Collaborative
Innovation Center for Genetics and Development, State Key Laboratory
of Genetic Engineering, Department of Microbiology, School of Life
Sciences, Fudan University, Shanghai 200433, China
| | - Rolf Müller
- Department
of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, 66123 Saarbrücken, Germany
| | - Youming Zhang
- Shandong
University−Helmholtz Institute of Biotechnology, State Key
Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, China
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Molecular and functional characterization of myxobacteria isolated from soil in India. 3 Biotech 2017; 7:112. [PMID: 28567623 DOI: 10.1007/s13205-017-0722-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/06/2017] [Indexed: 10/19/2022] Open
Abstract
This study reports the isolation of myxobacteria from soil collected from plains in north India. Based on the morphology and 16S rDNA sequence, the isolated myxobacteria were identified as Corallococcus sp., Pyxidicoccus sp., Myxococcus sp., Cystobacter sp. and Archangium sp. The myxobacteria were functionally characterized to assess their ability to produce antibacterial and anticancer metabolites. The isolates were found to be functionally versatile as they produced extracellular bioactive molecules that exhibited high frequency of activities against Bacillus cereus, Mycobacterium smegmatis, Enterobacter cloacae and Pseudomonas syringae. The strains also showed cytotoxic activity against the human cancer cell lines of liver, pancreas, prostrate, bone and cervix. These results indicate the importance of isolating diverse strains of myxobacteria from unexplored habitats to find novel bioactive compounds. Moreover, the bioactive molecules explored in this study are predominantly hydrophilic compounds, obviating the limitations of solubility-related aspect of drug discovery.
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Zhang MM, Qiao Y, Ang EL, Zhao H. Using natural products for drug discovery: the impact of the genomics era. Expert Opin Drug Discov 2017; 12:475-487. [PMID: 28277838 DOI: 10.1080/17460441.2017.1303478] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Evolutionarily selected over billions of years for their interactions with biomolecules, natural products have been and continue to be a major source of pharmaceuticals. In the 1990s, pharmaceutical companies scaled down their natural product discovery programs in favor of synthetic chemical libraries due to major challenges such as high rediscovery rates, challenging isolation, and low production titers. Propelled by advances in DNA sequencing and synthetic biology technologies, insights into microbial secondary metabolism provided have inspired a number of strategies to address these challenges. Areas covered: This review highlights the importance of genomics and metagenomics in natural product discovery, and provides an overview of the technical and conceptual advances that offer unprecedented access to molecules encoded by biosynthetic gene clusters. Expert opinion: Genomics and metagenomics revealed nature's remarkable biosynthetic potential and her vast chemical inventory that we can now prioritize and systematically mine for novel chemical scaffolds with desirable bioactivities. Coupled with synthetic biology and genome engineering technologies, significant progress has been made in identifying and predicting the chemical output of biosynthetic gene clusters, as well as in optimizing cluster expression in native and heterologous host systems for the production of pharmaceutically relevant metabolites and their derivatives.
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Affiliation(s)
- Mingzi M Zhang
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Yuan Qiao
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Ee Lui Ang
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Huimin Zhao
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore.,b Department of Chemical and Biomolecular Engineering , University of Illinois at Urbana-Champaign , Urbana , IL , USA
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Charousová I, Steinmetz H, Medo J, Javoreková S, Wink J. Soil myxobacteria as a potential source of polyketide-peptide substances. Folia Microbiol (Praha) 2017; 62:305-315. [DOI: 10.1007/s12223-017-0502-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/26/2017] [Indexed: 02/06/2023]
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Padmanaban VP, Verma P, Venkatabaskaran S, Keppayan T, Gopal D, Sekar AK, Ramalingam K. Antimicrobial potential and taxonomic investigation of piezotolerant Streptomyces sp. NIOT-Ch-40 isolated from deep-sea sediment. World J Microbiol Biotechnol 2017; 33:27. [DOI: 10.1007/s11274-016-2193-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/20/2016] [Indexed: 11/28/2022]
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Identification of Functions Affecting Predator-Prey Interactions between Myxococcus xanthus and Bacillus subtilis. J Bacteriol 2016; 198:3335-3344. [PMID: 27698086 DOI: 10.1128/jb.00575-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/28/2016] [Indexed: 12/14/2022] Open
Abstract
Soil bacteria engage each other in competitive and cooperative ways to determine their microenvironments. In this study, we report the identification of a large number of genes required for Myxococcus xanthus to engage Bacillus subtilis in a predator-prey relationship. We generated and tested over 6,000 individual transposon insertion mutants of M. xanthus and found many new factors required to promote efficient predation, including the specialized metabolite myxoprincomide, an ATP-binding cassette (ABC) transporter permease, and a clustered regularly interspaced short palindromic repeat (CRISPR) locus encoding bacterial immunity. We also identified genes known to be involved in predation, including those required for the production of exopolysaccharides and type IV pilus (T4P)-dependent motility, as well as chemosensory and two-component systems. Furthermore, deletion of these genes confirmed their role during predation. Overall, M. xanthus predation appears to be a multifactorial process, with multiple determinants enhancing predation capacity. IMPORTANCE Soil bacteria engage each other in complex environments and utilize multiple traits to ensure survival. Here, we report the identification of multiple traits that enable a common soil organism, Myxococcus xanthus, to prey upon and utilize nutrients from another common soil organism, Bacillus subtilis We mutagenized the predator and carried out a screen to identify genes that were required to either enhance or diminish capacity to consume prey. We identified dozens of genes encoding factors that contribute to the overall repertoire for the predator to successfully engage its prey in the natural environment.
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50
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Draft Genome Sequence of Thermogemmatispora onikobensis NBRC 111776T, an Aerial Mycelium- and Spore-Forming Thermophilic Bacterium Belonging to the Class Ktedonobacteria. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01156-16. [PMID: 27738048 PMCID: PMC5064121 DOI: 10.1128/genomea.01156-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Here, we report the draft genome sequence of Thermogemmatispora onikobensis NBRC 111776T, an aerial mycelium- and spore-forming thermophilic bacterium belonging to the class Ktedonobacteria. The genome contains five biosynthetic gene clusters coding for secondary metabolites, such as terpene, thiopeptide, lantipeptide, nonribosomal peptide, and lassopeptide, suggesting the potential to produce secondary metabolites.
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