1
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Wu Y, Wang M, Liu L. Advances on structure, bioactivity, and biosynthesis of amino acid-containing trans-AT polyketides. Eur J Med Chem 2023; 262:115890. [PMID: 37907023 DOI: 10.1016/j.ejmech.2023.115890] [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: 08/19/2023] [Revised: 10/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023]
Abstract
Trans-AT polyketides represent a class of natural compounds utilizing independent acyltransferase during their biosynthesis. They are well known for their diverse chemical structures and potent bioactivities. Trans-AT polyketides are synthesized through biosynthetic gene clusters predominantly composed of polyketide synthases (PKS), but often found in hybrid with non-ribosomal peptide synthetases (NRPS). This genetic hybridization results in the incorporation of amino acid residues into polyketide structures, significantly enhancing their structural diversity. Numerous amino acid-containing trans-AT polyketides have been identified, drawing significant attention to the mechanisms underlying amino acid incorporation and their impact on the biological activity of polyketides. Here, we discussed their origins, structures, biological activities, and the specific roles of amino acids in modulating both the bioactivity and biosynthesis of 38 trans-AT polyketides containing amino acids for the first time. This comprehensive analysis will serve as a crucial reference for the exploration of novel compounds and the improvement of structures and activities.
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Affiliation(s)
- Yunqiang Wu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Min Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
| | - Liwei Liu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China.
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2
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Im JH, Oh S, Bae ES, Um S, Lee SK, Ban YH, Oh DC. Discovery and structure elucidation of glycosyl and 5-hydroxy migrastatins from dung beetle gut Kitasatospora sp. J Ind Microbiol Biotechnol 2023; 50:kuad046. [PMID: 38093455 PMCID: PMC10750973 DOI: 10.1093/jimb/kuad046] [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: 10/07/2023] [Accepted: 12/12/2023] [Indexed: 12/27/2023]
Abstract
Two new macrocyclic secondary metabolites, glycosyl-migrastatin (1) and 5-hydroxy-migrastatin (2), were isolated from a gut bacterium Kitasatospora sp. JL24 in dung beetle Onthophagus lenzii. Based on a comprehensive analysis of the nuclear magnetic resonance (NMR), MS, and UV spectroscopic data, the planar structures of 1 and 2 were successfully identified as new derivatives of migrastatin. Compound 1 was the first glycosylated member of the migrastatin family. The absolute configuration of the sugar moiety was determined to be d-glucose through the analysis of coupling constants and ROESY correlations, followed by chemical derivatization and chromatographic comparison with authentic d- and l-glucose. Compound 2, identified as 5-hydroxy-migrastatin possessing an additional hydroxy group with a previously unreported chiral center, was assigned using Mosher's method through 19F NMR chemical shifts and confirmed with the modified Mosher's method. Genomic analysis of Kitasatospora sp. strain JL24 revealed a putative biosynthetic pathway involving an acyltransferase-less type I polyketide synthase biosynthetic gene cluster. ONE-SENTENCE SUMMARY Two secondary metabolites, glycosyl-migrastatin (1) and 5-hydroxy-migrastatin (2), were discovered from the gut bacterium Kitasatospora sp. JL24 in the dung beetle Onthophagus lenzii.
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Affiliation(s)
- Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Seoyoung Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Soohyun Um
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeon Hee Ban
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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3
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Ueoka R, Sondermann P, Leopold-Messer S, Liu Y, Suo R, Bhushan A, Vadakumchery L, Greczmiel U, Yashiroda Y, Kimura H, Nishimura S, Hoshikawa Y, Yoshida M, Oxenius A, Matsunaga S, Williamson RT, Carreira EM, Piel J. Genome-based discovery and total synthesis of janustatins, potent cytotoxins from a plant-associated bacterium. Nat Chem 2022; 14:1193-1201. [PMID: 36064972 PMCID: PMC7613652 DOI: 10.1038/s41557-022-01020-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Host-associated bacteria are increasingly being recognized as underexplored sources of bioactive natural products with unprecedented chemical scaffolds. A recently identified example is the plant-root-associated marine bacterium Gynuella sunshinyii of the chemically underexplored order Oceanospirillales. Its genome contains at least 22 biosynthetic gene clusters, suggesting a rich and mostly uncharacterized specialized metabolism. Here, in silico chemical prediction of a non-canonical polyketide synthase cluster has led to the discovery of janustatins, structurally unprecedented polyketide alkaloids with potent cytotoxicity that are produced in minute quantities. A combination of MS and two-dimensional NMR experiments, density functional theory calculations of 13C chemical shifts and semiquantitative interpretation of transverse rotating-frame Overhauser effect spectroscopy data were conducted to determine the relative configuration, which enabled the total synthesis of both enantiomers and assignment of the absolute configuration. Janustatins feature a previously unknown pyridodihydropyranone heterocycle and an unusual biological activity consisting of delayed, synchronized cell death at subnanomolar concentrations.
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Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Philipp Sondermann
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Stefan Leopold-Messer
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Yizhou Liu
- NMR Structure Elucidation, Process & Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Rei Suo
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Agneya Bhushan
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Lida Vadakumchery
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Ute Greczmiel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Yoko Yashiroda
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiromi Kimura
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Shinichi Nishimura
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan,Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yojiro Hoshikawa
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Minoru Yoshida
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan,Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Annette Oxenius
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - R. Thomas Williamson
- NMR Structure Elucidation, Process & Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Erick M. Carreira
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland,Correspondence and requests for materials should be addressed to J.P. or E.M.C.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland.
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4
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Li P, Chen M, Tang W, Guo Z, Zhang Y, Wang M, Horsman GP, Zhong J, Lu Z, Chen Y. Initiating polyketide biosynthesis by on-line methyl esterification. Nat Commun 2021; 12:4499. [PMID: 34301953 PMCID: PMC8302727 DOI: 10.1038/s41467-021-24846-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/09/2021] [Indexed: 12/04/2022] Open
Abstract
Aurantinins (ARTs) are antibacterial polyketides featuring a unique 6/7/8/5-fused tetracyclic ring system and a triene side chain with a carboxyl terminus. Here we identify the art gene cluster and dissect ART’s C-methyl incorporation patterns to study its biosynthesis. During this process, an apparently redundant methyltransferase Art28 was characterized as a malonyl-acyl carrier protein O-methyltransferase, which represents an unusual on-line methyl esterification initiation strategy for polyketide biosynthesis. The methyl ester bond introduced by Art28 is kept until the last step of ART biosynthesis, in which it is hydrolyzed by Art9 to convert inactive ART 9B to active ART B. The cryptic reactions catalyzed by Art28 and Art9 represent a protecting group biosynthetic logic to render the ART carboxyl terminus inert to unwanted side reactions and to protect producing organisms from toxic ART intermediates. Further analyses revealed a wide distribution of this initiation strategy for polyketide biosynthesis in various bacteria. Aurantinins are polyketides with unusual connectivities and broad antibacterial activity. Here the authors show the biosynthesis of aurantinins, which proceeds via an on-line methyl esterification at the terminus that enables the iterative chain elongations prior to condensation and cyclization.
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Affiliation(s)
- Pengwei Li
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Meng Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong, China
| | - Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Jin Zhong
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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5
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Williams EP, Bachvaroff TR, Place AR. A Global Approach to Estimating the Abundance and Duplication of Polyketide Synthase Domains in Dinoflagellates. Evol Bioinform Online 2021; 17:11769343211031871. [PMID: 34345159 PMCID: PMC8283056 DOI: 10.1177/11769343211031871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
Many dinoflagellate species make toxins in a myriad of different molecular configurations but the underlying chemistry in all cases is presumably via modular synthases, primarily polyketide synthases. In many organisms modular synthases occur as discrete synthetic genes or domains within a gene that act in coordination thus forming a module that produces a particular fragment of a natural product. The modules usually occur in tandem as gene clusters with a syntenic arrangement that is often predictive of the resultant structure. Dinoflagellate genomes however are notoriously complex with individual genes present in many tandem repeats and very few synthetic modules occurring as gene clusters, unlike what has been seen in bacteria and fungi. However, modular synthesis in all organisms requires a free thiol group that acts as a carrier for sequential synthesis called a thiolation domain. We scanned 47 dinoflagellate transcriptomes for 23 modular synthase domain models and compared their abundance among 10 orders of dinoflagellates as well as their co-occurrence with thiolation domains. The total count of domain types was quite large with over thirty-thousand identified, 29 000 of which were in the core dinoflagellates. Although there were no specific trends in domain abundance associated with types of toxins, there were readily observable lineage specific differences. The Gymnodiniales, makers of long polyketide toxins such as brevetoxin and karlotoxin had a high relative abundance of thiolation domains as well as multiple thiolation domains within a single transcript. Orders such as the Gonyaulacales, makers of small polyketides such as spirolides, had fewer thiolation domains but a relative increase in the number of acyl transferases. Unique to the core dinoflagellates, however, were thiolation domains occurring alongside tetratricopeptide repeats that facilitate protein-protein interactions, especially hexa and hepta-repeats, that may explain the scaffolding required for synthetic complexes capable of making large toxins. Clustering analysis for each type of domain was also used to discern possible origins of duplication for the multitude of single domain transcripts. Single domain transcripts frequently clustered with synonymous domains from multi-domain transcripts such as the BurA and ZmaK like genes as well as the multi-ketosynthase genes, sometimes with a large degree of apparent gene duplication, while fatty acid synthesis genes formed distinct clusters. Surprisingly the acyl-transferases and ketoreductases involved in fatty acid synthesis (FabD and FabG, respectively) were found in very large clusters indicating an unprecedented degree of gene duplication for these genes. These results demonstrate a complex evolutionary history of core dinoflagellate modular synthases with domain specific duplications throughout the lineage as well as clues to how large protein complexes can be assembled to synthesize the largest natural products known.
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Affiliation(s)
- Ernest P Williams
- Institute of Marine and Environmental Technologies, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Tsvetan R Bachvaroff
- Institute of Marine and Environmental Technologies, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Allen R Place
- Institute of Marine and Environmental Technologies, University of Maryland Center for Environmental Science, Baltimore, MD, USA
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6
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Kačar D, Cañedo LM, Rodríguez P, González EG, Galán B, Schleissner C, Leopold-Messer S, Piel J, Cuevas C, de la Calle F, García JL. Identification of trans-AT polyketide clusters in two marine bacteria reveals cryptic similarities between distinct symbiosis factors. Environ Microbiol 2021; 23:2509-2521. [PMID: 33734547 DOI: 10.1111/1462-2920.15470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/26/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022]
Abstract
Glutarimide-containing polyketides are known as potent antitumoral and antimetastatic agents. The associated gene clusters have only been identified in a few Streptomyces producers and Burkholderia gladioli symbiont. The new glutarimide-family polyketides, denominated sesbanimides D, E and F along with the previously known sesbanimide A and C, were isolated from two marine alphaproteobacteria Stappia indica PHM037 and Labrenzia aggregata PHM038. Structures of the isolated compounds were elucidated based on 1D and 2D homo and heteronuclear NMR analyses and ESI-MS spectrometry. All compounds exhibited strong antitumor activity in lung, breast and colorectal cancer cell lines. Subsequent whole genome sequencing and genome mining revealed the presence of the trans-AT PKS gene cluster responsible for the sesbanimide biosynthesis, described as sbn cluster. Strikingly, the modular architecture of downstream mixed type PKS/NRPS, SbnQ, revealed high similarity to PedH in pederin and Lab13 in labrenzin gene clusters, although those clusters are responsible for the production of structurally completely different molecules. The unexpected presence of SbnQ homologues in unrelated polyketide gene clusters across phylogenetically distant bacteria, raises intriguing questions about the evolutionary relationship between glutarimide-like and pederin-like pathways, as well as the functionality of their synthetic products.
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Affiliation(s)
- Dina Kačar
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Librada M Cañedo
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | - Pilar Rodríguez
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | - Elena G González
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | | | | | | | - Carmen Cuevas
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | | | - José L García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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7
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Helfrich EJN, Ueoka R, Chevrette MG, Hemmerling F, Lu X, Leopold-Messer S, Minas HA, Burch AY, Lindow SE, Piel J, Medema MH. Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria. Nat Commun 2021; 12:1422. [PMID: 33658492 PMCID: PMC7930024 DOI: 10.1038/s41467-021-21163-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 01/06/2021] [Indexed: 02/07/2023] Open
Abstract
Trans-acyltransferase polyketide synthases (trans-AT PKSs) are bacterial multimodular enzymes that biosynthesize diverse pharmaceutically and ecologically important polyketides. A notable feature of this natural product class is the existence of chemical hybrids that combine core moieties from different polyketide structures. To understand the prevalence, biosynthetic basis, and evolutionary patterns of this phenomenon, we developed transPACT, a phylogenomic algorithm to automate global classification of trans-AT PKS modules across bacteria and applied it to 1782 trans-AT PKS gene clusters. These analyses reveal widespread exchange patterns suggesting recombination of extended PKS module series as an important mechanism for metabolic diversification in this natural product class. For three plant-associated bacteria, i.e., the root colonizer Gynuella sunshinyii and the pathogens Xanthomonas cannabis and Pseudomonas syringae, we demonstrate the utility of this computational approach for uncovering cryptic relationships between polyketides, accelerating polyketide mining from fragmented genome sequences, and discovering polyketide variants with conserved moieties of interest. As natural combinatorial hybrids are rare among the more commonly studied cis-AT PKSs, this study paves the way towards evolutionarily informed, rational PKS engineering to produce chimeric trans-AT PKS-derived polyketides.
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Affiliation(s)
- Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
- Institute for Molecular Bio Science, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Franziska Hemmerling
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Xiaowen Lu
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Stefan Leopold-Messer
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Hannah A Minas
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Adrien Y Burch
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Steven E Lindow
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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8
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Nakou IT, Jenner M, Dashti Y, Romero‐Canelón I, Masschelein J, Mahenthiralingam E, Challis GL. Genomics-Driven Discovery of a Novel Glutarimide Antibiotic from Burkholderia gladioli Reveals an Unusual Polyketide Synthase Chain Release Mechanism. Angew Chem Int Ed Engl 2020; 59:23145-23153. [PMID: 32918852 PMCID: PMC7756379 DOI: 10.1002/anie.202009007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/18/2020] [Indexed: 11/07/2022]
Abstract
A gene cluster encoding a cryptic trans‐acyl transferase polyketide synthase (PKS) was identified in the genomes of Burkholderia gladioli BCC0238 and BCC1622, both isolated from the lungs of cystic fibrosis patients. Bioinfomatics analyses indicated the PKS assembles a novel member of the glutarimide class of antibiotics, hitherto only isolated from Streptomyces species. Screening of a range of growth parameters led to the identification of gladiostatin, the metabolic product of the PKS. NMR spectroscopic analysis revealed that gladiostatin, which has promising activity against several human cancer cell lines and inhibits tumor cell migration, contains an unusual 2‐acyl‐4‐hydroxy‐3‐methylbutenolide in addition to the glutarimide pharmacophore. An AfsA‐like domain at the C‐terminus of the PKS was shown to catalyze condensation of 3‐ketothioesters with dihydroxyacetone phosphate, thus indicating it plays a key role in polyketide chain release and butenolide formation.
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Affiliation(s)
- Ioanna T. Nakou
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
| | - Matthew Jenner
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
| | - Yousef Dashti
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Current Address: The Centre for Bacterial Cell Biology, Biosciences InstituteMedical SchoolNewcastle UniversityNewcastle upon TyneNE2 4AXUK
| | - Isolda Romero‐Canelón
- Institute of Clinical SciencesSchool of PharmacyUniversity of BirminghamBirminghamB15 2TTUK
| | - Joleen Masschelein
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Current Address: Laboratory for Biomolecular Discovery &, EngineeringVIB-KU Leuven Center for MicrobiologyDepartment of BiologyKU Leuven3001LeuvenBelgium
| | - Eshwar Mahenthiralingam
- Organisms and Environment DivisionCardiff School of BiosciencesCardiff UniversityCardiffCF10 3ATUK
| | - Gregory L. Challis
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
- Department of Biochemistry and Molecular BiologyARC Centre of Excellence for Innovations in Peptide and Protein ScienceMonash UniversityVictoria3800Australia
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9
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Nakou IT, Jenner M, Dashti Y, Romero‐Canelón I, Masschelein J, Mahenthiralingam E, Challis GL. Genomics‐Driven Discovery of a Novel Glutarimide Antibiotic from
Burkholderia gladioli
Reveals an Unusual Polyketide Synthase Chain Release Mechanism. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ioanna T. Nakou
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
| | - Matthew Jenner
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Warwick Integrative Synthetic Biology Centre University of Warwick Coventry CV4 7AL UK
| | - Yousef Dashti
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Current Address: The Centre for Bacterial Cell Biology, Biosciences Institute Medical School Newcastle University Newcastle upon Tyne NE2 4AX UK
| | - Isolda Romero‐Canelón
- Institute of Clinical Sciences School of Pharmacy University of Birmingham Birmingham B15 2TT UK
| | - Joleen Masschelein
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Current Address: Laboratory for Biomolecular Discovery &, Engineering VIB-KU Leuven Center for Microbiology Department of Biology KU Leuven 3001 Leuven Belgium
| | - Eshwar Mahenthiralingam
- Organisms and Environment Division Cardiff School of Biosciences Cardiff University Cardiff CF10 3AT UK
| | - Gregory L. Challis
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Warwick Integrative Synthetic Biology Centre University of Warwick Coventry CV4 7AL UK
- Department of Biochemistry and Molecular Biology ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Victoria 3800 Australia
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10
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Niehs SP, Kumpfmüller J, Dose B, Little RF, Ishida K, Flórez LV, Kaltenpoth M, Hertweck C. Insect‐Associated Bacteria Assemble the Antifungal Butenolide Gladiofungin by Non‐Canonical Polyketide Chain Termination. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sarah P. Niehs
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Jana Kumpfmüller
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Rory F. Little
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Laura V. Flórez
- Department for Evolutionary Ecology Institute of Organismic and Molecular Evolution Johannes Gutenberg University Mainz Hanns-Dieter-Hüsch-Weg 15 55128 Mainz Germany
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology Institute of Organismic and Molecular Evolution Johannes Gutenberg University Mainz Hanns-Dieter-Hüsch-Weg 15 55128 Mainz Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstr. 11a 07745 Jena Germany
- Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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11
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Niehs SP, Kumpfmüller J, Dose B, Little RF, Ishida K, Flórez LV, Kaltenpoth M, Hertweck C. Insect-Associated Bacteria Assemble the Antifungal Butenolide Gladiofungin by Non-Canonical Polyketide Chain Termination. Angew Chem Int Ed Engl 2020; 59:23122-23126. [PMID: 32588959 PMCID: PMC7756420 DOI: 10.1002/anie.202005711] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/10/2020] [Indexed: 12/17/2022]
Abstract
Genome mining of one of the protective symbionts (Burkholderia gladioli) of the invasive beetle Lagria villosa revealed a cryptic gene cluster that codes for the biosynthesis of a novel antifungal polyketide with a glutarimide pharmacophore. Targeted gene inactivation, metabolic profiling, and bioassays led to the discovery of the gladiofungins as previously‐overlooked components of the antimicrobial armory of the beetle symbiont, which are highly active against the entomopathogenic fungus Purpureocillium lilacinum. By mutational analyses, isotope labeling, and computational analyses of the modular polyketide synthase, we found that the rare butenolide moiety of gladiofungins derives from an unprecedented polyketide chain termination reaction involving a glycerol‐derived C3 building block. The key role of an A‐factor synthase (AfsA)‐like offloading domain was corroborated by CRISPR‐Cas‐mediated gene editing, which facilitated precise excision within a PKS domain.
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Affiliation(s)
- Sarah P Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Jana Kumpfmüller
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Rory F Little
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Laura V Flórez
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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12
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Lee B, Son S, Lee JK, Jang M, Heo KT, Ko SK, Park DJ, Park CS, Kim CJ, Ahn JS, Hwang BY, Jang JH, Hong YS. Isolation of new streptimidone derivatives, glutarimide antibiotics from Streptomyces sp. W3002 using LC-MS-guided screening. J Antibiot (Tokyo) 2019; 73:184-188. [PMID: 31853030 DOI: 10.1038/s41429-019-0264-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/19/2019] [Accepted: 11/27/2019] [Indexed: 11/09/2022]
Abstract
A LC-MS-guided screening led to the isolation of two new streptimidone derivatives (2 and 3) containing a glutarimide ring and two glutarimide ring-opened compounds (4 and 5) along with a known glutarimide-containing polyketide, streptimidone (1) from Streptomyces sp. W3002 strain. Their structures were elucidated by MS and NMR spectroscopic analyses and by comparison with data from the literature. Compound 2 is a non-hydroxylated analog at the C-5 position of streptimidone. The structure of 3 was determined as a streptimidone derivative possessing the α, β-unsaturated ketone moiety at positions C-5 and C-6. Compound 4 had similar chemical shifts and splitting patterns with 3, but the glutarimide ring is opened. Compound 5 closely resembles that of 4 with the only difference being the existence of an additional methoxy group instead of an amide group. Streptimidone (1) and 3 showed weak cytotoxic activity against three human cancer cell lines, respectively.
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Affiliation(s)
- Byeongsan Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,College of Pharmacy, Chungbuk National University, Cheongju, 28160, Korea
| | - Sangkeun Son
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea
| | - Jae Kyoung Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea
| | - Mina Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Korea
| | - Kyung Taek Heo
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Korea
| | - Sung-Kyun Ko
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Korea
| | - Dong-Jin Park
- Industrial Bio-materials Research Center, KRIBB, Daejeon, 34141, Korea
| | - Chan Sun Park
- Immunoregulatory Materials Research Center, KRIBB, Jeongeup, 56212, Korea
| | - Chang-Jin Kim
- KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Korea.,Industrial Bio-materials Research Center, KRIBB, Daejeon, 34141, Korea
| | - Jong Seog Ahn
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea
| | - Bang Yeon Hwang
- College of Pharmacy, Chungbuk National University, Cheongju, 28160, Korea
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea. .,KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Korea.
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13
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Zhang D, Yi W, Ge H, Zhang Z, Wu B. Bioactive Streptoglutarimides A-J from the Marine-Derived Streptomyces sp. ZZ741. JOURNAL OF NATURAL PRODUCTS 2019; 82:2800-2808. [PMID: 31584271 DOI: 10.1021/acs.jnatprod.9b00481] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The new streptoglutarimides A-J (1-10) and the known streptovitacin A (11) were isolated from a marine-derived actinomycete, Streptomyces sp. ZZ741. Structures of the isolated compounds were elucidated based on their HRESIMS data, extensive NMR spectroscopic analyses, ECD calculations, Mosher's method, and a single-crystal X-ray diffraction experiment. Streptoglutarimide H (8) and streptovitacin A (11) showed potent antiproliferative activity against human glioma U87MG and U251 cells with IC50 values of 1.5-3.8 μM for 8 and 0.05-0.22 μM for 11. All isolated compounds exhibited antimicrobial activity with MIC values of 9-11 μg/mL against methicillin-resistant Staphylococcus aureus, 8-12 μg/mL against Escherichia coli, and 8-20 μg/mL against Candida albicans.
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Affiliation(s)
- Di Zhang
- Ocean College, Zhoushan Campus , Zhejiang University , Zhoushan 316021 , People's Republic of China
| | - Wenwen Yi
- Ocean College, Zhoushan Campus , Zhejiang University , Zhoushan 316021 , People's Republic of China
| | - Hengju Ge
- Ocean College, Zhoushan Campus , Zhejiang University , Zhoushan 316021 , People's Republic of China
| | - Zhizhen Zhang
- Ocean College, Zhoushan Campus , Zhejiang University , Zhoushan 316021 , People's Republic of China
| | - Bin Wu
- Ocean College, Zhoushan Campus , Zhejiang University , Zhoushan 316021 , People's Republic of China
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14
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Abstract
Enzymes that catalyze a Michael-type addition in polyketide biosynthesis are summarized and discussed.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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15
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Challenges and opportunities for natural product discovery, production, and engineering in native producers versus heterologous hosts. J Ind Microbiol Biotechnol 2018; 46:433-444. [PMID: 30426283 DOI: 10.1007/s10295-018-2094-5] [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: 08/27/2018] [Accepted: 10/19/2018] [Indexed: 10/27/2022]
Abstract
Recent advances and emerging technologies for metabolic pathway engineering and synthetic biology have transformed the field of natural product discovery, production, and engineering. Despite these advancements, there remain many challenges in understanding how biosynthetic gene clusters are silenced or activated, including changes in the transcription of key biosynthetic and regulatory genes. This knowledge gap is highlighted by the success and failed attempts of manipulating regulatory genes within biosynthetic gene clusters in both native producers and heterologous hosts. These complexities make the choice of native producers versus heterologous hosts, fermentation medium, and supply of precursors crucial factors in achieving the production of the target natural products and engineering designer analogs. Nature continues to serve as inspiration for filling the knowledge gaps and developing new research strategies. By exploiting the evolutionary power of nature, alternative producers, with the desired genetic amenability and higher titers of the target natural products, and new strains, harboring gene clusters that encode evolutionary optimized congeners of the targeted natural product scaffolds, can be discovered. These newly identified strains can serve as an outstanding biotechnology platform for the engineered production of sufficient quantities of the target natural products and their analogs, enabling biosynthetic studies and potential therapeutic applications. These challenges and opportunities are showcased herein using fredericamycin, iso-migrastatin, platencin and platensimycin, the enediynes of C-1027, tiancimycin, and yangpumicin, and the leinamycin family of natural products.
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16
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Zhang B, Xu Z, Teng Q, Pan G, Ma M, Shen B. A Long-Range Acting Dehydratase Domain as the Missing Link for C17-Dehydration in Iso-Migrastatin Biosynthesis. Angew Chem Int Ed Engl 2017; 56:7247-7251. [PMID: 28464455 DOI: 10.1002/anie.201703588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Indexed: 11/05/2022]
Abstract
The dehydratase domains (DHs) of the iso-migrastatin (iso-MGS) polyketide synthase (PKS) were investigated by systematic inactivation of the DHs in module-6, -9, -10 of MgsF (i.e., DH6, DH9, DH10) and module-11 of MgsG (i.e., DH11) in vivo, followed by structural characterization of the metabolites accumulated by the mutants, and biochemical characterization of DH10 in vitro, using polyketide substrate mimics with varying chain lengths. These studies allowed us to assign the functions for all four DHs, identifying DH10 as the dedicated dehydratase that catalyzes the dehydration of the C17 hydroxy group during iso-MGS biosynthesis. In contrast to canonical DHs that catalyze dehydration of the β-hydroxy groups of the nascent polyketide intermediates, DH10 acts in a long-range manner that is unprecedented for type I PKSs, a novel dehydration mechanism that could be exploited for polyketide structural diversity by combinatorial biosynthesis and synthetic biology.
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Affiliation(s)
- Bo Zhang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Zhengren Xu
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Qihui Teng
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Guohui Pan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Ming Ma
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Department of Molecular Medicine, Natural Products Library Initiative, The Scripps Research Institute, Jupiter, FL, 33458, USA
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17
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Zhang B, Xu Z, Teng Q, Pan G, Ma M, Shen B. A Long-Range Acting Dehydratase Domain as the Missing Link for C17-Dehydration in Iso-Migrastatin Biosynthesis. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703588] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Bo Zhang
- Department of Chemistry; The Scripps Research Institute; Jupiter FL 33458 USA
| | - Zhengren Xu
- Department of Chemistry; The Scripps Research Institute; Jupiter FL 33458 USA
| | - Qihui Teng
- Department of Chemistry; The Scripps Research Institute; Jupiter FL 33458 USA
| | - Guohui Pan
- Department of Chemistry; The Scripps Research Institute; Jupiter FL 33458 USA
| | - Ming Ma
- Department of Chemistry; The Scripps Research Institute; Jupiter FL 33458 USA
| | - Ben Shen
- Department of Chemistry; The Scripps Research Institute; Jupiter FL 33458 USA
- Department of Molecular Medicine, Natural Products Library Initiative; The Scripps Research Institute; Jupiter FL 33458 USA
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18
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Pang B, Wang M, Liu W. Cyclization of polyketides and non-ribosomal peptides on and off their assembly lines. Nat Prod Rep 2016; 33:162-73. [PMID: 26604034 DOI: 10.1039/c5np00095e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modular polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are multifunctional megaenzymes that serve as templates to program the assembly of short carboxylic acids and amino acids in a primarily co-linear manner. The variation, combination, permutation and evolution of their functional units (e.g., modules, domains and proteins) along with their association with external enzymes have resulted in the generation of numerous versions of templates, the roles of which have not been fully recognized in the structural diversification of polyketides, non-ribosomal peptides and their hybrids present in nature. In this Highlight, we focus on the assembly-line enzymology and associated chemistry by providing examples of some newly characterized cyclization reactions that occur on and off the assembly lines during and after chain elongation for the purpose of elucidating the template effects of PKSs and NRPSs. A fundamental understanding of the underlying biosynthetic logic would facilitate the elucidation of chemical information contained within the PKS or NRPS templates and benefit the development of strategies for genome mining, biosynthesis-inspired chemical synthesis and combinatorial biosynthesis.
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Affiliation(s)
- Bo Pang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Min Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China. and Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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19
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Stulberg ER, Lozano GL, Morin JB, Park H, Baraban EG, Mlot C, Heffelfinger C, Phillips GM, Rush JS, Phillips AJ, Broderick NA, Thomas MG, Stabb EV, Handelsman J. Genomic and Secondary Metabolite Analyses of Streptomyces sp. 2AW Provide Insight into the Evolution of the Cycloheximide Pathway. Front Microbiol 2016; 7:573. [PMID: 27199910 PMCID: PMC4853412 DOI: 10.3389/fmicb.2016.00573] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/07/2016] [Indexed: 11/13/2022] Open
Abstract
The dearth of new antibiotics in the face of widespread antimicrobial resistance makes developing innovative strategies for discovering new antibiotics critical for the future management of infectious disease. Understanding the genetics and evolution of antibiotic producers will help guide the discovery and bioengineering of novel antibiotics. We discovered an isolate in Alaskan boreal forest soil that had broad antimicrobial activity. We elucidated the corresponding antimicrobial natural products and sequenced the genome of this isolate, designated Streptomyces sp. 2AW. This strain illustrates the chemical virtuosity typical of the Streptomyces genus, producing cycloheximide as well as two other biosynthetically unrelated antibiotics, neutramycin, and hygromycin A. Combining bioinformatic and chemical analyses, we identified the gene clusters responsible for antibiotic production. Interestingly, 2AW appears dissimilar from other cycloheximide producers in that the gene encoding the polyketide synthase resides on a separate part of the chromosome from the genes responsible for tailoring cycloheximide-specific modifications. This gene arrangement and our phylogenetic analyses of the gene products suggest that 2AW holds an evolutionarily ancestral lineage of the cycloheximide pathway. Our analyses support the hypothesis that the 2AW glutaramide gene cluster is basal to the lineage wherein cycloheximide production diverged from other glutarimide antibiotics. This study illustrates the power of combining modern biochemical and genomic analyses to gain insight into the evolution of antibiotic-producing microorganisms.
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Affiliation(s)
- Elizabeth R Stulberg
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
| | - Gabriel L Lozano
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
| | - Jesse B Morin
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
| | - Hyunjun Park
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| | - Ezra G Baraban
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
| | - Christine Mlot
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| | | | | | - Jason S Rush
- Department of Chemistry, Yale University New Haven, CT, USA
| | | | - Nichole A Broderick
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
| | - Michael G Thomas
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| | - Eric V Stabb
- Department of Microbiology, University of Georgia Athens, GA, USA
| | - Jo Handelsman
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT, USA
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20
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Sundaram S, Hertweck C. On-line enzymatic tailoring of polyketides and peptides in thiotemplate systems. Curr Opin Chem Biol 2016; 31:82-94. [DOI: 10.1016/j.cbpa.2016.01.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/21/2015] [Accepted: 01/15/2016] [Indexed: 11/26/2022]
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21
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Helfrich EJN, Piel J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 2016; 33:231-316. [DOI: 10.1039/c5np00125k] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
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Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
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22
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Zhang B, Yang D, Yan Y, Pan G, Xiang W, Shen B. Overproduction of lactimidomycin by cross-overexpression of genes encoding Streptomyces antibiotic regulatory proteins. Appl Microbiol Biotechnol 2015; 100:2267-77. [PMID: 26552797 DOI: 10.1007/s00253-015-7119-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/19/2015] [Accepted: 10/22/2015] [Indexed: 12/21/2022]
Abstract
The glutarimide-containing polyketides represent a fascinating class of natural products that exhibit a multitude of biological activities. We have recently cloned and sequenced the biosynthetic gene clusters for three members of the glutarimide-containing polyketides-iso-migrastatin (iso-MGS) from Streptomyces platensis NRRL 18993, lactimidomycin (LTM) from Streptomyces amphibiosporus ATCC 53964, and cycloheximide (CHX) from Streptomyces sp. YIM56141. Comparative analysis of the three clusters identified mgsA and chxA, from the mgs and chx gene clusters, respectively, that were predicted to encode the PimR-like Streptomyces antibiotic regulatory proteins (SARPs) but failed to reveal any regulatory gene from the ltm gene cluster. Overexpression of mgsA or chxA in S. platensis NRRL 18993, Streptomyces sp. YIM56141 or SB11024, and a recombinant strain of Streptomyces coelicolor M145 carrying the intact mgs gene cluster has no significant effect on iso-MGS or CHX production, suggesting that MgsA or ChxA regulation may not be rate-limiting for iso-MGS and CHX production in these producers. In contrast, overexpression of mgsA or chxA in S. amphibiosporus ATCC 53964 resulted in a significant increase in LTM production, with LTM titer reaching 106 mg/L, which is five-fold higher than that of the wild-type strain. These results support MgsA and ChxA as members of the SARP family of positive regulators for the iso-MGS and CHX biosynthetic machinery and demonstrate the feasibility to improve glutarimide-containing polyketide production in Streptomyces strains by exploiting common regulators.
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Affiliation(s)
- Bo Zhang
- School of Life Sciences, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Yijun Yan
- School of Life Sciences, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Guohui Pan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Wensheng Xiang
- School of Life Sciences, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China.
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA.
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, 33458, USA.
- Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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23
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Polyketide synthase chimeras reveal key role of ketosynthase domain in chain branching. Nat Chem Biol 2015; 11:949-51. [DOI: 10.1038/nchembio.1932] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/28/2015] [Indexed: 11/08/2022]
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24
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Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases. Proc Natl Acad Sci U S A 2015; 112:12693-8. [PMID: 26420866 DOI: 10.1073/pnas.1515460112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.
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25
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Abstract
Leinamycin (LNM) is a sulfur-containing antitumor antibiotic featuring an unusual 1,3-dioxo-1,2-dithiolane moiety that is spiro-fused to a thiazole-containing 18-membered lactam ring. The 1,3-dioxo-1,2-dithiolane moiety is essential for LNM's antitumor activity, by virtue of its ability to generate an episulfonium ion intermediate capable of alkylating DNA. We have previously cloned and sequenced the lnm gene cluster from Streptomyces atroolivaceus S-140. In vivo and in vitro characterizations of the LNM biosynthetic machinery have since established that: (i) the 18-membered macrolactam backbone is synthesized by LnmP, LnmQ, LnmJ, LnmI, and LnmG, (ii) the alkyl branch at C-3 of LNM is installed by LnmK, LnmL, LnmM, and LnmF, and (iii) leinamycin E1 (LNM E1), bearing a thiol moiety at C-3, is the nascent product of the LNM hybrid nonribosomal peptide synthetase (NRPS)-acyltransferase (AT)-less type I polyketide synthase (PKS). Sulfur incorporation at C-3 of LNM E1, however, has not been addressed. Here we report that: (i) the bioinformatics analysis reveals a pyridoxal phosphate (PLP)-dependent domain, we termed cysteine lyase (SH) domain (LnmJ-SH), within PKS module-8 of LnmJ; (ii) the LnmJ-SH domain catalyzes C-S bond cleavage by using l-cysteine and l-cysteine S-modified analogs as substrates through a PLP-dependent β-elimination reaction, establishing l-cysteine as the origin of sulfur at C-3 of LNM; and (iii) the LnmJ-SH domain, sharing no sequence homology with any other enzymes catalyzing C-S bond cleavage, represents a new family of PKS domains that expands the chemistry and enzymology of PKSs and might be exploited to incorporate sulfur into polyketide natural products by PKS engineering.
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Liu SP, Yu P, Yuan PH, Zhou ZX, Bu QT, Mao XM, Li YQ. Sigma factor WhiGch positively regulates natamycin production in Streptomyces chattanoogensis L10. Appl Microbiol Biotechnol 2015; 99:2715-26. [DOI: 10.1007/s00253-014-6307-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 12/06/2014] [Accepted: 12/09/2014] [Indexed: 12/22/2022]
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Zhou Z, Xu Q, Bu Q, Guo Y, Liu S, Liu Y, Du Y, Li Y. Genome mining-directed activation of a silent angucycline biosynthetic gene cluster in Streptomyces chattanoogensis. Chembiochem 2014; 16:496-502. [PMID: 25511454 DOI: 10.1002/cbic.201402577] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 01/01/2023]
Abstract
Genomic sequencing of actinomycetes has revealed the presence of numerous gene clusters seemingly capable of natural product biosynthesis, yet most clusters are cryptic under laboratory conditions. Bioinformatics analysis of the completely sequenced genome of Streptomyces chattanoogensis L10 (CGMCC 2644) revealed a silent angucycline biosynthetic gene cluster. The overexpression of a pathway-specific activator gene under the constitutive ermE* promoter successfully triggered the expression of the angucycline biosynthetic genes. Two novel members of the angucycline antibiotic family, chattamycins A and B, were further isolated and elucidated. Biological activity assays demonstrated that chattamycin B possesses good antitumor activities against human cancer cell lines and moderate antibacterial activities. The results presented here provide a feasible method to activate silent angucycline biosynthetic gene clusters to discover potential new drug leads.
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Affiliation(s)
- Zhenxing Zhou
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Zijingang Campus, 388 Yuhangtang Road, Hangzhou 310058 (China)
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Seo JW, Ma M, Kwong T, Ju J, Lim SK, Jiang H, Lohman JR, Yang C, Cleveland J, Zazopoulos E, Farnet CM, Shen B. Comparative characterization of the lactimidomycin and iso-migrastatin biosynthetic machineries revealing unusual features for acyltransferase-less type I polyketide synthases and providing an opportunity to engineer new analogues. Biochemistry 2014; 53:7854-65. [PMID: 25405956 PMCID: PMC4270375 DOI: 10.1021/bi501396v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Lactimidomycin (LTM, 1) and iso-migrastatin (iso-MGS, 2) belong to the glutarimide-containing polyketide family of natural products. We previously cloned and characterized the mgs biosynthetic gene cluster from Streptomyces platensis NRRL 18993. The iso-MGS biosynthetic machinery featured an acyltransferase (AT)-less type I polyketide synthase (PKS) and three tailoring enzymes (MgsIJK). We now report cloning and characterization of the ltm biosynthetic gene cluster from Streptomyces amphibiosporus ATCC 53964, which consists of nine genes that encode an AT-less type I PKS (LtmBCDEFGHL) and one tailoring enzyme (LtmK). Inactivation of ltmE or ltmH afforded the mutant strain SB15001 or SB15002, respectively, that abolished the production of 1, as well as the three cometabolites 8,9-dihydro-LTM (14), 8,9-dihydro-8S-hydroxy-LTM (15), and 8,9-dihydro-9R-hydroxy-LTM (13). Inactivation of ltmK yielded the mutant strain SB15003 that abolished the production of 1, 13, and 15 but led to the accumulation of 14. Complementation of the ΔltmK mutation in SB15003 by expressing ltmK in trans restored the production of 1, as well as that of 13 and 15. These results support the model for 1 biosynthesis, featuring an AT-less type I PKS that synthesizes 14 as the nascent polyketide intermediate and a cytochrome P450 desaturase that converts 14 to 1, with 13 and 15 as minor cometabolites. Comparative analysis of the LTM and iso-MGS AT-less type I PKSs revealed several unusual features that deviate from those of the collinear type I PKS model. Exploitation of the tailoring enzymes for 1 and 2 biosynthesis afforded two analogues, 8,9-dihydro-8R-hydroxy-LTM (16) and 8,9-dihydro-8R-methoxy-LTM (17), that provided new insights into the structure-activity relationship of 1 and 2. While 12-membered macrolides, featuring a combination of a hydroxyl group at C-17 and a double bond at C-8 and C-9 as found in 1, exhibit the most potent activity, analogues with a single hydroxyl or methoxy group at C-8 or C-9 retain most of the activity whereas analogues with double substitutions at C-8 and C-9 lose significant activity.
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Affiliation(s)
- Jeong-Woo Seo
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
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Heine D, Bretschneider T, Sundaram S, Hertweck C. Enzymatic Polyketide Chain Branching To Give Substituted Lactone, Lactam, and Glutarimide Heterocycles. Angew Chem Int Ed Engl 2014; 53:11645-9. [DOI: 10.1002/anie.201407282] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Indexed: 01/01/2023]
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Heine D, Bretschneider T, Sundaram S, Hertweck C. Enzymatische Polyketid-Kettenverzweigung zur Bildung substituierter Lacton-, Lactam- und Glutarimidheterocyclen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407282] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Sun D, Sun W, Yu Y, Li Z, Deng Z, Lin S. A new glutarimide derivative from marine sponge-derived Streptomyces anulatus S71. Nat Prod Res 2014; 28:1602-6. [DOI: 10.1080/14786419.2014.928877] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Dandan Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P.R. China
| | - Wei Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P.R. China
| | - Yinxian Yu
- Department of Orthopedic Surgery, Shanghai Frist People's Hospital, School of Medicine, Shanghai Jiao Tong University, 100 Haining Road, Shanghai 200080, P.R. China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P.R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P.R. China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P.R. China
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Van Wagoner RM, Satake M, Wright JLC. Polyketide biosynthesis in dinoflagellates: what makes it different? Nat Prod Rep 2014; 31:1101-37. [DOI: 10.1039/c4np00016a] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Yin M, Yan Y, Lohman JR, Huang SX, Ma M, Zhao GR, Xu LH, Xiang W, Shen B. Cycloheximide and actiphenol production in Streptomyces sp. YIM56141 governed by single biosynthetic machinery featuring an acyltransferase-less type I polyketide synthase. Org Lett 2014; 16:3072-5. [PMID: 24815182 PMCID: PMC4051428 DOI: 10.1021/ol501179w] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Cycloheximide (1) and
actiphenol (2)
have been isolated from numerous Streptomyces species.
Cloning, sequencing, and characterization of a gene cluster from Streptomyces sp. YIM65141 now establish that 1 and 2 production is governed by single biosynthetic
machinery. Biosynthesis of 1 features an acyltransferase-less
type I polyketide synthase to construct its carbon backbone but may
proceed via 2 as a key intermediate, invoking a provocative
reduction of a phenol to a cyclohexanone moiety in natural product
biosynthesis.
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Affiliation(s)
- Min Yin
- Department of Chemistry, ⊥Department of Molecular Therapeutics, and ¶Natural Products Library Initiative, The Scripps Research Institute , Jupiter, Florida 33458, United States
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Till M, Race PR. Progress challenges and opportunities for the re-engineering of trans-AT polyketide synthases. Biotechnol Lett 2014; 36:877-88. [PMID: 24557077 DOI: 10.1007/s10529-013-1449-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 12/23/2013] [Indexed: 12/13/2022]
Abstract
Polyketides are a structurally and functionally diverse family of bioactive natural products that are used extensively as pharmaceuticals and agrochemicals. In bacteria these molecules are biosynthesized by giant, multi-functional enzymatic complexes, termed modular polyketide synthases (PKSs), that function in assembly-line like fashion to fuse and tailor simple carboxylic acid monomers into a vast array of elaborate chemical scaffolds. Modifying PKSs through targeted synthase re-engineering is a promising approach for accessing functionally-optimized polyketides. Due to their highly mosaic architectures the recently identified trans-AT family of modular synthases appear inherently more amenable to re-engineering than their well studied cis-AT counterparts. Here, we review recent progress in the re-engineering of trans-AT PKSs, summarize opportunities for harnessing the biosynthetic potential of these systems, and highlight challenges that such re-engineering approaches present.
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Affiliation(s)
- M Till
- School of Biochemistry, Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK
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35
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Vinylogous chain branching catalysed by a dedicated polyketide synthase module. Nature 2013; 502:124-8. [DOI: 10.1038/nature12588] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/19/2013] [Indexed: 11/08/2022]
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36
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Improvement of natamycin production by engineering of phosphopantetheinyl transferases in Streptomyces chattanoogensis L10. Appl Environ Microbiol 2013; 79:3346-54. [PMID: 23524668 DOI: 10.1128/aem.00099-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Phosphopantetheinyl transferases (PPTases) are essential to the activities of type I/II polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) through converting acyl carrier proteins (ACPs) in PKSs and peptidyl carrier proteins (PCPs) in NRPSs from inactive apo-forms into active holo-forms, leading to biosynthesis of polyketides and nonribosomal peptides. The industrial natamycin (NTM) producer, Streptomyces chattanoogensis L10, contains two PPTases (SchPPT and SchACPS) and five PKSs. Biochemical characterization of these two PPTases shows that SchPPT catalyzes the phosphopantetheinylation of ACPs in both type I PKSs and type II PKSs, SchACPS catalyzes the phosphopantetheinylation of ACPs in type II PKSs and fatty acid synthases (FASs), and the specificity of SchPPT is possibly controlled by its C terminus. Inactivation of SchPPT in S. chattanoogensis L10 abolished production of NTM but not the spore pigment, while overexpression of the SchPPT gene not only increased NTM production by about 40% but also accelerated productions of both NTM and the spore pigment. Thus, we elucidated a comprehensive phosphopantetheinylation network of PKSs and improved polyketide production by engineering the cognate PPTase in bacteria.
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Wang B, Song Y, Luo M, Chen Q, Ma J, Huang H, Ju J. Biosynthesis of 9-Methylstreptimidone Involves a New Decarboxylative Step for Polyketide Terminal Diene Formation. Org Lett 2013; 15:1278-81. [PMID: 23438151 DOI: 10.1021/ol400224n] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bo Wang
- Key Laboratory of Marine Bio-resources Sustainable Utilization, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yongxiang Song
- Key Laboratory of Marine Bio-resources Sustainable Utilization, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Minghe Luo
- Key Laboratory of Marine Bio-resources Sustainable Utilization, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Qi Chen
- Key Laboratory of Marine Bio-resources Sustainable Utilization, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Junying Ma
- Key Laboratory of Marine Bio-resources Sustainable Utilization, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Hongbo Huang
- Key Laboratory of Marine Bio-resources Sustainable Utilization, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Jianhua Ju
- Key Laboratory of Marine Bio-resources Sustainable Utilization, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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Ma M, Kwong T, Lim SK, Ju J, Lohman JR, Shen B. Post-polyketide synthase steps in iso-migrastatin biosynthesis, featuring tailoring enzymes with broad substrate specificity. J Am Chem Soc 2013; 135:2489-92. [PMID: 23394593 PMCID: PMC3582021 DOI: 10.1021/ja4002635] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The iso-migrastatin (iso-MGS) biosynthetic gene cluster from Streptomyces platensis NRRL 18993 consists of 11 genes, featuring an acyltransferase (AT)-less type I polyketide synthase (PKS) and three tailoring enzymes MgsIJK. Systematic inactivation of mgsIJK in S. platensis enabled us to (i) identify two nascent products of the iso-MGS AT-less type I PKS, establishing an unprecedented novel feature for AT-less type I PKSs, and (ii) account for the formation of all known post-PKS biosynthetic intermediates generated by the three tailoring enzymes MgsIJK, which possessed significant substrate promiscuities.
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Affiliation(s)
- Ming Ma
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, USA
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Boronated tartrolon antibiotic produced by symbiotic cellulose-degrading bacteria in shipworm gills. Proc Natl Acad Sci U S A 2013; 110:E295-304. [PMID: 23288898 DOI: 10.1073/pnas.1213892110] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shipworms are marine wood-boring bivalve mollusks (family Teredinidae) that harbor a community of closely related Gammaproteobacteria as intracellular endosymbionts in their gills. These symbionts have been proposed to assist the shipworm host in cellulose digestion and have been shown to play a role in nitrogen fixation. The genome of one strain of Teredinibacter turnerae, the first shipworm symbiont to be cultivated, was sequenced, revealing potential as a rich source of polyketides and nonribosomal peptides. Bioassay-guided fractionation led to the isolation and identification of two macrodioloide polyketides belonging to the tartrolon class. Both compounds were found to possess antibacterial properties, and the major compound was found to inhibit other shipworm symbiont strains and various pathogenic bacteria. The gene cluster responsible for the synthesis of these compounds was identified and characterized, and the ketosynthase domains were analyzed phylogenetically. Reverse-transcription PCR in addition to liquid chromatography and high-resolution mass spectrometry and tandem mass spectrometry revealed the transcription of these genes and the presence of the compounds in the shipworm, suggesting that the gene cluster is expressed in vivo and that the compounds may fulfill a specific function for the shipworm host. This study reports tartrolon polyketides from a shipworm symbiont and unveils the biosynthetic gene cluster of a member of this class of compounds, which might reveal the mechanism by which these bioactive metabolites are biosynthesized.
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Wong FT, Jin X, Mathews II, Cane DE, Khosla C. Structure and mechanism of the trans-acting acyltransferase from the disorazole synthase. Biochemistry 2011; 50:6539-48. [PMID: 21707057 DOI: 10.1021/bi200632j] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 1.51 Å resolution X-ray crystal structure of the trans-acyltransferase (AT) from the "AT-less" disorazole synthase (DSZS) and that of its acetate complex at 1.35 Å resolution are reported. Separately, comprehensive alanine-scanning mutagenesis of one of its acyl carrier protein substrates (ACP1 from DSZS) led to the identification of a conserved Asp45 residue on the ACP, which contributes to the substrate specificity of this unusual enzyme. Together, these experimental findings were used to derive a model for the selective association of the DSZS AT and its ACP substrate. With a goal of structurally characterizing the AT-ACP interface, a strategy was developed for covalently cross-linking the active site Ser → Cys mutant of the DSZS AT to its ACP substrate and for purifying the resulting AT-ACP complex to homogeneity. The S86C DSZS AT mutant was found to be functional, albeit with a transacylation efficiency 200-fold lower than that of its wild-type counterpart. Our findings provide new insights as well as new opportunities for high-resolution analysis of an important protein-protein interface in polyketide synthases.
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Affiliation(s)
- Fong T Wong
- Department of Chemical Engineering, Department of Chemistry, and §Department of Biochemistry, Stanford University , Stanford, California 94305, United States
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Titer improvement of iso-migrastatin in selected heterologous Streptomyces hosts and related analysis of mRNA expression by quantitative RT-PCR. Appl Microbiol Biotechnol 2010; 89:1709-19. [PMID: 21132287 DOI: 10.1007/s00253-010-3025-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 11/11/2010] [Accepted: 11/18/2010] [Indexed: 10/18/2022]
Abstract
iso-Migrastatin (iso-MGS) has been actively pursued recently as an outstanding candidate of antimetastasis agents. Having characterized the iso-MGS biosynthetic gene cluster from its native producer Streptomyces platensis NRRL 18993, we have recently succeeded in producing iso-MGS in five selected heterologous Streptomyces hosts, albeit the low titers failed to meet expectations and cast doubt on the utility of this novel technique for large-scale production. To further explore and capitalize on the production capacity of these hosts, a thorough investigation of these five engineered strains with three fermentation media for iso-MGS production was undertaken. Streptomyces albus J1074 and Streptomyces lividans K4-114 were found to be preferred heterologous hosts, and subsequent analysis of carbon and nitrogen sources revealed that sucrose and yeast extract were ideal for iso-MGS production. After the initial optimization, the titers of iso-MGS in all five hosts were considerably improved by 3-18-fold in the optimized R2YE medium. Furthermore, the iso-MGS titer of S. albus J1074 (pBS11001) was significantly improved to 186.7 mg/L by a hybrid medium strategy. Addition of NaHCO(3) to the latter finally afforded an optimized iso-MGS titer of 213.8 mg/L, about 5-fold higher than the originally reported system. With S. albus J1074 (pBS11001) as a model host, the expression of iso-MGS gene cluster in four different media was systematically studied via the quantitative RT-PCR technology. The resultant comparison revealed the correlation of gene expression and iso-MGS production for the first time; synchronous expression of the whole gene cluster was crucial for optimal iso-MGS production. These results reveal new insights into the iso-MGS biosynthetic machinery in heterologous hosts and provide the primary data to realize large-scale production of iso-MGS for further preclinical studies.
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Iso-migrastatin Titer Improvement in the Engineered Streptomyces lividans SB11002 Strain by Optimization of Fermentation Conditions. BIOTECHNOL BIOPROC E 2010; 15:664-669. [PMID: 21625393 DOI: 10.1007/s12257-009-3129-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The heterologous production of iso-migrastatin (iso-MGS) was successfully demonstrated in an engineered S. lividans SB11002 strain, which was derived from S. lividans K4-114, following introduction of pBS11001, which harbored the entire mgs biosynthetic gene cluster. However, under similar fermentation conditions, the iso-MGS titer in the engineered strain was significantly lower than that in the native producer - Streptomyces platensis NRRL 18993. To circumvent the problem of low iso-MGS titers and to expand the utility of this heterologous system for iso-MGS biosynthesis and engineering, systematic optimization of the fermentation medium was carried out. The effects of major components in the cultivation medium, including carbon, organic and inorganic nitrogen sources, were investigated using a single factor optimization method. As a result, sucrose and yeast extract were determined to be the best carbon and organic nitrogen sources, resulting in optimized iso-MGS production. Conversely, all other inorganic nitrogen sources evaluated produced various levels of inhibition of iso-MGS production. The final optimized R2YE production medium produced iso-MGS with a titer of 86.5 mg/L, about 3.6-fold higher than that in the original R2YE medium, and 1.5 fold higher than that found within the native S. platensis NRRL 18993 producer.
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Magpusao AN, Desmond RT, Billings KJ, Fenteany G, Peczuh MW. Synthesis and evaluation of antimigratory and antiproliferative activities of lipid-linked [13]-macro-dilactones. Bioorg Med Chem Lett 2010; 20:5472-6. [PMID: 20709546 DOI: 10.1016/j.bmcl.2010.07.083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 12/21/2022]
Abstract
The biological activities of a family of novel, lipid-linked 13-membered-ring macro-dilactones are reported. These [13]-macro-dilactones were synthesized by diacylation of functionalized diols, followed by ring-closing metathesis under conditions we had previously reported. Antimigratory, cytostatic and cytotoxic activities of the compounds against cancer cells were evaluated. Compound 13 was the most potent in the series, while compound 10 had the broadest concentration range of subtoxic antiproliferative activity. These compounds share common structural components, namely the [13]-macro-dilactone templated by an octyl alpha-glucoside 4,6-diol.
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Zhao C, Coughlin JM, Ju J, Zhu D, Wendt-Pienkowski E, Zhou X, Wang Z, Shen B, Deng Z. Oxazolomycin biosynthesis in Streptomyces albus JA3453 featuring an "acyltransferase-less" type I polyketide synthase that incorporates two distinct extender units. J Biol Chem 2010; 285:20097-108. [PMID: 20406823 DOI: 10.1074/jbc.m109.090092] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The oxazolomycins (OZMs) are a growing family of antibiotics produced by several Streptomyces species that show diverse and important antibacterial, antitumor, and anti-human immunodeficiency virus activity. Oxazolomycin A is a peptide-polyketide hybrid compound containing a unique spiro-linked beta-lactone/gamma-lactam, a 5-substituted oxazole ring. The oxazolomycin biosynthetic gene cluster (ozm) was identified from Streptomyces albus JA3453 and localized to 79.5-kb DNA, consisting of 20 open reading frames that encode non-ribosomal peptide synthases, polyketide synthases (PKSs), hybrid non-ribosomal peptide synthase-PKS, trans-acyltransferases (trans-ATs), enzymes for methoxymalonyl-acyl carrier protein (ACP) synthesis, putative resistance genes, and hypothetical regulation genes. In contrast to classical type I polyketide or fatty acid biosynthases, all 10 PKS modules in the gene cluster lack cognate ATs. Instead, discrete ATs OzmM (with tandem domains OzmM-AT1 and OzmM-AT2) and OzmC were equipped to carry out all of the loading functions of both malonyl-CoA and methoxymalonyl-ACP extender units. Strikingly, only OzmM-AT2 is required for OzmM activity for OZM biosynthesis, whereas OzmM-AT1 seemed to be a cryptic AT domain. The above findings, together with previous results using isotope-labeled precursor feeding assays, are assembled for the OZM biosynthesis model to be proposed. The incorporation of both malonyl-CoA (by OzmM-AT2) and methoxymalonyl-ACP (by OzmC) extender units seemed to be unprecedented for this class of trans-AT type I PKSs, which might be fruitfully manipulated to create structurally diverse novel compounds.
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Affiliation(s)
- Chunhua Zhao
- Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
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Chen Y, Smanski MJ, Shen B. Improvement of secondary metabolite production in Streptomyces by manipulating pathway regulation. Appl Microbiol Biotechnol 2010; 86:19-25. [PMID: 20091304 DOI: 10.1007/s00253-009-2428-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2009] [Revised: 12/22/2009] [Accepted: 12/24/2009] [Indexed: 12/21/2022]
Abstract
Titer improvement is a constant requirement in the fermentation industry. The traditional method of "random mutation and screening" has been very effective despite the considerable amount of time and resources it demands. Rational metabolic engineering, with the use of recombinant DNA technology, provides a novel, alternative strategy for titer improvement that complements the empirical method used in industry. Manipulation of the specific regulatory systems that govern secondary metabolite production is an important aspect of metabolic engineering that can efficiently improve fermentation titers. In this review, we use examples from Streptomyces secondary metabolism, the most prolific source of clinically used drugs, to demonstrate the power and utility of exploiting natural regulatory networks, in particular pathway-specific regulators, for titer improvement. Efforts to improve the titers of fredericamycin, C-1027, platensimycin, and platencin in our lab are highlighted.
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Affiliation(s)
- Yihua Chen
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA
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