1
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Schmalhofer M, Vagstad AL, Zhou Q, Bode HB, Groll M. Polyketide Trimming Shapes Dihydroxynaphthalene-Melanin and Anthraquinone Pigments. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400184. [PMID: 38491909 PMCID: PMC11165489 DOI: 10.1002/advs.202400184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/28/2024] [Indexed: 03/18/2024]
Abstract
Pigments such as anthraquinones (AQs) and melanins are antioxidants, protectants, or virulence factors. AQs from the entomopathogenic bacterium Photorhabdus laumondii are produced by a modular type II polyketide synthase system. A key enzyme involved in AQ biosynthesis is PlAntI, which catalyzes the hydrolysis of the bicyclic-intermediate-loaded acyl carrier protein, polyketide trimming, and assembly of the aromatic AQ scaffold. Here, multiple crystal structures of PlAntI in various conformations and with bound substrate surrogates or inhibitors are reported. Structure-based mutagenesis and activity assays provide experimental insights into the three sequential reaction steps to yield the natural product AQ-256. For comparison, a series of ligand-complex structures of two functionally related hydrolases involved in the biosynthesis of 1,8-dihydroxynaphthalene-melanin in pathogenic fungi is determined. These data provide fundamental insights into the mechanism of polyketide trimming that shapes pigments in pro- and eukaryotes.
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Affiliation(s)
- Maximilian Schmalhofer
- TUM School of Natural SciencesDepartment of BioscienceCentre for Protein AssembliesChair of BiochemistryTechnical University of Munich85748GarchingGermany
| | - Anna L. Vagstad
- Eidgenössische Technische Hochschule (ETH) ZürichInstitute of MicrobiologyZürich8093Switzerland
| | - Qiuqin Zhou
- Department of Natural Products in Organismic InteractionsMax Planck Institute for Terrestrial Microbiology35043MarburgGermany
- Present address:
Center for Mass Spectrometry and Optical Spectroscopy (CeMOS)Mannheim University of Applied Sciences68163MannheimGermany
| | - Helge B. Bode
- Department of Natural Products in Organismic InteractionsMax Planck Institute for Terrestrial Microbiology35043MarburgGermany
- Molecular BiotechnologyDepartment of BiosciencesGoethe University Frankfurt60438FrankfurtGermany
- Department of ChemistryPhillips Universität Marburg35043MarburgGermany
- Center for Synthetic Microbiology (SYNMIKRO)Phillips Universität Marburg35043MarburgGermany
- Senckenberg Gesellschaft für Naturforschung60325FrankfurtGermany
| | - Michael Groll
- TUM School of Natural SciencesDepartment of BioscienceCentre for Protein AssembliesChair of BiochemistryTechnical University of Munich85748GarchingGermany
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2
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Feng Z. O-methyltransferases selectively modify anthraquinone natural products. Structure 2023; 31:507-508. [PMID: 37146572 DOI: 10.1016/j.str.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
In this issue of Structure, Huber et al. identify five O-methyltransferases, and three of them catalyze the sequential methylation of the Gram-negative bacterium-derived aromatic polyketide anthraquinone AQ-256. They present co-crystal structures with bound AQ-256 and its methylated derivatives, which explains the specificities of these O-methyltransferases.
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Affiliation(s)
- Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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3
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Huber EM, Kreling L, Heinrich AK, Dünnebacke M, Pöthig A, Bode HB, Groll M. A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments. Structure 2023; 31:573-583.e5. [PMID: 36963398 DOI: 10.1016/j.str.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/26/2023]
Abstract
Modification of the polyketide anthraquinone AQ-256 in the entomopathogenic Photorhabdus luminescens involves several O-methylations, but the biosynthetic gene cluster antA-I lacks corresponding tailoring enzymes. We here describe the identification of five putative, highly homologous O-methyltransferases encoded in the genome of P. luminescens. Activity assays in vitro and deletion experiments in vivo revealed that three of them account for anthraquinone tailoring by producing three monomethylated and two dimethylated species of AQ-256. X-ray structures of all five enzymes indicate high structural and mechanistic similarity. As confirmed by structure-based mutagenesis, a conserved histidine at the active site likely functions as a general base for substrate deprotonation and subsequent methyl transfer in all enzymes. Eight complex structures with AQ-256 as well as mono- and dimethylated derivatives confirm the substrate specificity patterns found in vitro and visualize how single amino acid differences in the active-site pockets impact substrate orientation and govern site-specific methylation.
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Affiliation(s)
- Eva M Huber
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany.
| | - Lukas Kreling
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Antje K Heinrich
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Maximilian Dünnebacke
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Alexander Pöthig
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Catalysis Research Center, Chair of Inorganic and Metal-Organic Chemistry, Ernst-Otto-Fischer-Str. 1, 85748 Garching, Germany
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Chemical Biology, Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany; Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany.
| | - Michael Groll
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany.
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4
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Cai Z, Zhao X, Zhou C, Fang T, Liu G, Luo J. Genome-Wide Mining of the Tandem Duplicated Type III Polyketide Synthases and Their Expression, Structure Analysis of Senna tora. Int J Mol Sci 2023; 24:ijms24054837. [PMID: 36902267 PMCID: PMC10003783 DOI: 10.3390/ijms24054837] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Senna tora is one of the homologous crops used as a medicinal food containing an abundance of anthraquinones. Type III polyketide synthases (PKSs) are key enzymes that catalyze polyketide formation; in particular, the chalcone synthase-like (CHS-L) genes are involved in anthraquinone production. Tandem duplication is a fundamental mechanism for gene family expansion. However, the analysis of the tandem duplicated genes (TDGs) and the identification and characterization of PKSs have not been reported for S. tora. Herein, we identified 3087 TDGs in the S. tora genome; the synonymous substitution rates (Ks) analysis indicated that the TDGs had recently undergone duplication. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the type III PKSs were the most enriched TDGs involved in the biosynthesis of the secondary metabolite pathways, as evidenced by 14 tandem duplicated CHS-L genes. Subsequently, we identified 30 type III PKSs with complete sequences in the S. tora genome. Based on the phylogenetic analysis, the type III PKSs were classified into three groups. The protein conserved motifs and key active residues showed similar patterns in the same group. The transcriptome analysis showed that the chalcone synthase (CHS) genes were more highly expressed in the leaves than in the seeds in S. tora. The transcriptome and qRT-PCR analysis showed that the CHS-L genes had a higher expression in the seeds than in other tissues, particularly seven tandem duplicated CHS-L2/3/5/6/9/10/13 genes. The key active-site residues and three-dimensional models of the CHS-L2/3/5/6/9/10/13 proteins showed slight variation. These results indicated that the rich anthraquinones in S. tora seeds might be ascribed to the PKSs' expansion from tandem duplication, and the seven key CHS-L2/3/5/6/9/10/13 genes provide candidate genes for further research. Our study provides an important basis for further research on the regulation of anthraquinones' biosynthesis in S. tora.
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Affiliation(s)
- Zeping Cai
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou 570228, China
| | - Xingkun Zhao
- College of Tropical Crops & College of Life Sciences, Hainan University, Haikou 570228, China
| | - Chaoye Zhou
- College of Tropical Crops & College of Life Sciences, Hainan University, Haikou 570228, China
| | - Ting Fang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou 570228, China
| | - Guodao Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (G.L.); (J.L.)
| | - Jiajia Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (G.L.); (J.L.)
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5
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Mund NK, Čellárová E. Recent advances in the identification of biosynthetic genes and gene clusters of the polyketide-derived pathways for anthraquinone biosynthesis and biotechnological applications. Biotechnol Adv 2023; 63:108104. [PMID: 36716800 DOI: 10.1016/j.biotechadv.2023.108104] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/27/2022] [Accepted: 01/23/2023] [Indexed: 01/28/2023]
Abstract
Natural anthraquinones are represented by a large group of compounds. Some of them are widespread across the kingdoms, especially in bacteria, fungi and plants, while the others are restricted to certain groups of organisms. Despite the significant pharmacological potential of several anthraquinones (hypericin, skyrin and emodin), their biosynthetic pathways and candidate genes coding for key enzymes have not been experimentally validated. Understanding the genetic and epigenetic regulation of the anthraquinone biosynthetic gene clusters in fungal endophytes would help not only understand their pathways in plants, which ensure their commercial availability, but also favor them as promising systems for prospective biotechnological production.
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Affiliation(s)
- Nitesh Kumar Mund
- Pavol Jozef Šafárik University in Košice, Faculty of Science, Institute of Biology and Ecology, Department of Genetics, Mánesova 23, 041 54 Košice, Slovakia
| | - Eva Čellárová
- Pavol Jozef Šafárik University in Košice, Faculty of Science, Institute of Biology and Ecology, Department of Genetics, Mánesova 23, 041 54 Košice, Slovakia.
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6
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Löhr NA, Urban MC, Eisen F, Platz L, Hüttel W, Gressler M, Müller M, Hoffmeister D. The Ketosynthase Domain Controls Chain Length in Mushroom Oligocyclic Polyketide Synthases. Chembiochem 2023; 24:e202200649. [PMID: 36507600 PMCID: PMC10108026 DOI: 10.1002/cbic.202200649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
The nonreducing iterative type I polyketide synthases (NR-PKSs) CoPKS1 and CoPKS4 of the webcap mushroom Cortinarius odorifer share 88 % identical amino acids. CoPKS1 almost exclusively produces a tricyclic octaketide product, atrochrysone carboxylic acid, whereas CoPKS4 shows simultaneous hepta- and octaketide synthase activity and also produces the bicyclic heptaketide 6-hydroxymusizin. To identify the region(s) controlling chain length, four chimeric enzyme variants were constructed and assayed for activity in Aspergillus niger as heterologous expression platform. We provide evidence that the β-ketoacyl synthase (KS) domain determines chain length in these mushroom NR-PKSs, even though their KS domains differ in only ten amino acids. A unique proline-rich linker connecting the acyl carrier protein with the thioesterase domain varies most between these two enzymes but is not involved in chain length control.
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Affiliation(s)
- Nikolai A Löhr
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Maximilian C Urban
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Frederic Eisen
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lukas Platz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Wolfgang Hüttel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Markus Gressler
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
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7
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Löhr NA, Eisen F, Thiele W, Platz L, Motter J, Hüttel W, Gressler M, Müller M, Hoffmeister D. Unprecedented Mushroom Polyketide Synthases Produce the Universal Anthraquinone Precursor. Angew Chem Int Ed Engl 2022; 61:e202116142. [PMID: 35218274 PMCID: PMC9325552 DOI: 10.1002/anie.202116142] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Indexed: 11/11/2022]
Abstract
(Pre-)anthraquinones are widely distributed natural compounds and occur in plants, fungi, microorganisms, and animals, with atrochrysone (1) as the key biosynthetic precursor. Chemical analyses established mushrooms of the genus Cortinarius-the webcaps-as producers of atrochrysone-derived octaketide pigments. However, more recent genomic data did not provide any evidence for known atrochrysone carboxylic acid (4) synthases nor any other polyketide synthase (PKS) producing oligocyclic metabolites. Here, we describe an unprecedented class of non-reducing (NR-)PKS. In vitro assays with recombinant enzyme in combination with in vivo product formation in the heterologous host Aspergillus niger established CoPKS1 and CoPKS4 of C. odorifer as members of a new class of atrochrysone carboxylic acid synthases. CoPKS4 catalyzed both hepta- and octaketide synthesis and yielded 6-hydroxymusizin (6), along with 4. These first mushroom PKSs for oligocyclic products illustrate how the biosynthesis of bioactive natural metabolites evolved independently in various groups of life.
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Affiliation(s)
- Nikolai A Löhr
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Frederic Eisen
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Wiebke Thiele
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lukas Platz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Jonas Motter
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Wolfgang Hüttel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Markus Gressler
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
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8
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Löhr NA, Eisen F, Thiele W, Platz L, Motter J, Hüttel W, Gressler M, Müller M, Hoffmeister D. Unprecedented Mushroom Polyketide Synthases Produce the Universal Anthraquinone Precursor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Nikolai A Löhr
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Frederic Eisen
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Wiebke Thiele
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Lukas Platz
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Jonas Motter
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Wolfgang Hüttel
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Markus Gressler
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Michael Müller
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Dirk Hoffmeister
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Pharmaceutical Microbiology at the Hans-Kn�ll-Institute Beutenbergstrasse 11a 07745 Jena GERMANY
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9
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Kang SH, Lee WH, Sim JS, Thaku N, Chang S, Hong JP, Oh TJ. De novo Transcriptome Assembly of Senna occidentalis Sheds Light on the Anthraquinone Biosynthesis Pathway. FRONTIERS IN PLANT SCIENCE 2022; 12:773553. [PMID: 35046973 PMCID: PMC8761625 DOI: 10.3389/fpls.2021.773553] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
Senna occidentalis is an annual leguminous herb that is rich in anthraquinones, which have various pharmacological activities. However, little is known about the genetics of S. occidentalis, particularly its anthraquinone biosynthesis pathway. To broaden our understanding of the key genes and regulatory mechanisms involved in the anthraquinone biosynthesis pathway, we used short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) to perform a spatial and temporal transcriptomic analysis of S. occidentalis. This generated 121,592 RNA-Seq unigenes and 38,440 Iso-Seq unigenes. Comprehensive functional annotation and classification of these datasets using public databases identified unigene sequences related to major secondary metabolite biosynthesis pathways and critical transcription factor families (bHLH, WRKY, MYB, and bZIP). A tissue-specific differential expression analysis of S. occidentalis and measurement of the amount of anthraquinones revealed that anthraquinone accumulation was related to the gene expression levels in the different tissues. In addition, the amounts and types of anthraquinones produced differ between S. occidentalis and S. tora. In conclusion, these results provide a broader understanding of the anthraquinone metabolic pathway in S. occidentalis.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Woo-Haeng Lee
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan, South Korea
| | - Joon-Soo Sim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Niha Thaku
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan, South Korea
| | - Saemin Chang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Jong-Pil Hong
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, South Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan, South Korea
- Genome-Based BioIT Convergence Institute, Asan, South Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, South Korea
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10
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Wuisan ZG, Kresna IDM, Böhringer N, Lewis K, Schäberle TF. Optimization of heterologous Darobactin A expression and identification of the minimal biosynthetic gene cluster. Metab Eng 2021; 66:123-136. [PMID: 33872780 DOI: 10.1016/j.ymben.2021.04.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/23/2021] [Accepted: 04/11/2021] [Indexed: 10/21/2022]
Abstract
Darobactin A (DAR) is a ribosomally synthesized and post-translationally modified peptide (RiPP) antibiotic, which was initially identified from bacteria belonging to the genus Photorhabdus. In addition, the corresponding biosynthetic gene cluster (BGC) was identified and subsequently detected in several bacteria genera. DAR represents a highly promising lead structure for the development of novel antibacterial therapeutic agents. It targets the outer membrane protein BamA and is therefore specific for Gram-negative bacteria. This, together with the convincing in vivo activities in mouse infection models, makes it a particular promising candidate for further research. To improve compound supply for further investigation of DAR and to enable production of novel derivatives, establishment of an efficient and versatile microbial production platform for these class of RiPP antibiotics is highly desirable. Here we describe design and construction of a heterologous production and engineering platform for DAR, which will ensure production yield and facilitates structure modification approaches. The known Gram-negative workhorses Escherichia coli and Vibrio natriegens were tested as heterologous hosts. In addition to that, DAR producer strains were generated and optimization of the expression constructs yielded production titers of DAR showing around 10-fold increase and 5-fold decrease in fermentation time compared to the original product description. We also report the identification of the minimal DAR BGC, since only two genes were necessary for heterologous production of the RiPP.
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Affiliation(s)
- Zerlina G Wuisan
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany
| | - I Dewa M Kresna
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany
| | - Nils Böhringer
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany; German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Kim Lewis
- Antimicrobial Discovery Center, Northeastern University, Department of Biology, Boston, MA, USA, 02115
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany; Branch for Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, 35394, Giessen, Germany; German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany.
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11
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Zhang H, Hantke V, Bruhnke P, Skellam EJ, Cox RJ. Chemical and Genetic Studies on the Formation of Pyrrolones During the Biosynthesis of Cytochalasans. Chemistry 2021; 27:3106-3113. [PMID: 33146923 PMCID: PMC7898483 DOI: 10.1002/chem.202004444] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Indexed: 01/17/2023]
Abstract
A key step during the biosynthesis of cytochalasans is a proposed Knoevenagel condensation to form the pyrrolone core, enabling the subsequent 4+2 cycloaddition reaction that results in the characteristic octahydroisoindolone motif of all cytochalasans. In this work, we investigate the role of the highly conserved α,β-hydrolase enzymes PyiE and ORFZ during the biosynthesis of pyrichalasin H and the ACE1 metabolite, respectively, using gene knockout and complementation techniques. Using synthetic aldehyde models we demonstrate that the Knoevenagel condensation proceeds spontaneously but results in the 1,3-dihydro-2H-pyrrol-2-one tautomer, rather than the required 1,5-dihydro-2H-pyrrol-2-one tautomer. Taken together our results suggest that the α,β-hydrolase enzymes are essential for first ring cyclisation, but the precise nature of the intermediates remains to be determined.
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Affiliation(s)
- Haili Zhang
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Verena Hantke
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Pia Bruhnke
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Elizabeth J. Skellam
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
- Current Address: Department of ChemistryUniversity of North Texas1508 W Mulberry30167DentonTexasUSA
| | - Russell J. Cox
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
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12
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Kang SH, Pandey RP, Lee CM, Sim JS, Jeong JT, Choi BS, Jung M, Ginzburg D, Zhao K, Won SY, Oh TJ, Yu Y, Kim NH, Lee OR, Lee TH, Bashyal P, Kim TS, Lee WH, Hawkins C, Kim CK, Kim JS, Ahn BO, Rhee SY, Sohng JK. Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nat Commun 2020; 11:5875. [PMID: 33208749 PMCID: PMC7674472 DOI: 10.1038/s41467-020-19681-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Senna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we reveal the genome sequence of S. tora at the chromosome level with 526 Mb (96%) assembled into 13 chromosomes. Comparison among related plant species shows that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identify a CHS-L gene contributing to the biosynthesis of anthraquinones. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea.
| | - Ramesh Prasad Pandey
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chang-Muk Lee
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Joon-Soo Sim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jin-Tae Jeong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong, 55365, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Myunghee Jung
- Department of Forest Science, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel Ginzburg
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kangmei Zhao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Tae-Jin Oh
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Yeisoo Yu
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
- DNACARE Co. Ltd, Seoul, 06730, Republic of Korea
| | - Nam-Hoon Kim
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Ok Ran Lee
- Department of Applied Plant Science, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Puspalata Bashyal
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Tae-Su Kim
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Woo-Haeng Lee
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Charles Hawkins
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Byoung Ohg Ahn
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Seung Yon Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Jae Kyung Sohng
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea.
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13
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Kang SH, Pandey RP, Lee CM, Sim JS, Jeong JT, Choi BS, Jung M, Ginzburg D, Zhao K, Won SY, Oh TJ, Yu Y, Kim NH, Lee OR, Lee TH, Bashyal P, Kim TS, Lee WH, Hawkins C, Kim CK, Kim JS, Ahn BO, Rhee SY, Sohng JK. Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nat Commun 2020. [PMID: 33208749 DOI: 10.1101/2020.04.27.063495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Senna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we reveal the genome sequence of S. tora at the chromosome level with 526 Mb (96%) assembled into 13 chromosomes. Comparison among related plant species shows that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identify a CHS-L gene contributing to the biosynthesis of anthraquinones. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea.
| | - Ramesh Prasad Pandey
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chang-Muk Lee
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Joon-Soo Sim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jin-Tae Jeong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong, 55365, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Myunghee Jung
- Department of Forest Science, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel Ginzburg
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kangmei Zhao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Tae-Jin Oh
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Yeisoo Yu
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
- DNACARE Co. Ltd, Seoul, 06730, Republic of Korea
| | - Nam-Hoon Kim
- Phyzen Genomics Institute, Seongnam, 13488, Republic of Korea
| | - Ok Ran Lee
- Department of Applied Plant Science, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Puspalata Bashyal
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Tae-Su Kim
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Woo-Haeng Lee
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea
| | - Charles Hawkins
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Byoung Ohg Ahn
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Seung Yon Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Jae Kyung Sohng
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, 31460, Republic of Korea.
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14
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Ishida K, Shabuer G, Schieferdecker S, Pidot SJ, Stinear TP, Knuepfer U, Cyrulies M, Hertweck C. Oak-Associated Negativicute Equipped with Ancestral Aromatic Polyketide Synthase Produces Antimycobacterial Dendrubins. Chemistry 2020; 26:13147-13151. [PMID: 32597507 PMCID: PMC7693217 DOI: 10.1002/chem.202001939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/26/2020] [Indexed: 11/07/2022]
Abstract
Anaerobic bacteria have only recently been recognized as a source of antibiotics; yet, the metabolic potential of Negativicutes (Gram-negative staining Firmicutes) such as the oak-associated Dendrosporobacter quercicolus has remained unknown. Genome mining of D. quercicolus and phylogenetic analyses revealed a gene cluster for a type II polyketide synthase (PKS) complex that belongs to the most ancestral enzyme systems of this type. Metabolic profiling, NMR analyses, and stable-isotope labeling led to the discovery of a new family of anthraquinone-type polyphenols, the dendrubins, which are diversified by acylation, methylation, and dimerization. Dendrubin A and B were identified as strong antibiotics against a range of clinically relevant, human-pathogenic mycobacteria.
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Affiliation(s)
- Keishi Ishida
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Gulimila Shabuer
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sebastian Schieferdecker
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, University of Melbourne, 792 Elizabeth Street, 3000, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne, 792 Elizabeth Street, 3000, Melbourne, Australia
| | - Uwe Knuepfer
- Biopilot Plant, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Michael Cyrulies
- Biopilot Plant, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany.,Institute for Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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15
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Bräuer A, Zhou Q, Grammbitter GLC, Schmalhofer M, Rühl M, Kaila VRI, Bode HB, Groll M. Structural snapshots of the minimal PKS system responsible for octaketide biosynthesis. Nat Chem 2020; 12:755-763. [DOI: 10.1038/s41557-020-0491-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/15/2020] [Indexed: 11/09/2022]
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16
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Zheng L, Jiang X, Zhang Q, Zhu Y, Zhang H, Zhang W, Saurav K, Liu J, Zhang C. Discovery and Biosynthesis of Neoenterocins Indicate a Skeleton Rearrangement of Enterocin. Org Lett 2019; 21:9066-9070. [PMID: 31657934 DOI: 10.1021/acs.orglett.9b03460] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Liujuan Zheng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xiaodong Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Kumar Saurav
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Jinsong Liu
- Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Institutions of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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